Comparison of Escherichia coli ST131 pulsotypes, by epidemiologic traits, 1967-2009.
Subject: Antibacterial agents (Health aspects)
Antibacterial agents (Analysis)
Drug resistance in microorganisms (Health aspects)
Drug resistance in microorganisms (Analysis)
Infection (Health aspects)
Infection (Analysis)
Drug resistance (Health aspects)
Drug resistance (Analysis)
Authors: Johnson, James R.
Nicolas-Chanoine, Marie-Helene
DebRoy, Chitrita
Castanheira, Mariana
Robicsek, Ari
Hansen, Glen
Weissman, Scott
Urban, Carl
Platell, Joanne
Trott, Darren
Zhanel, George
Clabots, Connie
Johnston, Brian D.
Kuskowski, Michael A.
Pub Date: 04/01/2012
Publication: Name: Emerging Infectious Diseases Publisher: U.S. National Center for Infectious Diseases Audience: Academic; Professional Format: Magazine/Journal Subject: Health Copyright: COPYRIGHT 2012 U.S. National Center for Infectious Diseases ISSN: 1080-6040
Issue: Date: April, 2012 Source Volume: 18 Source Issue: 4
Product: Product Code: 2834880 Bacteriostats NAICS Code: 325412 Pharmaceutical Preparation Manufacturing SIC Code: 2834 Pharmaceutical preparations
Accession Number: 286114909
Full Text: The prevalence of resistance to fluoroquinolones and extended-spectrum cephalosporins in Escherichia coli has increased dramatically over the past decade. This increase is largely the result of the widespread emergence of a single disseminated E. coli clonal group, designated sequence type (ST) 131 according to multilocus sequence typing (MLST) (1,2). E. coli ST131 is characterized by serotype O25b:H4 and often produces CTX-M-15 or other extended-spectrum [beta]-lactamases (ESBLs) (3-5). Unlike most other antimicrobial drug-resistant E. coli, ST131 derives from virulence-associated phylogenetic group B2 and typically exhibits multiple virulence factors, including adhesins, siderophores, toxins, and group 2 capsule (1-7). It thereby poses the dual threat of extensive antimicrobial drug resistance plus virulence.

By definition, ST131 is homogeneous with respect to housekeeping gene sequence across the 7 MLST loci; however, within-lineage genetic variation has been noted since ST131 was first described (3-5). Specifically, diversity of pulsed-field gel electrophoresis (PFGE) profiles has provided insights into the ecology of ST131. For example, the presence of ST131 isolates with similar PFGE profiles in widely dispersed locales and of isolates with quite different profiles in the same locale has suggested rapid and ongoing global dissemination of ST131 (3,8). Likewise, recovery of ST131 isolates with similar PFGE profiles from multiple household members (9-12) and from food animals (or retail meats) and humans (13) has suggested host-to-host or foodborne transmission, respectively, as potential mechanisms for dissemination of ST131.

However, relevant studies to date have included relatively few isolates, locales, and sources and limited time periods (2,6). In addition, the idiosyncratic nature of PFGE analysis precludes across-study comparisons. Thus, we analyzed 579 ST131 isolates from diverse sources according to a standardized PFGE protocol and then compared PFGE profiles with other characteristics, including geographic origin, time of collection, ecologic source, and antimicrobial drug-resistance traits.

Materials and Methods

Isolates

The 579 ST131 study isolates, some previously published (3,9-12,14-19), were compiled as a series of convenience samples from collaborators in diverse locales. The isolates came already identified as ST131 or as generic E. coli in need of screening for ST131 status. They derived mostly from collections assembled by investigators or reference laboratories on the basis of specific resistance phenotypes, O antigens, geographic origins, and/or clinical syndromes of interest. Some isolates were from cases or case series involving infected humans or animals with distinctive signs and symptoms and/or predisposing conditions (9-12,14,15).

Isolates were accompanied by data regarding date of isolation (or receipt in the reference laboratory), ecologic source (i.e., host species, food, or water), and locale of origin. For some isolates, data were available regarding resistance-associated characteristics, i.e., fluoroquinolone resistance; ESBL production; and presence of [bla.sub.CTX-M-15], which encodes the CTX-M-15 ESBL variant. If not provided, this information was newly generated.

ST131 Status

Of the 579 study isolates, 34 (5.9%) came already defined as ST131 by 7-locus MLST (http://mlst.ucc.ie/mlst/dbs/Ecoli). The remaining 545 (94.1%) were presumptively identified as ST131 in the study laboratory by PCR-based screening for ST131-specific single-nucleotide polymorphisms (SNPs) in gyrB and mdh (17). Full MLST was done de novo for 57 (10.5%) of these presumptive ST131 isolates, which represented diverse time periods, locales, sources, and resistance characteristics; in each instance, presumptive ST131 status was confirmed (SNP PCR specificity 100%; 95% CI 94%-100%). Thus, 91 (16%) isolates were directly confirmed by MLST to be ST131. Another 301 (52%) isolates represented pulsotypes with [greater than or equal to] 1 MLST-confirmed ST131 isolate, which indirectly confirmed their ST131 status. Therefore, in total, 392 (68%) isolates were directly or indirectly confirmed by MLST to be ST131. Of the 31 earliest isolates (1967-1997), including the 5 earliest isolates (1967-1986), 32% were directly confirmed by MLST to be ST131.

PFGE Analysis

PFGE analysis of JSaI-restricted total DNA of isolates was performed according to a standardized protocol (20) by a single observer in 1 laboratory. Profiles were captured and analyzed digitally by using BioNumerics software version 6.6 (Applied Maths, Austin, TX, USA). Marker lanes in each gel (E. coli O157:H7 strain g5244) enabled normalization within and across gels. Band positions were assigned manually, with computer assistance. The band tolerance setting, as derived empirically from analysis of multiple same-isolate profiles, was 1.15%.

Pairwise Dice similarity coefficients were used to define pulsotypes. Isolates exhibiting [greater than or equal to] 94% profile similarity ([approximately equal to] 3-band difference) to the index isolate for an established pulsotype, implying genetic similarity (21), were assigned to that pulsotype; others became the index isolate for a new pulsotype. Newly encountered pulsotypes were numbered sequentially. A PFGE profile dendrogram was constructed according to the unweighted pair group method for 87 (15%) of the isolates (selected randomly after inclusion of 2 representatives of each pulsotype with [greater than or equal to] 6 members) plus the earliest isolated (1967) and earliest published (1985) isolates (8).

Susceptibility Testing

Disk diffusion testing for ciprofloxacin susceptibility and ESBL production was performed on isolates of unknown fluoroquinolone or ESBL phenotype as described (22,23). Fluoroquinolone resistance was defined as nonsusceptibility to ciprofloxacin.

Statistical Analyses

Geographic origin was categorized as United States (with 4 subregions--West, Midwest, South, and Northeast--as defined by the US Census Bureau [www. census.gov/geo/www/us_regdiv.pdf]), Canada, and other international locales combined. Ecologic source was categorized as human, companion animal, food animal, other animal, food, and water. Year of isolation/submission was assessed both continuously and categorically (e.g., pre-1990 vs. later).

Comparisons of proportions were tested by using 2-tailed Fisher exact (unpaired comparisons) and McNemar (paired comparisons) tests. Comparisons involving continuous variables were tested by using the Mann Whitney U test (2-tailed). Other variables were assessed as independent predictors of selected pulsotype categories by using multivariable logistic regression analysis. The significance criterion was p<0.05.

