Multiplex PCR assay for identification of human diarrheagenic Escherichia coli

Evolution and zoonotic risk of O1:K1 and O2:K1 avian pathogenic Escherichia coli

The O1 and O2 serogroups of avian pathogenic E. coli (APEC) and human extraintestinal pathogenic E. coli (huExPEC) are closely related, but their evolutionary relationships need to be further elucidated. This study classified nineteen O1 and O2 APEC into rpoB sequence types (RSTs) and compared them with reference huExPEC using molecular prophage typing, virulence and antibiotic resistance gene profiling, and comparative genomics. Most O1:K1 and O2:K1 APEC (73.7 %) were classified as RST46-1 and RST47-9. RST47-9 is unique to Korean O1 APEC and likely derives from RST46-1 APEC. The six APEC showed high genome coverage/identity with the Korean RST46-1 huExPEC. Based on RST network and comparative genomics, we hypothesized that the O1 antigen first appeared in RST19-1 and O2 in RST24-1 E. coli in humans. Then, O1 and O2-antigen horizontally transferred to human RST46-1, where a unique K1 capsule (K1-cps) first appeared. The Korean APEC and huExPEC share evolutionary CRISPR spacers but differ in molecular antibiograms and prophage contents. Thus, RST46-1 huExPEC transmitted and evolved in poultry. The zoonotic risks remain unknown, but the substantial virulence of the RST46-1 APEC indicates that the reverse zoonotic risk of huExPEC in poultry is alarming.

Could Exotic Birds Play a Significant Role in the Emergence of Antibiotic-Resistant Microorganisms?

Despite limited studies, free-living birds are considered reservoirs of several diseases, including zoonotic diseases. Thus, we aimed to investigate the presence and characteristics of Campylobacter spp., Escherichia coli, and Salmonella spp. in wild birds assessing their potential risks to human and animal health. Fecal samples were collected from wild and exotic rescued birds, as well as exotic parrots from commercial breeding facilities. Campylobacter spp. and Salmonella spp. were not detected in the samples. E. coli was biochemically confirmed in 58.33% of the samples, resulting nine distinct isolates. PCR analysis identified no enteroinvasive or enteropathogenic E. coli strains, but two isolates were characterized as avian pathogenic E. coli (APEC). The isolates were inoculated into chicken embryos to determine their pathogenicity index, utilizing commensal and pathogenic E. coli strains as controls. All isolates demonstrated higher pathogenicity compared to probiotic bacteria and commensal E. coli. Specifically, two isolates exhibited pathogenicity levels comparable to the positive control (APEC ST131). Furthermore, for the minimum inhibitory concentration (MIC) test, we evaluated 7 antibiotics: ampicillin, ceftazidime, cefotaxime, ciprofloxacin, levofloxacin, colistin, and sulfamethoxazole combined with trimethoprim. Four isolates were classified as multidrug-resistant and the highest level of resistance was to fluoroquinolones. This work demonstrated that wild or captive exotic birds can excrete potentially pathogenic and/or multidrug-resistant E. coli, which may impact the health of other animals and humans.

An Outbreak of Shiga Toxin-Positive Enteroaggregative Escherichia coli O104:H4 Related Hemolytic Uremic Syndrome in Turkey: A Multicenter Study

INTRODUCTION

Serious outbreaks of Shiga toxin-producing Escherichia coli-associated hemolytic uremic syndrome (STEC-HUS) have been reported globally. In 2011, Germany experienced a significant outbreak of HUS caused by enteroaggregative E. coli (EAEC) O104:H4 strain. Since then, no other outbreaks of this strain have been reported. This study aims to evaluate pediatric patients affected by the second documented worldwide outbreak of STEC-HUS (EAEC O104:H4 serotype) contaminating local drinking water.

METHODS

Medical records of patients hospitalized in five pediatric intensive care units (PICUs) diagnosed with STEC-HUS between July and September 2022 were evaluated retrospectively.

RESULTS

Eighteen patients (14 girls and 4 boys) were enrolled in the study. The median age was 7.4 (Interquartile range [IQR] 1.3-17) years. Abdominal pain was the most common symptom (100%). The mean duration between symptom onset and development of STEC-HUS was 3 days (IQ 1-9). EAEC O104:H4 serotype was detected in the stool samples of 8 patients. Neurological involvement was observed in 3 patients, cardiac involvement in 2 patients, and both in 1 patient. Two patients required respiratory support and dialysis was performed in 16 (88.8%) patients. Plasmapheresis was administered to 2 patients, and eculizumab was given to four. No mortality was reported during follow-up; the mean durations of PICU and hospital stays were 11.3 and 31.6 days, respectively.

CONCLUSION

Outbreaks of HUS can have serious impacts on both mortality and morbidity. However, timely diagnosis and implementation of appropriate supportive care, including dialysis, respiratory support, and medical treatment for eligible patients, can lead to favorable outcomes.

Molecular characterization of common zoonotic protozoan parasites and bacteria causing diarrhea in dairy calves in Ningxia Hui Autonomous Region, China

Diarrhea caused by zoonotic pathogens is one of the most common diseases in dairy calves, threatening the health of young animals. Humans are also at risk, in particular children. To explore the pathogens causing diarrhea in dairy calves, the present study applied PCR-based sequencing tools to investigate the occurrence and molecular characteristics of three parasites (Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi) and three bacterial pathogens (Escherichia coli, Clostridium perfringens, and Salmonella spp.) in 343 fecal samples of diarrheic dairy calves from five farms in Lingwu County, Ningxia Hui Autonomous Region, China. The total positive rate of these pathogens in diarrheic dairy calves was 91.0% (312/343; 95% CI, 87.9-94.0), with C. perfringens (61.5%, 211/343; 95% CI, 56.3-66.7) being the dominant one. Co-infection with two to five pathogens was found in 67.3% (231/343; 95% CI, 62.4-72.3) of investigated samples. There were significant differences (p < 0.05) in the positive rates of Cryptosporidium spp. and diarrheagenic E. coli among farms, age groups, and seasons. Two Cryptosporidium species (C. parvum and C. bovis) and five gp60 subtypes of C. parvum (IIdA15G1, IIdA20G1, IIdA19G1, IIdA14G1, and a novel IIdA13G1) were identified. Two assemblages (assemblage E and zoonotic assemblage A) of G. duodenalis and six ITS genotypes of E. bieneusi (J, Henan-IV, EbpC, I, EbpA, and ESH-01) were observed. Four virulence genes (eaeA, stx1, stx2, and st) of diarrheagenic E. coli and one toxin type (type A) of C. perfringens were detected. Our study enriches our knowledge on the characteristics and zoonotic potential of diarrhea-related pathogens in dairy calves.

Characterization of diarrheagenic Escherichia coli from different cattle production systems in Brazil

Diarrheagenic E. coli (DEC) can cause severe diarrhea and is a public health concern worldwide. Cattle are an important reservoir for this group of pathogens, and once introduced into the abattoir environment, these microorganisms can contaminate consumer products. This study aimed to characterize the distribution of DEC [Shiga toxin-producing E. coli (STEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), and enteroaggregative E. coli (EAEC)] from extensive and intensive cattle production systems in Brazil. Samples (n = 919) were collected from animal feces (n = 200), carcasses (n = 600), meat cuts (n = 90), employee feces (n = 9), and slaughterhouse water (n = 20). Virulence genes were detected by PCR in 10% of animal samples (94/919), with STEC (n = 81) as the higher prevalence, followed by EIEC (n = 8), and lastly EPEC (n = 5). Animals raised in an extensive system had a higher prevalence of STEC (average 48%, sd = 2.04) when compared to animals raised in an intensive system (23%, sd = 1.95) (Chi-square test, P < 0.001). From these animals, most STEC isolates only harbored stx2 (58%), and 7% were STEC LEE-positive isolates that were further identified as O157:H7. This study provides further evidence that cattle are potential sources of DEC, especially STEC, and that potentially pathogenic E. coli isolates are widely distributed in feces and carcasses during the slaughter process.

Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections

Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance.

IMPORTANCE

Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.

