Adhesion of marine cryptic Escherichia isolates to human intestinal epithelial cells

Development of a multiplex droplet digital PCR assay for simultaneous detection and quantification of Escherichia coli, E. marmotae, and E. ruysiae in water samples

Escherichia coli are widely used by water quality managers as Fecal Indicator Bacteria, but current quantification methods do not differentiate them from benign, environmental Escherichia species such as E. marmotae (formerly named cryptic clade V) or E. ruysiae (cryptic clades III and IV). Reliable and specific techniques for their identification are required to avoid confounding microbial water quality assessments. To address this, a multiplex droplet digital PCR (ddPCR) assay targeting lipB (E. coli and E. ruysiae) and bglC (E. marmotae) was designed. The ddPCR performance was assessed using in silico analysis; genomic DNA from 40 local, international, and reference strains of target and non-target coliforms; and spiked water samples in a range relevant to water quality managers (1 to 1000 cells/100 mL). Results were compared to an analogous quantitative PCR (qPCR) and the Colilert method. Both PCR assays showed excellent sensitivity with a limit of detection of 0.05 pg/μL and 0.005 pg/μl for ddPCR and qPCR respectively, and of quantification of 0.5 pg/μL of genomic DNA. The ddPCR allowed differentiation and quantification of three Escherichia species per run by amplitude multiplexing and showed a high concordance with concentrations measured by Colilert once proportional bias was accounted for. In silico specificity testing underlined the possibility to further detect and distinguish Escherichia cryptic clade VI. Finally, the applicability of the ddPCR was successfully tested on environmental water samples where E. marmotae and E. ruysiae potentially confound E. coli counts based on the Most Probable Number method, highlighting the utility of this novel ddPCR as an efficient and rapid discriminatory test to improve water quality assessments.

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.

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.

EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations

The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.

Molecular typification of Escherichia coli from community-acquired urinary tract infections in Mexico

One hundred and five uropathogenic Escherichia coli (UPEC) strains from patients with community-acquired urinary tract infection were characterized according to their phylogenetic groups, virulence factors, serogroups, antibiotics resistance, and genotype. The pathogenic phylogenetic groups (B2, D, and F) were found in 71.4% of the tested strains. Among them, the main uropathogenic serogroups were O8, O25, and O75, in which 97.1% of the strains had a multidrug-resistant profile. Moreover, 16 virulence genes were analyzed using a combination of PCR assays, with the fimH, irp-2, iutA, aer, iucC, PAI, sat, iroN, usp, and cnf1 genes being mainly found in pathogenic phylogroups. The E. coli O25b-ST131 clone was identified in 32% of the strains assigned to the pathogenic phylogroup B2. Our findings demonstrate that virulence genes encoding adhesin components, iron acquisition systems, toxins, and pathogenicity-associated islands were highly prevalent among the pathogenic phylogroup of UPEC strains.

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.

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.

Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller

The genus Escherichia comprises five species and at least five lineages currently not assigned to any species, termed 'Escherichia cryptic clades'. We isolated an Escherichia strain from an international traveller and resolved the complete DNA sequence of the chromosome and an IncI multidrug resistance plasmid using Illumina and Nanopore whole-genome sequencing (WGS). Strain OPT1704T can be differentiated from existing Escherichia species using biochemical (VITEK2) and genomic tests [average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH)]. Phylogenetic analysis based on alignment of 16S rRNA sequences and 682 concatenated core genes showed similar results. Our analysis further revealed that strain OPT1704T falls within Escherichia cryptic clade IV and is closely related to cryptic clade III. Combining our analyses with publicly available WGS data of cryptic clades III and IV from Enterobase confirmed the close relationship between clades III and IV (>96 % interclade ANI), warranting assignment of both clades to the same novel species. We propose Escherichia ruysiae sp. nov. as a novel species, encompassing Escherichia cryptic clades III and IV (type strain OPT1704T=NCCB 100732T=NCTC 14359T).

Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

The evolution, habitat, and lifestyle of the cryptic clade II of Escherichia, which were first recovered at low frequency from non-human hosts and later from external environments, were poorly understood. Here, the genomes of selected strains were analyzed for preliminary indications of ecological differentiation within their population. We adopted the delta bitscore metrics to detect functional divergence of their orthologous genes and trained a random forest classifier to differentiate the genomes according to habitats (gastrointestinal vs external environment). Model was built with inclusion of other Escherichia genomes previously demonstrated to have exhibited genomic traits of adaptation to one of the habitats. Overall, gene degradation was more prominent in the gastrointestinal strains. The trained model correctly classified the genomes, identifying a set of predictor genes that were informative of habitat association. Functional divergence in many of these genes were reflective of ecological divergence. Accuracy of the trained model was confirmed by its correct prediction of the habitats of an independent set of strains with known habitat association. In summary, the cryptic clade II of Escherichia displayed genomic signatures that are consistent with divergent adaptation to gastrointestinal and external environments.

Tossed 'good luck' coins as vectors for anthropogenic pollution into aquatic environment

Superstition has it that tossing coins into wells or fountains brings good luck, thereby causing a potential accumulation of microbially contaminated metal particles in the water. Here, we characterized the microbiota and the resistance profile in biofilm on such coins and their surrounding sediments. The study site was a tidal marine lake within a touristic center located in a natural reserve area. Notwithstanding the fact that coin-related biofilms were dominated by typical marine taxa, coin biofilms had specific microbial communities that were different from the communities of the surrounding sediment. Moreover, the communities were different depending on whether the coin were made mainly of steel or of copper. Sequences affiliated with putative pathogens were found on every third coin but were not found in the surrounding sediment. Antibiotic resistance genes (ARGs) were detected on most of the coins, and interestingly, sediments close to the area where coins accumulate had a higher frequency of ARGs. We suggest that the surface of the coins might offer a niche for ARGs and faecal bacteria to survive, and, thus, tossed coins are a potential source and vector for ARGs into the surrounding environment.

The vertical distribution of tetA and intI1 in a deep lake is rather due to sedimentation than to resuspension

Lakes are exposed to anthropogenic pollution including the release of allochthonous bacteria into their waters. Antibiotic resistance genes (ARGs) stabilize in bacterial communities of temperate lakes, and these environments act as long-term reservoirs of ARGs. Still, it is not clear if the stabilization of the ARGs is caused by a periodical introduction, or by other factors regulated by dynamics within the water column. Here we observed the dynamics of the tetracycline resistance gene (tetA) and of the class 1 integron integrase gene intI1 a proxy of anthropogenic pollution in the water column and in the sediments of subalpine Lake Maggiore, together with several chemical, physical and microbiological variables. Both genes resulted more abundant within the bacterial community of the sediment compared to the water column and the water-sediment interface. Only at the inset of thermal stratification they reached quantifiable abundances in all the water layers, too. Moreover, the bacterial communities of the water-sediment interface were more similar to deep waters than to the sediments. These results suggest that the vertical distribution of tetA and intI1 is mainly due to the deposition of bacteria from the surface water to the sediment, while their resuspension from the sediment is less important.

Genomic and molecular characterisation of Escherichia marmotae from wild rodents in Qinghai-Tibet plateau as a potential pathogen