Results

Isolate Origins and Characteristics

The 579 ST131 study isolates were derived from humans (486 [84%]), animals (77 [13%]), environmental sources (15 [3%]), and an unknown source (n = 1). Animal uses included companion (22 [4%]), food (45 [8%]), and other (10 [2%]). Environmental sources included food (6 [1%]) and water (9 [2%]). Geographic origins included the United States (446 [77%]), Canada (53 [9%]), and other international locales (80 [14.1%]). The US isolates were from the West (59 [10%]; 9 centers, 4 states), Midwest (180 [31%] centers, 11 states), South (98 [17%] centers, 9 states), and Northeast (109 [19%] centers, 7 states). Isolates from Canada were from 9 centers in 8 provinces. Other international isolates were from 11 centers in 11 countries (Australia, Chile, France, South Korea, Lebanon, India, Italy, Peru, Portugal, Spain, Switzerland). Dates of isolation/submission ranged from 1967 through 2009 (median year 2007). Twenty (4%) isolates were isolated/submitted during 1967-1989, the 5 earliest during 1967, 1982, 1983, 1985, and 1986; 22 (4%) were isolated/submitted during 1990-1999; and 537 (93%) were isolated/submitted during 2000-2009. Overall, 462 (80%) isolates were fluoroquinolone-resistant, 272 (47%) were ESBL-producers, and 188 (33%) had [bla.sub.CTX-M-15].

Pulsotypes

XbaI PFGE analysis resolved 170 distinct pulsotypes, each accounting for 1 isolate (105 pulsotypes) to 136 isolates (1 pulsotype, type 968). The 105 single-isolate pulsotypes collectively accounted for 105 isolates (18% of total); the 65 multiple-isolate pulsotypes accounted for the remaining 474 isolates (82% of total). Among the multipleisolate pulsotypes, 12 contained [greater than or equal to] 6 isolates each (i.e., >1% of the population), collectively accounting for 327 isolates (56% of total). The multiple-isolate pulsotypes contained 62 clusters of isolates (each comprising 2-5 isolates; total 150 isolates) with indistinguishable profiles.

Temporal Patterns

Pulsotypes varied significantly by temporal occurrence. The 65 multiple-isolate pulsotypes and 12 high-prevalence pulsotypes were significantly associated with more recent dates of isolation/submission, relative to the low-prevalence and single-isolate pulsotypes (Table 1). Temporal variation was also evident among the 12 high-prevalence pulsotypes; 4 were significantly associated with later and 1 (type 955) with earlier occurrence (Table 1).

Analysis of temporal prevalence trends (Figure) showed that the 12 high-prevalence pulsotypes accounted collectively for only 5% of 20 isolates during the earliest period (1967-1989) but for 58% of isolates during subsequent years (p<0.001). Three of these pulsotypes (988, 800, 812) were the top 1, 2, or 3 most prevalent, overall and within each interval from 1990 forward. These 3 types appeared sequentially by overall pulsotype prevalence (i.e., in 1990-1999 for type 968, in 2000-2002 for type 800, and in 2005 for type 812) and, except for type 800 in 2003, were detected continuously after first appearing. After it appeared, type 968 maintained a consistently high prevalence ([greater than or equal to] 19%), whereas types 800 and 812 exhibited early prevalence spikes followed by sizeable drops. In contrast, the 9 other high-prevalence types appeared intermittently, which, depending on the pulsotype, was mostly in earlier years, later years, or sporadically throughout (Figure).

A temporal trend was also evident in the PFGE dendrogram (online Appendix Figure, wwwnc.cdc.gov/EID/article/18/1/11-1627-FA1.htm), which extended to 67% similarity. The more highly similar PFGE profiles in the upper region of the tree involved mostly recent isolates and higher prevalence pulsotypes, whereas the more basal, dissimilar profiles toward the lower region of the tree involved more older isolates (including isolates from 1967, 1982, 1985, and 1986) and low-prevalence pulsotypes.

Geographic Distribution

The pulsotypes primarily exhibited a broad geographic distribution, yet there was some geographic segregation. Table 2 shows the number of mutually exclusive geographic regions (among 6 total) in which each of the 65 multipleisolate pulsotypes were found. Only 18 of 65 multipleisolate pulsotypes were limited to a single geographic region (p<0.001 for occurrence in 1 vs. multiple regions, McNemar test). Moreover, these 18 pulsotypes included only 2 (13 pulsotypes), 3 (4 pulsotypes), or 4 (1 pulsotype) isolates each and represented <50% of pulsotypes within their size category. In contrast, all pulsotypes including [greater than or equal to] 5 isolates were found in multiple geographic regions, and 3 of the 6 pulsotypes comprising [greater than or equal to] 8 isolates spanned all 6 geographic regions (Table 2). Table 3 shows the overlap among regions by the number of shared pulsotypes and by the number of isolates in these pulsotypes. Each region overlapped partially with every other region (Table 3).

[FIGURE OMITTED]

Against this background of broad geographic distribution, substantial geographic segregation of pulsotypes was evident. For example, at the isolate level, each region was negatively associated with at least 1 other region; the US West and non-Canadian international sites exhibited the greatest number of such negative associations, suggesting somewhat locale-specific pulsotype populations in these regions (Table 3). The only positive association between nonoverlapping regions involved the US Midwest and Canada.

Table 4 provides a pulsotype-level analysis of these geographic associations. For example, the high-prevalence and multiple-isolate pulsotypes were collectively significantly overrepresented in Canada, and the high-prevalence pulsotypes were also significantly underrepresented in the United States, specifically, in the US West. Among individual high-prevalence pulsotypes, 968 was overrepresented in the US Midwest and underrepresented in the US West; 800 was over-represented in Canada and under-represented in the United States and the US West; 812 was over-represented in the US South; 987 was over-represented internationally (specifically in Australia, data not shown) and under-represented in the United States; and 1202 was over-represented in the US West (Table 4).

Source Distribution

In contrast with the generally broad geographic distribution of pulsotypes, the source distribution was more restricted, and source-specific segregation predominated over across-source commonality. For example, only 13 of 65 multiple-isolate pulsotypes spanned multiple sources (p<0.001, McNemar test); most of these included only 2 sources each, and none included >4 (of 6 possible) sources (Table 2).

Likewise, the by-source distribution of pulsotypes (Table 5) showed less overall commonality than did geographic distribution. Still, it showed multiple positive and negative associations at the isolate and the pulsotype level. Specifically, isolates from humans were associated positively with pulsotypes comprising isolates from water and negatively with pulsotypes comprising isolates from companion animals, food animals, or food. Isolates from companion animals were associated positively with pulsotypes containing isolates from other animals, and isolates from food animals were associated positively with pulsotypes containing isolates from food (Table 5). In addition, pulsotypes containing isolates from food animals were associated negatively with pulsotypes containing isolates from humans, but they were associated positively with pulsotypes containing isolates from food (Table 5).

Significant by-source segregation also was evident for individual pulsotypes (Table 6). Collectively, the multiple-isolate and high-prevalence pulsotypes were associated positively with humans and negatively with food animals and environmental sources, and high-prevalence pulsotypes were associated with companion animals. Furthermore, 5 high-prevalence pulsotypes were individually significantly distributed by source: type 968 was associated positively with pets and other animals and negatively with food animals and environmental sources, 800 was associated positively with humans and negatively with food animals, 812 was associated positively with humans, 1202 was associated negatively with humans and positively with food animals, and 955 was associated negatively with humans and positively with pets and environmental sources (Table 6). Five additional pulsotypes, comprising 2 food animal isolates each, were significantly associated with food animals (p = 0.004 for each; data not shown).

