A Comprehensive Account of Escherichia coli Sequence Type 131 in Wastewater Reveals an Abundance of Fluoroquinolone-Resistant Clade A Strains

Abstract

In the ten years since its discovery, the Escherichia coli clone sequence type 131 (ST131) has become a major international health threat, with the multidrug-resistant and extended-spectrum β-lactamase (ESBL)-producing clade C emerging as the globally dominant form. ST131 has previously been isolated from wastewater; however, most of these studies selectively screened for ESBL-producing organisms, thereby missing the majority of remaining ST131 clades. In this study, we used a high-throughput PCR-based screening strategy to comprehensively examine wastewater for the presence of ST131 over a 1-year period. Additional multiplex PCRs were used to differentiate clades and obtain an unbiased account of the total ST131 population structure within the collection. Furthermore, antimicrobial susceptibility profiles of all ST131-positive samples were tested against a range of commonly used antibiotics. From a total of over 3,762 E. coli wastewater samples, 1.86% (n = 70) tested positive for ST131, with the majority being clade A isolates. In total, 63% (n = 44) were clade A, 29% (n = 20) were clade B, 1% (n = 1) were clade C0, 6% (n = 4) were clade C1, and 1% (n = 1) were clade C2. In addition, a very high rate of resistance to commonly used antibiotics among wastewater isolates is reported, with 72.7% (n = 32) of clade A resistant to ciprofloxacin and high rates of resistance to gentamicin, sulfamethoxazole-trimethoprim, and tetracycline in clades that are typically sensitive to antibiotics. IMPORTANCE ST131 is a global pathogen. This clone causes urinary tract infections and is frequently isolated from human sources. However, little is known about ST131 from environmental sources. With the widely reported increase in antibiotic concentrations found in wastewater, there is additional selection pressure for the emergence of antibiotic-resistant ST131 in this niche. The unbiased screening approach reported herein revealed that previously antibiotic-sensitive lineages of ST131 are now resistant to commonly used antibiotics present in wastewater systems and may be capable of surviving UV sterilization. This is the most comprehensive account of ST131 in the wastewater niche to date and an important step in better understanding the ecology of this global pathogen.

Genomic comparisons of Escherichia coli ST131 from Australia

“…Research has emerged indicating that ST131 clades are niche associated, specifically that clade C has adapted to human hosts [ 3 ], clade B is zoonotic and dominates meat, pigs [ 18, 67 ] and poultry [ 19 ], and that clade A is predominantly environmental [ 10 ]. Others claim genetic commonality and a broad distribution across ecological niches and reservoirs [ 68, 69 ].…”

“…Furthermore, three clade A isolates possessed the dual parC- 1aAB gyrA- 1AB mutations previously only reported in clade C. These two mutations not only confer resistance to fluroquinolone but also improve fitness in the absence of antibiotics [ 87 ] and it is generally acknowledged that the combination of fluroquinolone and ESBL resistance propelled the global expansion of clade C [ 7 ]. It is therefore alarming that clade A may be following suit and should be monitored closely, especially when population estimates have flagged clade A as the dominant clade in Australia [ 37 ], and unbiased sampling methodologies have also identified clade A as dominant in the community in PR China [ 88 ] and domestic wastewater in Canada [ 10 ].…”

“…Clade A ( fimH 41), the most divergent of the three clades, probably emerged in Southeast Asia in the 1880s [ 9 ]. Recently, clade A isolates have been recovered from wastewater [ 10 ] that displayed resistance to drugs used to treat UTIs (fluoroquinolones, gentamicin, sulfamethoxazole-trimethoprim) [ 11–13 ]. In terms of lethality, clade A isolates with serotype O16:H5 are on a par with O25b:H4 in a mouse sepsis model of infection [ 6 ].…”

Trends in Population Dynamics ofEscherichia coliSequence Type 131, Calgary, Alberta, Canada, 2006–20161

“…Clade A is likely the ancestral lineage of ST131 and probably originated in Southeast Asia during the mid to late 1880s ( 30 ). Clade A isolates are generally sensitive to antimicrobial drugs and appear to occupy distinct ecologic niches, such as waste water ( 35 ). Results from this study show that clade A isolates have high not susceptible rates for trimethoprim/sulfamethoxazole, gentamicin, and tobramycin and were associated with community-associated and healthcare-associated urinary tract infections in younger patients.…”

The Darkest Place Is under the Candlestick-Healthy Urogenital Tract as a Source of Worldwide Disseminated Extraintestinal Pathogenic Escherichia coli Lineages

“…The detection of the fimH30 allele in clade B isolates is uncommon, but these recombination events have been occasionally observed in other collections [11,21]. Available data on the prevalence of ST131 subclades is largely biased by human clinical isolates, and clade C in particular [56][57][58]. However, there is evidence that non-human sources are underestimated and there is a specialization for each clade, including a foodborne origin for clade B-fimH22 [59] and wastewater for clade A-fimH41 [58], suggesting those as additional possible sources of acquisition.…”