Enterotoxigenic Escherichia coli and diffusely adherent E. coli as likely causes of a proportion of pathogen-negative travelers' diarrhea--a PCR-based study

Whole-Genome Analysis of blaNDM-Bearing Proteus mirabilis Isolates and mcr-1-Positive Escherichia coli Isolates Carrying blaNDM from the Same Fresh Vegetables in China

The global spread of colistin or carbapenem-resistant Enterobacteriaceae (CRE) has been a pressing threat to public health. Members of Enterobacteriaceae, especially Proteus mirabilis and Escherichia coli, have been prevalent foodborne pathogens and such pathogens from fresh vegetables have triggered foodborne illness in China. However, reports about CRE, especially P. mirabilis from fresh vegetables, are still lacking. In this study, we identified five bla_NDM-positive P. mirabilis and five bla_NDM-positive generic E. coli concurrently from five fresh vegetables in two markets from China, and four of the five E. coli also carried mcr-1. The 10 isolates were characterized with methods including antimicrobial susceptibility testing, conjugation, whole-genome sequencing and phylogenetic analysis. All 10 isolates were multidrug-resistant (MDR). bla_NDM-5 in five E. coli isolates and one P. mirabilis carrying bla_NDM-5 was located on similarly transferable IncX3 plasmids, while transferably untypable plasmids were the carriers of bla_NDM-1 in four P. mirabilis isolates from different types of vegetables/markets. mcr-1 in the four bla_NDM-₅-positive E. coli was located on similarly non-conjugative IncHI2 MDR plasmids lacking transfer region. Notably, ISCR1 complex class 1 integron capable of capturing bla_NDM-1 was found on all untypable plasmids from P. mirabilis, and five copies of ISCR1 complex class 1 integron containing bla_NDM-1 even occurred in one P. mirabilis, which showed high-level carbapenem resistance. Plasmid and phylogenetic analysis revealed that the bla_NDM-positive P. mirabilis and E. coli from fresh vegetables might be derived from animals and transmitted to humans via the food chain. The concurrence of bla_NDM-positive P. mirabilis and E. coli carrying both mcr-1 and bla_NDM in different types of fresh vegetables eaten raw is alarming and threatens food safety. Sustained surveillance of these foodborne pathogens among fresh vegetables is urgent to ensure the health of food consumers. We report for the first time the concurrence of bla_NDM-positive P. mirabilis and mcr-1-bearing E. coli carrying bla_NDM from the same fresh vegetables.

Multiplex PCR reveals a high prevalence of multiple pathogens in traveller's diarrhoea in children

OBJECTIVE

Traveller's diarrhoea (TD) is one of the most frequent illnesses affecting children returning from tropical countries. The purpose of this study was to assess the distribution of pathogens associated with TD in children using a multiplex PCR assay on stool samples.

DESIGN

All the children admitted for TD in two university hospitals from 1 August to 15October during 2014 and 2015 were included in a prospective study. Stool samples were tested by a multiplex PCR FilmArray GI panel detecting 22 pathogens. Performances for the detection of major enteropathogenic bacteria (Salmonella, Shigella and Campylobacter spp) by multiplex PCR and conventional culture methods were compared. The prevalence of extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae was also determined.

RESULTS

Fifty-nine children were included. In 58 cases (98%), at least one pathogen was identified, including 9 different enteropathogenic bacteria, 5 viruses and 2 parasites. Multiplex PCR enhanced the enteropathogenic bacteria detection by 25%. The most frequent pathogens were enteroaggregative Escherichia coli (n=32), enteropathogenic E. coli (n=26), enterotoxigenic E. coli (n=19), Salmonella enterica, enteroinvasive E. coli/Shigella (n=16 each), Cryptosporidium, sapovirus (n=11 each), Campylobacter jejuni, norovirus (n=10 each), rotavirus (n=9), Giardia (n=8) and Shiga-toxin-producing E. coli (n=4). Fifty-two coinfections were observed, notably including bacteria and viruses (n=21), multiple bacteria (n=14), or bacteria and parasites (n=10). ESBL were detected in 28 cases. Multiplex PCR could optimise the number of treated patients by 27% compared with stool cultures.

