A novel single-step multiplex polymerase chain reaction assay for the detection of diarrheagenic Escherichia coli

Phenotypic and Genotypic Characterization of Escherichia coli and Salmonella spp. Isolates from Pigs at Slaughterhouse and from Commercial Pork Meat in Portugal

Background: Foodborne diseases are a serious public health concern, and food-producing animals are a major source of contamination. Methods: The present study analysed Escherichia coli and Salmonella spp. isolated from faecal samples of 100 fattening pigs and from 52 samples of pork meat. Results: The results showed that the majority of the analysed meat samples were considered satisfactory in terms of microbiological quality (92.3% for E. coli and 94.2% for Salmonella spp.). Salmonella spp. was identified in 5.8% of the meat samples, whereas E. coli was detected in 89.5% of all samples (69.2% in meat and 100% in faecal samples). Furthermore, 1.9% of the faecal samples contained Shiga-toxin-producing E. coli and 3.9% contained enterotoxigenic E. coli. All sequenced isolates presented virulence genes for extraintestinal pathogenic E. coli. Moreover, 75.0% of E. coli isolates from meat and 71.8% from faeces samples showed antibiotic resistance, with 40.7% and 51.4%, respectively, being multidrug-resistant (MDR). The most prevalent resistances were to tetracycline, ampicillin, and sulfamethoxazole, and one E. coli isolate showed resistance to extended-spectrum β-lactamase. Conclusions: This study highlights the role of pigs as a potential source of human contamination and the importance of a One Health approach to ensure food safety and to promote public health.

High-resolution melting real-time polymerase chain reaction assays for subtyping of five diarrheagenic Escherichia coli by a single well in milk

Diarrheagenic Escherichia coli (DEC) is a kind of foodborne pathogen that poses a significant threat to both food safety and human health. To address the current challenges of high prevalence and difficult subtyping of DEC, this study developed a method that combined multiplex PCR with high-resolution melting (HRM) analysis for subtyping 5 kinds of DEC. The target genes are amplified by multiplex PCR in a single well, and HRM curve analysis was applied for distinct amplicons based on different melting temperature (Tm) values. The method enables discrimination of different DEC types based on characteristic peaks and distinct Tm values in the thermal melting curve. The assay exhibited 100% sensitivity and 100% specificity with a detection limit of 0.5 to 1 ng/μL. The results showed that different DNA concentrations did not influence the subtyping results, demonstrating this method owed high reliability and stability. In addition, the method was also used for the detection and subtyping of DEC in milk. This method streamlines operational procedures, shorts the detection time, and offers a novel tool for subtyping DEC.

Raw meat-based diet for pets: a neglected source of human exposure to Salmonella and pathogenic Escherichia coli clones carrying mcr, Portugal, September 2019 to January 2020

BackgroundThe pet industry is expanding worldwide, particularly raw meat-based diets (RMBDs). There are concerns regarding the safety of RMBDs, especially their potential to spread clinically relevant antibiotic-resistant bacteria or zoonotic pathogens.AimWe aimed to investigate whether dog food, including RMBD, commercially available in Portugal can be a source of Salmonella and/or other Enterobacteriaceae strains resistant to last-line antibiotics such as colistin.MethodsFifty-five samples from 25 brands (21 international ones) of various dog food types from 12 suppliers were screened by standard cultural methods between September 2019 and January 2020. Isolates were characterised by phenotypic and genotypic methods, including whole genome sequencing and comparative genomics.ResultsOnly RMBD batches were contaminated, with 10 of 14 containing polyclonal multidrug-resistant (MDR) Escherichia coli and one MDR Salmonella. One turkey-based sample contained MDR Salmonella serotype 1,4,[5],12:i:- ST34/cgST142761 with similarity to human clinical isolates occurring worldwide. This Salmonella exhibited typical antibiotic resistance (bla TEM + strA-strB + sul2 + tet(B)) and metal tolerance profiles (pco + sil + ars) associated with the European epidemic clone. Two samples (turkey/veal) carried globally dispersed MDR E. coli (ST3997-complexST10/cgST95899 and ST297/cgST138377) with colistin resistance (minimum inhibitory concentration: 4 mg/L) and mcr-1 gene on IncX4 plasmids, which were identical to other IncX4 circulating worldwide.ConclusionSome RMBDs from European brands available in Portugal can be a vehicle for clinically relevant MDR Salmonella and pathogenic E. coli clones carrying genes encoding resistance to the last-line antibiotic colistin. Proactive actions within the One Health context, spanning regulatory, pet-food industry and consumer levels, are needed to mitigate these public health risks.

Genomic characterization of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli from urban wastewater in Australia

This study investigates extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli isolates from Sydney's wastewater. These isolates exhibit resistance to critical antibiotics and harbor novel resistance mechanisms. The findings highlight the importance of wastewater-based surveillance in monitoring resistance beyond the clinical setting.

