Melvold, JA, Wyrsch, ER, McKinnon, J, Charles, IG & Djordjevic, SP 2017, 'Identification of a novel qnrA allele, qnrA8, in environmental Shewanella algae', Journal Of Antimicrobial Chemotherapy, vol. 72, no. 10, pp. 2949-2952.View/Download from: UTS OPUS or Publisher's site
Quinolones are recognized as one of the most widely prescribed classes of antibiotics used to treat infections caused by Gram-negative and Gram-positive bacteria.1 In humans, quinolones are used to treat infections of the urogenital, respiratory and gastroinestinal tracts as well as a range of anatomically diverse infections in swine, poultry, cattle and companion animals and in aquaculture.2 In the environment, fluoroquinolones break down slowly (half-life of ∼100 days) and it is possible to measure trace levels of the drug in exposed environments.3 The environmental impact of quinolones, particularly fluoroquinolones from humans, agriculture and pharmaceutical production facilities, is a cause of concern as residues and metabolic breakdown products released from the body of target species provides a selection pressure that impacts the ecology of non-target bacterial, invertebrate and vertebrate populations, where it can influence natural mutation rates and lateral gene transfer.2
Reid, CJ, Wyrsch, ER, Roy Chowdhury, P, Zingali, T, Liu, M, Darling, AE, Chapman, TA & Djordjevic, SP 2017, 'Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26.', Microbial Genomics, vol. 3, no. 12, pp. 1-13.View/Download from: UTS OPUS or Publisher's site
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.
Reid, C, Wyrsch, E, Chowdhury, PR, Zingali, T, Liu, M, Darling, A, Chapman, T & Djordjevic, S 2017, 'Porcine commensal Escherichia coli: A reservoir for class 1 integrons associated with IS26'.View/Download from: UTS OPUS or Publisher's site
Abstract Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial resistance and virulence-associated genes (VAGs) and the zoonotic potential of commensal Escherichia coli from swine is largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilisation of antimicrobial resistance genes between food animals and the environment. Here, we report whole genome sequence analysis of 141 E. coli from 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 genes bla TEM , 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 gene sul3 was 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 pathogenic E. coli (ExPEC) from humans. This study provides the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin, facilitating tracking of specific lineages and the mobile resistance genes they carry. Conflict of Interest Statement None to declare.
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...
Roy Chowdhury, P, McKinnon, J, Wyrsch, E, Hammond, JM, Charles, I & Djordjevic, S 2014, 'Genomic interplay in bacterial communities: implications for growth promoting practices in animal husbandry.', Frontiers in Microbiology, vol. 12, no. 5, pp. 394-394.View/Download from: UTS OPUS or Publisher's site