Escherichia coli in the Environment: Implications for Water Quality and Human Health

Stress in the City: Disentangling multi-stressor effects on an urbanized coral in a changing ocean

Reducing the negative impacts of global change on organismal physiology is a critical area of scientific investigation in the Anthropocene. Marine coastal ecosystems that exist downstream from urban centers are often subjected to excess nutrients, pathogens, and chemicals via runoff, which can harm organismal function, and may interact with climate change stress. To simultaneously investigate the individual and combined effects of locally-mediated (nutrient, bacterial) and globally-mediated (temperature) stressors on coral physiology, we conducted a multi-factor experiment utilizing the temperate, urban coral Astrangia poculata. Corals were incubated for 12 days with two levels of field-relevant nitrate concentrations at ambient (20 °C) and elevated (29 °C) temperatures, under fed or starved conditions. After 12 days, corals were challenged with an acute 4-h exposure to Escherichia coli, a known urban pathogen for A. poculata. Results show that the physiological impacts of E. coli exposure, nitrate, elevated temperatures, and starvation were interactive and nuanced. Elevated temperatures had the largest single factor impact, resulting in metabolic lethargy regardless of pathogen exposure, nitrate enrichment, or food level. However, corals under the combination of E. coli exposure, elevated nitrate, starvation, and high temperatures demonstrated metabolic hyperactivity, indicating energetic investment by hyper stressed corals in response to the pathogen. With this work, we move beyond pairwise interactions to demonstrate that the interactive effects of combined stressors may offer the key (and more realistic) answer to the fundamental question "How resilient will marine organisms be to locally-mediated stressors in an era of global change?"

Microbial risk assessment of fecal indicator bacteria in a highly polluted river: Santiago-Guadalajara River Basin

The Santiago-Guadalajara River, located in western Mexico, is one of the most polluted rivers in the country, with widespread fecal contamination that presents a potential risk to public health, food safety, and biodiversity. This study investigated the spatial and seasonal behavior of fecal indicator bacteria (FIB) in the Santiago-Guadalajara River Basin (SGRB) using the most probable number (MPN) microbiological quantification technique and measuring the tributary flow rates in the main stem of the river and tributaries. Twenty-five sampling sites were monitored from July 2021 to April 2022. The mean of the microbial counts (MPN/100 mL) at the basin was as follows: total coliforms 2.5 × 107, fecal coliforms 2.2 × 107, and E. coli 2.1 × 107. These FIB values position the Santiago-Guadalajara River as one of the most polluted rivers globally since it significantly exceeds the regulatory limits at the monitored sites, indicating insufficient sanitation infrastructure throughout the basin. A high level of correlation was found between FIB concentrations and monitored stream tributary flows, which allowed modeling the behavior of the FIB with respect to the flow regime throughout the basin. Quantitative microbial risk assessment revealed specific stations with elevated infection risks from Escherichia coli exposure. This field-based study provides valuable insights into the relationship between the variables that influence FIB concentrations in a highly polluted river and the potential risk to the exposed population.

Overview of Patagonian Red Octopus (Enteroctopus megalocyathus) Fisheries in Chilean Regions and Their Food Safety Aspects

Artisanal fisheries in southern Chile rely heavily on the Patagonian red octopus (Enteroctopus megalocyathus) as a valuable resource, contributing significantly to local economies. This octopus species accounts for 25-40% of Chilean octopus landings. It is a merobenthic species, characterized by a semelparous life cycle and a long brooding period, and it is distributed along the Pacific and Atlantic coasts of the southern tip of South America, inhabiting holes and crevices in rocky substrates. However, this fishery faces critical challenges to both its ecological sustainability and the food safety of octopus products. The primary fishing method, using hooks, poses a risk to reproductive capacity as it can capture brooding females. Food safety concerns arise from microbial contamination during pre- and post-harvest handling, bioaccumulation of toxins from algal blooms, and the presence of heavy metals in the marine environment. While evisceration effectively reduces the risk of consuming toxins and heavy metals, inadequate hygiene practices and insufficient ice usage throughout the production chain represent significant food safety risks. Chilean fishing Law No. 18892/1989 defines artisanal fishing and establishes territorial use rights in fisheries (TURFs) to promote sustainable extraction of benthic resources. Integrating training programs on post-harvest handling, hygiene practices, and food safety measures into the TURFs framework, along with targeted investments in infrastructure and technical assistance, is crucial to ensure the long-term sustainability of the E. megalocyathus fishery, protect consumer health, and maintain the economic viability and environmental sustainability of this vital resource for local communities.

Consideration of a Liquid Mutation-Accumulation Experiment to Measure Mutation Rates by Successive Serial Dilution

The mutation-accumulation (MA) experiment is a fixture of evolutionary biology, though its execution is laborious. MA experiments typically take between months and years to acquire sufficient mutations to measure DNA mutation rates and mutation spectra. MA experiments for many organisms rely on colony formation on agar plates and repetitive streaking, an environment which at first glance appears somewhat contrived, a poor imitation of actual environmental living conditions. We propose that a fully liquid-phase MA experiment may at times more accurately reflect the environment of an organism. We note also that whereas automation of streaking plates is a daunting prospect, automation of liquid handling, and serial dilution is already commonplace. In principle, this type of MA experiment can be automated so as to reduce the human capital requirements of measuring mutation rates. We demonstrate that a liquid MA recapitulates the mutation rate estimated for MMR-E. coli in liquid LB culture vs. plate Lysogeny Broth culture. We detect a modified mutation spectrum with a transition skew of 4.7:1 of A:T→G:C vs. G:C→A:T mutations, highlighting the potential role of tautomerization as a mechanism of DNA mutation.

Associations between fecal contamination of the household environment and enteric pathogen detection in children living in Maputo, Mozambique

Environmental exposure to enteric pathogens is generally assessed using fecal indicators but relationships between markers of fecal contamination and actual exposure to enteric pathogens remain poorly characterized. We investigated whether Escherichia coli and two human fecal markers (HF183 and Mnif) in urban Mozambican household soil and drinking water were associated with detection in child stool of eight bacteria, three viruses, and three protozoa measured by multiplex reverse-transcription PCR and soil transmitted helminths assessed by microscopy. We used mixed-effects logistic regression with marginal standardization to obtain a pooled estimate of the overall indicator-pathogen relationship while simultaneously estimating pathogen-specific associations that accounted for assessing multiple pathogens per sample. At least one pathogen was detected in 88% (169/192) of child stools. Increasing drinking water E. coli gene concentration was associated with higher Ascaris prevalence, while human HF183 in drinking water was weakly associated with lower prevalence of the most common pathogens but was infrequently detected. No fecal marker in soil was clearly associated with any pathogen. We did not find evidence to support human markers as reliable indicators of enteric pathogen carriage in a high-prevalence domestic setting and recommend targeting enteric pathogens directly.

An investigation of microbial groundwater contamination seasonality and extreme weather event interruptions using "big data", time-series analyses, and unsupervised machine learning

Temporal studies of groundwater potability have historically focused on E. coli detection rates, with non-E. coli coliforms (NEC) and microbial concentrations remaining understudied by comparison. Additionally, "big data" (i.e., large, diverse datasets that grow over time) have yet to be employed for assessing the effects of high return-period extreme weather events on groundwater quality. The current investigation employed ≈1.1 million Ontarian private well samples collected between 2010 and 2021, seeking to address these knowledge gaps via applying time-series decomposition, interrupted time-series analysis (ITSA), and unsupervised machine learning to five microbial contamination parameters: E. coli and NEC concentrations (CFU/100 mL) and detection rates (%), and the calculated NEC:E. coli ratio. Time-series decompositions revealed E. coli concentrations and the NEC:E. coli ratio as complementary metrics, with concurrent interpretation of their seasonal signals indicating that localized contamination mechanisms dominate during winter months. ITSA findings highlighted the importance of hydrogeological time lags: for example, a significant E. coli detection rate increase (2.4% vs 1.8%, p = 0.02) was identified 12 weeks after the May 2017 flood event. Unsupervised machine learning spatially classified annual contamination cycles across Ontarian subregions (n = 27), with the highest inter-cluster variability identified among E. coli detection rates and the lowest among NEC detection rates and the NEC:E. coli ratio. Given the spatiotemporal consistency identified for NEC and the NEC:E. coli ratio, associated interpretations and recommendations are likely transferable across large, heterogeneous regions. The presented study may serve as a methodological blueprint for future temporal investigations employing "big" groundwater quality data.

