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Staphylococcus aureus infections of the central nervous system are serious and can be fatal. S. aureus is commonly present in the nasal cavity, and after injury to the nasal epithelium it can rapidly invade the brain via the olfactory nerve. The trigeminal nerve constitutes another potential route of brain infection. The glia of these nerves, olfactory ensheathing cells (OECs) and trigeminal nerve Schwann cells (TgSCs), as well as astrocytes populating the glia limitans layer, can phagocytose bacteria. Whilst some glial responses to S. aureus have been studied, the specific responses of different glial types are unknown. Here, we compared how primary mouse OECs, TgSCs, astrocytes and microglia responded to S. aureus. All glial types internalized the bacteria within phagolysosomes, and S. aureus-conjugated BioParticles could be tracked with subtle but significant differences in time-course of phagocytosis between glial types. Live bacteria could be isolated from all glia after 24 h in culture, and microglia, OECs and TgSCs exhibited better protection against intracellular S. aureus survival than astrocytes. All glial types responded to the bacteria by cytokine secretion. Overall, OECs secreted the lowest level of cytokines, suggesting that these cells, despite showing strong capacity for phagocytosis, have immunomodulatory functions that can be relevant for neural repair.

Vibrio cholerae is the etiological agent of cholera, a severe diarrheal disease, which can occur as either an epidemic or sporadic disease. Cholera pandemic-causing V. cholerae O1 and O139 serogroups originated from the Indian subcontinent and spread globally and millions of lives are lost each year, mainly in developing and underdeveloped countries due to this disease. V. cholerae O1 is further classified as classical and El Tor biotype which can produce biotype specific cholera toxin (CT). Since 1961, the current seventh pandemic El Tor strains replaced the sixth pandemic strains resulting in the classical biotype strain that produces classical CT. The ongoing evolution of Atypical El Tor V. cholerae srains encoding classical CT is of global concern. The severity in the pathophysiology of these Atypical El Tor strains is significantly higher than El Tor or classical strains. Pathogenesis of V. cholerae is a complex process that involves coordinated expression of different sets of virulence-associated genes to cause disease. We are yet to understand the complete virulence profile of V. cholerae, including direct and indirect expression of genes involved in its survival and stress adaptation in the host. In recent years, whole genome sequencing has paved the way for better understanding of the evolution and strain distribution, outbreak identification and pathogen surveillance for the implementation of direct infection control measures in the clinic against many infectious pathogens including V. cholerae. This review provides a synopsis of recent studies that have contributed to the understanding of the evolution, distribution and genetics of the seventh pandemic Atypical El Tor V. cholerae strains.

The endometrial cavity is an upper genital tract site previously thought as sterile, however, advances in culture-independent, next-generation sequencing technology have revealed that this low-biomass site harbors a rich microbial community which includes multiple Lactobacillus species. These bacteria are considered to be the most abundant non-pathogenic genital tract commensals. Next-generation sequencing of the female lower genital tract has revealed significant variation amongst microbial community composition with respect to Lactobacillus sp. in samples collected from healthy women and women with urogenital conditions. The aim of this study was to evaluate our ability to characterize members of the genital tract microbial community to species-level taxonomy using variable regions of the 16S rRNA gene. Samples were interrogated for the presence of microbial DNA using next-generation sequencing technology that targets the V5–V8 regions of the 16S rRNA gene and compared to speciation using qPCR. We also performed re-analysis of published data using alternate variable regions of the 16S rRNA gene. In this analysis, we explore next-generation sequencing of clinical genital tract isolates as a method for high throughput identification to species-level of key Lactobacillus sp. Data revealed that characterization of genital tract taxa is hindered by a lack of a consensus protocol and 16S rRNA gene region target allowing comparison between studies.