Wildlife is a reservoir of emerging infectious diseases of humans and domestic animals. Marmota himalayana mainly resides 2800-4000 m above sea level in the Qinghai-Tibetan Plateau, and is the primary animal reservoir of plague pathogen Yersinia pestis. Recently we isolated a new species, Escherichia marmotae from the faeces of M. himalayana. In this study we characterised E. marmotae by genomic analysis and in vitro virulence testing to determine its potential as a human pathogen. We sequenced the genomes of the seven E. marmotae strains and found that they contained a plasmid that carried a Shigella-like type III secretion system (T3SS) and their effectors, and shared the same O antigen gene cluster as Shigella dysenterae 8 and E. coli O38. We also showed that E. marmotae was invasive to HEp-2 cells although it was much less invasive than Shigella. Thus E. marmotae is likely to be an invasive pathogen. However, E. marmotae has a truncated IpaA invasin, and lacks the environmental response regulator VirF and the IcsA-actin based intracellular motility, rendering it far less invasive in comparison to Shigella. E. marmotae also carried a diverse set of virulence factors in addition to the T3SS, including an IS1414 encoded enterotoxin gene astA with 37 copies, E. coli virulence genes lifA/efa, cif, and epeA, and the sfp gene cluster, Yersinia T3SS effector yopJ, one Type II secretion system and two Type VI secretion systems. Therefore, E. marmotae is a potential invasive pathogen.

Antibiotic resistance along an urban river impacted by treated wastewaters

Urban rivers are impacted ecosystems which may play an important role as reservoirs for antibiotic-resistant (AR) bacteria. The main objective of this study was to describe the prevalence of antibiotic resistance along a sewage-polluted urban river. Seven sites along the Zenne River (Belgium) were selected to study the prevalence of AR Escherichia coli and freshwater bacteria over a 1-year period. Culture-dependent methods were used to estimate E. coli and heterotrophic bacteria resistant to amoxicillin, sulfamethoxazole, nalidixic acid and tetracycline. The concentrations of these four antibiotics have been quantified in the studied river. The antibiotic resistance genes (ARGs), sul1, sul2, tetW, tetO, blaTEM and qnrS were also quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed an effect of treated wastewaters release on the spread of antibiotic resistance along the river. Although an increase in the abundance of both AR E. coli and resistant heterotrophic bacteria was observed from upstream to downstream sites, the differences were only significant for AR E. coli. A significant positive regression was also found between AR E. coli and resistant heterotrophic bacteria. The concentration of ARGs increased from upstream to downstream sites for both particle-attached (PAB) and free-living bacteria (FLB). Particularly, a significant increase in the abundance of four among six ARGs analyzed was observed after crossing urban area. Although concentrations of tetracycline significantly correlated with tetracycline resistance genes, the antibiotic levels were likely too low to explain this correlation. The analysis of ARGs in different fractions revealed a significantly higher abundance in PAB compared to FLB for tetO and sul2 genes. This study demonstrated that urban activities may increase the spread of antibiotic resistance even in an already impacted river.

IgA-coated E. coli enriched in Crohn's disease spondyloarthritis promote TH17-dependent inflammation

Peripheral spondyloarthritis (SpA) is a common extraintestinal manifestation in patients with active inflammatory bowel disease (IBD) characterized by inflammatory enthesitis, dactylitis, or synovitis of nonaxial joints. However, a mechanistic understanding of the link between intestinal inflammation and SpA has yet to emerge. We evaluated and functionally characterized the fecal microbiome of IBD patients with or without peripheral SpA. Coupling the sorting of immunoglobulin A (IgA)-coated microbiota with 16S ribosomal RNA-based analysis (IgA-seq) revealed a selective enrichment in IgA-coated Escherichia coli in patients with Crohn's disease-associated SpA (CD-SpA) compared to CD alone. E. coli isolates from CD-SpA-derived IgA-coated bacteria were similar in genotype and phenotype to an adherent-invasive E. coli (AIEC) pathotype. In comparison to non-AIEC E. coli, colonization of germ-free mice with CD-SpA E. coli isolates induced T helper 17 cell (TH17) mucosal immunity, which required the virulence-associated metabolic enzyme propanediol dehydratase (pduC). Modeling the increase in mucosal and systemic TH17 immunity we observed in CD-SpA patients, colonization of interleukin-10-deficient or K/BxN mice with CD-SpA-derived E. coli lead to more severe colitis or inflammatory arthritis, respectively. Collectively, these data reveal the power of IgA-seq to identify immunoreactive resident pathosymbionts that link mucosal and systemic TH17-dependent inflammation and offer microbial and immunophenotype stratification of CD-SpA that may guide medical and biologic therapy.

