scholarly journals Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread

2014 ◽  
Vol 80 (14) ◽  
pp. 4350-4362 ◽  
Author(s):  
Victoriya V. Volkova ◽  
Zhao Lu ◽  
Thomas Besser ◽  
Yrjö T. Gröhn
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Resistance Gene ◽  
Small Contribution ◽  
Worst Case ◽  
Content Type ◽  
E Coli ◽  
Infection Dynamics ◽  
Antimicrobial Resistance Genes ◽  
Generalized Transduction

ABSTRACTAnimal-associated bacterial communities are infected by bacteriophages, although the dynamics of these infections are poorly understood. Transduction by bacteriophages may contribute to transfer of antimicrobial resistance genes, but the relative importance of transduction among other gene transfer mechanisms is unknown. We therefore developed a candidate deterministic mathematical model of the infection dynamics of enteric coliphages in commensalEscherichia coliin the large intestine of cattle. We assumed the phages were associated with the intestine and were predominantly temperate. Model simulations demonstrated how, given the bacterial ecology and infection dynamics, most (>90%) commensal entericE. colibacteria may become lysogens of enteric coliphages during intestinal transit. Using the model and the most liberal assumptions about transduction efficiency and resistance gene frequency, we approximated the upper numerical limits (“worst-case scenario”) of gene transfer through specialized and generalized transduction inE. coliby enteric coliphages when the transduced genetic segment is picked at random. The estimates were consistent with a relatively small contribution of transduction to lateral gene spread; for example, generalized transduction delivered the chromosomal resistance gene to up to 8E. colibacteria/hour within the population of 1.47 × 108E. colibacteria/liter luminal contents. In comparison, the plasmidicblaCMY-2gene carried by ∼2% of entericE. coliwas transferred by conjugation at a rate at least 1.4 × 103times greater than our generalized transduction estimate. The estimated numbers of transductants varied nonlinearly depending on the ecology of bacteria available for phages to infect, that is, on the assumed rates of turnover and replication of entericE. coli.

scholarly journals Resistance Gene Transfer during Treatments for Experimental Avian Colibacillosis

2011 ◽  
Vol 56 (1) ◽  
pp. 189-196 ◽  
Author(s):  
Alexandra Dheilly ◽  
Laëtitia Le Devendec ◽  
Gwenaëlle Mourand ◽  
Axelle Bouder ◽  
Eric Jouy ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Resistance Gene ◽  
Gel Electrophoresis ◽  
Intestinal Tract ◽  
Pulsed Field Gel Electrophoresis ◽  
Content Type ◽  
E Coli ◽  
Plasmid Genes ◽  
Antimicrobial Treatments

ABSTRACTAn experiment was conducted in animal facilities to compare the impacts of four avian colibacillosis treatments—oxytetracycline (OTC), trimethoprim-sulfadimethoxine (SXT), amoxicillin (AMX), or enrofloxacin (ENR)—on the susceptibility ofEscherichia coliin broiler intestinal tracts. Birds were first orally inoculated with rifampin-resistantE. colistrains bearing plasmid genes conferring resistance to fluoroquinolones (qnr), cephalosporins (blaCTX-MorblaFOX), trimethoprim-sulfonamides, aminoglycosides, or tetracyclines. Feces samples were collected before, during, and after antimicrobial treatments. The susceptibilities ofE. colistrains were studied, and resistance gene transfer was analyzed. An increase in the tetracycline-resistantE. colipopulation was observed only in OTC-treated birds, whereas multiresistantE. coliwas detected in the dominantE. colipopulations of SXT-, AMX-, or ENR-treated birds. Most multiresistantE. colistrains were susceptible to rifampin and exhibited various pulsed-field gel electrophoresis profiles, suggesting the transfer of one of the multiresistance plasmids from the inoculated strains to otherE. colistrains in the intestinal tract. In conclusion, this study clearly illustrates how, inE. coli, “old” antimicrobials may coselect antimicrobial resistance to recent and critical molecules.

scholarly journals Impact of UV and Peracetic Acid Disinfection on the Prevalence of Virulence and Antimicrobial Resistance Genes in Uropathogenic Escherichia coli in Wastewater Effluents

2014 ◽  
Vol 80 (12) ◽  
pp. 3656-3666 ◽  
Author(s):  
Basanta Kumar Biswal ◽  
Ramzi Khairallah ◽  
Kareem Bibi ◽  
Alberto Mazza ◽  
Ronald Gehr ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Peracetic Acid ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Municipal Wastewaters ◽  
The Impact