Detection and characterization of potentially hybrid enteroaggregative Escherichia coli (EAEC) strains isolated from urinary tract infection

Uropathogenic Escherichia coli (UPEC) have the potential to receive the virulence markers of intestinal pathotypes and transform into various important hybrid pathotypes. This study aimed to investigate the frequency and characteristics of hybrid enteroaggregative E. coli (EAEC)/UPEC strains. Out of 202 UPEC strains, nine (4.5%) were detected as hybrid EAEC/UPEC. These strains carried one to four iron uptake systems. Among nine investigated pathogenicity islands (PAIs), PAI IV536, PAI II536, and PAI ICFT073 were found in 9 (100%), 3 (33.3%), and 1 (11.1%) strains, respectively. The chuA and sitA genes were detected in 5 (55.5%) and 3 (33.3%) hybrid strains, respectively. Six hybrid strains were found to be typical extraintestinal pathogenic E. coli (ExPEC) according to their virulence traits. Most of the hybrid strains belonged to the phylogenetic group E (6/9). Among the hybrid strains, seven (7/9) were able to form biofilm and adhere to cells; however, only two strains penetrated into the HeLa cells. Our findings reveal some of the virulence characteristics of hybrid strains that lead to fitness and infection in the urinary tract. These strains, with virulence factors of intestinal and non-intestinal pathotypes, may become emerging pathogens in clinical settings; therefore, further studies are needed to reveal their pathogenicity mechanisms and so that preventive measures can be taken.

Tracing the Evolutionary Pathways of Serogroup O78 Avian Pathogenic Escherichia coli

Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To trace these evolutionary pathways, we classified 3101 E. coli strains into 306 subgenotypes according to the numbers and types of single nucleotide polymorphisms (RST0 to RST63-1) relative to the consensus sequence (RST0) of the RNA polymerase beta subunit gene and performed network analysis. The E. coli strains showed four apparently different evolutionary pathways (I-1, I-2, I-3, and II). The thirty-two Korean O78 APEC strains tested in this study were classified into RST4-4 (45.2%), RST3-1 (32.3%), RST21-1 (12.9%), RST4-5 (3.2%), RST5-1 (3.2%), and RST12-6 (3.2%), and all RSTs except RST21-1 (I-2) may have evolved through the same evolutionary pathway (I-1). A comparative genomic study revealed the highest relatedness between O78 strains of the same RST in terms of genome sequence coverage/identity and the spacer sequences of CRISPRs. The early-appearing RST3-1 and RST4-4 prevalence among O78 APEC strains may reflect the early settlement of O78 E. coli in chickens, after which these bacteria accumulated virulence and antibiotic resistance genes to become APEC strains. The zoonotic risk of the conventional O78 APEC strains is low at present, but the appearance of genetically distinct and multiple virulence gene-bearing RST21-1 O78 APEC strains may alert us to a need to evaluate their virulence in chickens as well as their zoonotic risk.

Resistance and Virulence Surveillance in Escherichia coli Isolated from Commercial Meat Samples: A One Health Approach

Escherichia coli is a key indicator of food hygiene, and its monitoring in meat samples points to the potential presence of antimicrobial-resistant strains capable of causing infections in humans, encompassing resistance profiles categorized as serious threats by the Centers for Disease Control and Prevention (CDC), such as Extended-Spectrum Beta-Lactamase (ESBL)-a problem with consequences for animal, human, and environmental health. The objective of the present work was to isolate and characterize ESBL-producing E. coli strains from poultry, pork, and beef meat samples, with a characterization of their virulence and antimicrobial resistance profiles. A total of 450 meat samples (150 chicken, 150 beef, and 150 pork) were obtained from supermarkets and subsequently cultured in medium supplemented with cefotaxime. The isolated colonies were characterized biochemically, followed by antibiogram testing using the disk diffusion technique. Further classification involved biofilm formation and the presence of antimicrobial resistance genes (blaCTX-M, AmpC-type, mcr-1, and fosA3), and virulence genes (eaeA, st, bfpA, lt, stx1, stx2, aggR, iss, ompT, hlyF, iutA, iroN, fyuA, cvaC, and hylA). Statistical analysis was performed via the likelihood-ratio test. In total, 168 strains were obtained, with 73% originating from chicken, 22% from pork, and 17% from beef samples. Notably, strains exhibited greater resistance to tetracycline (51%), ciprofloxacin (46%), and fosfomycin (38%), apart from β-lactams. The detection of antimicrobial resistance in food-isolated strains is noteworthy, underscoring the significance of antimicrobial resistance as a global concern. More than 90% of the strains were biofilm producers, and strains carrying many ExPEC genes were more likely to be biofilm formers (OR 2.42), which increases the problem since the microorganisms have a greater chance of environment persistence and genetic exchange. Regarding molecular characterization, bovine samples showed a higher prevalence of blaCTX-M-1 (OR 6.52), while chicken strains were more likely to carry the fosA3 gene (OR 2.43, CI 1.17-5.05) and presented between 6 to 8 ExPEC genes (OR 2.5, CI 1.33-5.01) compared to other meat samples. Concerning diarrheagenic E. coli genes, two strains harbored eae. It is important to highlight these strains, as they exhibited both biofilm-forming capacities and multidrug resistance (MDR), potentially enabling colonization in diverse environments and causing infections. In conclusion, this study underscores the presence of β-lactamase-producing E. coli strains, mainly in poultry samples, compared to beef and pork samples. Furthermore, all meat sample strains exhibited many virulence-associated extraintestinal genes, with some strains harboring diarrheagenic E. coli (DEC) genes.

Development and application of the MIRA and MIRA-LFD detection methods of Spiroplasma eriocheiris

The tremor disease (TD) caused by Spiroplasma eriocheiris is the most destructive disease of the Chinese mitten crab, Eriocheir sinensis. This study attempts to construct Multienzyme Isothermal Rapid Amplification (MIRA), a quick and simple nucleic acid amplification method that operates at room temperature. Based on the gene sequences of S. eriocheiris, appropriate amplification primers were constructed and screened in this investigation. Both the relevant specific probe and the chosen specific amplification primers were designed and labeled. The MIRA and MIRA-LFD reaction conditions were then optimized. The result showed MIRA and MIRA-FFD could identify S. eriocheiris at 37 °C in 30 min and 15 min, respectively. To investigate the specificity of MIRA and MIRA-LFD, three Gram-negative bacteria (Bacillus subtilis, Bacillus thuringiensis, and Staphylococcus aureus), three Gram-positive bacteria (Escherichia coli, Aeromonas hydrophila, and Salmonella typhimurium) and S. eriocheiris were selected. The result showed MIRA and MIRA-LFD were highly specific to S. eriocheiris and did not react with other six pathogens. The sensitivities of PCR, MIRA, and MIRA-LFD were then evaluated. The result showed the detection limit of PCR is 1 ng/L whereas the detection limit of MIRA and MIRA-LFD is 10 pg/L. Finally, the established MIRA and MIRA-LFD detection methods had the advantages of being quick, sensitive, and specific for S. eriocheiris detection, as well as not requiring any specialized equipment.

Molecular Characterization of Cryptosporidium spp., Giardia duodenalis, Enterocytozoon bieneusi and Escherichia coli in Dairy Goat Kids with Diarrhea in Partial Regions of Shaanxi Province, China

Cryptosporidium spp., Giardia duodenalis, Enterocytozoon bieneusi and Escherichia coli are important diarrheal pathogens threatening the health of humans and various animals. Goats, especially pre-weaned goat kids, that carry these pathogens are important reservoirs related to human infection. In the present study, PCR-based sequencing techniques were applied to characterize Cryptosporidium spp., G. duodenalis, E. bieneusi and E. coli in 202 fecal samples of diarrheal kids for Guanzhong dairy goats from five locations in Shaanxi Province. The positive rates of Cryptosporidium spp., G. duodenalis, E. bieneusi and E. coli were 37.6% (76/202), 16.3% (33/202), 55.4% (112/202) and 78.7% (159/202) in these goat kids, respectively. Co-infection of two to four pathogens was found in 114 of 202 fecal samples. Significant differences (p < 0.001) in the positive rates of Cryptosporidium spp. and G. duodenalis were found among locations and age groups. Furthermore, two Cryptosporidium species (C. parvum and C. xiaoi), two G. duodenalis assemblages (E and A), nine E. bieneusi genotypes (CHG3, CHG1, BEB6, CHG5, CHG2, SX1, CHG28, COS-II and CD6) and two E. coli pathotypes (EPEC and EHEC) were identified. As for Cryptosporidium, two (IIdA19G1 and IIdA19G2) and two (XXIIIa and XXIIIg) subtypes were recognized in samples positive for C. parvum and C. xiaoi, respectively. A phylogenetic analysis based on the ITS locus of E. bieneusi indicated that all nine genotypes of E. bieneusi identified in this study belonged to the group 2. Four virulence factors (ehxA, eae, stx2 and stx1) of EPEC and EHEC were found in E. coli strains. Collectively, this study explored the colonization frequency of Cryptosporidium spp., G. duodenalis, E. bieneusi and E. coli in diarrheal kids of Guanzhong dairy goats in Shaanxi Province and expanded our understanding of the genetic composition and zoonotic potential of these pathogens in goats.

