Use of Escherichia coli BOX-PCR fingerprints to identify sources of fecal contamination of water bodies in the State of São Paulo, Brazil

Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR

Laguna Lake is an economically important resource in the Philippines, with reports of declining water quality due to fecal pollution. Currently, monitoring methods rely on counting fecal indicator bacteria, which does not supply information on potential sources of contamination. In this study, we predicted sources of Escherichia coli in lake stations and tributaries by establishing a fecal source library composed of rep-PCR DNA fingerprints of human, cattle, swine, poultry, and sewage samples (n = 1,408). We also evaluated three statistical methods for predicting fecal contamination sources in surface waters. Random forest (RF) outperformed k-nearest neighbors and discriminant analysis of principal components in terms of average rates of correct classification in two- (84.85%), three- (82.45%), and five-way (74.77%) categorical splits. Overall, RF exhibited the most balanced prediction, which is crucial for disproportionate libraries. Source tracking of environmental isolates (n = 332) revealed the dominance of sewage (47.59%) followed by human sources (29.22%), poultry (12.65%), swine (7.23%), and cattle (3.31%) using RF. This study demonstrates the promising utility of a library-dependent method in augmenting current monitoring systems for source attribution of fecal contamination in Laguna Lake. This is also the first known report of microbial source tracking using rep-PCR conducted in surface waters of the Laguna Lake watershed.

New Approaches for Escherichia coli Genotyping

Easy-to-perform, fast, and inexpensive methods of differentiation of Escherichia coli strains beyond the species level are highly required. Herein two new, original tools for genotyping of E. coli isolates are proposed. The first of the developed method, a PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) test uses a highly variable fliC gene, encoding the H antigen as a molecular target. The designing of universal pair of primers and selection of the optimal restriction enzyme RsaI was preceded by in silico comparative analysis of the sequences of the genes coding for 53 different serotypes of H-antigen (E. coli flagellin). The target fragments of E. coli genomes for MLST method were selected on the basis of bioinformatics analysis of complete sequences of 16 genomes of E. coli. Initially, seven molecular targets were proposed (seven pairs of primers) and five of them were found useful for effective genotyping of E. coli strains. Both developed methods revealed high differentiation power, and a high genetic diversity of the strains tested was observed. Within the group of 71 strains tested, 29 and 47 clusters were revealed with fliC RFLP-PCR and MLST methods, respectively. Differentiation of the strains with the reference BOX-PCR method revealed 31 different genotypes. The in silico analysis revealed that the discriminatory power of the new MLST method is comparable to the Pasteur and Achtman schemes and is higher than the discriminatory power of the method developed by Clermont. From the epidemiology point of view, the outcomes of our investigation revealed that in most cases, the patients were infected with unique strains, probably from environmental sources. However, some strains isolated from different patients of the wards of pediatrics, internal medicine, and neurology were classified to the same genotype when the results of all three methods were taken into account. It could suggest that they were transferred between the patients.

Effectiveness of BOX-PCR in Differentiating Genetic Relatedness among Salmonella enterica Serotype 4,[5],12:i:- Isolates from Hospitalized Patients and Minced Pork Samples in Northern Thailand