CONCLUSION

Multiplex PCR on stools revealed a high prevalence of diverse enteric pathogens and coinfections in children with TD. Major enteropathogenic bacteria were more frequently detected by multiplex PCR compared with conventional culture. Finally, this technique allows the start of appropriate and early antibiotic treatment and seems to optimise the number of correctly treated patients.

Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea

BACKGROUND

Travelers' diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 40% of TD patients. It is predicted that new pathogens may be causative agents of the disease.

RESULTS

We performed a comprehensive amplicon and whole genome shotgun (WGS) metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers, all of which were negative for the known etiologic agents of TD based on standard microbiological and immunological assays. Abnormal and diverse taxonomic profiles in TD samples were revealed. WGS reads were assembled and the resulting contigs were visualized using multiple query types. A semi-manual workflow was applied to isolate independent genomes from metagenomic pools. A total of 565 genome bins were extracted, 320 of which were complete enough to be characterized as cellular genomes; 160 were viral genomes. We made predictions of the etiology of disease for many of the individual subjects based on the properties and features of the recovered genomes. Multiple patients with low-diversity metagenomes were predominated by one to several E. coli strains. Functional annotation allowed prediction of pathogenic type in many cases. Five patients were co-infected with E. coli and other members of Enterobacteriaceae, including Enterobacter, Klebsiella, and Citrobacter; these may represent blooms of organisms that appear following secretory diarrhea. New "dark matter" microbes were observed in multiple samples. In one, we identified a novel TM7 genome that phylogenetically clustered with a sludge isolate; it carries genes encoding potential virulence factors. In multiple samples, we observed high proportions of putative novel viral genomes, some of which form clusters with the ubiquitous gut virus, crAssphage. The total relative abundance of viruses was significantly higher in healthy travelers versus TD patients.

CONCLUSION

Our study highlights the strength of assembly-based metagenomics, especially the manually curated, visualization-assisted binning of contigs, in resolving unusual and under-characterized pathogenic profiles of human-associated microbiomes. Results show that TD may be polymicrobial, with multiple novel cellular and viral strains as potential players in the diarrheal disease.

The determination of E. coli levels and pathotypes in water sources around Isparta province Turkey

In this study, a total of 57 water samples were collected over different months around the Isparta region. The levels of total and fecal coliform in these water samples were determined. According to an analysis of the results, although the pollution level of these water sources are not high in terms of their total coliform counts, they cannot be used as drinking water. In the water samples taken from Andık Creek, Darı Creek  Dam, and Eğirdir Lake, fecal counts were found to be similar to each other, it is possible to use these waters after refinement. However fecal coliform levels are high in water samples taken from Bezirgan Creek, and these waters cannot be used as drinking water. After the total and fecal coliform counts were determined, the most probable colonies that can be identified to be E. coli were chosen and confirmation tests were performed. In total, 397 colonies were isolated from water samples, and 55 of those were confirmed as E. coli strains. Also, 151 strains were determined to be part of the coliform group. E. coli strains were studied with a real-time PCR to determine some virulence genes. Analysis of the results showed that 29.2% of E. coli strains contained enteropathogenic/enterohemorrhagic E. coli virulence genes, and 14.5% of the isolated E. coli strains contained verotoxigenic E. coli virulence factors. Enteroinvasive E. coli virulence genes were contained in 1.8% of the E. coli strains, and it was found that 54.5% of the isolated E. coli strains contained none of the gene regions investigated.