PCR diagnostics are insufficient for the detection of Diarrhoeagenic Escherichia coli in Ibadan, Nigeria

Understanding the contribution of different diarrhoeagenic Escherichia coli pathotypes to disease burden is critical to mapping risk and informing vaccine development. Targeting select virulence genes by PCR is the diagnostic approach of choice in high-burden, least-resourced African settings. We compared the performance of a commonly-used multiplex protocol to whole genome sequencing (WGS). PCR was applied to 3,815 E. coli isolates from 120 children with diarrhoea and 357 healthy controls. Three or more isolates per specimen were also Illumina-sequenced. Following quality assurance, ARIBA and Virulencefinder database were used to identify virulence targets. Root cause analysis of deviant PCR results was performed by examining target sensitivity using BLAST, Sanger sequencing false-positive amplicons, and identifying lineages prone to false-positivity using in-silico multilocus sequence typing and a Single Nucleotide Polymorphism phylogeny constructed using IQTree. The sensitivity and positive predictive value of PCR compared to WGS ranged from 0-77.8% while specificity ranged from 74.5-94.7% for different pathotypes. WGS identified more enteroaggregative E. coli (EAEC), fewer enterotoxigenic E. coli (ETEC) and none of the Shiga toxin-producing E. coli detected by PCR, painting a considerably different epidemiological picture. Use of the CVD432 target resulted in EAEC under-detection, and enteropathogenic E. coli eae primers mismatched more recently described intimin alleles common in our setting. False positive ETEC were over-represented among West Africa-predominant ST8746 complex strains. PCR precision varies with pathogen genome so primers optimized for use in one part of the world may have noticeably lower sensitivity and specificity in settings where different pathogen lineages predominate.

Are non-lactose-fermenting Escherichia coli important diarrhoeal pathogens in children and adults?

Introduction

Diarrhoeagenic Escherichia coli (DEC) remains one of the major causes of acute diarrhoea episodes in developing countries. The percentage of acute diarrhoea cases caused by DEC is 30-40 % in these countries. Approximately 10% of E. coli isolates obtained from stool specimens have been reported to be non-lactose-fermenting (NLF). The available literature is sparse regarding the pathogenicity of NLF E. coli causing infectious diarrhoea.

Aim

We aimed to elucidate the importance of NLF E. coli in causing diarrhoea in both adults and children by detecting various DEC pathotypes among NLF E. coli in stool samples taken from gastroenteritis cases.

Material and Methods

A total of 376 NLF E. coli isolates from 3110 stool samples from diarrhoea/gastroenteritis patients were included in the study. Up to three NLF colonies that were not confirmed as Vibrio cholerae , Aeromonas spp., Salmonella spp. or Shigella spp., but were identified as E. coli using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), were carefully picked up from each MacConkey agar plate and then meticulously streaked onto freshly prepared, sterilized nutrient agar plates, and biochemical reactions were conducted. Multiplex PCR was conducted for the EAEC, EPEC, ETEC and EHEC pathotypes and PCR for the ipaH gene was conducted for EIEC. The disc diffusion method was used for antibiotic sensitivity testing.

Results

Using multiplex PCR and ipaH PCR, a total of 63 pathotypes of DEC were obtained, with EAEC being the most predominant (n=31) followed by EIEC (n=22), EPEC (n=8) and ETEC (n=2). To further differentiate EIEC from Shigella , additional biochemical tests were performed, including acetate utilization, mucate and salicin fermentation, and aesculin hydrolysis. Antimicrobial susceptibility testing (AST) showed that maximum resistance was seen against ciprofloxacin (82.5 %) followed by ampicillin (77.8 %) and cotrimoxazole (68.2 %), and minimum resistance was seen against ertapenem (4.8 %).

Conclusion

In our study two pathotypes (EAEC, EIEC) were predominant among NLF E. coli and these were not only important aetiological agents in children, but also in adults. Our study also sheds light on the epidemiology of EIEC, which is one of the most neglected DEC pathotypes, as hardly any microbiological laboratories process NLF E. coli for EIEC.

Conventional and advanced detection techniques of foodborne pathogens: A comprehensive review

Foodborne pathogens are a major public health concern and have a significant economic impact globally. From harvesting to consumption stages, food is generally contaminated by viruses, parasites, and bacteria, which causes foodborne diseases such as hemorrhagic colitis, hemolytic uremic syndrome (HUS), typhoid, acute, gastroenteritis, diarrhea, and thrombotic thrombocytopenic purpura (TTP). Hence, early detection of foodborne pathogenic microbes is essential to ensure a safe food supply and to prevent foodborne diseases. The identification of foodborne pathogens is associated with conventional (e.g., culture-based, biochemical test-based, immunological-based, and nucleic acid-based methods) and advances (e.g., hybridization-based, array-based, spectroscopy-based, and biosensor-based process) techniques. For industrial food applications, detection methods could meet parameters such as accuracy level, efficiency, quickness, specificity, sensitivity, and non-labor intensive. This review provides an overview of conventional and advanced techniques used to detect foodborne pathogens over the years. Therefore, the scientific community, policymakers, and food and agriculture industries can choose an appropriate method for better results.

Antimicrobial resistance, Extended-Spectrum β-Lactamase production and virulence genes in Salmonella enterica and Escherichia coli isolates from estuarine environment

The impact of antimicrobial resistance (AMR) on global public health has been widely documented. AMR in the environment poses a serious threat to both human and animal health but is frequently overlooked. This study aimed to characterize the association between phenotype and genotype of AMR, virulence genes and Extended-Spectrum β-Lactamase (ESBL) production from estuarine environment. The Salmonella (n = 126) and E. coli (n = 409) were isolated from oysters and estuarine water in Thailand. The isolates of Salmonella (96.9%) and E. coli (91.4%) showed resistance to at least one antimicrobial agent. Multidrug resistance (MDR) was 40.1% of Salmonella and 23.0% of E. coli. Resistance to sulfamethoxazole was most common in Salmonella (95.2%) and E. coli (77.8%). The common resistance genes found in Salmonella were sul3 (14.3%), followed by blaTEM (11.9%), and cmlA (11.9%), while most E. coli were blaTEM (31.5%) and tetA (25.4%). The ESBL production was detected in Salmonella (1.6%, n = 2) of which one isolate was positive to blaTEM-1. Eight E. coli isolates (2.0%) were ESBL producers, of which three isolates carried blaCTX-M-55 and one isolate was blaTEM-1. Predominant virulence genes identified in Salmonella were invA (77.0%), stn (77.0%), and fimA (69.0%), while those in E. coli isolates were stx1 (17.8%), lt (11.7%), and stx2 (1.2%). Logistic regression models showed the statistical association between resistance phenotype, virulence genes and ESBL production (p < 0.05). The findings highlighted that estuarine environment were potential hotspots of resistance. One Health should be implemented to prevent AMR bacteria spreading.

Genetic and Antimicrobial Resistance Profiles of Mammary Pathogenic E. coli (MPEC) Isolates from Bovine Clinical Mastitis

Mammary pathogenic E. coli (MPEC) is one of the main pathogens of environmental origin responsible for causing clinical mastitis worldwide. Even though E. coli are strongly associated with transient or persistent mastitis and the economic impacts of this disease, the virulence factors involved in the pathogenesis of MPEC remain unknown. Our aim was to characterize 110 MPEC isolates obtained from the milk of cows with clinical mastitis, regarding the virulence factor-encoding genes present, adherence patterns on HeLa cells, and antimicrobial resistance profile. The MPEC isolates were classified mainly in phylogroups A (50.9%) and B1 (38.2%). None of the isolates harbored genes used for diarrheagenic E. coli classification, but 26 (23.6%) and 4 (3.6%) isolates produced the aggregative or diffuse adherence pattern, respectively. Among the 22 genes investigated, encoding virulence factors associated with extraintestinal pathogenic E. coli pathogenesis, fimH (93.6%) was the most frequent, followed by traT (77.3%) and ompT (68.2%). Pulsed-field gel electrophoresis analysis revealed six pulse-types with isolates obtained over time, thus indicating persistent intramammary infections. The genes encoding beta-lactamases detected were as follows: bla_TEM (35/31.8%); bla_CTX-M-2/bla_CTX-M-8 (2/1.8%); bla_CTX-M-15 and bla_CMY-2 (1/0.9%); five isolates were classified as extended spectrum beta-lactamase (ESBL) producers. As far as we know, papA, shf, ireA, sat and bla_CTX-M-8 were detected for the first time in MPEC. In summary, the genetic profile of the MPEC studied was highly heterogeneous, making it impossible to establish a common genetic profile useful for molecular MPEC classification. Moreover, the detection of ESBL-producing isolates is a serious public health concern.

