Analysis of bacterial pathogens causing acute diarrhea on the basis of sentinel surveillance in Shanghai, China, 2006-2011

Aetiology of diarrhoea in children aged zero to nine years in low- and middle-income countries: A systematic review

Background

While diarrhoeal disease remains a leading cause of death in children aged <5 years in low- and middle-income countries (LMICs), it also poses significant health risks for older children, underscoring the importance of our study focusing on children aged <10 years. In this systematic review, we assessed common diarrhoea aetiologies in children aged <10 years in LMICs.

Methods

We identified relevant articles in PubMed, Embase, and Web of Science using pre-defined search criteria. We included case series and case-control studies of children aged <10 years with non-bloody, bloody, acute, persistent, and chronic diarrhoea. Articles that evaluated two or more diarrhoea pathogens in LMICs conducted between 1 January 1990 and 31 July 2020 were eligible for inclusion. We stratified combined data from case series and case-control studies by age and World Health Organization (WHO) regions.

Results

76 studies published between 1990-2020 were eligible for inclusion. Among these, eight were case-control studies. 56 papers focused only on children aged <5 years, while 20 also included children aged ≥5 years. The most common viral pathogens among <5 years old children were rotavirus, norovirus, adenovirus, and astrovirus. Bacterial pathogens included Escherichia coli, Salmonella enterica, Shigella species, and Campylobacter species, while parasitic pathogens included Cryptosporidium, Giardia, and Entamoeba species. Rotavirus was the most common viral pathogen among children across all age groups and every WHO region. Escherichia coli was prevalent in all age groups and was responsible for most diarrhoea cases in the African Region. Among parasitic pathogens, Entamoeba species and Giardia were prevalent in children aged three to five years, with the former a major cause of diarrhoea in the Eastern Mediterranean Region. Similarly, in children aged six to 10 years, bacterial pathogens, including Escherichia coli, Salmonella, and Shigella, suggest a continued significance of these pathogens beyond the age of five. Common viral pathogens for this group were rotavirus, norovirus, and sapovirus, although the number of studies for this age group is limited.

Conclusions

Escherichia coli, rotavirus, and Entamoeba species were the most common pathogens responsible for diarrhoea in children aged <5 years in LMICs. Future research should focus on characterising the pathogens responsible for causing diarrhoea in children aged six to 10 years stratified by geographic area of residence, i.e. WHO region and urban vs rural. Case-control or cohort studies covering a full 12-month period to account for seasonality are needed for a more accurate picture of diarrhoea aetiology among children.

Registration

PROSPERO (CRD42020204005).

Risk Factors and Effects of Climate Lag on Vibrio Parahaemolyticus Infection in Eastern Coastal Cities of China: A Study Based on Hangzhou City

Bacterial foodborne diseases caused by Vibrio parahaemolyticus pose persistent challenges to coastal cities in China. In this study, we employed multiple logistic regression analysis and distributed lag non-linear models (DLNM) to investigate the epidemiological characteristics and associated risk factors of vibriosis in the metropolitan area of Hangzhou from 2014 to 2018. Analysis of foodborne cases indicated that certain demographics and occupational factors, including age between 16 and 44 years; houseworkers or unemployed individuals; preference for aquatic and meat products; and dining in collective canteens or catering services contribute to an increased likelihood of V. parahaemolyticus infection. Moreover, a higher per capita GDP and exposure to high temperatures were identified as risk factors for vibriosis. This study highlights the significance of the daily mean temperature as a meteorological factor influencing V. parahaemolyticus infection, with varying lag effects observed depending on temperature conditions. At low temperatures, the risk of infection occurs after a lag of 21 days, whereas at high temperatures, the risk is highest on the same day, while the second infection risk period occurs after a lag of 21 days. These findings provide a spatiotemporal perspective of the risk analysis of foodborne diseases, with a daily timescale and street spatial scale, which contributes to the development of public health strategies and food safety protocols in coastal cities.

Descriptive study of foodborne disease using disease monitoring data in Zhejiang Province, China, 2016-2020

Background

This study aimed to identify the epidemiology, seasonality, aetiology and clinical characteristics of sporadic foodborne diseases in Zhejiang province during 2016–2020.

Methods

Descriptive statistical methods were used to analyze the data from surveillance network established by the Zhejiang Provincial Center for Disease Control and Prevention. There were 31 designated hospitals in all 11 cities which were selected using probability proportionate to size sampling method.

