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Application of Whole Genome Sequencing (WGS) Approach Against Identification of Foodborne Bacteria

  • Shiv Bharadwaj
  • Vivek Dhar Dwivedi
  • Nikhil KirtipalEmail author
Chapter

Abstract

Food quality and safety along with their associated hazards risks present a major concern worldwide associated with relative economical losses as well as potential danger to consumer’s health. In this context, antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. A lack of measures and reliable assays to evaluate and maintain a good control of antimicrobial resistance foodborne pathogens may affect the food industry economy and shatter consumer confidence. Hence, surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental, and food borne strains. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. It is imperative to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. This chapter summarizes the information on the method developed and application of the whole-genome sequencing (WGS) in the past few years focusing on surveillance of AMR in foodborne pathogenic bacteria. Emphasis is also posed with respect to the routine implementation of these next-generation sequencing methodologies on characterization of well-known food pathogens. Besides, potential advantages and disadvantages of the WGS have been discussed on the surveillance of AMR in foodborne pathogens.

Keywords

Antimicrobial resistance (AMR) Whole-genome sequencing (WGS) Food Safety Environment Foodborne Pathogens Strains Food Products Phenotypic Bacteria 

References

  1. Allard MW (2016) The future of whole genome sequencing for public health and the clinic. J Clin Microbiol:01082–01016Google Scholar
  2. Allard MW, Bell R, Ferreira CM, Gonzalez-Escalona N, Hoffmann M, Muruvanda T, Ottesen A, Ramachandran P, Reed E, Sharma S (2018) Genomics of foodborne pathogens for microbial food safety. Curr Opin Biotechnol 49:224–229CrossRefPubMedPubMedCentralGoogle Scholar
  3. Allard MW, Luo Y, Strain E, Li C, Keys CE, Son I, Stones R, Musser SM, Brown EW (2012) High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach. BMC Genomics 13(1):32CrossRefPubMedPubMedCentralGoogle Scholar
  4. Allard MW, Strain E, Melka D, Bunning K, Musser SM, Brown EW, Timme R (2016) Practical value of food pathogen traceability through building a whole-genome sequencing network and database. J Clin Microbiol 54(8):1975–1983CrossRefPubMedPubMedCentralGoogle Scholar
  5. Amos GC, Gozzard E, Carter CE, Mead A, Bowes MJ, Hawkey PM, Zhang L, Singer AC, Gaze WH, Wellington EM (2015) Validated predictive modelling of the environmental resistome. ISME J 9(6):1467CrossRefPubMedPubMedCentralGoogle Scholar
  6. European Food Safety Authority, European Centre for Disease Prevention and Control (2017) The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2016. EFSA J 15(12):e05077Google Scholar
  7. Brambilla G, Testa C (2014) Food safety/food security aspects related to the environmental release of pharmaceuticals. Chemosphere 115:81–87CrossRefPubMedPubMedCentralGoogle Scholar
  8. Carroll LM, Wiedmann M, den Bakker H, Siler J, Warchocki S, Kent D, Lyalina S, Davis M, Sischo W, Besser T (2017) Whole-genome sequencing of drug-resistant Salmonella enterica isolated from dairy cattle and humans in New York and Washington states reveals source and geographic associations. Appl Environ Microbiol AEM:00140–00117Google Scholar
  9. Chen Y, Mukherjee S, Hoffmann M, Kotewicz ML, Young S, Abbott J, Luo Y, Davidson MK, Allard M, McDermott P, Zhao S (2013) Whole-genome sequencing of gentamicin-resistant Campylobacter coli isolated from U.S. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes. Antimicrob Agents Chemother 57(11):5398–5405CrossRefPubMedPubMedCentralGoogle Scholar
