73 results on '"Toni A. Chapman"'
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2. Diet and irradiation effects on the bacterial community composition and structure in the gut of domesticated teneral and mature Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)
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Deane N. Woruba, Jennifer L. Morrow, Olivia L. Reynolds, Toni A. Chapman, Damian P. Collins, and Markus Riegler
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Sterile insect technique ,microbiome ,16S rRNA gene ,Enterobacteriaceae ,Acetobacteraceae ,Asaia sp. ,Microbiology ,QR1-502 - Abstract
Abstract Background Mass-rearing, domestication and gamma irradiation of tephritid fruit flies used in sterile insect technique (SIT) programmes can negatively impact fly quality and performance. Symbiotic bacteria supplied as probiotics to mass-reared fruit flies may help to overcome some of these issues. However, the effects of tephritid ontogeny, sex, diet and irradiation on their microbiota are not well known. Results We have used next-generation sequencing to characterise the bacterial community composition and structure within Queensland fruit fly, Bactrocera tryoni (Froggatt), by generating 16S rRNA gene amplicon libraries derived from the guts of 58 individual teneral and mature, female and male, sterile and fertile adult flies reared on artificial larval diets in a laboratory or mass-rearing environment, and fed either a full adult diet (i.e. sugar and yeast hydrolysate) or a sugar only adult diet. Overall, the amplicon sequence read volume in tenerals was low and smaller than in mature adult flies. Operational taxonomic units (OTUs), belonging to the families Enterobacteriaceae (8 OTUs) and Acetobacteraceae (1 OTU) were most prevalent. Enterobacteriaceae dominated laboratory-reared tenerals from a colony fed a carrot-based larval diet, while Acetobacteraceae dominated mass-reared tenerals from a production facility colony fed a lucerne chaff based larval diet. As adult flies matured, Enterobacteriaceae became dominant irrespective of larval origin. The inclusion of yeast in the adult diet strengthened this shift away from Acetobacteraceae towards Enterobacteriaceae. Interestingly, irradiation increased 16S rRNA gene sequence read volume. Conclusions Our findings suggest that bacterial populations in fruit flies experience significant bottlenecks during metamorphosis. Gut bacteria in teneral flies were less abundant and less diverse, and impacted by colony origin. In contrast, mature adult flies had selectively increased abundances for some gut bacteria, or acquired these bacteria from the adult diet and environment. Furthermore, irradiation augmented bacterial abundance in mature flies. This implies that either some gut bacteria were compensating for damage caused by irradiation or irradiated flies had lost their ability to regulate bacterial load. Our findings suggest that the adult stage prior to sexual maturity may be ideal to target for probiotic manipulation of fly microbiota to increase fly performance in SIT programmes.
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- 2019
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3. Commensal microbiota modulates larval foraging behaviour, development rate and pupal production in Bactrocera tryoni
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Juliano Morimoto, Binh Nguyen, Shabnam T. Tabrizi, Ida Lundbäck, Phillip W. Taylor, Fleur Ponton, and Toni A. Chapman
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Nutrition ,Larval behaviour ,Development ,Microbiota ,Microbiology ,QR1-502 - Abstract
Abstract Backround Commensal microbes can promote survival and growth of developing insects, and have important fitness implications in adulthood. Insect larvae can acquire commensal microbes through two main routes: by vertical acquisition from maternal deposition of microbes on the eggshells and by horizontal acquisition from the environment where the larvae develop. To date, however, little is known about how microbes acquired through these different routes interact to shape insect development. In the present study, we investigated how vertically and horizontally acquired microbiota influence larval foraging behaviour, development time to pupation and pupal production in the Queensland fruit fly (‘Qfly’), Bactrocera tryoni. Results Both vertically and horizontally acquired microbiota were required to maximise pupal production in Qfly. Moreover, larvae exposed to both vertically and horizontally acquired microbiota pupated sooner than those exposed to no microbiota, or only to horizontally acquired microbiota. Larval foraging behaviour was also influenced by both vertically and horizontally acquired microbiota. Larvae from treatments exposed to neither vertically nor horizontally acquired microbiota spent more time overall on foraging patches than did larvae of other treatments, and most notably had greater preference for diets with extreme protein or sugar compositions. Conclusion The integrity of the microbiota early in life is important for larval foraging behaviour, development time to pupation, and pupal production in Qflies. These findings highlight the complexity of microbial relations in this species, and provide insights to the importance of exposure to microbial communities during laboratory- or mass-rearing of tephritid fruit flies.
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- 2019
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4. Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs
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Ania T. Deutscher, Toni A. Chapman, Lucas A. Shuttleworth, Markus Riegler, and Olivia L. Reynolds
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Tephritidae ,SIT ,Gut microbiota ,Gut microbiome ,Host-microbe interaction ,Insect microbial symbiosis ,Microbiology ,QR1-502 - Abstract
Abstract Background The Sterile Insect Technique (SIT) is being applied for the management of economically important pest fruit flies (Diptera: Tephritidae) in a number of countries worldwide. The success and cost effectiveness of SIT depends upon the ability of mass-reared sterilized male insects to successfully copulate with conspecific wild fertile females when released in the field. Methods We conducted a critical analysis of the literature about the tephritid gut microbiome including the advancement of methods for the identification and characterization of microbiota, particularly next generation sequencing, the impacts of irradiation (to induce sterility of flies) and fruit fly rearing, and the use of probiotics to manipulate the fruit fly gut microbiota. Results Domestication, mass-rearing, irradiation and handling, as required in SIT, may change the structure of the fruit flies’ gut microbial community compared to that of wild flies under field conditions. Gut microbiota of tephritids are important in their hosts’ development, performance and physiology. Knowledge of how mass-rearing and associated changes of the microbial community impact the functional role of the bacteria and host biology is limited. Probiotics offer potential to encourage a gut microbial community that limits pathogens, and improves the quality of fruit flies. Conclusions Advances in technologies used to identify and characterize the gut microbiota will continue to expand our understanding of tephritid gut microbial diversity and community composition. Knowledge about the functions of gut microbes will increase through the use of gnotobiotic models, genome sequencing, metagenomics, metatranscriptomics, metabolomics and metaproteomics. The use of probiotics, or manipulation of the gut microbiota, offers significant opportunities to enhance the production of high quality, performing fruit flies in operational SIT programs.
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- 2019
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5. Next-Generation Sequencing reveals relationship between the larval microbiome and food substrate in the polyphagous Queensland fruit fly
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Rajib Majumder, Brodie Sutcliffe, Phillip W. Taylor, and Toni A. Chapman
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Medicine ,Science - Abstract
Abstract Insects typically host substantial microbial communities (the ‘microbiome’) that can serve as a vital source of nutrients and also acts as a modulator of immune function. While recent studies have shown that diet is an important influence on the gut microbiome, very little is known about the dynamics underpinning microbial acquisition from natural food sources. Here, we addressed this gap by comparing the microbiome of larvae of the polyphagous fruit fly Bactrocera tryoni (‘Queensland fruit fly’) that were collected from five different fruit types (sapodilla [from two different localities], hog plum, pomegranate, green apple, and quince) from North-east to South-east Australia. Using Next-Generation Sequencing on the Illumina MiSeq platform, we addressed two questions: (1) what bacterial communities are available to B. tryoni larvae from different host fruit; and (2) how does the microbiome vary between B. tryoni larvae and its host fruit? The abundant bacterial taxa were similar for B. tryoni larvae from different fruit despite significant differences in the overall microbial community compositions. Our study suggests that the bacterial community structure of B. tryoni larvae is related less to the host fruit (diet) microbiome and more to vertical transfer of the microbiome during egg laying. Our findings also suggest that geographic location may play a quite limited role in structuring of larval microbiomes. This is the first study to use Next-Generation Sequencing to analyze the microbiome of B. tryoni larvae together with the host fruit, an approach that has enabled greatly increased resolution of relationships between the insect’s microbiome and that of the surrounding host tissues.
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- 2019
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6. Using Genomics to Design a Pathovar-Specific Loop-Mediated Isothermal Amplification (LAMP) Assay, for the Improved Detection of Xanthomonas citri pv. citri
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John Webster, Monica A. Kehoe, Elisse Nogarotto, Linda Falconer, Nerida Jane Donovan, and Toni A. Chapman
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loop mediated isothermal amplification (LAMP) ,Xanthomonas ,Citrus Canker ,rapid diagnostic ,Biology (General) ,QH301-705.5 - Abstract
The ability to swiftly respond to pathogen incursions relies heavily on fast and accurate diagnostics. Current published assays for citrus bacterial canker do not target Xanthomonas citri pv. citri, the causative agent, with high specificity when testing Australian samples. While the current diagnostics are useful in countries where canker is endemic, the detection of canker in Australia requires an emergency response. Close relatives to X. citri pv. citri found in Australia may generate false positives with the current recommended diagnostic assays. Therefore, we developed a more specific detection tool for citrus bacterial canker to provide greater diagnostic confidence for surveillance and eradication efforts. We used genomic comparisons of 161 Xanthomonad genomes and identified and confirmed genomic regions specific for X. citri pv. citri by performing local alignments of unique regions to reference genomes. We then developed loop-mediated isothermal amplification primers and validated them against a panel of 190 isolates to confirm specificity. Our diagnostic assay showed 100% corroboration with the concurrently developed multiplex primers and represents an improved diagnostic method capable of effective citrus bacterial canker identification.
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- 2022
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7. Artificial Larval Diet Mediates the Microbiome of Queensland Fruit Fly
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Rajib Majumder, Brodie Sutcliffe, Saleh Mohammad Adnan, Bishwo Mainali, Bernard C. Dominiak, Phillip W. Taylor, and Toni A. Chapman
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Tephritidae ,gut bacteria ,Illumina sequencing ,development ,domestication ,mating ,Microbiology ,QR1-502 - Abstract
Larval diets used for artificial rearing can have a significant effect on insect biology. The Queensland fruit fly (aka “Qfly”), Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), is one of the greatest challenges for fruit growers in Australia. The sterile insect technique (SIT) is being developed to manage outbreaks in regions that remain free of Qfly and to reduce populations in regions where this species is endemic. Factory scale rearing is essential for SIT; however, artificial larval diets are known to affect the microbiome of Qfly, which may then affect fly performance. In this study, high-throughput Illumina sequencing was used to assess the Qfly microbiome in colonies reared, for five generations from nature, on two common artificial diets (carrot and gel). At generation five (G5), the microbiome was assessed in larvae, pupae, adult males and adult females and standard fly quality control parameters were assessed together with additional performance measures of mating propensity and survival under nutritional stress. At the genus level, bacterial communities were significantly different between the colonies reared on the two larval diets. However, communities converged at Phyla to family taxonomic levels. Bacterial genera of Morganella, Citrobacter, Providencia, and Burkholderia were highly abundant in all developmental stages of Qfly reared on the gel diet, when compared to the carrot diet. Despite abundance of these genera, a greater percentage of egg hatching, heavier pupal weight and a higher percentage of fliers were found in the Qfly reared on the gel diet. Mating propensity and survival under nutritional stress was similar for adult Qfly that had been reared on the two larval diets. Overall, our findings demonstrate that the artificial larval diet strongly influences the microbiome and quality control measures of Qfly, with likely downstream effects on performance of flies released in SIT programs.