Wastewater-based epidemiology (WBE) demonstrates potential for COVID-19 community transmission monitoring; however, data on the stability of SARS-CoV-2 RNA in wastewater are needed to interpret WBE results. The decay rates of RNA from SARS-CoV-2 and a potential surrogate, murine hepatitis virus (MHV), were investigated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in untreated wastewater, autoclaved wastewater, and dechlorinated tap water stored at 4, 15, 25, and 37 °C. Temperature, followed by matrix type, most greatly influenced SARS-CoV-2 RNA first-order decay rates (k). The average T90 (time required for 1-log10 reduction) of SARS-CoV-2 RNA ranged from 8.04 to 27.8 days in untreated wastewater, 5.71 to 43.2 days in autoclaved wastewater, and 9.40 to 58.6 days in tap water. The average T90 for RNA of MHV at 4 to 37 °C ranged from 7.44 to 56.6 days in untreated wastewater, 5.58–43.1 days in autoclaved wastewater, and 10.9 to 43.9 days in tap water. There was no statistically significant difference between RNA decay of SARS-CoV-2 and MHV; thus, MHV is suggested as a suitable persistence surrogate. Decay rate constants for all temperatures were comparable across all matrices for both viral RNAs, except in untreated wastewater for SARS-CoV-2, which showed less sensitivity to elevated temperatures. Therefore, SARS-CoV-2 RNA is likely to persist long enough in untreated wastewater to permit reliable detection for WBE application.

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen, and serotype O157:H7 is typically associated with severe disease. Australian STEC epidemiology differs from many other countries, as severe outbreaks and HUS cases appear to be more often associated with non-O157 serogroups. It is not known why Australian strains of O157 STEC might differ in virulence to international strains. Here we investigate the reduced virulence of Australian strains. Multiple genetic analyses were performed, including SNP-typing, to compare the core genomes of the Australian to the international isolates, and accessory genome analysis to determine any significant differences in gene presence/absence that could be associated with their phenotypic differences in virulence. The most distinct difference between the isolates was the absence of the stx2a gene in all Australian isolates, with few other notable differences observed in the core and accessory genomes of the O157 STEC isolates analyzed in this study. The presence of stx1a in most Australian isolates was another notable observation. Acquisition of stx2a seems to coincide with the emergence of highly pathogenic STEC. Due to the lack of other notable genotypic differences observed between Australian and international isolates characterized as highly pathogenic, this may be further evidence that the absence of stx2a in Australian O157 STEC could be a significant characteristic defining its mild virulence. Further work investigating the driving force(s) behind Stx prophage loss and acquisition is needed to determine if this potential exists in Australian O157 isolates.

Chronic wounds, particularly infected wounds are clinically very important due to their significant impact on health budgets as well as patients` health worldwide. Patients with diabetes mellitus, vascular diseases especially peripheral vascular disease and pressure ulcers are major categories of patients presenting with chronic wounds. It is known that there are multiple factors determining chronic wound prognosis. The presence of multiple types of pathogenic bacteria, with specific virulence and adherent (biofilm) properties, contribute a significant role to the development of chronic wounds. This review article is based on the research project entitled” An investigation of the impact of bacterial diversity, pathogenic determinants and biofilms on chronic wounds”. The research findings have been published in form of research papers as well as conference posters. The aim of this article is to highlight various important aspects of bacterial impact on wound healing.

Emerging antibiotic multi-resistance, increased travel and trade, and environmental changes have contributed to the prevalence of infectious diseases and rapid changes in the efficiency of therapeutics. We report detection of multi-resistant Staphylococus aureus and S. aureus strain sub-types using a microfluidic detection module with integrated thin film heater and DNA microarray, which enables surface-bound melting curve analysis. Successful discrimination between clinical S. aureus strain sub-types and between methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) was demonstrated. The microfluidic detection module is constructed completely on a plastic foil using roll-to-roll compatible fabrication methods that yield a very low-cost system.