  10. Dallman TJ, Byrne L, Ashton PM, Cowley LA, Perry NT, Adak G, Petrovska L, Ellis RJ, Elson R, Underwood A (2015) Whole-genome sequencing for national surveillance of shiga toxin–producing Escherichia coli O157. Clin Infect Dis 61(3):305–312CrossRefPubMedPubMedCentralGoogle Scholar
  11. Davis GS, Waits K, Nordstrom L, Weaver B, Aziz M, Gauld L, Grande H, Bigler R, Horwinski J, Porter S (2015) Intermingled Klebsiella pneumoniae populations between retail meats and human urinary tract infections. Clin Infect Dis 61(6):892–899CrossRefPubMedPubMedCentralGoogle Scholar
  12. Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, Kooistra-Smid AM, Raangs EC, Rosema S, Veloo AC (2017) Application of next generation sequencing in clinical microbiology and infection prevention. J Biotechnol 243:16–24CrossRefPubMedPubMedCentralGoogle Scholar
  13. Edirmanasinghe R, Finley R, Parmley EJ, Avery BP, Carson C, Bekal S, Golding G, Mulvey MR (2017) A whole-genome sequencing approach to study cefoxitin-resistant salmonella enterica serovar heidelberg isolates from various sources. Antimicrob Agents Chemother 61(4)Google Scholar
  14. Ellington M, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden M, Hopkins KL (2017) The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect 23(1):2–22CrossRefPubMedPubMedCentralGoogle Scholar
  15. Fox EM, Casey A, Jordan K, Coffey A, Gahan CG, McAuliffe O (2017) Whole genome sequence analysis; an improved technology that identifies underlying genotypic differences between closely related Listeria monocytogenes strains. Innovative Food Sci Emerg Technol 44:89–96CrossRefGoogle Scholar
  16. Franz E, Gras LM, Dallman T (2016) Significance of whole genome sequencing for surveillance, source attribution and microbial risk assessment of foodborne pathogens. Curr Opin Food Sci 8:74–79CrossRefGoogle Scholar
  17. Gandhi M, Chikindas ML (2007) Listeria: a foodborne pathogen that knows how to survive. Int J Food Microbiol 113(1):1–15CrossRefPubMedPubMedCentralGoogle Scholar
  18. Gantzhorn MR, Olsen JE, Thomsen LE (2015) Importance of sigma factor mutations in increased triclosan resistance in Salmonella Typhimurium. BMC Microbiol 15(1):105CrossRefPubMedPubMedCentralGoogle Scholar
  19. Gašo-Sokač D, Kovač S, Josić D (2010) Application of proteomics in food technology and food biotechnology: process development, quality control and product safety. Food Technol Biotechnol 48(3)Google Scholar
  20. Giacometti J, Tomljanović AB, Josić D (2013) Application of proteomics and metabolomics for investigation of food toxins. Food Res Int 54(1):1042–1051CrossRefGoogle Scholar
  21. Gordon N, Price J, Cole K, Everitt R, Morgan M, Finney J, Kearns A, Pichon B, Young B, Wilson D (2014) Prediction of Staphylococcus aureus antimicrobial resistance from whole genome sequencing. J Clin Microbiol JCM:03117–03113Google Scholar
  22. Havelaar AH, Brul S, De Jong A, De Jonge R, Zwietering MH, Ter Kuile BH (2010) Future challenges to microbial food safety. Int J Food Microbiol 139:S79–S94CrossRefPubMedPubMedCentralGoogle Scholar
  23. He T, Wei R, Zhang L, Sun L, Pang M, Wang R, Wang Y (2017) Characterization of NDM-5-positive extensively resistant Escherichia coli isolates from dairy cows. Vet Microbiol 207:153–158CrossRefPubMedPubMedCentralGoogle Scholar
  24. Hoffmann M, Zhao S, Pettengill J, Luo Y, Monday SR, Abbott J, Ayers SL, Cinar HN, Muruvanda T, Li C (2014) Comparative genomic analysis and virulence differences in closely related Salmonella enterica serotype Heidelberg isolates from humans, retail meats, and animals. Genome Biol Evol 6(5):1046–1068CrossRefPubMedPubMedCentralGoogle Scholar