Antimicrobial Drug Resistance

Fluoroquinolone resistance, ESBL production, and [bla.sub.CTX-M-15] also segregated significantly by pulsotype in varied patterns (Table 7). The high-prevalence and multipleisolate pulsotypes collectively and type 968 were associated positively with fluoroquinolone resistance but indifferently with ESBL production and [bla.sub.CTX-M-15]. In contrast, type 800 was associated positively with fluoroquinolone resistance but negatively with ESBL production and [bla.sub.CTX-M-15], whereas types 905, 812, and 919 were associated positively with all 3 traits, and type 987 was associated negatively with all 3 traits (Table 7).

Multivariable Analysis

All 3 resistance traits, plus several source groups and geographic regions, exhibited significant associations with year of isolation/submission (Table 1), suggesting possible confounding by temporal correlations among variables. Thus, we used multivariable logistic regression analysis to assess for independent associations of selected predictor variables with pulsotype. Separate models were constructed for the 3 most prevalent pulsotypes, the high-frequency pulsotypes, and the multiple-isolate pulsotypes, by using as candidate predictor variables 1 representative from each epidemiologic or resistance category (year, ecologic source, locale, fluoroquinolone phenotype, and ESBL status). ESBL status was a significant predictor in all 5 resulting models, as was fluoroquinolone resistance in 4 models (fluoroquinolone resistance was excluded from the fifth model because of its 100% prevalence in pulsotype 812), year in 3 models, and human source in 2 models (Table 8). In contrast, US origin (the representative geographic variable) was not a significant predictor in any model.

Indistinguishable PFGE Profile Isolates

We also assessed associations with other variables for the 7 largest clusters of isolates with indistinguishable PFGE profiles; each cluster contained 4-5 isolates. Of the 31 constituent isolates, 28 were recent (2007-2009) and the other 3 were from 2002 or 2004. Of the 7 clusters, 6 included isolates from multiple locales, from multiple continents in 3 instances. In contrast, only 3 clusters came from multiple host species. Whereas each cluster was internally homogeneous for fluoroquinolone phenotype (6 all-resistant clusters, 1 all-susceptible cluster), 4 were internally heterogeneous according to ESBL and/or blaCTX-M-15 status.

Discussion

We used PFGE analysis to define population structure among 579 diverse E. coli ST131 isolates and then assessed temporal, geographic, ecologic, and resistance trait associations for the various pulsotypes, i.e., presumed sub-ST genetic lineages. Our findings support 4 main conclusions. First, although ST131 is highly diverse at the pulsotype level, a small number of high-frequency pulsotypes predominate, and pulsotype 968 accounts for 24% of the population. Second, pulsotypes differ in prevalence over time; high-prevalence pulsotypes tend to occur in more recent years, consistent with recent emergence and expansion, implying greater fitness. Third, whereas broad geographic distribution predominates over locale-specific segregation, implying widespread dispersal rather than localized endemicity, segregation by ecologic source predominates over across-source commonality, implying niche adaptation rather than broad host-range capability and interspecies transmission. Fourth, resistance traits (i.e., fluoroquinolone resistance, ESBL production, and [bla.sub.CTX-M-15]) are highly pulsotype-specific, suggesting predominantly subclonal distribution.

The striking prevalence disparities among pulsotypes suggest that certain pulsotypes, especially the exceptionally successful pulsotype 968, possess fitness advantages over others. In retrospect, pulsotype 968 accounted for all previously reported household clusters, 3 of which involved serious or fatal disease in [greater than or equal to] 1 household members (9-12). A possible founder effect for type 968 is unlikely because the pulsotypes that were detected earliest were mostly low-prevalence types; higher prevalence pulsotypes appeared only later, seemingly outcompeting the low-prevalence types. In regard to possible fitness advantages, ESBL production and [bla.sub.CTX-M-15] were significantly associated with several high-prevalence pulsotypes and were present in most or all of their members (Table 7). However, they were not significantly associated with (predominant) pulsotype 968 and so are unlikely the main explanation for the recent expansion of ST131, of which pulsotype 968 was the single main component (Figure). In contrast, fluoroquinolone resistance was significantly associated with each of the 4 most prevalent pulsotypes and collectively with the 12 high-prevalence and 65 multiple-isolate pulsotypes. Thus, fluoroquinolone resistance may have made a major contribution to the recent expansion of ST131.

Although the predominant pattern was broad dispersal of pulsotypes, localized segregation also occurred. These trends imply considerable ongoing dissemination and intermixing of ST131 lineages among locales (sufficient to largely preclude establishment of locale-specific populations) but with variable degrees of intermixing versus segregation by locale and pulsotype. For example, the US Midwest and Canada shared pulsotypes more extensively than did other regions. Conversely, non-Canadian international locales and the US West had less pulsotype commonality with other regions (i.e., had more highly locale-specific populations) than did other locales. Several high-prevalence pulsotypes similarly exhibited distinct patterns of distribution and were variably concentrated in specific regions. Similar patterns have been described previously for ST131 but in lesser detail and without statistical analysis (3,6,8,17,24,25). The undefined mechanisms for the ongoing dispersal of ST131, possibly including international travel and commerce, wild bird migration, and foodborne or waterborne transmission, and its limited locale-specific segregation by pulsotype warrant study.

The associations of specific pulsotypes with different ecologic sources are relevant to the dispersal mechanisms of ST131. In contrast to the striking geographic dissemination of pulsotypes, we also found some evidence of niche segregation. Positive associations for niche segregation were found between humans and water, companion animals and other animals, and food animals and food. In contrast, negative associations were found between humans and most other sources, companion animals or other animals and food or food animals, and water and companion animals or food animals. These findings implicate humans as the source for ST131 isolates found in water and implicate food animals as the source for isolates found in food. In contrast, and consistent with findings in most, but not all, previous studies (13,26-28), these findings indicate that food animals and food are not major sources of ST131 for humans. They also suggest no special pet-human commonality of ST131 pulsotypes, notwithstanding some well-documented overlap (29). This argues against pets and the food supply as major vehicles for dissemination of ST131 strains among humans. Indeed, in 1 study, 7% of healthy humans were found to be colonized intestinally with an ST131 strain (30); thus, humans may be the main reservoir for human-associated strains. A larger, more current, and more systematically assembled study population is needed to confirm the findings of the present study.

Until now, the earliest reported isolate of ST131 was from a patient with urosepsis in 1985 (8). Here, we report 3 earlier isolations, from 1967, 1982, and 1983, none of which were from a high-prevalence pulsotype. This finding documents the presence of ST131 decades before its emergence as a disseminated human pathogen and suggests an opportunity to compare early isolates with recent isolates for characteristics that might confer enhanced fitness, possibly contributing to the emergence of ST131.

Our study had limitations. First, the population was a convenience sample with multiple possible sources of bias. Second, despite considerable diversity, the population was not balanced; it predominantly comprised recent isolates from human in the United States, reducing both generalizability and power for comparisons involving other times, sources, and regions. Third, minimal associated data (especially clinical details) were available for many isolates, limiting the possible epidemiologic analyses. Fourth, PFGE profiles reflect genetic relationships only indirectly and require subjective interpretation. Fifth, the multiple comparisons could have produced spurious associations by chance alone. However, the proportion of comparisons yielding a significant p value was much greater, and the associated p values much smaller, than should occur by chance alone. Last, the 94% PFGE similarity pulsotype criterion was somewhat arbitrary and possibly suboptimal; however, an alternate 100% similarity criterion yielded qualitatively similar conclusions.

Our study also had strengths. The population was the largest reported to date for ST131 (2) and the most extensively distributed by time, source, and region. The PFGE analysis was conducted by 1 experienced observer in 1 laboratory by using software that enabled concurrent comparisons for all isolates. Diverse univariable and multivariable statistical approaches were used, pulsotypes were analyzed collectively and individually, and PFGE profiles were assessed by using 2 similarity thresholds (94% and 100%) and in a dendrogram.