Results

During the study period, the surveillance system received 75,124 cases with 4826 (6.42%) hospitalizations from 31 hospitals. The most common cause was Norovirus, 6120 cases (42.56%), followed by Salmonella, 3351 cases (23.30%). A significant seasonal trend was observed for the V. parahaemolyticus, with the highest rates over the summer period, peaking in August, 1171 cases (38.75%), a similar trend was also observed with Salmonella and Diarrheagenic E. coli. Norovirus infections showed the highest rate in November (904, 14.77%) and March (660,10.78%), the lowest in August, 215 cases (3.51%). Patients between 19 ~ 40 years were more likely to infected by Norovirus, V. parahaemolyticus and Diarrheagenic E. coli, patients below 1 year were the highest among patients with Salmonella infection, 881 cases (26.3%). The Norovirus, V. parahaemolyticus and Diarrheagenic E. coli infection with the highest positive detection rates among the workers were observed. The largest number cases of food categories were from aquatic product infection. The private home was the most common exposure setting.

Conclusion

Our study highlighted the necessity for conducting an active, comprehensive surveillance for pathogens in all age groups, to monitor the changing dynamics in the epidemiology and aetiology of foodborne diseases to guide policies that would reduce related illnesses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-14226-1.

Clinical application of a multiplex genetic pathogen detection system remaps the aetiology of diarrhoeal infections in Shanghai

Background

Culture-based diagnostic methods cannot achieve rapid and precise diagnoses for the identification of multiple diarrhoeal pathogens (DPs). A high-throughput multiplex genetic detection system (HMGS) was adapted and evaluated for the simultaneous identification and differentiation of infectious DPs and a broad analysis of DP infection aetiology.

Results

DP-HMGS was highly sensitive and specific for DP detection compared with culture-based techniques and was similar to singleplex real-time PCR. The uniform level of sensitivity of DP-HMGS for all DPs allowed us to remap the aetiology of acute diarrhoeal infections in Shanghai, correcting incidences of massively underdiagnosed DP species with accuracy approaching that of sequencing-based methods. The most frequent DPs were enteropathogenic Escherichia coli, rotavirus and Campylobacter jejuni. DP-HMGS detected two additional causes of infectious diarrhoea that were previously missed by routine culture-based methods: enterohemorrhagic E. coli and Yersinia enterocolitica. We demonstrated the age dependence of specific DP distributions, especially the distributions of rotavirus, intestinal adenovirus and Clostridium difficile in paediatric patients as well as those of dominant bacterial infections in adults, with a distinct “top 3” pattern for each age group. Finally, the multiplexing capability and high sensitivity of DP-HMGS allowed the detection of infections co-induced by multiple pathogens (approximately 1/3 of the cases), with some DPs preferentially co-occurring as infectious agents.

Conclusions

DP-HMGS has been shown to be a rapid, specific, sensitive and appropriate method for the simultaneous screening/detection of polymicrobial DP infections in faecal specimens. Widespread use of DP-HMGS is likely to advance routine diagnostic and clinical studies on the aetiology of acute diarrhoea.

Electronic supplementary material

The online version of this article (10.1186/s13099-018-0264-7) contains supplementary material, which is available to authorized users.

Epidemiology, aetiology and seasonality of infectious diarrhoea in adult outpatients through active surveillance in Shanghai, China, 2012-2016: a cross-sectional study

OBJECTIVES

This study aimed to identify the epidemiology, clinical characteristics, aetiology and seasonality of sporadic infectious diarrhoea in adults in Shanghai.

SETTING

This study was based on a city-wide, active continuous hospital-based diarrhoea surveillance network established by Shanghai Municipal Center for Disease Control and Prevention. There were 22 sentinel hospitals in all 16 districts (9 primary-level hospitals, 6 secondary-level hospitals and 7 tertiary-level hospitals) which were selected using probability proportionate to size sampling method.

PARTICIPANTS

From 1 May 2012 to 31 May 2016, 90 713 patients were included in this study. Among 8797 patients whose stool samples were collected and detected, 4392 patients were male.

RESULTS

The positive rate was 47.96%. Bacterial and viral infections accounted for 27.19% and 69.07% separately. Norovirus was the most common pathogen (43.10%), followed by rotavirus, Vibrio parahaemolyticus, diarrhoeagenic Escherichia coli (DEC) and Salmonella spp. Patients between 30-44 and 45-59 years were more likely to have infectious diarrhoea and viral diarrhoea. Those aged 30-44 years were the most likely to get infected with V. parahaemolyticus (adjusted OR, aOR vs 60+ years: 2.04, 95% CI 1.47 to 2.78) and norovirus (aOR vs 60+ years: 1.32, 95% CI 1.12 to 1.56). Bacterial (except V. parahaemolyticus) diarrhoea was characterised by fever, abdominal pain and loose stool; while viral diarrhoea was characterised by nausea, vomiting and watery stool. A seasonal distribution of infectious diarrhoea was observed with larger peaks in winter and smaller peaks in summer. Winter peaks were mainly due to norovirus and rotavirus, and summer peaks were due to bacterial infections. An emerging spring peak of norovirus around March was observed in the past 3 years.