Salmonella enterica Serotype 4,[5],12:i:-, a monophasic variant of S. Typhimurium, with high virulence and multidrug resistance is distributed globally causing pathogenicity to both humans and domesticated animals. BOX-A1R-based repetitive extragenic palindromic-PCR (BOX)-PCR proved to be superior to three other repetitive element-based PCR typing methods, namely, enterobacterial repetitive intergenic consensus (ERIC)-, poly-trinucleotide (GTG)₅-, and repetitive extragenic palindromic (REP)-PCR (carried out under a single optimized amplification condition), in differentiating genetic relatedness among S. 4,[5],12:i:- isolates from feces of hospitalized patients (n=12) and isolates from minced pork samples of S. 4,[5],12:i:- (n=6), S. Typhimurium (n=6), and Salmonella Serogroup B (n=4) collected from different regions of northern Thailand. Construction of phylogenetic trees from amplicon size patterns allowed allocation of Salmonella isolates into clusters of similar genetic relatedness, with BOX-PCR generating more unique clusters for each serotype than the other three typing methods. BOX-, (GTG)₅-, and REP-PCR indicated significant genetic relatedness between S. 4,[5],12:i:- isolates 1 and 9 from hospitalized patients and S. 4,[5],12:i:- isolate en 29 from minced pork, suggesting a possible route of transmission. Thus, BOX-PCR provides a suitable molecular typing method for discriminating genetic relatedness among Salmonella spp. of the same and different serotypes and should be suitable for application in typing and tracking route of transmission in Salmonella outbreaks.

Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops

The impact of microbially contaminated irrigation water on risks to produce safety and public health is a complex issue that is not well understood. This study tracked fecal indicators, pathogenic bacteria, and total bacterial communities from a creek water irrigation source to irrigated produce to assess the impact of irrigation events on soil and produce-associated microbiota. Kale and radishes were drip-irrigated using Mid-Atlantic creek water in October 2017. Plant and soil samples were collected immediately before and after irrigation, and for 3 consecutive days thereafter. All samples (n = 134), including irrigation water, were tested for generic Escherichia coli and total coliforms (TC) using standard membrane filtration or direct plating, and for Salmonella enterica and Listeria monocytogenes by selective enrichment. DNA extracted from all samples was PCR-amplified for the V3-V4 region of the 16S rRNA gene for bacterial community profiling. In soil, TC levels were significantly higher immediately and 3 days post-irrigation compared to pre-irrigation (p < 0.01). E. coli levels in soil increased after irrigation, but the difference was not significant (p = 0.31), and die-off was not observed. No E. coli were detected on kale leaves. TC increased over the study period on radish roots (p < 0.01) but not kale leaves (p = 0.43). Although target pathogens were detected in irrigation water, S. enterica was detected from only one post-irrigation kale sample and L. monocytogenes was not detected in the field. The 16S rRNA gene sequencing data revealed differences in bacterial community structure and composition across sample types and showed that radish soil and root surface bacterial communities were more strongly influenced by irrigation compared to kale samples. This study provides insights into the impact of irrigation water on fresh produce microbiota, revealing that, although irrigation did influence crop-associated microbiota (especially below ground) in the field, bacterial pathogens were not likely transferred to the crop.

Multidrug-resistant Escherichia coli isolated from canine faeces in a public park in Quito, Ecuador

OBJECTIVES

This study focused on estimating the prevalence of extended-spectrum β-lactamases (ESBLs), plasmid-mediated AmpC β-lactamases, carbapenemases and MCR-1-producing Escherichia coli in canine faeces from a public park in Quito, Ecuador.

METHODS

Phenotypic and genotypic characterisation of E. coli isolated from 50 canine faecal samples recovered from a city park in Quito was performed. In addition, a multiple choice survey was conducted among 50 dog owners.

RESULTS

Of the 50 faecal samples, 20 (40.0%) presented E. coli resistant to ceftriaxone. Moreover, 23 E. coli isolates were recovered for further analysis. All of the isolates showed as multidrug-resistant (MDR) phenotype (resistant to three or more antibiotic families). Resistance to carbapenems, tigecycline and amikacin was not observed. No major clonal relatedness was observed among the resistant isolates. The ESBL genes bla_CTX-M-15, bla_CTX-M-55 and bla_CTX-M-65 were the most common. Two isolates harboured the bla_CMY-2 gene and one isolate harboured both mcr-1 and bla_CTX-M-65. Statistical analysis showed that older people were more conscious of collecting and disposing of dog faeces than subjects aged <35 years (P < 0.05).