Spectroscopic characterization of bacterial colonies through UV hyperspectral imaging techniques

Introduction

Plate culturing and visual inspection are the gold standard methods for bacterial identification. Despite the growing attention on molecular biology techniques, colony identification using agar plates remains manual, interpretative, and heavily reliant on human experience, making it prone to errors. Advanced imaging techniques, like hyperspectral imaging, offer potential alternatives. However, the use of hyperspectral imaging in the VIS-NIR region has been hindered by sensitivity to various components and culture medium changes, leading to inaccurate results. The application of hyperspectral imaging in the ultraviolet (UV) region has not been explored, despite the presence of specific absorption and emission peaks in bacterial components.

Methods

To address this gap, we developed a predictive model for bacterial colony detection and identification using UV hyperspectral imaging. The model utilizes hyperspectral images acquired in the UV wavelength range of 225-400 nm, processed with principal component analysis (PCA) and discriminant analysis (DA). The measurement setup includes a hyperspectral imager, a PC for automated data analysis, and a conveyor belt system to transport agar plates for automated analysis. Four bacterial species (Escherichia coli, Staphylococcus, Pseudomonas, and Shewanella) were cultured on two different media, Luria Bertani and Tryptic Soy, to train and validate the model.

Results

The PCA-DA-based model demonstrated high accuracy (90%) in differentiating bacterial species based on the first three principal components, highlighting the potential of UV hyperspectral imaging for bacterial identification.

Discussion

This study shows that UV hyperspectral imaging, coupled with advanced data analysis techniques, offers a robust and automated alternative to traditional methods for bacterial identification. The model's high accuracy emphasizes the untapped potential of UV hyperspectral imaging in microbiological analysis, reducing human error and improving reliability in bacterial species differentiation.

Detection and collection of shiga toxin-producing Escherichia coli using foam concentration without membrane filtration

Information on Shiga toxin-producing Escherichia coli (STEC) in river water is scarce, and it is essential to understand its actual status in river water. This study investigated a method for the highly efficient recovery of STEC from river water in its active state by combining a coagulation and foam concentration and a selective medium. The method was applied to three rivers, and STEC-positive Escherichia coli (E. coli) were obtained from all rivers. Ten E. coli harboring one of the pathogenic genes (stx2, eae) were detected in the Oyodo River's upstream and midstream and the Kaeda River's midstream. Furthermore, antimicrobial agent susceptibility testing was performed on these ten strains using ten antimicrobial agents. Nine strains showed intermediate resistance to at least one antibiotic, and one was multidrug-resistant. This study's coagulation and foam concentration and selective medium detection methods can efficiently collect STEC in river water and recover it in an active state without conventional membrane filtration. Isolating and cultivating this STEC strain will provide crucial information for antimicrobial agent susceptibility testing, target gene testing, and whole-genome analysis.

Somatic coliphages as bioindicators of contamination in Lake Guamuez, Colombia

Lake Guamuez is the second largest lake in Colombia and economically supports hundreds of families in the area. The main activities carried out in the region have focused on tourism, agriculture, livestock, and rainbow trout production; however, these activities have been associated with contamination of the lake. This research aimed to evaluate the water quality of Lake Guamuez using somatic coliphages (SCs) as bioindicators. For this purpose, periodic sampling was carried out for 6 months at nine strategic points of the lake. For the detection of SCs, the method described in 9211 D of the Standard Methods for the Examination of Water and Wastewater was used. The genomic variability and presence of virulence genes in the isolated SCs were determined. Water contamination in the lake is evident, and the SCs titer is greater in areas with a high flow of anthropogenic activities. An important degree of genetic diversity and a high prevalence of virulence genes could be observed among the SCs analyzed. The results when compared with guidelines and water quality standards from various countries showed concentrations of SCs higher than those allowed. The high prevalence of gastrointestinal diseases in the region suggests a link to water contamination.

Exploring the effects of cellulose sources on silver reduction and the bacterial removal of nanocellulose-based hydrogel beads

With water access challenged, there is a need to develop efficient and sustainable alternatives for water purification. Here, cellulose nanofibrils (CNFs) isolated from three source materials (softwood, soybean hulls and oat straw) were compared for the generation of hydrogels beads, and compared as support and reducing agent for silver nanoparticles formation. The silver-functionalized hydrogel beads (Ag-CNFs) were characterized, and the surface energy and specific surface area were evaluated. Antimicrobial testing was conducted to assess the efficacy of the Ag-CNFs against E. coli. The results showed that the Ag-CNFs had a higher specific surface area and lower surface energy compared with unmodified CNFs. Softwood-based Ag-CNFs exhibited the highest silver content and specific surface area, while the soybean hull based showed the highest hydrophobic character. The silver-functionalized soybean hull beads (Ag-sbCNF) showed the highest efficacy in reducing the growth of bacteria. Overall, this study highlights the potential of silver-functionalized CNFs hydrogel beads as a promising environmentally friendly and sustainable material for water filtration and disinfection. The findings also suggest that lower surface energy of the Ag-CNFs play an important role in their antimicrobial effect on tested water by enabling shorter retention, providing useful insights into the design of future water filtration materials.

Associations between weather extremes and faecal contamination along pathogen transmission pathways in rural Bangladeshi households: a prospective observational study

BACKGROUND

Weather extremes are predicted to influence pathogen exposure but their effects on specific faecal-oral transmission pathways are not well investigated. We evaluated associations between extreme rain and temperature during different antecedent periods (0-14 days) and Escherichia coli along eight faecal-oral pathways in rural Bangladeshi households.

METHODS

We used data from the WASH Benefits Bangladesh cluster-randomised controlled trial (NCT01590095). E coli was enumerated in hand rinses from children younger than 5 years and their mothers, food, stored drinking water, tubewells, captured flies, ponds, and courtyard soil using IDEXX Quanti-Tray/2000 in nine rounds over 3·5 years and spatiotemporally matched to daily weather data. We used generalised linear models with robust standard errors to estimate E coli count ratios (ECRs) associated with extreme rain and temperature, defined as greater than the 90th percentile of daily values during the study period.

FINDINGS

A total of 26 659 samples were collected during the study period. Controlling for temperature, extreme rain on the sampling day was associated with increased E coli in food (ECR=3·13 [95% CI 1·63-5·99], p=0·0010), stored drinking water (ECR=1·98 [1·36-2·88], p=0·0004), and ponds (ECR=3·46 [2·34-5·11], p<0·0001), and reduced E coli in soil (ECR=0·36 [0·24-0·53], p<0·0001). Extreme rain the day before sampling was associated with reduced E coli in tubewells (ECR=0·10 [0·02-0·62], p=0·014). Associations were similar for rainfall 1-7 days before sampling and slightly attenuated for rainfall 14 days before sampling. Controlling for rainfall, extreme temperature on the sampling day was associated with increased E coli in stored drinking water (ECR=1·49 [1·05-2·12], p=0·025) and food (ECR=3·01 [1·51-6·01], p=0·0020). Associations with temperature were similar for all antecedent periods and particularly pronounced for food. Neither rainfall nor temperature were consistently associated with E coli on hands and flies.