CONCLUSION

Viral infections were predominant, and norovirus played a leading role. A seasonal distribution was observed and an emerging spring peak of norovirus was noted. Our findings highlight the necessity for conducting an active, comprehensive surveillance in adults, to monitor changing dynamics in the epidemiology and aetiology of infectious diarrhoea.

Virulence gene profiles and molecular genetic characteristics of diarrheagenic Escherichia coli from a hospital in western China

Background

Diarrheagenic Escherichia coli (DEC) is one of the most important etiological agents of diarrheal diseases. In this study we investigated the prevalence, virulence gene profiles, antimicrobial resistance, and molecular genetic characteristics of DEC at a hospital in western China.

Methods

A total of 110 Escherichia coli clinical isolates were collected from the First Affiliated Hospital of Chengdu Medical College from 2015 to 2016. Microbiological methods, PCR, antimicrobial susceptibility test, pulsed-field gel electrophoresis and multilocus sequence typing were used in this study.

Results

Molecular analysis of six DEC pathotype marker genes showed that 13 of the 110 E. coli isolates (11.82%) were DEC including nine (8.18%) diffusely adherent Escherichia coli (DAEC) and four (3.64%) enteroaggregative Escherichia coli (EAEC). The adherence genes fimC and fimH were present in all DAEC and EAEC isolates. All nine DAEC isolates harbored the virulence genes fyuA and irp2 and four (44.44%) also carried the hlyA and sat genes. The virulence genes fyuA, irp2, cnf1, hlyA, and sat were found in 100%, 100%, 75%, 50%, and 50% of EAEC isolates, respectively. In addition, all DEC isolates were multidrug resistant and had high frequencies of antimicrobial resistance. Molecular genetic characterization showed that the 13 DEC isolates were divided into 11 pulsed-field gel electrophoresis patterns and 10 sequence types.

Conclusions

To the best of our knowledge, this study provides the first report of DEC, including DAEC and EAEC, in western China. Our analyses identified the virulence genes present in E. coli from a hospital indicating their role in the isolated DEC strains’ pathogenesis. At the same time, the analyses revealed, the antimicrobial resistance pattern of the DEC isolates. Thus, DAEC and EAEC among the DEC strains should be considered a significant risk to humans in western China due to their evolved pathogenicity and antimicrobial resistance pattern.

Bacterial pathogen spectrum of acute diarrheal outpatients in an urbanized rural district in Southwest China

OBJECTIVES

To conduct a one-year pathogen surveillance of acute diarrheal disease based on outpatient clinics in township hospitals in rural Hongta District of Yunnan Province, China.

METHODS

Fecal specimens of acute diarrhea cases and relevant epidemiological information were collected. Salmonella, Shigella, Vibrio, Aeromonas, Plesiomonas shigelloides and diarrheogenic Escherichia coli (DEC) were examined.

RESULTS

Among the 797 stool specimens sampled, 198 samples (24.8%) were positive in pathogen isolation, and 223 strains were isolated. The order of isolation rates from high to low were DEC, Aeromonas, P. shigelloides, Salmonella, Shigella and Vibrio. The overall positive rate in middle school students and preschool children was relatively high; while the overall positive rate of less than 1-year-old infants and above 55 years olds was relatively low. The isolates were analyzed by pulsed-field gel electrophoresis (PFGE). Some cases had the same or very close onset time, and the isolates had similar PFGE patterns, suggesting a possible outbreak once occurred but was not detected by the current infectious disease reporting system.

CONCLUSIONS

Pathogen infection and transmission in rapidly urbanized rural areas is a serious issue. There is a great need for a more sensitive and accurate mode of monitoring, reporting and outbreak identification of diarrheal disease.

