in

A database for risk assessment and comparative genomic analysis of foodborne Vibrio parahaemolyticus in China

  • 1.

    Letchumanan, V., Chan, K. G. & Lee, L. H. Vibrio parahaemolyticus: a review on the pathogenesis, prevalence, and advance molecular identification techniques. Front. Microbiol. 5, 705, https://doi.org/10.3389/fmicb.2014.00705 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  • 2.

    DePaola, A., Hopkins, L. H., Peeler, J. T., Wentz, B. & McPhearson, R. M. Incidence of Vibrio parahaemolyticus in U.S. coastal waters and oysters. Appl. Environ. Microbiol. 56, 2299–2302 (1990).

    CAS  Article  Google Scholar 

  • 3.

    Daniels, N. A. et al. Emergence of a new Vibrio parahaemolyticus serotype in raw oysters: a prevention quandary. JAMA. 284, 1541–1545, https://doi.org/10.1001/jama.284.12.1541 (2000).

    CAS  Article  PubMed  Google Scholar 

  • 4.

    McLaughlin, J. B. et al. Outbreak of Vibrio parahaemolyticus gastroenteritis associated with Alaskan oysters. N. Engl. J. Med. 353, 1463–1470, https://doi.org/10.1056/NEJMoa051594 (2005).

    CAS  Article  PubMed  Google Scholar 

  • 5.

    Ralph, A. & Currie, B. J. Vibrio vulnificus and V. parahaemolyticus necrotising fasciitis in fishermen visiting an estuarine tropical northern Australian location. J. Infect. 54, e111–114, https://doi.org/10.1016/j.jinf.2006.06.015 (2007).

    Article  PubMed  Google Scholar 

  • 6.

    Akther, F. et al. Major tdh(+)Vibrio parahaemolyticus serotype changes temporally in the Bay of Bengal estuary of Bangladesh. Infect. Genet. Evol. 41, 153–159, https://doi.org/10.1016/j.meegid.2016.04.003 (2016).

    Article  PubMed  Google Scholar 

  • 7.

    Caburlotto, G. et al. Occurrence and molecular characterisation of Vibrio parahaemolyticus in crustaceans commercialised in Venice area, Italy. Int. J. Food Microbiol. 220, 39–49, https://doi.org/10.1016/j.ijfoodmicro.2015.12.007 (2016).

    CAS  Article  PubMed  Google Scholar 

  • 8.

    Arakawa, E. et al. Emergence and prevalence of a novel Vibrio parahaemolyticus O3:K6 clone in Japan. Jpn. J. Infect. Dis. 52, 246–247 (1999).

    CAS  PubMed  Google Scholar 

  • 9.

    Leal, N. C. et al. Vibrio parahaemolyticus serovar O3:K6 gastroenteritis in northeast Brazil. J. Appl. Microbiol. 105, 691–697, https://doi.org/10.1111/j.1365-2672.2008.03782.x (2008).

    CAS  Article  PubMed  Google Scholar 

  • 10.

    Shaw, K. S., Sapkota, A. R., Jacobs, J. M., He, X. & Crump, B. C. Recreational swimmers’ exposure to Vibrio vulnificus and Vibrio parahaemolyticus in the Chesapeake Bay, Maryland, USA. Environ. Int. 74, 99–105, https://doi.org/10.1016/j.envint.2014.09.016 (2015).

    Article  PubMed  Google Scholar 

  • 11.

    Liu, J. et al. Trends of foodborne diseases in China: lessons from laboratory-based surveillance since 2011. Front. Med. 12, 48–57, https://doi.org/10.1007/s11684-017-0608-6 (2018).

    Article  PubMed  Google Scholar 

  • 12.

    Paudyal, N. et al. A meta-analysis of major foodborne pathogens in Chinese food commodities between 2006 and 2016. Foodborne Pathog. Dis. 15, 187–197, https://doi.org/10.1089/fpd.2017.2417 (2018).

    CAS  Article  PubMed  Google Scholar 

  • 13.

    Deng, C., Deng, Y. & Yi, J. Analysis of microbial food poisoning from 2010 to 2016 in Sanya city. Hainan Med. J. 28, 2723–2725 (2017).

    Google Scholar 

  • 14.

