Objective: To understand the virulence gene and drug resistance profile of Shigella sonnei outbreak in Huainan city, and conduct pathogenic traceability analysis. Methods: Water samples and feces related to an infectious diarrhea outbreak in Huainan city in August 2020 were collected for multiple pathogen detection. Virulence gene, drug sensitivity, pulse-field gel electrophoresis and whole genome sequencing of Shigella isolates were analyzed respectively. Results: 38 strains of Shigella sonnei were detected in 56 samples of mucilage feces with a positive rate 67.86%, and all serotypes were Shigella sonnei Phase I. Three strains of Shigella sonnei were detected by fluorescence PCR in the Gram-negative (GN) bacterial enrichment solution of terminal water and well water. Virulence genes were ipaH positive (38), ipaH/ial (31) and ipaH/ial/sen positive (1), respectively. The drug resistance spectrum showed that 9 of 14 antibiotics were 100% resistant, and only imipenem, chloramphenicol, ceftazidime and ciprofloxacin were effective drugs. XbaⅠ restriction enzyme map type of 36 isolates was completely consistent, and the ST type analysis of 3 strains was ST152. Whole genome sequencing and analysis verified that the outbreak was caused by a single clonal group of strains, and revealed that the isolates of the outbreak were clustered into a large cluster with 3 Chinese strains and 1 Korean strain in the database, far away from the strains of other countries. Conclusion: The outbreak is caused by a single clone of Shigella sonnei, which are low virulence strains and have multiple drug resistance.
Disease Outbreaks ; Dysentery, Bacillary/microbiology* ; Humans ; Shigella ; Shigella sonnei/genetics* ; Water/pharmacology*

Shigella flexneri, S. sonnei, S. dysenteriae, and S. boydii. Conventional treatment regimens for Shigella have been less effective due to the development of resistant strains against antibiotics. Therefore, an effective vaccine for the long term control of Shigella transmission is urgently needed.MATERIALS AND METHODS: In this study, a reverse vaccinology approach was employed to identify most conserved and immunogenic outer membrane proteins (OMPs) of S. flexneri 2a.RESULTS: Five OMPs including fepA, ompC, nlpD_1, tolC, and nlpD_2 were identified as potential vaccine candidates. Protein-protein interactions analysis using STRING software (https://string-db.org/) revealed that five of these OMPs may potentially interact with other intracellular proteins which are involved in beta-lactam resistance pathway. B- and T-cell epitopes of the selected OMPs were predicted using BCPred as well as Propred I and Propred (http://crdd.osdd.net/raghava/propred/), respectively. Each of these OMPs contains regions which are capable to induce B- and T-cell immune responses.CONCLUSION: Analysis acquired from this study showed that five selected OMPs have great potential for vaccine development against S. flexneri infection. The predicted immunogenic epitopes can also be used for development of peptide vaccines or multi-epitope vaccines against human shigellosis. Reverse vaccinology is a promising strategy for the discovery of potential vaccine candidates which can be used for future vaccine development against global persistent infections.]]>
Anti-Bacterial Agents ; beta-Lactam Resistance ; Computational Biology ; Dysentery, Bacillary ; Enterobacteriaceae ; Epitopes ; Epitopes, T-Lymphocyte ; Humans ; Membrane Proteins ; Membranes ; Shigella flexneri ; Shigella ; T-Lymphocytes ; Vaccines ; Vaccines, Subunit

