Evidence for coexistence of distinct Escherichia coli populations in various aquatic environments and their survival in estuary water

The efficacy of current treatment processes to remove, inactivate, or reduce environmental bloom-forming Escherichia coli

Escherichia coli is excreted in high numbers from the intestinal tract of humans, other mammals, and birds. Traditionally, it had been thought that E. coli could grow only within human or animal hosts and would perish in the environment. Therefore, the presence of E. coli in water has become universally accepted as a key water quality indicator of fecal pollution. However, recent research challenges the assumption that the presence of E. coli in water is always an indicator of fecal contamination, with some types of E. coli having evolved to survive and grow in aquatic environments. These strains can form blooms in water storages, resulting in high E. coli counts even without fecal contamination. Although these bloom-forming strains lack virulence genes and pose little threat to public health, their presence in treated water triggers the same response as fecal-derived E. coli. Yet, little is known about the effectiveness of treatment processes in removing or inactivating them. This study evaluated the effectiveness of current treatment processes to remove bloom-forming strains, in comparison to fecal-derived strains, with conventional coagulation-flocculation-sedimentation and filtration investigated. Second, the effectiveness of current disinfection processes-chlorination, chloramination, and ultraviolet (UV) light to disinfect bloom-forming strains in comparison to fecal-derived strains-was assessed. These experiments showed that the responses of bloom isolates were not significantly different from those of fecal E. coli strains. Therefore, commonly used water treatment and disinfection processes are effective to remove bloom-forming E. coli strains from water.IMPORTANCEThe presence of Escherichia coli in water has long been used globally as a key indicator of fecal pollution and for quantifying water safety. Traditionally, it was believed that E. coli could only thrive within hosts and would perish outside, making its presence in water indicative of fecal contamination. However, recent research has unveiled strains of E. coli capable of surviving and proliferating in aquatic environments, forming blooms even in the absence of fecal contamination. While these bloom-forming strains lack the genes to be pathogenic, their detection in source or drinking water triggers the same response as fecal-derived E. coli. Yet, little is known about the efficacy of treatment processes in removing them. This study evaluated the effectiveness of conventional treatment and disinfection processes in removing bloom-forming strains compared to fecal-derived strains. Results indicate that these commonly used processes are equally effective against both types of E. coli, reassuring that bloom-forming E. coli strains can be eliminated from water.

Systematic review and meta-analyses of the role of drinking water sources in the environmental dissemination of antibiotic-resistant Escherichia coli in Africa

Escherichia coli are pathogenic and antibiotic-resistant organisms that can spread to humans through water. However, there is sparse synthesised information on the dissemination of antibiotic-resistant E. coli through drinking water in Africa. This review provides an overview of the environmental spread of antimicrobial-resistant E. coli through drinking water in Africa. We performed a systematic review based on PRISMA guidelines, and 40 eligible studies from 12 countries were identified until June 2023. Four electronic databases (PubMed, Elsevier, AJOL, and DOAJ) were searched. Studies that employed phenotypic tests (n = 24/40) in identifying the bacterium outstripped those that utilised genome-based methods (n = 13). Of the 40 studies, nine and five, respectively, assessed the bacterium for antimicrobial resistance (AMR) phenotype and genotype. Multiple antibiotic resistance indices of 0.04-0.1 revealed a low level of antibiotic resistance. The detection of multidrug-resistant E. coli carrying resistance genes in certain water sources suggests that AMR-surveillance expansion should include drinking water.

Identification of novel inhibitors against Escherichia coli utilizing HisC as a target from histidine biosynthesis pathway

Escherichia coli is a gram-negative bacterial pathogen that poses a significant challenge both clinically and epidemiologically. Large numbers of multi-drug resistant E. coli have emerged in the last decade, because of the selection pressure generated by the inadequate use of antibiotics. Although research to combat antibiotic resistance has been going on extensively but still lags in the rate of development of newer antibiotics. Therefore, newer approaches are required to speed up the rate of discovery of antibiotics. Computational methods for screening of inhibitors have made a significant contribution to the discovery of novel antimicrobials. The present study utilized histidinol-phospho aminotransferase (HisC) as a target. HisC is an enzyme that plays a crucial role in the biosynthesis of histidine and its absence in mammals makes it an attractive drug target. A ZINC library of 5000 natural compounds was screened against HisC (PDB ID: 1FG7) using PyRx and the first 500 hits were selected for secondary screening after sorting the result on the basis of binding score. Fifteen compounds passed the secondary filter ADME and out of these five passed toxicity filters; the best among five hits was selected on the basis of its binding score and inhibition constants. Further, molecular dynamics simulations and free binding were computed of selected five compounds and two natural compounds ZINC402598829 and ZINC31157928 complexed with HisC were found as highly stable. Overall, our results indicated that these natural sources could be used as potential HisC inhibitors.Communicated by Ramaswamy H. Sarma.

The burden of hospital acquired infections and antimicrobial resistance

The burden of Hospital care-associated infections (HCAIs) is becoming a global concern. This is compounded by the emergence of virulent and high-risk bacterial strains such as "ESKAPE" pathogens - (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), especially within Intensive care units (ICUs) that house high-risk and immunocompromised patients. In this review, we discuss the contributions of AMR pathogens to the increasing burden of HCAIs and provide insights into AMR mechanisms, with a particular focus on last-resort antibiotics like polymyxins. We extensively discuss how structural modifications of surface-membrane lipopolysaccharides and cationic interactions influence and inform AMR, and subsequent severity of HCAIs. We highlight some bacterial phenotypic survival mechanisms against polymyxins. Lastly, we discuss the emergence of plasmid-mediated resistance as a phenomenon making mitigation of AMR difficult, especially within the ICUs. This review provides a balanced perspective on the burden of HCAIs, associated pathogens, implication of AMR and factors influencing emerging AMR mechanisms.

Dynamics of antibiotic resistance markers and Escherichia coli invasion in riverine heterotrophic biofilms facing increasing heat and flow stagnation

As motivation to address environmental dissemination of antimicrobial resistance (AMR) is mounting, there is a need to characterize mechanisms by which AMR can propagate under environmental conditions. Here we investigated the effect of temperature and stagnation on the persistence of wastewater-associated antibiotic resistance markers in riverine biofilms and the invasion success of genetically-tagged Escherichia coli. Biofilms grown on glass slides incubated in-situ downstream of a wastewater treatment plant effluent discharge point were transferred to laboratory-scale flumes fed with filtered river water under potentially stressful temperature and flow conditions: recirculation flow at 20 °C, stagnation at 20 °C, and stagnation at 30 °C. After 14 days, quantitative PCR and amplicon sequencing were used to quantify bacteria, biofilms diversity, resistance markers (sul1, sul2, ermB, tetW, tetM, tetB, blaCTX-M-1, intI1) and E. coli. Resistance markers significantly decreased over time regardless of the treatment applied. Although invading E. coli were initially able to colonize the biofilms, its abundance subsequently declined. Stagnation was associated with a shift in biofilm taxonomic composition, but there was no apparent effect of flow conditions or the simulated river-pool warming (30 °C) on AMR persistence or invasion success of E. coli. Results however indicated that antibiotic resistance markers in the riverine biofilms decreased under the experimental conditions in the absence of exposure to external inputs of antibiotics and AMR.

Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland

Natural ecosystems can become significant reservoirs and/or pathways for antimicrobial resistance (AMR) dissemination, with the potential to affect nearby microbiological, animal, and ultimately human communities. This is further accentuated in environments that provide direct human exposure, such as drinking water. To date, however, few studies have investigated AMR dissemination potential and the presence of co-selective stressors (e.g., metals/metalloids) in groundwater environments of human health significance. Accordingly, the present study analysed samples from rural (drinking) groundwater supplies (i.e., private wells) in the Republic of Ireland, where land use is dominated by livestock grazing activities. In total, 48 Escherichia coli isolates tested phenotypically for antimicrobial susceptibility in an earlier study were further subject to whole genome sequencing (WGS) and corresponding water samples were further analysed for trace metal/metalloid concentrations. Eight isolates (i.e., 16.7%) were genotypically resistant to antimicrobials, confirming prior phenotypic results through the identification of ten antimicrobial resistance genes (ARGs); namely: aph(3″)-lb (strA; n=7), aph(6)-Id (strA; n = 6), blaTEM (n = 6), sul2 (n = 6), tetA (n = 4), floR (n = 2), dfrA5 (n = 1), tetB (n = 1), and tetY (n = 1). Additional bioinformatic analysis revealed that all ARGs were plasmid-borne, except for two of the six sul2 genes, and that 31.2% of all tested isolates (n = 15) and 37.5% of resistant ones (n = 3) carried virulence genes. Study results also found no significant relationships between metal concentrations and ARG abundance. Additionally, just one genetic linkage was identified between ARGs and a metal resistance gene (MRG), namely merA, a mercury-resistant gene found on the same plasmid as blaTEM, dfrA5, strA, strB, and sul2 in the only isolate of inferred porcine (as opposed to bovine) origin. Overall, findings suggest that ARG (and MRG) acquisition may be occurring prior to groundwater ingress, and are likely a legacy issue arising from agricultural practices.

Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework

The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.

Genomic analysis of phylogroup D Escherichia coli strains using novel de-novo reference-based guided assembly

Escherichia coli are highly diverse bacteria with different pathogenic types, serotypes and phylogenetic types/phylotypes. In recent years, infections with E. coli have increased worldwide and so has the emergence of antibiotic resistant strains. In the present study we have assembled, annotated and analysed genome sequences of three strains of the phylogroup D of E. coli. These strains were isolated from the river Yamuna, a prominent anthropogenic urban river of northern India. These strains showed varied antibiotic susceptibilities, one was susceptible to all the antibiotics tested except ampicillin while of the other two, one was multi-β-lactam resistant and the other was multi-drug resistant (resistant to multiple β-lactams, fluoroquinolones and kanamycin). The short-sequence reads were assembled into contigs using the de-novo approach and further, scaffolding of contigs was performed by using the best reference genome for a particular isolate which resulted in a significant increase in the N50 value of each assembly. The bioinformatics assembly approach used in this study could be easily applied to study other bacterial genomes.

Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro

Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain-dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.

Macrophytes and their wrack as a habitat for faecal indicator bacteria and Vibrio in coastal marine environments

Waterborne pathogenic bacteria, including faecal indicator bacteria and potentially pathogenic Vibrio, are a global concern for diseases transmitted through water. A systematic review was conducted to analyse publications that investigated these bacteria in relation to macrophytes (seagrasses and macroalgae) in coastal marine environments. The highest quantities of FIB were found on brown algae and seagrasses, and the highest quantities of Vibrio bacteria were on red algae. The most extensively studied macrophyte group was brown algae, green algae were the least researched. Macrophyte wrack was found to favor the presence of FIB, but there is a lack of information about Vibrio quantities in this environment. To understand the role of Vibrio bacteria that are pathogenic to humans, molecular methods complementary to cultivation methods should be used. Further research is needed to understand the underlying mechanisms of FIB and potentially pathogenic Vibrio with macrophytes and their microbiome in the coastal marine environment.

Fate of microbial contamination in a South European Coastal Lagoon (Ria Formosa) under the influence of treated effluents dispersal

AIM

Assessment of the fate of microbial contamination driven from treated wastewater disposal at a highly productive zone on a South European coastal lagoon (Ria Formosa).

METHODS AND RESULTS

Microbial indicators of contamination (Total coliforms, Escherichia coli, and Enterococci) were evaluated monthly during September 2018-September 2020 at three study areas (Faro, Olhão, and Tavira) under different wastewater discharge flows and hydrodynamic conditions. Additional data on E. coli monitoring in bivalves, available from the national institution responsible for their surveillance was also considered. The maximum microbial contamination was found at Faro, the highest-load and less-flushed study area, contrasting the lowest contamination at Olhão, a lower-load and strongly flushed area. The wastewater impact decreased along the spatial dispersal gradients and during high water, particularly at Faro and Tavira study areas, due to a considerable dilution effect. Microbial contamination at Olhão increased during the summer, while at the other study areas seasonal evidence was not clear. Data also indicate that E. coli in bivalves from bivalve production zones next to the three study areas reflected the differentiated impact of the wastewater treatment plants effluents on the water quality of those areas.

CONCLUSIONS

Effluent loads together with local hydrodynamics, water temperature, solar radiation, precipitation, and land runoff as well as seabirds populations and environmentally adapted faecal or renaturelized bacterial communities, contributed to microbial contamination of the study areas.

First Identification of bla NDM-1 Producing Escherichia coli ST 9499 Isolated from Musca domestica in the Urban Center of Rio de Janeiro, Brazil

The present study presents phenotypic and molecular characterization of a multidrug-resistant strain of Escherichia coli (Lemef26), belonging to sequence type ST9499 carrying a blaNDM-1 carbapenem resistance gene. The bacterium was isolated from a specimen of Musca domestica, collected in proximity to a hospital in Rio de Janeiro City, Brazil. The strain was identified as E. coli by matrix-assisted laser desorption-ionization time of flight mass spectrometry (Maldi-TOF-MS) and via genotypic analysis (Whole-Genome Sequencing-WGS), followed by phylogenetic analysis, antibiotic resistance profiling (using phenotypic and genotypic methods) and virulence genotyping. Interestingly, the blaNDM-1 was the only resistance determinant detected using a panel of common resistance genes, as evaluated by PCR. In contrast, WGS detected genes conferring resistance to aminoglycosides, fluoroquinolones, quinolones, trimethoprim, beta-lactams, chloramphenicol, macrolides, sulfonamide, tetracycline, lincosamide and streptogramin B. Conjugation experiments demonstrated the transfer of carbapenem resistance, via acquisition of the blaNDM-1 sequence, to a sensitive receptor strain of E. coli, indicating that blaNDM-1 is located on a conjugative plasmid (most likely of the IncA/C incompatibility group, in association with the transposon Tn3000). Phylogenetic analyses placed Lemef26 within a clade of strains exhibiting allelic and environment diversity, with the greatest level of relatedness recorded with a strain isolated from a human source suggesting a possible anthropogenic origin. Analysis of the virulome revealed the presence of fimbrial and pilus genes, including a CFA/I fimbriae (cfaABCDE), common pilus (ecpABCDER), laminin-bind fimbrae (elfADG), hemorrhagic pilus (hcpABC) and fimbrial adherence determinants (stjC) indicates the ability of strain Lemef26 to colonize animal hosts. To the best of our knowledge, this study represents the first report of blaNDM-1 carbapenemase gene in an E. coli strain isolated from M. domestica. In concordance with the findings of previous studies on the carriage of MDR bacteria by flies, the data presented herein provide support to the idea that flies may represent a convenient means (as sentinel animals) for the monitoring of environmental contamination with multidrug-resistant bacteria.

Comparative Genomic Analyses of Escherichia coli from a Meat Processing Environment in Relation to Their Biofilm Formation and Persistence

We investigated the phylogeny of biofilm forming (BF) and nonbiofilm forming (NBF) Escherichia coli (n = 114) from a beef processing environment as well as genetic elements in their BF and persistence via a comparative genomic analysis. Phylogroup B1 made up the largest proportion of both the BF (73.8%) and NBF (50.9%) groups. E. coli from all of the sources that were examined had mixed phylogroups, except for those that were recovered from equipment after cleaning, which were exclusively from phylogroup B1. Both the core genome and gene content trees showed a tree-wide spread of BF strains, with clusters, including both BF and NBF strains. Genome-wide association studies (GWAS) via Scoary or Pyseer did not find any genes or mutations that were overrepresented in the BF group. A retrospective analysis of phenotypes found a significant correlation (P < 0.05) between BF ability and curli production, cellulose synthesis, and/or mobility. However, the BF group also included strains that were negative for curli and cellulose and/or missing encoding genes for the two traits. All curli and cellulose encoding genes were present in most genomes, regardless of their BF status. The degree of motility was correlated with both curli and cellulose production, and 80 common genes were overrepresented in all three of the trait-positive groups. A PTS enzyme II, a subsidiary gluconate catabolism pathway, and an iron-dicitrate transport system were more abundant in the persisting E. coli group. These findings suggest gene function redundancy in E. coli for biofilm formation as well as additional substrate utilization and iron acquisition in its persistence. IMPORTANCE The persistence of potentially hazardous bacteria is a major challenge for meat processing environments, which are conducive for biofilm formation. Marker genes/phenotypes are commonly used to differentiate biofilm forming E. coli strains from their nonbiofilm forming counterparts. We took a comparative genomic analysis approach to analyze E. coli strains that were from the same environment but were differentiated by their biofilm forming ability. A diversification of the genes involved in the biofilm formation of E. coli was observed. Even though there is a correlation on the population level between biofilm formation and the expression of curli and cellulose, uncertainties exist on the individual strain level. Novel substrate utilization and iron acquisition could contribute to the persistence of E. coli. These findings not only advance our understanding of the ecology of E. coli with respect to its persistence but also show that a marker gene/phenotype driven approach for the biofilm control of E. coli may not be prudent.

