Investigation and Identification of Food Poisoning Caused by Clostridium botulinum Type B1 in Shenzhen, China.

Clostridium botulinum produces botulinum neurotoxins (BoNTs), which cause people who ingest them to become seriously ill and sometimes die. In recent years, sporadic food poisoning cases associated with C. botulinum have occurred across the world. In 2016, two men were admitted to our hospital in Shenzhen, China, with foodborne botulism. In this study, we report on these two typical C. botulinum-related food poisoning incidents and the steps taken to identify and characterize the causative pathogen. We characterized the bacterial pathogen isolated from the first patient using cooked meat medium and egg yolk agar bacterial cultures under anaerobic conditions, and morphologically identified the isolate using Gram staining. The in vivo bioassay results in mice showed that the minimum lethal dose of the BoNTs produced by our isolate was 0.001-0.0001 mg/mL (LD50 of the culture was estimated to be 1.5812 mg/kg). Whole genome sequencing (WGS) results showed that the isolate was identified as C. botulinum B1 Okra. The causative strain was successfully isolated from the intestinal lavage fluid collected from the initial patient.

Comparative evaluation of six nucleic acid amplification kits for SARS-CoV-2 RNA detection.

BACKGROUND: SARS-CoV-2 is a newly emerged coronavirus, causing the coronavirus disease 2019 (COVID-19) outbreak in December, 2019. As drugs and vaccines of COVID-19 remain in development, accurate virus detection plays a crucial role in the current public health crisis. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) kits have been reliably used for detection of SARS-CoV-2 RNA since the beginning of the COVID-19 outbreak, whereas isothermal nucleic acid amplification-based point-of-care automated kits have also been considered as a simpler and rapid alternative. However, as these kits have only been developed and applied clinically within a short timeframe, their clinical performance has not been adequately evaluated to date. We describe a comparative study between a newly developed cross-priming isothermal amplification (CPA) kit (Kit A) and five RT-qPCR kits (Kits B-F) to evaluate their sensitivity, specificity, predictive values and accuracy. METHODS: Fifty-two clinical samples were used including throat swabs (n = 30), nasal swabs (n = 7), nasopharyngeal swabs (n = 7) and sputum specimens (n = 8), comprising confirmed (n = 26) and negative cases (n = 26). SARS-CoV-2 detection was simultaneously performed on each sample using six nucleic acid amplification kits. The sensitivity, specificity, positive/negative predictive values (PPV/NPV) and the accuracy for each kit were assessed using clinical manifestation and molecular diagnoses as the reference standard. Reproducibility for RT-qPCR kits was evaluated in triplicate by three different operators using a SARS-CoV-2 RNA-positive sample. On the basis of the six kits' evaluation results, CPA kit (Kit A) and two RT-qPCR Kits (Kit B and F) were applied to the SARS-CoV-2 detection in close-contacts of COVID-19 patients. RESULTS: For Kit A, the sensitivity, specificity, PPV/NPV and accuracy were 100%. Among the five RT-qPCR kits, Kits B, C and F had good agreement with the clinical diagnostic reports (Kappa ≥ 0.75); Kits D and E were less congruent (0.4 ≤ Kappa < 0.75). Differences between all kits were statistically significant (P < 0.001). The reproducibility of RT-qPCR kits was determined using a coefficients of variation (CV) between 0.95% and 2.57%, indicating good reproducibility. CONCLUSIONS: This is the first comparative study to evaluate CPA and RT-qPCR kits' specificity and sensitivity for SARS-CoV-2 detection, and could serve as a reference for clinical laboratories, thus informing testing protocols amid the rapidly progressing COVID-19 pandemic.

Integrated Whole-Genome Sequencing Infrastructure for Outbreak Detection and Source Tracing of Salmonella enterica Serotype Enteritidis.