Objective There is a paucity of data characterizing the microbiota of the female upper genital tract, which controversially is described as a sterile site. We examine whether the fallopian tube harbours an endogenous microbial community. Design This prospective study collected from women undergoing total hysterectomy or salpingectomy-oophorectomy. Setting Private hospital gynaecology department. Patients Fallopian tubes were collected from women diagnosed with benign disease or for prophylaxis. Interventions Samples were interrogated for the presence of microbial DNA using a next generation sequencing technology approach to exploit the V5 to V9 regions of the 16S rRNA gene. Main outcome measures The fallopian tube microbiota was characterized using traditional culture techniques and next generation sequencing. Results Bacteria were isolated from 50% of cultured samples, and 100% of samples returned positive PCR results. Only 68% of the culture isolates could be confidently identified using automated diagnostic equipment in a clinical microbiology laboratory. Monomicrobial communities were identified only for cultured isolates (50%). Pyrosequencing revealed that all communities were polymicrobial. Lactobacillus spp. were not present in all groups, nor were they the most dominant isolates. Distinct differences in the microbial communities were evident for left compared to right fallopian tubes, ampulla versus isthmus, pre- and post- menopausal tissue, and in secretory phase fallopian tubes with and without Mirena intrauterine devices in situ (all p < 0.05). Conclusion The female upper genital tract is not sterile. Distinct microbial community profiles in the fallopian tubes of healthy women suggest that this genital tract site supports an endogenous microbiota.

This study aimed to characterise the microbial community within the endometrial cavity and endocervix in women with menorrhagia or dysmenorrhea. Paired endocervical and endometrial biopsy samples were collected from women undergoing operative hysteroscopy and/or laparoscopy. Samples were cohorted based on pathology, indications for surgery, and histological dating of the endometrium. Samples were interrogated for the presence of microbial DNA using a two-step next generation sequencing technology approach to exploit the V5–V8 regions of the 16S rRNA gene. Pyrosequencing revealed that the endocervix and endometrium share a minor microbial community, but that each site harbours a separate and distinct microbial population (p = 0.024). This was also the case for women with menorrhagia and dysmenorrhea (p = 0.017). Lactobacillus spp. were the most abundant microbial taxa present in 50% of the cohorts, and across all endocervical groups. Members of the genera Prevotella, Fusobacterium and Jonquetella were the most abundant taxa identified in samples collected from nulliparous women. It can be concluded that the female upper genital tract is not sterile. Microbial community profiling revealed differences in the endometrial microbial community profiles for: (1) the endocervix compared to the endometrium, and (2), women with menorrhagia versus dysmenorrhea. The distinct microbial community profiles in these women may offer insight into the pathology and clinical management of dysfunctional menstrual bleeding.

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen, and serotype O157:H7 is typically associated with severe disease. Australia is unique in its STEC epidemiology, as severe cases are typically associated with non-O157 serogroups, and locally acquired O157 isolates are H-negative/nonmotile. The H-negative phenotype and reduced severity of disease compared to that associated with H7/motile strains are distinct features of Australian O157 strains, but the molecular mechanism behind this phenotype has not been reported. Accurate characterization of the H-negative phenotype is important in epidemiological surveillance of STEC. Serotyping is moving away from phenotype-based methods, as next generation sequencing allows rapid extrapolation of serotype through in silico detection of the O-antigen processing genes, wzx, wzy, wzm, and wzt, and the H-antigen gene, fliC. The detection and genotyping of fliC alone is unable to determine the motility of the strain. Typically, most Australian O157:H-negative strains carry an H7 genotype yet phenotypically are nonmotile; thus, many are mischaracterized as H7 strains by in silico serotyping tools. Comparative genomic analysis of flagellar genes between Australian and international isolates was performed and an insertion at nucleotide (nt) 125 in the flgF gene was identified in H-negative isolates. Chi-square results showed that this insertion was significantly associated with the H-negative phenotype (P 0.0001). Phylogenetic analysis was also completed and showed that the Australian H-negative isolates with the insertion in flgF represent a clade within the O157 serogroup, distinct from O157:H7 serotypes. This study provides a genetic target for inferring the nonmotile phenotype of Australian O157 STEC, which increases the predictive value of in silico serotyping.