Listeria monocytogenes, Escherichia coli and Coagulase Positive Staphylococci in Cured Raw Milk Cheese from Alentejo Region, Portugal

Traditional cheeses are part of the Portuguese gastronomic identity, and raw milk of autochthonous species is a common primary ingredient. Here, we investigated the presence of Listeria monocytogenes, Coagulase Positive Staphylococci (CPS) and pathogenic Escherichia coli, as well as of indicator microorganisms (E. coli and other Listeria spp.) in 96 cured raw milk cheeses from the Alentejo region. Whole genome sequencing (WGS) of pathogenic E. coli and Listeria spp. as well as antimicrobial resistance (AMR) screening of E. coli isolates was also performed. L. monocytogenes, CPS > 104 cfu/g and Extraintestinal E. coli were detected in 15.6%, 16.9% and 10.1% of the samples, respectively. Moreover, L. monocytogenes > 102 cfu/g and Staphylococcal enterotoxins were detected in 4.2% and 2.2% of the samples, respectively. AMR was observed in 27.3% of the E. coli isolates, six of which were multidrug resistant. WGS analysis unveiled clusters of high closely related isolates for both L. monocytogenes and L. innocua (often correlating with the cheese producer). This study can indicate poor hygiene practices during milk collection/preservation or during cheese-making procedures and handling, and highlights the need of more effective prevention and control measures and of multi-sectoral WGS data integration, in order to prevent and detect foodborne bacterial outbreaks.

Genotypic and Phenotypic Characterization of Pathogenic Escherichia coli, Salmonella spp., and Campylobacter spp., in Free-Living Birds in Mainland Portugal

Birds are potential carriers of pathogens affecting humans and agriculture. Aiming to evaluate the occurrence of the top three most important foodborne pathogens in free-living birds in Portugal, we investigated 108 individual fecal samples from free-living birds and one pooled sample of gull feces (n = 50) for the presence of Escherichia coli (pathogenic and non-pathogenic), Salmonella spp. and Campylobacter spp. Virulence- and antimicrobial resistance- (AMR) associated genes were detected by PCR and Whole-Genome Sequencing (WGS), and phenotypic (serotyping and AMR profiles) characterization was performed. Overall, 8.9% of samples tested positive for pathogenic E. coli, 2.8% for Salmonella spp., and 9.9% for Campylobacter spp. AMR was performed on all pathogenic isolates and in a fraction of non-pathogenic E. coli, being detected in 25.9% of them. Ten of the tested E. coli isolates were multidrug-resistant (MDR), and seven of them were Extended-spectrum β-lactamase (ESBL) producers. Among Salmonella (n = 3) and Campylobacter (n = 9), only one strain of C. jejuni was identified as MDR. Most of the identified serotypes/sequence types had already been found to be associated with human disease. These results show that free-living birds in Portugal may act as carriers of foodborne pathogens linked to human disease, some of them resistant to critically important antimicrobials.

Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. in Two Natural Conservation Centers of Wildlife in Portugal: Genotypic and Phenotypic Characterization

Human-wildlife coexistence may increase the potential risk of direct transmission of emergent or re-emergent zoonotic pathogens to humans. Intending to assess the occurrence of three important foodborne pathogens in wild animals of two wildlife conservation centers in Portugal, we investigated 132 fecal samples for the presence of Escherichia coli (Shiga toxin-producing E. coli (STEC) and non-STEC), Salmonella spp. and Campylobacter spp. A genotypic search for genes having virulence and antimicrobial resistance (AMR) was performed by means of PCR and Whole-Genome Sequencing (WGS) and phenotypic (serotyping and AMR profiles) characterization. Overall, 62 samples tested positive for at least one of these species: 27.3% for STEC, 11.4% for non-STEC, 3.0% for Salmonella spp. and 6.8% for Campylobacter spp. AMR was detected in four E. coli isolates and the only Campylobacter coli isolated in this study. WGS analysis revealed that 57.7% (30/52) of pathogenic E. coli integrated genetic clusters of highly closely related isolates (often involving different animal species), supporting the circulation and transmission of different pathogenic E. coli strains in the studied areas. These results support the idea that the health of humans, animals and ecosystems are interconnected, reinforcing the importance of a One Health approach to better monitor and control public health threats.

Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin

Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.

First study on virulence genes, antimicrobial resistance, and integrons in Escherichia coli isolated from cage, free-range, and organic commercial eggs in Phayao Province, Thailand

Background and Aim:

Antimicrobial resistance (AMR) is a global problem that affects human and animal health, and eggs can act as a vehicle for pathogenic and non-pathogenic resistant bacteria in the food chain. Escherichia coli is an indicator of food contamination with fecal materials as well as the occurrence and levels of AMR. This study aimed to investigate the presence of AMR, integrons, and virulence genes in E. coli isolated from eggshell samples of three egg production systems, from supermarkets in Thailand.