Thus, within a large, diverse collection of E. coli ST131 isolates, we documented extensive PFGE profile diversity and a predominance of certain high-prevalence pulsotypes (particularly pulsotype 968, 24% overall) that exhibited distinctive temporal patterns of emergence. Notwithstanding some geographic localization, pulsotypes were extensively dispersed by region. In contrast, they were more highly source specific; in particular, isolates from humans exhibited almost no commonality with isolates from food animals or foods. Pulsotype 968 was much more closely associated with fluoroquinolone resistance than with ESBL production or [bla.sub.CTX-M-15], suggesting a greater role for fluoroquinolone resistance than ESBLs in the expansion of this dominant pulsotype and ST131 in general. These findings considerably advance our understanding of the genetic structure, ecology, geographic distribution, and emergence of this widely disseminated antimicrobial drug-resistant pathogen, which represents a growing public health threat.

The MASTER (Macrorestriction Analysis of ST131 for Epidemiologic Research) Investigators who contributed data include Jo-Ellyn Abraham (Abbott-Northwestern Hospital, Minneapolis, Minnesota, USA), Javier Adachi (The University of Texas MD Anderson Cancer Center, Houston, Texas, USA), Aristides Assimacopoulos (University of South Dakota, Souix Falls, South Dakota, USA), Robert L. Bergsbaken (Health Partners and Regions Medical Center, St. Paul, Minnesota, USA), Jorge Blanco (University of Santiago de Compostela, Lugo, Spain), Michael Cooperstock (University of Missouri School of Medicine, Columbia, Missouri, USA), Paul Edelstein (Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA), Peter T. Ender (St. Luke's Hospital and Health Network, Bethlehem, Pennsylvania, USA), Nancy Hansen (Creighton University, Omaha, Nebraska, USA), John Holter (Veterans Affairs Medical Center, Minneapolis), Thomas M. Hooton (University of Miami, Miami, Florida, USA), Michelle Hulse (Childrens Hospital, Minneapolis), James H. Jorgensen and James S. Lewis II (University Health System, San Antonio, Texas, USA), Karen Lolans (Rush Medical School, Chicago, Illinois, USA), Sybille Miller (Leesburg Veterinary Internal Medicine, Leesburg, Virginia, USA), Rob Owens (Cubist Pharmaceuticals, Falmouth, Maine, USA), Elizabeth Palavecino (Wake Forest University Baptist Medical Center, Winston-Salem, North Carolina, USA), David Paterson (University of Pittsburgh, Pittsburgh, Pennsylvania, USA, and Queensland University, Brisbane, Queensland, Australia), Johann D. D. Pitout (Calgary Laboratory Services, Calgary, Alberta, Canada), John P. Quinn (Pfizer Global Research, Groton, Connecticut, USA), James Rice (The Scripps Research Institute, La Jolla, California, USA), Daniel F. Sahm (Eurofins-Medinet, Chantilly, Virginia, USA), and Karen Vigil (University of Texas Health Sciences Center at Houston, Houston)

This material is based on work supported by the Office of Research and Development, Medical Research Service, Department of Veterans Affairs (J.R.J.). Dave Prentiss (Minneapolis VA Medical Center) prepared the figures.

J.R.J. received research funding from Merck and Rochester Medical Group; J.S.L. received research funding and/or honoraria from Merck, Ortho-McNeil, and Pfizer; J.P.Q. is an employee of Astra-Zeneca and a shareholder in Pfizer Global Research.

Dr Johnson is professor of medicine and senior associate director of the infectious diseases fellowship program at the University of Minnesota and head of the molecular epidemiology laboratory at the Minneapolis VA Medical Center. His research focuses on the molecular epidemiology, ecology, evolution, and virulence of extraintestinal pathogenic and antimicrobial drug-resistant E. coli.

References

(1.) Peirano G, Pitout JDD. Molecular epidemiology of Escherichia coli producing CTX-M p-lactamases: the worldwide emergence of clone ST131 O25:H4. Int J Antimicrob Agents. 2010;35:316-21. http:// dx.doi.org/10.1016/j.ijantimicag.2009.11.003

(2.) Rogers BA, Sidjabat HE, Paterson DL. Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain. J Antimicrob Chemother. 2011;66:1-14. http://dx.doi.org/10.1093/ jac/dkq415

(3.) Nicolas-Chanoine MH, Blanco J, Leflon-Guibout V, Demarty R, Alonso MP, Cani9a MM, et al. Intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15. J Antimicrob Chemother. 2008;61:273-81. http://dx.doi.org/10.1093/jac/dkm464

(4.) Clermont O, Lavollay M, Vimont S, Deschamps C, Forestier C, Branger C, et al. The CTX-M-15producing Escherichia coli diffusing clone belongs to a highly virulent B2 phylogenetic subgroup. J Antimicrob Chemother. 2008;61:1024-8. http://dx.doi.org/10.1093/jac/dkn084

(5.) Coque TM, Novais A, Carattoli A, Poirel L, Pitout J, Peixe L, et al. Dissemination of clonally related Escherichia coli strains expressing extended-spectrum p-lactamase CTX-M-15. Emerg Infect Dis. 2008;14:195-200. http://dx.doi.org/10.3201/eid1402.070350

(6.) Gibreel TM, Dodgson AR, Cheesbrough J, Fox AJ, Bolton FJ, Upton M. Population structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli from northwest England. J Antimicrob Chemother. 2012;67:346-56. http://dx.doi.org/10.1093/jac/dkr451

(7.) Totsika M, Beatson SA, Sarkar S, Phan MD, Petty NK, Bachmann N, et al. Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: genome analysis and virulence mechanisms. PLoS ONE. 2011;6:e26578. http://dx.doi. org/10.1371/journal.pone.0026578

(8.) Johnson JR, Johnston B, Clabots C, Kuskowski MA, Castanheira M. Escherichia coli sequence type ST131 as the major cause of serious multidrug-resistant E. coli infections in the United States (2007). Clin Infect Dis. 2010;51:286-94. http://dx.doi.org/10.1086/653932

(9.) Johnson JR, Anderson JT, Clabots C, Johnston B, Cooperstock M. Within-household sharing of a fluoroquinolone-resistant Escherichia coli sequence type ST131 strain causing pediatric osteoarticular infection. Pediatr Infect Dis J. 2010;29:473-5. http://dx.doi. org/10.1097/INF.0b013e3181c89bd7

(10.) Ender PT, Gajanana D, Johnston B, Clabots C, Tamarkin FJ, Johnson JR. Transmission of extended-spectrum beta-lactamase-producing Escherichia coli (sequence type ST131) between a father and daughter resulting in septic shock and emphysematous pyelonephritis. J Clin Microbiol. 2009;47:3780-2. http://dx.doi.org/10.1128/JCM.01361-09

(11.) Owens RC, Johnson JR, Stogstill P, Yarmus L, Lolans K, Quinn J. Community transmission in the United States of a CTX-M-15-producing sequence type ST131 Escherichia coli strain resulting in death. J Clin Microbiol. 2011;49:3406-8. http://dx.doi.org/10.1128/JCM.00993-11

(12.) Johnson JR, Miller S, Johnston B, Clabots C. DebRoy C. Sharing of Escherichia coli sequence type ST131 and other multidrug-resistant and urovirulent E. coli strains among dogs and cats within a household. J Clin Microbiol. 2009;47:3721-5. http://dx.doi.org/10.1128/JCM.01581-09

(13.) Platell JL, Johnson JR, Cobbold RN, Trott DJ. Multidrug-resistant extraintestinal pathogenic Escherichia coli of sequence type ST131 in animals and foods. Vet Microbiol. 2011;153:99-108. http:// dx.doi.org/10.1016/j.vetmic.2011.05.007