Background Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for analysis. However, the speed of existing analysis pipelines may limit our ability to work with these quantities of data. Furthermore, the limited coverage of existing 16S databases may hamper our ability to characterise these communities, particularly in the context of complex or poorly studied environments. Results In this article we present the SigClust algorithm, a novel clustering method involving the transformation of sequence reads into binary signatures. When compared to other published methods, SigClust yields superior cluster coherence and separation of metagenomic read data, while operating within substantially reduced timeframes. We demonstrate its utility on published Illumina datasets and on a large collection of labelled wound reads sourced from patients in a wound clinic. The temporal analysis is based on tracking the dominant clusters of wound samples over time. The analysis can identify markers of both healing and non-healing wounds in response to treatment. Prominent clusters are found, corresponding to bacterial species known to be associated with unfavourable healing outcomes, including a number of strains of Staphylococcus aureus. Conclusions SigClust identifies clusters rapidly and supports an improved understanding of the wound microbiome without reliance on a reference database. The results indicate a promising use for a SigClust-based pipeline in wound analysis and prediction, and a possible novel method for wound management and treatment.

Aims: To determine whether cultivation-dependent and -independent analyses identifying fallopian tube bacteria were associated with visually observable microbial cells in situ using scanning electron microscopy. Patients: Fallopian tubes were collected from pre- and post-menopausal women undergoing salpingectomies for benign disease or as prophylaxis. Materials and Methods: Fresh fallopian tube samples were processed for scanning electron microscopy to characterize fallopian tube ultrastructure. Histopathology was used to exclude fallopian tube abnormalities and for menstrual cycle staging of the endometrium. Results: Scanning electron microscopy revealed observable microbial cells in Fallopian tube samples. Conclusions: In the absence of inflammatory pathology, the Fallopian tube harbours a visually observable microbial population, which correlates with cultivation-dependent and cultivation-independent data, further refuting the sterility of this anatomical niche.

Background: Wound infection results in delayed wound healing. The development of infection in chronic wounds can be influenced by many factors that impair the host’s ability to defend or related to the bacterial ability to cause harm. These factors can be comorbidities, psychosocial factors, the bacterial virulence, bacterial load or microbial synergy. This study explored the factors related to the likelihood of the development of infection in participants with chronic leg ulcers...

Chronic wounds present a significant risk to the patient and a substantial drain on health budgets, with the problem likely to worsen markedly with increased incidence of type II diabetes. The wound fluid microbiome is known to influence wound healing outcomes, but is poorly characterised. Next Generation Sequencing approaches yield abundant data from wound samples, but progress in understanding these microbial communities may be hampered by the speed of existing analysis pipelines and limitations on coverage by 16S databases. This paper presents SigClust, a novel clustering method based on binary signatures derived from sequence reads. SigClust yields superior cluster coherence and separation of metagenomic read data in timeframes substantially reduced from those of alternative methods. We demonstrate its utility in the wound context on a preliminary set of labelled patient data. We show how a time course analysis based on tracking the dominant clusters over successive wound samples can identify markers of both successful wound healing and wounds refractory to treatment. Clusters prominent in these analyses are found to correspond to bacterial species known to be implicated as a determinant of wound outcomes, notably a number of strains of Staphylococcus aureus. The clusters obtained rapidly via SigClust support improved understanding of the wound microbiome without direct reliance on a reference database, offering the promise of a SigClust-based pipeline for wound analysis and prediction, and potentially novel methods for wound treatment and management.

