Pathogenic potential, genetic diversity, and population structure of Escherichia coli strains isolated from a forest-dominated watershed (Comox Lake) in British Columbia, Canada

Phylogenetic groups and extraintestinal virulence genes of inflow Escherichia coli entering a municipal drinking water treatment facility (St. Paul, MN, USA)

Extraintestinal pathogenic Escherichia coli (ExPEC), a leading cause of urinary tract infections, sepsis and neonatal meningitis, circulates between diverse hosts and the environment. Consequently, identifying ExPEC reservoirs and transmission pathways has potentially great public health importance. Here, we used PCR-based methods to characterize 104 E. coli isolates from inflow water to the St. Paul, MN (USA), municipal drinking water treatment plant. Isolates were analysed for major phylogenetic groups and multiple extraintestinal virulence genes. Additionally, from the 65 (of 104) water samples that yielded multiple E. coli colonies, we screened E. coli population DNA for virulence genes. Thirty-three percent of isolates represented virulence-associated groups B2 and D, and 8% (95% CI: 3%, 15%) qualified molecularly as ExPEC. The ExPEC isolates, all from group B2 or D, had a median virulence gene score of 11.0 and collectively contained all but four of the 28 studied extraintestinal virulence genes. Population DNA screening increased the proportion of samples positive for individual virulence genes and, presumptively, for ExPEC [14% (95% CI: 10%, 30%) vs. 8%, P=0.03]. These findings identify a previously underappreciated potential mechanism for community-wide dissemination of ExPEC and underscore the importance of consistent disinfection of municipal drinking water.

Abundance of fecal indicator bacteria and diversity of Escherichia coli associated with poultry farms and pasture land cover in streams of northwestern South Carolina

Livestock can contribute fecal indicator bacteria (FIB) to waterbodies. However, few studies have examined the relationship between watershed land use or land cover involving livestock production and the genetic diversity of Escherichia coli in freshwater ecosystems. Our major goal was to determine if FIB abundance and E. coli phylogenetic group distributions in headwater streams are related to livestock production in rural watersheds in South Carolina. In both 2017 and 2018, grab samples were collected from streams at summer baseflow. In 2017, we collected samples from watersheds with or without poultry rearing facilities (PRFs). In 2018, we collected samples from streams draining watersheds with mixed forest and pasture cover and from streams in mostly forested watersheds. In both summers, we measured concentrations of total coliforms, E. coli, and Enterococcus. We also categorized E. coli isolates into one of four phylogenetic groups (A, B1, B2, D). Streams with PRFs in their watersheds had significantly higher concentrations of Enterococcus but not total coliforms or E. coli than streams in watersheds without PRFs. Also, B2 isolates were less frequent and B1 isolates were more frequent in watersheds with PRFs than in those without. Streams draining mixed forest/pasture watersheds had significantly higher concentrations of total coliforms and E. coli but not Enterococcus, as well as higher frequencies of B1 isolates, than streams in mostly forested watersheds. Overall, the most frequent E. coli phylogenetic groups in watersheds with animal production appeared consistent with the phylogenetic groups that are especially abundant in poultry or mammalian livestock feces.

Multi-Drug Resistant Escherichia coli, Biosecurity and Anti-Microbial Use in Live Bird Markets, Abeokuta, Nigeria

Live bird markets (LBM) remain a critical link from farm to fork in the poultry value chain, which oftentimes promotes indiscriminate antimicrobial use (AMU) and resistance (AMR). In this study, we assessed biosecurity practices, AMU, and associated these with multidrug resistant (MDR) E. coli in LBMs in Abeokuta, Ogun State. A cross-sectional survey among live bird sellers (LBS) in eight LBMs was conducted using a semi-structured questionnaire. Also, cloacal samples (n = 200) were randomly collected and pooled for bacteriological detection of MDR E. coli in live chickens of consenting LBS. Susceptibility to 14 antimicrobials belonging to 6 different classes was determined using the disk diffusion method. Biosecurity level and AMU were generally low. LBS less than 46 years were 6.8- fold more likely to fall within the poor biosecurity level (Crudes odds ratio = 6.8; 95% CI; 1.20-38.56; p = 0.03) than others. An informal or primary school education increased the odds of having a poor practice of AMU by 15.1 folds (Crudes odds ratio = 15.1; 95% CI; 2.73-84.18; p = 0.002) than those with secondary or tertiary. The prevalence of E. coli and MDR E. coli at the LBM level were 80% and 56.3%, respectively. Extremely high resistance rates were observed for ceftazidime (96.9%) and imipenem (90.6%). The odds of MDR E. coli increased eight-fold in poultry kept by LBS who use AMs as prophylaxis. This current data could be useful for the development of targeted behavioral risk communication and mitigation strategies for AMR to impede the potential horizontal transfer of AMR genes to humans through animal-sourced food.