(14.) Johnson JR, Johnston B, Clabots C, Kuskowski MA, Pendyala S, DebRoy C, et al. Escherichia coli sequence type ST131 as an emerging fluoroquinolone-resistant uropathogen among renal transplant recipients. Antimicrob Agents Chemother. 2010;54:546-50. http:// dx.doi.org/10.1128/AAC.01089-09

(15.) Vigil KJ, Johnson JR, Johnston BD, Kontoyiannis DP, Mulanovich VE, Raad II, et al. Escherichia coli pyomyositis: an emerging entity among patients with hematologic malignancies. Clin Infect Dis. 2010;50:374-80. http://dx.doi.org/10.1086/649866

(16.) Urban C, Mariano N, Bradford PA, Tuckman M, Segal-Maurer S, Wehbeh W, et al. Identification of CTX-M p-lactamases in Escherichia coli from hospitalized patients and residents of long-term care facilities. Diagn Microbiol Infect Dis. 2010;66:402-6. http:// dx.doi.org/10.1016/j.diagmicrobio.2009.11.012

(17.) Johnson JR, Menard M, Johnston B, Kuskowski MA, Nichol K, Zhanel GG. Epidemic clonal groups of Escherichia coli as a cause of antimicrobial-resistant urinary tract infections in Canada, 2002-2004. Antimicrob Agents Chemother. 2009;53:2733-9. http:// dx.doi.org/10.1128/AAC.00297-09

(18.) Sidjabat HE, Paterson DL, Adams-Haduch JM, Ewan L, Pasculle AW, Muto CA, et al. Molecular epidemiology of CTX-M-producing Escherichia coli isolates at a tertiary medical center in western Pennsylvania. Antimicrob Agents Chemother. 2009;53:4733-9. http://dx.doi.org/10.1128/AAC.00533-09

(19.) Lewis JS II, Herrera M, Wickes B, Patterson JE, Jorgensen JH. First report of the emergence of CTX-M-type extended-spectrum beta-lactamases (ESBLs) as the predominant ESBL isolated in a US health care system. Antimicrob Agents Chemother. 2007;51:4015-21. http://dx.doi.org/10.1128/AAC.00576-07

(20.) Ribot EM, Fair MA, Gautom R, Cameron DN, Hunter SB, Swami nathan B, et al. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog Dis. 2006;3:59-67. http://dx.doi.org/10.1089/fpd.2006.3.59

(21.) Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, et al. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol. 1995;33:2233-9.

(22.) Clinical Laboratory Standards Institute. Performance standards for antimicrobial disk susceptibility tests; approved standard-tenth edition. M02-A10. Wayne (PA): The Institute; 2009.

(23.) Clinical Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing; nineteenth informational supplement. M100-S19. Wayne (PA): The Institute; 2009.

(24.) Blanco M, Alonso MP, Nicolas-Chanoine MH, Dahbi G, Mora A, Blanco JE, et al. Molecular epidemiology of Escherichia coli producing extended-spectrum p-lactamases in Lugo (Spain): dissemination of clone O25b:H4-ST131 producing CTX-M-15. J Antimicrob Chemother. 2009;63:1135-41. http://dx.doi.org/10.1093/jac/dkp122

(25.) Manges AR, Tabor H, Tellis P, Vincent C, Tellier P-P. Endemic and epidemic lineages of Escherichia coli that cause urinary tract infections. Emerg Infect Dis. 2008;14:1575-83. http://dx.doi. org/10.3201/eid1410.080102

(26.) Dhanji H, Murphy NM, Doumith M, Durmus S, Lee SS, Hope R, et al. Cephalosporin resistance mechanisms in Escherichia coli isolated from raw chicken imported into the UK. J Antimicrob Che mother. 2010;65:2534-7. http://dx.doi.org/10.1093/jac/dkq376

(27.) Mora A, Herrera A, Mamani R, Lopez C, Alonso MP, Blanco JE, et al. Recent emergence of clonal group O25b:K1:H4-B2-ST131 ibeA strains among Escherichia coli poultry isolates, including CTX-M-9producing strains, and comparison with clinical human isolates. Appl Environ Microbiol. 2010;76:6991-7. http://dx.doi. org/10.1128/AEM.01112-10

(28.) Vincent C, Boerlin P, Daignault D, Dozois CM, Dutil L, Galana kis C, et al. Food reservoir for Escherichia coli causing urinary tract infections. Emerg Infect Dis. 2010;16:88-95. http://dx.doi. org/10.3201/eid1601.091118

(29.) Platell JL, Cobbold RN, Johnson JR, Heisig A, Heisig P, Clabots C, et al. Commonality among fluoroquinolone-resistant sequence type ST131 extraintestinal Escherichia coli isolates from humans and companion animals in Australia. Antimicrob Agents Chemother. 2011;55:3782-7. http://dx.doi.org/10.1128/AAC.00306-11

(30.) Leflon-Guibout V, Blanco J, Amaqdouf K, Mora A, Guize L, Nicolas-Chanoine MH. Absence of CTX-M enzymes but high prevalence of clones, including clone ST131, among fecal Escherichia coli isolates from healthy subjects living in the area of Paris, France. J Clin Microbiol. 2008;46:3900-5. http://dx.doi.org/10.1128/JCM.0073408

James R. Johnson, Marie-Helene Nicolas-Chanoine, Chitrita DebRoy, Mariana Castanheira Ari Robicsek, Glen Hansen, Scott Weissman, Carl Urban, Joanne Platell, Darren Trott, George Zhanel Connie Clabots, Brian D. Johnston, Michael A. Kuskowski, and the MASTER Investigators [1]

[1] MASTER (Macrorestriction Analysis of ST131 for Epidemiologic Research) Investigators who contributed data are listed at the end of this article.

Author affiliations: Veterans Affairs Medical Center, Minneapolis, Minnesota, USA (J.R. Johnson, C. Clabots, B.D. Johnston, M.A. Kuskowski); University of Minnesota, Minneapolis (J.R. Johnson, B.D. Johnston, M.A. Kuskowski); Hopital Beaujon, Clichy, France (M.-H. Nicolas-Chanoine); The Pennsylvania State University, College Park, Pennsylvania, USA (C. DebRoy); JMI Laboratories, North Liberty, Iowa, USA (M. Castanheira); NorthShore University HealthSystem, Evanston, Illinois, USA (A. Robicsek); Hennepin County Medical Center, Minneapolis (G. Hansen); University of Washington, Seattle, Washington, USA (S. Weissman); New York Hospital Queens, Flushing, New York, USA (C. Urban); New York University School of Medicine, New York, New York, USA (C. Urban); University of Queensland, Brisbane, Queensland, Australia (J. Platell); University of Adelaide, Adelaide, South Australia, Australia (D. Trott); and University of Manitoba, Winnipeg, Manitoba, Canada (G. Zhanel)

DOI: http://dx.doi.org/ 10.3201/eid1804.111627

Address for correspondence: James R. Johnson, VA Medical Center, Infectious Diseases (111F), 1 Veterans Dr, Minneapolis, MN 55417, USA; email: johns007@umn.edu
Table 1. Association of year of isolation-submission with pulsotype
and other characteristics for 579 Escherichia coli sequence type
isolates, 1967-2009 *

Associated                Characteristic absent
characteristic,
specific trait           No.        Year, median
([double dagger])      isolates       (range)

Pulsotype
  High-prevalence        252      2007 (1967-2009)
  Multiple-isolate       105      2007 (1967-2009)
  968                    443      2007 (1967-2009)
  812                    547      2007 (1967-2009)
  987                    568      2007 (1967-2009)
  955                    572      2007 (1967-2009)
  1160                   573      2007 (1967-2009)