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- 2020
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8. Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements
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Veronica M. Jarocki, Cameron J. Reid, Toni A. Chapman, and Steven P. Djordjevic
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aEPEC ,ST302 ,mobile genetic elements ,IncHI2 plasmid ,IncFIB ,ETT2 ,Microbiology ,QR1-502 - Abstract
aEPEC are associated with persistent diarrhea, and diarrheal outbreaks in both humans and animals worldwide. They are differentiated from typical EPEC by the lack of bundle-forming pili, and from EHEC by the lack of phage-mediated stx toxins. However, phylogenetic analyses often associate aEPEC with EHEC, promoting the hypothesis that aEPEC are the progenitors of EHEC, which is supported by aEPEC conversion to EHEC by stx-carrying phages. While aEPEC can cause disease outright, the potential to acquire stx, one of the most potent bacterial toxins known, merits close monitoring. Escherichia coli ST302 (O108:H9, O182:H9, O45:H9) are aEPEC that have been isolated from diarrheic human, pig and rabbit hosts, as well as in healthy pigs, however, no study to date has focused on E. coli ST302 strains. Through WGS and hybrid assembly we present the first closed chromosome, and two circularized plasmids of an ST302 strain - F2_18C, isolated from a healthy pig in Australia. A phylogenetic analysis placed E. coli ST302 strains in proximity to EHEC ST32 (O145:H28) strains. Public databases were interrogated for WGSs of E. coli ST302 strains and short-read gene screens were used to compare their virulence-associated gene (VAG) and antimicrobial resistance gene (ARG) cargo. E. coli ST302 strains carry diverse VAGs, including those that typically associated with extraintestinal pathogenic E. coli (ExPEC). Plasmid comparisons showed that pF2_18C_FIB shared homology with EHEC virulence plasmids such as pO103 while pF2_18C_HI2 is a large multidrug resistance IncHI2:ST3 plasmid. A comparison of 33 HI2:ST3 plasmids demonstrated that those of Australian origin have not acquired resistances to extended-spectrum beta-lactams, colistin, fosfomycin or rifampicin, unlike those originating from Asia. F2_18C was shown to carry two additional pathogenicity islands – ETT2, and the STEC-associated PAICL3, plasmid-associated heavy metal resistance genes, as well as several unoccupied stx-phage attachment sites. This study sheds light on the virulence and AMR potential of E. coli ST302 strains and informs AMR genomic surveillance.
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- 2020
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9. Dynamics of the Queensland Fruit Fly Microbiome through the Transition from Nature to an Established Laboratory Colony
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Rajib Majumder, Phillip W. Taylor, and Toni A. Chapman
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Bactrocera tryoni ,Tephritidae ,high-throughput Illumina sequencing ,domestication ,sterile insect technique ,gel-based diet ,Biology (General) ,QH301-705.5 - Abstract
The transition from nature to laboratory or mass rearing can impose significant physiological and evolutionary impact on insects. The Queensland fruit fly (also known as ‘Qfly’), Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), is a serious economic pest that presents major challenges for horticulture industries in Australia. The sterile insect technique (SIT) is being developed to manage outbreaks in regions that remain free of Qfly and to suppress populations in regions where this species is endemic. The biology of Qfly is intimately connected to its microbiome. Therefore, changes in the microbiome that occur through domestication have implications for SIT. There are numerous studies of the microbiome in Qfly larvae and adults, but there is little information on how the microbiome changes as Qfly laboratory colonies are established. In this study, high-throughput Illumina sequencing was used to assess the Qfly microbiome in colonies reared from wild larvae, collected from fruit, for five generations, on a gel-based larval diet. Beta diversity analysis showed that the bacterial communities from Generation 5 (G5) clustered separately from earlier generations. At the genus level, bacterial communities were significantly different between the generations and mostly altered at G5. However, communities were found similar at phyla to family taxonomic levels. We observed high abundance of Morganella and Burkholderia at the genus level in the larval and pupal stages respectively at G5, but these were not detected in earlier generations. Overall, our findings demonstrate that the domestication process strongly affects the Qfly microbiome and prompts questions about the functional relationship between the Qfly and its microbiome, as well as implications for the performance of insects that have been domesticated and mass-reared for SIT programs.
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- 2022
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10. Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae
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Ania T. Deutscher, Catherine M. Burke, Aaron E. Darling, Markus Riegler, Olivia L. Reynolds, and Toni A. Chapman
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Diptera ,Tephritidae ,Bactrocera tryoni ,Sterile insect technique ,Host–microbe interactions ,Insect–microbe interactions ,Microbial ecology ,QR100-130 - Abstract
Abstract Background Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome. Read lengths of previous fruit fly next-generation sequencing (NGS) studies have limited the resolution of microbiome studies, and the diversity within populations is often overlooked. In this study, we used a new near full-length (> 1300 nt) 16S rRNA gene amplicon NGS approach to characterize gut bacterial communities of individual B. tryoni larvae from two field populations (developing in peaches) and three domesticated populations (mass- or laboratory-reared on artificial diets). Results Near full-length 16S rRNA gene sequences were obtained for 56 B. tryoni larvae. OTU clustering at 99% similarity revealed that gut bacterial diversity was low and significantly lower in domesticated larvae. Bacteria commonly associated with fruit (Acetobacteraceae, Enterobacteriaceae, and Leuconostocaceae) were detected in wild larvae, but were largely absent from domesticated larvae. However, Asaia, an acetic acid bacterium not frequently detected within adult tephritid species, was detected in larvae of both wild and domesticated populations (55 out of 56 larval gut samples). Larvae from the same single peach shared a similar gut bacterial profile, whereas larvae from different peaches collected from the same tree had different gut bacterial profiles. Clustering of the Asaia near full-length sequences at 100% similarity showed that the wild flies from different locations had different Asaia strains. Conclusions Variation in the gut bacterial communities of B. tryoni larvae depends on diet, domestication, and horizontal acquisition. Bacterial variation in wild larvae suggests that more than one bacterial species can perform the same functional role; however, Asaia could be an important gut bacterium in larvae and warrants further study. A greater understanding of the functions of the bacteria detected in larvae could lead to increased fly quality and performance as part of the SIT.
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- 2018
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11. Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia
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Ethan R. Wyrsch, Cameron J. Reid, Matthew Z. DeMaere, Michael Y. Liu, Toni A. Chapman, Piklu Roy Chowdhury, and Steven P. Djordjevic
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Escherichia coli ,antimicrobial resistance (AMR) ,plasmid ,genomics ,epidemiology ,Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
IncHI2 ST3 plasmids are known carriers of multiple antimicrobial resistance genes. Complete plasmid sequences from multiple drug resistant Escherichia coli circulating in Australian swine is however limited. Here we sequenced two related IncHI2 ST3 plasmids, pSDE-SvHI2, and pSDC-F2_12BHI2, from phylogenetically unrelated multiple-drug resistant Escherichia coli strains SvETEC (CC23:O157:H19) and F2_12B (ST93:O7:H4) from geographically disparate pig production operations in New South Wales, Australia. Unicycler was used to co-assemble short read (Illumina) and long read (PacBio SMRT) nucleotide sequence data. The plasmids encoded three drug-resistance loci, two of which carried class 1 integrons. One integron, hosting drfA12-orfF-aadA2, was within a hybrid Tn1721/Tn21, with the second residing within a copper/silver resistance transposon, comprising part of an atypical sul3-associated structure. The third resistance locus was flanked by IS15DI and encoded neomycin resistance (neoR). An oqx-encoding transposon (quinolone resistance), similar in structure to Tn6010, was identified only in pSDC-F2_12BHI2. Both plasmids showed high sequence identity to plasmid pSTM6-275, recently described in Salmonella enterica serotype 1,4,[5],12:i:- that has risen to prominence and become endemic in Australia. IncHI2 ST3 plasmids circulating in commensal and pathogenic E. coli from Australian swine belong to a lineage of plasmids often in association with sul3 and host multiple complex antibiotic and metal resistance structures, formed in part by IS26.
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- 2019
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12. Comparative Genomics of Xanthomonas citri pv. citri A* Pathotype Reveals Three Distinct Clades with Varying Plasmid Distribution
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John Webster, Daniel Bogema, and Toni A. Chapman
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Xanthomonas citri ,A* pathotype ,plasmid ,complete genome ,pan-genome ,phylogenomics ,Biology (General) ,QH301-705.5 - Abstract
Citrus bacterial canker (CBC) is an important disease of citrus cultivars worldwide that causes blister-like lesions on host plants and leads to more severe symptoms such as plant defoliation and premature fruit drop. The causative agent, Xanthomonas citri pv. citri, exists as three pathotypes—A, A*, and Aw—which differ in their host range and elicited host response. To date, comparative analyses have been hampered by the lack of closed genomes for the A* pathotype. In this study, we sequenced and assembled six CBC isolates of pathotype A* using second- and third-generation sequencing technologies to produce complete, closed assemblies. Analysis of these genomes and reference A, A*, and Aw sequences revealed genetic groups within the A* pathotype. Investigation of accessory genomes revealed virulence factors, including type IV secretion systems and heavy metal resistance genes, differentiating the genetic groups. Genomic comparisons of closed genome assemblies also provided plasmid distribution information for the three genetic groups of A*. The genomes presented here complement existing closed genomes of A and Aw pathotypes that are publicly available and open opportunities to investigate the evolution of X. citri pv. citri and the virulence factors that contribute to this serious pathogen.
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- 2020
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13. Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring
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Tiziana Zingali, Cameron J. Reid, Toni A. Chapman, Daniela Gaio, Michael Liu, Aaron E. Darling, and Steven P. Djordjevic
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porcine E. coli ,commensal E. coli ,class 1 integron ,microbial genomic epidemiology ,antimicrobial resistance ,Biology (General) ,QH301-705.5 - Abstract
Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1+). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1+ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to β-lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1+ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.