CONCLUSION

The finding of MDR E. coli in dog faeces in a city park in Ecuador illustrates the importance of analysing canine faeces in public settings (e.g. parks, playgrounds) as part of surveillance programmes for MDR E. coli. In addition, this research might be a sentinel sampling method to gain a better understanding of community sources of antibiotic-resistant Enterobacteriaceae at human-animal-environment interfaces.

Genetic diversity of Escherichia coli isolates from surface water and groundwater in a rural environment

The genetic characteristics among Escherichia coli strains can be grouped by origin of isolation. Then, it is possible to use the genotypes as a tool to determine the source of water contamination. The aim of this study was to define water aptitude for human consumption in a rural basin and to assess the diversity of E. coli water populations. Thus, it was possible to identify the main sources of fecal contamination and to explore linkages with the hydrogeological environment and land uses. The bacteriological analysis showed that more than 50% of samples were unfit for human consumption. DNA fingerprinting analysis by BOX-PCR indicated low genotypic diversity of E. coli isolates taken from surface water and groundwater. The results suggested the presence of a dominant source of fecal contamination. The relationship between low genotypic diversity and land use would prove that water contamination comes from livestock. The genetic diversity of E. coli isolated from surface water was less than that identified in groundwater because of the different hydraulic features of both environments. Furthermore, each one of the two big strain groups identified in this basin is located in different sub-basins, showing that hydrological dynamics exerts selective pressure on bacteria DNA.

Occurrence and Dispersal of Indicator Bacteria on Cucumbers Grown Horizontally or Vertically on Various Mulch Types

No data exist on the impact of cultivation practices on food safety risks associated with cucumber. Cucumbers are typically grown horizontally over a mulch cover, with fruit touching the ground, but this vining plant grows well in vertical systems. To assess whether production system affects bacterial dispersal onto plants, field trials were conducted over 2 years. Cucumber cultivar 'Marketmore 76' was grown horizontally on plastic, straw, or bare ground or vertically on trellises installed on bare ground in soil previously amended with raw dairy manure. Fruit, flower, leaf, and soil samples were collected to quantify Escherichia coli , thermotolerant coliforms, and enterococci by direct plating. E. coli isolates were characterized by BOX-PCR to evaluate relatedness among strains. Although thermotolerant coliforms and enterococci were significantly less abundant on fruit in year 1 (P < 0.05), this result was not seen in year 2 when more rain was recorded. Instead, fruit from straw-mulched beds had higher levels of enterococci compared with fruit grown on bare ground (P < 0.05). Leaves on bare ground occasionally had more bacteria than did leaves on plastic mulch beds (P < 0.05). Production system did not impact flower-associated bacterial levels. E. coli isolates (n =127) were genotyped, generating 21 distinct fingerprints. Vertical production did not appear to be a barrier for E. coli dispersal to the crop, as suggested by numerous related isolates from soil and flowers on bare ground, straw-mulched, and trellised beds (subcluster B1). None of the isolates from soil and flowers in this subcluster were related to isolates recovered from fruit, showing that flower colonization does not necessarily lead to fruit colonization. One cluster of isolates contained those from flowers and fruits but not soil, indicating a source other than manure-amended soil. Straw may be a source of E. coli ; a number of closely related E. coli isolates were retrieved from soil and fruits from straw-mulched beds. Our approach revealed E. coli dispersal patterns and could be used to assess bacterial transmission in other production systems.

Metrics Proposed To Prevent the Harvest of Leafy Green Crops Exposed to Floodwater Contaminated with Escherichia coli