Niche Preference of Escherichia coli in a Peri-Urban Pond Ecosystem

Escherichia coli comprises diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond, as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used the uidA and mutS sequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity/virulence genes (stxI, stxII, eaeA, hlyA, ST, and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azithromycin. Our results showed that isolates from water, sediment, and water plants were similar by phylogroup distribution, virulence gene distribution, and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail, and aquatic environments. Collectively these data support niche preference of E. coli isolates occurring in this ecosystem.

Tracking Fecal Bacterial Dispersion from Municipal Wastewater to Peri-Urban Farms during Monsoon Rains in Hue City, Vietnam

Disease outbreaks attributed to monsoon flood-induced pathogen exposure are frequently reported, especially in developing cities with poor sanitation. Contamination levels have been monitored in past studies, yet the sources, routes, and extents of contamination are not always clear. We evaluated pollution from municipal wastewater (MWW) discharge and investigated fecal contamination by Escherichia coli (E. coli) in three agricultural fields on the outskirts of Hue City, Vietnam. After E. coli concentration was determined in irrigation water (IRW), MWW, soil, vegetables (VEG), and manure, its dispersion from MWW was tracked using multilocus sequence typing (MLST) and phylogenetic analyses during the wet and dry seasons. IRW was severely contaminated; 94% of the samples were positive with E. coli exceeding the stipulated standards, while VEG contamination was very low in both seasons. The confirmed total number of isolates was comparable between the seasons; however, results from MLST and phylogenetic clustering revealed more links between the sites and samples to MWW during the wet season. The wet season had four mixed clusters of E. coli isolates from multiple locations and samples linked to MWW, while only one mixed cluster also linking MWW to IRW was observed during the dry season. The most prevalent sequence type (ST) complex 10 and two others (40 and 155) have been associated with disease outbreaks, while other STs have links to major pathotypes. Irrigation canals are significant routes for E. coli dispersion through direct links to the urban drainage-infested river. This study clarified the genotype of E. coli in Hue city, and the numerous links between the samples and sites revealed MWW discharge as the source of E. coli contamination that was enhanced by flooding.

A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts

E. coli is one of the most common species of bacteria colonizing humans and animals. The singularity of E. coli 's genus and species underestimates its multifaceted nature, which is represented by different strains, each with different combinations of distinct virulence factors. In fact, several E. coli pathotypes, or hybrid strains, may be associated with both subclinical infection and a range of clinical conditions, including enteric, urinary, and systemic infections. E. coli may also express DNA-damaging toxins that could impact cancer development. This review summarizes the different E. coli pathotypes in the context of their history, hosts, clinical signs, epidemiology, and control. The pathotypic characterization of E. coli in the context of disease in different animals, including humans, provides comparative and One Health perspectives that will guide future clinical and research investigations of E. coli infections.

Human Mucosal IgA Immune Responses against Enterotoxigenic Escherichia coli

Infection with enterotoxigenic Escherichia coli (ETEC) is a major contributor to diarrheal illness in children in low- and middle-income countries and travelers to these areas. There is an ongoing effort to develop vaccines against ETEC, and the most reliable immune correlate of protection against ETEC is considered to be the small intestinal secretory IgA response that targets ETEC-specific virulence factors. Since isolating IgA from small intestinal mucosa is technically and ethically challenging, requiring the use of invasive medical procedures, several other indirect methods are used as a proxy for gauging the small intestinal IgA responses. In this review, we summarize the literature reporting on anti-ETEC human IgA responses observed in blood, activated lymphocyte assayss, intestinal lavage/duodenal aspirates, and saliva from human volunteers being experimentally infected with ETEC. We describe the IgA response kinetics and responder ratios against classical and noncanonical ETEC antigens in the different sample types and discuss the implications that the results may have on vaccine development and testing.