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- 2020
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14. Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia
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Tiziana Zingali, Toni A. Chapman, John Webster, Piklu Roy Chowdhury, and Steven P. Djordjevic
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IncHI2 ,plasmid ,porcine ,mefB ,complex resistance locus ,multiple drug resistance ,Biology (General) ,QH301-705.5 - Abstract
Antibiotic resistance genes (ARGs) including those from the blaCTX-M family and mcr-1 that encode resistance to extended spectrum β–lactams and colistin, respectively, have been linked with IncHI2 plasmids isolated from swine production facilities globally but not in IncHI2 plasmids from Australia. Here we describe the first complete sequence of a multiple drug resistance Australian IncHI2-ST4 plasmid, pTZ41_1P, from a commensal E. coli from a healthy piglet. pTZ41_1P carries genes conferring resistance to heavy-metals (copper, silver, tellurium and arsenic), β-lactams, aminoglycosides and sulphonamides. The ARGs reside within a complex resistance locus (CRL) that shows considerable sequence identity to a CRL in pSDE_SvHI2, an IncHI2:ST3 plasmid from an enterotoxigenic E. coli with serotype O157:H19 of porcine origin that caused substantial losses to swine production operations in Australia in 2007. pTZ41_1P is closely related to IncHI2 plasmids found in E. coli and Salmonella enterica from porcine, avian and human sources in Europe and China but it does not carry genes encoding resistance to clinically-important antibiotics. We identified regions of IncHI2 plasmids that contribute to the genetic plasticity of this group of plasmids and highlight how they may readily acquire new resistance gene cargo. Genomic surveillance should be improved to monitor IncHI2 plasmids.
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- 2020
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15. Microbiome of the Queensland Fruit Fly through Metamorphosis
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Rajib Majumder, Brodie Sutcliffe, Phillip W. Taylor, and Toni A. Chapman
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gut bacteria and fungi ,yeast and yeast like ,Next-Generation Sequencing ,Biology (General) ,QH301-705.5 - Abstract
Bactrocera tryoni (Froggatt) (Queensland fruit fly, or “Qfly”) is a highly polyphagous tephritid fruit fly and a serious economic pest in Australia. Qfly biology is intimately linked to the bacteria and fungi of its microbiome. While there are numerous studies of the microbiome in larvae and adults, the transition of the microbiome through the pupal stage remains unknown. To address this knowledge gap, we used high-throughput Next-Generation Sequencing (NGS) to examine microbial communities at each developmental stage in the Qfly life cycle, targeting the bacterial 16S rRNA and fungal ITS regions. We found that microbial communities were similar at the larval and pupal stage and were also similar between adult males and females, yet there were marked differences between the larval and adult stages. Specific bacterial and fungal taxa are present in the larvae and adults (fed hydrolyzed yeast with sugar) which is likely related to differences in nutritional biology of these life stages. We observed a significant abundance of the Acetobacteraceae at the family level, both in the larval and pupal stages. Conversely, Enterobacteriaceae was highly abundant (>80%) only in the adults. The majority of fungal taxa present in Qfly were yeasts or yeast-like fungi. In addition to elucidating changes in the microbiome through developmental stages, this study characterizes the Qfly microbiome present at the establishment of laboratory colonies as they enter the domestication process.
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- 2020
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16. Molecular Techniques for the Detection and Differentiation of Host and Parasitoid Species and the Implications for Fruit Fly Management
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Olivia L. Reynolds, Jessica L. Micallef, Toni A. Chapman, and Cheryl Jenkins
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Diptera ,Tephritidae ,parasitoid ,biological control ,DNA barcode ,PCR ,microsatellites ,Science - Abstract
Parasitoid detection and identification is a necessary step in the development and implementation of fruit fly biological control strategies employing parasitoid augmentive release. In recent years, DNA-based methods have been used to identify natural enemies of pest species where morphological differentiation is problematic. Molecular techniques also offer a considerable advantage over traditional morphological methods of fruit fly and parasitoid discrimination as well as within-host parasitoid identification, which currently relies on dissection of immature parasitoids from the host, or lengthy and labour-intensive rearing methods. Here we review recent research focusing on the use of molecular strategies for fruit fly and parasitoid detection and differentiation and discuss the implications of these studies on fruit fly management.
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- 2012
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17. Investigating the defoliating‐like (DL) VCG2A pathotype of Verticillium dahliae through identification and prediction of secreted proteins from genomes of Australian isolates
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John Webster, Pearl Dadd‐Daigle, Toni A. Chapman, and Karen Kirkby
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Genetics ,Plant Science ,Horticulture ,Agronomy and Crop Science - Published
- 2022
18. The Verticillium wilt problem in Australian cotton
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P. Dadd-Daigle, Karen Kirkby, P. Roy Chowdhury, Toni A. Chapman, and Maurizio Labbate
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0106 biological sciences ,0301 basic medicine ,business.industry ,fungi ,food and beverages ,Plant Science ,Biology ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Agronomy ,Agriculture ,Verticillium dahliae ,Verticillium wilt ,business ,010606 plant biology & botany - Abstract
Verticillium dahliae is a soil-borne phytopathogen and the causal agent of Verticillium wilt. It affects many agriculturally important crops around the world, including cotton. In Australia, the billion-dollar cotton industry is increasingly impacted by Verticillium wilt. Internationally it has been reported that the defoliating V. dahliae Vegetative Compatibility Group (VCG) 1A causes severe damage to cotton. In Australia however, the non-defoliating VCG2A is causing more severe damage to crops in fields than the defoliating VCG1A. This review examines the current research to understand the Australian V. dahliae situation, including current classification systems, genetic analyses and management strategies. It appears that virulence cannot be defined solely by VCG in Australian Verticillium dahliae isolates causing disease in cotton, and that the industry must continually adapt their practices in order to keep the disease under control.
- Published
- 2021
19. Genomic Acquisitions in Emerging Populations of Xanthomonas vasicola pv. vasculorum Infecting Corn in the United States and Argentina
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Janet Ziegle, Adrien Rieux, Jan E. Leach, Alvaro L. Pérez-Quintero, Frank F. White, Kirk Broders, Mary Ortiz-Castro, Sanzhen Liu, Guangxi Wu, Christine Chang, Toni A Chapman, Jillian M. Lang, Zhao Peng, and Maria Cristina Plazas
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Comparative genomics ,Genetics ,education.field_of_study ,Phylogenetic tree ,Population ,Xanthomonas vasicola ,Plant Science ,Biology ,Genome ,Horizontal gene transfer ,education ,Agronomy and Crop Science ,Prophage ,Bacterial leaf streak - Abstract
Xanthomonas vasicola pv. vasculorum is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this pathogen have greatly increased in the past years in South America and in the United States. The rapid spread of this disease in North and South America may be due to more favorable environmental conditions, susceptible hosts and/or genomic changes that favored the spread. To understand whether genetic mechanisms exist behind the recent spread of X. vasicola pv. vasculorum, we used comparative genomics to identify gene acquisitions in X. vasicola pv. vasculorum genomes from the United States and Argentina. We sequenced 41 genomes of X. vasicola pv. vasculorum and the related sorghum-infecting X. vasicola pv. holcicola and performed comparative analyses against all available X. vasicola genomes. Time-measured phylogenetic analyses showed that X. vasicola pv. vasculorum strains from the United States and Argentina are closely related and arose from two introductions to North and South America. Gene content comparisons identified clusters of genes enriched in corn X. vasicola pv. vasculorum that showed evidence of horizontal transfer including one cluster corresponding to a prophage found in all X. vasicola pv. vasculorum strains from the United States and Argentina as well as in X. vasicola pv. holcicola strains. In this work, we explore the genomes of an emerging phytopathogen population as a first step toward identifying genetic changes associated with the emergence. The acquisitions identified may contain virulence determinants or other factors associated with the spread of X. vasicola pv. vasculorum in North and South America and will be the subject of future work.
- Published
- 2020
20. Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig
- Author
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Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, Graeme J. Eamens, Linda Falconer, Toni A. Chapman, Steven Djordjevic, and Aaron E. Darling
- Subjects
Multidisciplinary ,General Science & Technology ,Swine ,Microbiota ,Probiotics ,Animals ,Dysbiosis ,Female ,Weaning ,Phylogeny ,Anti-Bacterial Agents ,Gastrointestinal Microbiome - Abstract
Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.
- Published
- 2022
21. Diet and irradiation effects on the bacterial community composition and structure in the gut of domesticated teneral and mature Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)
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Damian Collins, Jennifer L. Morrow, Toni A. Chapman, Olivia L. Reynolds, Deane N. Woruba, and Markus Riegler
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0106 biological sciences ,Microbiology (medical) ,DNA, Bacterial ,Male ,Asaia sp ,media_common.quotation_subject ,lcsh:QR1-502 ,Zoology ,microbiome ,01 natural sciences ,Microbiology ,Acetobacteraceae ,DNA, Ribosomal ,lcsh:Microbiology ,Domestication ,03 medical and health sciences ,Sterile insect technique ,Enterobacteriaceae ,Tephritidae ,RNA, Ribosomal, 16S ,Animals ,Metamorphosis ,Phylogeny ,030304 developmental biology ,media_common ,Bactrocera tryoni ,0303 health sciences ,Larva ,biology ,Bacteria ,Sequence Analysis, RNA ,Research ,fungi ,High-Throughput Nucleotide Sequencing ,biology.organism_classification ,Animal Feed ,Gastrointestinal Microbiome ,010602 entomology ,Female ,16S rRNA gene ,Symbiotic bacteria - Abstract
Background Mass-rearing, domestication and gamma irradiation of tephritid fruit flies used in sterile insect technique (SIT) programmes can negatively impact fly quality and performance. Symbiotic bacteria supplied as probiotics to mass-reared fruit flies may help to overcome some of these issues. However, the effects of tephritid ontogeny, sex, diet and irradiation on their microbiota are not well known. Results We have used next-generation sequencing to characterise the bacterial community composition and structure within Queensland fruit fly, Bactrocera tryoni (Froggatt), by generating 16S rRNA gene amplicon libraries derived from the guts of 58 individual teneral and mature, female and male, sterile and fertile adult flies reared on artificial larval diets in a laboratory or mass-rearing environment, and fed either a full adult diet (i.e. sugar and yeast hydrolysate) or a sugar only adult diet. Overall, the amplicon sequence read volume in tenerals was low and smaller than in mature adult flies. Operational taxonomic units (OTUs), belonging to the families Enterobacteriaceae (8 OTUs) and Acetobacteraceae (1 OTU) were most prevalent. Enterobacteriaceae dominated laboratory-reared tenerals from a colony fed a carrot-based larval diet, while Acetobacteraceae dominated mass-reared tenerals from a production facility colony fed a lucerne chaff based larval diet. As adult flies matured, Enterobacteriaceae became dominant irrespective of larval origin. The inclusion of yeast in the adult diet strengthened this shift away from Acetobacteraceae towards Enterobacteriaceae. Interestingly, irradiation increased 16S rRNA gene sequence read volume. Conclusions Our findings suggest that bacterial populations in fruit flies experience significant bottlenecks during metamorphosis. Gut bacteria in teneral flies were less abundant and less diverse, and impacted by colony origin. In contrast, mature adult flies had selectively increased abundances for some gut bacteria, or acquired these bacteria from the adult diet and environment. Furthermore, irradiation augmented bacterial abundance in mature flies. This implies that either some gut bacteria were compensating for damage caused by irradiation or irradiated flies had lost their ability to regulate bacterial load. Our findings suggest that the adult stage prior to sexual maturity may be ideal to target for probiotic manipulation of fly microbiota to increase fly performance in SIT programmes.