Objective: To analyze the pathogenic surveillance programs and related factors on bacillary dysentery in Beijing, 2008-2017, to provide evidence for the practices of diagnosis, treatment and prevention of the disease. Methods: Analysis was conducted on surveillance data of bacillary dysentery, collected from the surveillance areas of national bacillary dysentery in Beijing. Shigella positive rate of stool samples were used as the gold standard while detection rate of Shigella, diagnostic accordance rate and resistance were computed on data from the surveillance programs. Chi-square test was used to compare the rates and unconditional logistic regression was used to analyze the related factors of Shigella infection. Results: Both the reported incidence rate on bacillary dysentery and detection rate of Shigella in diarrhea patients showed significantly decreasing trend, from 2008 to 2017. The accordance rate of bacillary dysentery was only 7.80% (111/1 423). Shigella sonnei was the most frequently isolated strain (73.95%, 159/215) followed by Shigella flexnery. Results from the multivariate logistic regression of Shigella positive rate revealed that among those patients who were routine test of stool positive vs. routine test of stool positive (OR=1.863, 95%CI: 1.402-2.475), onset from July to October vs. other months'time (OR=7.271, 95%CI: 4.514-11.709) temperature ≥38 ℃vs. temperature <38 ℃(OR=4.516, 95%CI: 3.369-6.053) and age from 6 to 59 years old vs. other ages (OR=1.617, 95%CI: 1.085-2.410), presenting higher positive detection rates of Shigella from the stool tests. The resistant rates on ampicillin and nalidixic acid were 97.57% (201/206) and 94.90% (186/196), both higher than on other antibiotics. The resistant rates on ciprofloxacin (16.33%, 32/196), ofloxacin (9.57%, 11/115) and on amoxilin (15.05%, 31/206) were relatively low. The resistant rate appeared higher on Shigella flexnery than on Shigella sonnei. The proportion of strains with resistance on 3 more drugs, was 30.00%(21/70). Conclusions: The diagnostic accordance rate of bacillary dysentery in Beijing was low, with severe resistance of Shigella. Our findings suggested that clinicians should take multiple factors into account in their practices about epidemiological history, clinical symptom and testing results for diarrhea patients.
Adolescent ; Adult ; Anti-Bacterial Agents/therapeutic use* ; Beijing/epidemiology* ; Child ; China/epidemiology* ; Dysentery, Bacillary/prevention & control* ; Feces/microbiology* ; Humans ; Middle Aged ; Population Surveillance/methods* ; Sentinel Surveillance ; Shigella/isolation & purification* ; Shigella flexneri/isolation & purification* ; Shigella sonnei/isolation & purification* ; Young Adult

BACKGROUND: In many developing countries, shigellosis is endemic and also occurs in epidemics and treatment of multidrug-resistant (MDR) isolates are important. The aims of this study were to determine the antimicrobial susceptibility, prevalence of class 1 and 2 integrons and the clonal relatedness of isolates. MATERIALS AND METHODS: Antimicrobial susceptibility tests were performed by disc diffusion method. Polymerase chain reaction (PCR)-sequencing technique was employed for detection and characterization of integrons. The genetic relatedness was evaluated by using enterobacterial repetitive intergenic consensus (ERIC) PCR. RESULTS: There was a high percentage of resistance to trimethoprim-sulfamethoxazole (TMP/SMX) (93.7%), ampicillin (AMP) (87.3%), streptomycin (STR) (84.5%) and tetracycline (TET) (78.9%). Multidrug resistant phenotype was seen in 95.1% of total isolates. Most common MDR profile was TMP/SMX/STR/AMP resistant pattern. Among the 142 Shigella spp. analyzed in this study, 28 isolates were positive for class 1 integron with two types of gene cassette arrays (dfrA17/aadA5 = 31.7% and dfrA7 = 3.8%). The class 2 integron was more frequently detected among the isolates (94.7%) with dfrA1/sat1/aadA1 (69.4%) and dfrA1/sat1 (30.6%) gene cassettes. ERIC-PCR results showed 6, 5, 4 and 3 main genotypes among S. flexneri, S. sonnei, S. boydii and S. dysenteriae isolates, respectively. CONCLUSIONS: Our findings revealed that multidrug resistant Shigella species with high prevalence of class 2 integron were very common in Iran. In addition, ERIC-PCR patterns showed limited variety of clones are responsible for shigellosis in the region of the study.
Ampicillin ; Clone Cells ; Consensus ; Developing Countries ; Diffusion ; Dysentery, Bacillary ; Genotype ; Integrons ; Iran* ; Methods ; Phenotype ; Polymerase Chain Reaction ; Prevalence ; Shigella* ; Streptomycin ; Tetracycline ; Trimethoprim, Sulfamethoxazole Drug Combination