Molecular diversity and profile analysis of virulence-associated genes in some Klebsiella pneumoniae isolates

The noticeable increase in the occurrence of multidrug-resistant Klebsiella pneumoniae strains separated from different hospitals in Taif city, (Saudi Arabia) demonstrates the limitation of antibiotics used for bacterial eradication. The aim of the present study is to detect the virulence genes in some K. pneumoniae isolates that collected from different hospitals in Taif governorate in Saudi Arabia. A total of 134 clinical samples were used to isolate about twenty three K. pneumoniae strains from various clinical specimens throw six months. They were identified by microbiological method as K. pneumoniae and confirmed with 16S rRNA sequencing analysis. The antimicrobial susceptibility of K. pneumoniae isolates was determined. The existence of virulence genes (AcrAB, tolC, arb, OmpK35, RmpA, fimH-1, entB, K2, irP-1 and Mdtk) were performed by PCR. The multidrug-resistant strains were detected in 16 (69.5%), that showed the presence of the most virulence genes. The multidrug-resistant isolates showed resistance against Ampicillin (96%), Amox-Clav (90%), Cephalothin (90%), Cefuroxime (90%), Ceftriaxone (85%), Aztreonam (87%), Cefepime (80%), Ceftazidime (80%), and Trim-Sulf (82%). Molecular diversity between K. pneumoniae isolates was determined using Rep-PCR markers technique. Thirty eight bands were resulted from the rep-PCR primers. Out of them, 31 bands were polymorphic with a polymorphism average of 81.6%. Total loci detected for each primer varied from 11 to 15 loci, and the loci size ranging from 200 to 2000 bp. These data may present novel epidemiological information regarding the clonal nature of K. pneumoniae separated from Taif governorate hospitals, Saudi Arabia.

Continuous Flow-Constructed Wetlands for the Treatment of Swine Waste Water

The microbiological quality of treated waste water is always a concern when waste water is disposed to the environment. However, when treated appropriately, such water can serve many purposes to the general population. Therefore, the treatment and removal of contaminants from swine waste water by continuous flow-constructed wetlands involves complex biological, physical, and chemical processes that may produce better quality water with reduced levels of contaminants. Swine waste contains E. coli populations and other bacterial contaminants originating from swine houses through constructed wetlands, but little is known about E. coli population in swine waste water. To assess the impacts of seasonal variations and the effect of the wetland layout/operations on water quality, E. coli isolates were compared for genetic diversity using repetitive extragenic palindromic polymerase chain reaction (REP-PCR). None of the isolates was confirmed as Shiga toxin producing E. coli O157:H7 (STEC); however, other pathotypes, such as enterotoxigenic E. coli (ETEC) were identified. Using a 90% similarity index from REP-PCR, 69 genotypes out of 421 E. coli isolates were found. Our data showed that the E. coli population was significantly (p = 0.036) higher in November than in March and August in most of the wetland cells. Furthermore, there was a significant (p = 0.001) reduction in E. coli populations from wetland influent to the final effluent. Therefore, the use of continuous flow-constructed wetlands may be a good treatment approach for reducing contaminants from different waste water sources.

Environmental Escherichia coli: ecology and public health implications-a review

Escherichia coli is classified as a rod-shaped, Gram-negative bacterium in the family Enterobacteriaceae. The bacterium mainly inhabits the lower intestinal tract of warm-blooded animals, including humans, and is often discharged into the environment through faeces or wastewater effluent. The presence of E. coli in environmental waters has long been considered as an indicator of recent faecal pollution. However, numerous recent studies have reported that some specific strains of E. coli can survive for long periods of time, and potentially reproduce, in extraintestinal environments. This indicates that E. coli can be integrated into indigenous microbial communities in the environment. This naturalization phenomenon calls into question the reliability of E. coli as a faecal indicator bacterium (FIB). Recently, many studies reported that E. coli populations in the environment are affected by ambient environmental conditions affecting their long-term survival. Large-scale studies of population genetics revealed the diversity and complexity of E. coli strains in various environments, which are affected by multiple environmental factors. This review examines the current knowledge on the ecology of E. coli strains in various environments with regard to its role as a FIB and as a naturalized member of indigenous microbial communities. Special emphasis is given on the growth of pathogenic E. coli in the environment, and the population genetics of environmental members of the genus Escherichia. The impact of environmental E. coli on water quality and public health is also discussed.