INTERPRETATION

In rural Bangladesh, measures to control enteric infections following weather extremes should focus on water treatment and safe storage to reduce contamination of drinking water and food stored at home and on reducing exposure to surface waters.

FUNDING

Bill & Melinda Gates Foundation, National Institutes of Health, World Bank.

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.

Comparison of liquid and filter sampling techniques for recovery of Bacillus spores and Escherichia coli from environmental water

Historically, detecting water contamination has involved collecting and directly analyzing liquid samples, but recent advances in filter sampling methods offer numerous potential advantages. Emerging technologies, including environmental DNA (eDNA) samplers, could be used for remote microbial contamination sampling, but work is needed to determine if target microorganisms can be recovered from filters at comparable levels to traditional sampling methods. In this study, Escherichia coli and a surrogate for Bacillus anthracis spores were sampled from synthetic stormwater and quantified using both direct liquid and filter methods, and dwell time tests compared microorganism persistence in water and on filters. At nearly all tested timepoints, the recoveries of spores from membrane filters were within 0.5 log10 colony forming units per sample (CFU/sample) compared to the liquid-only samples, suggesting that the use of filter sampling is a feasible alternative to liquid-based sampling, and samples were held for up to 4 weeks without significant sample degradation. Recoveries for E. coli remained relatively consistent for ∼3 days in phosphate buffered saline (PBS), in synthetic stormwater, and on membrane filters, but decreases in recoveries were observed for samples held for >3 days. These results indicate that emerging water sampling technologies, which reduce logistical burdens and offer potential cost savings, can be leveraged to characterize biological contamination in water matrices with multiple types of microbiological agents.

Phenotypic and genomic comparison of three human outbreak and one cattle-associated Shiga toxin-producing Escherichia coli O157:H7

Escherichia coli O157:H7-adulterated food products are associated with disease outbreaks in humans. Although cattle feces are a source for E. coli O157:H7 contamination, it is unclear if human-associated outbreak isolates differentially colonize and shed in the feces of cattle from that of non-outbreak isolates. It is also unclear if phenotypes, such as biofilm formation, cell attachment, or toxin production, differentiate environmental E. coli O157:H7 isolates from those associated with human illness. The objective of this study was to compare the genotypes and phenotypes of a diverse set of E. coli O157:H7 isolates, with the intent of identifying differences that could inform cattle colonization and fecal shedding, along with virulence potential in humans. Isolates differed in attachment phenotypes on human Caco-2 cells and bovine-derived recto-anal junction squamous epithelial cells, with curli having a strong impact on attachment to the human-derived cell line. The prototypical E. coli O157 isolate EDL933 had the greatest expression of the adhesin gene iha, yet it had decreased expression of the virulence genes stx2, eae, and ehxA compared the lineage I/II isolates RM6067W and/or FRIK1989. Strong or weak biofilm production was not associated with significant differences in cattle colonization or shedding, suggesting biofilms may not play a major role in cattle colonization. No significant differences in cattle colonization and fecal shedding were detected, despite genomic and in vitro phenotypic differences. The outbreak isolate associated with the greatest incidence of hemolytic uremic syndrome, RM6067W, induced the greatest Vero cell cytotoxicity and had the greatest stx2 gene expression.

IMPORTANCE

Foodborne illness has major impacts on global health and imposes financial hardships on food industries. Escherichia coli serotype O157:H7 is associated with foodborne illness. Cattle feces are a source of E. coli O157:H7, and routine surveillance has led to an abundance of E. coli O157:H7 genomic data. The relationship between E. coli O157:H7 genome and phenotype is not clearly discerned for cattle colonization/shedding and improved understanding could lead to additional strategies to limit E. coli O157:H7 in the food chain. The goal of the research was to evaluate genomic and phenotypic attributes of E. coli O157:H7 associated with cattle colonization and shedding, environmental persistence, and human illness. Our results indicate variations in biofilm formation and in vitro cellular adherence was not associated with differences in cattle colonization or shedding. Overall, processes involved in cattle colonization and various phenotypes in relation to genotype are complex and remain not well understood.

Antibiotic resistance of E. coli isolates from different water sources in Mbarara, Uganda

Escherichia coli is widely used as an indicator of recent faecal pollution of water. Most E. coli strains are commensals; however, isolates in water samples have been shown to carry antibiotic resistance determinants. In total, 47 E. coli were isolated from selected drinking water sources in Mbarara, Uganda. The isolates were examined for their susceptibility to seven antibiotics and the presence of nine antibiotic-resistance genes (mostly β-lactamase genes) and class 1 integrons. Isolates showed a high resistance to ampicillin of 55.5% and a high sensitivity to azithromycin and gentamicin at 98 and 96%, respectively. PCR analysis showed the presence of extended-spectrum β-lactamase genes blaCTX-M-32 and blaCMY-2 in 64 and 36% of the isolates. The carbapenemase genes blaOXA-48, blaVIM-2, blaNDM-1, and blaKPC-3 were either not detected or only in a very small number of the isolates, whereas class 1 integrons were present in 68% of the isolates. This study proves that antimicrobial resistance exists in E. coli in water used for drinking purposes in Mbarara city. There is a need for public health actors to improve the surveillance of microbiological quality of drinking water to minimize health risks.

Pepper mild mottle virus as an effective tool in microbial source tracking for deficient domestic on-site water treatment systems

Pollution from domestic on-site wastewater treatment systems (OWTS) is a significant contaminant pressure in many rural catchments. However, due to their design, and dispersed proliferation, it is difficult to assess their impact. Water testing methodologies employ bacterial culturing methods and chemical analysis which may lose resolution and/or specificity being confounded by diffuse agricultural sources within a rural environment. In this study, we successfully assessed the applicability of Pepper Mild Mottle Virus (PMMoV) as a human faecal source tracker for deficient on-site wastewater treatment systems. The transport of PMMoV was first studied in the effluent of a 30 cm deep soil column which was dosed for 510 days with primary influent from a conventional septic system. The removal of PMMoV through the 30 cm deep soil column was quantified with a 5-day seeding trial employing primary influent mixed with PMMoV sourced from Tabasco pepper product ®. The trial was then carried out at field scale with the seeding solution dosed into an operational percolation trench receiving septic tank effluent which had been instrumented for porewater sampling. Samples were taken at depths of 10 cm, 30 cm, and 50 cm across the length of the trench at distances of 1 m, 7.5 m, and 17.5 m from the inlet of the trench. PMMoV was detected on all days of the trial, with a peak concentration of 1 × 106 found at the rear of the trench on day 2 of the seeding trial. Finally, to assess the effectiveness of PPMoV as a microbial source tracking tool from a water receptor perspective, three rural catchments with high densities of OWTSs were sampled and analysed for hourly variations in biological parameters which included total coliforms, Escherichia coli, PMMoV, and chemical parameters total organic carbon, total nitrogen, and total carbon. PMMoV was detected in all river samples over a 24-hour period, thereby indicating its suitability as a tracer of human wastewater effluent in such environments with multiple diffuse sources.

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.