Predominance of Multidrug Resistant Escherichia coli of Environmental Phylotype in Different Environments of Dhaka, Bangladesh

Considering the ecological diversity of E. coli, the main aim of this study was to determine the prevalence, phylogroup diversity, and antimicrobial susceptibility of E. coli isolated from 383 different clinical and environmental sources. In total, varied prevalence was observed of the 197 confirmed E. coli that were isolated (human-100%, animal-67.5%, prawn-49.23%, soil-30.58%, and water-27.88%). Of these isolates, 70 (36%) were multidrug-resistant (MDR). MDR E. coli was significantly associated with their sources (χ² = 29.853, p = 0.001). Humans (51.67%) and animals (51.85%) carried more MDR E. coli than other environments. The eae gene indicative of recent fecal contamination was not detected in any isolate, indicating that these E. coli isolates could be present in these environments for a long time and became naturalized. Phylogroup B1 (48.22%) was the predominant group, being present in all hosts analyzed and with the commensal E. coli group A (26.9%) representing the second predominant group. According to chi-square analysis, phylogroup B1 was significantly associated with E. coli from humans (p = 0.024), soil (p < 0.001) and prawn samples (p < 0.001). Human samples were significantly associated with phylogroup B1 (p = 0.024), D (p < 0.001), and F (p = 0.016) of E. coli strains, whereas phylogroup A (p < 0.001), C (p < 0.001), and E (p = 0.015) were associated with animal samples. Correspondence analysis results also indicated the association of these phylogroups with their hosts/sources. The findings of this study exhibited a non-random distribution of phylogenetic groups, though the diversity index was highest for human E. coli phylogroups.

Genetic Determinants of Escherichia coli Survival in Beach Sand

Escherichia coli contain a high level of genetic diversity and are generally associated with the guts of warm-blooded animals but have also been isolated from secondary habitats outside hosts. We used E. coli isolates from previous in situ microcosm experiments conducted under actual beach conditions and performed population-level genomic analysis to identify accessory genes associated with survival within the beach sand environment. E. coli strains capable of surviving had been selected for by seeding isolates originating from sand, sewage, and gull waste (n = 528; 176 from each source) into sand, which was sealed in microcosm chambers and buried for 45 days in the backshore beach of Lake Michigan. In the current work, survival-associated genes were identified by comparing the pangenome of viable E. coli populations at the end of the microcosm experiment with the original isolate collection and identifying loci enriched in the out put samples. We found that environmental survival was associated with a wide variety of genetic factors, with the majority corresponding to metabolism enzymes and transport proteins. Of the 414 unique functions identified, most were present across E. coli phylogroups, except B2 which is often associated with human pathogens. Gene modules that were enriched in surviving populations included a betaine biosynthesis pathway, which produces an osmoprotectant, and the GABA (gamma-aminobutyrate) biosynthesis pathway, which aids in pH homeostasis and nutrient use versatility. Overall, these results demonstrate that the genetic flexibility within this species allows for survival in the environment for extended periods. IMPORTANCE Escherichia coli is commonly used as an indicator of recent fecal pollution in recreational water despite its known ability to survive in secondary environments, such as beach sand. These long-term survivors from sand reservoirs can be introduced into the water column through wave action or runoff during precipitation events, thereby impacting the perception of local water quality. Current beach monitoring methods cannot differentiate long-term environmental survivors from E. coli derived from recent fecal input, resulting in inaccurate monitoring results and unnecessary beach closures. This work identified the genetic factors that are associated with long-term survivors, providing insight into the mechanistic basis for E. coli accumulation in beach sand. A greater understanding of the intrinsic ability of E. coli to survive long-term and conditions that promote such survival will provide evidence of the limitations of beach water quality assessments using this indicator.

Distribution of faecal indicator bacteria in tropical waters of Peninsular Malaysia and their decay rates in tropical seawater

We investigated the appropriateness of faecal indicator bacteria in tropical waters. We compared total coliform (undetectable to 7.2 × 10⁵ cfu 100 mL^-1), faecal coliform (undetectable to 6.1 × 10⁵ cfu 100 mL^-1) and enterococci (undetectable to 3.1 × 10⁴ cfu 100 mL^-1) distribution in Peninsular Malaysia. Faecal indicator bacteria was highest in freshwater, and lowest in seawater (q > 4.18, p < 0.01). We also measured the decay rates of Escherichia coli and Enterococcus faecium in microcosms. In seawater, average decay rate for E. coli was 0.084 ± 0.029 h^-1, and higher than E. faecium (0.048 ± 0.024 h^-1) (t = 2.527, p < 0.05). Grazing accounted for 54 % of both E. coli and E. faecium decay. E. coli decayed in the <0.02 μm seawater fraction (0.023 ± 0.012 h^-1) but E. faecium sometimes grew. Seawater warming further uncoupled the response from both E. coli and E. faecium as E. faecium grew and E. coli decayed with warming. Our results suggested that the prevalence of faecal indicator bacteria in tropical waters was not due to faecal pollution alone, and this will have serious implications towards the use of these faecal indicator bacteria.

Escherichia cryptic clade II through clade VIII: Rapid detection and prevalence in feces and surface water

Bacteria of the cryptic lineage of genus Escherichia, or Escherichia cryptic clades (cryptic clades), are phenotypically indistinguishable from Escherichia coli (E. coli) using standard biochemical tests. Except for clade I (C-I), cryptic clades were hypothetically believed to be environmental but not enteric. If so, they would hinder the interpretation of current E. coli-based water quality (fecal pollution) monitoring in the United States because environmental bacteria do not indicate the presence of harmful fecal material. This study was performed to develop a rapid method for the detection of cryptic clades and to investigate their potential impact on water quality monitoring. By whole-genome comparison, one gene, named ecc (Escherichiacryptic clades), was identified to be unique to C-II through C-VIII. An end-point polymerase chain reaction (PCR) method, eccPCR, was developed by targeting the ecc. The results of in-silico and wet tests demonstrated 100 % sensitivity and specificity of the eccPCR to detect C-II through C-VIII. Based on the EPA Method 1603, 519 presumptive E. coli isolates were obtained from the fecal samples of 13 different host species and 192 isolates from surface water samples taken at four locations in a watershed of mid-Missouri. As indicated by the eccPCR amplification, the overall prevalence of C-II through C-VIII in the presumptive E. coli isolates was estimated to be about 0.6 % in the fecal samples and about 1.6 % in the water samples. Therefore, the potential impact of cryptic clades on water quality monitoring may be limited if EPA Method 1603 is used. Furthermore, clades C-II through C-VIII in stream water samples were found repeatedly only at a single sampling site, but neither at the upstream sites nor five kilometers downstream of the site. The data do not support nor reject the environmental hypothesis about cryptic clades. Further study is needed to determine the implication of the observation.

Detection and characterization of ESBL-producing Escherichia coli and additional co-existence with mcr genes from river water in northern Thailand

Background

Extended-spectrum β-lactamase producing Escherichia coli (ESBL-producing E. coli) have emerged, causing human and animal infections worldwide. This study was conducted to investigate the prevalence and molecular genetic features of ESBL-producing and multidrug-resistant (MDR) E. coli in river water.

Methods

A total of 172 E. coli samples were collected from the Kok River and Kham River in Chiang Rai, Thailand, during a 10-month period (2020-2021).