The Virulence Regulator Rns Activates the Expression of CS14 Pili

Although many viral and bacterial pathogens cause diarrhea, enterotoxigenic E. coli (ETEC) is one of the most frequently encountered in impoverished regions where it is estimated to kill between 300,000 and 700,000 children and infants annually. Critical ETEC virulence factors include pili which mediate the attachment of the pathogen to receptors in the intestinal lumen. In this study we show that the ETEC virulence regulator Rns positively regulates the expression of CS14 pili. Three Rns binding sites were identified upstream of the CS14 pilus promoter centered at -34.5, -80.5, and -155.5 relative to the Rns-dependent transcription start site. Mutagenesis of the promoter proximal site significantly decreased expression from the CS14 promoter. In contrast, the contribution of Rns bound at the promoter distal site was negligible and largely masked by occupancy of the promoter proximal site. Unexpectedly, Rns bound at the site centered at -80.5 had a slight but statistically significant inhibitory effect upon the pilin promoter. Nevertheless, this weak inhibitory effect was not sufficient to overcome the substantial promoter activation from Rns bound to the promoter proximal site. Thus, CS14 pili belong to a group of pili that depend upon Rns for their expression.

Pathogenesis of human diffusely adhering Escherichia coli expressing Afa/Dr adhesins (Afa/Dr DAEC): current insights and future challenges

The pathogenicity and clinical pertinence of diffusely adhering Escherichia coli expressing the Afa/Dr adhesins (Afa/Dr DAEC) in urinary tract infections (UTIs) and pregnancy complications are well established. In contrast, the implication of intestinal Afa/Dr DAEC in diarrhea is still under debate. These strains are age dependently involved in diarrhea in children, are apparently not involved in diarrhea in adults, and can also be asymptomatic intestinal microbiota strains in children and adult. This comprehensive review analyzes the epidemiology and diagnosis and highlights recent progress which has improved the understanding of Afa/Dr DAEC pathogenesis. Here, I summarize the roles of Afa/Dr DAEC virulence factors, including Afa/Dr adhesins, flagella, Sat toxin, and pks island products, in the development of specific mechanisms of pathogenicity. In intestinal epithelial polarized cells, the Afa/Dr adhesins trigger cell membrane receptor clustering and activation of the linked cell signaling pathways, promote structural and functional cell lesions and injuries in intestinal barrier, induce proinflammatory responses, create angiogenesis, instigate epithelial-mesenchymal transition-like events, and lead to pks-dependent DNA damage. UTI-associated Afa/Dr DAEC strains, following adhesin-membrane receptor cell interactions and activation of associated lipid raft-dependent cell signaling pathways, internalize in a microtubule-dependent manner within urinary tract epithelial cells, develop a particular intracellular lifestyle, and trigger a toxin-dependent cell detachment. In response to Afa/Dr DAEC infection, the host epithelial cells generate antibacterial defense responses. Finally, I discuss a hypothetical role of intestinal Afa/Dr DAEC strains that can act as "silent pathogens" with the capacity to emerge as "pathobionts" for the development of inflammatory bowel disease and intestinal carcinogenesis.

Characterization of the human gut microbiome during travelers' diarrhea

Alterations in the gut microbiota are correlated with ailments such as obesity, inflammatory bowel disease, and diarrhea. Up to 60% of individuals traveling from industrialized to developing countries acquire a form of secretory diarrhea known as travelers' diarrhea (TD), and enterotoxigenic Escherichia coli (ETEC) and norovirus (NoV) are the leading causative pathogens. Presumably, TD alters the gut microbiome, however the effect of TD on gut communities has not been studied. We report the first analysis of bacterial gut populations associated with TD. We examined and compared the gut microbiomes of individuals who developed TD associated with ETEC, NoV, or mixed pathogens, and TD with no pathogen identified, to healthy travelers. We observed a signature dysbiotic gut microbiome profile of high Firmicutes:Bacteroidetes ratios in the travelers who developed diarrhea, regardless of etiologic agent or presence of a pathogen. There was no significant difference in α-diversity among travelers. The bacterial composition of the microbiota of the healthy travelers was similar to the diarrheal groups, however the β-diversity of the healthy travelers was significantly different than any pathogen-associated TD group. Further comparison of the healthy traveler microbiota to those from healthy subjects who were part of the Human Microbiome Project also revealed a significantly higher Firmicutes:Bacteriodetes ratio in the healthy travelers and significantly different β-diversity. Thus, the composition of the gut microbiome in healthy, diarrhea-free travelers has characteristics of a dysbiotic gut, suggesting that these alterations could be associated with factors such as travel.

