Rapid genetic typing of diarrheagenic Escherichia coli using a two-tube modified molecular beacon based multiplex real-time PCR assay and its clinical application

High-resolution melting real-time PCR 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 polymerase chain reaction (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 0.5-1 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.

Enteropathogenic Escherichia coli is a predominant pathotype in healthy pigs in Hubei Province of China

AIM

This study aims to investigate the prevalence of intestinal pathogenic Escherichia coli (InPEC) in healthy pig-related samples and evaluate the potential virulence of the InPEC strains.

METHODS AND RESULTS

A multiplex PCR method was established to identify different pathotypes of InPEC. A total of 800 rectal swab samples and 296 pork samples were collected from pig farms and slaughterhouses in Hubei province, China. From these samples, a total of 21 InPEC strains were isolated, including 19 enteropathogenic E. coli (EPEC) and 2 shiga toxin-producing E. coli (STEC) strains. By whole-genome sequencing and in silico typing, it was shown that the sequence types and serotypes were diverse among the strains. Antimicrobial susceptibility assays showed that 90.48% of the strains were multi-drug resistant. The virulence of the strains was first evaluated using the Galleria mellonella larvae model, which showed that most of the strains possessed medium to high pathogenicity. A moderately virulent EPEC isolate was further selected to characterize its pathogenicity using a mouse model, which suggested that it could cause significant diarrhea. Bioluminescence imaging (BLI) was then used to investigate the colonization dynamics of this EPEC isolate, which showed that the EPEC strain could colonize the mouse cecum for up to 5 days.

Genomic Epidemiology and Antimicrobial Susceptibility Profile of Enterotoxigenic Escherichia coli From Outpatients With Diarrhea in Shenzhen, China, 2015-2020

Enterotoxigenic Escherichia coli (ETEC) is the leading cause of severe diarrhea in children and the most common cause of diarrhea in travelers. However, most ETEC infections in Shenzhen, China were from indigenous adults. In this study, we characterized 106 ETEC isolates from indigenous outpatients with diarrhea (77% were adults aged >20 years) in Shenzhen between 2015 and 2020 by whole-genome sequencing and antimicrobial susceptibility testing. Shenzhen ETEC isolates showed a remarkable high diversity, which belonged to four E. coli phylogroups (A: 71%, B1: 13%, E: 10%, and D: 6%) and 15 ETEC lineages, with L11 (25%, O159:H34/O159:H43, ST218/ST3153), novel L2/4 (21%, O6:H16, ST48), and L4 (15%, O25:H16, ST1491) being major lineages. Heat-stable toxin (ST) was most prevalent (76%, STh: 60% STp: 16%), followed by heat-labile toxin (LT, 17%) and ST + LT (7%). One or multiple colonization factors (CFs) were identified in 68 (64%) isolates, with the common CFs being CS21 (48%) and CS6 (34%). Antimicrobial resistance mutation/gene profiles of genomes were concordant with the phenotype testing results of 52 representative isolates, which revealed high resistance rate to nalidixic acid (71%), ampicillin (69%), and ampicillin/sulbactam (46%), and demonstrated that the novel L2/4 was a multidrug-resistant lineage. This study provides novel insight into the genomic epidemiology and antimicrobial susceptibility profile of ETEC infections in indigenous adults for the first time, which further improves our understanding on ETEC epidemiology and has implications for the development of vaccine and future surveillance and prevention of ETEC infections.

Cholera: under diagnosis and differentiation from other diarrhoeal diseases

BACKGROUND

Globally 1.4 billion people are at risk from cholera in countries where the disease is endemic, with an estimated 2.8 million cases annually. The disease is significantly under reported due to economic, social and political disincentives as well as poor laboratory resources and epidemiological surveillance in those regions. In addition, identification of cholera from other diarrhoeal causes is often difficult due to shared pathology and symptoms with few reported cases in travellers from Northern Europe.

METHODS

A search of PubMed and Ovid Medline for publications on cholera diagnosis from 2010 through 2017 was conducted. Search terms included were cholera, Rapid Diagnostic Test (RDT), multiplex PCR and diagnosis of diarrhoea. Studies were included if they are published in English, French or Spanish.

RESULTS

An increase of RDT study publications for diarrhoeal disease and attempted test validations were seen over the publication period. RDTs were noted as having varied selectivity and specificity, as well as associated costs and local resource requirements that can prohibit their use.

CONCLUSIONS

Despite opportunities to employ RDTs with high selectivity and specificity in epidemic areas, or in remote locations without access to health services, such tests are limited to surveillance use. This may represent a missed opportunity to discover the true global presence of Vibrio cholerae and its role in all cause diarrhoeal disease in underdeveloped countries and in travellers to those areas. The wider applicability of RDTs may also represent an opportunity in the wider management of traveller's diarrhoea.