As an important foodborne pathogen, Salmonella enterica serotype Enteritidis is recognized as one of the most common causes of human salmonellosis globally. Outbreak detection for this highly homogenous serotype, however, has remained challenging. Rapid advances in sequencing technologies have presented whole-genome sequencing (WGS) as a significant advancement for source tracing and molecular typing of foodborne pathogens. A retrospective analysis was conducted using Salmonella Enteritidis isolates (n = 65) from 11 epidemiologically confirmed outbreaks and a collection of contemporaneous sporadic isolates (n = 258) during 2007-2017 to evaluate the performance of WGS in delineating outbreak-associated isolates. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis revealed well-supported clades in concordance with epidemiological evidence and pairwise distances of ≤3 SNPs for all outbreaks. WGS-based framework of outbreak detection was thus proposed and applied prospectively to investigate isolates (n = 66) from nine outbreaks during 2018-2019. We further demonstrated the superior discriminatory power and accuracy of WGS to resolve and delineate outbreaks for pragmatic food source tracing. The proposed integrated WGS framework is the first in China for Salmonella Enteritidis and has the potential to serve as a paradigm for outbreak detection and source tracing of Salmonella throughout the stages of food production, as well as expanded to other foodborne pathogens.

Whole-Genome Analysis of Salmonella enterica Serovar Enteritidis Isolates in Outbreak Linked to Online Food Delivery, Shenzhen, China, 2018.

In July 2018, an outbreak of 10 cases of Salmonella enterica serovar Enteritidis infection occurred in Shenzhen, China. Outbreak investigation complemented by whole-genome sequencing traced the source to food ordered online. Our investigation highlights the role of online food delivery platforms as a new mode of foodborne disease transmission.

[Rapid identification of 15 common S. enterica Salmonella serovars by multiplex real-time PCR].

OBJECTIVE: Multiplex real-time PCR for the identification of 15 Salmonella serovars was developed. METHODS: Through the Salmonella genome comparison, 12 membrane proteins STM4497 gene can be used to identify 15 Salmonella serovars, and these 12 genes were respectively listed as A-L genes. Then primers were designed according to A-L gene conserved sequences, and then multiplex real-time PCR was established assessed with the evaluation of the limit detection, sensitivity, specificity, and repeatability. The 206 Salmonella strains were identified using multiplex real-time PCR with the comparison of the serum slide agglutination assay. RESULTS: The limit detection of multiplex PCR ranged from 1. 1×10~(-3)-1. 2×10~(-3) ng/µL. The target genes were 100% specificity, and the relative standard deviation was lower than 2. 97%. Compared with the serum slide agglutination assay, Kappa ranged 0. 92-1. 00. CONCLUSION: The multiplex real-time PCR can be used to identify 15 Salmonella serovars, which is rapid, accurate and specific.

Multiplex ligation reaction based on probe melting curve analysis: a pragmatic approach for the identification of 30 common Salmonella serovars.

BACKGROUND: While Salmonella serotyping is of paramount importance for the disease intervention of salmonellosis, a fast and easy-to-operate molecular serotyping solution remains elusive. We have developed a multiplex ligation reaction based on probe melting curve analysis (MLMA) for the identification of 30 common Salmonella serovars. METHODS: Serovar-specific primers and probes were designed based on a comparison of gene targets (wzx and wzy encoding for somatic antigen biosynthesis; fliC and fljB for flagellar antigens) from 5868 Salmonella genomes. The ssaR gene, a type III secretion system component, was included for the confirmation of Salmonella. RESULTS: All gene targets were detected and gave expected Tm values during assay evaluation. Cross reactions were not demonstrated between the 30 serovars (n = 211), or with an additional 120 serovars (n = 120) and other Enterobacteriaceae (n = 3). The limit of identification for all targets ranged from using 1.2 ng/µL to 1.56 ng/µL of DNA. The intra- and inter-assay standard deviations and the coefficients of variation were no more than 0.5 °C and less than 1% respectively, indicating high reproducibility. From consecutive outpatient stool samples (n = 3590) collected over a 10-month period at 11 sentinel hospitals in Shenzhen, China, we conducted a multicenter study using the traditional Salmonella identification workflow and the MLMA assay workflow in parallel. From Salmonella isolates (n = 496, 13.8%) derived by both workflows, total agreement (kappa = 1.0) between the MLMA assay and conventional serotyping was demonstrated. CONCLUSIONS: With an assay time of 2.5 h, this simple assay has shown promising potential to provide rapid and high-throughput identification of Salmonella serovars for clinical and public health laboratories to facilitate timely surveillance of salmonellosis.

Phenotypic and Genotypic Characterization of Clinical Enterotoxigenic Escherichia coli Isolates from Shenzhen, China.

BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) is one of the major causes of infectious diarrhea in developing countries. This study aimed to characterize the prevalence and phenotypic and genotypic features of ETEC isolates from Shenzhen, China. METHODS: ETEC isolates were obtained from acute diarrheal patients and evaluated for enterotoxin, classical colonization factors (CFs), serotypes, antimicrobial susceptibility, and multilocus sequencing typing (MLST). RESULTS: A total of 168 (1.3%) ETEC strains were isolated from 13,324 diarrheal outpatients during 2009 and 2014. A vast majority of ETEC-infected patients (82.1%) belonged to the age ranging 20-59 years and only six patients were children aged <5 years. Heat-stable toxin (ST) was most frequently detected (81.5%), followed by heat-labile toxin (LT) (13.1%). One or multiple colonization factors (CFs) were identified in 91 ETEC strains (54.2%). The most frequently detected CF was CS6 (with or without other CFs) (84/91), followed by CS21 (14/91). The most common serotype was O159:H34 (n = 36), followed by O148:H28 (n = 25) and O27:H7 (n = 17). High resistant rate was observed to nalidixic acid (77.4%), cephalothin (41.7%), ampicillin (34.5%), and tetracycline (21.4%). Antimicrobial resistance profiles differed among different serogroups. Sequence type (ST) 10 complex, integrated with connected ST218, ST48, ST4, and ST1312 subgroups, covered 73 (43.5%) isolates. CONCLUSIONS: ETEC isolates in Shenzhen of China appeared highly diverse, yet some isolates belonged to well-defined clonal groups sharing a unique set of virulence factors, serotypes, and MLST sequence types. Facing the challenge of ETEC antigenic diversity and geographic variation, novel molecules and/or classical antigens designed by novel strategies might contribute to ETEC vaccine development.

The evaluation and application of multilocus variable number tandem repeat analysis (MLVA) for the molecular epidemiological study of Salmonella enterica subsp. enterica serovar Enteritidis infection.

BACKGROUND: Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the most prevalent Salmonella serotypes that cause gastroenteritis worldwide and the most prevalent serotype causing Salmonella infections in China. A rapid molecular typing method with high throughput and good epidemiological discrimination is urgently needed for detecting the outbreaks and finding the source for effective control of S. Enteritidis infections. METHODS: In this study, 194 strains which included 47 from six outbreaks that were well-characterized epidemiologically were analyzed with pulse field gel electrophoresis (PFGE) and multilocus variable number tandem repeat analysis (MLVA). Seven VNTR loci published by the US Center for Disease Control and Prevention (CDC) were used to evaluate and develop MLVA scheme for S. Enteritidis molecular subtyping by comparing with PFGE, and then MLVA was applied to the suspected outbreaks detection. All S. Enteritidis isolates were analyzed with MLVA to establish a MLVA database in Shenzhen, Guangdong province, China to facilitate the detection of S. Enteritidis infection clusters. RESULTS: There were 33 MLVA types and 29 PFGE patterns among 147 sporadic isolates. These two measures had Simpson indices of 0.7701 and 0.8043, respectively, which did not differ significantly. Epidemiological concordance was evaluated by typing 47 isolates from six epidemiologically well-characterized outbreaks and it did not differ for PFGE and MLVA. We applied the well established MLVA method to detect two S. Enteritidis foodborne outbreaks and find their sources successfully in 2014. A MLVA database of 491 S. Enteritidis strains isolated from 2004 to 2014 was established for the surveillance of clusters in the future. CONCLUSIONS: MLVA typing of S. Enteritidis would be an effective tool for early warning and epidemiological surveillance of S. Enteritidis infections.

Feasibility of Using Multiple-Locus Variable-Number Tandem-Repeat Analysis for Epidemiology Study of Vibrio parahaemolyticus Infections.