High number of diarrhoeal co-infections in travellers to Benin, West Africa

Background

Travellers’ diarrhoea (TD) is the most frequent health problem among travellers to the tropics. Using routine techniques, the aetiology mostly remains unresolved, whereas modern molecular methods enable reducing the number of equivocal cases considerably. While many studies address the aetiology of TD in Asian, Central American and North African tourist resorts, only few focus on Western Africa.

Methods

Stool samples from 45 travellers travelling in Benin, West Africa, were analyzed by a new multiplex qPCR assay for Salmonella, Yersinia, Campylobacter, Vibrio cholerae, Shigella or enteroinvasive (EIEC), enterohaemorrhagic (EHEC), enterotoxigenic (ETEC), enteroaggregative (EAEC), and enteropathogenic Escherichia coli (EPEC).

Results

All 18 pre-travel samples proved negative for bacterial pathogens. Of the 39/45 (87%) travellers having had TD, EPEC was detected in post-travel samples in 30 (77%) cases, EAEC in 23 (59%), ETEC in 22 (56%), Shigella or EIEC in 7 (18%), EHEC in two (5%), and Salmonella in one (3%). In 31(79%) of the TD cases two or more bacterial pathogens were identified. Two (8%) samples remained negative: both patients had taken antimicrobials for TD.

Conclusions

EPEC, EAEC and ETEC were the most common findings. 79% of the cases had a co-infection. As modern diagnostics reveals in most patients a multitude of pathogens, the role of each pathogen should be re-evaluated.

A quantitative polymerase chain reaction assay for rapid detection of 9 pathogens directly from stools of travelers with diarrhea

BACKGROUND & AIMS

Every year, 80 million tourists traveling to tropical and subtropical areas contract traveler's diarrhea (TD). Forty percent to 80% of cases are caused by bacteria, yet clinical diagnostic tests are available to identify only a few of the strains that cause TD. We aimed to develop a quantitative polymerase chain reaction (qPCR) assay to identify all major pathogens in stool samples.

METHODS

We developed a low-cost, high-throughput, multiplex qPCR assay for simultaneous detection of 9 bacterial pathogens in stool samples: Salmonella, Yersinia, Campylobacter, and Vibrio cholerae, as well as Shigella or enteroinvasive Escherichia coli, enterohemorrhagic E coli, enterotoxigenic E coli (ETEC), enteroaggregative E coli (EAEC), and enteropathogenic E coli (EPEC). The assay was validated using positive (n = 245) and negative (n = 243) control strains, as well as preselected positive and negative stool samples. In addition, stool samples were collected from 96 returning travelers with TD. The findings were compared with those from routine diagnostic tests.

RESULTS

The assay detected the bacterial strains with 100% sensitivity and specificity, compared with results from the reference tests. Of all stool samples collected from travelers with TD, EPEC was found in 47%, EAEC in 46%, ETEC in 22%, enterohemorrhagic E coli in 7%, Campylobacter in 6%, Shigella or enteroinvasive E coli in 2%, and Salmonella in 2%. Multiple pathogens were found in 37% of all samples.