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments-a Review

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.

The "Cryptic" Escherichia

In 2009, five monophyletic Escherichia clades were described and referred to as "cryptic" based on the inability to distinguish them from representative E. coli isolates using diagnostic biochemical reactions. Since this original publication, a number of studies have explored the genomic, transcriptomic, and phenotypic diversity of cryptic clade isolates to better understand their phylogenetic, physiological, and ecological distinctiveness with respect to previously named Escherichia species. This chapter reviews the original discovery of the cryptic clades, discusses available evidence that some are environmentally adapted, and evaluates current support for taxonomic designations of these microorganisms. The importance of these clades to clinical research, epidemiology, population genetics, and microbial speciation is also discussed.

Distribution of Escherichia coli in a coastal lagoon (Venice, Italy): Temporal patterns, genetic diversity and the role of tidal forcing

Despite its worldwide importance as fecal indicator in aquatic systems, little is known about the diversity of Escherichia coli in the environment and the factors driving its spatial distribution. The city of Venice (Italy), lying at the forefront of a large European lagoon, is an ideal site to study the mechanisms driving the fate of fecal bacteria, due to the huge fluxes of tourists, the city's unique architecture (causing poor efficiency of sewages treatment), and the long branching network of canals crossing the city. We summarize the results of a multi-year investigation to study the temporal dynamics of E. coli around the city, describe the population structure (by assigning isolates to their phylogenetic group) and the genotypic diversity, and explore the role of environmental factors in determining its variability. E. coli abundance in water was highly variable, ranging from being undetectable up to 10(4) Colony Forming Units (CFU) per 100 ml. Abundance did not display significant relationships with the water physico-chemical variables. The analysis of the population structure showed the presence of all known phylogroups, including extra-intestinal and potentially pathogenic ones. The genotypic diversity was very high, as likely consequence of the heterogeneous input of fecal bacteria from the city, and showed site-specific patterns. Intensive sampling during the tidal fluctuations highlighted the prominent role of tides, rather than environmental variables, as source of spatial variation, with a more evident influence in water than sediments. These results, the first providing information on the genetic properties, spatial heterogeneity and influence of tides on E. coli populations around Venice, have implications to manage the fecal pollution, and the associated waterborne disease risks, in coastal cities lying in front of lagoons and semi-enclosed basins.

Understanding the association of Escherichia coli with diverse macroalgae in the lagoon of Venice

Recent studies provided evidence that the macroalga Cladopohora in lakes hosts associated Escherichia coli, with consequences on the environmental and human health. We expanded these investigations to other macroalgae (Ulva spp., Sargassum muticum and Undaria pinnatifida) widespread in the lagoon of Venice (Italy). Attached E. coli were abundant, accounting up to 3,250 CFU gram⁻¹ of alga. Macroalgal-associated isolates belonged to all E. coli phylogroups, including pathogenic ones, and to Escherichia cryptic clades. Attached E. coli showed potential to grow even at in situ temperature on macroalgal extracts as only source of carbon and nutrients, and ability to produce biofilm in vitro. The genotypic diversity of the attached isolates was high, with significant differences between algae and the overlying water. Our evidences suggest that attached populations consist of both resident and transient strains, likely resulting from the heterogeneous input of fecal bacteria from the city. We report that cosmopolitan and invasive macroalgae may serve as source of E. coli, including pathogenic genotypes, and that this habitat can potentially support their growth. Considering the global diffusion of the macroalgae here studied, this phenomenon is likely occurring in other coastal cities worldwide and deserves further investigations from either the sanitary and ecological perspectives.