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.

•

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.

Impact of integrated water, sanitation, hygiene, health and nutritional interventions on diarrhoea disease epidemiology and microbial quality of water in a resource-constrained setting in Kenya: A controlled intervention study

Objectives

We assessed the impact of water, hygiene and sanitation (WASH), maternal, new‐born and child health (MNCH), nutrition and early childhood development (ECD) on diarrhoea and microbial quality of water in a resource‐constrained rural setting in Kenya.

Methods

Through a controlled intervention study, we tested faecal and water samples collected from both the intervention and control sites before and after the interventions using microbiological, immunological and molecular assays to determine the prevalence of diarrhoeagenic agents and microbial quality of water. Data from the hospital registers were used to estimate all‐cause diarrhoea prevalence.

Results

After the interventions, we observed a 58.2% (95% CI: 39.4–75.3) decline in all‐cause diarrhoea in the intervention site versus a 22.2% (95% CI: 5.9–49.4) reduction of the same in the control site. Besides rotavirus and pathogenic Escherichia coli, the rate of isolation of other diarrhoea‐causing bacteria declined substantially in the intervention site. The microbial quality of community and household water improved considerably in both the intervention (81.9%; 95% CI: 74.5%–87.8%) and control (72.5%; 95% CI: 64.2%–80.5%) sites with the relative improvements in the intervention site being slightly larger.

Conclusions

The integrated WASH, MNCH, nutrition and ECD interventions resulted in notable decline in all‐cause diarrhoea and improvements in water quality in the rural resource‐limited population in Kenya. This indicates a direct public health impact of the interventions and provides early evidence for public health policy makers to support the sustained implementation of these interventions.

Escherichia coli Clonal Variability Based on Genetic Diversity Pattern with Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction Methods for Traveler’s Diarrhea Cases in Bali

BACKGROUND: Bali is a favorite tourism destination in the world. As a major tourist destination, the incidence of illness that afflicts tourists greatly affects the image of tourism. Diarrhea is a health problem that is most often experienced and is a major obstacle for foreign tourists when traveling, especially to Bali. Escherichia coli (E. coli) bacteria cause diarrhea more often than viruses in some developing countries. Genetic differences can affect the characteristics of E. coli, especially in relation to the medical field. AIM: We would like to assess the genetic diversity of the different pathogenic E. coli from various clinical isolates including those from traveler’s diarrhea in Bali, Indonesia. MATERIALS AND METHODS: One of the molecular techniques used in this study is to use enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). The sample in this study was the feces of foreign tourists with traveler’s diarrhea in Bali. This study carried out research procedures in the form of Isolation of E. coli genome DNA from culture, amplification of E. coli 16S rRNA encoding genes, sequencing of E. coli 16S rRNA encoding genes, phylogenetic tree construction, and then analysis of E. coli genetic diversity with ERIC-PCR sequences. RESULTS: The results showed that the ERIC-PCR method was more discriminatory than other methods to analyze the genetic diversity of E. coli from fecal samples of patients with traveler’s diarrhea. It was found that clonal variability based on the genetic similarity of all sample E. coli isolates varied from 0% to 100%. CONCLUSIONS: This shows that the source of transmission and the strains of E. coli that cause it comes from diverse populations.

Gut Commensal Escherichia coli, a High-Risk Reservoir of Transferable Plasmid-Mediated Antimicrobial Resistance Traits

Background

Escherichia coli (E. coli), the main human gut microorganism, is one of the evolved superbugs because of acquiring antimicrobial resistance (AMR) determinants via horizontal gene transfer (HGT).

Purpose

This study aimed to screen isolates of gut commensal E. coli from healthy adult individuals for antimicrobial susceptibility and plasmid-mediated AMR encoding genes.

Methods

Gut commensal E. coli bacteria were isolated from fecal samples that were taken from healthy adult individuals and investigated phenotypically for their antimicrobial susceptibility against diverse classes of antimicrobials using the Kirby Bauer disc method. PCR-based molecular assays were carried out to detect diverse plasmid-carried AMR encoding genes and virulence genes of different E. coli pathotypes (eaeA, stx, ipaH, est, elt, aggR and pCVD432). The examined AMR genes were β-lactam resistance encoding genes (bla_CTX-M1, bla_TEM, bla_CMY-2), tetracycline resistance encoding genes (tetA, tetB), sulfonamides resistance encoding genes (sul1, sulII), aminoglycoside resistance encoding genes (aac(3)-II, aac(6′)-Ib-cr) and quinolones resistance encoding genes (qnrA, qnrB, qnrS).

Results

PCR results revealed the absence of pathotypes genes in 56 isolates that were considered gut commensal isolates. E. coli isolates showed high resistance rates against tested antimicrobial agents belonging to both β-lactams and sulfonamides (42/56, 75%) followed by quinolones (35/56, 62.5%), tetracyclines (31/56, 55.4%), while the lowest resistance rate was to aminoglycosides (24/56, 42.9%). Antimicrobial susceptibility profiles revealed that 64.3% of isolates were multidrug-resistant (MDR). High prevalence frequencies of plasmid-carried AMR genes were detected including bla_TEM (64%) sulI (60.7%), qnrA (51.8%), aac(3)-II (37.5%), and tetA (46.4%). All isolates harbored more than one gene with the most frequent genetic profile among isolates was bla_TEM-bla_CTX-M1-like-qnrA-qnrB-tetA-sulI.

Conclusion

Results are significant in the evaluation of plasmid-carried AMR genes in the human gut commensal E. coli, suggesting a potential human health risk and the necessity of strict regulation of the use of antibiotics in Egypt. Commensal E. coli bacteria may constitute a potential reservoir of AMR genes that can be transferred to other bacterial species.

Clinical, Sociodemographic and Environmental Risk Factors for Acute Bacterial Diarrhea among Adults and Children over Five Years in Bangladesh

In 2016, diarrheal disease was the eighth leading cause of mortality globally accounting for over 1.6 million deaths with the majority of deaths in adults and children over 5 years. This study aims to investigate the clinical, sociodemographic, and environmental risk factors associated with common bacterial acute diarrhea among adults and children over 5. Data were collected from March 2019 to March 2020 in patients over 5 years presenting with acute gastroenteritis at icddr,b. Stool samples were collected from each patient for culture and polymerase chain reaction (PCR) testing. Bivariate associations between independent variables and stool-testing indicating bacterial etiology were calculated. This analysis included 2,133 diarrheal patients of whom a bacterial enteropathogen was identified in 1,537 (72%). Detection of bacteria was associated with: younger age (OR 0.92; 95% CI: 0.88-0.96), lower mean arterial pressure (OR 0.84; 95% CI: 0.79-0.89), heart rate (OR 1.06; 95% CI: 1.01-1.10), percentage dehydration (OR 1.33; 95% CI: 1.13-1.55), respiration rate (OR 1.23; 95% CI: 1.04-1.46), lower mid-upper arm circumference (OR 0.97; 95% CI: 0.94-0.99), confused/lethargic mental status (OR 1.85; 95% CI: 1.11-3.25), rice watery stool (OR 1.92; 95% CI: 1.54-2.41), and vomiting more than three times in the past 24 hours (OR 1.30; 95% CI: 1.06-1.58). Higher monthly income (OR 0.92; 95% CI: 0.86-0.98), > 8 years of education (OR 0.79; 95% CI: 0.63-1.00), and having more than five people living at home (OR 0.80; 95% CI: 0.66-0.98) were associated with lower odds of bacterial diarrhea. These findings may help guide the development of predictive tools to aid in identifying patients with bacterial diarrhea for timely and appropriate use of antibiotics.

Faradaic-free electrokinetic nucleic acid amplification (E-NAAMP) using localized on-chip high frequency Joule heating

We present a novel Faradaic reaction-free nucleic acid amplification (NAA) method for use with microscale liquid samples. Unlike previous Joule heating methods where the electrodes produce electrolysis gaseous by-products and require both the electrodes be isolated from a sample and the venting of produced electrolysis gas, our electrokinetic Nucleic Acid Amplification (E-NAAMP) method alleviates these issues using a radio frequency (RF) alternating current electric field. In this approach, a pair of microscale thin film gold electrodes are placed directly in contact with a nucleic acid reaction mixture. A high frequency (10-40 MHz) RF potential is then applied across the electrode pair to induce a local Ohmic current within the sample and drive the sample temperature to increase by Joule heating. The temperature increase is sustainable in that it can be generated for several hours of constant use without generating any pH change to the buffer or any microscopically observable gaseous electrolysis by-products. Using this RF Joule heating approach, we demonstrate successful direct thermal amplification using two popular NAA biochemical reactions: loop-mediated isothermal amplification and polymerase chain reaction. Our results demonstrate that a simple microscale electrode structure can be used for thermal regulation for NAA reactions without observable electrolytic reactions, minimal enzyme activity loss and sustained (>50 h use per device) continuous operations without electrode delamination. As such, E-NAAMP offers substantial miniaturization of the heating elements for use in microfluidic or miniaturized NAA reaction systems.