Prevalence and Molecular Characterization of Campylobacter spp. Isolated from Patients with Diarrhea in Shunyi, Beijing

Bacterial pathogens have been confirmed as the major cause of acute diarrhea among outpatients in China. In this study, 370 stool samples from the patients aged from 15 to 87 years old with diarrhea were collected over 12 months (from May 2016 to April 2017) in two hospitals in Shunyi, Beijing. Bacterial isolation was performed for the common enteric pathogens: Campylobacter, Salmonella, Shigella, Diarrheagenic Escherichia coli, and Vibrio parahaemolyticus for 370 samples. The filtration method was used for the Campylobacter isolation in this study. The prevalence and molecular characterization of the Campylobacter were investigated. The isolation ratio for Campylobacter, Salmonella, Shigella, Diarrheagenic E. coli, and V. parahaemolyticus was 7.0% (26/370), 6.2% (23/370), 0.3% (1/370), 7.3% (27/370), and 10.3% (38/370), respectively. Based on the isolation result, Campylobacter positive cases presented in almost every month of the whole year and the isolation ratio was the highest among the tested pathogens during October to March. There was no significant difference between genders of Campylobacter positive cases. More Campylobacter positive cases presented dehydration compared with those who were positive for Salmonella. Twenty-six Campylobacter isolates were obtained in this study and 24 of these were Campylobacter jejuni. The antibiotic susceptibility tests indicated that 83.3% (20/24) of the isolates exhibited resistance to three or more types of antibiotic. Twenty STs were identified for the 26 Campylobacter isolates and four novel STs were identified in this study. No clonal cluster was found among these isolates. This is the first study for Campylobacter isolated using the filtration method in China which indicated the Campylobacter infection might be seriously under-ascertained in the diarrheal patients in China.

Etiology of travellers' diarrhea

Eleven published studies of the etiology of travellers' diarrhea (TD) were reviewed define the etiology of TD and to exam newly developed technology such as Real-Time multiplex polymerase chain reaction (PCR) to identify multiple pathogens in one assay to define the cause of TD. Using PCR methods bacterial pathogens were found in 72% of patients acquiring diarrhea in Latin America and in 80% in travellers with illness acquired in Southeast Asia). In these studies, enterotoxigenic Escherichia coli as the predominant pathogen (42% in Latin America and 28% in Southeast Asia). Ciprofloxacin-resistant Campylobacter was commonly associated with TD in Southeast Asia. Multiplex PCR has improved the detection of enteropathogens and allowed better assessment returning travellers hospitalized with TD and those with persistent diarrhea.

The 12 Gastrointestinal Pathogens Spectrum of Acute Infectious Diarrhea in a Sentinel Hospital, Shenzhen, China

Acute infectious gastroenteritis is one of the most common diseases among all ages, particularly in developing countries. The pathogen spectrum may differ among different regions and seasons. To investigate the etiology of acute diarrhea in Shenzhen, a prospective study was conducted from August 2014 to September 2015. Stools from 412 patients with diarrhea (286 of whom were adults) including the general epidemiological information of the patients were collected. The 19 pathogens were detected by conventional culture method or multiplex PCR assay, which included five viruses (rotavirus, adenovirus, sapovirus, norovirus, and astrovirus), 11 bacterial pathogens (Salmonella, Campylobacter jejuni, Shigella, Listeria monocytogenes, Vibrio parahaemolyticus, Vibrio cholera, Enterohemorrhagic (EHEC), enteropathogenic (EPEC), enteroinvasive (EIEC), enterotoxigenic (ETEC); and enteroaggregative Escherichia coli (EAEC)) and three parasites (Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum). A potential pathogen and coinfection was found in 41.5 and 7.0% of cases, respectively. The bacterial infection was the dominant cause of diarrhea (32.3%), and the three most frequently identified organisms were Salmonella (12.1%), ETEC (8.0%), and Campylobacter jejuni (4.9%). Salmonella enteritidis was the leading serotype of Salmonella sp. Norovirus (8.3%) and sapovirus (2.2%) were the most common viral pathogens, followed by adenovirus (1.5%) and rotavirus (1.2%). No EHEC, L. monocytogenes, V. cholera, Shigella, and parasites were found. The single most important causes of diarrhea were Salmonella spp. and Campylobacter jejuni, which points toward the need for testing and surveillance for these pathogens in this region.

Multi-Typing of Enterobacteria Harboring LT and ST Enterotoxin Genes Isolated from Mexican Children

Enterotoxigenic Escherichia coli is the most common cause of diarrhea in children younger than 5 years in the developing world. We used 16S rRNA gene sequencing, the Biolog^® system, and an Amplified Ribosomal DNA Restriction Analysis (ARDRA) to identify 69 enterobacteria isolated from the feces of healthy children up to 12 years old and 54 enterobacteria isolated from stool samples obtained from children up to 5 years old with diarrhea from Morelia, Michoacán, Mexico. In the diarrheic group, 18 isolates belonged to the enterotoxigenic pathotype, 1 isolate had both LT (heat labile toxin) gene and ST (heat stable toxin) gene, and 17 had the ST gene. The identity of most of the strains harboring the ST gene was E. coli, and 3 of the strains were identified as Morganella morganii. The ST toxin gene of one of the strains identified as M. morganii showed 100% identity with an ST toxin gene of E. coli. The ARDRA was a very useful tool to differentiate between E. coli and M. morganii. The phenotypic and genetic analyses of the isolates using the Biolog^® system and Random Amplified Polymorphic DNA, respectively, showed physiological variation among the studied strains and genetic differences between subgroups.