- Published
- 2019
22. Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs
- Author
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Lucas A. Shuttleworth, Ania T. Deutscher, Toni A. Chapman, Olivia L. Reynolds, and Markus Riegler
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Male ,0106 biological sciences ,Microbiology (medical) ,Cost effectiveness ,lcsh:QR1-502 ,Review ,Gut microbiota ,Gut flora ,Bacterial Physiological Phenomena ,Insect Control ,01 natural sciences ,Microbiology ,digestive system ,lcsh:Microbiology ,Domestication ,Sexual Behavior, Animal ,03 medical and health sciences ,Sterile insect technique ,Host-microbe interaction ,Tephritidae ,Insect microbial symbiosis ,Animals ,Pest Control, Biological ,030304 developmental biology ,0303 health sciences ,Gut microbiome ,biology ,business.industry ,Probiotics ,fungi ,Mass-rearing ,Microbial symbiont ,biology.organism_classification ,Gastrointestinal Microbiome ,Biotechnology ,010602 entomology ,SIT ,Microbial population biology ,Metagenomics ,Metaproteomics ,Female ,PEST analysis ,business - Abstract
Background The Sterile Insect Technique (SIT) is being applied for the management of economically important pest fruit flies (Diptera: Tephritidae) in a number of countries worldwide. The success and cost effectiveness of SIT depends upon the ability of mass-reared sterilized male insects to successfully copulate with conspecific wild fertile females when released in the field. Methods We conducted a critical analysis of the literature about the tephritid gut microbiome including the advancement of methods for the identification and characterization of microbiota, particularly next generation sequencing, the impacts of irradiation (to induce sterility of flies) and fruit fly rearing, and the use of probiotics to manipulate the fruit fly gut microbiota. Results Domestication, mass-rearing, irradiation and handling, as required in SIT, may change the structure of the fruit flies’ gut microbial community compared to that of wild flies under field conditions. Gut microbiota of tephritids are important in their hosts’ development, performance and physiology. Knowledge of how mass-rearing and associated changes of the microbial community impact the functional role of the bacteria and host biology is limited. Probiotics offer potential to encourage a gut microbial community that limits pathogens, and improves the quality of fruit flies. Conclusions Advances in technologies used to identify and characterize the gut microbiota will continue to expand our understanding of tephritid gut microbial diversity and community composition. Knowledge about the functions of gut microbes will increase through the use of gnotobiotic models, genome sequencing, metagenomics, metatranscriptomics, metabolomics and metaproteomics. The use of probiotics, or manipulation of the gut microbiota, offers significant opportunities to enhance the production of high quality, performing fruit flies in operational SIT programs.
- Published
- 2019
23. Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes
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Kay Anantanawat, Toni A. Chapman, Aaron E. Darling, Matthew Z. DeMaere, Steven P. Djordjevic, and Daniela Gaio
- Subjects
Proteome ,Swine ,medicine.medical_treatment ,gut microbiome ,Zoology ,Weaning ,Biology ,Genome ,law.invention ,post-weaning ,03 medical and health sciences ,Probiotic ,law ,medicine ,Animals ,Microbiome ,Phylogeny ,Research Articles ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,carbohydrate active enzymes ,Prebiotic ,030302 biochemistry & molecular biology ,General Medicine ,Metabolism ,Gastrointestinal Microbiome ,Microbial Communities ,Metagenomics ,Metagenome ,Composition (visual arts) ,co-assembly ,time series ,Genome, Bacterial ,shotgun metagenomics - Abstract
Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a
- Published
- 2021
24. A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
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Tiziana Zingali, Linda Falconer, Steven P. Djordjevic, Michael Liu, Matthew Z. DeMaere, Daniela Gaio, Kay Anantanawat, Toni A. Chapman, G.J. Eamens, and Aaron E. Darling
- Subjects
Swine ,medicine.drug_class ,AcademicSubjects/SCI02254 ,Antibiotics ,Health Informatics ,Weaning ,Gut flora ,Data Note ,law.invention ,Microbiology ,03 medical and health sciences ,Probiotic ,Antibiotic resistance ,law ,medicine ,Animals ,Microbiome ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,biology ,030306 microbiology ,Probiotics ,biology.organism_classification ,Gastrointestinal Microbiome ,Computer Science Applications ,Diarrhea ,Metagenomics ,AcademicSubjects/SCI00960 ,Metagenome ,Female ,Sample collection ,medicine.symptom - Abstract
Background Early weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. As an alternative to antibiotic treatment, studies have previously investigated the potential of probiotics for the prevention of postweaning diarrhea. In order to describe the post-weaning gut microbiota, and to study the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we sampled and processed over 800 faecal time-series samples from 126 piglets and 42 sows. Results Here we report on the largest shotgun metagenomic dataset of the pig gut lumen microbiome to date, consisting of >8 Tbp of shotgun metagenomic sequencing data. The animal trial, the workflow from sample collection to sample processing, and the preparation of libraries for sequencing, are described in detail. We provide a preliminary analysis of the dataset, centered on a taxonomic profiling of the samples, and a 16S-based beta diversity analysis of the mothers and the piglets in the first 5 weeks after weaning. Conclusions This study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. Besides investigating the effects of the probiotic and intramuscular antibiotic treatment, the dataset can be explored to assess a wide range of ecological questions with regards to antimicrobial resistance, host-associated microbial and phage communities, and their dynamics during the aging of the host.
- Published
- 2021
25. Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes
- Author
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Matthew Z. DeMaere, Toni A. Chapman, Aaron E. Darling, Kay Anantanawat, Daniela Gaio, and Steven P. Djordjevic
- Subjects
Genetics ,Metagenomics ,Post weaning ,Composition (visual arts) ,Metabolism ,Microbiome ,Biology ,Genome - Abstract
Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50,000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5% of which were classified as >70% complete with a
- Published
- 2021
26. Fruit host-dependent fungal communities in the microbiome of wild Queensland fruit fly larvae
- Author
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Brodie Sutcliffe, Toni A. Chapman, Rajib Majumder, and Phillip W. Taylor
- Subjects
0301 basic medicine ,Range (biology) ,030106 microbiology ,lcsh:Medicine ,Zoology ,Microbiology ,Article ,Pichia ,Hanseniaspora ,03 medical and health sciences ,Symbiosis ,Ascomycota ,Animals ,Microbiome ,lcsh:Science ,Illumina dye sequencing ,Candida ,Bactrocera tryoni ,Larva ,Multidisciplinary ,biology ,Ecology ,Host Microbial Interactions ,Host (biology) ,lcsh:R ,fungi ,Tephritidae ,Australia ,Penicillium ,Zygosaccharomyces ,biology.organism_classification ,030104 developmental biology ,Fruit ,lcsh:Q ,Mycobiome - Abstract
Bactrocera tryoni (Froggatt), the Queensland fruit fly (Qfly), is a highly polyphagous tephritid fly that is widespread in Eastern Australia. Qfly physiology is closely linked with its fungal associates, with particular relationship between Qfly nutrition and yeast or yeast-like fungi. Despite animal-associated fungi typically occurring in multi-species communities, Qfly studies have predominately involved the culture and characterisation of single fungal isolates. Further, only two studies have investigated the fungal communities associated with Qfly, and both have used culture-dependant techniques that overlook non-culturable fungi and hence under-represent, and provide a biased interpretation of, the overall fungal community. In order to explore a potentially hidden fungal diversity and complexity within the Qfly mycobiome, we used culture-independent, high-throughput Illumina sequencing techniques to comprehensively, and holistically characterized the fungal community of Qfly larvae and overcome the culture bias. We collected larvae from a range of fruit hosts along the east coast of Australia, and all had a mycobiome dominated by ascomycetes. The most abundant fungal taxa belonged to the genera Pichia (43%), Candida (20%), Hanseniaspora (10%), Zygosaccharomyces (11%) and Penicillium (7%). We also characterized the fungal communities of fruit hosts, and found a strong degree of overlap between larvae and fruit host communities, suggesting that these communities are intimately inter-connected. Our data suggests that larval fungal communities are acquired from surrounding fruit flesh. It is likely that the physiological benefits of Qfly exposure to fungal communities is primarily due to consumption of these fungi, not through syntrophy/symbiosis between fungi and insect ‘host’.
- Published
- 2020
27. Community composition and development of the post-weaning piglet gut microbiome
- Author
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Daniela Gaio, Matthew Z DeMaere, Kay Anantanawat, Graeme J Eamens, Michael Liu, Tiziana Zingali, Linda Falconer, Toni A Chapman, Steven P Djordjevic, and Aaron E Darling
- Abstract
BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. Studies have previously investigated the effects of probiotics as alternatives to antibiotic treatment for the prevention of post-weaning diarrhea. In order to describe the post-weaning gut microbiota, and the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we processed over 800 faecal time-series samples from 126 piglets and 42 sows, generating over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework.ResultsFactors such as age, litter effects, and breed, by significantly correlating with gut microbial community shifts, can be major confounding factors in the assessment of treatment effects. Intramuscular antibiotic treatment and probiotic treatments were found to correlate with alpha and beta diversity, as well as with a transient establishment of Mollicutes and Lactobacillales, respectively. We found the abundance of certain taxa to correlate with weight gain.ConclusionsOur findings demonstrate that breed, litter, and age, are important contributors to variation in the community composition, and that treatment effects of the antibiotic and probiotic treatments were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The current study shows, by means of a phylogenetic diversity framework, that the post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.