ABSTRACTWastewater discharges may increase the populations of pathogens, includingEscherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenicEscherichia coli(UPEC), the most abundantE. colipathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766E. coliisolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm2and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.

scholarly journals Dissemination of the blaNDM-5 Gene via IncX3-Type Plasmid among Enterobacteriaceae in Children

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Dongxing Tian ◽  
Bingjie Wang ◽  
Hong Zhang ◽  
Fen Pan ◽  
Chun Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Klebsiella Pneumoniae ◽  
Pediatric Patients ◽  
Transmission Mechanism ◽  
Klebsiella Aerogenes ◽  
Content Type ◽  
E Coli

ABSTRACT The continuous emergence of novel New Delhi metallo-β-lactamase-5 (NDM-5)-producing Enterobacteriaceae isolates is receiving more and more public attention. Twenty-two NDM-5-producing strains were identified from 146 carbapenemase-producing Enterobacteriaceae (CRE) strains isolated from pediatric patients between January and March 2017, indicating that the blaNDM-5 gene has spread to children. All 22 isolates, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, showed significantly high resistance to β-lactam antibiotics (except aztreonam) but remained susceptible to tigecycline and colistin. K. pneumoniae and K. aerogenes strains were respectively defined as homologous clonal isolates by pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) results confirmed the genetic relatedness with all K. pneumoniae strains belonging to sequence type (ST) 48. Two E. coli isolates (ST617 and ST1236) were considered genetically unrelated. Twenty-two blaNDM-5 plasmids were positive for the IncX3 amplicon and showed almost identical profiles after digestion with HindIII and EcoRI. Four representative strains (K. pneumoniae K725, K. aerogenes CR33, E. coli Z214, and E. coli Z244) were selected for further study. Plasmids harboring blaNDM-5 showed strong stability in both clinical isolates and transconjugants, without apparent plasmid loss after 100 serial generations. S1-PFGE followed by Southern blot analysis demonstrated that the blaNDM-5 gene was located on an ∼46-kb plasmid. Plasmid sequences of pNDM-K725, pNDM-CR33, and pNDM-Z214 were almost identical but were slightly different from that of pNDM-Z244. Compared with pNDM-Z244, ΔISAba125 and partial copies of IS3000 were missing. The genetic backgrounds of the blaNDM-5 gene in four strains were slightly different from that of the typical pNDM_MGR194. This study comprehensively characterized the horizontal gene transfer of the blaNDM-5 gene among different Enterobacteriaceae isolates in pediatric patients, and the IncX3-type plasmid was responsible for the spread. IMPORTANCE The emergence of CRE strains resistant to multiple antibiotics is considered a substantial threat to human health. Therefore, all the efforts to provide a detailed molecular transmission mechanism of specific drug resistance can contribute positively to prevent the further spread of multidrug-resistant bacteria. Although the new superbug harboring blaNDM-5 has been reported in many countries, it was mostly identified among E. coli strains, and the gene transfer mechanism has not been fully recognized and studied. In this work, we identified 22 blaNDM-5-positive strains in different species of Enterobacteriaceae, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, which indicated the horizontal gene transfer of blaNDM-5 among Enterobacteriaceae strains in pediatric patients. Moreover, blaNDM-5 was located on a 46-kb IncX3 plasmid, which is possibly responsible for this widespread horizontal gene transfer. The different genetic contexts of the blaNDM-5 gene indicated some minor evolutions of the plasmid, based on the complete sequences of the blaNDM-5 plasmids. These findings are of great significance to understand the transmission mechanism of drug resistance genes, develop anti-infection treatment, and take effective infection control measures.

scholarly journals Prevalence of Antimicrobial Resistance and Transfer of Tetracycline Resistance Genes in Escherichia coli Isolates from Beef Cattle

2015 ◽  
Vol 81 (16) ◽  
pp. 5560-5566 ◽  
Author(s):  
Seung Won Shin ◽  
Min Kyoung Shin ◽  
Myunghwan Jung ◽  
Kuastros Mekonnen Belaynehe ◽  
Han Sang Yoo
Keyword(s):  
Escherichia Coli ◽  
South Korea ◽  
Beef Cattle ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Tetracycline Resistance ◽  
Tetracycline Resistance Gene ◽  
Content Type ◽  
E Coli ◽  
Tetracycline Resistance Genes