Change in the Structure of Escherichia coli Population and the Pattern of Virulence Genes along a Rural Aquatic Continuum

The aim of this study was to investigate the diversity of the Escherichia coli population, focusing on the occurrence of pathogenic E. coli, in surface water draining a rural catchment. Two sampling campaigns were carried out in similar hydrological conditions (wet period, low flow) along a river continuum, characterized by two opposite density gradients of animals (cattle and wild animals) and human populations. While the abundance of E. coli slightly increased along the river continuum, the abundance of both human and ruminant-associated Bacteroidales markers, as well as the number of E. coli multi-resistant to antibiotics, evidenced a fecal contamination originating from animals at upstream rural sites, and from humans at downstream urban sites. A strong spatial modification of the structure of the E. coli population was observed. At the upstream site close to a forest, a higher abundance of the B2 phylogroup and Escherichia clade strains were observed. At the pasture upstream site, a greater proportion of both E and B1 phylogroups was detected, therefore suggesting a fecal contamination of mainly bovine origin. Conversely, in downstream urban sites, A, D, and F phylogroups were more abundant. To assess the occurrence of intestinal pathogenic strains, virulence factors [afaD, stx1, stx2, eltB (LT), estA (ST), ipaH, bfpA, eae, aaiC and aatA] were screened among 651 E. coli isolates. Intestinal pathogenic strains STEC O174:H21 (stx2) and EHEC O26:H11 (eae, stx1) were isolated in water and sediments close to the pasture site. In contrast, in the downstream urban site aEPEC/EAEC and DAEC of human origin, as well as extra-intestinal pathogenic E. coli belonging to clonal group A of D phylogroup, were sampled. Even if the estimated input of STEC (Shiga toxin-producing E. coli) - released in water at the upstream pasture site - at the downstream site was low, we show that STEC could persist in sediment. These results show that, the run-off of small cattle farms contributed, as much as the wastewater effluent, in the dissemination of pathogenic E. coli in both water and sediments, even if the microbiological quality of the water was good or to average quality according to the French water index.

Engineering a natural Saccharomyces cerevisiae strain for ethanol production from inulin by consolidated bioprocessing

BACKGROUND

The yeast Saccharomyces cerevisiae is an important eukaryotic workhorse in traditional and modern biotechnology. At present, only a few S. cerevisiae strains have been extensively used as engineering hosts. Recently, an astonishing genotypic and phenotypic diversity of S. cerevisiae was disclosed in natural populations. We suppose that some natural strains can be recruited as superior host candidates in bioengineering. This study engineered a natural S. cerevisiae strain with advantages in inulin utilization to produce ethanol from inulin resources by consolidated bioprocess. Rational engineering strategies were employed, including secretive co-expression of heterologous exo- and endo-inulinases, repression of a protease, and switch between haploid and diploid strains.

RESULTS

Results from co-expressing endo- and exo-inulinase genes showed that the extracellular inulinase activity increased 20 to 30-fold in engineered S. cerevisiae strains. Repression of the protease PEP4 influenced cell physiology in late stationary phase. Comparison between haploid and diploid engineered strains indicated that diploid strains were superior to haploid strains in ethanol production albeit not in production and secretion of inulinases. Ethanol fermentation from both inulin and Jerusalem artichoke tuber powder was dramatically improved in most engineered strains. Ethanol yield achieved in the ultimate diploid strain JZD-InuMKCP was close to the theoretical maximum. Productivity achieved in the strain JZD-InuMKCP reached to 2.44 and 3.13 g/L/h in fermentation from 200 g/L inulin and 250 g/L raw Jerusalem artichoke tuber powder, respectively. To our knowledge, these are the highest productivities reported up to now in ethanol fermentation from inulin resources.

CONCLUSIONS

Although model S. cerevisiae strains are preferentially used as hosts in bioengineering, some natural strains do have specific excellent properties. This study successfully engineered a natural S. cerevisiae strain for efficient ethanol production from inulin resources by consolidated bioprocess, which indicated the feasibility of natural strains used as bioengineering hosts. This study also presented different properties in enzyme secretion and ethanol fermentation between haploid and diploid engineering strains. These findings provided guidelines for host selection in bioengineering.