Results

We detected 45.3% of E. coli to be MDR. The prevalence of ESBL-producers was 22%. Among those ESBL-producing strains, CTX-M-15 (44.7%) was predominantly found, followed by CTX-M-55 (26.3%), CTX-M-14 (18.4%), and CTX-M-27 (10.5%). The bla _TEM-1 and bla _TEM-116 genes were found to be co-harbored with the bla _CTX-M genes. Mobile elements, i.e., ISEcp1 and Tn3, were observed. Twelve plasmid replicons were found, predominantly being IncF (76.3%) and IncFIB (52.6%). Whole genome sequencing of ten selected isolates revealed the co-existence of ESBL with mcr genes in two ESBL-producing E. coli. A wide diversity of MLST classifications was observed. An mcr-1.1-pap2 gene cassette was found to disrupt the PUF2806 domain-containing gene, while an mcr-3.4 contig on another isolate contained the nimC/nimA-mcr-3.4-dgkA core segment.

Discussion

In conclusion, our data provides compelling evidence of MDR and ESBL-producing E. coli, co-existing with mcr genes in river water in northern Thailand, which may be disseminated into other environments and so cause increased risks to public health.

Lactic Acid Resistance and Population Structure of Escherichia coli from Meat Processing Environment

To explore the effect of beef processing on Escherichia coli populations in relation to lactic acid resistance, this study investigated the links among acid response, phylogenetic structure, genome diversity, and genotypes associated with acid resistance of meat plant E. coli. Generic E. coli isolates (n = 700) were from carcasses, fabrication equipment, and beef products. Acid treatment was carried out in Luria-Bertani broth containing 5.5% lactic acid (pH 2.9). Log reductions of E. coli ranged from <0.5 to >5 log CFU/mL (median: 1.37 log). No difference in lactic acid resistance was observed between E. coli populations recovered before and after a processing step or antimicrobial interventions. E. coli from the preintervention carcasses were slightly more resistant than E. coli isolated from equipment, differing by <0.5 log unit. Acid-resistant E. coli (log reduction <1, n = 45) had a higher prevalence of genes related to energy metabolism (ydj, xap, ato) and oxidative stress (fec, ymjC) than the less resistant E. coli (log reduction >1, n = 133). The ydj and ato operons were abundant in E. coli from preintervention carcasses. In contrast, fec genes were abundant in E. coli from equipment surfaces. The preintervention E. coli contained phylogroups A and B1 in relatively equal proportions. Phylogroup B1 predominated (95%) in the population from equipment. Of note, E. coli collected after sanitation shared either the antigens of O8 or H21. Additionally, genome diversity decreased after chilling and equipment sanitation. Overall, beef processing did not select for E. coli resistant to lactic acid but shaped the population structure. IMPORTANCE Antimicrobial interventions have significantly reduced the microbial loads on carcasses/meat products; however, the wide use of chemical and physical biocides has raised concerns over their potential for selecting resistant populations in the beef processing environment. Phenotyping of acid resistance and whole-genome analysis described in this study demonstrated beef processing practices led to differences in acid resistance, genotype, and population structure between carcass- and equipment-associated E. coli but did not select for the acid-resistant population. Results indicate that genes coding for the metabolism of long-chain sugar acids (ydj) and short-chain fatty acids (ato) were more prevalent in carcass-associated than equipment-associated E. coli. These results suggest E. coli from carcasses and equipment surfaces have been exposed to different selective pressures. The findings improve our understanding of the microbial ecology of E. coli in food processing environments and in general.

Molecular and metabolic characteristics of wastewater associated Escherichia coli strains

We previously characterized the genetic diversity of Escherichia coli strains isolated from septic tanks in the Canberra region, Australia. In this study, we used repetitive element palindromic (REP) PCR fingerprinting to identify dominant REP-types belonging to phylogroups A and B1 strains across septic tanks. Subsequently, 76 E. coli strains were selected for whole-genome sequencing and phenotype microarrays. Comparative genome analysis was performed to compare septic tank E. coli genomes with a collection of 433 E. coli isolates from different hosts and freshwater. Clonal complexes (CCs) 10 (n = 15) and 399 (n = 10) along with sequence type (ST) 401 (n = 9) were the common lineages in septic tanks. CC10 strains have been detected from animal hosts and freshwater, whereas CC399 and ST401 strains appeared to be associated with septic tanks as they were uncommon in isolates from other sources. Comparative genome analysis revealed that CC399 and ST401 were genetically distinct from other isolates and carried an abundance of niche-specific traits involved in environmental adaptation. These strains also showed distinct metabolic characteristics, such as the ability to utilize pectin, which may provide a fitness advantage under nutrient-limited conditions. The results of this study characterized the adaptive mechanisms allowing E. coli to persist in wastewater.

Draft Genome Sequences of Multidrug-Resistant Escherichia coli Strains Isolated from River Water in Malaysia

Antimicrobial resistance has become a primary concern in clinical and public health. Escherichia coli is one of the bacteria that carries and disseminates antimicrobial resistance genes to the community. Here, we report the draft genome sequence of three multidrug-resistant E. coli strains that were isolated from river water in Malaysia.

To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131

BACKGROUND

Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile.

RESULTS

Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131.

CONCLUSIONS

This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.

Naturalized Escherichia coli in Wastewater and the Co-evolution of Bacterial Resistance to Water Treatment and Antibiotics

Antibiotic resistance represents one of the most pressing concerns facing public health today. While the current antibiotic resistance crisis has been driven primarily by the anthropogenic overuse of antibiotics in human and animal health, recent efforts have revealed several important environmental dimensions underlying this public health issue. Antibiotic resistant (AR) microbes, AR genes, and antibiotics have all been found widespread in natural environments, reflecting the ancient origins of this phenomenon. In addition, modern societal advancements in sanitation engineering (i.e., sewage treatment) have also contributed to the dissemination of resistance, and concerningly, may also be promoting the evolution of resistance to water treatment. This is reflected in the recent characterization of naturalized wastewater strains of Escherichia coli-strains that appear to be adapted to live in wastewater (and meat packing plants). These strains carry a plethora of stress-resistance genes against common treatment processes, such as chlorination, heat, UV light, and advanced oxidation, mechanisms which potentially facilitate their survival during sewage treatment. These strains also carry an abundance of common antibiotic resistance genes, and evidence suggests that resistance to some antibiotics is linked to resistance to treatment (e.g., tetracycline resistance and chlorine resistance). As such, these naturalized E. coli populations may be co-evolving resistance against both antibiotics and water treatment. Recently, extraintestinal pathogenic strains of E. coli (ExPEC) have also been shown to exhibit phenotypic resistance to water treatment, seemingly associated with the presence of various shared genetic elements with naturalized wastewater E. coli. Consequently, some pathogenic microbes may also be evolving resistance to the two most important public health interventions for controlling infectious disease in modern society-antibiotic therapy and water treatment.

Public health implications of plasmid-mediated quinolone and aminoglycoside resistance genes in Escherichia coli inhabiting a major anthropogenic river of India

Presence of antimicrobial resistance (AMR) genes in Escherichia coli inhabiting anthropogenic rivers is an important public health concern because plasmid-mediated AMR genes can easily spread to other pathogens by horizontal gene transfer. Besides β -lactams, quinolones and aminoglycosides are the major antibiotics against E. coli. In the present study, we have investigated the presence of plasmid-mediated quinolone resistance (PMQR) and aminoglycoside resistance genes in E. coli isolated from a major river of northern India. Our results revealed that majority of the strains were phenotypically susceptible for fluoroquinolones and some aminoglycosides like amikacin, netilmicin, tobramycin and gentamicin. However, 16.39% of the strains were resistant for streptomycin, 8.19% for kanamycin and 3.30% for gentamicin. Of the various PMQR genes investigated, only qnrS1 was present in 24.59% of the strains along with ISEcl2 . Aminoglycoside-resistance genes like strA-strB were found to be present in 16.39%, aphA1 in 8.19% and aacC 2 in only 3.30% of the strains. Though, no co-relation was observed between phenotypic resistance for fluorquinolones and presence of PMQR genes, phenotypic resistance for streptomycin, kanamycin and gentamicin exactly co-related with the presence of the genes strA-strB , aphA1 and aacC2 , respectively. Moreover, all the AMR genes discerned in aquatic E. coli were found to be situated on conjugative plasmids and, thus easily transferrable. Our study accentuates the importance of routine surveillance of urban rivers to curtail the spread of AMR genes in aquatic pathogens.

