Commonality among Fluoroquinolone-Resistant Sequence Type ST131 Extraintestinal Escherichia coli Isolates from Humans and Companion Animals in Australia ᰔ †

Escherichia coli sequence type 131 (ST131), an emergent multidrug-resistant extraintestinal pathogen, has spread epidemically among humans and was recently isolated from companion animals. To assess for humancompanion animal commonality among ST131 isolates, 214 fluoroquinolone-resistant extraintestinal E. coli isolates (205 from humans, 9 from companion animals) from diagnostic laboratories in Australia, provisionally identified as ST131 by PCR, selectively underwent PCR-based O typing and bla CTX-M-15 detection. A subset then underwent multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) analysis, extended virulence genotyping, antimicrobial susceptibility testing, and fluoroquinolone resistance genotyping. All isolates were O25b positive, except for two O16 isolates and one O157 isolate, which (along with six O25b-positive isolates) were confirmed by MLST to be ST131. Only 12% of isolates (25 human, 1 canine) exhibited bla CTX-M-15 . PFGE analysis of 20 randomly selected human and all 9 companion animal isolates showed multiple instances of >94% profile similarity across host species; 12 isolates (6 human, 6 companion animal) represented pulsotype 968, the most prevalent ST131 pulsotype in North America (representing 23% of a large ST131 reference collection). Virulence gene and antimicrobial resistance profiles differed minimally, without host species specificity. The analyzed ST131 isolates also exhibited a conserved, host species-independent pattern of chromosomal fluoroquinolone resistance mutations. However, eight (89%) companion animal isolates, versus two (10%) human isolates, possessed the plasmid-borne qnrB gene (P < 0.001). This extensive across-species strain commonality, plus the similarities between Australian and non-Australian ST131 isolates, suggest that ST131 isolates are exchanged between humans and companion animals both within Australia and intercontinentally

Clonal group distribution of fluoroquinolone-resistant Escherichia coli among humans and companion animals in Australia

Objectives: To determine the phylogenetic group distribution and prevalence of three major globally disseminated clonal groups [clonal group A (CGA) and O15:K52:H1, associated with phylogenetic group D, and sequence type ST131, associated with phylogenetic group B2] among fluoroquinolone-resistant extra-intestinal Escherichia coli isolates from humans and companion animals in Australia. Methods: Clinical extra-intestinal fluoroquinolone-resistant E. coli isolates were obtained from humans (n = 582) and companion animals (n  = 125), on Australia's east coast (October 2007–October 2009). Isolates were tested for susceptibility to seven antimicrobial agents, and for phylogenetic group, O type and clonal-group-specific single nucleotide polymorphisms by PCR. Results: The fluoroquinolone-resistant isolates were typically resistant to multiple agents (median of four). Analysis revealed that clonal group ST131 accounted for a large subset of the human isolates (202/585, 35%), but for a much smaller proportion of the companion animal isolates (9/125, 7.2%; P ≤ 0.001). In contrast, CGA and O15:K52:H1 were uncommon among both human (7.2%) and companion animal (0.8%) isolates. Conclusions: In Australia, a large proportion (42%) of recent fluoroquinolone-resistant extra-intestinal E. coli isolates from humans are represented by three major globally disseminated clonal groups, predominantly ST131, which by contrast is comparatively rare among fluoroquinolone-resistant E. coli from companion animals. In conjunction with Australia's ban on fluoroquinolone use in livestock, these results argue against a major domestic food animal or companion animal source for fluoroquinolone-resistant extra-intestinal E. coli among humans in Australia. However, both humans and companion animals are involved in the intercontinental emergence and dissemination of ST131.Joanne L. Platell, Rowland N. Cobbold, James R. Johnson and Darren J. Trot

Fluoroquinolone-resistant extraintestinal Escherichia coli clinical isolates representing the O15:K52:H1 clonal group from humans and dogs in Australia