Materials and Methods:

A total of 750 hen’s egg samples were purchased from supermarkets in Phayao Province: Cage eggs (250), free-range eggs (250), and organic eggs (250). Each sample was soaked in buffered peptone water (BPW), and the BPW samples were incubated at 37°C for 18–24 h. All samples were tested for E. coli by the standard conventional culture method. Then, all identified E. coli were tested for antimicrobial susceptibility to 15 antimicrobial agents by the agar disk diffusion method. All E. coli strains were subsequently found to have virulence genes and Classes 1 and 2 integrons by polymerase chain reaction.

Results:

Among the eggshell samples, 91 samples were identified as having E. coli (cage eggs, 24 strains; free-range eggs, 27 strains; and organic eggs, 40 strains). Then, among the E. coli strains, 47 (51.6%) were positive for at least one virulence gene. The proportion of AMR in the eggshell samples was 91.2% (83/91), and streptomycin (STR), ampicillin (AMP), and tetracycline (TET) had a high degree of resistance. Among the E. coli strains, 27 (29.7%) strains were positive for class 1 or 2 integrons, and integron-positive strains were commonly found in STR-, AMP-, and TET-resistant strains. Multidrug resistance (MDR) was detected in 57.1% (52/91) of the E. coli strains, with STR-AMP-TET (5.5%) as the most frequent pattern. The proportion of MDR in cage eggs was 75.0% (18/24), which was higher than in both free-range and organic eggs. On the other hand, 53.2% (25/47) of E. coli carrying virulence genes had MDR, distributed across the production systems as follows: Cage eggs, 76.9% (10/13); free-range eggs, 63.6% (7/11); and organic eggs, 34.8% (8/23).

Conclusion:

Escherichia coli was detected in eggshell samples from all three egg production systems. The high level of virulence genes, AMR, and integrons indicated the possibility of dissemination of AMR among pathogenic and commensal E. coli through eggshells. These findings could be a major concern to farmers, food handlers, and consumers, especially regarding raw egg consumption.

A one-step multiplex PCR-based assay for simultaneous detection and classification of virulence factors to identify five diarrheagenic E. coli pathotypes

Human diarrhea-causing strains of Escherichia coli are referred to as diarrheagenic E. coli (DEC). DEC can be divided into five main categories based on distinct epidemiological and clinical features, specific virulence determinants, and association with certain serotypes. In the present study, a simple and rapid one-step single reaction multiplex PCR (mPCR) assay was developed for the simultaneous identification and differentiation of five currently established DEC pathotypes causing gastrointestinal diseases. The mPCR incorporated 10 primer pairs to amplify 10 virulence genes specific to the different pathotypes (i.e., stx1 and stx2 for EHEC, elt and sth for ETEC, eaeA and bfpA for EPEC, aggR and astA for EAEC, and ipaH and invE for EIEC) and to generate DNA fragments of sufficiently different sizes to be unequivocally resolved. All strains were detected at concentrations ranging from 10⁴ to 10⁷ CFU/mL. To demonstrate the utility of the mPCR assay, 236 clinically isolated strains of DEC from two hospitals were successfully categorized. One-step mPCR technique reduced the cost and effort involved in the identification of various virulence factors in DEC. Thus, we demonstrated that the newly developed mPCR assay has the potential to be introduced as a diagnostic tool that can be utilized for the detection of DEC as an additional check in clinical laboratories and for confirmation in health and environment institutes, health centers, and reference laboratories.

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We developed a one-step single reaction mPCR to detect DEC strains.

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10 prominently expressed genes characteristic to the five pathotypes were assayed.

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All the strains were detected at concentrations ranging from 10⁴ to 10⁷ CFU/mL.

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We show cost- and time-effective detection of DEC in clinical cultured samples.

Genotyping Based on CRISPR Loci Diversity and Pathogenic Potential of Diarrheagenic Escherichia coli

Diarrheagenic Escherichia coli (DEC) can cause epidemic diarrhea worldwide. The pathogenic potential of different strains is diverse and the continuous emergence of pathogenic strains has brought serious harm to public health. Accurately distinguishing and identifying DEC with different virulence is necessary for epidemiological surveillance and investigation. Clustered regularly interspaced short palindromic repeats (CRISPR) typing is a new molecular method that can distinguish pathogenic bacteria excellently and has shown great promise in DEC typing. The purpose of this study was to investigate the discrimination of CRISPR typing method for DEC and explore the pathogenicity potential of DEC based on CRISPR types (CT). The whole genome sequences of 789 DEC strains downloaded from the database were applied CRISPR typing and serotyping. The D value (Simpson’s index) with 0.9709 determined that CRISPR typing had a higher discrimination. Moreover, the same H antigen strains with different O seemed to share more identical spacers. Further analyzing the strains CRISPR types and the number of virulence genes, it was found that there was a significant correlation between the CRISPR types and the number of virulence genes (p < 0.01). The strains with the largest number of virulence genes concentrated in CT25 and CT56 and the number of virulence genes in CT264 was the least, indicating that the pathway potential of different CRISPR types was variable. Combined with the Caco-2 cell assay of the laboratory strains, the invasion capacity of STEC strains of different CRISPR types was different and there was no significant difference in the invasion rate between different CRISPR type strains (p > 0.05). In the future, with the increase of the number of strains that can be studied experimentally, the relationship between CRISPR types and adhesion and invasion capacities will be further clarified.