Molecular diversity survey on diarrheagenic Escherichia coli isolates among children with gastroenteritis in Fars, Iran

Aim: To differentiate Escherichia coli isolates from diarrheal pediatric patients in clinical laboratories. Materials & methods: Patients with watery diarrhea were selected for sampling and tested for diarrheagenic E. coli (DEC) by API kit. DEC isolates were tested for phylotyping, pathotyping and presence of determined virulence-encoding genes by specific molecular methods. Results: About 50% of isolates were detected as DECs (>55 and >31% were categorized B2 and D phylotypes respectively). Enterotoxigenic E. coli was the most and enteroinvasive E. coli was the lowest prevalent pathotypes. csg and fim genes were the most present virulence factors. Conclusion: Typing of E. coli isolates from stool specimens will help to determine the diversity of diarrheal pathogens and take proper decisions to reduce the health burden of diarrheal diseases.

Surveillance and Reduction Control of Escherichia coli and Diarrheagenic E. coli During the Pig Slaughtering Process in China

The microbial contamination of pork during the slaughter process, especially that of the hygiene indicator bacteria, Escherichia coli, is closely related to the safety and quality of the meat. Some diarrheagenic E. coli can cause serious foodborne diseases, and pose a significant threat to human life and health. In order to ascertain the current status of E. coli and diarrheagenic E. coli contamination during the pig slaughter process in China, we conducted thorough monitoring of large-sized slaughterhouses, as well as small- or medium-sized slaughterhouses, in different provinces of China from 2019 to 2020. The overall positive rate of E. coli on the pork surface after slaughter was very high (97.07%). Both the amount of E. coli contamination and the positive ratio of diarrheagenic E. coli in large-sized slaughterhouses (7.50–13.33 CFU/cm², 3.44%) were lower than those in small- or medium-sized slaughterhouses (74.99–133.35 CFU/cm², 5.71%). Combined with the current status of sanitary control in slaughterhouses, we determined that pre-cooling treatment significantly reduced E. coli and diarrheagenic E. coli in pork after slaughter, while microbiological testing reduced E. coli. Based on our monitoring data, China urgently needs to establish relevant standards to better control microbial contamination during pig slaughtering progress. This study provided a theoretical basis for the hygiene quality management of the pig slaughter industry in China.

Occurrence of Hybrid Diarrhoeagenic Escherichia coli Associated with Multidrug Resistance in Environmental Water, Johannesburg, South Africa

This study was undertaken to determine the virulence and antibiotic resistance profiles of diarrhoeagenic Escherichia coli (DEC) in environmental waters of Johannesburg, South Africa. Samples were collected and cultured on selective media. An 11-plex PCR assay was used to differentiate five DEC, namely: enteroaggregative (EAEC), enterohaemorrhagic (EHEC), enteroinvasive (EIEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). The antibiotic resistance profile of isolates was determined using the VITEK®-2 automated system. The virulence profiles of 170 E. coli tested showed that 40% (68/170) were commensals and 60% (102/170) were pathogenic. EPEC had a prevalence of 19.2% (32/170), followed by ETEC 11.4% (19/170), EAEC 6% (10/170) and EHEC 3% (5/170). Hybrid DEC carrying a combination of simultaneously two and three pathogenic types was detected in twenty-eight and nine isolates, respectively. The antibiotic susceptibility testing showed isolates with multidrug resistance, including cefuroxime (100%), ceftazidime (86%), cefotaxime (81%) and cefepime (79%). This study highlighted the widespread occurrence of DEC and antibiotic resistance strains in the aquatic ecosystem of Johannesburg. The presence of hybrid pathotypes detected in this study is alarming and might lead to more severe diseases. There is a necessity to enhance surveillance in reducing the propagation of pathogenic and antibiotic-resistant strains in this area.

Determining the microbial and chemical contamination in Ecuador's main rivers

One major health issue is the microbial and chemical contamination of natural freshwater, particularly in Latin American countries, such as Ecuador, where it is still lacking wastewater treatment plants. This study analyzed the water quality in twelve rivers of Ecuador (Coastal, Andean, and Amazonian regions). All rivers showed levels of E. coli and total coliforms above the maximum limit according to International and Ecuadorian legislations. The most polluted rivers were Zamora, Esmeraldas and Machángara. Also, E. coli pathotypes were found in six rivers. Several physicochemical and metal parameters were detected in high levels, such as COD_TOTAL (in eight rivers), TSS (in six rivers), TS (in two rivers), Al (in nine rivers), Zn (in eight rivers), Pb (in three rivers), Cu (in three rivers), Fe (in two rivers), and Mn (in Machángara River). Our results agree with other studies in Latin America (such as Colombia, Brazil, and Peru) reporting similar contamination in water resources used for agriculture, livestock, and human consumption. Overall, Guayas, Guayllabamba, and Machángara Rivers showed the highest levels of physicochemical parameters (such as COD_TOTAL and TSS) and metal concentrations (such as copper, zinc, aluminum, iron, and manganese). Further studies should evaluate contamination sources and public health impact.

Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador

Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.

Prevalence of pathogenic Klebsiella pneumoniae based on PCR capsular typing harbouring carbapenemases encoding genes in Uganda tertiary hospitals

BACKGROUND

Klebsiella pneumoniae is an opportunistic pathogen that has been implicated as one of commonest cause of hospital and community acquired infections. The K. pneumoniae infections have considerably contributed to morbidity and mortality in patients with protracted ailments. The capacity of K. pneumoniae to cause diseases depends on the presence of an array virulence factors. Coexistence and expression of virulence factors and genetic determinants of antibiotic resistance complicates treatment outcomes. Thus, emergence of pathogenic MDR K. pneumoniae poses a great threat to the healthcare system. However, the carriage of antibiotic resistance among pathogenic K. pneumoniae is yet to be investigated in Uganda. We sought to investigate the carbapenem resistance profiles and pathogenic potential based on capsular serotypes of K. pneumoniae clinical isolates.

METHODS

This was a cross sectional study involving use of archived Klebsiella pneumoniae isolates collected between January and December, 2019 at four tertiary hospitals in Uganda. All isolates were subject to antimicrobial susceptibility assays to determine phenotypic antibiotic resistance, pentaplex PCR to detect carbapenemases encoding genes and heptaplex PCR to identify capsular serotypes K1, K2, K3, K5, K20, K54 and K57.

RESULTS

The study found an overall phenotypic carbapenem resistance of 23.3% (53/227) and significantly higher genotypic resistance prevalence of 43.1% (98/227). Over all, the most prevalent gene was blaOXA-48-like (36.4%), followed by blaIMP-type (19.4%), blaVIM-type (17.1%), blaKPC-type (14.0%) and blaNDM-type (13.2%). blaVIM-type and blaOXA-48-like conferred phenotypic resistance in all isolates and 38.3% of isolates that harbored them respectively. Capsular multiplex PCR revealed that 46.7% (106/227) isolates were pathogenic and the predominantly prevalent pathotype was K5 (18.5%) followed by K20 (15.1%), K3 (7.1%), K2 (3.1%) and K1 (2.2%). Of the 106 capsular serotypes, 37 expressed phenotypic resistance; thus, 37 of the 53 carbapenem resistant K. pneumoniae were pathogenic.

CONCLUSION

The high prevalence of virulent and antibiotic resistant K. pneumoniae among clinical isolates obtained from the four tertiary hospital as revealed by this study pose a great threat to healthcare. Our findings underline the epidemiological and public health risks and implications of this pathogen.

