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 blaCTX-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 >
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 blaCTX-M-15
were significantly associated with several high-prevalence pulsotypes and were present in most or all of their members (). 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 (). 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 blaCTX-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.