CONCLUSIONS

We developed a low-cost, high-throughput qPCR assay for use in routine diagnostic analysis and research. It detects the pathogenic bacteria most commonly associated with TD in stool samples with 100% sensitivity and specificity, compared with reference methods. The assay requires 4 hours, whereas current detection methods require 1 to 7 days. At least 1 TD pathogen was identified in stool samples from 76% of returning travelers, whereas conventional methods found a pathogen in only 17%. The most commonly detected bacteria were EPEC, EAEC, and ETEC.

Advances in the treatment of travelers' diarrhea

Diarrhea is the most common complaint reported by travelers from industrialized countries visiting developing nations. High-risk areas for travelers' diarrhea (TD) include South Asia, Sub-Saharan Africa, and Latin America, while moderate-risk areas include Southeast Asia, Middle East, Oceania and the Caribbean. Bacterial pathogens are the major cause of TD. Recent advances in the therapy for diarrhea include a better understanding of the potential benefit of symptomatic and antimicrobial therapy. The mainstay of treatment includes antibacterial therapy with one of three drugs, a fluoroquinolone, rifaximin, or azithromycin. Probiotics have been used in preliminary studies for both treatment and prevention of TD, but more studies are needed with these biologic agents. The aim of this review is to identify the recent advances in the therapy of TD and to provide recommendations for treatment during international travel.

Management of the returning traveler with diarrhea

Traveler's diarrhea (TD) strikes 20-60% of travelers visiting developing countries. It occurs shortly after the return and can be distinguished into two categories: acute and persistent TD. Acute TD, mostly caused by bacterial and viral pathogens, is usually mild and self-limited, and deserves empirical symptomatic and/or antibiotic therapy in selected cases. Fluoroquinolones are progressively superseded in this indication by azithromycin, a well tolerated macrolide active against most bacteria responsible for TD, including the quinolone-resistant species of Campylobacter jejuni that are now pervasive, especially in Southeast Asia and India. Persistent TD in the returning traveler is much rarer than its acute counterpart and may be associated with three types of causes. Persistent infections, among which Giardia and possibly Entamoeba predominate, account for a significant proportion of cases. Postinfectious processes represent a second cause and comprise temporary lactose malabsorption and postinfectious irritable bowel syndrome, now considered a major cause of persistent TD. Finally, apparently unrelated chronic diseases causing diarrhea are occasionally unmasked by TD and represent a third type of persistent TD, among which the well established case of incident inflammatory bowel disease poses intriguing pathogenesis questions. This review discusses recent advances in the field and provides practical recommendations for the management of TD in adult, immunocompetent returning travelers.

Incidence, etiology, and determinants associated with acute diarrhea among French forces deployed to Chad

BACKGROUND

This study assesses, for the first time, the incidence, etiology, and determinants associated with traveler's diarrhea (TD) among French forces deployed to N'Djamena, Chad.

METHODS

A prospective study was conducted based on physician consultation for diarrhea during a 5-month French forces mandate. Diarrhea was defined as ≥3 loose stools in a 24-hour period or ≥2 loose stools within the last 8 hours. For each diarrheic episode, an anonymous physician-administered questionnaire was completed and a stool sample collected. Samples were tested for parasites, bacteria, and enteric viruses. Global incidence rate was calculated using the mean number of soldiers based in N'Djamena (n = 1,024) over the 5-month period, as denominator. Incidence rates were also estimated for each of the eleven 2-week periods of stay. A case-crossover analysis estimated determinants associated with diarrhea.

RESULTS

A total of 240 cases of diarrhea were notified by military physicians, resulting in a global incidence rate of 49 cases per 1,000 person-months (PM). The cumulative individual risk of developing diarrhea during the study period was 0.23. The incidence per 2-week stay began at 8.8/1,000 PM, rose to 54.4/1,000 PM after 1 month, and decreased after 2 months. Of the 240 cases reported, stool samples were obtained for 196 cases. Pathogens were identified in 40% of samples; enteric viruses were predominant (28.1%). Three determinants were associated with diarrhea by multivariate analysis: diarrhea in the close circle [OR: 3.8 (2.0-7.0)]; always eating at the military mess [OR: 0.2 (0.1-0.5)]; or staying in a temporary encampment [OR: 0.3 (0.1-0.8)].