Comparative analysis of virulence determinants, phylogroups, and antibiotic susceptibility patterns of typical versus atypical Enteroaggregative E. coli in India

Enteroaggregative Escherichia coli (EAEC) is an evolving enteric pathogen that causes acute and chronic diarrhea in developed and industrialized nations in children. EAEC epidemiology and the importance of atypical EAEC (aEAEC) isolation in childhood diarrhea are not well documented in the Indian setting. A comparative analysis was undertaken to evaluate virulence, phylogeny, and antibiotic sensitivity among typical tEAEC versus aEAEC. A total of 171 EAEC isolates were extracted from a broad surveillance sample of diarrheal (N = 1210) and healthy children (N = 550) across North India. Polymerase chain reaction (PCR) for the aggR gene (master regulator gene) was conducted to differentiate tEAEC and aEAEC. For 21 virulence genes, we used multiplex PCR to classify possible virulence factors among these strains. Phylogenetic classes were identified by a multiplex PCR for chuA, yjaA, and a cryptic DNA fragment, TspE4C2. Antibiotic susceptibility was conducted by the disc diffusion method as per CLSI guidelines. EAEC was associated with moderate to severe diarrhea in children. The prevalence of EAEC infection (11.4%) was higher than any other DEC group (p = 0.002). tEAEC occurrence in the diarrheal group was higher than in the control group (p = 0.0001). tEAEC strain harbored more virulence genes than aEAEC. astA, aap, and aggR genes were most frequently found in the EAEC from the diarrheal population. Within tEAEC, this gene combination was present in more than 50% of strains. Also, 75.8% of EAEC strains were multidrug-resistant (MDR). Phylogroup D (43.9%) and B1 (39.4%) were most prevalent in the diarrheal and control group, respectively. Genetic analysis revealed EAEC variability; the comparison of tEAEC and aEAEC allowed us to better understand the EAEC virulence repertoire. Further microbiological and epidemiological research is required to examine the pathogenicity of not only typical but also atypical EAEC.

Enteroaggregative E. coli (EAEC) are an increasingly important cause of diarrhea. E. coli belonging to this category cause watery diarrhea, which is often persistent and can be inflammatory. It is also associated with traveler’s diarrhea in children and adults in middle and high-income countries. EAEC are defined by their ability to adhere to epithelial cells in a characteristic stacked brick-like pattern. However, the identification of these pathogenic strains remains elusive because of its heterogeneous nature. Genes that could contribute to the pathogenicity of EAEC encode adhesions, toxins, and other factors. Due to the heterogeneity of EAEC strains and differing host immune responses, not all EAEC infections are symptomatic. A critical factor in both recognizing EAEC pathogenesis and defining typical EAEC (tEAEC) strains is AggR, a transcriptional control for many EAEC virulence genes. The central role of aggR in virulence confers a strong priority to understand its pathogenicity. To identify EAEC, the CVD432 probe has been used. The CVD432 is a DNA probe from pAA plasmid of EAEC, has been reported to be specific for the detection of EAEC. The lack of sensitivity comes from the genetic heterogeneity of the EAEC strains and the wide geographic dispersal of strains. In our study, we performed a large surveillance of EAEC from North India among the pediatric population. Samples were collected by the microbiology staff at the Postgraduate Institute of Medical Education and Research (PGIMER) and referral system labs in Chandigarh (Manimajra), Punjab (Ludhiana), Haryana (Panchkula and Ambala Cantt), Himachal Pradesh (Hamirpur, Shimla, and Tanda), and Uttarakhand (Rishikesh, Rudrapur, and Haridwar)]. PGIMER is the largest tertiary care hospital in North India and serves patients from across Punjab, Jammu and Kashmir, Himachal Pradesh and Haryana. EAEC infections were detected using molecular methods. In our finding, astA, aap, and aggR genes were most frequently found in the EAEC from the diarrheal population. Within tEAEC, this gene combination is present in more than 50% of strains and helps to differentiate tEAEC from aEAEC. Our collection of EAEC strains helps in finding an appropriate marker for the early detection of EAEC. Our signature sequence (astA, aap, and aggR) will be ideal as focus genes for EAEC identification, as well as tEAEC and aEAEC. The multidrug resistance (MDR) was observed in 75.8% of the EAEC strains. tEAEC exhibits resistance to a greater number of antibiotics with respect to aEAEC. The phylogenetic analysis revealed that EAEC phylogeny is diverse and dispersed in all the phylogroups.

High Prevalence of blaCTX-M-15 Gene among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Causing Extraintestinal Infections in Bangladesh

The emergence of multidrug-resistant (MDR) Escherichia coli (E. coli) clonal lineages with high virulence potential is alarming. Lack of sufficient data on molecular epidemiology of such pathogens from countries with high infection burden, such as Bangladesh, hinders management and infection control measures. In this study, we assessed the population structure, virulence potential and antimicrobial susceptibility of clinical E. coli isolates from Dhaka, Bangladesh. A high prevalence of MDR (69%) and extended-spectrum β-lactamase production (ESBL) (51%) was found. Most E. coli isolates were susceptible to amikacin (95%), meropenem (94%) and nitrofurantoin (89%) antibiotics. A high prevalence of ST131 (22%) and ST95 (9%) followed by ST69 (4%) and ST73 (3%) was observed. Phylogroups B2 (46%), B1 (16%), D (10%) and F (9%) were prominent. bla_CTX-M-15 (52%) and bla_NDM-1 (5%) were the most prevalent ESBL and carbapenem resistance genes, respectively. Moreover, the predominant pathotype identified was extraintestinal pathogenic E. coli (ExPEC) (41%) followed by enteric pathogens (11%). In conclusion, our results suggest the transmission of clonal E. coli groups amidst diverse E. coli population that are associated with high virulence potential and MDR phenotype. This is of high concern and mandates more efforts towards molecular surveillance of antimicrobial resistance (AMR) in clinically significant pathogens.

Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh

The avian pathogenic Escherichia coli (APEC) strains are the chief etiology of colibacillosis worldwide. The present study investigated the circulating phylotypes, existence of virulence genes (VGs), and antimicrobial resistance (AMR) in 392 APEC isolates, obtained from 130 samples belonged to six farms using both phenotypic and PCR-based molecular approaches. Congo red binding (CRB) assay confirmed 174 APEC isolates which were segregated into ten, nine, and eight distinct genotypes by RAPD assay (discriminatory index, DI = 0.8707), BOX-PCR (DI = 0.8591) and ERIC-PCR (DI = 0.8371), respectively. The combination of three phylogenetic markers (chuA, yjaA and DNA fragment TspE4.C2) classified APEC isolates into B23 (37.36%), A1 (33.91%), D2 (11.49%), B22 (9.20%), and B1 (8.05%) phylotypes. Majority of the APEC isolates (75-100%) harbored VGs (ial, fimH, crl, papC, and cjrC). These VGs (papC and cjrC) and phylotypes (D2 and B2) of APEC had significant (p = 0.004) association with colibacillosis. Phylogenetic analysis showed two distinct clades (clade A and clade B) of APEC, where clade A had 98-100% similarity with E. coli APEC O78 and E. coli EHEC strains, and clade B had closest relationship with E. coli O169:H41 strain. Interestingly, phylogroups B2 and D2 were found in the APEC strains of both clades, while the strains from phylogroups A1 and B1 were found in clade A only. In this study, 81.71% of the isolates were biofilm formers, and possessed plasmids of varying ranges (1.0 to 54 kb). In vitro antibiogram profiling revealed that 100% isolates were resistant to ≥3 antibiotics, of which 61.96%, 55.24%, 53.85%, 51.16% and 45.58% isolates in phylotypes B1, D2, B22, B23, and A1, respectively, were resistant to these antimicrobials. The resistance patterns varied among different phylotypes, notably in phylotype B22, showing the highest resistance to ampicillin (90.91%), nalidixic acid (90.11%), tetracycline (83.72%), and nitrofurantoin (65.12%). Correspondence analysis also showed significant correlation among phylotypes with CRB (p = 0.008), biofilm formation (p = 0.02), drug resistance (p = 0.03), and VGs (p = 0.06). This report demonstrated that B2 and A1 phylotypes are dominantly circulating APEC phylotypes in Bangladesh; however, B2 and D2 are strongly associated with the pathogenicity. A high prevalence of antibiotic-resistant APEC strains from different phylotypes suggest the use of organic antimicrobial compounds, and/or metals, and the rotational use of antibiotics in poultry farms in Bangladesh.