Severe outbreak of bovine neonatal diarrhea in a dairy calf rearing unit with multifactorial etiology

This study describes the etiological diversity observed in a severe neonatal diarrhea outbreak with morbidity and mortality rates of 80 and 20%, respectively, with detection of mixed infections with viral, bacterial, and protozoan disease agents in a dairy calf rearing unit. Diarrheic fecal samples were collected from eight 5 to 18 days of age calves and were submitted to the investigation of the presence of rotavirus A (RVA), bovine coronavirus (BCoV), bovine kobuvirus (BKV), bovine viral diarrhea virus 1 and 2 (BVDV-1 and BVDV-2), enteropathogenic Escherichia coli (ETEC), Salmonella sp., and Cryptosporidium spp. Fragments of the small intestine of one calf with diarrhea that spontaneously died were submitted for histopathological analyses. The most frequent infectious agent detected in diarrheic fecal samples was BKV (8/8—100%), followed by RVA (5/8—62.5%), BVDV (5/8—62.5%), Cryptosporidium parvum (5/8—62.5%), ETEC (4/8—50%), and Cryptosporidium ryanae (1/8—12.5%). These etiological agents were found in mixed infections with two or more pathogens per diarrheic fecal sample. The association of viral and protozoan pathogens was the most frequently identified (37.5%) in these samples, followed by viral and bacterial (25%); viral, bacterial, and protozoan (25%); and only viral agents (12.5%). BCoV and Salmonella sp. were not identified in the diarrheic fecal samples analyzed. Additionally, histopathology of the small intestine diagnosed chronic lymphocytic enteritis. In conclusion, in calf rearing units, the adoption and strict monitoring of health management practices are critical to the success of this calf creation system.

Prevalence and Characterization of Quinolone-Resistance Determinants in Escherichia coli Isolated from Food-Producing Animals and Animal-Derived Food in the Philippines

Antimicrobial resistance to quinolones, which constitutes a threat to public health, has been increasing worldwide. In this study, we investigated the prevalence of quinolone-resistant determinants in Escherichia coli not susceptible to quinolones and isolated from food-producing animals and food derived from them, in the Philippines. A total of 791 E. coli strains were isolated in 56.4% of 601 beef, chicken, pork, egg, and milk samples, as well as environmental, cloacal, and rectal swab-collected samples from supermarkets, open markets, abattoirs, and poultry, swine, and buffalo farms. Using the disc diffusion method, it was determined that 78.6% and 55.4% of the isolates were resistant to at least one antimicrobial and multiple drugs, respectively. In 141 isolates not susceptible to quinolones, 115 (81.6%) harbored quinolone-resistant determinants and had mutations predominantly in the quinolone-resistance determining regions (QRDRs) of gyrA and parC. Plasmid-mediated, quinolone resistance (PMQR) and Qnr family (qnrA1, qnrB4, and qnrS1) genes were detected in all isolates. Forty-eight sequence types were identified in isolates harboring mutations in QRDR and/or PMQR genes by multilocus sequence typing analysis. Moreover, 26 isolates harboring mutations in QRDR and/or PMQR genes belonged mostly to phylogroup B1 and Enteroaggregative E. coli. In conclusion, a high prevalence of E. coli was found in food-producing animals and products derived from them, which could potentially spread high-risk clones harboring quinolone-resistance determinants.

Antimicrobial resistance and genomic characterisation of Escherichia coli isolated from caged and non-caged retail table eggs in Western Australia