- Published
- 2020
28. Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig
- Author
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Michael Liu, Matthew Z. DeMaere, Linda Falconer, Tiziana Zingali, Daniela Gaio, Kay Anantanawat, Steven P. Djordjevic, Aaron E. Darling, Graeme J. Eamens, and Toni A. Chapman
- Subjects
0301 basic medicine ,Litter (animal) ,biology ,medicine.drug_class ,030106 microbiology ,Antibiotics ,Zoology ,Gut flora ,biology.organism_classification ,Gut microbiome ,Breed ,law.invention ,03 medical and health sciences ,Probiotic ,030104 developmental biology ,Metagenomics ,law ,medicine ,Weaning - Abstract
BackgroundIntensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Besides leading to antimicrobial resistance (AMR), orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. However, although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life.MethodsShotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 piglets and 42 sows were analysed in a phylogenetic framework to characterise the developing gut microbial community composition of post-weaning piglets. We assessed the effects of intramuscular antibiotic treatment and probiotic oral treatment on the diversity of these gut microbial communities using alpha and beta diversity measures.ResultsDifferences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment.DiscussionThe discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.
- Published
- 2020
29. Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring
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Steven P. Djordjevic, Tiziana Zingali, Michael Liu, Cameron J. Reid, Toni A. Chapman, Daniela Gaio, and Aaron E. Darling
- Subjects
Microbiology (medical) ,microbial genomic epidemiology ,Integron ,medicine.disease_cause ,Microbiology ,Genome ,Article ,class 1 integron ,03 medical and health sciences ,Antibiotic resistance ,Virology ,medicine ,antimicrobial resistance ,Insertion sequence ,Gene ,Escherichia coli ,lcsh:QH301-705.5 ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,biology ,porcine E. coli ,030306 microbiology ,Multiple drug resistance ,lcsh:Biology (General) ,commensal E. coli ,biology.protein - Abstract
Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1+). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1+ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1+ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.
- Published
- 2020
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- View/download PDF
30. Virulence not linked with vegetative compatibility groups in Australian cotton Verticillium dahliae isolates
- Author
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William S. Cuddy, P. Dadd-Daigle, D Collins, Maurizio Labbate, P. A. Lonergan, Toni A. Chapman, S Roser, P Bhattacharya, and Karen Kirkby
- Subjects
0607 Plant Biology, 0701 Agriculture, Land and Farm Management, 0703 Crop and Pasture Production ,biology ,Compatibility (mechanics) ,Virulence ,food and beverages ,Plant Science ,Verticillium dahliae ,biology.organism_classification ,Agronomy and Crop Science ,Microbiology ,Conidium - Abstract
Verticillium dahliae, the causal agent of Verticillium wilt, is a soil-borne ascomycete that infects numerous agriculturally important crops globally, including cotton. As a billion-dollar industry, cotton is economically important to Australia and the management of disease such as Verticillium wilt is key for the success of the industry. Internationally, defoliating V. dahliae isolates belonging to Vegetative Compatibility Group (VCG) 1A cause severe damage to cotton, while non-defoliating VCG2A isolates result in significantly less disease. However, in Australia, VCG2A is causing more severe damage to crops in the field than the defoliating VCG1A. This study aimed to replicate field observations in controlled greenhouse conditions. We examined and compared disease symptoms on a range of Australian commercial cotton varieties when inoculated with different V. dahliae VCGs. Seedlings were root dipped in conidial suspensions and assessed over seven weeks. The final disease score, disease over time and root length were analysed. Plant mortality resulted from both V. dahliae VCG1A and VCG2A isolates across all cotton varieties used, confirming that there are virulent VCG2A isolates present in Australia. To our knowledge, although virulent on other plant hosts, V. dahliae VCG2A has not previously been reported to be highly virulent in cotton. We infer that virulence cannot be defined solely by VCG in Australian V. dahliae isolates causing disease in cotton.
- Published
- 2020
31. Microbiome of the Queensland Fruit Fly through Metamorphosis
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Phillip W. Taylor, Rajib Majumder, Brodie Sutcliffe, and Toni A. Chapman
- Subjects
0106 biological sciences ,0301 basic medicine ,Microbiology (medical) ,Next-Generation Sequencing ,gut bacteria and fungi ,media_common.quotation_subject ,yeast and yeast like ,Zoology ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,Article ,03 medical and health sciences ,Virology ,Microbiome ,Metamorphosis ,Domestication ,lcsh:QH301-705.5 ,media_common ,Bactrocera tryoni ,Larva ,biology ,fungi ,biology.organism_classification ,Pupa ,030104 developmental biology ,Taxon ,lcsh:Biology (General) ,PEST analysis - Abstract
Bactrocera tryoni (Froggatt) (Queensland fruit fly, or &ldquo, Qfly&rdquo, ) is a highly polyphagous tephritid fruit fly and a serious economic pest in Australia. Qfly biology is intimately linked to the bacteria and fungi of its microbiome. While there are numerous studies of the microbiome in larvae and adults, the transition of the microbiome through the pupal stage remains unknown. To address this knowledge gap, we used high-throughput Next-Generation Sequencing (NGS) to examine microbial communities at each developmental stage in the Qfly life cycle, targeting the bacterial 16S rRNA and fungal ITS regions. We found that microbial communities were similar at the larval and pupal stage and were also similar between adult males and females, yet there were marked differences between the larval and adult stages. Specific bacterial and fungal taxa are present in the larvae and adults (fed hydrolyzed yeast with sugar) which is likely related to differences in nutritional biology of these life stages. We observed a significant abundance of the Acetobacteraceae at the family level, both in the larval and pupal stages. Conversely, Enterobacteriaceae was highly abundant (>, 80%) only in the adults. The majority of fungal taxa present in Qfly were yeasts or yeast-like fungi. In addition to elucidating changes in the microbiome through developmental stages, this study characterizes the Qfly microbiome present at the establishment of laboratory colonies as they enter the domestication process.
- Published
- 2020
32. Genomic Acquisitions in Emerging Populations of
- Author
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Alvaro L, Perez-Quintero, Mary, Ortiz-Castro, Jillian M, Lang, Adrien, Rieux, Guangxi, Wu, Sanzhen, Liu, Toni A, Chapman, Christine, Chang, Janet, Ziegle, Zhao, Peng, Frank F, White, Maria Cristina, Plazas, Jan E, Leach, and Kirk, Broders
- Subjects
South Africa ,Xanthomonas ,Argentina ,Genomics ,South America ,Zea mays ,Phylogeny ,United States ,Plant Diseases - Published
- 2020
33. Commensal microbiota modulates larval foraging behaviour, development rate and pupal production in Bactrocera tryoni
- Author
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Binh Nguyen, Fleur Ponton, Shabnam Tarahi Tabrizi, Phillip W. Taylor, Ida Lundbäck, Juliano Morimoto, and Toni A. Chapman
- Subjects
Microbiology (medical) ,media_common.quotation_subject ,Foraging ,lcsh:QR1-502 ,Zoology ,Insect ,Development ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Larval behaviour ,Animals ,Symbiosis ,Phylogeny ,030304 developmental biology ,media_common ,Nutrition ,Bactrocera tryoni ,0303 health sciences ,Larva ,biology ,Bacteria ,030306 microbiology ,Research ,Microbiota ,fungi ,Tephritidae ,Pupa ,Larval foraging behaviour ,biology.organism_classification ,Gastrointestinal Microbiome ,Female ,Consummatory Behavior - Abstract
Backround Commensal microbes can promote survival and growth of developing insects, and have important fitness implications in adulthood. Insect larvae can acquire commensal microbes through two main routes: by vertical acquisition from maternal deposition of microbes on the eggshells and by horizontal acquisition from the environment where the larvae develop. To date, however, little is known about how microbes acquired through these different routes interact to shape insect development. In the present study, we investigated how vertically and horizontally acquired microbiota influence larval foraging behaviour, development time to pupation and pupal production in the Queensland fruit fly (‘Qfly’), Bactrocera tryoni. Results Both vertically and horizontally acquired microbiota were required to maximise pupal production in Qfly. Moreover, larvae exposed to both vertically and horizontally acquired microbiota pupated sooner than those exposed to no microbiota, or only to horizontally acquired microbiota. Larval foraging behaviour was also influenced by both vertically and horizontally acquired microbiota. Larvae from treatments exposed to neither vertically nor horizontally acquired microbiota spent more time overall on foraging patches than did larvae of other treatments, and most notably had greater preference for diets with extreme protein or sugar compositions. Conclusion The integrity of the microbiota early in life is important for larval foraging behaviour, development time to pupation, and pupal production in Qflies. These findings highlight the complexity of microbial relations in this species, and provide insights to the importance of exposure to microbial communities during laboratory- or mass-rearing of tephritid fruit flies.
- Published
- 2019
34. Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real-time qPCR assay to detect the genus Dickeya and Dickeya dianthicola
- Author
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Gamze Boluk, Shefali Dobhal, John Rascoe, Mohammad Arif, Michael J. Stulberg, Anne M. Alvarez, Brooke Babler, Mark K. Nakhla, Michael J. Melzer, Alex B. Crockford, and Toni A. Chapman
- Subjects
Dickeya ,Computational biology ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,Genome ,03 medical and health sciences ,Species Specificity ,Limit of Detection ,TaqMan ,False positive paradox ,medicine ,media_common.cataloged_instance ,Multiplex ,European union ,Plant Diseases ,Solanum tuberosum ,media_common ,030304 developmental biology ,Comparative genomics ,0303 health sciences ,Genus Dickeya ,biology ,030306 microbiology ,Pathogenic bacteria ,Genomics ,General Medicine ,biology.organism_classification ,Multiplex Polymerase Chain Reaction ,Gammaproteobacteria ,Genome, Bacterial ,Biotechnology - Abstract
AimsDickeya species are high consequence plant pathogenic bacteria listed among the quarantine pathogens of the European Union; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate, and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. Therefore, a multiplex TaqMan qPCR was developed for sensitive detection of Dickeya spp. and specifically, D. dianthicola.Methods and ResultsA signature genomic region for the genus Dickeya (mglA/mglC) and unique genomic region for D. dianthicola (alcohol dehydrogenase) were identified using a whole genome based comparative genomics approach. The developed multiplex TaqMan qPCR was validated using extensive inclusivity and exclusivity panels, and naturally/artificially infected samples to confirm broad range detection capability and specificity. Both sensitivity and spiked assays showed detection limit of 10 fg DNA.ConclusionThe developed multiplex assay is sensitive and reliable to detect Dickeya spp. and D. dianthicola with no false positives or false negatives. It was able to detect mixed infection from naturally and artificially infected plant materials.Significance and ImpactThe developed assay will serve as a practical tool for screening of propagative material, monitoring the presence and distribution, and quantification of target pathogens in a breeding program. The assay also has applications in routine diagnostics, biosecurity and microbial forensics.