Antimicrobial-resistant extraintestinal pathogenic Escherichia coli (ExPEC) impact both human and veterinary medicine. One ExPEC clonal group that has become increasingly multidrug-resistant is serotype O15:K52:H1. Accordingly, we sought O15:K52:H1 strains among fluoroquinolone-resistant (FQ) E. coli clinical isolates from humans (n=582) and dogs (n=120) in Australia. The phylogenetic group D isolates (267/702; 38%) were screened for O15:K52:H1-specific single-nucleotide polymorphisms (SNPs) in fumC and the O15 rfb variant. The 34 so-identified O15:K52:H1 isolates (33 human, 1 canine) underwent antimicrobial susceptibility profiling, virulence genotyping, and macrorestriction profiling. Although susceptibility profiles varied, the 34 isolates were closely related by pulsed-field gel electrophoresis and exhibited typical O15:K52:H1-associated virulence profiles (complete pap operon, F16 papA allele, papG allele II, iha, fimH, sat, fyuA, iutA, kpsMII, ompT). The canine isolate closely resembled human isolates. Thus, O15:K52:H1 strains contribute to the FQ ExPEC population in Australia and may potentially be transferred between humans and dogs

Prominence of an O75 Clonal Group (Clonal Complex 14) among Non-ST131 Fluoroquinolone-Resistant Escherichia coli Causing Extraintestinal Infections in Humans and Dogs in Australia

Fluoroquinolone (FQ)-resistant extraintestinal pathogenic Escherichia coli (FQ r ExPEC) strains from phylogenetic group B2 are undergoing epidemic spread. Isolates belonging to phylogenetic group B2 are generally more virulent than other E. coli isolates; therefore, resistance to FQs among group B2 isolates is concerning. Although clonal expansion of sequence type 131 (ST131) is a major factor, the contribution of additional clonal groups has not been quantified. Group B2 FQ r ExPEC isolates from humans ( n = 250) and dogs ( n = 12) in Australia were screened for ST131, a recently recognized and rapidly emerging multidrug-resistant and virulent clonal group that is important in both human and companion animal medicine. Non-ST131 isolates underwent virulence genotyping, PCR-based O typing, partial multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and FQ resistance mechanism analysis. Of 49 non-ST131 isolates (45 human, 4 canine), 49% (24 human, 2 canine) represented O-type O75 and exhibited conserved virulence genotypes (F10 papA allele, iha , fimH , sat , vat , fyuA , iutA , kpsM II, usp , ompT , malX , K1/K5 capsule) and MLST allele profiles corresponding with clonal complex CC14. Two clusters, each containing canine and human isolates, were identified by PFGE (differentiated by K1 and K5 capsules). Australian FQ r O75 isolates exhibited commonality with an historical FQ-susceptible O75 urosepsis isolate (also CC14). The isolation from humans and dogs of highly similar FQ r derivatives of the classic O75:K1/K5 (CC14) ExPEC lineage suggests recent acquisition of FQ resistance and potential cross-host-species transfer. This lineage should be targeted with ST131 in future epidemiological investigations of FQ r ExPEC

Commonality among Fluoroquinolone-Resistant Sequence Type ST131 Extraintestinal Escherichia coli Isolates from Humans and Companion Animals in Australia

Escherichia coli sequence type 131 (ST131), an emergent multidrug-resistant extraintestinal pathogen, has spread epidemically among humans and was recently isolated from companion animals. To assess for human-companion animal commonality among ST131 isolates, 214 fluoroquinolone-resistant extraintestinal E. coli isolates (205 from humans, 9 from companion animals) from diagnostic laboratories in Australia, provisionally identified as ST131 by PCR, selectively underwent PCR-based O typing and bla CTX-M-15 detection. A subset then underwent multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) analysis, extended virulence genotyping, antimicrobial susceptibility testing, and fluoroquinolone resistance genotyping. All isolates were O25b positive, except for two O16 isolates and one O157 isolate, which (along with six O25b-positive isolates) were confirmed by MLST to be ST131. Only 12% of isolates (25 human, 1 canine) exhibited bla CTX-M-15 . PFGE analysis of 20 randomly selected human and all 9 companion animal isolates showed multiple instances of ≥94% profile similarity across host species; 12 isolates (6 human, 6 companion animal) represented pulsotype 968, the most prevalent ST131 pulsotype in North America (representing 23% of a large ST131 reference collection). Virulence gene and antimicrobial resistance profiles differed minimally, without host species specificity. The analyzed ST131 isolates also exhibited a conserved, host species-independent pattern of chromosomal fluoroquinolone resistance mutations. However, eight (89%) companion animal isolates, versus two (10%) human isolates, possessed the plasmid-borne qnrB gene ( P < 0.001). This extensive across-species strain commonality, plus the similarities between Australian and non-Australian ST131 isolates, suggest that ST131 isolates are exchanged between humans and companion animals both within Australia and intercontinentally