Molecular and Conventional Analysis of Acute Diarrheal Isolates Identifies Epidemiological Trends, Antibiotic Resistance and Virulence Profiles of Common Enteropathogens in Shanghai

Objective: To investigate prevalence of acute diarrhea in Shanghai and analyze virulence associated-genes and antibiotic resistance of major enteropathogens using combination of conventional and molecular epidemiology methods. Method: The 412 stool specimens were obtained by systematic sampling from diarrhea patients throughout entire year 2016. Bacterial and viral pathogens were identified and bacterial isolates were cultured and screened for antibiotic resistance profiles. Two most prevalent bacteria, Vibrio parahaemolyticus and Salmonella were further typed by multi-locus sequence typing (MLST) and analyzed for presence of virulence-associated genes. The association between virulence genes, resistance phenotypes and genetic diversities was analyzed. Results: Among stool specimens testing positive for pathogens (23.1%), 59 bacterial and 36 viral pathogens were identified. V. parahaemolyticus (27/412, 6.6%), Salmonella (23/412, 5.6%) and norovirus GII (21/412, 5.1%) were three most-commonly found. Most bacterial isolates exhibited high levels of antibiotic resistance with high percentage of MDR. The drug resistance rates of V. parahaemolyticus and Salmonella isolates to cephalosporins were high, such as 100.0 and 34.8% to CFX, 55.6 and 43.4% to CTX, 92.6 and 95.7% to CXM, respectively. The most common resistance combination of V. parahaemolyticus and Salmonella was cephalosporins and quinolone. The dominant sequence types (STs) of V. parahaemolyticus and Salmonella were ST3 (70.4%) and ST11 (43.5%), respectively. The detection rates of virulence genes in V. parahaemolyticus were tlh (100%) and tdh (92.6%), without trh and ureR. Most of the Salmonella isolates were positive for the Salmonella pathogenicity islands (SPIs) genes (87-100%), and some for Salmonella plasmid virulence (SPV) genes (34.8% for spvA and spvB, 43.5% for spvC). In addition, just like the drug resistance, virulence genes exhibited wide-spread distribution among the different STs albeit with some detectable frequency linkage among Salmonella STs. Conclusion: Bacterial infections are still the major cause of severe diarrheas in Shanghai. The most common bacteria V. parahaemolyticus and Salmonella show molecular characteristics consistent with preselection of highly virulent types with exceedingly high level of antibiotic resistance.

Characteristics of diarrheagenic Escherichia coli among children under 5 years of age with acute diarrhea: a hospital based study

BACKGROUND

Diarrhea is the leading infectious cause of childhood morbidity and mortality. Among bacterial agents, diarrheagenic Escherichia coli (DEC) is the major causal agent of childhood diarrhea in developing countries, particularly in children under the age of 5 years. Here, we performed a hospital-based prospective study to explore the pathotype distribution, epidemiological characteristics and antibiotic resistance patterns of DEC from < 5-year-old diarrheal children.

METHODS

Between August 2015 and September 2016, 684 stool samples were collected from children (< 5 years old) with acute diarrhea. All samples were cultured and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and biochemical tests. PCR was used for subtyping, and enteropathogenic E. coli (EPEC) isolates were identified simultaneously with serology. Furthermore, antimicrobial sensitivity tests and sequencing of antibiotic resistance-related genes were conducted.

RESULTS

DEC strains were identified in 7.9% of the 684 stool samples. Among them, the most commonly detected pathotype was EPEC (50.0% of DEC), of which 77.8% were classified as atypical EPEC (aEPEC). Age and seasonal distribution revealed that DEC tended to infect younger children and to occur in summer/autumn periods. Multidrug-resistant DEC isolates were 66.7%; resistance rates to ampicillin, co-trimoxazole, cefazolin, cefuroxime, cefotaxime, and ciprofloxacin were ≥ 50%. Among 5 carbapenem-resistant DEC, 60.0% were positive for carbapenemase genes (2 blaNDM-1 and 1 blaKPC-2). Among 30 cephalosporin-resistant DEC, 93.3% were positive for extended-spectrum β-lactamase (ESBL) genes, with blaTEM-1 and blaCTX-M-55 being the most common types. However, no gyrA or gyrB genes were detected in 16 quinolone-resistant isolates. Notably, aEPEC, which has not received much attention before, also exhibited high rates of drug resistance (81.0%, 66.7%, and 14.3% for ampicillin, co-trimoxazole , and carbapenem resistance, respectively).

CONCLUSIONS

EPEC was the most frequent DEC pathotype in acute diarrheal children, with aEPEC emerging as a dominant diarrheal agent in central China. Most DEC strains were multidrug-resistant, making even ciprofloxacin unsuitable for empiric treatment against DEC infection. Among carbapenem-resistant DEC strains, those harboring blaNDM-1 and blaKPC-2 were the main causal agents. blaTEM-1 and blaCTX-M-55 were the major genetic determinants associated with high levels of cephalosporin resistance.