Potential pathogens, antimicrobial patterns and genotypic diversity of Escherichia coli isolates in constructed wetlands treating swine wastewater

Escherichia coli populations originating from swine houses through constructed wetlands were analyzed for potential pathogens, antimicrobial susceptibility patterns, and genotypic diversity. Escherichia coli isolates (n = 493) were screened for the presence of the following virulence genes: stx1, stx2 and eae (Shiga toxin-producing E. coli [STEC]), heat-labile enterotoxin (LT) genes and heat stable toxin STa and STb (enterotoxigenic E. coli (ETEC), cytotoxin necrotizing factors 1 and 2 (cnf1 and cnf2 [necrotoxigenic E. coli- NTEC]), as well as O and H antigens, and the presence of the antibiotic resistance genes blaTEM, blaSHV, blaCMY-2, tet A, tet B, tet C, mph(A), aadA, StrA/B, sul1, sul2 and sul3. The commensal strains were further screened for 16 antimicrobials and characterized by BOX AIR-1 PCR for unique genotypes. The highest antibiotic resistance prevalence was for tetracycline, followed by erythromycin, ampicillin, streptomycin, sulfisoxazole and kanamycin. Our data showed that most of the isolates had high distribution of single or multidrug-resistant (MDR) genotypes. Therefore, the occurrence of MDR E. coli in the wetland is a matter of great concern due to possible transfer of resistance genes from nonpathogenic to pathogenic strains or vice versa in the environment.

Prevalence and Characterization of Shiga Toxin-Producing and Enteropathogenic Escherichia coli in Shellfish-Harvesting Areas and Their Watersheds

more strains formed a strong biofilm at 18 than at 30°C. Finally, more than 85% of analyzed strains were found to be sensitive to the 16 tested antibiotics. These data suggest the low risk of human infection by STEC if shellfish from these shellfish-harvesting areas were consumed.

Molecular characterization of microbial contaminants isolated from Umbilical Cord Blood Units for transplant

Disposal of Umbilical Cord Blood Units due to microbial contamination is a major problem in Cord Blood Banks worldwide as it reduces the number of units available for transplantation. Additionally, economic losses are generated as result of resources and infrastructure used to obtain such units. Umbilical Cord Blood Units that showed initial microbial contamination were subject to strains isolation, identification, and characterization by sequencing the 16S rRNA gene and Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR). Moreover, tests of antimicrobial resistance/sensitivity and phenotypic activities that may play an important role in microbial infection were performed. Microbial contamination was detected in 120 Umbilical Cord Blood Units (2.31%) in the period from 2003 to 2013. The most frequently isolated strains were Enterococcus faecium, followed by Staphylococcus epidermidis, Escherichia coli, Enterococcus faecalis, Staphylococcus haemoliticus, Klebsiella pneumoniae, Enterococcus durans, Lactobacillus helveticus, Enterococcus hiriae and Roseomonas genomospecies 5. The ERIC-PCR assays revealed a wide genetic diversity in some strains although belonging to the same genus and specie, indicating different sources of contamination. Broad-spectrum penicillins, third generation cephalosporins, aminoglycosides, and fluoroquinolones showed lower inhibitory activity on the tested strains. All strains were proteolytic, 67.69% were amylase-positive, 27.6% hemolysis-positive, and 34.71% nuclease-positive. The most common sources of contamination were: vaginal flora, digestive tract, and skin flora, highlighting the need for staff training in good manufacturing practices in collection SCU since all contaminants identified are part of the microbial flora of the donors. Implications and consequences in the therapeutic use of Umbilical Cord Blood Units for transplantation contaminated by multiresistant bacteria in immunocompromised patients are discussed.

Investigation on the temporal variation and source tracking of faecal bacteria in a forest dominated watershed (Comox Lake), British Columbia, Canada

AIMS

The aims of this study were to investigate the temporal variation in Escherichia coli density and its sources at the drinking water intake of Comox Lake for a period of 3 years (2011-2013).

METHODS AND RESULTS

Density of E. coli was assessed by standard membrane filtration method. Source tracking of E. coli were done by using BOX-A1R-based rep-PCR DNA fingerprinting method. Over the years, the mean E. coli density ranged from nondetectable to 9·8 CFU 100 ml(-1) . The density of E. coli in each of the years did not show any significant difference (P > 0·05); however, a comparatively higher density was observed during the fall. Wildlife was (64·28%, 153/238) identified as the major contributing source of E. coli, followed by human (18·06%, 43/238) and unknown sources (17·64%, 42/238). Although the sources were varied by year and season, over all, the predominant contributing sources were black bear, human, unknown, elk, horse and gull.

CONCLUSIONS

The findings of this investigation identified the multiple animal sources contributing faecal bacteria into the drinking water intake of Comox Lake and their varying temporal occurrence.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study can reliably inform the authorities about the most vulnerable period (season) of faecal bacterial loading and their potential sources in the lake for improving risk assessment and pollution mitigation.