Implementation of the WHO Tricycle protocol for surveillance of extended-spectrum β-lactamase producing Escherichia coli in humans, chickens, and the environment in Madagascar: a prospective genomic epidemiology study

BACKGROUND

Antimicrobial resistance (AMR) is a major public health threat, affecting not only people but also animals and the environment. The One Health dimension of AMR is well known; however, data are lacking on the circulation of resistance-conferring genes, particularly in low-income countries. In 2017, WHO proposed a protocol called Tricycle, focusing on extended-spectrum β-lactamase (ESBL)-Escherichia coli surveillance in the three sectors (humans, animals, and the environment). We implemented Tricycle in Madagascar to assess ESBL-E coli prevalence and describe intrasector and intersector circulation of ESBL-E coli and plasmids.

METHODS

In this prospective study, we collected blood culture data from hospitalised patients with a suspected bloodstream infection processed from May 1, 2018, to April 30, 2019, and rectal swabs from healthy pregnant women from July 30, 2018, to April 27, 2019, both from three hospitals in Antananarivo, Madagascar; and caeca from farm chickens and surface waters from the Ikopa river, wastewater, and slaughterhouse effluents in the Antananarivo area, Madagascar, from April 9, 2018, to April 30, 2019. All samples were tested for ESBL-E coli. The genomes of all isolates were sequenced using a short-read method on NextSeq 500 and NovaSeq 6000 platforms (Illumina, San Diego, CA, USA) and those carrying plasmid replicons using an additional long-read method on a MinION platform (Oxford Nanopore Technologies, Oxford, UK). We characterised genomes of isolated strains (sequence type, resistance and virulence gene content, and plasmid replicons). We then compared isolates using the variant calling method (single-nucleotide polymorphism).

FINDINGS

Data from 1056 blood cultures were collected and 289 pregnant women, 246 chickens, and 28 surface waters were sampled. Of the blood cultures, 18 contained E coli, of which seven (39%) were ESBL. ESBL-E coli was present in samples from 86 (30%) of 289 pregnant women, 140 (57%) of 246 chickens, and 28 (100%) of 28 surface water samples. The wet season (November to April) was associated with higher rates of carriage in humans (odds ratio 3·08 [1·81-5·27]) and chickens (2·79 [1·65-4·81]). Sequencing of 277 non-duplicated isolates (82 from pregnant women, 118 from chickens, and 77 from environmental samples) showed high genetic diversity (90 sequence types identified) with sector-specific genomic features. Single nucleotide polymorphism (SNP) analysis revealed that 169 (61%) of 277 isolates grouped into 44 clusters (two or more isolates) of closely related isolates (<40 SNPs), of which 24 clusters contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were all blaCTX-M variants (215 [78%] of 277 being blaCTX-M-15) and were located on a plasmid in 113 (41%) of 277 isolates. These ESBL-carrying plasmids were mainly IncF (63 [55%] of 114; one strain carried two plasmids) and IncY (42 [37%] of 114). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) pMLST subtypes, and the IncY plasmids, which were all highly conserved, were observed in isolates of differing genetic backgrounds from all sectors and were transferable in vitro by conjugation.

INTERPRETATION

Despite sector-specific population structures, both ESBL-E coli strains and plasmids are circulating among humans, chickens, and the environment in Antananarivo, Madagascar. The Tricycle protocol can be implemented in a low-income country and represents a powerful tool for investigating dissemination of AMR from a One Health perspective.

FUNDING

Fondation Mérieux and INSERM, Université Paris Cité.

Comparison of methods proposed for monitoring cefotaxime-resistant Escherichia coli in the water environment

Escherichia coli is a promising subject for globally coordinated surveillance of antimicrobial resistance (AMR) in water environments due to its clinical relevance and widespread use as an indicator of fecal contamination. Cefotaxime-resistant E. coli was recently evaluated favorably for this purpose by the World Health Organization TriCycle Protocol, which specifies tryptone bile x-glucuronide (TBX) medium and incubation at 35°C. We assessed comparability with the U.S. Environmental Protection Agency-approved method for E. coli quantification, which uses membrane-thermotolerant E. coli (mTEC) agar and incubation at 44.5°C, in terms of recovery of E. coli and cefotaxime-resistant E. coli from wastewater influent and surface waters. Total E. coli concentrations in wastewater influent were 106-108 CFU/100 mL, while cefotaxime-resistant E. coli were ~100-fold lower. Total E. coli in surface waters were ~102 CFU/100 mL, and cefotaxime-resistant isolates were near the limit of detection (0.4 CFU/100 mL). Total and putative cefotaxime-resistant E. coli concentrations did not differ significantly between media or by incubation method; however, colonies isolated on mTEC were more frequently confirmed to species (97.1%) compared to those from TBX (92.5%). Incubation in a water bath at 44.5°C significantly decreased non-specific background growth and improved confirmation frequency on both media (97.4%) compared to incubation at 35°C (92.3%). This study helps to advance globally coordinated AMR in water environments and suggests that the TriCycle Protocol is adaptable to other standard methods that may be required in different locales, while also offering a means to improve specificity by decreasing the frequency of false-positive identification of cefotaxime-resistant E. coli by modifying incubation conditions.IMPORTANCEAs antibiotic-resistant bacteria in water environments are increasingly recognized as contributors to the global antibiotic resistance crisis, the need for a monitoring subject that captures antibiotic resistance trends on a global scale increases. The World Health Organization TriCycle Protocol proposes the use of cefotaxime-resistant Escherichia coli isolated on tryptone bile x-glucuronide agar. The U.S. Environmental Protection Agency (USEPA) criteria for safe recreational waters also use E. coli as an indicator but specify the use of mTEC agar at a higher incubation temperature (44.5°C vs 35°C). We assessed the comparability of these methods for isolating total and cefotaxime-resistant E. coli, finding overall good agreement and performance, but significantly higher specificity toward E. coli selection with the use of the USEPA incubation protocol and mTEC agar. This study is the first to directly compare these methods and provides evidence that the methods may be used interchangeably for global surveillance of antibiotic resistance in the environment.

Two synonymous single-nucleotide polymorphisms promoting fluoroquinolone resistance of Escherichia coli in the environment

Single-nucleotide polymorphism (SNP) is one of the core mechanisms that respond to antibiotic resistance of Escherichia coli (E. coli), which is a major issue in environmental pollution. A specific type of SNPs, synonymous SNPs, have been generally considered as the "silent" SNPs since they do not change the encoded amino acid. However, the impact of synonymous SNPs on mRNA splicing, nucleo-cytoplasmic export, stability, and translation was gradually discovered in the last decades. Figuring out the mechanism of synonymous SNPs in regulating antibiotic resistance is critical to improve antimicrobial therapy strategies in clinics and biological treatment strategies of antibiotic-resistant E. coli-polluted materials. With our newly designed antibiotic resistant SNPs prediction algorithm, Multilocus Sequence Type based Identification for Phenotype-single nucleotide polymorphism Analysis (MIPHA), and in vivo validation, we identified 2 important synonymous SNPs 522 G>A and 972 C>T, located at hisD gene, which was previously predicted as a fluoroquinolone resistance-related gene without a detailed mechanism in the E. coli samples with environmental backgrounds. We first discovered that hisD causes gyrA mutation via the upregulation of sbmC and its downstream gene umuD. Moreover, those 2 synonymous SNPs of hisD cause its own translational slowdown and further reduce the expression levels of sbmC and its downstream gene umuD, making the fluoroquinolone resistance determining region of gyrA remains unmutated, ultimately causing the bacteria to lose their ability to resist drugs. This study provided valuable insight into the role of synonymous SNPs in mediating antibiotic resistance of bacteria and a new perspective for the treatment of environmental pollution caused by drug-resistant bacteria.

Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes

Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.

Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment

Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations.

IMPORTANCE

Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.