High Resolution Melt Assays to Detect and Identify Vibrio parahaemolyticus, Bacillus cereus, Escherichia coli, and Clostridioides difficile Bacteria

Over one hundred bacterial species have been determined to comprise the human microbiota in a healthy individual. Bacteria including Escherichia coli, Bacillus cereus, Clostridioides difficile, and Vibrio parahaemolyticus are found inside of the human body and B. cereus and E. coli are also found on the skin. These bacteria can act as human pathogens upon ingestion of contaminated food or water, if they enter an open wound, or antibiotics, and environment or stress can alter the microbiome. In this study, we present new polymerase chain reaction (PCR) high-resolution melt (HRM) assays to detect and identify the above microorganisms. Amplified DNA from C. difficile, E. coli, B. cereus, and V. parahaemolyticus melted at 80.37 ± 0.45 °C, 82.15 ± 0.37 °C, 84.43 ± 0.50 °C, and 86.74 ± 0.65 °C, respectively. A triplex PCR assay was developed to simultaneously detect and identify E. coli, B. cereus, and V. parahaemolyticus, and cultured microorganisms were successfully amplified, detected, and identified. The assays demonstrated sensitivity, specificity, reproducibility, and robustness in testing.

Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION - Promising Strategies for Multiplex Identification of Viable Pathogens in Food

Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in food remains a major challenge. A novel strategy is developed through direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION to achieve real-time multiplex identification of viable pathogens in food. Specifically, this study reports an optimized universal Nanopore sample extraction and library preparation protocol applicable to both Gram-positive and Gram-negative pathogenic bacteria, demonstrated using a cocktail culture of E. coli O157:H7, Salmonella enteritidis, and Listeria monocytogenes, which were selected based on their impact on economic loss or prevalence in recent outbreaks. Further evaluation and validation confirmed the accuracy of direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing using Sanger sequencing and selective media. The study also included a comparison of different bioinformatic pipelines for metatranscriptomic and amplicon genomic analysis. MEGAN without rRNA mapping showed the highest accuracy of multiplex identification using the metatranscriptomic data. EPI2ME also demonstrated high accuracy using multiplex RT-PCR amplicon sequencing. In addition, a systemic comparison was drawn between Nanopore sequencing of the direct metatranscriptome RNA-seq and RT-PCR amplicons. Both methods are comparable in accuracy and time. Nanopore sequencing of RT-PCR amplicons has higher sensitivity, but Nanopore metatranscriptome sequencing excels in read length and dealing with complex microbiome and non-bacterial transcriptome backgrounds.

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.

Case Report: Bacillus pumilus-Caused Bacteremia in a Patient with Food Poisoning

Bacillus pumilus has rarely been reported as a cause of human infections. We report a case of a B. pumilus causing food poisoning in an adult male. A 51-year-old Japanese man complained of severe abdominal cramps, fever with chills, diarrhea, dizziness, and loss of appetite after eating reheated rice with stewed minced meat purchased from a Kenyan restaurant. Bacillus pumilus was isolated from blood culture and was identified using a biochemical test and 16S rRNA gene sequencing analysis. The patient was treated with probiotics and ciprofloxacin and recovered after 3 days. To our knowledge, this is the first report describing the potential role of B. pumilus as a foodborne pathogen in Kenya and highlights the importance of good hygiene and food preparation practices.

Metagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes

Escherichia coli is a leading contributor to infectious diarrhea and child mortality worldwide, but it remains unknown how alterations in the gut microbiome vary for distinct E. coli pathotype infections and whether these signatures can be used for diagnostic purposes. Further, the majority of enteric diarrheal infections are not diagnosed with respect to their etiological agent(s) due to technical challenges. To address these issues, we devised a novel approach that combined traditional, isolate-based and molecular-biology techniques with metagenomics analysis of stool samples and epidemiological data. Application of this pipeline to children enrolled in a case-control study of diarrhea in Ecuador showed that, in about half of the cases where an E. coli pathotype was detected by culture and PCR, E. coli was likely not the causative agent based on the metagenome-derived low relative abundance, the level of clonality, and/or the virulence gene content. Our results also showed that diffuse adherent E. coli (DAEC), a pathotype that is generally underrepresented in previous studies of diarrhea and thus, thought not to be highly virulent, caused several small-scale diarrheal outbreaks across a rural to urban gradient in Ecuador. DAEC infections were uniquely accompanied by coelution of large amounts of human DNA and conferred significant shifts in the gut microbiome composition relative to controls or infections caused by other E. coli pathotypes. Our study shows that diarrheal infections can be efficiently diagnosed for their etiological agent and categorized based on their effects on the gut microbiome using metagenomic tools, which opens new possibilities for diagnostics and treatment.IMPORTANCEE. coli infectious diarrhea is an important contributor to child mortality worldwide. However, diagnosing and thus treating E. coli infections remain challenging due to technical and other reasons associated with the limitations of the traditional culture-based techniques and the requirement to apply Koch's postulates. In this study, we integrated traditional microbiology techniques with metagenomics and epidemiological data in order to identify cases of diarrhea where E. coli was most likely the causative disease agent and evaluate specific signatures in the disease-state gut microbiome that distinguish between diffuse adherent, enterotoxigenic, and enteropathogenic E. coli pathotypes. Therefore, our methodology and results should be highly relevant for diagnosing and treating diarrheal infections and have important applications in public health.

Microbial safety status of Serro artisanal cheese produced in Brazil

Considering the growing consumption of artisanal foods worldwide, we aimed to evaluate the microbial safety of Serro artisanal cheese (SAC), produced in Minas Gerais State, Brazil. This cheese is produced with raw milk using 1 of 2 natural starter cultures: "pingo" and "rala." A total of 53 SAC samples (pingo = 8; rala = 45) were obtained from different farmers and subjected to conventional and molecular assays to detect and enumerate Listeria monocytogenes, Salmonella spp., coagulase-positive staphylococci (CPS), diarrheagenic Escherichia coli, Mycobacterium tuberculosis, and Brucella abortus. The SAC samples were also subjected to an ELISA to detect classical staphylococcal enterotoxins (CSE: SEA, SEB, SEC, SED, SEE) and to PCR assays to detect staphylococcal enterotoxin-related genes (sea, seb, sec, sed, see). Coagulase-positive staphylococci isolates were obtained and tested by the same assays to detect their potential in CSE production and presence of CSE-related genes. None of the SAC samples showed any of the screened food-borne pathogens and zoonotic agents, and none showed the presence of CSE by phenotypic and genotypic approaches. Despite the absence of microbial hazards, mean counts of CPS in SAC samples were 5.2 log cfu/g (pingo starter) and 4.6 log cfu/g (rala starter), indicating poor hygiene practices during production. None of the tested CPS isolates (n = 116) produced CSE or presented CSE-related genes. Despite the relative microbial safety, hygienic conditions during SAC production must be improved to meet official guidelines established in Brazil.

Multidrug-resistant Shigella infection in pediatric patients with diarrhea from central Iran

Background:Shigella spp. are primary pathogens of diarrhea in children worldwide. Emergence of resistance to fluoroquinolones and third-generation cephalosporins is crucial in the management of pediatric shigellosis. We determined the prevalence and the antibiotic resistance patterns of Shigella species isolated from pediatric patients in central Iran.

Materials and methods: Pediatric diarrhea samples (n=230) were cultured on MacConkey and XLD agar media and in GN broth. Genus-specific PCR for ipaH was also used for detection directly from fecal specimens. Antibiotic resistance and the frequency of ESBL and AmpC genes were determined.

Results: Out of the 230 samples, 19 (8.2%) cases of Shigella spp. were identified using culture. Twenty-six samples were positive by PCR (11.3%), S. flexneri (4/19; 21%) and S. sonnei (15/19; 78.9%) being the most detected. The highest antibiotic resistance rates were found for cotrimoxazole (19/19; 100%), ampicillin (16/19; 84.2%), cefixime (13/19; 68.4%) and ceftriaxone (12/19; 63.1%). Ten cases showed phenotypic ESBL presence and all these strains were positive for bla_TEM, bla_CTX-M-1, and bla_CTX-M-15. Three strains were AmpC positive, all of which harbored bla_CMY-2 and two contained bla_CIT. Of the 19 Shigella isolates 5 (26.3%), 2 (10.5%), and 1 (5.2%) were phenotypically resistant to nalidixic acid, ciprofloxacin, and norfloxacin, respectively. Class 1 integron was found in 18 (94.7%) isolates whereas class 2 integron was found in 19 (100%) strains.

Conclusion: We found a considerable presence of Shigella species with elevated antibiotic resistance levels. In particular, the resistance to third-generation cephalosporins (ESBL) and ciprofloxacin must be taken seriously.

Prevalence of pathogenic Escherichia coli from salad vegetable and fruits sold in Jakarta

OBJECTIVE

Escherichia coli is a normal inhabitant of mammalian's gut, but some strains acquired virulence factor and became pathogenic. Enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), and enteroaggregative E. coli (EAEC) are among pathogenic strains of E. coli. Vegetables and fruits could be sources of transmission. Samples were collected and subjected to three-tubes Most Probable Number (MPN) analysis followed by Multiplex PCR. Six sets of primer encoding virulence genes were used: stx, ipah, aggr, eae, elt and est.