Prevalence and Diversity of Antibiotic Resistant Escherichia coli From Anthropogenic-Impacted Larut River

Aquatic environments, under frequent anthropogenic pressure, could serve as reservoirs that provide an ideal condition for the acquisition and dissemination of antibiotic resistance genetic determinants. We investigated the prevalence and diversity of antibiotic-resistant Escherichia coli by focusing on their genetic diversity, virulence, and resistance genes in anthropogenic-impacted Larut River. The abundance of E. coli ranged from (estimated count) Est 1 to 4.7 × 105 (colony-forming units per 100 ml) CFU 100 ml−1 to Est 1 to 4.1 × 105 CFU 100 ml−1 with phylogenetic group B1 (46.72%), and A (34.39%) being the most predominant. The prevalence of multiple antibiotic resistance phenotypes of E. coli, with the presence of tet and sul resistance genes, was higher in wastewater effluents than in the river waters. These findings suggested that E. coli could be an important carrier of the resistance genes in freshwater river environments. The phylogenetic composition of E. coli and resistance genes was associated with physicochemical properties and antibiotic residues. These findings indicated that the anthropogenic inputs exerted an effect on the E. coli phylogroup composition, diversification of multiple antibiotic resistance phenotypes, and the distribution of resistance genes in the Larut River.

Genetic and Ecological Diversity of Escherichia coli and Cryptic Escherichia Clades in Subtropical Aquatic Environments

Escherichia coli not only inhabit the large intestines of human and warm-blooded animals but could also persist in the external environment. However, current knowledge was largely based on host-associated strains. Moreover, cryptic Escherichia clades that were often misidentified as E. coli by conventional diagnostic methods were discovered. Failure to distinguish them from E. coli sensu stricto could lead to inaccurate conclusions about the population genetics of E. coli. Based on seven housekeeping genes, we determine the genetic and ecological diversity of E. coli and cryptic clades as they occupy aquatic habitats with different characteristics and human impact levels in subtropical Hong Kong. Contrary to previous reports, clade II was the most abundant cryptic lineage co-isolated with E. coli, being especially abundant in relatively pristine subtropical aquatic environments. The phylogenetically distinct cryptic clades and E. coli showed limited recombination and significant genetic divergence. Analyses indicated that these clade II strains were ecologically differentiated from typical E. coli; some may even represent novel environmental Escherichia clades that were closely related to the original clade II strains of fecal origins. E. coli of diverse origins exhibited clonality amidst divergent genotypes STs, echoing other studies in that recombination in housekeeping genes was insufficient to disrupt phylogenetic signals of the largely clonal E. coli. Notably, environmental E. coli were less diverse than fecal isolates despite contributing many new alleles and STs. Finally, we demonstrated that human activities influenced the distribution of E. coli and clade II in a small aquatic continuum. Moving from relatively pristine sites toward areas with higher human disturbance, the abundance of clade II isolates and new E. coli genotypes reduces, while E. coli bearing class I integrons and belonging to CCs of public health concern accumulates. Altogether, this work revealed the new genetic diversity of E. coli and cryptic clades embedded in selected subtropical aquatic habitats, especially relatively pristine sites, which will aid a more thorough understanding of the extent of their genetic and functional variations in relation to diverse habitats with varied conditions.

Prevalence, diversity and genetic structure of Escherichia coli isolates from septic tanks

The present study investigated the diversity and genetic structure of Escherichia coli isolates from 100 septic tanks in the Canberra region, Australia. The physicochemical characteristics of the septic tanks were determined to examine the extent to which environmental factors might influence E. coli prevalence, diversity and population structure. The results of this study indicated that the temperature of the septic tank could explain some of the variation observed in the number of E. coli isolates recovered per septic tank, whereas pH was an important driver of E. coli diversity. Conductivity, pH and household size had a significant impact on E. coli population structure, and household size significantly affected the probability of detecting human-associated E. coli lineages [sequence types (STs) 69, 73, 95 and 131] in septic tanks. Phylogroup A and B1 strains were not randomly distributed among septic tanks, and the strong negative association between them may indicate intraspecific competition. The findings of this study suggest that the combination of environmental factors and intraspecific interactions may influence the distribution and genetic structure of E. coli in the environment.

AB5 Enterotoxin-Mediated Pathogenesis: Perspectives Gleaned from Shiga Toxins

Foodborne diseases affect an estimated 600 million people worldwide annually, with the majority of these illnesses caused by Norovirus, Vibrio, Listeria, Campylobacter, Salmonella, and Escherichia coli. To elicit infections in humans, bacterial pathogens express a combination of virulence factors and toxins. AB₅ toxins are an example of such toxins that can cause various clinical manifestations, including dehydration, diarrhea, kidney damage, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Treatment of most bacterial foodborne illnesses consists of fluid replacement and antibiotics. However, antibiotics are not recommended for infections caused by Shiga toxin-producing E. coli (STEC) because of the increased risk of HUS development, although there are conflicting views and results in this regard. Lack of effective treatment strategies for STEC infections pose a public health threat during outbreaks; therefore, the debate on antibiotic use for STEC infections could be further explored, along with investigations into antibiotic alternatives. The overall goal of this review is to provide a succinct summary on the mechanisms of action and the pathogenesis of AB₅ and related toxins, as expressed by bacterial foodborne pathogens, with a primary focus on Shiga toxins (Stx). The role of Stx in human STEC disease, detection methodologies, and available treatment options are also briefly discussed.

Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes

Antimicrobial resistance (AMR) is a major global public health concern, shared by a large number of human and animal health actors. Within the framework of a One Health approach, actions should be implemented in the environmental realm, as well as the human and animal realms. The Government of France commissioned a report to provide policy and decision makers with an evidential basis for recommending or taking future actions to mitigate AMR in the environment. We first examined the mechanisms that underlie the emergence and persistence of antimicrobial resistance in the environment. This report drew up an inventory of the contamination of aquatic and terrestrial environments by AMR and antibiotics, anticipating that the findings will be representative of some other high-income countries. Effluents of wastewater treatment plants were identified as the major source of contamination on French territory, with spreading of organic waste products as a more diffuse and incidental contamination of aquatic environments. A limitation of this review is the heterogeneity of available data in space and time, as well as the lack of data for certain sources. Comparing the French Measured Environmental Concentrations (MECs) with predicted no effect concentrations (PNECs), fluoroquinolones and trimethoprim were identified as representing high and medium risk of favoring the selection of resistant bacteria in treated wastewater and in the most contaminated rivers. All other antibiotic molecules analyzed (erythromycin, clarithromycin, azithromycin, tetracycline) were at low risk of resistance selection in those environments. However, the heterogeneity of the data available impairs their full exploitation. Consequently, we listed indicators to survey AMR and antibiotics in the environment and recommended the harmonization of sampling strategies and endpoints for analyses. Finally, the objectives and methods used for the present work could comprise a useful example for how national authorities of countries sharing common socio-geographic characteristics with France could seek to better understand and define the environmental dimension of AMR in their particular settings.

Elucidating the resistance repertoire, biofilm production, and phylogenetic characteristics of multidrug-resistant Escherichia coli isolated from community ponds: A study from West Bengal, India

This study details about the phenotypic and molecular characteristics of multidrug-resistant (MDR) Escherichia coli in the fresh community pond water (n = 257) collected from three districts of West Bengal, India. In total, 57 isolates were MDR of which 38 emerged as extended spectrum and 7 as AmpC-type β-lactamase producers in phenotypic assay. Among β-lactamase genes, blaCTXM-1was predominant (87.71%) followed by blaAmpC (77.2%) and blaTEM-1 (22.8%). Six MDR strains carried metallo-β-lactamase (MBL, blaNDM-1) gene. Tissue culture plate assay confirmed strong biofilm (SP) production in four MDR and one non-MDR isolates. In PCR-based replicon typing (PBRT), multiple plasmids of diverse replicon types (Frep, FIB, I1, FIA, K/B, HI1, and Y) were identified. The enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR)-based phylogenetic analysis revealed a high degree of genetic divergence among the MDR isolates. Multiplex PCR-based phylogrouping categorized 11 isolates as virulent (B2/D/F), which carried blaCTXM-1 gene and three had blaNDM-1 gene. Relative transcriptional activity of AcrAB efflux pump was significantly elevated among the SP and MBL producers. The presence of MDR E. coli isolates, particularly those resistant to carbapenem, in pond water used for daily domestic and household work, is a cause of concern as these pathogens may sneak into human food chain causing life-threatening infections. PRACTITIONER POINTS: Multidrug-resistant biofilm producing E. coli isolated from community pond water. A few of them were carbapenem-resistant and belonged to virulent (B2/D) types. Expression of AcrAB efflux pumps was found significantly elevated among biofilm producers and carbapenem-resistant population.

Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves

Intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing, and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over 6 months. We characterized the bacterial clones and plasmids carrying bla_ESBL genes with a combination of genotyping methods, whole genome sequencing, and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [bla_CTX-M-1 (64.7%), bla_CTX-M-14 (33.5%), or bla_CTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and bla_CTX-M-carrying plasmids, few bla_CTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario "clone versus plasmid spread" depended on the farm. Thus, epistatic interactions between resistance genes, plasmids, and bacterial clones contribute to optimize fitness in specific environments. IMPORTANCE The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated, but the ecological and evolutionary forces at play in nature are less studied. In this context, we performed a field work on temporal intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli in veal farms. Veal calves are animals with one of the highest levels of ESBL producing E. coli fecal carriage, due to early high antibiotic exposure. We were able to show that calves were colonized successively by different ESBL-producing E. coli clones, and that two main scenarios were at play in the spread of bla_CTX-M genes among calves: efficient colonization of several calves by a few bacterial clones and successful plasmid spread in various bacterial clones. Such knowledge should help develop new strategies to fight the emergence of antibiotic-resistance.

Virulence and phylogenetic analysis of enteric pathogenic Escherichia coli isolated from children with diarrhoea in South Africa

BACKGROUND

Diarrhoeagenic E. coli pose a significant risk to human health. As such, determining the source(s) of these bacteria when isolated from patients with diarrhoea is an important step in disease prevention.

OBJECTIVES

This study aimed to identify the presence of genes coding for virulence and phylogroups among E. coli isolated from children hospitalised due to diarrhoea in Limpopo, South Africa.

METHODS

E. coli isolates were identified by VITEK®-2 automated system. An 11-gene multiplex PCR was used to differentiate five pathogenic types of E. coli: enteroaggregative (EAEC), enteroinvasive (EIEC), enterohaemorrhagic (EHEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). Clermont quadruplex PCR method was used to identify phylogroups of isolates.

RESULTS

From the 133 isolates tested, 79 were confirmed as E. coli of which (19.0%, 15/79) were commensals and 81.0% (64/79) isolates were positive for at least one pathotype of which ETEC was predominant (16.5%, 13/79), followed by EAEC (10.1%, 8/79), EPEC (7.6%, 6/79) and EHEC (2.5%, 2/79). Hybrid pathotypes were also detected and EAEC/ETEC was predominant (25.3%, 20/79). Phylogroup B2 was predominant (30.4%, 24/79), followed by group B1 (22.8%, 18/79), phylogroup C and E both had (12.7%, 10/79) each. Just over six percent (5/79) of isolates were non-typable.

CONCLUSION

There was a high distribution of diarrhoeagenic E. coli associated with different phylogroups among children living in Limpopo province, South Africa. This emphasises the importance of future monitoring of virulence and phylogroup distribution of E. coli isolates in this province in particular and South Africa as a whole.

Genomic and Phenotypic Analysis of Heat and Sanitizer Resistance in Escherichia coli from Beef in Relation to the Locus of Heat Resistance

The locus of heat resistance (LHR) can confer heat resistance to Escherichia coli to various extents. This study investigated the phylogenetic relationships and the genomic and phenotypic characteristics of E. coli with or without LHR recovered from beef by direct plating or from enrichment broth at 42°C. LHR-positive E. coli isolates (n = 24) were subjected to whole-genome sequencing by short and long reads. LHR-negative isolates (n = 18) from equivalent sources as LHR-positive isolates were short-read sequenced. All isolates were assessed for decimal reduction time at 60°C (D_60°C) and susceptibility to the sanitizers E-SAN and Perox-E. Selected isolates were evaluated for growth at 42°C. The LHR-positive and -negative isolates were well separated on the core genome tree, with 22/24 positive isolates clustering into three clades. Isolates within clade 1 and 2, despite their different D_60°C values, were clonal, as determined by subtyping (multilocus sequence typing [MLST], core genome MLST, and serotyping). Isolates within each clade are of one serotype. The LHR-negative isolates were genetically diverse. The LHR-positive isolates had a larger (P < 0.001) median genome size by 0.3 Mbp (5.0 versus 4.7 Mbp) and overrepresentation of genes related to plasmid maintenance, stress response, and cryptic prophages but underrepresentation of genes involved in epithelial attachment and virulence. All LHR-positive isolates harbored a chromosomal copy of LHR, and all clade 2 isolates had an additional partial copy of LHR on conjugative plasmids. The growth rates at 42°C were 0.71 ± 0.02 and 0.65 ± 0.02 log(OD) h^-1 for LHR-positive and -negative isolates, respectively. No meaningful difference in sanitizer susceptibility was noted between LHR-positive and -negative isolates. IMPORTANCE Resistant bacteria are serious food safety and public health concerns. Heat resistance conferred by the LHR varies largely among different strains of E. coli. The findings in this study show that genomic background and composition of LHR, in addition to the presence of LHR, play an important role in the degree of heat resistance in E. coli and that strains with certain genetic backgrounds are more likely to acquire and maintain the LHR. Also, caution should be exercised when recovering E. coli at elevated temperatures, as the presence of LHR may confer growth advantages to some strains. Interestingly, the LHR-harboring strains seem to have evolved further from their primary animal host to adapt to their secondary habitat, as reflected by fewer genes involved in virulence and epithelial attachment. The phylogenetic relationships among the isolates point toward multiple mechanisms for acquisition of LHR by E. coli, likely prior to its being deposited on meat.

Environmental adaptation of E. coli within private groundwater sources in southeastern Ontario: Implications for groundwater quality monitoring and human health

Groundwater quality monitoring typically employs testing for the presence of E. coli as a fecal indicator of recent ingress of human or animal fecal material. The efficacy of fecal indicator organisms is based on the primary criteria that the organism does not reproduce in the aquatic environment. However, recent studies have reported that E. coli may proliferate (i.e., has adapted to) in the external environment, including soil and surface water. To date, the presence of environmentally-adapted E. coli in groundwater has not been examined. The current study employed Clermont phylotyping and the presence of six accessory genes to identify the likely presence of adapted E. coli in private groundwater sources. E. coli isolates (n = 325) from 76 contaminated private water wells located in a southeastern Ontario watershed were compared with geographically analogous human and animal fecal E. coli isolates (n = 234). Cryptic clades III-V, a well-described environmentally-adapted Escherichia population, were identified in three separate groundwater wells, one of which exclusively comprised this adapted population. Dimensionality reduction (via Principal Component Analysis) was used to develop an "E. coli adaptation model", comprising three distinct components (groundwater, animal feces, human feces) and suggests adaptation occurs frequently in the groundwater environment. Model findings indicate that 23/76 (30.3%) wells had an entirely adapted community. Accordingly, the use of E. coli as a FIO returned a false positive result in these instances, while an additional 23/76 (30.3%) wells exhibited some evidence of adaptation (i.e., not all isolates were adapted) representing an over-estimate of the magnitude (concentration) of contamination. Study findings highlight the need to further characterize environmentally-adapted E. coli in the groundwater environment and the potential implications with respect to water quality policy, legislation and determinants of human health risk both regionally and internationally.