Investigating Escherichia coli habitat transition from sediments to water in tropical urban lakes

Background

Escherichia coli is a commonly used faecal indicator bacterium to assess the level of faecal contamination in aquatic habitats. However, extensive studies have reported that sediment acts as a natural reservoir of E. coli in the extraintestinal environment. E. coli can be released from the sediment, and this may lead to overestimating the level of faecal contamination during water quality surveillance. Thus, we aimed to investigate the effects of E. coli habitat transition from sediment to water on its abundance in the water column.

Methods

This study enumerated the abundance of E. coli in the water and sediment at five urban lakes in the Kuala Lumpur-Petaling Jaya area, state of Selangor, Malaysia. We developed a novel method for measuring habitat transition rate of sediment E. coli to the water column, and evaluated the effects of habitat transition on E. coli abundance in the water column after accounting for its decay in the water column.

Results

The abundance of E. coli in the sediment ranged from below detection to 12,000 cfu g-1, and was about one order higher than in the water column (1 to 2,300 cfu mL-1). The habitat transition rates ranged from 0.03 to 0.41 h-1. In contrast, the E. coli decay rates ranged from 0.02 to 0.16 h-1. In most cases (>80%), the habitat transition rates were higher than the decay rates in our study.

Discussion

Our study provided a possible explanation for the persistence of E. coli in tropical lakes. To the best of our knowledge, this is the first quantitative study on habitat transition of E. coli from sediments to water column.

Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water

Although enteric bacteria normally reside within the animal intestine, the ability to persist extraintestinally is an essential part of their overall lifestyle, and it might contribute to transmission between hosts. Despite this potential importance, few genetic determinants of extraintestinal growth and survival have been identified, even for the best-studied model, Escherichia coli. In this work, we thus used a genome-wide library of barcoded transposon insertions to systematically identify functional clusters of genes that are crucial for E. coli fitness in lake water. Our results revealed that inactivation of pathways involved in maintaining outer membrane integrity, nucleotide biosynthesis, and chemotaxis negatively affected E. coli growth or survival in this extraintestinal environment. In contrast, inactivation of another group of genes apparently benefited E. coli growth or persistence in filtered lake water, resulting in higher abundance of these mutants. This group included rpoS, which encodes the general stress response sigma factor, as well as genes encoding several other global transcriptional regulators and RNA chaperones, along with several poorly annotated genes. Based on this co-enrichment, we identified these gene products as novel positive regulators of RpoS activity. We further observed that, despite their enhanced growth, E. coli mutants with inactive RpoS had reduced viability in lake water, and they were not enriched in the presence of the autochthonous microbiota. This highlights the duality of the general stress response pathway for E. coli growth outside the host.

Surveillance of Escherichia coli in different types of chicken and duck hatcheries: one health outlook

Escherichia coli is an important zoonotic bacterium that significantly impacts one health concept. E. coli is normally detected in the gut of warm-blooded animals, but some serotypes can cause diseases in humans and animals. Moreover, it can continue for a long time in different environments, replicate in water, and survive outside different hosts. In this study, 171 samples collected from 10 different types of poultry hatcheries (automatic, semiautomatic, and manual "traditional" types) were examined for the prevalence of E. coli. PCR was applied to verify the E. coli isolates via 16S rRNA gene-specific primers. From the gathered samples, 62 E. coli isolates were recovered (36.3%). The highest prevalence was met with the manual "traditional" hatcheries (57.1%) with no significance difference (P = 0.243) in the 3 types of hatcheries. The incidence of E. coli varied significantly in different tested avian types and breeds. The prevalence was 35.7% in duck hatcheries and 37% in chicken hatcheries, with significant differences between breeds of both species (P = 0.024 and 0.001, respectively). The identification of zoonotic E. coli serotypes in this study is concerning, highlighting the need for collaborative efforts across various sectors, including social, environmental, and governance, to promote the adoption of the one health principle in the chicken business. Periodical surveillance, biosecurity measures at the hatcheries and farm levels, and boosting the immunity of birds were recommended to limit the risk of E. coli spread from avian sources to humans.

Carbohydrate-protein interaction-based detection of pathogenic bacteria using a biodegradable self-powered biosensor

Battery-free and biodegradable sensors can detect biological elements in remote areas. The triboelectric nanogenerator (TENG) can potentially eliminate the need for a battery by simply converting the abundant vibrations from nature or human motion into electricity. A biodegradable sensor system integrated with TENG to detect commonly found disease-causing bacteria (E. coli) in the environment is showcased herein. In this system, D-mannose functionalized 3D printed polylactic acid (PLA) with the brush-painted silver electrode was used to detect E. coli by a simple carbohydrate-protein interaction mechanism. The adsorption capacity of D-mannose is generally altered by varying the concentration of E. coli resulting in changes in resistance. Thus, the presented biosensor can detect bacterial concentrations by monitoring the output current. The PLA TENG generates an output of 70 V, 800 nA, and 22 nC, respectively. In addition, tap water and unpasteurized milk samples are tested for detecting bacteria, and the output is measured at 6 μA and 5 μA, respectively. Further, the biosensor was tested for biodegradability in soil compost by maintaining constant temperature and humidity. This study not only proposes an efficient and fast method for screening E. coli but also gives important insights into the ability to degrade and long-term reliability of TENG-based sensor platforms.

Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings

IMPORTANCE

The importance of clean water cannot be overstated. It is a vital resource for maintaining health and well-being. Unfortunately, water sources contaminated with fecal discharges from animal and human origin due to a lack of wastewater management pose a significant risk to communities, as they can become a means of transmission of pathogenic bacteria like enterotoxigenic E. coli (ETEC). ETEC is frequently found in polluted water in countries with a high prevalence of diarrheal diseases, such as Bolivia. This study provides novel insights into the circulation of ETEC between diarrheal cases and polluted water sources in areas with high rates of diarrheal disease. These findings highlight the Choqueyapu River as a potential reservoir for emerging pathogens carrying antibiotic-resistance genes, making it a crucial area for monitoring and intervention. Furthermore, the results demonstrate the feasibility of a low-cost, high-throughput method for tracking bacterial pathogens in low- and middle-income countries, making it a valuable tool for One Health monitoring efforts.

Scale of analysis drives the observed ratio of spatial to non-spatial variance in microbial water quality: insights from two decades of citizen science data

AIMS

While fecal indicator bacteria (FIB) testing is used to monitor surface water for potential health hazards, observed variation in FIB levels may depend on the scale of analysis (SOA). Two decades of citizen science data, coupled with random effects models, were used to quantify the variance in FIB levels attributable to spatial versus temporal factors.

METHODS AND RESULTS

Separately, Bayesian models were used to quantify the ratio of spatial to non-spatial variance in FIB levels and identify associations between environmental factors and FIB levels. Separate analyses were performed for three SOA: waterway, watershed, and statewide. As SOA increased (from waterway to watershed to statewide models), variance attributable to spatial sources generally increased and variance attributable to temporal sources generally decreased. While relationships between FIB levels and environmental factors, such as flow conditions (base versus stormflow), were constant across SOA, the effect of land cover was highly dependent on SOA and consistently smaller than the effect of stormwater infrastructure (e.g. outfalls).

CONCLUSIONS

This study demonstrates the importance of SOA when developing water quality monitoring programs or designing future studies to inform water management.

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.