Resistance
  FQ                     117      2003 (1967-2009)
  ESBL                   307      2007 (1967-2009)
  [bla.sub.CTX-M-15]     391      2007 (1967-2009)

Source ([section])
  Human                   92      2003 (1982-2009)
  Pet                    556      2007 (1982-2009)
  Food animal            533      2007 (1985-2009)
  Food/water             563      2007 (1982-2009)

Region
  United States          133      2005 (1998-2009)
    West                 520      2007 (1967-2009)
    Midwest              399      2007 (1967-2009)
  Canada                 526      2007 (1967-2009)
  International          499      2007 (1967-2009)

Associated               Characteristic present
characteristic,
specific trait           No.        Year, median      p value
([double dagger])      isolates       (range)        ([dagger])

Pulsotype
  High-prevalence        327      2007 (1987-2009)     <0.001
  Multiple-isolate       474      2007 (1982-2009)     <0.001
  968                    136      2008 (1992-2009)     <0.001
  812                     32      2007 (2005-2009)      0.03
  987                     11      2008 (1998-2008)      0.004
  955                     7       2002 (1993-2005)      0.001
  1160                    6       2008 (2004-2009)      0.04

Resistance
  FQ                     462      2007 (2000-2009)     <0.001
  ESBL                   272      2007 (2000-2009)      0.001
  [bla.sub.CTX-M-15]     188      2007 (2000-2009)      0.048

Source ([section])
  Human                  486      2007 (1985-2009)     <0.001
  Pet                     22      2008 (2002-2009)     <0.001
  Food animal             45      1997 (1982-2009)     <0.001
  Food/water              15      2003 (1993-2007)     <0.001

Region
  United States          446      2007 (1967-2009)      0.007
    West                  59      2007 (1982-2007)     <0.001
    Midwest              180      2008 (1986-2009)     <0.001
  Canada                  53      2004 (1998-2004)     <0.001
  International           80      2008 (2002-2009)     <0.001

* ST, sequence type; FQ, fluoroquinolone; ESBL, extended-spectrum
[beta]-lactamase; [bla.sub.CTX-M-15], gene encoding the CTX-M-15
ESBL; high-prevalence, pulsotypes with [greater than or equal to] 6
isolates each; multiple-isolate, pulsotypes with [greater than or
equal to] 2 isolates each; international, non-US locales other than
Canada.

([dagger]) Characteristics shown are those that yielded p<0.05
(Mann-Whitney U test, 2-tailed).

([double dagger]) High-prevalence pulsotypes 800, 905, 1202, 807,
919, 595, and 797; other animal source; and origin from the US South
or US Northeast did not exhibit a significant association with year.

([section]) Total for all source variables is 578 rather than 579
because source was unknown for 1 isolate.

Table 2. Geographic origin and ecologic source of 65 pulsotypes
among 579 Escherichia coli ST131 isolates, 1967-2009 *

                                                No. pulsotypes
                                                 with isolate
                                                from indicated
                                                no. geographic
                                                   regions
                                                  ([dagger])

No. isolates per                    No.
pulsotype                       pulsotypes       1        2

2                                   28           13       15
3                                   12           4        8
4                                   10           1        3
5                                    3           0        2
6                                    3           0        0
7                                    3           0        0
[greater than or equal to] 8         6           0        1

                               No. pulsotypes with isolate from
                               indicated no. geographic regions
                                        ([dagger])

No. isolates per
pulsotype                        3       4       5       6

2                               NA      NA      NA      NA
3                                0      NA      NA      NA
4                                5       1      NA      NA
5                                1       0       0      NA
6                                0       2       1       0
7                                0       1       2       0
[greater than or equal to] 8     1       0       1       3

                                      No. pulsotypes with
                                   isolates from indicated
                                     no. ecologic sources
                                      ([double dagger])

No. isolates per
pulsotype                        1       2       3       4

2                               26       2      NA      NA
3                               10       2       0      NA
4                                9       0       0       1
5                                1       2       0       0
6                                2       1       0       0
7                                2       0       1       0
[greater than or equal to] 8     1       3       2       0

* ST, sequence type; NA, not applicable (no. regions or source
groups exceeds no. isolates in pulsotype).

([dagger]) The 6 geographic regions included the US West, Midwest,
South, and Northeast; Canada; and other international sites
(collectively).

([double dagger]) The 5 source groups included humans, companion
animals, food animals, other animals, and food and water combined.

Table 3. Segregation, by geographic region, of multiple-isolate
pulsotypes and of Escherichia coli ST131 isolates from the
pulsotypes, 1967-2009 *

        Multiple-isolate              No. isolates, by geographic
        pulsotype group                 region, from pulsotype
                                              group (474)

           Total no.    Total no.

           pulsotypes    isolates
Source      in group     in group          US               W
region        (65)        (474)          (358)             (47)

US             61          463             NA               47

  West         24          348            272               NA
                                      ([dagger])#

  MW           38          408            309               33
                                                       ([dagger])##

  South        23          350            272               23
                                                       ([dagger])##

  NE           31          368            287               23
                                      ([dagger])#      ([dagger])##

CAN            15          279            201               10
                                      ([dagger])##     ([dagger])##

INT            20          336            231               17
                                      ([dagger])##     ([dagger])##

        Multiple-isolate              No. isolates, by geographic
        pulsotype group                 region, from pulsotype
                                              group (474)

           Total no.    Total no.

           pulsotypes    isolates
Source      in group     in group          MW               S
region        (65)        (474)          (139)             (84)

US             61          463            139               84
                                      ([dagger])#

  West         24          348            105               62

  MW           38          408             NA               74

  South        23          350            108               NA

  NE           31          368            106               68

CAN            15          279             92               52
                                      ([dagger])#

INT            20          336            102               58

        Multiple-isolate              No. isolates, by geographic
        pulsotype group                 region, from pulsotype
                                              group (474)

           Total no.    Total no.

           pulsotypes    isolates
Source      in group     in group          NE              CAN
region        (65)        (474)           (88)             (52)

US             61          463             88               50

  West         24          348             58               41

  MW           38          408             63               47
                                      ([dagger])##

  South        23          350             57               43
                                      ([dagger])##

  NE           31          368             NA               43

CAN            15          279             47               NA

INT            20          336             54               41
                                      ([dagger])##

        Multiple-isolate             No. isolates,
        pulsotype group              by geographic
                                      region, from
                                       pulsotype
           Total no.    Total no.     group (474)

           pulsotypes    isolates
Source      in group     in group         INT
region        (65)        (474)           (64)

US             61          463             55
                                        ([double
                                       dagger])##

  West         24          348             35
                                        ([double
                                       dagger])##

  MW           38          408             52

  South        23          350             35
                                        ([double
                                       dagger])##

  NE           31          368             38
                                        ([double
                                       dagger])##

CAN            15          279             26
                                     ([section])##

INT            20          336             NA

        Multiple-isolate                    No. pulsotypes,
        pulsotype group                  by geographic region,
                                            among isolate
                                              group (65)
           Total no.    Total no.

           pulsotypes    isolates
Source      in group     in group          US               W
region        (65)        (474)           (61)             (24)

US             61          463             NA

  West         24          348             24               NA

  MW           38          408             38               15
                                      ([dagger])#

  South        23          350             23               10

  NE           31          368             31               12

CAN            15          279             14               5

INT            20          336             17               14

        Multiple-isolate                    No. pulsotypes,
        pulsotype group                  by geographic region,
                                            among isolate
                                              group (65)
           Total no.    Total no.

           pulsotypes    isolates
Source      in group     in group          MW               S
region        (65)        (474)           (38)             (23)

US             61          463

  West         24          348

  MW           38          408             NA

  South        23          350             17               NA

  NE           31          368             17               12

CAN            15          279             11               7

INT            20          336             14               8

        Multiple-isolate                    No. pulsotypes,
        pulsotype group                  by geographic region,
                                            among isolate
                                              group (65)
           Total no.    Total no.

           pulsotypes    isolates
Source      in group     in group          NE              CAN
region        (65)        (474)           (31)             (15)

US             61          463

  West         24          348

  MW           38          408

  South        23          350

  NE           31          368             NA

CAN            15          279             8                NA

INT            20          336             10               5

* Values in parentheses are n values. Boldface indicates significant
associations; boldface Italics indicate negative associations. Blank
spaces indicate duplicated comparisons (mirror image of matrix). ST,
sequence type; US, United States; W, West; MW, Midwest; S, South;
NE, Northeast; CAN, Canada; INT, international (non-US locales other
than Canada); NA, not applicable.