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- 2019
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- View/download PDF
35. Developmental Stage-Specific Microbiota Profile of a Polyphagous Fly
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Toni A. Chapman, Juliano Morimoto, Fleur Ponton, Rajib Majumder, Ida Lundbäck, Jack Horlick, and Phillip W. Taylor
- Subjects
Developmental stage ,Symbiosis ,Evolutionary biology ,media_common.quotation_subject ,fungi ,Endopterygota ,Microbiome ,Biology ,Metamorphosis ,biology.organism_classification ,media_common - Abstract
Gut bacteria play a key role in insect fitness, but the changes in gut microbiome profile across developmental stages of holometabolous insects remains little explored. Understanding changes in the microbiome across life stages is an important step toward understanding the associated shifts in functional relationships and trade-offs. Here, we characterised the microbiome of larvae, pupae, and adults of the highly polyphagous fruit fly Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) using next-generation sequencing. We sampled individuals from colonies that had been recently introduced to the laboratory environment from naturally infested fruits at generations one (‘G1’) and five (‘G5’). Alpha diversity increased across developmental stages at both G1 and G5, with maximum diversity in adults. Community composition changed across developmental stages and between generations. In G1, larval and pupal microbiomes were dominated by the genus Asaia whereas adult microbiomes were dominated by Enterobacter. In G5, larval and pupal microbiomes contained a high relative abundance of Asaia, but pupae also had a high relative abundance of Staphylococcus and Burkholderia, and there were no dominant patterns in adults. Our findings provide insights into the developmental stage-dependent microbiome associations of a polyphagous fly, and how host-symbiont interactions change at each life stage through the transition from nature to laboratory environments.
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- 2019
36. Next-Generation Sequencing reveals relationship between the larval microbiome and food substrate in the polyphagous Queensland fruit fly
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Brodie Sutcliffe, Rajib Majumder, Phillip W. Taylor, and Toni A. Chapman
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0301 basic medicine ,DNA, Bacterial ,media_common.quotation_subject ,Science ,030106 microbiology ,Zoology ,Insect ,Microbiology ,DNA sequencing ,Article ,03 medical and health sciences ,Symbiosis ,Animals ,Microbiome ,media_common ,Bactrocera tryoni ,Larva ,Multidisciplinary ,biology ,Host Microbial Interactions ,Host (biology) ,fungi ,Tephritidae ,Australia ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,biology.organism_classification ,Diet ,Gastrointestinal Microbiome ,030104 developmental biology ,Microbial population biology ,Fruit ,Medicine - Abstract
Insects typically host substantial microbial communities (the ‘microbiome’) that can serve as a vital source of nutrients and also acts as a modulator of immune function. While recent studies have shown that diet is an important influence on the gut microbiome, very little is known about the dynamics underpinning microbial acquisition from natural food sources. Here, we addressed this gap by comparing the microbiome of larvae of the polyphagous fruit fly Bactrocera tryoni (‘Queensland fruit fly’) that were collected from five different fruit types (sapodilla [from two different localities], hog plum, pomegranate, green apple, and quince) from North-east to South-east Australia. Using Next-Generation Sequencing on the Illumina MiSeq platform, we addressed two questions: (1) what bacterial communities are available to B. tryoni larvae from different host fruit; and (2) how does the microbiome vary between B. tryoni larvae and its host fruit? The abundant bacterial taxa were similar for B. tryoni larvae from different fruit despite significant differences in the overall microbial community compositions. Our study suggests that the bacterial community structure of B. tryoni larvae is related less to the host fruit (diet) microbiome and more to vertical transfer of the microbiome during egg laying. Our findings also suggest that geographic location may play a quite limited role in structuring of larval microbiomes. This is the first study to use Next-Generation Sequencing to analyze the microbiome of B. tryoni larvae together with the host fruit, an approach that has enabled greatly increased resolution of relationships between the insect’s microbiome and that of the surrounding host tissues.
- Published
- 2019
37. Genomic sequence analysis reveals diversity of Australian Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli
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Toni A. Chapman, Brendan Rodoni, R. Roach, Cherie Gambley, Ross Mann, and Roger G. Shivas
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0106 biological sciences ,Xanthomonas ,lcsh:QH426-470 ,Sequence analysis ,lcsh:Biotechnology ,Virulence ,Biology ,Polymorphism, Single Nucleotide ,01 natural sciences ,Genome ,03 medical and health sciences ,Solanum lycopersicum ,Phylogenetics ,lcsh:TP248.13-248.65 ,Secretion system ,Genetics ,Phylogeny ,Plant Diseases ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,Genetic diversity ,Phylogenetic tree ,Pan genome ,Pan-genome ,Biodiversity ,Genomics ,Cell wall degrading enzymes ,lcsh:Genetics ,Capsicum ,Genome, Bacterial ,CAZymes ,Research Article ,Plasmids ,010606 plant biology & botany ,Biotechnology - Abstract
Background The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. The aim of this study was to confirm the identities of these Australian Xanthomonas species and classify them in comparison to overseas isolates. Analysis of whole genome sequence allows for the investigation of bacterial population structure, pathogenicity and gene exchange, resulting in better management strategies and biosecurity. Results Phylogenetic analysis of the core genome alignments and SNP data grouped strains in distinct clades. Patterns observed in average nucleotide identity, pan genome structure, effector and carbohydrate active enzyme profiles reflected the whole genome phylogeny and highlight taxonomic issues in X. perforans and X. euvesicatoria. Circular sequences with similarity to previously characterised plasmids were identified, and plasmids of similar sizes were isolated. Potential false positive and false negative plasmid assemblies were discussed. Effector patterns that may influence virulence on host plant species were analysed in pathogenic and non-pathogenic xanthomonads. Conclusions The phylogeny presented here confirmed X. vesicatoria, X. arboricola, X. euvesicatoria and X. perforans and a clade of an uncharacterised Xanthomonas species shown to be genetically distinct from all other strains of this study. The taxonomic status of X. perforans and X. euvesicatoria as one species is discussed in relation to whole genome phylogeny and phenotypic traits. The patterns evident in enzyme and plasmid profiles indicate worldwide exchange of genetic material with the potential to introduce new virulence elements into local bacterial populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5600-x) contains supplementary material, which is available to authorized users.
- Published
- 2019
38. Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia
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Cameron J. Reid, Piklu Roy Chowdhury, Matthew Z. DeMaere, Steven P. Djordjevic, Michael Liu, Ethan R. Wyrsch, and Toni A. Chapman
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Transposable element ,lcsh:TX341-641 ,Locus (genetics) ,Drug resistance ,Biology ,Horticulture ,Management, Monitoring, Policy and Law ,medicine.disease_cause ,Integron ,Plasmid ,antimicrobial resistance (AMR) ,plasmid ,Escherichia coli ,genomics ,medicine ,Genetics ,Global and Planetary Change ,lcsh:TP368-456 ,Ecology ,Nucleic acid sequence ,biology.organism_classification ,lcsh:Food processing and manufacture ,Salmonella enterica ,biology.protein ,epidemiology ,lcsh:Nutrition. Foods and food supply ,Agronomy and Crop Science ,Food Science - Abstract
© Copyright © 2019 Wyrsch, Reid, DeMaere, Liu, Chapman, Roy Chowdhury and Djordjevic. IncHI2 ST3 plasmids are known carriers of multiple antimicrobial resistance genes. Complete plasmid sequences from multiple drug resistant Escherichia coli circulating in Australian swine is however limited. Here we sequenced two related IncHI2 ST3 plasmids, pSDE-SvHI2, and pSDC-F2_12BHI2, from phylogenetically unrelated multiple-drug resistant Escherichia coli strains SvETEC (CC23:O157:H19) and F2_12B (ST93:O7:H4) from geographically disparate pig production operations in New South Wales, Australia. Unicycler was used to co-assemble short read (Illumina) and long read (PacBio SMRT) nucleotide sequence data. The plasmids encoded three drug-resistance loci, two of which carried class 1 integrons. One integron, hosting drfA12-orfF-aadA2, was within a hybrid Tn1721/Tn21, with the second residing within a copper/silver resistance transposon, comprising part of an atypical sul3-associated structure. The third resistance locus was flanked by IS15DI and encoded neomycin resistance (neoR). An oqx-encoding transposon (quinolone resistance), similar in structure to Tn6010, was identified only in pSDC-F2_12BHI2. Both plasmids showed high sequence identity to plasmid pSTM6-275, recently described in Salmonella enterica serotype 1,4,[5],12:i:- that has risen to prominence and become endemic in Australia. IncHI2 ST3 plasmids circulating in commensal and pathogenic E. coli from Australian swine belong to a lineage of plasmids often in association with sul3 and host multiple complex antibiotic and metal resistance structures, formed in part by IS26.
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- 2019
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39. Genomic acquisitions in emerging populations ofXanthomonas vasicolapv.vasculoruminfecting corn in the U.S. and Argentina
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Zhao Peng, Maria Cristina Plazas, Jillian M. Lang, Sanzhen Liu, Frank F. White, Guangxi Wu, Janet Ziegle, Mary Ortiz-Castro, Kirk Broders, Alvaro L. Pérez-Quintero, Toni A. Chapman, Christine Chang, and Jan E. Leach
- Subjects
Comparative genomics ,Genetics ,Phylogenetic tree ,Horizontal gene transfer ,Xanthomonas vasicola ,Virulence ,Biology ,Genome ,Bacterial leaf streak ,Prophage - Abstract
Xanthomonas vasicolapv.vasculorum (Xvv)is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this bacteria have greatly increased in the past years in South America and in the U.S., where it is now present in most of the corn producing states. Phenotypic characterization showed that the emerging U.S. and South American Xvvpopulations may have increased virulence in corn compared to older strains. To understand the genetic mechanisms behind the increased virulence in this group, we used comparative genomics to identify gene acquisitions inXvvgenomes from the U.S. and Argentina. We sequenced 41 genomes ofXvvand the related sorghum-infectingX. vasicolapv.holcicola(Xvh).A comparison of all availableX. vasicolagenomes showed the phylogenetic relationships in the group and identified clusters of genes associated with the emergingXvvpopulations. The newly acquired gene clusters showed evidence of horizontal transfer toXvvand included candidate virulence factors. One cluster, in particular, corresponded to a prophage transferred fromXvhto allXvvfrom Argentina and the U.S. The prophage contains putative secreted proteins, which represent candidates for virulence determinants in these populations and await further molecular characterization.
