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Spoilage of postharvest strawberries by fungal pathogens is a major global concern. This study employed culture‐dependent and culture‐independent methods to identify postharvest fungal communities of strawberries in Western Australia (WA). Ripe strawberries from eight varieties were sampled twice, early and late in the growing season, from 20 farms in two growing regions. At the first sampling time, traditional isolation and identification demonstrated a high abundance of Botrytis and Cladosporium in Region 1. Mucor was abundant at the second sampling time in Region 1 and both times in Region 2. Metabarcoding confirmed variety‐specific fungal communities in WA strawberries. Botrytis and Cladosporium were predominant in Region 1 and Region 2 samples with more than 50% read abundance except on variety Suncoast. No Mucor sequences were detected using metabarcoding, although they were isolated from all samples using culture‐based methods. Sisquoc, a hydroponic variety, had a significantly higher fungal diversity than the soil‐grown varieties. Varieties Suncoast and Albion exhibited the lowest fungal diversity compared to others. This study demonstrated the value of using culture‐dependent and culture‐independent methods to investigate the complexity of fungal microbiomes of postharvest strawberries. [ABSTRACT FROM AUTHOR]

The SpTransformer (SpTrf) gene family in the purple sea urchin, Strongylocentrotus purpuratus, encodes immune response proteins. The genes are clustered, surrounded by short tandem repeats, and some are present in genomic segmental duplications. The genes share regions of sequence and include repeats in the coding exon. This complex structure is consistent with putative local genomic instability. Instability of the SpTrf gene cluster was tested by 10 days of growth of Escherichia coli harboring bacterial artificial chromosome (BAC) clones of sea urchin genomic DNA with inserts containing SpTrf genes. After the growth period, the BAC DNA inserts were analyzed for size and SpTrf gene content. Clones with multiple SpTrf genes showed a variety of deletions, including loss of one, most, or all genes from the cluster. Alternatively, a BAC insert with a single SpTrf gene was stable. BAC insert instability is consistent with variations in the gene family composition among sea urchins, the types of SpTrf genes in the family, and a reduction in the gene copy number in single coelomocytes. Based on the sequence variability among SpTrf genes within and among sea urchins, local genomic instability of the family may be important for driving sequence diversity in this gene family that would be of benefit to sea urchins in their arms race with marine microbes. [ABSTRACT FROM AUTHOR]

Vibriosis caused by luminous Vibrio species is one of the biggest challenges to shrimp industry in Bangladesh. This study aimed to characterize whole microbial communities from Vibrio‐infected black tiger shrimp (Penaeus monodon) using 16S rRNA‐based amplicon sequencing. A total of 36 disease‐free and infected shrimp were collected from six different hatcheries in Bagerhat, Bangladesh. A final pool of 12 samples (n = 6) was created by homogenization of the hepatopancreas samples from three shrimps collected from each hatchery for the same group. The amplicon sequencing data revealed significant (p <.05) decrease of alpha diversity measurements and subsequent effects (p <.05) on the hepatopancreas microbiota in the infected group, compared to control shrimp. Proteobateria and Aeromonas were the most dominant bacteria at phylum and genus level in both groups and identified as core microbiota in the community. Two bacterial groups at phyla level and eight at genus level were found associated with the alteration of hepatopancreas microbial communities and associated gene functions in vibriosis‐infected shrimp, revealed by differential abundance and KEGG pathway analysis. The overwhelming abundance of Citroibacter, Shewanella and Candidatus lineages in vibriosis‐infected shrimp needs further investigations. [ABSTRACT FROM AUTHOR]

This study was conducted to characterize the causative agent of streptococcosis in tilapia (Oreochromis niloticus) and control of Streptococcus infection by means of garlic (Allium sativum) supplementation. The morphological, biochemical and polymerase chain reaction amplification confirmed 11 isolates belong to Streptococcus iniae from the infected fish eyes and tissue samples. Random screening of 12 well‐known medicinal plant parts against S. iniae revealed the garlic extract as the most effective herbal recovery against Streptococcus infection. In vivo challenge test with dietary supplementation of garlic powder significantly improved survival rates of fish against S. iniae infections, and modulate the microbial community and cytokine gene expression profiling in the intestine of the experimental tilapia. Among the two garlic supplemented treatments, 1.0 g garlic supplemented diet significantly increased (p < 0.05) the survival rates of tilapia and the gut bacterial operational transitional units abundance for Proteobacteria and Tenericutes, the phyla associated with healthy intestinal flora. The bacterial diversity index also found high with garlic supplemented diets. Significant upregulations of IL‐10 and IL‐17F gene expression in the intestinal tissue were observed with 1.0 g garlic supplemented diet where IL‐8 and IL‐1β expression levels were relatively static. The dietary supplementation of garlic, therefore, could be effective in the prevention of S. iniae infection in fish. [ABSTRACT FROM AUTHOR]