Vibrio parahaemolyticus causes foodborne gastroenteritis, which is often associated with the consumption of raw or undercooked shellfish. Molecular typing can provide critical information for detecting outbreaks and for source attribution. In this study, we describe the development and evaluation of an optimized multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) for the characterization of V. parahaemolyticus isolates. The discriminatory power of MLVA was compared to that of pulsed-field gel electrophoresis (PFGE) by typing 73 sporadic isolates. Epidemiologic concordance was evaluated by typing 23 isolates from five epidemiologically well-characterized outbreaks. The optimized MLVA was applied in early warning, epidemiological surveillance, and source tracking for V. parahaemolyticus infections. There was no significant difference in the discriminatory power of PFGE and MLVA with six or eight VNTR loci for the sporadic isolates. All isolates within an outbreak were indistinguishable by MLVA with six loci, except for one outbreak. Typically, the epidemiological survey could be initiated according to PFGE clusters. We applied MLVA with six loci on 22 isolates in two PFGE clusters. Isolates in one PFGE cluster were distinguished by MLVA. Although a follow-up investigation showed that both clusters had no epidemiological concordance, MLVA decreased the frequency of initiation of epidemiological surveys, thereby reducing labor costs. The ability of MLVA to trace the source of infection was evaluated by isolates from two outbreaks and shrimp samples. The isolates from one of outbreaks and a shrimp had the same MLVA type, suggesting that an epidemiological survey was initiated. Data from the epidemiological investigation subsequently indicated that contaminated shrimp from a nearby city (Dongguan) might be the source of the outbreak. In conclusion, these results indicate that the optimized MLVA may be a promising tool for early warning and epidemiological surveillance of V. parahaemolyticus infections.

Association of CRISPR/Cas evolution with Vibrio parahaemolyticus virulence factors and genotypes.

Clustered regularly interspaced short palindromic repeats (CRISPR), which is considered to be an immune system for bacteria, has been widely used as a tool for genome editing and genotyping. It has also been reported to be associated with virulence factors in some bacteria. To understand the role of CRISPR in the virulence and evolution of pathogenic Vibrio parahaemolyticus, 154 V. parahaemolyticus strains isolated from clinical samples and 54 strains from food samples taken in Shenzhen, China were subjected to a correlation analysis of CRISPR and virulence factors TDH and TRH. We also performed multilocus sequence typing (MLST) for genotype analysis. Six different CRISPR sequence types (CSTs) of V. parahaemolyticus were identified, and CSTs were found to be significantly associated with the virulence factors tested and MLST genotype. Therefore, CSTs provide insight into the evolution of V. parahaemolyticus. Moreover, identification of CSTs may lend insight into the virulence potential of strains.

Risk Factors for Vibrio parahaemolyticus Infection in a Southern Coastal Region of China.

OBJECTIVES: The objectives of the study were to identify dietary and medical risk factors for Vibrio parahaemolyticus (VP) infection in the coastal city Shenzhen in China. METHODS: In April-October 2012, we conducted a case-control study in two hospitals in Shenzhen, China. Laboratory-confirmed VP cases (N = 83) were matched on age, sex, and other social factors to healthy controls (N = 249). Subjects were interviewed using a questionnaire on medical history; contact with seawater; clinical symptoms and outcome; travel history over the past week; and dietary history 3 days prior to onset. Laboratory tests were used to culture, serotype, and genotype VP strains. We used logistic regression to calculate the odds ratios for the association of VP infection with potential risk factors. RESULTS: In multivariate analysis, VP infection was associated with having pre-existing chronic disease (adjusted odds ratio [aOR], 6.0; 95% confidence interval [CI], 1.5-23.7), eating undercooked seafood (aOR, 8.0; 95% CI, 1.3-50.4), eating undercooked meat (aOR, 29.1; 95% CI, 3.0-278.2), eating food from a street food vendor (aOR, 7.6; 95% CI, 3.3-17.6), and eating vegetable salad (aOR, 12.1; 95% CI, 5.2-28.2). CONCLUSIONS: Eating raw (undercooked) seafood and meat is an important source of VP infection among the study population. Cross-contamination of VP in other food (e.g., vegetables and undercooked meat) likely plays a more important role. Intervention should be taken to lower the risks of cross-contamination with undercooked seafood/meat, especially targeted at people with low income, transient workers, and people with medical risk factors.

Vibrio parahaemolyticus, Southern Coastal Region of China, 2007-2012.

We analyzed the prevalence and characteristics of Vibrio parahaemolyticus among patients with acute infectious diarrhea in the southern coastal region of China. V. parahaemolyticus was the leading cause of bacterial infectious diarrhea in this region during 2007-2012. Serotype O3:K6 strains were most common, followed by serotypes O4:K8 and O3:K29.