ABSTRACTThe aim of this study was to investigate the prevalence and transferability of resistance in tetracycline-resistantEscherichia coliisolates recovered from beef cattle in South Korea. A total of 155E. coliisolates were collected from feces in South Korea, and 146 were confirmed to be resistant to tetracycline. The tetracycline resistance genetet(A) (46.5%) was the most prevalent, followed bytet(B) (45.1%) andtet(C) (5.8%). Strains carryingtet(A) plustet(B) andtet(B) plustet(C) were detected in two isolates each. In terms of phylogenetic grouping, 101 (65.2%) isolates were classified as phylogenetic group B1, followed in decreasing order by D (17.4%), A (14.2%), and B2 (3.2%). Ninety-one (62.3%) isolates were determined to be multidrug resistant by the disk diffusion method. MIC testing using the principal tetracyclines, namely, tetracycline, chlortetracycline, oxytetracycline, doxycycline, and minocycline, revealed that isolates carryingtet(B) had higher MIC values than isolates carryingtet(A). Conjugation assays showed that 121 (82.9%) isolates could transfer a tetracycline resistance gene to a recipient via the IncFIB replicon (65.1%). This study suggests that the high prevalence of tetracycline-resistantE. coliisolates in beef cattle is due to the transferability of tetracycline resistance genes betweenE. colipopulations which have survived the selective pressure caused by the use of antimicrobial agents.

scholarly journals Emergence of Colistin Resistance Gene mcr-1 in Cronobacter sakazakii Producing NDM-9 and in Escherichia coli from the Same Animal

2016 ◽  
Vol 61 (2) ◽  
Author(s):  
Bao-Tao Liu ◽  
Feng-Jing Song ◽  
Ming Zou ◽  
Zhi-Hui Hao ◽  
Hu Shan
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Cronobacter Sakazakii ◽  
Colistin Resistance ◽  
Content Type ◽  
E Coli ◽  
Carbapenem Resistant

ABSTRACT We report the presence of mcr-1 in Escherichia coli and carbapenem-resistant Cronobacter sakazakii from the same diseased chicken. The mcr-1 gene linked with ISApl1 was located on two different IncI2 plasmids, including one multidrug plasmid in E. coli, whereas fosA3-bla NDM-9 was on an IncB/O plasmid in C. sakazakii. The development of the fosA3-bla NDM-9 resistance region was mediated by IS26. The colocation of mcr-1 or bla NDM-9 with other resistance genes will accelerate the dissemination of the two genes.

scholarly journals Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

2020 ◽  
Vol 6 (7) ◽  
Author(s):  
Bede Constantinides ◽  
Kevin K. Chau ◽  
T. Phuong Quan ◽  
Gillian Rodger ◽  
Monique I. Andersson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Type Species ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Antimicrobial Resistance Genes

Escherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonized with diverse populations of E. coli , Klebsiella pneumoniae and Klebsiella oxytoca , including both antimicrobial-resistant and susceptible strains. Using whole-genome sequencing of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies, which may vary as a result of different inputs and selection pressures. Whole-genome sequencing of 46 contemporaneous patient isolates identified one (2 %; 95 % CI 0.05–11 %) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10 % of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including bla CTX-M, bla SHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention. This article contains data hosted by Microreact.

scholarly journals Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Max Laurence Cummins ◽  
Piklu Roy Chowdhury ◽  
Marc Serge Marenda ◽  
Glenn Francis Browning ◽  
Steven Philip Djordjevic
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Genomic Island ◽  
Sequence Type ◽  
Genomic Islands ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACT Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry blaNDM-1, blaVEB-6, and blaCTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3′ end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli. The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023. IMPORTANCE SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the Enterobacteriaceae. SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3′ end of trmE. For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.

scholarly journals Genotypic-Phenotypic Discrepancies between Antibiotic Resistance Characteristics of Escherichia coli Isolates from Calves in Management Settings with High and Low Antibiotic Use

2011 ◽  
Vol 77 (10) ◽  
pp. 3293-3299 ◽  
Author(s):  
Margaret A. Davis ◽  
Thomas E. Besser ◽  
Lisa H. Orfe ◽  
Katherine N. K. Baker ◽  
Amelia S. Lanier ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antibiotic Use ◽  
Dairy Calf ◽  
Bacterial Populations ◽  
Content Type ◽  
Exact Test ◽  
E Coli ◽  
Fisher’S Exact Test