Aim: Klebsiella pneumoniae is considered to be one of the most frequent bacterial species associated with urinary tract infections (UTIs) and recurrent UTIs (RUTIs) worldwide. The present study aimed to comprehensively characterize K. pneumoniae isolates from women suffering from UTI and RUTIs. Methodology and results: A total of 15 clinical isolates, collected from different hospitals in Bangladesh, were tested for biochemical features, and amplified by PCR. Antibiogram assay was performed by disk-diffusion assay. Phylogenetic and functional features were analyzed using bioinformatics platform. XLSTAT was used for principal component analysis (PCA). PCR amplification using Klebsiella hemolysin gene (khe) confirmed the presence of K. pneumoniae in agarose gel with expected product size of 486 kb. Antibiogram assay revealed all K. pneumoniae isolates to be completely resistant to six out of ten relevant drugs namely ampicillin, cephradine, chloramphenicol, erythromycin, kanamycin and sulfamethoxazole used for treating UTIs in Bangladesh. Sequencing of 16S rRNA gene of clinically significant K. pneumoniae isolates showed a high level of sequence divergence among the isolates from UTI and RUTIs as well as functional features such as SNP variants and restriction sites. Conclusion, significance and impact of study: We surmise that the results could be used as a pipeline for further research in the identification of K. pneumoniae associated with UTI and RUTIs, and treatment of infection. [ABSTRACT FROM AUTHOR]

Aerolysin (aer) is one of the most important and abundant virulence factors in the infection of fish by Aeromonas veronii. A comprehensive study on the molecular characterization and pathogenicity of the aer gene from 34 A. veronii isolates from diseased carp and catfish was carried out and its interactome was analysed to observe the functional correlations between aer and other proteins within the A. veronii network. The PCR‐based amplification of aer from the 34 isolates of A. veronii showed more aer‐positive isolates from catfish with a high pathogenic potential in the in vivo challenge test than the carp fish. The analysis of aer gene sequence from challenged fish revealed significant sequence divergence according to the types and geographical distribution of the fish. The networking analysis of aer from the model A. veronii B565 revealed histidine kinase (cheA) as the most functional interacting partner. The study of the interaction between aer from the experimental A. veronii and cheA demonstrated that the A chain of cheA plays a more important role than the corresponding B chain during contact, and a linker sequence of 15 residues controlled the entire interaction process. Therefore, cheA could be an excellent drug target for controlling A. veronii infection of fish. [ABSTRACT FROM AUTHOR]

Background: Acute respiratory infection (ARI) is a leading cause of morbidity and mortality in children in low and middle‐income countries. Human metapneumovirus (hMPV) is one of the most common viral etiological agents for ARIs in children. Objectives: In this study, we explored the genotypic diversity and the epidemiology of hMPV among infants in Dhaka, Bangladesh. Study Design: Between December 2014 and August 2016, a total of 3810 mid‐turbinate nasal swab samples were collected from infants (0 to 6 months of age) who met clinical ARI criteria, as a part of a prospective ARI cohort study. hMPV was detected using polymerase chain reaction, and genotyped by sequencing and phylogenetic analysis. Results: hMPV was identified in 206 (5.4%) nasal swab specimens. One‐tenth of the hMPV‐positive swabs (n = 19) were also positive for other respiratory viruses. hMPV activity peaked in January and September in 2015; however, no seasonal pattern of hMPV infection was detected. Phylogenetic analyses of the N and F gene‐fragments revealed that the hMPV strains circulating in Dhaka, Bangladesh, belonged to three genotypes: A2b, A2c, and B1. Genotype A (57%) was the predominant hMPV genotype circulating in Bangladesh during the study period. Conclusion: This study describes both the epidemiology of hMPV infection and its genotypic strain diversity in Dhaka, Bangladesh. 1.We describe the molecular epidemiology of hMPV infection among infants in Bangladesh.2.hMPV contributes 5.4% of the studied ARI infections and there were three hMPV genotypes; A2b, A2c and B1 circulating in the country. [ABSTRACT FROM AUTHOR]