RESULTS

From this study we found, the highest maximum number for the MPN result reached > 1100 MPN/mL and the lowest is 3 MPN/mL. From first multiplex PCR showed 65 salad vegetable samples, 7.69% were positive and from the 63 fruit samples, 11.11% were positive. From second multiplex PCR for 76 isolates, 55 (72.37%) isolates were aggR positive (EAEC), 12 (15.79%) isolates were eae positive (EPEC), and 9 (11.84%) were elt positive (ETEC). Antimicrobial resistance assay showed that 83.33% of the isolates were multi resistant. Resistances are observed to 10 μg Ampicillin (22.22%), 5 μg Ciprofloxacin (11.11%), 10 μg Gentamycin (33.33%), 30 μg Kanamycin (38.89%), 10 μg Streptomycin (55.56%), 5 μg Trimethoprim (16.67%), and 300 U Polymyxin B (61.11%).

Locals get travellers' diarrhoea too: risk factors for diarrhoeal illness and pathogenic Escherichia coli infection across an urban-rural gradient in Ecuador

OBJECTIVES

Diarrhoea is a common and well-studied cause of illness afflicting international travellers. However, traveller's diarrhoea can also result from travel between high and low disease transmission regions within a country, which is the focus of this study.

METHODS

We recruited participants for a case-control study of diarrhoea at four sites along an urban-rural gradient in Northern Ecuador: Quito, Esmeraldas, Borbón and rural communities outside of Borbón. At each of these sites, approximately 100 subjects with diarrhoea (cases) were recruited from Ministry of Health clinics and were age-matched with subjects visiting the same clinics for other complaints (controls).

RESULTS

Travellers to urban destinations had higher risk of diarrhoea and diarrhoeagenic Escherichia coli (DEC) infections. Travel to Quito was associated with diarrhoea (aOR = 2.01, 95% CI = 1.10-3.68) and travel to Guayaquil (another urban centre in Ecuador) was associated with Diffuse Adherent E. coli infection (OR = 2.09, 95% CI = 1.01-4.33). Compared to those not travelling, urban origins were also associated with greater risk of diarrhoea in Esmeraldas (aOR = 2.28, 95% CI = 1.20-4.41), and with higher risk of diarrhoeagenic E. coli infections in Quito (aOR = 2.61, 95% CI = 1.16-5.86), with >50% of travel from Quito and Esmeraldas specified to another urban destination.

CONCLUSIONS

This study suggests that individuals travelling from lower-transmission regions (rural areas) to higher transmission regions (urban centres) within a single country are at a greater risk of acquiring a diarrhoea-related illness. Investments to improve water, sanitation and hygiene conditions in urban areas could have impacts on outlying rural areas within a given country.

Rotavirus analyses by SYBR Green real-time PCR and microbiological contamination in bivalves cultivated in coastal water of Amazonian Brazil

The contamination of mussels and oysters by viruses and bacteria is often associated with water contamination and gastroenteritis in humans. The present study evaluated viral and bacterial contamination in 380 samples, from nine mollusk-producing regions in coastal water north of the Brazilian Amazon. Rotavirus contamination was studied for groups A to H, using a two-step SYBR Green RT-qPCR (quantitative reverse transcription polymerase chain reaction), and bacterial families Enterobacteriaceae, Vibrionaceae, and Aeromonadaceae by classical and molecular methods. From the 19 pools analyzed, 26.3% (5/19) were positive for group A Rotavirus, I2 genotype for VP6 region, without amplifications for groups B-H. Bacteriological analysis identified Escherichia coli isolates in 89.5% (17/19) with identification of atypical enteropathogenic E. coli aEPEC in 10.5% (2/19), Salmonella (Groups C1 and G) (10.5%, 2/19), Vibrio alginolyticus (57.9%, 11/19) V. parahaemolyticus (63.2%, 12/19), V. fluvialis (42.1%, 8/19), V. vulnificus (10.5%, 2/19), V. cholerae non-O1, non O139(10.5%, 2/19) and Aeromonas salmonicida (52.6%, 10/19). All the samples investigated presented some level of contamination by enterobacteria, rotavirus, or both, and these results may reflect the level of contamination in the Northern Amazon Region, due to the natural maintenance of some of these agents or by the proximity with human populations and their sewer.

Development of a multiplex PCR targeting eae, stx and cdt genes in genus Escherichia and detection of a novel cdtB gene in Providencia rustigianii

This study was aimed to develop a multiplex PCR (m-PCR) for the detection of Escherichia coli attaching and effacing (eae), Shiga toxin (stx) and cytolethal distending toxin (cdt) genes encoding important virulence factors of diarrheagenic E. coli such as EPEC, STEC, and Escherichia albertii. For this purpose, the m-PCR was designed to detect eae, all the subtypes of stx (stx1, stx2a-g except stx2f) and cdt (I-V) genes. The m-PCR was validated with 58 and 55 target gene-positive and negative strains of different sources, respectively. Sensitivity and specificity of the m-PCR were 100%. The m-PCR could also detect the eae, stx and cdt genes in bacteria spiked into stool specimens with or without enrichment culture. Clinical specimens collected from children with diarrhea were tested by the m-PCR, and 27 eae and 32 cdt genes were detected. Among them, three cdt-II and one untypable cdt gene-positive bacteria were isolated and identified as E. albertii and Providencia rustigianii, respectively. This is the first report demonstrating the presence of cdtB gene in P. rustigianii. These results indicate that the m-PCR is useful for surveillance of eae, stx and cdt gene-positive bacteria, not only EPEC, STEC and E. albertii but also P. rustigianii.

Survey on pathogenic Escherichia coli and Salmonella spp. in captive cockatiels (Nymphicus hollandicus)

We surveyed healthy captive cockatiels (Nymphicus hollandicus) for Escherichia coli and Salmonella spp. Cloacal swabs were collected from 94 cockatiels kept in commercial breeders, private residencies and pet shops in the cities of São Paulo/SP and Niterói/RJ (Brazil). Three strains of E. coli from each individual were tested for the presence of ExPEC-, APEC- and DEC-related genes. We evaluated the bla_TEM, bla_SHV, bla_OXA, bla_CMY, bla_CTX-M, tetA, tetB, aadA, aphA, strAB, sul1, sul2, sul3, qnrA, qnrD, qnrB, qnrS, oqxAB, aac (6)'-Ib-cr, qepA resistance genes and markers for plasmid incompatibility groups. Salmonella spp. was not detected. E. coli was isolated in 10% of the animals (9/94). Four APEC genes (ironN, ompT, iss and hlyF) were detected in two strains (2/27-7%), and iss (1/27-4%) in one isolate. The highest resistance rates were observed with amoxicillin (22/27-82%), ampicillin (21/27-79%), streptomycin (18/27-67%), tetracycline (11/27-41%). Multiresistance was verified in 59% (16/27) of the isolates. We detected strAB, bla_TEM, tetA, tetB, aadA, aphaA, sul1, sul2, sul3 resistance genes and plasmid Inc groups in 20 (74%) of the strains. E. coli isolated from these cockatiels are of epidemiological importance, since these pets could transmit pathogenic and multiresistant microorganisms to humans and other animals.

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.

Multiplex PCR for the simultaneous detection of the Enterobacterial gene wecA, the Shiga Toxin genes (stx1 and stx2) and the Intimin gene (eae)

OBJECTIVES

The aetiology of several human diarrhoeas has been increasingly associated with the presence of virulence factors rather than with the bacterial species hosting the virulence genes, exemplified by the sporadic emergence of new bacterial hosts. Two important virulence factors are the Shiga toxin (Stx) and the E. coli outer membrane protein (Eae) or intimin, encoded by the stx and eae genes, respectively. Although several polymerase chain reaction (PCR) protocols target these virulence genes, few aim at detecting all variants or have an internal amplification control (IAC) included in a multiplex assay. The objective of this work was to develop a simple multiplex PCR assay in order to detect all stx and eae variants, as well as to detect bacteria belonging to the Enterobacteriaceae, also used as an IAC.

RESULTS

The wecA gene coding for the production of the Enterobacterial Common Antigen was used to develop an Enterobacteriaceae specific qPCR. Universal primers for the detection of stx and eae were developed and linked to a wecA primer pair in a robust triplex PCR. In addition, subtyping of the stx genes was achieved by subjecting the PCR products to restriction digestion and semi-nested duplex PCR, providing a simple screening assay for human diarrhoea diagnostic.