ABSTRACTWe hypothesized that bacterial populations growing in the absence of antibiotics will accumulate more resistance gene mutations than bacterial populations growing in the presence of antibiotics. If this is so, the prevalence of dysfunctional resistance genes (resistance pseudogenes) could provide a measure of the level of antibiotic exposure present in a given environment. As a proof-of-concept test, we assayed field strains ofEscherichia colifor their resistance genotypes using a resistance gene microarray and further characterized isolates that had resistance phenotype-genotype discrepancies. We found a small but significant association between the prevalence of isolates with resistance pseudogenes and the lower antibiotic use environment of a beef cow-calf operation versus a higher antibiotic use dairy calf ranch (Fisher's exact test,P= 0.044). Other significant findings include a very strong association between the dairy calf ranch isolates and phenotypes unexplained by well-known resistance genes (Fisher's exact test,P< 0.0001). Two novel resistance genes were discovered inE. coliisolates from the dairy calf ranch, one associated with resistance to aminoglycosides and one associated with resistance to trimethoprim. In addition, isolates resistant to expanded-spectrum cephalosporins but negative forblaCMY-2had mutations in the promoter regions of the chromosomalE. coliampCgene consistent with reported overexpression of native AmpC beta-lactamase. Similar mutations in hospitalE. coliisolates have been reported worldwide. Prevalence or rates ofE. coliampCpromoter mutations may be used as a marker for high expanded-spectrum cephalosporin use environments.

scholarly journals Metrics Proposed To Prevent the Harvest of Leafy Green Crops Exposed to Floodwater Contaminated with Escherichia coli

2016 ◽  
Vol 82 (13) ◽  
pp. 3746-3753 ◽  
Author(s):  
Mary Theresa Callahan ◽  
Shirley A. Micallef ◽  
Manan Sharma ◽  
Patricia D. Millner ◽  
Robert L. Buchanan
Keyword(s):  
Escherichia Coli ◽  
The United States ◽  
Green Products ◽  
Worst Case ◽  
Probable Number ◽  
Content Type ◽  
E Coli ◽  
Flood Zone ◽  
Flooding Event ◽  
Bacterial Movement

ABSTRACTThe California Leafy Green Products Handler Marketing Agreement (LGMA) requires leafy green crops within 9 m of the edge of a flooded field not be harvested due to potential contamination (California Leafy Green Products Handler Marketing Board,Commodity Specific Flood Safety Guidelines for the Production and Harvest of Lettuce and Leafy Greens, 2012). Further, previously flooded soils should not be replanted for 60 days. In this study, the suitability of the LGMA metrics for farms in the Mid-Atlantic region of the United States was evaluated. The upper end of a spinach bed (in Beltsville, MD) established on a −5% grade was flooded with water containing 6 log CFU/mlEscherichia colito model a worst-case scenario of bacterial movement through soil.Escherichia coliprevalence in soil and on foliar tissue was determined by most probable number (MPN) analysis at distances up to 9 m from the edge of the flood for 63 days. WhileE. coliwas quickly detected at the 9-m distance within 1 day in the spring trial and within 3 days in the fall trial, noE. coliwas detected on plants outside the flood zone after 14 days. On day 63 for the two trials,E. colipopulations in the flood zone soil were higher in the fall than in the spring. Regression analysis predicted that the time required for a 3-log MPN/g (dry weight) decrease inE. colipopulations inside the flood zone was within the 60-day LGMA guideline in the spring but would require 90 days in the fall. Overall, data suggest that the current guidelines should be revised to include considerations of field and weather conditions that may promote bacterial movement and survival.IMPORTANCEThis study tracked the movement ofEscherichia colifrom floodwater across a horizontal plane of soil and the potential for the contamination of distant leafy green produce. The purpose of this study was to address the validity of the California Leafy Green Products Handler Marketing Agreement recommendations for the harvest of leafy green crops after a flooding event. These recommendations were based on the turning radius of farming equipment but did not take into consideration the potential subsurface movement of pathogens in the water through soil. This research shows that further considerations of field slope, temperature, and additional rainfall events may be necessary to provide appropriate guidelines to prevent the harvest of leafy green crops contaminated by enteric pathogens in floodwaters. This study may be used to provide a framework for comprehensive recommendations to growers for good harvesting practices after a flooding event.

scholarly journals Genomic comparisons of Escherichia coli ST131 from Australia

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Dmitriy Li ◽  
Ethan R. Wyrsch ◽  
Paarthiphan Elankumaran ◽  
Monika Dolejska ◽  
Marc S. Marenda ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Type Species ◽  
Companion Animals ◽  
Snp Analysis ◽  
Complete Class ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Antimicrobial Resistance Genes

Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron–integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462–1014 bp), highlighting the ongoing evolution of this element. The module intI1–dfrA17–aadA5–qacEΔ1–sul1–ORF–chrA–padR–IS1600–mphR–mrx–mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically bla CTX-M-15 and bla CTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.

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