Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia

Wyrsch, Ethan R.; Reid, Cameron J.; DeMaere, Matthew Z.; Liu, Michael Y.; Chapman, Toni A.; Chowdhury, Piklu Roy; Djordjevic, Steven P.

doi:10.3389/fsufs.2019.00018

Cited by 22 publications

(46 citation statements)

References 82 publications

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“…The IS26 flanked integron type D containing bla OXA−10 was identical to three unpublished Chinese E. coli plasmid sequences isolated from poultry, river water and an unknown source (gb| CP033636.1, gb| CP010168.1, gb| KY421937.1). Integron type E was previously described in three MDR E. coli on HI2 plasmids in Australian swine (Billman-Jacobe et al, 2018;Wyrsch et al, 2019). Integron type F was identical to that described on the chromosome of multiple O104:H4 E. coli responsible for the 2011 produceassociated outbreak in Germany (Roy Chowdhury et al, 2015).…”

Section: Class 1 Integrons Are Associated With Is26 and Have Diverse mentioning

confidence: 82%

“…This arrangement comprised a partial copy of Tn1721 followed by intI1-dfrA12-orfF-aadA2-qacE 1-sul1-orf5-tniB-tniA-IS26. Upstream of this resistance region were a copper/silver resistance operon and numerous hypothetical proteins similar to those described in HI2 plasmids from Australia and China (Fang et al, 2016;Billman-Jacobe et al, 2018;Wyrsch et al, 2019). Integron type F was present in two ST7576 strains and consisted of an IS1 inverted repeat, a Tn3like transposase gene tnpA, a recombinase family protein gene then intI1-dfrA7-qacE 1-sul1-IS26.…”

Section: Class 1 Integronsmentioning

confidence: 95%

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Whole Genome Sequencing of Escherichia coli From Store-Bought Produce

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The role of agriculture in the transfer of drug resistant pathogens to humans is widely debated and poorly understood. Escherichia coli is a valuable indicator organism for contamination and carriage of antimicrobial resistance (AMR) in foods. Whilst whole genome sequences for E. coli from animals and associated meats are common, sequences from produce are scarce. Produce may acquire drug resistant E. coli from animal manure fertilizers, contaminated irrigation water and wildlife, particularly birds. Whole genome sequencing was used to characterize 120 tetracycline (TET) resistant E. coli from store-bought, ready-to-eat cilantro, arugula and mixed salad from two German cities. E. coli were recovered on the day of purchase and after 7 days of refrigeration. Cilantro was far more frequently contaminated with TET-resistant E. coli providing 102 (85%) sequenced strains. Phylogroup B1 dominated the collection (n = 84, 70%) with multi-locus sequence types B1-ST6186 (n = 37, 31%), C-ST165 (n = 17, 14%), B1-ST58 (n = 14, 12%), B1-ST641 (n = 8, 7%), and C-ST88 (n = 5, 4%) frequently identified. Notably, seven strains of diverse sequence type (ST) carried genetic indicators of ColV virulence plasmid carriage. A number of previously identified and novel integrons associated with insertion elements including IS26 were also identified. Storage may affect the lineages of E. coli isolated, however further studies are needed. Our study indicates produce predominantly carry E. coli with a commensal phylogroup and a variety of AMR and virulence-associated traits. Genomic surveillance of bacteria that contaminate produce should be a matter of public health importance in order to develop a holistic understanding of the environmental dimensions of AMR.

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Section: Class 1 Integrons Are Associated With Is26 and Have Diverse mentioning

confidence: 82%

Section: Class 1 Integronsmentioning

confidence: 95%

Whole Genome Sequencing of Escherichia coli From Store-Bought Produce

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“…VAGs identified in E. coli from sows and piglets were previously reported in multiple pathotypes of E. coli [ 47 , 48 , 49 , 73 , 74 ], and the carriage of multiple VAGs in commensal E. coli strains is consistent with our earlier study [ 25 ]. Reliance on antibiotics and metals to prevent outbreaks of infectious disease is likely to not only maintain high carriage levels of class 1 integrons in plasmids that also carry heavy metal resistance genes and IS 26 [ 25 , 74 , 75 ], but it may yield a more severe disease presentation by driving the evolution of MDR hybrid E. coli with virulence attributes derived from different pathovar designations. Indeed, Australia has already experienced one such episode in early 2000s when an MDR enterotoxigenic E. coli (ETEC) O157:H19-ST4245 (ST23 complex) that was phylogenetically more closely related to serogroup O78 avian pathogenic E. coli (APEC) and distant from enterohaemorrhagic E. coli (EHEC,) O157:H7, caused widespread mortalities in several swine production operations [ 76 ].…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring

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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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“…This plasmid was typed by pMLST as HI2:ST3, a lineage known as a major contributor in transferring complex class 1 integrons conferring AMR (Zhao H. et al, 2018) pF2_18C_HI2 is very similar to three HI2:ST3 plasmids circulating in Australian pig farms (Dyall-Smith et al, 2017;Billman-Jacobe et al, 2018;Wyrsch et al, 2019) (Figure 6A). pF2_18C_H12 carries the same AMR profile as pSDE-SvHI2, isolated from a severe ETEC strain (Wyrsch et al, 2019), and differs to a pSDC-F2_12BHI2, isolated from a commensal E. coli strain (Wyrsch et al, 2019), and pSTM6-275, isolated from Salmonella enterica subsp. Enterica Typhimurium (Dyall-Smith et al, 2017), by lacking aminoglycoside resistance gene aph(3 )-Ia and fluoroquinolone resistance genes oqxAB in the former, and beta-lactam resistance gene blaTEM-1B in the latter.…”

Section: Discussionmentioning

confidence: 99%

“…In addition to the LEE, EHEC and EPEC possess various non-LEE (nle)-encoded effector genes. nle genes are frequently carried on prophage elements and contribute to virulence by interfering with host signaling pathways, apoptosis and phagocytosis (Wong et al, 2011) as well as disrupting host cell cytoskeleton and tight junctions (Gomes et al, 2016). However, EHEC differ from EPEC in that they possess phage-associated Shiga toxins (stx), which contribute to the hemorrhagic colitis and hemolytic uremic syndrome (HUS) associated with EHEC infections (Mayer et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements

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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 bundleforming 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 shortread 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 PAI CL3 , plasmid-associated heavy metal resistance genes, as well as several unoccupied stxphage 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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Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia

Cited by 22 publications

References 82 publications

Whole Genome Sequencing of Escherichia coli From Store-Bought Produce

Whole Genome Sequencing of Escherichia coli From Store-Bought Produce

Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring

Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements

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