Degradation of indole via a two-component indole oxygenase system from Enterococcus hirae GDIAS-5

Animal farming copiously generates indoles, which contribute to odor and pose a challenge for deodorization. While biodegradation is widely accepted, there is a lack of suitable indole-degrading bacteria for animal husbandry. In this study, we aimed to construct genetically engineered strains with indole-degrading abilities. Enterococcus hirae GDIAS-5 is a highly efficient indole-degrading bacterium, which functions via a monooxygenase YcnE presumably contributes to indole oxidation. However, the efficiency of engineered Escherichia coli expressing YcnE for indole degradation is lower than that of GDIAS-5. To improve its efficacy, the underlying indole-degradation mechanisms in GDIAS-5 were analyzed. An ido operon that responds to a two-component indole oxygenase system was identified. In vitro experiments showed that the reductase component of YcnE, YdgI, can improve the catalytic efficiency. The reconstruction of the two-component system in E. coli exhibited higher indole removal efficiency than GDIAS-5. Furthermore, isatin, the key intermediate metabolite in indole degradation, might be degraded via a novel isatin-acetaminophen-aminophenol pathway involving an amidase whose coding gene is located near the ido operon. The two-component anaerobic oxidation system, upstream degradation pathway, and engineering strains investigated in this study provide important insights into indole degradation metabolism and offer efficient resources for achieving bacterial odor elimination.

Comparison of antibiotic-resistant Escherichia coli and extra-intestinal pathogenic E. coli from main river basins under different levels of the sewer system development

Antimicrobial-resistant Escherichia coli in the aquatic environments is considered a strong indicator of sewage or animal waste contamination and antibiotic pollution. Sewer construction and wastewater treatment plant (WWTP) infrastructure may serve as concentrated point sources of contamination of antibiotic-resistant bacteria and antibiotic resistance genes. In this study, we focused on the distribution of antimicrobial-resistant E. coli in two rivers with large drainage areas and different urbanisation levels. E. coli from Kaoping River with drainage mainly from livestock farming had higher resistance to antibiotics (e.g. penicillins, tetracyclines, phenicols, aminoglycosides, and sulpha drugs) and presented more positive detection of antibiotic-resistance genes (e.g. ampC, blaTEM, tetA, and cmlA1) than that from Tamsui River. In Kaoping River with a lower percentage of sewer construction nearby (0-30%) in contrast to a higher percentage of sewer construction (55-92%) in Tamsui River, antimicrobial-resistant E. coli distribution was related to livestock farming waste. In Tamsui River, antimicrobial resistant E. coli isolates were found more frequently in the downstream drainage area of WWTPs with secondary water treatment than that of WWTPs with tertiary water treatment. The Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR showed that the fingerprinting group was significantly related to the sampling site (p < 0.01) and sampling date (p < 0.05). By utilising ERIC-PCR in conjunction with antibiotic susceptibility and antibiotic-resistance gene detection, the relationship among different strains of E. coli could be elucidated. Furthermore, we identified the presence of six extra-intestinal pathogenic E. coli isolates and antibiotic-resistant E. coli isolates near drinking water sources, posing a potential risk to public health through community transmission. In conclusion, this study identified environmental factors related to antibiotic-resistant bacteria and antibiotic-resistance gene contamination in rivers during urban development. The results facilitate the understanding of specific management of different waste streams across different urban areas. Periodic surveillance of the effects of WWTPs and livestock waste containing antibiotic-resistant bacteria and antibiotic-resistance genes on river contamination is necessary.

Detection of tetracycline resistance genes and their diversity in Escherichia coli isolated from pig farm waste in Banten province, Indonesia

Background and Aim

Livestock waste in the form of feces and liquid represents an important reservoir of antibiotic resistance genes (ARGs). Because many ARGs can be horizontally transferred to other pathogens, livestock waste plays an essential role in the emergence and transmission of various ARGs in the environment. Therefore, this study aimed to detect and assess the diversity of tet genes in Escherichia coli isolated from pig farm waste in Banten province, Indonesia.

Materials and Methods

Solid waste (feces) and wastewater were collected from 44 pig farms in Banten province. The isolation and identification of E. coli referred to the Global Tricycle Surveillance extended-spectrum beta-lactamase E. coli World Health Organization (2021) guidelines. tet genes were detected using quantitative real-time polymerase chain reaction after dividing pig farms in the province into four clusters based on their adjacent areas and characteristics.

Results

tetA, tetB, tetC, tetM, tetO, and tetX were detected in solid waste and wastewater from pig farms, whereas tetE was not detected in either sample type. tetX (100%) and tetO (75%) were the most dominant genes in solid waste, whereas wastewater samples were dominated by tetA, tetM, tetO, and tetX (prevalence of 50% each). Furthermore, eight tet gene patterns were found in pig farm waste (prevalence of 12.5% each).

Conclusion

The results showed a high prevalence of tetO and tetX in solid waste and wastewater from pig farms in Banten province. This significant prevalence and diversity indicated the transmission of tet genes from pigs to the environment, posing a serious threat to public health.

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.

High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers

Contamination of water with bacterial, viral, and protozoan pathogens can cause human diseases. Both humans and nonhumans can release these pathogens through their feces. To identify the sources of fecal contamination in the water environment, microbial source tracking (MST) approaches have been developed; however, the relationship between MST markers and pathogens is still not well understood most likely due to the lack of comprehensive datasets of pathogens and MST marker concentrations. In this study, we developed a novel microfluidic quantitative PCR (MFQPCR) platform for the simultaneous quantification of 37 previously validated MST markers, two fecal indicator bacteria (FIB), 22 bacterial, 11 viral, and five protozoan pathogens, and three internal amplification/process controls in many samples. The MFQPCR chip was applied to analyze pathogen removal rates during the wastewater treatment processes. In addition, multiple host-specific MST markers, FIB, and pathogens were successfully quantified in human and avian-impacted surface waters. While the genes for pathogens were relatively infrequently detected, positive correlations were observed between some potential pathogens such as Clostridium perfringens and Mycobacterium spp., and human MST markers. The MFQPCR chips developed in this study, therefore, can provide useful information to monitor and improve water quality.

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.

Versatile dual-channel loop-mediated isothermal amplification assay featuring smartphone imaging enables determination of fecal indicator bacteria in environmental waters

Rapid diagnostic assays are often a critical tool for monitoring water quality in developing and developed countries. Conventional testing requires 24-48 h for incubation, resulting in delayed remediation and increasing the likelihood of negative outcomes. In this study, we report a workflow for detection of E. coli, a common indicator of fecal contamination. Following large volume filtration, E. coli is then solubilized enabling the facile isolation and recovery of genetic material by a thin film microextraction (TFME) device featuring a polymeric ionic liquid (PIL) sorbent. Rapid recovery of pure nucleic acids is achieved using a PIL sorbent with high affinity for DNA to significantly increase mass transfer and facilitate adsorption and desorption of DNA. Downstream detection is performed by a versatile, dual channel loop mediated isothermal amplification (LAMP) assay featuring a colorimetric dye and a sequence-specific molecular beacon. A portable LAMP companion box enables consistent isothermal heating and endpoint smartphone imaging while being powered by a single 12-V battery. Programmable LEDs are switched from white or blue light to facilitate the independent imaging of the colorimetric dye or fluorometric probe following amplification. The methodology positively identified E. coli in environmental samples spiked to concentrations of 6600 colony forming units (CFU) per milliliter and 660 CFU/mL with 100% and 22% positivity, respectively.