Spreading of Pandemic Vibrio parahaemolyticus O3:K6 and Its Serovariants: A Re-analysis of Strains Isolated from Multiple Studies

In China, V. parahaemolyticus has been a leading cause of foodborne outbreaks and bacterial infectious diarrhea since the 1990s, and most infections have been associated with the pandemic V. parahaemolyticus O3:K6 and its serovariants. However, a comprehensive overview of the sero-prevalence and genetic diversity of the pandemic V. parahaemolyticus clone in China is lacking. To compensate for this deficiency, pandemic isolates in both clinical and environmental Chinese samples collected from multiple studies were analyzed in this study. Surprisingly, as many as 27 clinical pandemic serovariants were identified and were widely distributed across nine coastal provinces and two inland provinces (Beijing and Sichuan). O3:K6, O4:K68, and O1:KUT represented the predominant clinical serovars. Only four environmental pandemic serovariants had previously been reported, and they were spread throughout Shanghai (O1:KUT, O3:K6), Jiangsu (O3:K6, O4:K48), Zhejiang (O3:K6), and Guangdong (O4:K9). Notably, 24 pandemic serovariants were detected within a short time frame (from 2006 to 2012). The pandemic isolates were divided into 15 sequence types (STs), 10 of which fell within clonal complex (CC) 3. Only three STs (ST3, ST192, and ST305) were identified in environmental isolates. Substantial serotypic diversity was mainly observed among isolates within pandemic ST3, which comprised 21 combinations of O/K antigens. The pandemic O3:K6 serotype showed a high level of sequence diversity, which was shared by eight different STs (ST3, ST227, ST431, ST435, ST487, ST489, ST526, and ST672). Antimicrobial susceptibility testing revealed that most isolates shared similar antibiotic susceptibility profiles. They were resistant to ampicillin but sensitive to most other drugs that were tested. In conclusion, the high levels of serotypic and genetic diversity of the pandemic clone suggest that the involved regions are becoming important reservoirs for the emergence of novel pandemic strains. We underscore the need for routine monitoring to prevent pandemic V. parahaemolyticus infection, which includes monitoring antimicrobial responses to avoid excessive misuse of antibiotics. Further investigations are also needed to delineate the specific mechanisms underlying the possible seroconversion of pandemic isolates.

Viral and Bacterial Etiology of Acute Diarrhea among Children under 5 Years of Age in Wuhan, China

BACKGROUND

Acute diarrhea remains the serious problem in developing countries, especially among children under 5 years of age. Currently, only two or three common diarrhea pathogens were screened at most hospitals in China. The aim of this study was to provide a wide variety of diarrhea pathogens and their antimicrobial resistance patterns in children under 5 years of age.

METHODS

Totally 381 stool samples collected from Tongji Hospital between July 1, 2014 and June 30, 2015 were tested by culture and/or polymerase chain reaction for eight kinds of bacteria and five kinds of viruses. An antimicrobial sensitivity test was performed using dilution method recommended by the Clinical and Laboratory Standards Institute.

RESULTS

Viral infections were mainly identified in infants (0-11 months), whereas bacterial infections were more prevalent in the age of 24-59 months. About 69.8% of samples were positive for at least one pathogen, 51.7% of samples were virus positive, followed by bacteria positive cases (19.4%), and 12.6% of cases displayed co-infections with two viruses or a virus and a bacterium. Rotavirus was the most prevalent pathogen, followed closely by norovirus, while Salmonella was the most commonly isolated bacteria, followed by diarrheagenic Escherichia coli (DEC) and Campylobacter. More than 40% of Salmonella spp. and DEC isolates were resistant to first-line antibiotics (ampicillin, trimethoprim-sulfamethoxazole, and tetracycline). Around 10% of Salmonella spp. isolates were resistant to ceftriaxone and ciprofloxacin simultaneously. Campylobacter spp. displayed high resistance to ciprofloxacin but kept low resistance to azithromycin and doxycycline.

CONCLUSIONS

The etiology of acute diarrhea varies in children of different age groups. The high frequency of infection with viruses suggests the urgent demand for new viral vaccine development. Proper use of antibiotics in the treatment of acute diarrhea is crucial due to the high level of antibiotic resistance.

A large outbreak of acute gastroenteritis caused by the human norovirus GII.17 strain at a university in Henan Province, China

Background

Human noroviruses are a major cause of viral gastroenteritis and are the main etiological agents of acute gastroenteritis outbreaks. An increasing number of outbreaks and sporadic cases of norovirus have been reported in China in recent years. There was a large acute gastroenteritis outbreak at a university in Henan Province, China in the past five years. We want to identify the source, transmission routes of the outbreak by epidemiological investigation and laboratory testing in order to provide the effective control measures.

Methods

The clinical cases were investigated, and analysed by descriptive epidemiological methods according to factors such as time, department, grade and so on. Samples were collected from clinical cases, healthy persons, the environment, water, and food at the university. These samples were tested for potential bacteria and viruses. The samples that tested positive for norovirus were selected for whole genome sequencing and the sequences were then analysed.