BACKGROUND: In many developing countries, shigellosis is endemic and also occurs in epidemics and treatment of multidrug-resistant (MDR) isolates are important. The aims of this study were to determine the antimicrobial susceptibility, prevalence of class 1 and 2 integrons and the clonal relatedness of isolates. MATERIALS AND METHODS: Antimicrobial susceptibility tests were performed by disc diffusion method. Polymerase chain reaction (PCR)-sequencing technique was employed for detection and characterization of integrons. The genetic relatedness was evaluated by using enterobacterial repetitive intergenic consensus (ERIC) PCR. RESULTS: There was a high percentage of resistance to trimethoprim-sulfamethoxazole (TMP/SMX) (93.7%), ampicillin (AMP) (87.3%), streptomycin (STR) (84.5%) and tetracycline (TET) (78.9%). Multidrug resistant phenotype was seen in 95.1% of total isolates. Most common MDR profile was TMP/SMX/STR/AMP resistant pattern. Among the 142 Shigella spp. analyzed in this study, 28 isolates were positive for class 1 integron with two types of gene cassette arrays (dfrA17/aadA5 = 31.7% and dfrA7 = 3.8%). The class 2 integron was more frequently detected among the isolates (94.7%) with dfrA1/sat1/aadA1 (69.4%) and dfrA1/sat1 (30.6%) gene cassettes. ERIC-PCR results showed 6, 5, 4 and 3 main genotypes among S. flexneri, S. sonnei, S. boydii and S. dysenteriae isolates, respectively. CONCLUSIONS: Our findings revealed that multidrug resistant Shigella species with high prevalence of class 2 integron were very common in Iran. In addition, ERIC-PCR patterns showed limited variety of clones are responsible for shigellosis in the region of the study.
Ampicillin ; Clone Cells ; Consensus ; Developing Countries ; Diffusion ; Dysentery, Bacillary ; Genotype ; Integrons ; Iran* ; Methods ; Phenotype ; Polymerase Chain Reaction ; Prevalence ; Shigella* ; Streptomycin ; Tetracycline ; Trimethoprim, Sulfamethoxazole Drug Combination

BACKGROUND: We attempted to determine the characteristics of diarrheal pathogens according to species, seasonal variations, and patient age using multiplex PCR for the epidemiologic study of diarrheal disease in Jeju Island. METHODS: From March 2015 to Feb 2017, stool specimens were collected from 537 diarrheal patients older than 16 years. Multiplex PCR was used to identify pathogens and found Group A Rotavirus, enteric Adenovirus, Norovirus GI/GII, Astrovirus, Salmonella spp., Shigella spp., Vibrio spp., Campylobacter spp., Clostridium difficile toxin B (CDB), Clostridium perfringens, Yersinia enterocolitica, Aeromonas spp., Escherichia coli O157:H7, and verocytotoxin-producing E. coli (VTEC). RESULTS: Pathogens were isolated from 221 of 537 samples (41.2%); 9.3% were positive only for viral pathogens; 30.2%, only for bacterial pathogens; and 1.7%, for both viral and bacterial pathogens. Bacteria were more prevalent in spring, summer, and autumn, but viral pathogens were more prevalent in winter. Overall prevalence were Campylobacter spp. (26.7%), Clostridium perfringens (23.9%); Norovirus GII (11.4%), CDB (8.2%), Aeromonas spp. (6.3%), Group A Rotavirus (5.1%), Salmonella spp. (3.9%), Astrovirus (3.9%), Norovirus GI (3.1%), Vibrio spp (2.7%), enteric Adenovirus (1.6%), Shigella spp. (1.2%), VTEC (1.2%), and Yersinia enterocolitica (0.4%). Group A Rotavirus and Norovirus GII were more prevalent in winter and early spring. Campylobacter spp., CDB, and C. perfringens were detected frequently, without seasonal variation. CONCLUSION: Bacterial pathogens are more prevalent than viruses in acute diarrhea in adults living in Jeju Island, especially in spring, summer, and autumn. Viral pathogens are prevalent in winter. Campylobacter spp., CDB, and Clostridium perfringens are the major pathogens occurring without seasonal variations. These data will be helpful in identifying diarrheal pathogens and for treatments and prevention strategies.
Adenoviridae ; Adult* ; Aeromonas ; Bacteria ; Campylobacter ; Clostridium difficile ; Clostridium perfringens ; Diarrhea ; Epidemiologic Studies* ; Epidemiology ; Escherichia coli ; Humans ; Multiplex Polymerase Chain Reaction* ; Norovirus ; Prevalence ; Rotavirus ; Salmonella ; Seasons ; Shiga-Toxigenic Escherichia coli ; Shigella ; Vibrio ; Yersinia enterocolitica