CONCLUSIONS

This study found a high frequency of enteric viruses and a high risk of person-to-person transmission associated with diarrhea. Eating at the military mess or staying in a temporary encampment conferred a protective effect. In addition to food-borne disease prevention, stringent hygiene measures are required to break transmission of diarrhea during military deployments.

Microbial etiology of travelers' diarrhea in Mexico, Guatemala, and India: importance of enterotoxigenic Bacteroides fragilis and Arcobacter species

This study examined established enteric pathogens, Arcobacter species and enterotoxigenic Bacteroides fragilis (ETBF), in 201 U.S. and European travelers with acute diarrhea acquired in Mexico, Guatemala, and India. Arcobacter butzleri and ETBF were detected in 8% and 7% of diarrhea cases, respectively.

The epidemiology of travelers' diarrhea in Incirlik, Turkey: a region with a predominance of heat-stabile toxin producing enterotoxigenic Escherichia coli

This study evaluated travelers' diarrhea among US military personnel on short-term deployment to Incirlik Air Base, Turkey, from June through September 2002. Upon reporting for care for travelers' diarrhea, subjects were enrolled into the study and completed a series of questionnaires and provided stool specimens for pathogen identification and antimicrobial susceptibility testing. Fifty-three percent of the 202 participating subjects had a pathogen isolated from their stool. Enterotoxigenic Escherichia coli (ETEC) was the predominant pathogen (41%), followed by Campylobacter spp. (12%). The most common ETEC phenotype recovered was stable toxin (ST) CS6 (47% of all ETEC). Most (91.1%) of the cases presented with water diarrhea regardless of isolated pathogen. However, there were some differences in nongastrointestinal symptoms among subjects with Campylobacter spp. All illnesses were well managed with antibiotics with or without loperamide with a median time to the last unformed stool of 9 h (interquartile range, 1-32 h). We found no food or environmental factors associated with a differential risk of infection with a specific pathogen. Travelers' diarrhea among a US military population in and around Incirlik, Turkey, can commonly be attributed to ETEC and Campylobacter spp. The high proportion of ST-only-producing CS6 ETEC in this region highlights the pathogen's worldwide diversity. Future studies of travelers' diarrhea in this population should adapt more novel microbiologic techniques such as polymerase chain reaction and enhanced culture methods to increase the likelihood of identifying pathogenic E. coli.

Systematic review: the epidemiology and clinical features of travellers' diarrhoea

BACKGROUND

Travellers' diarrhoea is the most common medical complaint among persons venturing into developing areas from industrialized regions.

AIM

To review recent developments dealing with microbiological, clinical, pathophysiological and therapeutic aspects of travellers' diarrhoea.

METHODS

The author's extensive file plus a review of publications listed in PubMed on January 22, 2009 on the topic of travellers' diarrhoea were reviewed.

RESULTS

Travellers' diarrhoea is largely caused by detectable and undetected bacterial enteropathogens, explaining the remarkable effectiveness of antibacterial agents in prophylaxis and therapy of the illness. A number of host genetic polymorphisms have been recently linked with susceptibility to travellers' diarrhoea. Novel antisecretory agents are being developed for treatment considering their physiological effects in acute diarrhoea. All travellers should be armed with one of three antibacterial drugs, ciprofloxacin, rifaximin or azithromycin, before their trips to use in self therapy should diarrhoea occur during travel. Loperamide may treat milder forms of travellers' diarrhoea and can be employed with antibacterial drugs.

CONCLUSIONS

Diarrhoea will continue to plague international travellers to high-risk regions. More studies of the incidence rate, relative important of the various pathogens by geographical region of the world, host risk factors and optimal therapeutic approach are needed.