Foodborne exposure to antimicrobial-resistant bacteria is a growing global health concern. Escherichia coli (E. coli) is well recognised as an indicator of food contamination with faecal materials. In the present study, we investigated the occurrence of E. coli in table eggs sold at retail supermarkets in Western Australia (WA). A total of 2172 visually clean and intact retail eggs were purchased between October 2017 and June 2018. A single carton containing a dozen eggs was considered as a single sample resulting a total of 181 samples. The shells and contents of each sample were separately pooled and tested using standard culture-based methods. Overall, generic E. coli was detected in 36 (19.8%; 95% confidence interval: 14.3; 26.4) of the 181 tested retail egg samples. We characterised 100 of the recovered E. coli isolates for their phenotypic antimicrobial resistance using minimum inhibitory concentration (MIC). A subset of E. coli isolates (n = 14) were selected on the basis of their MIC patterns, and were further characterised using whole genome sequencing (WGS). Fifty-seven (57%) of the recovered generic E. coli isolates (n = 100) were resistant to at least one of the 14 antimicrobials included in the MIC testing panel, of which 22 isolates (22%) showed multi-class resistance. The highest frequencies of non-susceptibility of E. coli isolated from WA retailed eggs were against tetracycline (49%) and ampicillin (36%). WGS revealed that tet(A) and bla_TEM-1B genes were present in most of the isolates exhibiting phenotypic resistance to tetracycline and ampicillin, respectively. The majority (98%) of the characterised E. coli isolates were susceptible to ciprofloxacin and azithromycin, and none were resistant to the cephalosporin antimicrobials included in the MIC panel. Two isolates demonstrated reduced susceptibility to ciprofloxacin, with MICs of 0.125 and 0.25 mg/L, and WGS revealed the presence of plasmid mediated qnrs1 gene in both isolates. This is the first report on detection of non-wild-type resistance to fluoroquinolones in supermarket eggs in Australia; one of the two isolates was from a cage-laid eggs sample while the other was from a barn-laid retail eggs sample. Fluoroquinolones have never been permitted for use in poultry farms in Australia. Thus, the detection of low-level ciprofloxacin-resistant E. coli in the absence of local antimicrobial selection pressure at the Australian layer farms warrants further research on the potential role of the environment or human-related factors in the transmission of antimicrobial resistance. The results of this study add to the local and global understanding of antimicrobial resistance spread in foods of animal origin.

Coinfection with Human Norovirus and Escherichia coli O25:H4 Harboring Two Chromosomal blaCTX-M-14 Genes in a Foodborne Norovirus Outbreak in Shizuoka Prefecture, Japan

ABSTRACT

Hospital-acquired infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are a global problem. Healthy people can carry ESBL-producing E. coli in the intestines; thus, E. coli from healthy people can potentially cause hospital-acquired infections. Therefore, the transmission routes of ESBL-producing E. coli from healthy persons should be determined. A foodborne outbreak of human norovirus (HuNoV) GII occurred at a restaurant in Shizuoka, Japan, in 2018. E. coli O25:H4 was isolated from some of the HuNoV-infected customers. Pulsed-field gel electrophoresis showed that these E. coli O25:H4 strains originated from one clone. Because the only epidemiological link among the customers was eating food from this restaurant, the customers were concurrently infected with E. coli O25:H4 and HuNoV GII via the restaurant food. Whole genome analysis revealed that the E. coli O25:H4 strains possessed genes for regulating intracellular iron and expressing the flagellum and flagella. Extraintestinal pathogenic E. coli often express these genes on the chromosome. Additionally, the E. coli O25:H4 strains had plasmids harboring nine antimicrobial resistance genes. These strains harbored ESBL-encoding blaCTX-M-14 genes on two loci of the chromosome and had higher ESBL activity. Multilocus sequence typing and fimH subtyping revealed that the E. coli O25:H4 strains from the outbreak belonged to the subclonal group, ST131-fimH30R, which has been driving ESBL epidemics in Japan. Because the E. coli O25:H4 strains isolated in the outbreak belonged to a subclonal group spreading in Japan, foods contaminated with ESBL-producing E. coli might contribute to spreading these strains among healthy persons. The isolated E. coli O25:H4 strains produced ESBL and contained plasmids with multiple antimicrobial resistance genes, which may make it difficult to select antimicrobials for treating extraintestinal infections caused by these strains.

HIGHLIGHTS

Virulence Profiles of Diarrheagenic Escherichia coli Isolated from the Western Region of Ghana

Diarrheagenic Escherichia coli (DEC), an important agent of infectious diarrhea, is constantly evolving, making its periodic monitoring necessary. However, the DEC genotypes in Ghana remain uncharacterized. We focused on characterizing the molecular serotypes, virulence factors, multilocus sequence types, and the phylogenetic relatedness among different DEC pathotypes recovered from stool samples of pediatric patients with symptoms of diarrhea from the Western region of Ghana. We detected all five common DEC pathotypes, with the majority of the isolates being enterotoxigenic E. coli (ETEC) harboring the heat-labile enterotoxin gene. The DEC strains exhibited diverse serotypic identity with novel and previously reported outbreak strains. Sequence types (ST) ST38, ST316, and ST1722 were most prevalent, and clonal complex 10 (CC10) was the most common CC. A close evolutionary distance was observed among most of the isolates. Coli surface antigen 6 was the most prevalent (44%, n = 11) ETEC-specific colonization factor. Nearly all the isolates harbored lpfA, and the frequencies of other virulence genes such as pap and cnf1 were 7.9% and 18.4%, respectively. This study provides insights into the important and novel genotypes circulating in the Western region of Ghana that should be monitored for public health.

Evolution of diarrheagenic Escherichia coli pathotypes in India

CONTEXT:

Diarrheagenic Escherichia coli (DEC) is the leading cause of infectious diarrhea in developing countries. On the basis of virulence and phenotypic characteristics, the DEC is categorized into multiple pathotypes. Each pathotype has different pathogenesis and geographical distribution. Thus, the proper management of disease relies on rapid and accurate identification of DEC pathotypes.