Results

From 4 March to 3 April 2015, a total of 753 acute diarrhoea cases were reported at the university; the attack rate was 3.29%. The epidemic curve showed two peaks, with the main peak occurring between 10 and 20 March, accounting for 85.26% of reported cases. The rates of norovirus detection in samples from confirmed cases, people without symptoms, and environmental samples were 32.72%, 17.39%, and 9.17%, respectively. The phylogenetic analysis showed that the norovirus belonged to the genotype GII.17.

Conclusions

This is the largest and most severe outbreak caused by genotype GII.17 norovirus in recent years in China. The GII.17 viruses displayed high epidemic activity and have become a dominant strain in China since the winter of 2014, having replaced the previously dominant GII.4 Sydney 2012 strain.

Electronic supplementary material

The online version of this article (doi:10.1186/s40249-017-0236-z) contains supplementary material, which is available to authorized users.

Case-control study of diarrheal disease etiology in individuals over 5 years in southwest China

Background

Acute diarrhea is one of the major public health problems worldwide. Most of studies on acute diarrhea have been made on infants aged below 5 years and few efforts have been made to identify the etiological agents of acute diarrhea in people over five, especially in China.

Methods

271 diarrhea cases and 149 healthy controls over 5 years were recruited from four participating hospitals between June 2014 and July 2015. Each stool specimen was collected to detect a series of enteric pathogens, involving five viruses (Rotavirus group A, RVA; Norovirus, NoV; Sapovirus, SaV; Astrovirus, As; and Adenovirus, Ad), seven bacteria (diarrheagenic Escherichia coli, DEC; non-typhoidal Salmonella, NTS; Shigella spp.; Vibrio cholera; Vibrio parahaemolyticus; Aeromonas spp.; and Plesiomonas spp.) and three protozoa (Cryptosporidium spp., Giardia lamblia, G. lamblia, and Blastocystis hominis, B. hominis). Standard microbiological and molecular methods were applied to detect these pathogens. Data was analyzed using Chi square, Fisher-exact tests and logistic regressions.

Results

The prevalence of at least one enteric pathogen was detected in 29.2% (79/271) acute diarrhea cases and in 12.1% (18/149) in healthy controls (p < 0.0001). Enteric viral infections (14.4%) were the most common in patients suffering from acute diarrhea, followed by bacteria (13.7%) and intestinal protozoa (4.8%). DEC (12.5%) was the most common causative agent in diarrhea cases, followed by NoV GII (10.0%), RVA (7.4%) and B. hominis (4.8%). The prevalence of co-infection was statistically higher (p = 0.0059) in the case group (7.7%) than in the healthy control (1.3%). RVA–NoV GII (3.0%) was the most common co-infection in symptomatic cases.

Conclusions

DEC was the most predominant pathogen in diarrhea cases, but it was largely overlooked because the lack of laboratory capacities. Because of the high prevalence of co-infections, it is recommended the urgent development of alternative laboratory methods to assess polymicrobial infections. Such methodological improvements will result in a better prevention and treatment strategies to control diarrhea illness in China.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-016-0141-1) contains supplementary material, which is available to authorized users.

Population analysis of clinical and environmental Vibrio parahaemolyticus isolated from eastern provinces in China by removing the recombinant SNPs in the MLST loci

Vibrio parahaemolyticus is a common seafood-borne pathogenic bacterium which causes gastroenteritis in humans. Continuous surveillance on the molecular characters of the clinical and environmental V. parahaemolyticus strains needs to be conducted for the epidemiological and genetic purposes. To generate a picture of the population distribution of V. parahaemolyticus in eastern China isolated from clinical cases of gastroenteritis and environmental samples, we investigated the genetic and evolutionary relationships of the strains using the commonly used multi-locus sequence typing (MLST, in which seven house-keeping genes are used in the protocol). A highly genetic diversity within the V. parahaemolyticus population was observed but ST3 was still dominant in the clinical strains, and 103 new sequence types (ST) were found in the clinical strains by searching in the global V. parahaemolyticus MLST database. With these genetically diverse strains, we estimated the recombination rates of the loci in MLST analysis. The locus recA was found to be subject to exceptionally high rate of recombination, and the recombinant single nucleotide polymorphisms (SNPs) were also identified within the seven loci. The phylogenetic tree of the strains was re-constructed using the maximum likelihood method by removing the recombination SNPs of the seven loci, and the minimum spanning tree was re-constructed with the six loci without recA. Some changes were observed in comparison with the previously used methods, suggesting that the homologous recombination has roles in shaping the clonal structure of V. parahaemolyticus. We propose the recombination-free SNPs strategy in the clonality analysis of V. parahaemolyticus, especially when using the maximum likelihood method.