Simultaneous detection of five enteric viruses associated with gastroenteritis by use of a PCR assay: a single real-time multiplex reaction and its clinical application.

We developed a highly sensitive reverse transcription and multiplex real-time PCR (rtPCR) assay that can identify five viruses, including six genogroups, in a single reaction: norovirus genogroups I and II; sapovirus genogroups I, II, IV, and V; human rotavirus A; adenovirus serotypes 40 and 41; and human astrovirus. In comparison to monoplex rtPCR assays, the sensitivities and specificities of the multiplex rtPCR ranged from 75% to 100% and from 99% to 100%, respectively, evaluated on 812 clinical stool specimens.

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

BACKGROUND: Diarrheagenic Escherichia coli (DEC), including Enterotoxigenic E.coli (ETEC), Enteroaggregative E.coli (EAEC), Enteropathogenic E.coli (EPEC), Enterohemolysin E.coli (EHEC) and Enteroinvasive E.coli (EIEC) causes diarrhea or hemolytic uremic syndromes among infants and travelers around the world. A rapid, reliable and repeatable method is urgent for identifying DEC so as to provide the reference for responding to diarrheal disease outbreak and the treatment of the diarrheal patients associated with DEC. METHODS: In this study, specific primers and modified molecular beacon probes of nine specific virulence genes, whose 5'end were added with homo tail sequence, were designed; and a two-tube modified molecular beacon based multiplex real-time PCR (rtPCR) assay for the identification of five Escherichia coli pathotypes, including ETEC, EAEC, EPEC, EHEC and EIEC was developed and optimized. Totally 102 bacterial strains, including 52 reference bacterial strains and 50 clinical strains were detected to confirm whether the target genes selected were specific. Then detection limits of the assay were tested. Lastly, the assay was applied to the detection of 11860 clinical samples to evaluate the specificity and sensitivity of the developed assay compared with the conventional PCR. RESULTS: The target genes were 100% specific as assessed on 102 bacterial strains since no cross-reactions were observed. The detection limits ranged from 88 CFU/mL (EHEC) to 880 CFU/mL (EPEC). Compared with the conventional PCR, the specificity and sensitivity of the multiplex rtPCR was 100% and over 99%, respectively. The coefficient of variation (CV) for each target gene ranged from 0.45% to 1.53%. 171 positive clinical samples were mostly identified as ETEC (n = 111, 64.9%) and EPEC (n = 38, 22.2%), which were the dominating pathotypes of DEC strains. CONCLUSION: The developed multiplex rtPCR assay for the identification of DEC was high sensitive and specific and could be applied to the rapid identification of DEC in clinical and public health laboratories.

A modified molecular beacons-based multiplex real-time PCR assay for simultaneous detection of eight foodborne pathogens in a single reaction and its application.

Foodborne disease outbreaks are often caused by one of the major pathogens. Early identification of the causal pathogen is crucial for disease control and prevention. We describe a real-time polymerase chain reaction (rtPCR) assay that can identify, in a single reaction, up to eight common foodborne bacterial pathogens, including Salmonella enterica subsp. enterica, Listeria monocytogenes, Escherichia coli O157, Vibrio parahaemolyticus, V. vulnificus, Campylobacter jejuni, Enterobacter sakazakii, and Shigella spp. This multiplex rtPCR assay takes advantage of modified molecular beacons and the multicolor combinational probe coding strategy to discriminate each pathogen and the homo-tag assisted non-dimer (HAND) system to prevent dimer formation. The detection limits of the assay ranged from 1.3×10(3) colony-forming units (CFU)/g stool (L. monocytogenes) to 1.6×10(4) CFU/g stool (Shigella spp.). The target genes were 100% specific as assessed on 986 reference strains covering 41 species since no cross-reactions were observed. The assay was applied to the detection of foodborne pathogens in 11,167 clinical samples and the results were compared with culture methods for further validation. The sensitivity and specificity of the rtPCR were 100% and 99%, respectively. When performed in a 96-well rtPCR system, more than 90 samples could be analyzed within 3 h. Given the high accuracy, sensitivity, specificity, and short turn-around time, the established assay could be used for the rapid and reliable identification of the causative pathogens responsible for a certain foodborne disease outbreak and rapid screening of these major foodborne pathogens in laboratory-based surveillance of outpatient clinical samples or even food samples.