  25. Hussain A, Shaik S, Ranjan A, Nandanwar N, Tiwari SK, Majid M, Baddam R, Qureshi IA, Semmler T, Wieler LH (2017) Risk of transmission of antimicrobial resistant Escherichia coli from commercial broiler and free-range retail chicken in India. Front Microbiol 8:2120CrossRefPubMedPubMedCentralGoogle Scholar
  26. Hyden P, Pietzka A, Lennkh A, Murer A, Springer B, Blaschitz M, Indra A, Huhulescu S, Allerberger F, Ruppitsch W (2016) Whole genome sequence-based serogrouping of Listeria monocytogenes isolates. J Biotechnol 235:181–186CrossRefPubMedPubMedCentralGoogle Scholar
  27. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM (2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 52(5):1501–1510CrossRefPubMedPubMedCentralGoogle Scholar
  28. Joseph S, Forsythe S (2012) Insights into the emergent bacterial pathogen Cronobacter spp., generated by multilocus sequence typing and analysis. Front Microbiol 3:397CrossRefPubMedPubMedCentralGoogle Scholar
  29. Kahlmeter G, Brown DF, Goldstein FW, MacGowan AP, Mouton JW, Österlund A, Rodloff A, Steinbakk M, Urbaskova P, Vatopoulos A (2003) European harmonization of MIC breakpoints for antimicrobial susceptibility testing of bacteria. J Antimicrob Chemother 52(2):145–148CrossRefPubMedPubMedCentralGoogle Scholar
  30. Karkman A, Do TT, Walsh F, Virta MP (2018) Antibiotic-resistance genes in waste water. Trends Microbiol 26(3):220–228CrossRefPubMedPubMedCentralGoogle Scholar
  31. Köser CU, Ellington MJ, Peacock SJ (2014) Whole-genome sequencing to control antimicrobial resistance. Trends Genet 30(9):401–407CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kuchenmüller T, Hird S, Stein C, Kramarz P, Nanda A, Havelaar A (2009) Estimating the global burden of foodborne diseases-a collaborative effort. Eurosurveillance 14(18):19195CrossRefPubMedPubMedCentralGoogle Scholar
  33. Kwong JC, Mercoulia K, Tomita T, Easton M, Li HY, Bulach DM, Stinear TP, Seemann T, Howden BP (2016) Prospective whole-genome sequencing enhances national surveillance of Listeria monocytogenes. J Clin Microbiol 54(2):333–342CrossRefPubMedPubMedCentralGoogle Scholar
  34. Lim SY, Yap K-P, Thong KL (2016) Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food. Gut Pathog 8(1):65CrossRefPubMedPubMedCentralGoogle Scholar
  35. Liu KC, Jinneman KC, Neal-McKinney J, Wu WH, Rice DH (2016) Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance. Genom Data 8:123–125CrossRefPubMedPubMedCentralGoogle Scholar
  36. Losada L, DebRoy C, Radune D, Kim M, Sanka R, Brinkac L, Kariyawasam S, Shelton D, Fratamico PM, Kapur V (2016) Whole genome sequencing of diverse Shiga toxin-producing and non-producing Escherichia coli strains reveals a variety of virulence and novel antibiotic resistance plasmids. Plasmid 83:8–11CrossRefPubMedPubMedCentralGoogle Scholar
  37. Moran-Gilad J (2017) Whole genome sequencing (WGS) for food-borne pathogen surveillance and control–taking the pulse. Eurosurveillance 22(23)Google Scholar
  38. Oniciuc E, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos J, Alvarez-Ordóñez A (2018) The present and future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for surveillance of antimicrobial resistant microorganisms and antimicrobial resistance genes across the food chain. Genes 9(5):268CrossRefGoogle Scholar
  39. World Health Organization (2018) Whole genome sequencing for foodborne disease surveillance: landscape paper. WHO, GenevaGoogle Scholar