Pseudomonas aeruginosa is a Gram-negative pathogen and the major cause of mortality in patients with cystic fibrosis. The mechanisms that P. aeruginosa strains use to regulate intracellular zinc have an effect on infection, antibiotic resistance, and the propensity to form biofilms. However, zinc homeostasis in P. aeruginosa strains of variable infectivity has not been compared. In the present study, zinc homeostasis in P. aeruginosa Trent, a highly infectious clinical strain, was compared to that of a laboratory P. aeruginosa strain,ATCC27853. Trent was able to tolerate higher concentrations of additional zinc in rich media than ATCC27853. Further, pre-adaptation to additional zinc enhanced the growth of Trent at non-inhibitory concentrations but the impact of pre-adaption in on the growth of ATCC27853 under the same conditions was minimal. The results establish clear differences in zinc induced responses in Trent and ATCC27853, and how zinc homeostasis can be a promising target for the development of novel antimicrobial strategies for P. aeruginosa infection in cystic fibrosis patients.

Objective There is a paucity of research on patients presenting with uninfected diabetic foot ulcers (DFU) that go on to develop infection. We aimed to investigate the incidence and risk factors for developing infection in a large regional cohort of patients presenting with uninfected DFUs. Methods We performed a secondary analysis of data collected from a validated prospective state-wide clinical diabetic foot database in Queensland (Australia). Patients presenting for their first visit with an uninfected DFU to a Diabetic Foot Service in one of thirteen Queensland regions between January 2012 and December 2013 were included. Socio-demographic, medical history, foot disease history, DFU characteristics and treatment variables were captured at the first visit. Patients were followed until their DFU healed, or if their DFU did not heal for 12-months, to determine if they developed a foot infection in that period. Results Overall, 853 patients were included; mean(standard deviation) age 62.9(12.8) years, 68.0% male, 90.9% type 2 diabetes, 13.6% indigenous Australians. Foot infection developed in 342 patients for an overall incidence of 40.1%; 32.4% incidence in DFUs healed <3 months, 55.9% in DFUs healed between 3–12 months (p<0.05). Independent risk factors (Odds Ratio (95% confidence interval)) for developing infection were: DFUs healed between 3–12 months (2.3 (1.6–3.3)), deep DFUs (2.2 (1.2–3.9)), peripheral neuropathy (1.8 (1.1–2.9)), previous DFU history (1.7 (1.2–2.4)), foot deformity (1.4 (1.0–2.0)), female gender (1.5 (1.1–2.1)) and years of age (0.98 (0.97–0.99)) (all p<0.05). Conclusions A considerable proportion of patients presenting with an uninfected DFU will develop an infection prior to healing. To prevent infection clinicians treating patients with uninfected DFUs should be particularly vigilant with those presenting with deep DFUs, previous DFU history, peripheral neuropathy, foot deformity, younger age, female gender and DFUs that hav

Guided bone regeneration (GBR) is a surgical procedure utilizing occlusive membranes for providing space maintenance and enabling selective repopulation of the damaged area. While this technique is effective in regenerating bone, bacterial infiltration occurs frequently and can compromise the regenerative outcome. In this study, the authors describe the development and characterization of a GBR membrane made of medical grade polycaprolactone (mPCL) electrospun fibers with antibacterial and immunomodulatory properties. This is achieved by the immobilization of the antibiotic azithromycin into the membrane via a solvent evaporation technique leading to a sustained release of the drug over 14 d. In vitro testing shows that this controlled release of azithromycin is proficient at inhibiting the growth of Staphylococcus aureus for 14 d. Implantation of azithromycin loaded mPCL membrane in a rodent calvarial defect induces macrophage polarization toward the M2 phenotype after one week and results in significantly more bone regeneration eight weeks post-surgery. The results suggest that this antibacterial membrane should be effective at preventing infection and also impacts on the macrophage polarization enhancing bone regeneration. The drug loading technique developed in this study is simple, effective with a strong potential for clinical translation and can be applied to different types of scaffolds and implants for applications in craniofacial and orthopedics applications.