Fluoroquinolone-resistant extraintestinal pathogenic Escherichia coli, including O25b-ST131, isolated from faeces of hospitalized dogs in an Australian veterinary referral centre

To determine rates of carriage of fluoroquinolone-resistant Escherichia coli and extraintestinal pathogenic E. coli (ExPEC) among dogs in a specialist referral hospital and to examine the population structure of the isolates. Fluoroquinolone-resistant faecal E. coli isolates (n = 232, from 23 of 123 dogs) recovered from hospitalized dogs in a veterinary referral centre in Sydney, Australia, over 140 days in 2009 were characterized by phylogenetic grouping, virulence genotyping and random amplified polymorphic DNA (RAPD) analysis. The RAPD dendrogram for representative isolates showed one group B2-associated cluster and three group D-associated clusters; each contained isolates with closely related ExPEC-associated virulence profiles. All group B2 faecal isolates represented the O25b-ST131 clonal group and were closely related to recent canine extraintestinal ST131 clinical isolates from the east coast of Australia by RAPD analysis. Hospitalized dogs may carry fluoroquinolone-resistant ExPEC in their faeces, including those representing O25b-ST131

Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli

BACKGROUND. Fluoroquinolone-resistant Escherichia coli are increasingly prevalent. Their clonal origins—potentially critical for control efforts—remain undefined. METHODS. Antimicrobial resistance profiles and fine clonal structure were determined for 236 diverse-source historical (1967–2009) E. coli isolates representing sequence type ST131 and 853 recent (2010–2011) consecutive E. coli isolates from 5 clinical laboratories in Seattle, Washington, and Minneapolis, Minnesota. Clonal structure was resolved based on fimH sequence (fimbrial adhesin gene: H subclone assignments), multilocus sequence typing, gyrA and parC sequence (fluoroquinolone resistance-determining loci), and pulsed-field gel electrophoresis. RESULTS. Of the recent fluoroquinolone-resistant clinical isolates, 52% represented a single ST131 subclonal lineage, H30, which expanded abruptly after 2000. This subclone had a unique and conserved gyrA/parC allele combination, supporting its tight clonality. Unlike other ST131 subclones, H30 was significantly associated with fluoroquinolone resistance and was the most prevalent subclone among current E. coli clinical isolates, overall (10.4%) and within every resistance category (11%–52%). CONCLUSIONS. Most current fluoroquinolone-resistant E. coli clinical isolates, and the largest share of multidrug-resistant isolates, represent a highly clonal subgroup that likely originated from a single rapidly expanded and disseminated ST131 strain. Focused attention to this strain will be required to control the fluoroquinolone and multidrug-resistant E. coli epidemic.James R. Johnson, Veronika Tchesnokova, Brian Johnston, Connie Clabots, Pacita L. Roberts, Mariya Billig, Kim Riddell, Peggy Rogers, Xuan Qin, Susan Butler-Wu, Lance B. Price, Maliha Aziz, Marie-Hélène Nicolas-Chanoine, Chitrita DebRoy, Ari Robicsek, Glen Hansen, Carl Urban, Joanne Platell, Darren J. Trott, George Zhanel, Scott J. Weissman, Brad T. Cookson, Ferric C. Fang, Ajit P. Limaye, Delia Scholes, Sujay Chattopadhyay, David C. Hooper, and Evgeni V. Sokurenk