  40. Ortiz S, López-Alonso V, Rodríguez P, Martínez-Suárez JV (2016) The connection between persistent, disinfectant-resistant Listeria monocytogenes strains from two geographically separate Iberian pork processing plants: evidence from comparative genome analysis. Appl Environ Microbiol 82(1):308–317CrossRefPubMedPubMedCentralGoogle Scholar
  41. Piras C, Roncada P, Rodrigues PM, Bonizzi L, Soggiu A (2016) Proteomics in food: quality, safety, microbes, and allergens. Proteomics 16(5):799–815CrossRefPubMedPubMedCentralGoogle Scholar
  42. Qin SS, Wang Y, Zhang QJ, Chen X, Shen ZQ, Deng FR, Wu CM, Shen JZ (2012) Identification of a novel genomic island conferring resistance to multiple aminoglycoside antibiotics in campylobacter coli. Antimicrob Agents Chemother 56(10):5332–5339CrossRefPubMedPubMedCentralGoogle Scholar
  43. Ranieri ML, Shi C, Switt AIM, Den Bakker HC, Wiedmann M (2013) Comparison of typing methods with a new procedure based on sequence characterization for Salmonella serovar prediction. J Clin Microbiol 51(6):1786–1797CrossRefPubMedPubMedCentralGoogle Scholar
  44. Sekse C, Holst-Jensen A, Dobrindt U, Johannessen GS, Li W, Spilsberg B, Shi J (2017) High throughput sequencing for detection of foodborne pathogens. Front Microbiol 8:2029CrossRefPubMedPubMedCentralGoogle Scholar
  45. Seltenrich N (2015) New link in the food chain? Marine plastic pollution and seafood safety. Environ Health Perspect 123(2):A34CrossRefPubMedPubMedCentralGoogle Scholar
  46. Smid E, Kleerebezem M (2014) Production of aroma compounds in lactic fermentations. Annu Rev Food Sci Technol 5:313–326CrossRefPubMedPubMedCentralGoogle Scholar
  47. Swaminathan B, Barrett TJ, Hunter SB, Tauxe RV, Force CPT (2001) PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis 7(3):382CrossRefPubMedPubMedCentralGoogle Scholar
  48. Taboada EN, Graham MR, Carriço JA, Van Domselaar G (2017) Food safety in the age of next generation sequencing, bioinformatics, and open data access. Front Microbiol 8:909CrossRefPubMedPubMedCentralGoogle Scholar
  49. Tran-Dien A, Le Hello S, Bouchier C, Weill FX (2018) Early transmissible ampicillin resistance in zoonotic Salmonella enterica serotype Typhimurium in the late 1950s: a retrospective, whole-genome sequencing study. Lancet Infect Dis 18(2):207–214CrossRefPubMedPubMedCentralGoogle Scholar
  50. Wilson A, Gray J, Chandry PS, Fox EM (2018) Phenotypic and genotypic analysis of antimicrobial resistance among listeria monocytogenes isolated from Australian food production chains. Genes 9(2):80CrossRefGoogle Scholar
  51. Yao H, Liu DJ, Wang Y, Zhang QJ, Shen ZQ (2017) High prevalence and predominance of the aph(2″)-if gene conferring aminoglycoside resistance in campylobacter. Antimicrob Agents Chemother 61(5)Google Scholar
  52. Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, Lund O, Larsen MV, Aarestrup FM (2012) Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 68(4):771–777CrossRefPubMedPubMedCentralGoogle Scholar
  53. Zhao S, Tyson GH, Chen Y, Li C, Mukherjee S, Young S, Lam C, Folster JP, Whichard JM, McDermott PF (2016) Whole-genome sequencing analysis accurately predicts antimicrobial resistance phenotypes in campylobacter spp. Appl Environ Microbiol 82(2):459–466CrossRefPubMedPubMedCentralGoogle Scholar
  54. Zuker CS (2015) Food for the brain. Cell 161(1):9–11CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Shiv Bharadwaj
    • 1
  • Vivek Dhar Dwivedi
    • 2
  • Nikhil Kirtipal
    • 3
    Email author
  1. 1.Department of Biotechnology, College of Life and Applied SciencesYeungnam UniversityGyeongbuk-doRepublic of Korea
  2. 2.Center for BioinformaticsPathfinder Research and Training FoundationGreater NoidaIndia
  3. 3.Department of BiotechnologyModern Institute of TechnologyRishikeshIndia

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