A baseline study of spatial variability of bacteria (total coliform, E. coli, and Enterococcus spp.) as biomarkers of pollution in ten tropical Atlantic beaches: concern for environmental and public health

Coastal water quality in urban cities is increasingly impacted by human activities such as agricultural runoff, sewage discharges, and poor sanitation. However, environmental factors controlling bacteria abundance remain poorly understood. The study employed multiple indicators to assess ten beach water qualities in Ghana during minor wet seasons. Environmental parameters (e.g. temperature, electrical conductivity, total dissolved solids) were measured in situ using the Horiba multiple parameter probe. Surface water samples were collected to measure total suspended solids, nutrients, and chlorophyll-a via standard methods and bacteria determination through membrane filtration. Environmental parameters measured showed no significant variation for the sample period. However, bacteria loads differ significantly (p = 0.024) among the beaches and influenced significantly by nitrate (55.3%, p = 0.02) and total dissolved solids (17.1%, p = 0.017). The baseline study detected an increased amount of total coliforms and faecal indicator bacteria (Escherichia coli and Enterococcus spp.) in beach waters along the coast of Ghana, suggesting faecal contamination, which can pose health risks. The mean ± standard deviations of bacteria loads in beach water are total coliforms (4.06 × 10³ ± 4.16 × 10³ CFU/100 mL), E. coli (7.06 × 10² ± 1.72 × 10³ CFU/100 mL), and Enterococcus spp. (6.15 × 10² ± 1.75 × 10³ CFU/100 mL). Evidence of pollution calls for public awareness to prevent ecological and health-related risks and policy reforms to control coastal water pollution. Future research should focus on identifying the sources of contamination in the tropical Atlantic region.

The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure

To get a global picture of the population structure of the Escherichia coli phylogroup E, encompassing the O157:H7 EHEC lineage, we analysed the whole genome of 144 strains isolated from various continents, hosts and lifestyles and representative of the phylogroup diversity. The strains possess 4331 to 5440 genes with a core genome of 2771 genes and a pangenome of 33 722 genes. The distribution of these genes among the strains shows an asymmetric U-shaped distribution. E phylogenetic strains have the largest genomes of the species, partly explained by the presence of mobile genetic elements. Sixty-eight lineages were delineated, some of them exhibiting extra-intestinal virulence genes and being virulent in the mouse sepsis model. Except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes. Most of the strains were devoid of acquired resistance genes, but eight strains possessed extended-spectrum beta-lactamase genes. Human strains belong to specific lineages, some of them being virulent and antibiotic-resistant [sequence type complexes (STcs) 350 and 2064]. The E phylogroup mimics all the features of the species as a whole, a phenomenon already observed at the STc level, arguing for a fractal population structure of E. coli.

Unraveling the ecological processes modulating the population structure of Escherichia coli in a highly polluted urban stream network

Escherichia coli dynamics in urban watersheds are affected by a complex balance among external inputs, niche modulation and genetic variability. To explore the ecological processes influencing E. coli spatial patterns, we analyzed its abundance and phylogenetic structure in water samples from a stream network with heterogeneous urban infrastructure and environmental conditions. Our results showed that environmental and infrastructure variables, such as macrophyte coverage, DIN and sewerage density, mostly explained E. coli abundance. Moreover, main generalist phylogroups A and B1 were found in high proportion, which, together with an observed negative relationship between E. coli abundance and phylogroup diversity, suggests that their dominance might be due to competitive exclusion. Lower frequency phylogroups were associated with sites of higher ecological disturbance, mainly involving simplified habitats, higher drainage infrastructure and septic tank density. In addition to the strong negative relationship between phylogroup diversity and dominance, the occurrence of these phylogroups would be associated with increased facilitated dispersal. Nutrients also contributed to explaining phylogroup distribution. Our study proposes the differential contribution of distinct ecological processes to the patterns of E. coli in an urban watershed, which is useful for the monitoring and management of fecal pollution.

A review of the taxonomy, genetics, and biology of the genus Escherichia and the type species Escherichia coli

Historically, bacteriologists have relied heavily on biochemical and structural phenotypes for bacterial taxonomic classification. However, advances in comparative genomics have led to greater insights into the remarkable genetic diversity within the microbial world, and even within well-accepted species such as Escherichia coli. The extraordinary genetic diversity in E. coli recapitulates the evolutionary radiation of this species in exploiting a wide range of niches (i.e., ecotypes), including the gastrointestinal system of diverse vertebrate hosts as well as non-host natural environments (soil, natural waters, wastewater), which drives the adaptation, natural selection, and evolution of intragenotypic conspecific specialism as a strategy for survival. Over the last few years, there has been increasing evidence that many E. coli strains are very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of E. coli as a distinct species, the vast genomic (diverse pan-genome and intragenotypic variability), phenotypic (e.g., metabolic pathways), and ecotypic (host-/niche-specificity) diversity, comparable to the diversity observed in known species complexes, suggest that E. coli is better represented as a complex. Herein we review the taxonomic classification of the genus Escherichia and discuss how phenotype, genotype, and ecotype recapitulate our understanding of the biology of this remarkable bacterium.

Selective survival of Escherichia coli phylotypes in freshwater beach sand

Escherichia coli is used as an indicator of fecal pollution at beaches despite evidence of long-term survival in sand. This work investigated the basis for survival of E. coli through field microcosm experiments and phylotypic characterization of more than >1400 E. coli isolated from sand, sewage, and gulls, enabling identification of long-surviving populations and environmental drivers of their persistence. Microcosms containing populations of E. coli from each source (n=176) were buried in the backshore of Lake Michigan for 45 & 96 days under several different nutrient treatments, including unaltered native sand, sterile autoclaved sand and baked nutrient depleted sand. Availability of carbon and nitrogen and competition with the indigenous community were major factors that influenced E. coli survival. E. coli Clermont phylotypes B1 and A were the most dominant phylotypes surviving seasonally (>6 weeks), regardless of source and nutrient treatment, whereas cryptic clade and D/E phylotypes survived over winter (>300 days). Autoclaved sand, presumably supplying nutrients through increased availability, promoted growth and the presence of the indigenous microbial community reduced this effect. Screening of 849 sand E. coli from four freshwater beaches demonstrated that B1, but also D/E, were the most common phylotypes recovered. Analysis by qPCR for the Gull2, Lachno3 and HB human markers demonstrated only 25% of the samples had evidence of gull waste and none of the samples had evidence of human waste. These findings suggest prevalence of E. coli in the sand could be attributed more to long term surviving populations than to new fecal pollution.IMPORTANCE Fecal pollution monitoring still relies upon the enumeration of E. coli, despite the fact that this organism can survive for prolonged periods and has been shown to be easily transported from sand into surrounding waters through waves and runoff, thus no longer represents recent fecal pollution events. Here, we experimentally demonstrate that regardless of host source, certain genetically distinct subgroups, or phylotypes, survive longer than others under conditions typical of Great Lakes beach sites. We found nutrients were a major driver of survival and could actually promote growth, and the presence of native microorganisms modulated these effects. These insights into the dynamics and drivers of survival will improve the interpretation of E. coli measurements at beaches and inform strategies that could focus on reducing nutrient inputs to beaches or maintaining a robust natural microbiome in beach sand.

The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing

Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of E. coli in the environment. In this study, we used whole genome sequencing to investigate the links between E. coli and recent faecal contamination in drinking water. We sequenced 103 E. coli isolates sampled from 9 water supplies in rural Kitui County, Kenya, including points of collection (n = 14) and use (n = 30). Biomarkers for definitive source tracking remain elusive, so we analysed the phylogenetic grouping, multi-locus sequence types (MLSTs), allelic diversity, and virulence and antimicrobial resistance (AMR) genes of the isolates for insight into their likely source. Phylogroup B1, which is generally better adapted to water environments, is dominant in our samples (n = 69) and allelic diversity differences (z = 2.12, p = 0.03) suggest that naturalised populations may be particularly relevant at collection points with lower E. coli concentrations (<50 / 100mL). The strains that are more likely to have originated from human and/or recent faecal contamination (n = 50), were found at poorly protected collection points (4 sites) or at points of use (12 sites). We discuss the difficulty of interpreting health risk from E. coli grab samples, especially at household level, and our findings support the use of E. coli risk categories and encourage monitoring that accounts for sanitary conditions and temporal variability.