- Published
- 2019
- Full Text
- View/download PDF
40. Interactions between ecological factors in the developmental environment modulate pupal and adult traits in a polyphagous fly
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Anh Than, Phillip W. Taylor, Toni A. Chapman, Fleur Ponton, Binh Nguyen, and Juliano Morimoto
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0106 biological sciences ,Nutritional composition ,Body weight ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Frugivore ,Dry weight ,lcsh:QH540-549.5 ,microbiota ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Nature and Landscape Conservation ,Original Research ,Bactrocera tryoni ,0303 health sciences ,Larva ,density ,Ecology ,biology ,fungi ,biology.organism_classification ,crowding ,Pupa ,animal–microbe competition ,larval competition ,lcsh:Ecology ,Sex ratio - Abstract
In holometabolous insects, adult fitness depends on the quantity and quality of resource acquired at the larval stage. Diverse ecological factors can influence larval resource acquisition, but little is known about how these factors in the larval environment interact to modulate larval development and adult traits. Here, we addressed this gap by considering how key ecological factors of larval density, diet nutritional composition, and microbial growth interact to modulate pupal and adult traits in a polyphagous tephritid fruit fly, Bactrocera tryoni (aka “Queensland fruit fly”). Larvae were allowed to develop at two larval densities (low and high), on diets that were protein‐rich, standard, or sugar‐rich and prepared with or without preservatives to inhibit or encourage microbial growth, respectively. Percentage of adult emergence and adult sex ratio were not affected by the interaction between diet composition, larval density, and preservative treatments, although low preservative content increased adult emergence in sugar‐rich diets but decreased adult emergence in protein‐rich and standard diets. Pupal weight, male and female adult dry weight, and female (but not male) body energetic reserves were affected by a strong three‐way interaction between diet composition, larval density, and preservative treatment, whereby in general, low preservative content increased pupal weight and female lipid storage in sugar‐rich diets particularly at low‐larval density and differentially modulated the decrease in adult body weight caused by larval density across diets. Our findings provide insights into the ecological factors modulating larval development of a polyphagous fly species and shed light into the ecological complexity of the larval developmental environment in frugivorous insects.
- Published
- 2018
41. Pathogenicity and copper tolerance in Australian Xanthomonas species associated with bacterial leaf spot
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Brendan Rodoni, Toni A. Chapman, Ross Mann, Roger G. Shivas, R. Roach, and Cherie Gambley
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0106 biological sciences ,Genetics ,biology ,food and beverages ,Bacterial growth ,biology.organism_classification ,01 natural sciences ,Phenotype ,010602 entomology ,Plasmid ,Protein sequencing ,Xanthomonas ,Leaf spot ,Agronomy and Crop Science ,Gene ,Function (biology) ,010606 plant biology & botany - Abstract
Recent studies into the distribution of Xanthomonas species causing Bacterial Leaf Spot (BLS) in Australian solanaceous crops detail varied genomic profiles that may influence pathogenicity. These genomic studies are expanded upon here by reporting the pathogenicity, race and copper tolerance of the previously sequenced Xanthomonas strains. Capsicum (Yolo Wonder), tomato (Grosse Lisse) and differential lines of capsicum (Early Cal-Wonder) were used to determine pathogenicity and race. Copper tolerance of 44 Xanthomonas strains was measured by observing bacterial growth on copper sulphate amended media. Protein sequence associated with these traits was detected using genomic analysis and compared using protein alignments. Only strains of X. euvesicatoria (16 strains) were found to be pathogenic on both tomato and capsicum. These were determined to be race 4 and 9. High copper tolerance was detected in the majority of Xanthomonas strains tested. Multiple copper resistance and avirulence proteins were detected in genomic sequence. Relatively few of these were associated with plasmid sequences. The genomic basis for copper tolerance was determined to be complex, as the tolerance thresholds did not directly correlate with gene number or presence. Similarly, pathogenicity of the strains was also not always clearly linked with presence or absence of specific Avr genes. This study highlights the need for detailed and ongoing investigations into the function of these proteins and how they produce the phenotypes that affect crop production.
- Published
- 2020
42. Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae
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Olivia L. Reynolds, Markus Riegler, Toni A. Chapman, Aaron E. Darling, Catherine Burke, and Ania T. Deutscher
- Subjects
0301 basic medicine ,Microbiology (medical) ,030106 microbiology ,Zoology ,Gut flora ,Microbiology ,lcsh:Microbial ecology ,Bactrocera tryoni ,03 medical and health sciences ,Sterile insect technique ,Illumina ,Insect–microbe interactions ,Tephritidae ,RNA, Ribosomal, 16S ,Animals ,Microbiome ,Symbiosis ,Larva ,Genome ,biology ,Research ,Microbiota ,Diptera ,fungi ,High-Throughput Nucleotide Sequencing ,Host–microbe interactions ,Microbial symbiont ,biology.organism_classification ,16S ribosomal RNA ,Gastrointestinal Microbiome ,030104 developmental biology ,Acetic acid bacteria ,Acetobacteraceae ,lcsh:QR100-130 ,PEST analysis - Abstract
Background Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome. Read lengths of previous fruit fly next-generation sequencing (NGS) studies have limited the resolution of microbiome studies, and the diversity within populations is often overlooked. In this study, we used a new near full-length (> 1300 nt) 16S rRNA gene amplicon NGS approach to characterize gut bacterial communities of individual B. tryoni larvae from two field populations (developing in peaches) and three domesticated populations (mass- or laboratory-reared on artificial diets). Results Near full-length 16S rRNA gene sequences were obtained for 56 B. tryoni larvae. OTU clustering at 99% similarity revealed that gut bacterial diversity was low and significantly lower in domesticated larvae. Bacteria commonly associated with fruit (Acetobacteraceae, Enterobacteriaceae, and Leuconostocaceae) were detected in wild larvae, but were largely absent from domesticated larvae. However, Asaia, an acetic acid bacterium not frequently detected within adult tephritid species, was detected in larvae of both wild and domesticated populations (55 out of 56 larval gut samples). Larvae from the same single peach shared a similar gut bacterial profile, whereas larvae from different peaches collected from the same tree had different gut bacterial profiles. Clustering of the Asaia near full-length sequences at 100% similarity showed that the wild flies from different locations had different Asaia strains. Conclusions Variation in the gut bacterial communities of B. tryoni larvae depends on diet, domestication, and horizontal acquisition. Bacterial variation in wild larvae suggests that more than one bacterial species can perform the same functional role; however, Asaia could be an important gut bacterium in larvae and warrants further study. A greater understanding of the functions of the bacteria detected in larvae could lead to increased fly quality and performance as part of the SIT. Electronic supplementary material The online version of this article (10.1186/s40168-018-0463-y) contains supplementary material, which is available to authorized users.
- Published
- 2018
43. Emerging Pathogens and Diseases: Where do they come from?
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James P. Stack, Toni A Chapman, Brendan Rodoni, Rachel Mann, and Grant R. Smith
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business.industry ,Open access publishing ,Internet privacy ,General Medicine ,business - Published
- 2018
44. Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26
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Tiziana Zingali, Ethan R. Wyrsch, Cameron J. Reid, Piklu Roy Chowdhury, Steven P. Djordjevic, Toni A. Chapman, Aaron E. Darling, and Michael Liu
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0301 basic medicine ,Microbial Evolution and Epidemiology: Population Genomics ,Whole genome sequence analysis ,Swine ,microbial genomic epidemiology ,medicine.disease_cause ,Integron ,Integrons ,Feces ,Drug Resistance, Multiple, Bacterial ,Zoonoses ,Genetics ,0303 health sciences ,Virulence ,General Medicine ,commensal E. coli ,Environmental Pollutants ,Research Article ,Gene Transfer, Horizontal ,IS26 ,Sequence analysis ,030106 microbiology ,Genomics ,Biology ,Microbiology ,03 medical and health sciences ,Antibiotic resistance ,Genetic variation ,Escherichia coli ,medicine ,Animals ,Humans ,antimicrobial resistance ,Symbiosis ,Gene ,030304 developmental biology ,Whole genome sequencing ,Whole Genome Sequencing ,030306 microbiology ,Australia ,Genetic Variation ,Mutagenesis, Insertional ,030104 developmental biology ,Carriage ,Food Microbiology ,biology.protein ,animal E. coli - Abstract
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial resistance and virulence-associated genes (VAGs) and the zoonotic potential of commensalEscherichia colifrom swine is largely unknown. Furthermore, little is known about the role of commensalE. colias contributors to the mobilisation of antimicrobial resistance genes between food animals and the environment. Here, we report whole genome sequence analysis of 141E. colifrom the faeces of healthy pigs. Most strains belonged to phylogroups A and B1 and carried i) a class 1 integron; ii) VAGs linked with extraintestinal infection in humans; iii) antimicrobial resistance genesblaTEM, aphAl, cmlA, strAB, tet(A)A,dfrA12, dfrA5, sul1, sul2, sul3; iv)IS26;and v) heavy metal resistance genes (merA, cusA, terA). Carriage of the sulphonamide resistance genesul3was notable in this study. The 141 strains belonged to 42 multilocus sequence types, but clonal complex 10 featured prominently. Structurally diverse class 1 integrons that were frequently associated with IS26 carried unique genetic features that were also identified in extraintestinal pathogenicE. coli(ExPEC) from humans. This study provides the first detailed genomic analysis and point of reference for commensalE. coliof porcine origin, facilitating tracking of specific lineages and the mobile resistance genes they carry.Conflict of Interest StatementNone to declare.