Impact of co-infections with enteric pathogens on children suffering from acute diarrhea in southwest China

Background

Acute diarrhea is a global health problem, resulting in high morbidity and mortality in children. It has been suggested that enteric pathogen co-infections play an important role in gastroenteritis, but most research efforts have only focused on a small range of species belonging to a few pathogen groups. This study aimed to assess the impact of co-infections with a broad range of enteric pathogens on children aged below five years who suffer from acute diarrhea in southwest China.

Method

A total of 1020 subjects (850 diarrhea cases and 170 healthy controls) were selected from four sentinel hospitals in Kunming, Yunnan province, southwest China, from June 2014 to July 2015. Stool specimens were collected to detect five virus (rotavirus group A, RVA; norovirus, NoV; Sapovirus, SaV; astrovirus, As; and adenovirus, Ad), seven bacterial (diarrheagenic Escherichia coli, DEC; non-typhoidal Salmonella, NTS; Shigella spp.; Vibrio cholera; Vibrio parahaemolyticus; Aeromonas spp.; and Plesiomonas spp.), and three protozoan (Cryptosporidium spp., Giardia lamblia, and Blastocystis hominis, B. hominis) species using standard microbiologic and molecular methods. Data were analyzed using the partial least square regression technique and chi-square test.

Results

At least one enteric pathogen was detected in 46.7 % (n = 397) of acute gastroenteritis cases and 13.5 % (n = 23) of healthy controls (χ² = 64.4, P < 0.05). Single infection with RVA was associated with acute diarrhea (26.5 % vs. 5.8 %, P < 0.05). The prevalence of a single infection with B. hominis in diarrhea cases was higher than in healthy controls (3.1 % vs. 0.5 %, OR = 4.7, 95 % CI: 1.01–112.0). Single infection with NoV GII was not associated with diarrhea (4.4 % vs. 3.5 %, OR = 1.2, 95 % CI: 0.5–3.3). Single infections with bacterial species were not observed. The prevalence of co-infections with two enteric pathogens in diarrhea cases was higher than in asymptomatic children (20.1 % vs. 5.3 %, P < 0.05). RVA-NoV GII was the most common co-infection in symptomatic children (4.4 %), with it aggravating the severity of diarrhea.

Conclusions

Although it is clear that RVA has an overwhelming impact on diarrhea illnesses in children, co-infection with other enteric pathogens appears to also aggravate diarrhea severity. These findings should serve as evidence for public health services when planning and developing intervention programs.

Electronic supplementary material

The online version of this article (doi:10.1186/s40249-016-0157-2) contains supplementary material, which is available to authorized users.

Prevalence and antibiotic resistance of bacterial pathogens isolated from childhood diarrhea in Beijing, China (2010-2014)

BACKGROUND

Diarrhea is one of the main causes of morbidity and mortality among children less than 5 years of age worldwide, and its causes vary by region. This study aimed to determine the etiologic spectrum, prevalent characteristics and antimicrobial resistance patterns of common enteropathogenic bacteria from diarrheagenic children in Beijing, the capital of China.

METHODS

Stool samples were collected from 2524 outpatients who were aged 0-5 years in Beijing, China during 2010-2014. Microbiological methods, real-time PCR and antimicrobial susceptibility test were used to identify the bacterial causes and antimicrobial resistance patterns in the isolates.

RESULTS

Of the 2524 patients screened, we identified the causes of 269 cases (10.7 %) as follows: diarrheagenic Escherichia coli (4.6 %), Salmonella (4.3 %), Shigella (1.4 %) and Vibrio parahaemolyticus (0.4 %). Atypical EPEC, Salmonella enteritidis, Shigella sonnei and serotype O3:K6 were the most common serogroups or serotypes of the four etiological bacteria. The prevalence of pathogens was correlated with age, season and clinical symptoms. The highest proportion of all causative bacteria was found in children aged 3-5 years and in summer. The clinical symptoms associated with specific bacterial infection, such as fever; abdominal pain; vomiting; and watery, mucus, and bloody stool, were observed frequently in diarrheal patients. Salmonella showed moderate rates of resistance (40-60 %) to ampicillin, nalidixic acid, streptomycin and sulfisoxazole. Resistance to at least three antimicrobials was found in 50 % of isolates. Of the top three serotypes in Salmonella, high-level antimicrobial resistance to single and multiple antibiotics was more common among Salmonella typhimurium and Salmonella 1, 4, [5], 12:i:- than among S. enteritidis. More than 90 % of Shigella isolates showed more alarming resistance to most antibiotics, with a widened spectrum compared to Salmonella.