Environmental risk assessment for fecal contamination sources in urban and peri-urban estuaries, in Escambia and Santa Rosa counties, FL, USA

Fecal pollution of estuaries and adjacent creeks and streams is of significant concern along the Gulf of Mexico. The prospective threat to human life and water quality impairment via fecal pollution is a substantial danger to the strength and resistance of coastline areas. Pensacola, FL, has a prosperous coastal tourism industry that is utilized for numerous other uses, such as recreational watersports and boating, seafood, and shellfish harvesting. However, the frequency and severity of fecal contamination present possible socio-economic issues, specifically financial hardships. Therefore, understanding the source, abundance, and fate of fecal microbial pollutants in aquatic systems signifies an imperative initial stage for detecting the host sources and techniques to lessen their transport from the landscape. This research aimed to quantify the fecal indicator bacteria (FIB), Escherichia coli, and perform microbiological fecal source tracking to verify if the fecal inputs are of either animal or human host origin. Surface water samples were taken from urban and peri-urban creeks for two sampling periods (February 2021 and January 2022), and IDEXX Colilert-18 (USEPA Standard Method 9223) was used for E. coli enumeration. DNA extractions were obtained from each sample, and quantitative PCR was utilized for fecal microbial source tracking (MST) to detect human, dog, ruminant, and bird host-specific Bacteroides DNA. The result indicates elevated quantities of FIB, E. coli, that surpass the threshold considered safe regarding human health. E. coli at six sites over the two sampling periods exceeded the impairment threshold, reaching as high as 866.4 MPN/100 ml. Fecal source tracking identified human host fecal contamination at four of nine sites, dogs at three of nine, and birds at one site. However, those sites with sources identified via MST all had E. coli levels below impairment thresholds. No sites were determined to be positive for ruminant as a source or for the pathogen Helicobacter pylori. No canine host fecal inputs were found in January 2022, and only one site with human sewage. Our results highlight the utility of MST in assessing bacterial inputs to water bodies and the challenges.

The impact of combined sewer outflows on urban water quality: Spatio-temporal patterns of fecal coliform in indianapolis

Many urban waterways with older stormwater drainage systems receive a significant amount of untreated or poorly treated waste from Combined Sewer Outflow (CSO) systems during precipitation events. The input of effluent waste from CSO to urban water streams during storm events often leads to elevated fecal coliform, specifically Escherichia Coli (E. Coli) in these waterways. The aim of the study is to examine fecal coliform concentration, water chemistry, and water quality parameters to better understand spatio-temporal patterns of fecal coliform associated with CSO events in three waterways from Indianapolis, Indiana (USA). The waterways are Pleasant Run Creek (PRW), Fall Creek (FC) and White River (WR). The sampling occurred biweekly over one year for PRW, nine months for FC, and an intense (∼every three days) sub-analysis of the presumed peak period of fecal coliform growth (July) for WR. All PRW and FC sampling sites significantly exceeded the EPA contact standard limit of 200 CFU/100 mL for fecal coliform concentrations during the sampling period. We found no relationship between fecal coliform levels and the number or density of CSO outfalls above a given site. The most significant predictors of increased fecal coliform concentrations were precipitation on the sampling day and cumulative degree days. The most significant predictors of decreased fecal coliform were maximum precipitation during the ten-day window prior to sampling and median discharge during a three-day window prior to sampling. These findings suggest a push-pull balance within the system where CSO activation and seasonal gradients replenish and promote fecal coliform growth. At the same time, large hydrologic events act to flush and dilute fecal coliform concentrations. The results from this study help us to better understand how different drivers influence fecal coliform growth and how this information can be potentially used to predict and remediate the conditions of urban water streams.

Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments

The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.

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.

Survival behavior of six enterotoxigenic Escherichia coli strains in soil and biochar-amended soils

Some Escherichia coli serotypes are important human pathogens causing diarrhea or in some cases, life threatening diseases. E. coli is also a typical indicator microorganism, routinely used for assessing the microbiological quality of water especially to indicate fecal contamination. The soil is a sink and route of transmission to water and food resources and it is thus important to understand the survival of enterotoxigenic E. coli strains in soil. This study monitored the survival of six E. coli strains in sandy and loam soil. Furthermore, since biochar is a commonly used soil conditioner, the study investigated the impact of biochar amendment (15%) on the survival of the E. coli strains in (biochar-amended) sandy and loam soils. Addition of biochar affected the physicochemical properties of both soils, altering potassium levels, calcium, magnesium, sodium as well as levels of other metal ions. It increased the organic matter of loam soil from 44 g/dm³ to 52 g/dm³, and increased the pH of both sandy and loam soils. Survival and persistence of the E. coli strains generally varied according to soil type, with strains generally surviving better (P ≤ 0.05) in loam soil compared to in sandy soil. In loam soil and biochar amended loam soils, E. coli strains remained culturable until the 150th day with counts ranging between 3.00 and 5.94 ± 0.04 log CFU/g. The effects of biochar on the physicochemical properties of soil and the response of the E. coli strains to biochar amendment was variable depending on soil type.

Development of two microbial source tracking markers for detection of wastewater-associated Escherichia coli isolates

Escherichia coli has been used as an indicator of fecal pollution in environmental waters. However, its presence in environmental waters does not provide information on the source of water pollution. Identifying the source of water pollution is paramount to be able to effectively reduce contamination. The present study aimed to identify E. coli microbial source tracking (MST) markers that can be used to identify domestic wastewater contamination in environmental waters. We first analyzed wastewater E. coli genomes sequenced by us (n = 50) and RefSeq animal E. coli genomes of fecal origin (n = 82), and identified 144 candidate wastewater-associated marker genes. The sensitivity and specificity of the candidate marker genes were then assessed by screening the genes in 335 RefSeq wastewater E. coli genomes and 3318 RefSeq animal E. coli genomes. We finally identified two MST markers, namely W_nqrC and W_clsA_2, which could be used for detection of wastewater-associated E. coli isolates. These two markers showed higher performance than the previously developed human wastewater-associated E. coli markers H8 and H12. When used in combination, W_nqrC and W_clsA_2 showed specificity of 98.9 % and sensitivity of 25.7 %. PCR assays to detect W_nqrC and W_clsA_2 were also developed and validated. The developed PCR assays are potentially useful for detecting E. coli isolates of wastewater origin in environmental waters, though users should keep in mind that the sensitivity of these markers is not high. Further studies are needed to assess the applicability of the developed markers to a culture-independent approach.

Potential Application of the WST-8-mPMS Assay for Rapid Viable Microorganism Detection

To ensure clean drinking water, viable pathogens in water must be rapidly and efficiently screened. The traditional culture or spread-plate process-the conventional standard for bacterial detection-is laborious, time-consuming, and unsuitable for rapid detection. Therefore, we developed a colorimetric assay for rapid microorganism detection using a metabolism-based approach. The reaction between a viable microorganism and the combination of 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium sodium salt (WST-8) and 1-methoxy-5-methylphenazinium methyl sulfate (mPMS) results in a color change. In combination with a microplate reader, WST-8-mPMS reactivity was leveraged to develop a colorimetric assay for the rapid detection of various bacteria. The detection limit of the WST-8-mPMS assay for both gram-negative and gram-positive bacteria was evaluated. This WST-8-mPMS assay can be used to perform colorimetrical semi-quantitative detection of various bacterial strains in buffers or culture media within 1 h without incubation before the reaction. The easy-to-use, robust, rapid, and sensitive nature of this novel assay demonstrates its potential for practical and medical use for microorganism detection.