- Published
- 2017
45. Phylogenetic and molecular insights into the evolution of multidrug-resistant porcine enterotoxigenic Escherichia coli in Australia
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Mitchell D. Groves, Toni A. Chapman, Darren J. Trott, John M. Fairbrother, Ren Zhang, David Jordan, Sam Abraham, Matthew G. Smith, and David M. Gordon
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Microbiology (medical) ,Genotype ,Swine ,Virulence Factors ,Microbial Sensitivity Tests ,Biology ,Serogroup ,medicine.disease_cause ,Integron ,Microbiology ,Evolution, Molecular ,Antibiotic resistance ,Drug Resistance, Multiple, Bacterial ,Enterotoxigenic Escherichia coli ,medicine ,Animals ,Cluster Analysis ,Pharmacology (medical) ,Typing ,Escherichia coli Infections ,Swine Diseases ,Molecular Epidemiology ,Molecular epidemiology ,Australia ,General Medicine ,bacterial infections and mycoses ,Random Amplified Polymorphic DNA Technique ,RAPD ,Multiple drug resistance ,Infectious Diseases ,Genes, Bacterial ,biology.protein ,Multilocus sequence typing ,Multilocus Sequence Typing - Abstract
This study investigated the phylogeny and molecular epidemiology of Australian porcine enterotoxigenic Escherichia coli (ETEC) isolates (n = 70) by performing multilocus sequence typing (MLST), random amplified polymorphic DNA (RAPD) analysis, virulence gene analysis, plasmid, bacteriocin, integron and antimicrobial resistance gene typing, and antimicrobial susceptibility phenotyping. Isolates of the most commonly observed O serogroup (O149) were highly clonal with a lower frequency of antimicrobial resistance compared with the less common O141 serogroup isolates, which were more genetically diverse and resistant to a greater array of antimicrobials. The O149 and O141 isolates belonged to sequence types (STs) ST100 and ST1260, respectively. A small number of new STs were identified for the least common serogroups, including O157 (ST4245), O138 (ST4244), O139 (ST4246) and O8 (ST4247). A high frequency of plasmid replicons was observed among all ETEC isolates. However, O149 isolates predominantly carried IncFIB, I1, HI1 and FIC, whereas O141 isolates carried a more varied array, including IncI1, FIB, FIC, HI1, I1, Y and, most significantly, A/C. O141 isolates also possessed a greater diversity of bacteriocins, with almost one-half of the isolates carrying colicin E3 (44.4%; 12/27) and E7 (48.1%; 13/27). This study shows that Australian porcine ETEC are distinct from isolates obtained in other parts of the world with respect to the MLST profile and the absence of resistance to critically important antimicrobials, including third-generation cephalosporins and fluoroquinolones.
- Published
- 2014
46. Genomic microbial epidemiology is needed to comprehend the global problem of antibiotic resistance and to improve pathogen diagnosis
- Author
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Piklu Roy Chowdhury, Steven P. Djordjevic, Toni A. Chapman, Ethan R. Wyrsch, Ian G. Charles, and Jeffrey M. Hammond
- Subjects
0301 basic medicine ,Microbiology (medical) ,medicine.medical_specialty ,medicine.drug_class ,030106 microbiology ,Antibiotics ,Virulence ,Disease ,Review ,Biology ,genomic epidemiology ,medicine.disease_cause ,Microbiology ,03 medical and health sciences ,Antibiotic resistance ,Epidemiology ,medicine ,Escherichia coli ,environmental pollutants ,multiple antibiotic resistance ,Pathogen ,agriculture ,animal production ,Antimicrobial ,030104 developmental biology - Abstract
© 2016 Wyrsch, Roy Chowdhury, Chapman, Charles, Hammond and Djordjevic. Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.
- Published
- 2016
47. Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease
- Author
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Piklu Roy Chowdhury, Steven P. Djordjevic, Ian G. Charles, Paul Worden, Matthew Z. DeMaere, Aaron E. Darling, and Toni A. Chapman
- Subjects
0301 basic medicine ,Microbiology (medical) ,Gastrointestinal Diseases ,Swine ,Bacterial Toxins ,Molecular Sequence Data ,030106 microbiology ,Virulence ,Locus (genetics) ,Biology ,medicine.disease_cause ,Microbiology ,Zoonosis ,03 medical and health sciences ,Bacterial Proteins ,medicine ,Animals ,Humans ,Amino Acid Sequence ,Horses ,Phylogeny ,Swine Diseases ,Comparative genomics ,Clostridioides difficile ,Toxin ,Clostridium difficile ,medicine.disease ,Toxin-negative isolates ,Parasitology ,Horizontal gene transfer ,Clostridium Infections ,Horse Diseases ,CDI ,Sequence Alignment ,Research Article - Abstract
Background Clostridium difficile infections (CDI) are a significant health problem to humans and food animals. Clostridial toxins ToxA and ToxB encoded by genes tcdA and tcdB are located on a pathogenicity locus known as the PaLoc and are the major virulence factors of C. difficile. While toxin-negative strains of C. difficile are often isolated from faeces of animals and patients suffering from CDI, they are not considered to play a role in disease. Toxin-negative strains of C. difficile have been used successfully to treat recurring CDI but their propensity to acquire the PaLoc via lateral gene transfer and express clinically relevant levels of toxins has reinforced the need to characterise them genetically. In addition, further studies that examine the pathogenic potential of toxin-negative strains of C. difficile and the frequency by which toxin-negative strains may acquire the PaLoc are needed. Results We undertook a comparative genomic analysis of five Australian toxin-negative isolates of C. difficile that lack tcdA, tcdB and both binary toxin genes cdtA and cdtB that were recovered from humans and farm animals with symptoms of gastrointestinal disease. Our analyses show that the five C. difficile isolates cluster closely with virulent toxigenic strains of C. difficile belonging to the same sequence type (ST) and have virulence gene profiles akin to those in toxigenic strains. Furthermore, phage acquisition appears to have played a key role in the evolution of C. difficile. Conclusions Our results are consistent with the C. difficile global population structure comprising six clades each containing both toxin-positive and toxin-negative strains. Our data also suggests that toxin-negative strains of C. difficile encode a repertoire of putative virulence factors that are similar to those found in toxigenic strains of C. difficile, raising the possibility that acquisition of PaLoc by toxin-negative strains poses a threat to human health. Studies in appropriate animal models are needed to examine the pathogenic potential of toxin-negative strains of C. difficile and to determine the frequency by which toxin-negative strains may acquire the PaLoc. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0653-3) contains supplementary material, which is available to authorized users.
- Published
- 2016
48. First report of the presence of Verticillium dahliae VCG1A in Australia
- Author
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Toni A. Chapman, Karen Kirkby, Grant A. Chambers, Rafael M. Jiménez-Díaz, and Cotton Research and Development Corporation (Australia)
- Subjects
0106 biological sciences ,0301 basic medicine ,Veterinary medicine ,biology ,Verticillium wilt ,food and beverages ,Virulence ,Plant Science ,Cotton ,biology.organism_classification ,01 natural sciences ,Defoliating ,03 medical and health sciences ,030104 developmental biology ,Non-defoliating ,Disease severity ,Botany ,Verticillium dahliae ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
For 32 years, cotton grown in NSW has been monitored for Verticillium wilt, with isolates of Verticillium dahliae Kleb. stored in the NSW Department of Primary Industries culture collection. An increase in disease severity in the 2013/14 season suggests a more virulent pathogenic strain may have been introduced. Eight V. dahliae isolates were selected for vegetative compatibility group (VCG) analysis using molecular assays and nit mutant testing. Two of the eight isolates were identified as the highly virulent defoliating VCG1A, making this the first record of VCG1A in Australia., This research was made possible through funding from the Cotton Research and Development Corporation (CRDC).
- Published
- 2016
49. Molecular Characterization of Escherichia coli Strains That Cause Symptomatic and Asymptomatic Urinary Tract Infections
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James Chin, Toni A. Chapman, Sam Abraham, Mark A. Schembri, Makrina Totsika, Ren Zhang, and Amanda N. Mabbett
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Microbiology (medical) ,Genotype ,Virulence Factors ,Virulence ,Bacteriuria ,Biology ,medicine.disease_cause ,Microbiology ,Plasmid ,Bacteriocins ,Bacteriocin ,Escherichia ,Escherichia coli ,medicine ,Cluster Analysis ,Humans ,Escherichia coli Infections ,Asymptomatic Diseases ,Bacteriology ,Microcin ,medicine.disease ,biology.organism_classification ,Virology ,Random Amplified Polymorphic DNA Technique ,Molecular Typing ,Urinary Tract Infections ,Plasmids - Abstract
The differences between Escherichia coli strains associated with symptomatic and asymptomatic urinary tract infections (UTIs) remain to be properly determined. Here we examined the prevalence of plasmid types and bacteriocins, as well as genetic relatedness, in a defined collection of E. coli strains that cause UTIs. Comparative analysis identified a subgroup of strains with a high number of virulence genes (VGs) and microcins M/H47. We also identified associations between microcin genes, VGs, and specific plasmid types.
- Published
- 2012
50. Genetic relatedness and virulence gene profiles of Escherichia coli strains isolated from septicaemic and uroseptic patients
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J. Faoagali, Mohammad Katouli, Nubia L. Ramos, Helen V. Smith, Toni A. Chapman, James Chin, M. L. Saayman, J. R. Tucker, and Annelie Brauner
- Subjects
DNA, Bacterial ,Microbiology (medical) ,Genotype ,Virulence Factors ,Virulence ,Biology ,medicine.disease_cause ,Bacterial Adhesion ,Cell Line ,Microbiology ,Sepsis ,Genetic variation ,Escherichia coli ,medicine ,Cluster Analysis ,Humans ,Gene ,Escherichia coli Infections ,Phylogeny ,Genetics ,Phylogenetic tree ,Escherichia coli Proteins ,General Medicine ,DNA Fingerprinting ,Bacterial Typing Techniques ,Random Amplified Polymorphic DNA Technique ,RAPD ,Phenotype ,Infectious Diseases ,DNA profiling ,Urinary Tract Infections - Abstract
We investigated the relationship between clonality and virulence factors (VFs) of a collection of Escherichia coli strains isolated from septicaemic and uroseptic patients with respect to their origin of translocation. Forty septicaemic and 30 uroseptic strains of E. coli were tested for their phylogenetic groupings, genetic relatedness using randomly amplified polymorphic DNA (RAPD), biochemical fingerprinting method (biochemical phenotypes [BPTs]), adherence to HT-29 cells and the presence of 56 E. coli VF genes. Strains belonging to phylogenetic groups B2 and D constituted 93% of all strains. Fifty-four (77%) strains belonged to two major BPT/RAPD clusters (A and B), with cluster A carrying significantly (P = 0.0099) more uroseptic strains. The degree of adhesion to HT-29 cells of uroseptic strains was significantly (P = 0.0012) greater than that of septicaemic strains. Of the 56 VF genes tested, pap genes was the only group that were found significantly (P < 0.0001) more often among uroseptic isolates. Phylogenetic group B2 contained a significantly higher number of strains carrying pap genes than those in group D. We conclude that uroseptic E. coli are clonally different from septicaemic strains, carry more pap genes and predominantly adhere more to the HT-29 cell model of the gut.
- Published
- 2009
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