CONCLUSION

Constant antibiotic surveillance is warranted because the bacteria were highly resistant to various antimicrobials. Our study contributes to the strengthening of the existing surveillance system and provides aid for effective prevention and control strategies for childhood diarrhea.

Evaluation of PCR Based Assays for the Improvement of Proportion Estimation of Bacterial and Viral Pathogens in Diarrheal Surveillance

Diarrhea can be caused by a variety of bacterial, viral and parasitic organisms. Laboratory diagnosis is essential in the pathogen-specific burden assessment. In the pathogen spectrum monitoring in the diarrheal surveillance, culture methods are commonly used for the bacterial pathogens' detection whereas nucleic acid based amplification, the non-cultural methods are used for the viral pathogens. Different methodology may cause the inaccurate pathogen spectrum for the bacterial pathogens because of their different culture abilities with the different media, and for the comparison of bacterial vs. viral pathogens. The application of nucleic acid-based methods in the detection of viral and bacterial pathogens will likely increase the number of confirmed positive diagnoses, and will be comparable since all pathogens will be detected based on the same nucleic acid extracts from the same sample. In this study, bacterial pathogens, including diarrheagenic Escherichia coli (DEC), Salmonella spp., Shigella spp., Vibrio parahaemolyticus and V. cholerae, were detected in 334 diarrheal samples by PCR-based methods using nucleic acid extracted from stool samples and associated enrichment cultures. A protocol was established to facilitate the consistent identification of bacterial pathogens in diarrheal patients. Five common enteric viruses were also detected by RT-PCR, including rotavirus, sapovirus, norovirus (I and II), human astrovirus, and enteric adenovirus. Higher positive rates were found for the bacterial pathogens, showing the lower proportion estimation if only using culture methods. This application will improve the quality of bacterial diarrheagenic pathogen survey, providing more accurate information pertaining to the pathogen spectrum associated with finding of food safety problems and disease burden evaluation.

Identification of Bufavirus-1 and Bufavirus-3 in Feces of Patients with Acute Diarrhea, China

Bufavirus (BuV) is a newly discovered human parvovirus that has been detected in some countries. The current study was designed to understand the epidemic of BuV in China. Totally 1877 fecal specimens were collected from pediatric and adult patients with acute diarrhea in two large hospitals from 2010 to 2014. BuV was detected in 0.5% (9/1877) of the fecal samples by PCR and subsequent sequencing. The positive patients had a wide age range from 1 month through 60 years (median 24 years old) and 6 were male. A geographic specific pattern was obvious, with significantly higher frequency of BuV presented in Northern than in Southern China. Four BuV-1 and five BuV-3 were determined. Mixed-infections of BuV with sapovirus and novavirus were found in 2 cases, respectively. A temporal clustering was identified, with most positive detection focused in the cold weather. These findings have expanded the current knowledge on the geographic boundaries of BuV circulation.

Acute gastroenteritis outbreak caused by a GII.6 norovirus

AIM: To report an acute gastroenteritis outbreak caused by a genogroup 2 genotype 6 (GII.6) strain norovirus in Shanghai, China.

METHODS: Noroviruses are responsible for approximately half of all reported gastroenteritis outbreaks in many countries. Genogroup 2 genotype 4 strains are the most prevalent. Rare outbreaks caused by GII.6 strains have been reported. An acute gastroenteritis outbreak occurred in an elementary school in Shanghai in December of 2013. Field and molecular epidemiologic investigations were conducted.

RESULTS: The outbreak was limited to one class in an elementary school located in southwest Shanghai. The age of the students ranged from 9 to 10 years. The first case emerged on December 10, 2013, and the last case emerged on December 14, 2013. The cases peaked on December 11, 2013, with 21 new cases. Of 45 students in the class, 32 were affected. The main symptom was gastroenteritis, and 15.6% (5/32) of the cases exhibited a fever. A field epidemiologic investigation showed the pathogen may have been transmitted to the elementary school from employees in a delicatessen via the first case student, who had eaten food from the delicatessen one day before the gastroenteritis episodes began. A molecular epidemiologic investigation identified the cause of the gastroenteritis as norovirus strain GII.6; the viral sequence of the student cases showed 100% homology with that of the shop employees. Genetic relatedness analyses showed that the new viral strain is closely related to previously reported GII.6 sequences, especially to a strain reported in Japan.

CONCLUSION: This is the first report to show that norovirus strain GII.6 can cause a gastroenteritis outbreak. Thus, the prevalence of GII.6 noroviruses requires attention.