Can supervise: YES
Wyrsch, ER, Reid, CJ, DeMaere, MZ, Liu, MY, Chapman, TA, Roy Chowdhury, P & Djordjevic, SP 2019, 'Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia', Frontiers in Sustainable Food Systems, vol. 3.View/Download from: UTS OPUS or Publisher's site
Deutscher, AT, Burke, CM, Darling, AE, Riegler, M, Reynolds, OL & Chapman, TA 2018, 'Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae.', Microbiome, vol. 6, no. 1.View/Download from: UTS OPUS or Publisher's site
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 bac...
Chowdhury, PR, DeMaere, M, Chapman, T, Worden, P, Charles, IG, Darling, AE & Djordjevic, SP 2016, 'Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease', BMC MICROBIOLOGY, vol. 16.View/Download from: UTS OPUS or Publisher's site
Wyrsch, E, Roy Chowdhury, P, Chapman, TA, Charles, IG, Hammond, JM & Djordjevic, SP 2016, 'Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis', Frontiers in Microbiology, vol. 7, no. 843.View/Download from: UTS OPUS or Publisher's site
Wyrsch, E, Roy Chowdhury, P, Abraham, S, Santos, J, Darling, AE, Charles, IG, Chapman, TA & Djordjevic, SP 2015, 'Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs.', BMC Genomics, vol. 16, pp. 1-11.View/Download from: UTS OPUS or Publisher's site
BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) are a major economic threat to pig production globally, with serogroups O8, O9, O45, O101, O138, O139, O141, O149 and O157 implicated as the leading diarrhoeal pathogens affecting pigs below four weeks of age. A multiple antimicrobial resistant ETEC O157 (O157 SvETEC) representative of O157 isolates from a pig farm in New South Wales, Australia that experienced repeated bouts of pre- and post-weaning diarrhoea resulting in multiple fatalities was characterized here. Enterohaemorrhagic E. coli (EHEC) O157:H7 cause both sporadic and widespread outbreaks of foodborne disease, predominantly have a ruminant origin and belong to the ST11 clonal complex. Here, for the first time, we conducted comparative genomic analyses of two epidemiologically-unrelated porcine, disease-causing ETEC O157; E. coli O157 SvETEC and E. coli O157:K88 734/3, and examined their phylogenetic relationship with EHEC O157:H7. RESULTS: O157 SvETEC and O157:K88 734/3 belong to a novel sequence type (ST4245) that comprises part of the ST23 complex and are genetically distinct from EHEC O157. Comparative phylogenetic analysis using PhyloSift shows that E. coli O157 SvETEC and E. coli O157:K88 734/3 group into a single clade and are most similar to the extraintestinal avian pathogenic Escherichia coli (APEC) isolate O78 that clusters within the ST23 complex. Genome content was highly similar between E. coli O157 SvETEC, O157:K88 734/3 and APEC O78, with variability predominantly limited to laterally acquired elements, including prophages, plasmids and antimicrobial resistance gene loci. Putative ETEC virulence factors, including the toxins STb and LT and the K88 (F4) adhesin, were conserved between O157 SvETEC and O157:K88 734/3. The O157 SvETEC isolate also encoded the heat stable enterotoxin STa and a second allele of STb, whilst a prophage within O157:K88 734/3 encoded the serum survival gene bor. Both isolates harbor a large repertoire of antibi...
Background Clostridium difficile is the leading cause of infectious diarrhea in humans and responsible for large outbreaks of enteritis in neonatal pigs in both North America and Europe. Disease caused by C. difficile typically occurs during antibiotic therapy and its emergence over the past 40 years is linked with the widespread use of broad-spectrum antibiotics in both human and veterinary medicine. Results We sequenced the genome of Clostridium difficile 5.3 using the Illumina Nextera XT and MiSeq technologies. Assembly of the sequence data reconstructed a 4,009,318 bp genome in 27 scaffolds with an N50 of 786 kbp. The genome has extensive similarity to other sequenced C. difficile genomes, but also has several genes that are potentially related to virulence and pathogenicity that are not present in the reference C. difficile strain. Conclusion Genome sequencing of human and animal isolates is needed to understand the molecular events driving the emergence of C. difficile as a gastrointestinal pathogen of humans and food animals and to better define its zoonotic potential.