([dagger]) p [less than or equal to] 0.05 for indicated region vs.
all other regions (Fisher exact test).

([double dagger]) p [less than or equal to] 0.001 for indicated
region vs. all other regions (Fisher exact test).

([section]) p [less than or equal to] 0.01 for indicated region vs.
all other regions (Fisher exact test).

Note: Significant associations indicated with #; negative
associations indicated with ##.

Table 4. Distribution, by geographic region, of Escherichia coli
ST131 isolates from different pulsotype groups and from individual
pulsotypes, 1967-2009 *

                                      High-          Multiple-
                     Total          prevalence        isolate
                   isolates,       pulsotypes,      pulsotypes,
Region              N = 579          n = 327          n = 474

US                  446 (77)         239 (73)         358 (80)
                                   ([dagger])#

  West              59 (10)           22 (7)          47 (10)
                                   ([dagger])#

  MW                180 (31)         56 (31)          139 (29)

  South             98 (17)          64 (20)          84 (18)

  NE                109 (19)         53 (16)          88 (19)

CAN                  53 (9)          42 (13)          52 (11)
                                   ([section])#     ([section])#

INT                 80 (14)          46 (14)          64 (14)

                      Individual high-prevalence pulsotypes

Region            968, n = 136     800, n = 82      812, n = 32

US                  107 (79)         55 (67)          25 (78)
                                     ([double
                                    dagger])#
  West               4 (7)            3 (4)            5 (16)
                  ([section])#       ([double
                                    dagger])#
  MW                53 (39)          24 (29)           7 (22)
                    ([double
                   dagger])#

  South             26 (19)          17 (21)           8 (25)
                                                    ([dagger])#
  NE                24 (18)          11 (13)           5 (16)

CAN                 14 (10)          20 (24)             0
                                   ([section])#

INT                 15 (11)           7 (9)            7 (23)

                      Individual high-
                   prevalence pulsotypes

Region            987, n = 11      1202, n = 8

US                   1 (9)           8 (100)
                  ([section])#

  West                 0              4 (50)
                                   ([dagger])#

  MW                 1 (9)            2 (25)

  South                0              2 (25)

  NE                   0                0

CAN                    0                0

INT                 10 (91)             0
                  ([section])#

* Values are no (%) isolates. Boldface indicates p<0.05 in
comparison with all other isolates (Fisher exact test). Pulsotypes
are those among the 12 high-prevalence pulsotypes that exhibited a
significant association with [greater than or equal to] 1 geographic
region. ST, sequence type; US, United States; MW, US Midwest; NE, US
Northeast; CAN, Canada; INT, international (non-US locales other
than Canada).

([dagger]) p [less than or equal to] 0.01 for indicated pulsotype
group or pulsotype vs. all others (Fisher exact test).

([double dagger]) p<0.05 for indicated pulsotype group or pulsotype
vs. all others (Fisher exact test).

([section]) p [less than or equal to] 0.001 for indicated pulsotype
group or pulsotype vs. all others (Fisher exact test).

Note: p<0.05 in comparison with all other isolates (Fisher exact
test) indicated with #.

Table 5. Segregation, by ecologic source, of multiple-isolate
pulsotypes and of Escherichia coli ST131 isolates from the
pulsotypes, 1967-2009 *

                      No.           Total no.

Ecologic          pulsotypes,       isolates,
source               n = 65          n = 474

HU                     57              453

CA                     8               216

FA                     13               43

OA                     2               140

Food                   2                11

Water                  2                84

                                   No. isolates

Ecologic              HU,              CA,              FA,
source              n = 412           n = 21           n = 28

HU                     NA               19               12
                                                    ([dagger])##

CA                    178               NA               8
                    ([double
                   dagger])##

FA                     7                3                NA
                  ([dagger])##

OA                    118               13               1
                                     ([double       ([dagger])#
                                    dagger])#

Food                   1                2                3
                  ([dagger])##                      ([section])#

Water                  82               0                0
                  ([dagger])#     ([section])##       ([double
                                                     dagger])##

                                   No. isolates

Ecologic              OA,             Food,            Water,
source               n = 7            n = 4            n = 2

HU                     7                1                2
                                   ([dagger])##

CA                     6                3                0
                  ([section])#

FA                     1                4                0
                                   ([dagger])#

OA                     NA               1                0

Food                   1                NA               0

Water                  0                0                NA

                        No. pulsotypes comprising isolates

Ecologic              HU,              CA,              FA,
source               n = 57           n = 8            n = 13

HU                     NA

CA                     7                NA

FA                     5                2               NA.
                  ([dagger])#

OA                     2                1                1

Food                   1                1                2
                                                    ([section])#

Water                  2                0                0

                        No. pulsotypes
                     comprising isolates

Ecologic              OA,             Food,
source               n = 2            n = 2

HU

CA

FA

OA                     NA

Food                   1                NA

Water                  0                0

* Blank spaces indicate duplicated comparisons (mirror image of
matrix). Boldface indicates significant associations; boldface
italics indicate negative associations. ST, sequence type; HU,
human; CA, companion animal; FA, food animal; OA, other animal; NA,
not applicable.

([dagger]) p [less than or equal to] 0.001 for indicated source vs.
all other sources (Fisher exact test).

([double dagger]) p [less than or equal to] 0.01 for indicated
source vs. all other sources (Fisher exact test).

([section]) p [less than or equal to] 0.05 for indicated source vs.
all other sources (Fisher exact test).

Note: Significant associations indicated by #; negative associations
indicated with ##.