Recently, there has been a growing demand for natural preservatives because of increased consumer interest in health. In this study, we produced Lactobacillus rhamnosus cell-free supernatant (LCFS) and evaluated and compared its antimicrobial activity with existing natural preservatives against pathogenic microorganisms and in chicken breast meat contaminated with Escherichia coli and Staphylococcus aureus. Lactobacillus rhamnosus cell-free supernatant possessed 30 units of lysozyme activity and contained 18,835 mg/L of lactic acid, 2,051 mg/L of citric acid and 5,060 mg/L of acetic acid. Additionally, LCFS inhibited the growth of fourteen pathogenic bacteria, S. aureus, Bacillus cereus, Listeria monocytogenes, Vibrio parahaemolyticus, Listeria innocua, S. epidermidis, L. ivanovii, E. coli, Pseudomonas aeruginosa, Shigella sonnei, Shi. flexneri, Proteus vulgaris, Pseudomonas fluorescens, and Klebsiella pneumoniae. The antibacterial activity of LCFS was stronger than that of egg white lysozyme (EWL), Durafresh (DF) and grapefruit seed extract (GSE). Additionally, LCFS maintained its antimicrobial activity after heat treatment at 50℃~95℃ and at pH values of 3~9. Moreover, LCFS inhibited the growth of E. coli and S. aureus in chicken breast meat. In conclusion, it is expected that LCFS, which contains both lysozyme and three organic acids, will be useful as a good natural preservative in the food industry.
Acetic Acid ; Bacillus cereus ; Bacteria ; Breast ; Chickens ; Citric Acid ; Citrus paradisi ; Egg White ; Escherichia coli ; Food Industry ; Hot Temperature ; Hydrogen-Ion Concentration ; Klebsiella pneumoniae ; Lactic Acid ; Lactobacillus rhamnosus ; Lactobacillus ; Listeria ; Listeria monocytogenes ; Meat ; Muramidase ; Proteus vulgaris ; Pseudomonas aeruginosa ; Pseudomonas fluorescens ; Shigella sonnei ; Staphylococcus aureus ; Vibrio parahaemolyticus

Objective: To understand the etiological characteristics of bacterial diarrhea in different areas, including large cities, mid-sized/small cities and rural area, in China. Methods: A cross-sectional surveillance was conducted in 17 provinces of China from 2010 to 2014. The acute diarrhea outpatients were selected from clinics or hospitals in large cities, mid-sized/small cities, including rural-urban fringe zones, and rural areas. The demographical and clinical characteristics of the patients were collected by using questionnaire, and stool samples were taken from them for laboratory detection of 17 kinds of bacteria. The differences in pathogen positive rates (PPR) and pathogen spectrum across the cases from three-type areas were compared. The different infection risk in different cases were analyzed with unconditional logistic regression model. Results: In our study, we enrolled 9 253 cases from large cities, 5 138 cases from rural areas and 13 683 cases from midsized/small cites. The pathogen with largest differences in infection rate across the three-type areas was Shigella (S.) flexneri (rural area: 5.81%, mid-sized/small city: 2.78%, large city: 0.46%), followed by Aeromonas (A.) hydrophila (rural area: 2.14%, mid-sized/small city: 0.96%, large city: 0.48%). Compared with cases in large cities, the cases in mid-sized/small cities and rural areas had higher infection risks for S. flexneri (mid-sized/small city: OR=6.481, 95%CI: 4.666-9.002, rural area: OR=11.304, 95%CI: 8.018-15.938) and A. hydrophila (mid-sized/small city: OR=1.992, 95%CI:1.401-2.832, rural area: OR=4.083, 95%CI: 2.833-5.884). The constituent ratio of diarrheagenic Escherichia coli and Salmonella increased with the urbanization development, while the ratios of Shigella and A. hydrophila had an opposite trend. S. sonnei (60.00%) was the predominant serogroup of Shigella in urban infections, while S. flexneri (77.37%) was the predominant serogroup in rural infections. Conclusion: The differences in pathogen spectrum of bacterial diarrhea were obvious across large cities, mid-sized/small cities and rural areas in China, especially the differences in the infection rates of S. flexneri and A. hydrophila.
Adolescent ; Adult ; Bacterial Infections/microbiology* ; Child ; China/epidemiology* ; Cross-Sectional Studies ; Diarrhea/microbiology* ; Dysentery/epidemiology* ; Escherichia coli/pathogenicity* ; Feces/virology* ; Female ; Humans ; Male ; Middle Aged ; Prevalence ; Rural Population ; Salmonella/pathogenicity* ; Shigella/pathogenicity* ; Suburban Population ; Urban Population