Detection and genetic analysis of Escherichia coli from Tonle Sap Lake and its tributaries in Cambodia: Spatial distribution, seasonal variation, pathogenicity, and antimicrobial resistance

As an indicator of fecal contamination, Escherichia coli was monitored in Tonle Sap Lake, Cambodia, and its tributaries during low- and high-water seasons, focusing on the impacts on floating villagers inhabiting boathouses. E. coli concentrations in the floating villages (3.6 × 10³ and 5.7 × 10³ CFU/100 mL during the low- and high-water seasons, respectively) were significantly higher than those in other lake sites (4.0 × 10¹ and 7.0 × 10⁰ CFU/100 mL during the low- and high-water seasons, respectively) and rivers (3.3 × 10² and 8.9 × 10² CFU/100 mL during the low- and high-water seasons, respectively), most likely because fecal materials from the boathouses were discharged without treatment. At most of the lake sampling sites remote from the boathouses, the E. coli concentration was lower during the high-water season than that during the low-water season, due to dilution by lake water. E. coli colonies detected during monitoring were isolated for pathotyping, antimicrobial susceptibility testing, beta-lactamase gene detection, and multilocus sequencing typing (MLST). Of the 659 E. coli isolates, 101 (15.3%) were diarrheagenic E. coli (DEC). The prevalence of DEC (52.2%) in the floating villages during the low-water season was higher than that during the high-water season (4.2%) and that in other sites during both seasons (10.6-21.3%). The DEC isolates from the floating villages during the low-water season showed high antimicrobial resistance, including ampicillin (83.4%) and ciprofloxacin (83.4%), and frequently possessed a beta-lactamase gene (bla_TEM) (83.4%). MLST analysis indicated that the predominant sequence type (ST) of DEC isolates from the floating villages possibly originated from humans, whereas more diverse STs were detected in isolates from other sites. We revealed the wide presence of diarrheagenic and antimicrobial-resistant E. coli in Tonle Sap Lake and identified a considerable infection risk in floating villages, especially during the low-water season.

Antibacterial Properties and Potential Mechanism of Serum from Chinese Alligator

The Chinese alligator (Alligator sinensis) is an ancient reptile with strong immunity that lives in wetland environments. This study tested the antibacterial ability of Chinese alligator serum (CAS) against Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa and analyzed the potential underlying mechanisms. Results showed that the CAS had a marked antibacterial effect on K. pneumoniae, E. coli, and P. aeruginosa, while S. aureus was only mildly affected. However, these effects disappeared when Protease K was added to the serum. The serum proteome analysis revealed that the antibacterial ability of CAS was produced by interactions among various proteins and that the complement proteins played a major antibacterial role. Therefore, we made relevant predictions about the structure and function of complement component 3. In addition, sequence alignment and phylogenetic analysis of complement component 3d (C3d) in four mammalian species and two alligator species showed that the amino acids that make up the acid pocket on the concave surface of alligator C3d are not identical to those in mammals. This study provided evidence that CAS elicits significant antibacterial effects against some pathogens and provides the basis for further development of novel antibacterial drugs.

Levels of Escherichia coli as Bio-Indicator of Contamination of Fish Food and Antibiotic Resistance Pattern Along the Value Chain in Northwest Ethiopia

INTRODUCTION

Microbiological contamination in fish origin foods is the leading risk for public health. Among the range of pathogenic bacterial species that cause fish food borne diseases is Escherichia coli. The pathogenic strains of Escherichia coli cause diarrhea by producing and releasing toxins and can also be the cause of food spoilage in fish.

METHODS

A cross-sectional study was conducted to assess hygienic practices of fish handlers, to evaluate bacterial load and antimicrobial resistance patterns of Escherichia coli along the fish value chain in Northwest Ethiopia. Systematic and purposive sampling techniques were used for uncooked and cooked fish samples respectively.

RESULTS

From a total of 180 fish samples, 36 (20%) were positive for Escherichia coli. From 115 uncooked and 65 cooked fish samples examined, 27 (23.5%) and 9 (13.8%) had E. coli respectively. The highest mean bacterial count was observed in raw fish samples (6.13 × 10⁵ cfu/g), followed by cooked fish samples (2.81 × 10⁴ cfu/g). Among the interviewed fish handlers, 83.3%, 76.7% and 80% of respondents had good knowledge and attitude towards using a clean cutting-and-filleting board, storing raw and cooked foods separately and using an apron for reducing the risk of fish contamination, respectively. All 36 isolates were 100% sensitive to ciprofloxacin and gentamycin. Of the Escherichia coli isolates subjected to tetracycline, 55.6% were resistant, 8.3% were intermediate and 36.1% were susceptible.

CONCLUSION AND RECOMMENDATION

This study revealed that there was a lack hygienic practice and high Escherichia coli profiles were observed. Hence, it could be wise to advise the fish harvesters, fish traders, hotels and restaurants about fish food safety practices from harvesting to consumption to improve fish food safety practices and quality standards of fish harvested and sold in northwest Ethiopia.

A 22-Site Comparison of Land-Use Practices, E-coli and Enterococci Concentrations

Land-use practices can greatly impact water quality. Escherichia (E.) coli and Enterococcus are accepted water quality indicators. However, surprisingly little research has been conducted comparing both organisms' population density relationships to land use practices and water quality. Stream water grab samples were collected monthly (n = 9 months) from 22 stream monitoring sites draining varying land use practice types in a representative mixed-land-use watershed of the northeastern United States. E. coli and enterococci colony forming units (CFU per 100 mL) were estimated (n = 396) and statistically analyzed relative to land use practices, hydroclimate, and pH, using a suite of methods, including correlation analysis, Principal Components Analysis (PCA), and Canonical Correspondence Analysis (CCA). Correlation analyses indicated significant (p < 0.05) relationships between fecal indicator bacteria concentrations, water quality metrics and land use practices but emphasized significant (p < 0.05) negative correlations between pH and instream enterococci concentrations. PCA and CCA results indicated consistent spatial differences between fecal indicator bacteria concentrations, pH, and land use/land cover characteristics. The study showed that pH could be considered an integrated proxy variable for past (legacy) and present land use practice influences. Results also bring to question the comparability of E-coli and enterococci relative to dominant land use practices and variations in pH and provide useful information that will help guide land use practice and water pollutant mitigation decision making.

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.

Dynamic multivariate analysis for pollution assessment and river habitat conservation in the Vietnamese La Buong watershed

Analysis of temporal patterns of high-dimensional time-series water quality data is essential for pollution management worldwide. This study has applied dynamic factor analysis (DFA) and cluster analysis (CA) to analyze time-series water quality data monitored at the five stations installed along the La Buong river in Southern Vietnam. Application of the DFA identified two types of temporal patterns, one of the run-off driven parameters (total suspended solid (TSS), turbidity, and iron) and the other of diffuse source pollution. The association of the variables like BOD₅ and COD at most stations to the run-off-driven parameters revealed their sharing of drivers. On the contrary, separating variables like phosphate (PO₄³) at the three upstream stations from the run-off patterns suggested their local point-source origin. The DFA-derived factors were later used in the time-point CA to explore the seasonality of water quality parameters and their pollution intensities compared to regulatory levels. The result suggested intensification in wet season of Fe, TSS, BOD₅, and COD concentrations at most sites, which are unobservable in run-off detached parameters like reactive nitrogen, phosphate (PO₄^3-), and E. coli. These findings generated robust insights to support water quality management for river habitat conservation.

DNA fingerprinting using BOX-A1R and (GTG)5 primers identify spatial variations of fecal contamination along Pasig River, Philippines

Pasig River is one of the most economically important rivers in Metro Manila, Philippines. It traverses some of the region's major cities, and because of its strategic location, it is utilized as a means of transportation, as a source of water for domestic and industrial uses, and for recreational purposes. However, due to population growth, industrialization, and land use, the river's water quality is deteriorating. Wastes that pollute the river pose health risks to the people that benefit from it. To prevent the river's further degradation, it is essential to identify the origin of contamination. In this study, the sources of fecal contamination in Pasig River were identified using BOX-A1R and (GTG)₅ primers in the DNA fingerprinting of Escherichia coli isolated from the river. Results showed the dominance of human contamination (percent composition = 65.55%), followed by agricultural sources (percent composition = 23.48%), and the lowest was from sewage (percent composition = 10.98%). The results of this research can help in evaluating public health risks and can be used as a scientific basis for policymaking and implementation for the rehabilitation and improvement of Pasig River.