AIMS:

The aim of the study was to determine the prevalence of DEC pathotypes in India.

MATERIALS AND METHODS:

A cross-sectional study was carried out between January 2008 and December 2012 at Jawaharlal Nehru Medical College and KLES Dr. Prabhakar Kore Hospital and Medical Research Center, Belgaum (Karnataka), India. A total of 300 stool samples were collected from diarrhea patients with age >3 months. The DEC was identified by both conventional and molecular methods.

RESULTS:

Of 300 samples, E. coli were detected in 198 (66%) and 170 (56.6%) samples by culture and polymerase chain reaction, respectively. Among DEC (n = 198) isolates, eae gene (59.5%) was the most prevalent followed by stx (27.7%), east (27.2%), elt (12.6%), est (10.6%), ipaH (5.5%), and eagg (1.5%) genes. On the basis of virulence genes, enteropathogenic E. coli (33.8%) was the most common pathotype followed by Shiga toxin-producing E. coli (STEC, 23.2%), enterotoxigenic E. coli (ETEC, 13.6%), enteroinvasive E. coli (5.5%), enteroaggregative heat-stable enterotoxin 1-harboring E. coli (EAST1EC, 4.5%), STEC/ETEC (3.5%), STEC/enteroaggregative E. coli (STEC/EAEC, 1.0%), and EAEC (0.05%).

CONCLUSIONS:

The hybrid DEC is potentially more virulent than basic pathotypes. The pathotyping should be included in clinical settings for the proper management of DEC-associated diarrhea.

Identification of diarrheagenic Escherichia coli by a new multiplex PCR assay and capillary electrophoresis

Diarrheagenic Escherichia coli (DEC) is a set of the most common pathogens causing diarrhea. DEC strains are classified into five pathotypes based on the possession of different virulence genes: enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC) or Shiga toxin-producing E. coli (STEC), enteroaggregative E. coli (EAEC), enterotoxigenic E. coli (ETEC), and enteroinvasive E. coli (EIEC). The development of an easy-to-use method to detect the specific virulence genes and distinguish the pathotypes is essential for the diagnosis and surveillance of DEC infections. In this study, a multiplex PCR assay (mPCR) specific to nine virulence genes and an internal control was designed for the identification of five DEC pathotypes. A temperature switch PCR (TSP) strategy was used in the PCR amplification. The PCR products were detected by capillary electrophoresis. The limit of detection (LOD) of the 10-plex reaction was 5 × 10³ copies/reaction for stx2 and 5 × 10² copies/reaction for the other targets. The mPCR showed very high specificity, and inclusivity and exclusivity were both 100%. When the mPCR assay was used for the detection of 221 cryopreserved diarrhea specimens, DEC colonies were detected from 49 specimens, and the positive rate was 22.2%. The mPCR assay was sensitive and specific, and the amplified product could be analyzed easily. Thus, this method could be used effectively to identify the suspected colonies of DEC in the primary culture of the specimen.

Comparative Evaluation of Seegene Allplex Gastrointestinal, Luminex xTAG Gastrointestinal Pathogen Panel, and BD MAX Enteric Assays for Detection of Gastrointestinal Pathogens in Clinical Stool Specimens

CONTEXT.—

Infectious gastroenteritis is caused by various pathogens, including bacteria, viruses, and parasites.

OBJECTIVE.—

To compare the performance of Seegene Allplex Gastrointestinal (24 targets: 13 bacteria, 5 viruses, and 6 parasites in 4 panels), Luminex xTAG Gastrointestinal Pathogen Panel (15 targets: 9 bacteria, 3 viruses, and 3 parasites), and BD MAX Enteric panel (5 bacteria and 3 parasites). We estimated the agreement among 3 molecular assays.

DESIGN.—

A total of 858 stool samples (554 bacterial/parasite and 304 viral pathogens) were included. A consensus positive/negative was defined as concordant results from at least 2 tests. To evaluate the agreement among the assays, κ value was calculated.

RESULTS.—

The overall positive percentage agreements of Seegene, Luminex, and BD MAX were 94% (258 of 275), 92% (254 of 275), and 78% (46 of 59), respectfully. For Salmonella, Luminex showed low negative percentage agreement because of frequent false positives (n = 31) showing low median fluorescent intensity. For viruses, positive/negative percentage agreements of Seegene and Luminex were 99%/96% and 93%/99%, respectively. Compared with routine microbiology testing, Seegene, Luminex, and BD MAX additionally identified 39, 40, and 12 pathogens, respectively. Sixty-one cases (16 cases with Seegene, 51 cases with Luminex, and 1 case with BD MAX) showed positive results for multiple pathogens, but only 3 were consensus positive.