Effects of Escherichia coli pollution on decomposition of aquatic plants: Variation due to microbial community composition and the release and cycling of nutrients

Determination of the effects of Escherichia coli (E. coli) pollution on agricultural pond ecosystems with vegetation at different life stages is essential for the protection of ecological functions. However, no comprehensive study has yet shown the responses of epiphytic microbial communities to E. coli invasion during plant decay. Thus, this study was conducted to clarify variation in the decay of the following aquatic plants-Myriophyllum aquaticum, Nymphaea tetragona and Phragmites australis after E. coli pollution. Exogenous E. coli especially shifted the epiphytic microbial composition and distribution of P. australis. Stronger effects of E. coli on the archaeal community (edges/nodes = 0.818 < 1, modularity = 0.654; lower clustered structure, 0.389) were found than on the bacterial community (edges/nodes = 1.538 > 1, modularity = 1.291 > 0.654; higher clustered, 0.593). During plant decomposition, E. coli weakened methanogenesis by regulating the network of core genera Methanobacterium and Methanospirillum (spearman, P <  0.05), stimulated the accumulation of organic matters in water (P <  0.05). Similarly, nitrification and denitrification increased and decreased through network regulation in relative biomass of genera Devosia and Desulfovibrio (P <  0.05), respectively. The results provided theoretical supports for eutrophication management in pond ecosystems threatened by E. coli pollution.

Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring

In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.

High Prevalence of Human-Associated Escherichia coli in Wetlands Located in Eastern France

Escherichia coli that are present in the rivers are mostly brought by human and animal feces. Contamination occurs mostly through wastewater treatment plant (WWTP) outflows and field amendment with sewage sludge or manure. However, the survival of these isolates in river-associated wetlands remains unknown. Here, we assessed E. coli population structure in low-anthropized wetlands located along three floodplains to identify the major source of contamination of wetlands, whose functioning is different from the rivers. We retrieved 179 E. coli in water samples collected monthly from 19 sites located in eastern France over 1 year. Phylogroups B1 and B2 were dominant in the E. coli population, while phylogroup A was dominant in isolates resistant to third-generation cephalosporins, which harbored the extended-spectrum β-lactamase (ESBL) encoding genes bla_CTX–M–15 and bla_CTX–M–27 in half of the cases. The high proportion of isolates from human source can be attributed to WWTP outflows and the spread of sewage sludge. We analyzed the distribution of the isolates belonging to the most human-associated phylogroups (B2 and D) on a phylogenetic tree of the whole species and compared it with that of isolates retrieved from patients and from WWTP outflows. The distribution of the three E. coli populations was similar, suggesting the absence of a specific population in the environment. Our results suggest that a high proportion of E. coli isolates that reach and survive in low-anthropized environments such as wetlands are from human source. To the best of our knowledge, this is the first study assessing E. coli contamination and resistance genes in natural freshwater wetlands.

Uneven genotypic diversity of Escherichia coli in fecal sources limits the performance of a library-dependent method of microbial source tracking on the southwestern French Atlantic coast

To develop a library-dependent method of tracking fecal sources of contamination of beaches on the Atlantic coast of southwestern France, a library of 6368 Escherichia coli isolates was constructed from samples of feces, from 40 known human or animal sources collected in the vicinity of Arcachon Bay in 2010, and in French Basque Country, Landes, and Béarn, between 2017 and 2018. Different schemes of source identification were tested: use of the complete or filtered reference library; characterization of the isolates by genotypic or proteomic profiling based on ERIC-PCR or MALDI-TOF mass spectrometry, respectively; isolate by isolate assignment using either classifiers based on the Pearson similarity or SVM (support vector machine). With the exception of one source identification scheme, which was discarded since it used self-assignment, all tested schemes resulted in low rates of correct classification (<35%) and significant rates of incorrect classification (>15%). The heterogeneous coverage of E. coli genotypic diversity between sources and the uneven distribution of E. coli genotypes in the library likely explain the difficulties encountered in identifying the sources of fecal contamination. Shannon diversity index of sources ranged from 0 for several wildlife species sampled once to 3.03 for sewage treatment plant effluents sampled on various occasions, showing discrepancies between sources. The uneven genotypic composition of the library was attested by the value of the Pielou index (0.54), the high proportion of nondiscriminatory genotypes (>91% of the isolates), and the very low proportion of discriminatory genotypes (<3%). Since efforts made to constitute such a library are not affordable for routine analyses, the results question the relevance of developing such a method for identifying sources of fecal contamination on such a coastline.

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.

Previous large scale studies on the evolution of E. coli focused on clinical isolates emphasizing virulence and antibiotic resistance in medically important lineages. Yet, most E. coli strains are either human commensals or not associated with humans at all. Here, we analyzed a large collection of non-clinical isolates of the species to assess the mechanisms of gene repertoire diversification in the light of isolation sources and phylogeny. We show that gene repertoires evolve so rapidly by the high turnover of mobile genetic elements that epidemiologically indistinguishable strains can be phenotypically extremely heterogeneous, illustrating the velocity of bacterial adaptation and the importance of accounting for the information on the whole genome at the epidemiological scale. Phylogeny and habitat shape the genetic diversification of E. coli to similar extents. Surprisingly, freshwater strains seem specifically adapted to this environment, breaking the paradigm that E. coli environmental isolates are systematically fecal contaminations. As a consequence, the evolution of this species is also shaped by environmental habitats, and it may diversify by acquiring genes and mobile elements from environmental bacteria (and not just from gut bacteria). This may facilitate the acquisition of virulence factors and antibiotic resistance in the strains that become pathogenic.

Antimicrobial Resistance Traits of Escherichia coli Isolated from Dairy Manure and Freshwater Ecosystems Are Similar to One Another but Differ from Associated Clinical Isolates

Antimicrobial resistance (AMR) is a prevalent global health problem across human and veterinary medicine. The One Health approach to AMR is necessary to mitigate transmission between sources of resistance and decrease the spread of resistant bacteria among humans, animals, and the environment. Our primary goal was to identify associations in resistance traits between Escherichia coli isolated from clinical (n = 103), dairy manure (n = 65), and freshwater ecosystem (n = 64) environments within the same geographic location and timeframe. Clinical E. coli isolates showed the most phenotypic resistance (47.5%), followed by environmental isolates (15.6%) and manure isolates (7.7%), with the most common resistances to ampicillin, ampicillin-sulbactam, and cefotaxime antibiotics. An isolate subset was screened for extended spectrum beta-lactamase (ESBL) production resulting in the identification of 35 ESBL producers. The most common ESBL gene identified was bla_TEM-1. Additionally, we found nine different plasmid replicon types including IncFIA-FIB, which were frequently associated with ESBL producer isolates. Molecular phylotyping revealed a significant portion of clinical E. coli were associated with phylotype B2, whereas manure and environmental isolates were more diverse. Manure and environmental isolates were significantly different from clinical isolates based on analyzed traits, suggesting more transmission occurs between these two sources in the sampled environment.

The response of nitrogen cycling and bacterial communities to E. coli invasion in aquatic environments with submerged vegetation

The effects of exogenous Escherichia coli on nitrogen cycling (N-cycling) in freshwater remains unclear. Thus, seven ecosystems, six with submerged plants-Potamogeton crispus (PC) and Myriophyllum aquaticum (MA)-and one with no plants were set up. Habitats were assessed before and after E. coli addition (10⁷ colony-forming units/mL). E. coli colonization of freshwater ecosystems had significant effects on bacterial community structure in plant surface biofilms and surface sediments (ANOVA, P < 0.05). It reduced the relative abundance of nitrosification bacteria (-70.94 ± 26.17%) and nitrifiers (-47.86 ± 23.68%) in biofilms which lead to significant reduction of ammoxidation in water (P < 0.05). The N-cycling intensity from PC systems was affected more strongly by E. coli than were MA systems. Furthermore, the coupling coefficient of exogenous E. coli to indigenous N-cycling bacteria in sediments (6.061, average connectivity degree) was significantly weaker than that in biofilms (9.852). Additionally, at the genus level, E. coli were most-closely associated with N-cycling bacteria such as Prosthecobacter, Hydrogenophaga, and Bacillus in sediments and biofilms according to co-occurrence bacterial network (Spearman). E. coli directly changed their abundance, so that the variability of species composition of N-cycling bacterial taxa was triggered, as well. Overall, exogenous E. coli repressed ammoxidation, but promoted ammonification and denitrification. Our results provided new insights into how pathogens influence the nitrogen cycle in freshwater ecosystems.

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

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.