Introduction: Alcaligenes faecalis is a common environmental bacteria that often infects human as an opportunistic pathogen. It rarely causes Urinary Tract Infection (UTI) in human; however, infection brings severe outcomes. Also, the treatment of A. faecalis associated infections with common antibiotics can be difficult due to a high level of antibiotic resistance. Aim: Molecular characterisation of A. faecalis isolate from women suffering from Recurrent Urinary Tract Infections (RUTIs). Materials and Methods: The study has been conducted in the USDA-laboratory of the Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh. The present study conducted from July 2017 to December 2017, characterised an A. faecalis strain from the women suffering from RUTIs by applying 16s rRNA gene sequencing and phylogenetic analysis. Antibiogram profiling was done by means of disk diffusion assay. Analysis of in-silico SNP variants was done using Geneious software. Results: The isolates were resistant to seven out of ten commercial antibiotics used to treat UTI in Bangladesh. Phylogenetic and evolutionary distance data analysis revealed a close proximity of the study AF1 strain with other A. faecalis strains identified from the environment, especially from a previously characterised water sample. In-silico variants search found nine potentials of Single Nucleotide Polymorphism (SNPs) in the studied strain compared to other environmental A. faecalis bacteria characterised from India, South-Korea, Japan, Mexico and Brazil. Conclusion: The present study revealed the transmission of environmental opportunistic pathogens to human and cause chronic infections in Bangladesh. [ABSTRACT FROM AUTHOR]

Multidrug-resistant bacteria, particularly extended-spectrum-beta-lactamase-producing (ESBL) bacteria, pose a significant global public health challenge. Klebsiella pneumoniae (KPN) is frequently implicated in cases of this resistance. This study aimed to investigate the presence of drug and metal resistance genes in clinical K. pneumoniae isolate Kp04 and comparative genomics of clinical KPN isolates characterized from Bangladesh. A total of 12 isolates were collected. Disk-diffusion assay showed that all five isolates were resistant to 14 out of 21 tested antibiotics and sensitive to only three-tigecycline, imipenem, and meropenem. KPN Kp04 was positive for both bla SHV and bla CTX-M ESBL genes in PCR. All five isolates produced PCR amplicons of the correct size for ampicillin (ampC), tetracycline (tetC), fluoroquinolone (qnrS), and aminoglycoside (aadA) resistance genes. The whole genome of Kp04 was sequenced using the MiSeq Platform (V3 kit, 2 × 300 cycles). We utilized different databases to detect Antibiotic-Resistant Genes (ARGs), virulence factor genes (VFGs), and genomic functional features of the Kp04 strain. Whole-genome sequencing identified 75 ESBL, virulence, and multiple drug-resistant (MDR) genes including bla SHV , tetA, oqxA, oqxB, aadA, sul1-5, and mphA in KPN Kp04 isolate. Pan-genomic analysis of 43 Bangladeshi KPN isolates showed similarities between Dhaka and Chattogram isolates regarding virulence and antibiotic-resistant genes. Our results indicate the transmission of similar virulent KPN strains in Dhaka and Chattogram. This study would provide valuable information about drug sensitivity, antibiotic, and metal resistance features of K. pneumoniae circulated among hospitalized patients in Bangladeshi megacities., Competing Interests: Declarations. Conflict of interest: The authors declare no conflict of interest., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Aerolysin (aer) is one of the most important and abundant virulence factors in the infection of fish by Aeromonas veronii. A comprehensive study on the molecular characterization and pathogenicity of the aer gene from 34 A. veronii isolates from diseased carp and catfish was carried out and its interactome was analysed to observe the functional correlations between aer and other proteins within the A. veronii network. The PCR-based amplification of aer from the 34 isolates of A. veronii showed more aer-positive isolates from catfish with a high pathogenic potential in the in vivo challenge test than the carp fish. The analysis of aer gene sequence from challenged fish revealed significant sequence divergence according to the types and geographical distribution of the fish. The networking analysis of aer from the model A. veronii B565 revealed histidine kinase (cheA) as the most functional interacting partner. The study of the interaction between aer from the experimental A. veronii and cheA demonstrated that the A chain of cheA plays a more important role than the corresponding B chain during contact, and a linker sequence of 15 residues controlled the entire interaction process. Therefore, cheA could be an excellent drug target for controlling A. veronii infection of fish., (© 2019 John Wiley & Sons Ltd.)