    Xu, X. et al. Prevalence, pathogenicity, and serotypes of Vibrio parahaemolyticus in shrimp from Chinese retail markets. Food Control. 46, 81–85, https://doi.org/10.1016/j.foodcont.2014.04.042 (2014).

    Article  Google Scholar 

  • 15.

    Xie, T., Wu, Q., Xu, X., Zhang, J. & Guo, W. Prevalence and population analysis of Vibrio parahaemolyticus in aquatic products from South China markets. FEMS Microbiol. Lett. 362, https://doi.org/10.1093/femsle/fnv178 (2015).

  • 16.

    Xu, X., Cheng, J., Wu, Q., Zhang, J. & Xie, T. Prevalence, characterization, and antibiotic susceptibility of Vibrio parahaemolyticus isolated from retail aquatic products in North China. BMC Microbiol. 16, 32, https://doi.org/10.1186/s12866-016-0650-6 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 17.

    Xie, T., Xu, X., Wu, Q., Zhang, J. & Cheng, J. Prevalence, molecular characterization, and antibiotic susceptibility of Vibrio parahaemolyticus from Ready-to-Eat foods in China. Front. Microbiol. 7, 549, https://doi.org/10.3389/fmicb.2016.00549 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  • 18.

    Pang, R. et al. Comparative genomic analysis reveals the potential risk of Vibrio parahaemolyticus isolated from Ready-To-Eat foods in China. Front. Microbiol. 10, 186, https://doi.org/10.3389/fmicb.2019.00186 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  • 19.

    Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477, https://doi.org/10.1089/cmb.2012.0021 (2012).

    MathSciNet  CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 20.

    Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30, 2068–2069, https://doi.org/10.1093/bioinformatics/btu153 (2014).

    CAS  Article  PubMed  Google Scholar 

  • 21.

    Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 31, 3691–3693, https://doi.org/10.1093/bioinformatics/btv421 (2015).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 22.

    Nabil-Fareed, A., Zhemin, Z., Sergeant, M. J. & Achtman, M. A genomic overview of the population structure of Salmonella. PLoS Genet. 14, e1007261, https://doi.org/10.1371/journal.pgen.1007261 (2018).

    CAS  Article  Google Scholar 

  • 23.

    Nakamura, T., Yamada, K. D., Tomii, K. & Katoh, K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. 34, 2490–2492, https://doi.org/10.1093/bioinformatics/bty121 (2018).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 24.

    Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One. 5, e9490, https://doi.org/10.1371/journal.pone.0009490 (2010).

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 25.

    Pang, R. & Wu, Q. A database for risk assessment and comparative genomic analysis of foodborne Vibrio parahaemolyticus in China. figshare https://doi.org/10.6084/m9.figshare.12210287 (2020).

  • 26.

    Pang, R. & Wu, Q. Genome assemblies and annotations of food-borne Vibrio parahaemolyticus strains. figshare https://doi.org/10.6084/m9.figshare.12004416 (2020).

  • 27.

    Pang, R. et al. Comparative genomic analysis of foodborne Vibrio parahaemolyticus in China. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP253458 (2020).

  • 28.

    Chen, Y. et al. Foodborne disease outbreaks in 2006 report of the National Foodborne Disease Surveillance Network, China. Wei Sheng Yan Jiu. 39, 331–334 (2010).

    PubMed  Google Scholar 

  • 29.

    Li, L. et al. Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus. BMC Genomics. 15, 1135, https://doi.org/10.1186/1471-2164-15-1135 (2014).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 30.

    McInerney, J. O., McNally, A. & O’Connell, M. J. Why prokaryotes have pangenomes. Nat. Microbiol. 2, 17040, https://doi.org/10.1038/nmicrobiol.2017.40 (2017).

    CAS  Article  PubMed  Google Scholar 

  • 31.

    Gonzalez-Escalona, N., Jolley, K. A., Reed, E. & Martinez-Urtaza, J. Defining a core genome multilocus sequence typing scheme for the global epidemiology of Vibrio parahaemolyticus. J. Clin. Microbiol. 55, 1682–1697, https://doi.org/10.1128/JCM.00227-17 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 


  • Source: Ecology - nature.com

    Antarctic sea ice may not cap carbon emissions as much as previously thought

    A champion of renewable energy