Objective: To analyze the effect of the identification and evaluation of Escherichia (E.) coli and Shigella, based on the upstream flanking sequences of CRISPR1. Methods: Both CRISPR and cas sequences were obtained through the BLAST with repeating sequences against the publicly complete genome in GenBank that related to E. coli and Shigella. Clustal X was used to perform multi-sequences alignment of the flanking sequences. PCR method was used to amplify the upstream flanking sequences of CRISPR1 in order to appraise the effect of identification and evaluation of upstream flanking sequences on E. coli and Shigella, which were based on the upstream flanking sequences of CRISPR1. Results: The results showed that 73.4% of the strains containing the I-E CRISPR/Cas that belonged to the phylogroups A, B1, D while 8.4% strains carried the I-F CRISPR/Cas. Another 17.2% of the strains owned CRISPR3-4 (non-CRISPR/Cas) only belonged to the phylogroups B2. All the Shigella strains carried I-E CRISPR/Cas. More than 99% of similarity the CRISPR1 upstream-flanking sequences was seen in E. coli (except B2) and Shigella and E. coli (B2). Both sensitivity and specificity were greater than 91% after PCR amplification in the region to identify the E.coli and Shigella. Conclusion: The upstream of CRISPR1 could achieve a preliminary identification effect on E.coli and Shigella.
Clustered Regularly Interspaced Short Palindromic Repeats/genetics* ; DNA, Bacterial/genetics* ; Escherichia coli/isolation & purification* ; Genotype ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA ; Shigella/isolation & purification*

A field survey studying intestinal parasites in humans and microbial pathogen contamination at environment was performed in a Laotian rural village to identify potential risks for disease outbreaks. A parasitological investigation was conducted in Ban Lak Sip village, Luang Prabang, Lao PDR involving fecal samples from 305 inhabitants as well as water samples taken from 3 sites of the local stream. Water analysis indicated the presence of several enteric pathogens, i.e., Aeromonas spp., Vibrio spp., E. coli H7, E. coli O157: H7, verocytotoxin-producing E. coli (VTEC), Shigella spp., and enteric adenovirus. The level of microbial pathogens contamination was associated with human activity, with greater levels of contamination found at the downstream site compared to the site at the village and upstream, respectively. Regarding intestinal parasites, the prevalence of helminth and protozoan infections were 68.9% and 27.2%, respectively. Eight helminth taxa were identified in fecal samples, i.e., 2 tapeworm species (Taenia sp. and Hymenolepis diminuta), 1 trematode (Opisthorchis sp.), and 5 nematodes (Ascaris lumbricoides, Trichuris trichiura, Strongyloides stercoralis, trichostrongylids, and hookworms). Six species of intestinal protists were identified, i.e., Blastocystis hominis, Cyclospora spp., Endolimax nana, Entamoeba histolytica/E. dispar, Entamoeba coli, and Giardia lamblia. Questionnaires and interviews were also conducted to determine risk factors of infection. These analyses together with a prevailing infection level suggested that most of villagers were exposed to parasites in a similar degree due to limited socio-economic differences and sharing of similar practices. Limited access to effective public health facilities is also a significant contributing factor.
Adenoviridae ; Aeromonas ; Ancylostomatoidea ; Ascaris lumbricoides ; Blastocystis hominis ; Cestoda ; Cyclospora ; Disease Outbreaks ; Endolimax ; Entamoeba ; Entamoeba histolytica ; Giardia lamblia ; Helminths ; Human Activities ; Humans ; Hymenolepis ; Parasites ; Prevalence ; Protozoan Infections ; Public Health ; Risk Factors ; Rivers ; Shigella ; Strongyloides stercoralis ; Trichuris ; Vibrio ; Water*