CONCLUSIONS.—

These multiplex molecular assays appear to be promising tools for the detection and identification of multiple gastrointestinal pathogens simultaneously. However, careful interpretation of positive results for multiple pathogens is required.

Detection and Categorization of Diarrheagenic Escherichia coli with Auto-microfluidic Thin-film Chip Method

Diarrheagenic Escherichia coli (DEC) causes human diarrhea symptom in both healthy and immunocompromised individuals. An auto-microfluidic thin-film chip (AMTC) instrument integrating one-step multiplex PCR (mPCR) with reverse dot blot hybridization (RDBH) was developed for high-throughput detection of DEC. The novel mPCR method was developed by designing 14 specific primers and corresponding probes. 14 indexes including an endogenous gene (uidA) and 13 pathogenic genes (stx1, stx2, escV, ipaH, invE, estB, lt, pic, aggR, astA, bfpB, sth and stp) of DEC were detected. This one-step mPCR + RDBH approach is useful for simultaneous detection of numerous target genes in a single sample, whose specificity and availability have been confirmed on the positive control of 11 DEC strains. In addition, with 300 diarrheal stool samples being detected by this method, 21 were found to contain five major DEC strains. Compared with monoplex PCR and previous one-step mPCR approach, this method could detect ipaH and estB, and compared with current commercial kit, the relevance ratio of DEC detected by the AMTC method was increased by 1% in stool samples. Furthermore, the novel integration AMTC device could be a valuable detection tool for categorization of E. coli.

Short communication: Detection of stx2 and elt genes in bovine milk by using a multiplex PCR system

The aim of this study was to detect 2 important toxin genes from diarrheagenic Escherichia coli (DEC) in bovine milk using a new multiplex PCR. To standardize the multiplex PCR, the stx2 and elt genes were investigated for the detection of Shiga toxin-producing Escherichia coli (STEC) and enterotoxigenic E. coli (ETEC), respectively. The DNA template was prepared with a thermal procedure (boiling) and a commercial kit. Samples consisted of UHT and pasteurized milk, both skimmed, and STEC and ETEC were tested in concentrations between 10¹ and 10⁹ cfu/mL. With the thermal procedure, the multiplex PCR system detected both pathotypes of E. coli at 10⁹ cfu/mL in UHT and pasteurized milk. When the commercial kit was used for template preparation, STEC and ETEC could be detected at concentrations as low as 10⁴ cfu/mL in UHT and pasteurized milk. Negative controls (Listeria monocytogenes, Salmonella Typhimurium, Salmonella Enteritidis, and Escherichia coli strain APEC 13) were not amplified with the multiplex PCR. These results indicate that the multiplex PCR was a rapid (less than 6 h) and efficient method to detect STEC and ETEC in milk using different methods for DNA preparation; however, the commercial kit was more sensitive than the thermal procedure.

Detection and risk assessment of diarrheagenic E. coli in recreational beaches of Brazil

Marine beaches are important recreational and economic resources in Brazil, but the beaches' water quality is negatively impacted by the discharge of domestic sewage effluent. The occurrence of diarrheagenic Escherichiacoli among the E. coli isolated from three Brazilian marine beaches was investigated. Multiplex and single step PCR were used to screen 99 E. coli isolates for ten target toxin genes. Six toxin genes, stx1, eae, estp, esth, astA, and bfpA, were identified in 1% to 35% of the isolates. A quantitative microbial risk assessment (QMRA) of human exposure to diarrheagenic E. coli during marine recreation was carried out. The results indicated that the diarrheagenic E. coli risk is well below the U.S. EPA's recommended daily recreational risk benchmark. However, the overall recreational health risk due to all pathogens in the water could be much higher and exceeded the U.S. EPA's benchmark.

Detection of Dientamoeba fragilis in Portuguese children with acute gastroenteritis between 2011 and 2013

Dientamoeba fragilis is an inhabitant of human gastrointestinal tract with a worldwide distribution. The first description considered this protozoan a rare and harmless commensal, since then it has struggled to gain recognition as a pathogen. Commercial multiplex real-time PCR was used to detect D. fragilis in fecal samples from hospitalized children (⩽18 years) with acute gastrointestinal disease, admitted to two hospitals of Lisbon area, with different demographic characteristics. A total of 176 children were studied, 103 (58·5%) male, 144 (81·8%) children between 0 and 5 years and 32 (18·2%) above 6 years old. The overall protozoa frequency considering the four tested microorganisms were 8·5% (15/176), and the most frequently found protozoan was D. fragilis, 6·3% (11/176). Dientamoeba fragilis frequency was higher among older children (21·9%), than younger children (2·8%), and greater in boys (6·8%) than in girls (5·5%). All positive children presented with diarrhoea associated with vomiting, fever and abdominal pain. Infection was associated with the age of children (P < 0·001), school attendance (P = 0·002) and consumption of certain foods (P = 0·014), e.g. cakes with crème and ham. The frequency of diantamoebiasis found in a cohort of hospitalized Portuguese children, with acute gastrointestinal disease, could be considered a very high value when compared with the protozoan frequency normally associated with this pathology.