Characterization of Staphylococcus aureus strains associated with food poisoning in Shenzhen, China.

To characterize isolates of Staphylococcus aureus that were associated with staphylococcal food poisoning between 2006 and 2009 in Shenzhen, Southern China, a total of 52 Staphylococcus aureus isolates from 11 outbreaks were analyzed by using multilocus sequence typing (MLST), spa typing, and pulsed-field gel electrophoresis (PFGE). PCR analysis was used to analyze the staphylococcal enterotoxin (SE) genes sea to sei, and antimicrobial susceptibility testing was also performed. ST6 was the most dominant sequence type (ST), constituting 63.5% (34/52) of all of the isolates in 7 outbreaks. The next most common ST was ST943, which constituted 23.1% (12/52) of the isolates that were collected from 3 outbreaks. t701, t091, and t2360 were the most predominant spa types, constituting 67.3% (35/52) of the isolates that were collected from 11 outbreaks. Three PFGE types, (types A, B, and C) were the most frequently observed types, constituting 84.6% (44/52) of all of the isolates. The enterotoxin gene that we detected most frequently was sea (45/52; 86.5%). Four SE gene profiles were observed, including sea (n = 45), sec-seh (n = 3), seb (n = 2), and seg-sei (n = 2). With respect to antibiotic resistance, penicillin resistance was the most common (96.2%; 50/52), followed by resistance to tetracycline (28.8%; 15/52). Approximately 30.8% (16/52) of the isolates were resistant to at least two antibiotics, and 7.7% (4/52) of the isolates were resistant to three or more drugs. The two predominant S. aureus lineages, (i) PFGE types A and B with ST6 and (ii) PFGE type C with ST943, were identified in the outbreaks.

[Development of a xMAP liquid chip assay for the rapid identification of 7 common foodborne pathogens and its application].

OBJECTIVE: To develop an assay for the simultaneous detection of 7 common foodborne pathogens with xMAP liquid chip in a single-tube reaction. METHODS: Seven specific primers and probes were designed and synthesized based on the target gene sequences from GenBank. Target bacterial sequences were amplified by asymmetric PCR. The biotinylated products were hybridized to seven probe beads in a multiplex reaction and analyzed by using streptavidin conjugated to a fluorescent reporter molecule. The developed liquid chip xMAP assay was used to test 140 strains of bacteria and then 56 food samples. RESULTS: No cross-reaction and false signals were observed. The detection limit was 1 - 100 pg and 10(5) - 10(6) cfu/ml. The results tested by xMAP were in accordance with the traditional culture method. CONCLUSION: The processing of xMAP liquid chip assay, including DNA preparation and sample detection, could be finished within 3.5 hours and could be applied to the classification and identification of foodborne pathogens in the food safety monitoring.

[Characteristics of Salmonella enterica serovar Senftenberg lacking Salmonella pathogenicity island 1].

OBJECTIVE: To study the characteristics of the strains of Salmonella enterica (S. enterica) serovar Senftenberg lacking Salmonella pathogenicity island 1 (SPI-1). METHODS: A total of 10 strains of S. enterica serovar Senftenberg were isolated from 10 cases of diarrhea patients. Pulsed field gel electrophoresis (PFGE), PCR, sequencing techniques and cell invasion test were adapted to study the molecular types and invasiveness of the genes and cells; and made a comparison between the 10 strains and the strains (C02013) isolated in Shenzhen in 2002. RESULTS: The 10 Senftenberg isolated (S09007-S09012, S09014-S09017) in Shanghai showed three PFGE patterns, which were significantly different from the strains isolated in Shenzhen. PCR-amplified results indicated the invasion gene (invA), secreted effector protein gene (sipA) and gene fragments as fhlA-hilA, hilA-spaP and spaP-invH in the 10 strains of SPI-1 were all negative. The sequencing results revealed that the 10 strains isolated in Shanghai lacked most parts of SPI-1 genes, as fragments from orgA to invH and parts of orgA gene itself; however, compared with strains isolated in Shenzhen, the sprB-orgC gene existed. The missing parts of genes were replaced by a simple insertion sequence (IS) of 1000 bp in the strains isolated both in Shenzhen in 2002 and in Shanghai in 2006. The invasiveness rates of the 10 strains (S09007-S09012, S09014-S09017) towards Hela cells were (0.0053 ± 0.0024)%, (0.0046 ± 0.0006)%, (0.0047 ± 0.0003)%, (0.0064 ± 0.0012)%, (0.0065 ± 0.0011)%, (0.0070 ± 0.0020)%, (0.0115 ± 0.0030)%, (0.0099 ± 0.0039)%, (0.0180 ± 0.0135)% and (0.0031 ± 0.0012)%, respectively; which were all significantly lower than the rate of invA-positive control strain STM1344 ((5.0800 ± 0.6333)%); lower or close to the rate of invA-lacked artificial-mutated strain STMinvA-((0.0193 ± 0.0045)%). CONCLUSION: SPI-1 genes are not essential for the diarrhea caused by S. enterica serovar Senftenberg.