Table 6. Distribution, by ecologic source, of Escherichia coli ST131
isolates among different pulsotype groups and individual pulsotypes,
1967-2009 *

                                No. (%) isolates

                                      High-          Multiple-
                     Total          prevalence        isolate
Ecologic           isolates,       pulsotypes,      pulsotypes,
source              N = 579          n = 327          n = 474

Human               486 (84)         290 (89)         412 (87)
                                  ([dagger]) **    ([dagger]) **

Comp. animal         22 (4)         19 (6)# **         21 (4)

Food animal          45 (8)           8 (2)            28 (6)
                                  ([dagger]) **    ([dagger]) **

Other animal        10 (1.7)          6 (2)           7 (1.5)

Food/water          15 (2.6)          4 (1)%           6 (1)
                                     ([double      ([dagger]) **
                                   dagger]) **

Food                6 (1.0)          3 (0.9)          4 (0.8)

Water               9 (1.6)          1 (0.3)          2 (0.4)
                                  ([section]) **   ([dagger]) **

                                No. (%) isolates

                      Individual high-prevalence pulsotypes

Ecologic
source            968, n = 136     800, n = 82      812, n = 32

Human               117 (86)         81 (99)          31 (97)
                                  ([dagger]) **       ([double
                                                    dagger]) **

Comp. animal        13 (10)             0              1 (3)
                 ([dagger]) **

Food animal            0                0                0
                 ([dagger]) **    ([dagger]) **

Other animal         6 (4)              0                0
                 ([section]) **

Food/water             0              1 (1)              0
                    ([double
                  dagger]) **

Food                   0                0                0

Water                  0              1 (1)              0

                        No. (%) isolates

                   Individual high-prevalence
                           pulsotypes
Ecologic
source            1202, n = 8       955, n = 7

Human                1 (13)           0 (0)
                 ([dagger]) **

Comp. animal         1 (8)            2 (29)
                                  ([section]) **

Food animal          6 (75)           2 (29)
                 ([dagger]) **

Other animal           0                0

Food/water             0              3 (43)

Food                   0              3 (43)
                                  ([dagger]) **

Water                  0                0

* Boldface indicates p<0.05 in comparison with all other isolates.
Pulsotypes are those, among the 12 high-prevalence pulsotypes, that
exhibited a significant association with [greater than or equal to]
1 source group. ST, sequence type; comp., companion.

([dagger]) p<0.001 for indicated pulsotype group or pulsotype vs.
all others (Fisher exact test).

([double dagger]) p [less than or equal to] 0.05 for indicated
pulsotype group or pulsotype vs. all others (Fisher exact test).

([section]) p [less than or equal to] 0.01 for indicated pulsotype
group or pulsotype vs. all others (Fisher exact test).

Note: p<0.05 in comparison with all other isolates is indicated
with **.

Table 7. Distribution, by antimicrobial drug resistance trait, of
Escherichia coliST131 isolates among different pulsotype groups and
individual pulsotypes, 1967-2009 *

                                     No. (%) isolates

Antimicrobial                             High-          Multiple-
drug                   Total no.        prevalence        isolate
resistance             isolates,       pulsotypes,      pulsotypes,
trait                   N = 579          n = 327          n = 474

FQ-R                    462 (80)        293 (90)f         401 (85)
                                       ([dagger])#      ([dagger])#

ESBL                    272 (47)         144 (44)         219 (46)

[bla.sub.CTX-M-15]      188 (33)         102 (31)         156 (33)

                                     No. (%) isolates

Antimicrobial              Individual high-prevalence pulsotypes
drug
resistance                968,             800,             812,
trait                   n = 136           n = 82           n = 32

FQ-R                    133 (98)         81 (99)             32
                      ([dagger])#      ([dagger])#

ESBL                    62 (46)          12 (15)          30 (94)
                                       ([dagger])#      ([dagger])#

[bla.sub.CTX-M-15]      38 (28)           5 (6)           28 (88)
                                       ([dagger])#      ([dagger])#

                                     No. (%) isolates

Antimicrobial              Individual high-prevalence pulsotypes
drug
resistance                905,             987,            1202,
trait                    n = 19           n = 11           n = 8

FQ-R                    19 (100)            0              1 (13)
                        ([double       ([dagger])#      ([dagger])#
                       dagger])#

ESBL                    17 (90)             0              3 (38)
                      ([dagger])#      ([dagger])#

[bla.sub.CTX-M-15]      16 (84)             0                0
                      ([dagger])#        ([double         ([double
                                        dagger])#        dagger])#

                                     No. (%) isolates

Antimicrobial              Individual high-prevalence pulsotypes
drug
resistance                919,             955,             797,
trait                    n = 7            n = 7            n = 6

FQ-R                    7 (100)           1 (14)             0
                      ([section])#     ([dagger])#      ([dagger])#

ESBL                    7 (100)           2 (29)             0
                      ([section])#     ([section])#       ([double
                                                         dagger])#

[bla.sub.CTX-M-15]       6 (86)             0                0
                      ([section])#

* Boldface indicates p<0.05 in comparison with all other isolates.
Pulsotypes shown are those, among the 12 high-prevalence pulsotypes,
that exhibited a significant association with [greater than or equal
to] 1 resistance trait. ST, sequence type; FQ-R, fluoroquinolone
resistance; ESBL, extended-spectrum p-lactamase production;
[bla.sub.CTX-M-15], gene encoding CTX-M-15.

([dagger]) p [less than or equal to] 0.001 for indicated pulsotype
group or pulsotype vs. all others (Fisher exact test).

([double dagger]) p [less than or equal to] 0.05 for indicated
pulsotype group or pulsotype vs. all others (Fisher exact test).

([section]) p [less than or equal to] 0.01 for indicated pulsotype
group or pulsotype vs. all others (Fisher exact test).

Note: p<0.05 in comparison with all other isolates is indicated with #.

Table 8. Results of multivariable logistic regression analysis for
predictors of selected pulsotype categories among 579 Escherichia
coli ST131 isolates, 1967-2009 *

Outcome variable, significant
predictor variables ([dagger])     Odds ratio (95% CI)     p value

Pulsotype 968
  Human source                      0.20 (0.09-0.46)       <0.001
  FQ-R                            55.04 (10.63-285.03)     <0.001
  ESBL production                   0.63 (0.41-0.90)        0.03

Pulsotype 800
  Human source                     10.61 (1.32-85.48)       0.03
  FQ-R                             46.50 (3.75-576.74)      .003
  ESBL production                   0.10 (0.05-0.19)       <0.001

Pulsotype 812
  Year of isolation/submission      1.47 (1.07-2.03)        0.02
  ESBL production                  17.53 (4.02-76.07)      <0.001

High-prevalence pulsotypes
  Year of isolation/submission      1.09 (1.03-1.55)        0.003
  FQ-R                              4.04 (2.22-7.34)       <0.001
  ESBL production                   0.47 (0.32-0.70)       <0.001

Multiple-isolate pulsotypes
  Year of isolation/submission      1.07 (1.02-1.13)        0.009
  FQ-R                              3.42 (1.76-6.66)       <0.001
  ESBL production                   0.42 (0.24-0.71)        0.001

                                         Nagelkerke
Outcome variable, significant       [R.sup.2] for model
predictor variables ([dagger])       ([double dagger])

Pulsotype 968                               0.18
  Human source
  FQ-R
  ESBL production

Pulsotype 800                               0.31
  Human source
  FQ-R
  ESBL production

Pulsotype 812                               0.21
  Year of isolation/submission
  ESBL production

High-prevalence pulsotypes                  0.16
  Year of isolation/submission
  FQ-R
  ESBL production

Multiple-isolate pulsotypes                 0.13
  Year of isolation/submission
  FQ-R
  ESBL production

* ST, sequence type; FQ-R, fluoroquinolone resistance-resistant;
ESBL, extended-spectrum p-lactamase; high-prevalence pulsotypes, 12
pulsotypes that contained [greater than or equal to] 6 isolates
([greater than or equal to] 1% of population) each; multiple-
isolate pulsotypes, 65 pulsotypes that contained [greater than or
equal to] 1 isolate each.

([dagger]) Variables shown are those that yielded p values of <0.05.
With 1 exception, each model included the following candidate
predictor variables: human source (vs. other sources), US origin
(vs. Canada or other international locale origin), year of
isolation-submission, FQ-R, and ESBL production. All pulsotype 812
isolates were FQ-R; thus, FQ-R could not be included in that model.

([double dagger]) Nagelkerke [R.sup.2] provides an estimate of the
total amount of variance accounted for by the model, i.e., the
model's explanatory power. Values range from 0 (no explanatory
power) to 1.0 (complete prediction).
Gale Copyright: Copyright 2012 Gale, Cengage Learning. All rights reserved.