Comparing the microbiological status of pre- and postharvest produce from small organic production

Consumption of locally, organically grown produce is increasing in popularity. Organic farms typically produce on a small scale, have limited resources, and adopt low technology harvest and postharvest handling practices. Data on the food safety risk associated with hand harvesting, field packing, and packing-house handling with minimal treatment, at this production scale, are lacking. We followed produce from small organic farms from the field through postharvest handling and packing. Pre- and postharvest produce (177 samples) and water (29 samples) were collected and analyzed quantitatively for Escherichia coli, total coliforms (TC), aerobic bacteria (APC), yeasts, molds (M), and enteric pathogens. No pathogens were recovered. E. coli was detected in 3 (3.6%) of 83 preharvest produce samples, 2 (6.3%) of 32 unwashed and 0 of 42 washed postharvest produce samples, and 10 (34.5%) of 29 water samples. No correlation was found between bacterial levels in irrigation water and those on produce. Postharvest handling without washing was a factor for APC and M counts on tomatoes, with lower frequencies postharvest. Postharvest handling with washing was a factor for leafy greens for TC counts, with higher frequencies postharvest. APC (P = 0.03) and yeast (P = 0.05) counts were higher in preharvest than in unwashed postharvest tomatoes. Washed postharvest leafy greens had higher M counts (P = 0.03) and other washed produce had higher TC counts (P = 0.01) than did their preharvest counterparts. Barriers were found to the use of sanitizer in wash water for leafy greens among small farms using organic practices. Hand harvesting and dry handling did not appear to be associated with a significant food safety risk, but washed leafy greens carried higher levels of some microbial indicators, possibly because of the lack of sanitizer in the wash water. The development of resources and materials customized for this sector of growers could enhance dissemination of information on best practices for handling of leafy greens.

Relationship among Shigella spp. and enteroinvasive Escherichia coli (EIEC) and their differentiation

Shigellosis produces inflammatory reactions and ulceration on the intestinal epithelium followed by bloody or mucoid diarrhea. It is caused by enteroinvasive E. coli (EIEC) as well as any species of the genus Shigella, namely, S. dysenteriae, S. flexneri, S. boydii, and S. sonnei. This current species designation of Shigella does not specify genetic similarity. Shigella spp. could be easily differentiated from E. coli, but difficulties observed for the EIEC-Shigella differentiation as both show similar biochemical traits and can cause dysentery using the same mode of invasion. Sequencing of multiple housekeeping genes indicates that Shigella has derived on several different occasions via acquisition of the transferable forms of ancestral virulence plasmids within commensal E. coli and form a Shigella-EIEC pathovar. EIEC showed lower expression of virulence genes compared to Shigella, hence EIEC produce less severe disease than Shigella spp. Conventional microbiological techniques often lead to confusing results concerning the discrimination between EIEC and Shigella spp. The lactose permease gene (lacY) is present in all E. coli strains but absent in Shigella spp., whereas β-glucuronidase gene (uidA) is present in both E. coli and Shigella spp. Thus uidA gene and lacY gene based duplex real-time PCR assay could be used for easy identification and differentiation of Shigella spp. from E. coli and in particular EIEC.

A sensitive and specific molecular tool for detection of both typical and atypical enteroaggregative Escherichia coli

A multiplex PCR has been standardized and evaluated for the identification of both typical and atypical enteroaggregative Escherichia coli (EAEC). The assay detecting aaiA, aaiG, aggR and aatA presented 94.8% of sensitivity, 94.3% of specificity and was able to efficiently detect both groups of EAEC among E. coli isolated from stool cultures.

Development and accuracy of quantitative real-time polymerase chain reaction assays for detection and quantification of enterotoxigenic Escherichia coli (ETEC) heat labile and heat stable toxin genes in travelers' diarrhea samples

Enterotoxigenic Escherichia coli (ETEC), the leading bacterial pathogen of travelers' diarrhea, is routinely detected by an established DNA hybridization protocol that is neither sensitive nor quantitative. Quantitative real-time polymerase chain reaction (qPCR) assays that detect the ETEC toxin genes eltA, sta1, and sta2 in clinical stool samples were developed and tested using donor stool inoculated with known quantities of ETEC bacteria. The sensitivity of the qPCR assays is 89%, compared with 22% for the DNA hybridization assay, and the limits of detection are 10,000-fold lower than the DNA hybridization assays performed in parallel. Ninety-three clinical stool samples, previously characterized by DNA hybridization, were tested using the new ETEC qPCR assays. Discordant toxin profiles were observed for 22 samples, notably, four samples originally typed as ETEC negative were ETEC positive. The qPCR assays are unique in their sensitivity and ability to quantify the three toxin genes in clinical stool samples.