[Development of modified molecular beacon based real-time PCR assay for the rapid detection of Salmonella choleraesuis and Salmonella paratyphi C].

OBJECTIVE: To develop real-time PCR assay based on modified molecular beacon for simultaneous detection of S. choleraesuis and S. paratyphi C. The established method was applied to the rapid detection of S. choleraesuis in food and stool samples of food poisoning, and then was applied to the identification of Salmonella C. METHODS: Based on the sequences (CP000857.1) published in GenBank, Two sets of primers and modified molecular beacon were designed. The Real-time PCR assay for the simultaneous detection of S. paratyphi C and S. choleraesuis was developed with optimized PCR procedures and PCR components, while other 11 different bacterial species were as the control. Then the sensitivity and specificity of the assay were tested using 77 Samonella strains. The assay was applied to the detection of 70 food samples. RESULTS: The limit of detection achieved was 10 fg/reaction or 20 CUF/reaction, Only Salmonella paratyphi C and Salmonella choleraesuis strains generated fluorescent signals. No cross-reaction was observed with other 11 bacterium, the sensitivity and specificity were both 100%. No samples among 70 food samples were found Salmonella positive by both real-time PCR assay and traditional culture method. It could be finished within 2 hours from template preparation to detection and the overall test would be finished within one day. CONCLUSION: The real-time PCR assay was rapid, sensitive and specific. It could be applied to the rapid diagnosis of S. paratyphi C and S. choleraesuis in food and stool samples of food poisoning and the identification of Salmonella C to guarantee food safety.

Simultaneous Identification of Clinically Common Vibrio parahaemolyticus Serotypes Using Probe Melting Curve Analysis.

The dynamic nature of Vibrio parahaemolyticus epidemiology has presented a unique challenge for disease intervention strategies. Despite the continued rise of disease incidence and outbreaks of vibriosis, as well as the global emergence of pandemic clones and serovariants with enhanced virulence, there is a paucity of molecular methods for the serotyping of V. parahaemolyticus strains to improve disease surveillance and outbreak investigations. We describe the development of a multiplex ligation reaction based on probe melting curve analysis (MLMA) for the simultaneous identification of 11 clinically most common V. parahaemolyticus serotypes spanning a 10-year period. Through extensive sequence analyses using 418 genomes, specific primers and probes were designed for a total of 22 antigen gene targets for the O- and K- serogroups. Additionally, the toxR gene was incorporated into the assay for the confirmation of V. parahaemolyticus. All gene targets were detected by the assay and gave expected Tm values, without any cross reactions between the 11 clinically common serotypes or with 38 other serotypes. The limit of identification for all gene targets ranged from 0.1 to 1 ng/µL. The intra- and inter-assay standard deviations and the coefficients of variation were no more than 1°C and <1% respectively, indicating a highly reproducible assay. A multicenter double-blind clinical study was conducted using the traditional V. parahaemolyticus identification workflow and the MLMA assay workflow in parallel. From consecutive diarrheal stool specimens (n = 6118) collected over a year at 10 sentinel hospitals, a total of 153 V. parahaemolyticus isolates (2.5%) were identified by both workflows. A total agreement (kappa = 1.0) between the serotypes identified by the MLMA assay and conventional serological method was demonstrated. This is the first molecular assay to simultaneously identify multiple clinically important V. parahaemolyticus serotypes, which satisfies the acute need for a practical, rapid and robust identification of V. parahaemolyticus serotypes to facilitate the timely detection of vibriosis outbreaks and surveillance.