The California Leafy Green Products Handler Marketing Agreement (LGMA) requires leafy green crops within 9 m of the edge of a flooded field not be harvested due to potential contamination (California Leafy Green Products Handler Marketing Board, Commodity Specific Flood Safety Guidelines for the Production and Harvest of Lettuce and Leafy Greens, 2012). Further, previously flooded soils should not be replanted for 60 days. In this study, the suitability of the LGMA metrics for farms in the Mid-Atlantic region of the United States was evaluated. The upper end of a spinach bed (in Beltsville, MD) established on a -5% grade was flooded with water containing 6 log CFU/ml Escherichia coli to model a worst-case scenario of bacterial movement through soil. Escherichia coli prevalence in soil and on foliar tissue was determined by most probable number (MPN) analysis at distances up to 9 m from the edge of the flood for 63 days. While E. coli was quickly detected at the 9-m distance within 1 day in the spring trial and within 3 days in the fall trial, no E. coli was detected on plants outside the flood zone after 14 days. On day 63 for the two trials, E. coli populations in the flood zone soil were higher in the fall than in the spring. Regression analysis predicted that the time required for a 3-log MPN/g (dry weight) decrease in E. coli populations inside the flood zone was within the 60-day LGMA guideline in the spring but would require 90 days in the fall. Overall, data suggest that the current guidelines should be revised to include considerations of field and weather conditions that may promote bacterial movement and survival.

IMPORTANCE

This study tracked the movement of Escherichia coli from floodwater across a horizontal plane of soil and the potential for the contamination of distant leafy green produce. The purpose of this study was to address the validity of the California Leafy Green Products Handler Marketing Agreement recommendations for the harvest of leafy green crops after a flooding event. These recommendations were based on the turning radius of farming equipment but did not take into consideration the potential subsurface movement of pathogens in the water through soil. This research shows that further considerations of field slope, temperature, and additional rainfall events may be necessary to provide appropriate guidelines to prevent the harvest of leafy green crops contaminated by enteric pathogens in floodwaters. This study may be used to provide a framework for comprehensive recommendations to growers for good harvesting practices after a flooding event.

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

AIMS

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

METHODS AND RESULTS

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

CONCLUSIONS

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

SIGNIFICANCE AND IMPACT OF THE STUDY

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

Escherichia coli Strains Isolated from the Uteri Horn, Mouth, and Rectum of Bitches Suffering from Pyometra: Virulence Factors, Antimicrobial Susceptibilities, and Clonal Relationships among Strains

Pyometra is recognized as one of the main causes of disease and death in the bitch, and Escherichia coli is the major pathogen associated with this disease. In this study, 70 E. coli isolates from the uteri horn, mouth, and rectum of bitches suffering from the disease and 43 E. coli isolates from the rectum of clinically healthy bitches were examined for the presence of uropathogenic virulence genes and susceptibility to antimicrobial drugs. DNA profiles of isolates from uteri horn and mouth in bitches with pyometra were compared by REP, ERIC, and BOX-PCR. Virulence gene frequencies detected in isolates from canine pyometra were as follows: 95.7% fim, 27.1% iss, 25.7% hly, 18.5% iuc, and 17.1% usp. Predominant resistance was determined for cephalothin, ampicillin, and nalidixic acid among the isolates from all sites examined. Multidrug resistance was found on ∼50% pyometra isolates. Using the genotypic methods some isolates from uteri, pus, and saliva of the same bitch proved to have identical DNA profiles which is a reason for concern due to the close relationship between household pets and humans.

Gulls identified as major source of fecal pollution in coastal waters: a microbial source tracking study

Gulls were reported as sources of fecal pollution in coastal environments and potential vectors of human infections. Microbial source tracking (MST) methods were rarely tested to identify this pollution origin. This study was conducted to ascertain the source of water fecal contamination in the Berlenga Island, Portugal. A total of 169 Escherichia coli isolates from human sewage, 423 isolates from gull feces and 334 water isolates were analyzed by BOX-PCR. An average correct classification of 79.3% was achieved. When an 85% similarity cutoff was applied 24% of water isolates were present in gull feces against 2.7% detected in sewage. Jackknifing resulted in 29.3% of water isolates classified as gull, and 10.8% classified as human. Results indicate that gulls constitute a major source of water contamination in the Berlenga Island. This study validated a methodology to differentiate human and gull fecal pollution sources in a real case of a contaminated beach.