Analysis of virulence potential of Escherichia coli O145 isolated from cattle feces and hide samples based on whole genome sequencing

English version

Autoři: Pragathi B. Shridhar ^aff001; Jay N. Worley ^aff002; Xin Gao ^aff002; Xun Yang ^aff002; Lance W. Noll ^aff003; Xiaorong Shi ^aff001; Jianfa Bai ^aff003; Jianghong Meng ^aff002; T. G. Nagaraja ^aff001
Působiště autorů: Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, United States of America ^aff001; Joint Institute for Food Safety and Applied Nutrition and Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States of America ^aff002; Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, Kansas, United States of America ^aff003
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0225057

Souhrn

Escherichia coli O145 serogroup is one of the big six non-O157 Shiga toxin producing E. coli (STEC) that causes foodborne illnesses in the United States and other countries. Cattle are a major reservoir of STEC, which harbor them in their hindgut and shed in the feces. Cattle feces is the main source of hide and subsequent carcass contaminations during harvest leading to foodborne illnesses in humans. The objective of our study was to determine the virulence potential of STEC O145 strains isolated from cattle feces and hide samples. A total of 71 STEC O145 strains isolated from cattle feces (n = 16), hide (n = 53), and human clinical samples (n = 2) were used in the study. The strains were subjected to whole genome sequencing using Illumina MiSeq platform. The average draft genome size of the fecal, hide, and human clinical strains were 5.41, 5.28, and 5.29 Mb, respectively. The average number of genes associated with mobile genetic elements was 260, 238, and 259, in cattle fecal, hide, and human clinical strains, respectively. All strains belonged to O145:H28 serotype and carried eae subtype γ. Shiga toxin 1a was the most common Shiga toxin gene subtype among the strains, followed by stx2a and stx2c. The strains also carried genes encoding type III secretory system proteins, nle, and plasmid-encoded virulence genes. Phylogenetic analysis revealed clustering of cattle fecal strains separately from hide strains, and the human clinical strains were more closely related to the hide strains. All the strains belonged to sequence type (ST)-32. The virulence gene profile of STEC O145 strains isolated from cattle sources was similar to that of human clinical strains and were phylogenetically closely related to human clinical strains. The genetic analysis suggests the potential of cattle STEC O145 strains to cause human illnesses. Inclusion of more strains from cattle and their environment in the analysis will help in further elucidation of the genetic diversity and virulence potential of cattle O145 strains.

Klíčová slova:

Sequence analysis – Bacteriophages – Cattle – Toxins – Antimicrobial resistance – Serum proteins – Escherichia coli – Genome sequencing

Zdroje

1. Brooks JT, Sowers EG, Wells JG, Greene KD, Griffin PM, Hoekstra RM, et al. Non-O157 Shiga toxin-producing Escherichia coli infections in the United States, 1983–2002. The Journal of infectious diseases. 2005;192(8):1422–9. doi: 10.1086/466536 16170761.

2. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson M-A, Roy SL, et al. Foodborne illness acquired in the United States—major pathogens. Emerging infectious diseases. 2011;17(1):7–15. doi: 10.3201/eid1701.P11101 21192848.

3. USDA-FSIS. Shiga toxin producing E. coli in certain raw beef products, 75 (2011).

4. Beutin L, Zimmermann S, Gleier K. Human infections with Shiga toxin-producing Escherichia coli other than serogroup O157 in Germany. Emerging Infectious Diseases. 1998;4(4):635–9. 9866741

5. Rivero MA, Passucci JA, Rodriguez EM, Parma AE. Role and clinical course of verotoxigenic Escherichia coli infections in childhood acute diarrhoea in Argentina. J Med Microbiol. 2010;59(Pt 3):345–52. Epub 2009/10/24. doi: 10.1099/jmm.0.015560-0 19850706.

6. De Schrijver K, Buvens G, Posse B, Van den Branden D, Oosterlynck O, De Zutter L, et al. Outbreak of verocytotoxin-producing E. coli O145 and O26 infections associated with the consumption of ice cream produced at a farm, Belgium, 2007. Euro Surveill. 2008;13.

7. Luna RE, Mody R. Non-O157 Shiga toxin-producing E. coli (STEC) outbreaks, United States. In: Department of Health and human services CfDCaPC, editor. Centers for Disease Control and Prevention, Atlanta.2010.

8. Yoder J, Roberts V, Craun GF, Hill V, Hicks L, Alexander NT, et al. Surveillance for waterborne disease and outbreaks associated with drinking water and water not intended for drinking—United States, 2005–2006. Morb.Mortal. Wkly. Rep; 2008. p. 39–69.

9. Taylor EV, Nguyen TA, Machesky KD, Koch E, Sotir MJ, Bohm SR, et al. Multistate outbreak of Escherichia coli O145 infections associated with romaine lettuce consumption, 2010. J Food Prot. 2013;76. doi: 10.4315/0362-028x.jfp-12-503 23726187

10. Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, et al. Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. BMC Genomics. 2014;15(1):17. doi: 10.1186/1471-2164-15-17 24410921

11. Carter MQ, Quinones B, He X, Zhong W, Louie JW, Lee BG, et al. An Environmental Shiga Toxin-Producing Escherichia coli O145 Clonal Population Exhibits High-Level Phenotypic Variation That Includes Virulence Traits. Applied and Environmental Microbiology. 2016;82(4):1090–101. doi: 10.1128/AEM.03172-15 26637597

12. Elder RO, Keen JE, Siragusa GR, Barkocy-Gallagher GA, Koohmaraie M, Laegreid WW. Correlation of enterohemorrhagic Escherichia coli O157 prevalence in feces, hides, and carcasses of beef cattle during processing. Proceedings of the National Academy of Sciences. 2000;97(7):2999–3003. doi: 10.1073/pnas.97.7.2999

13. Jacob ME, Renter DG, Nagaraja TG. Animal- and truckload-level associations between Escherichia coli O157:H7 in feces and on hides at harvest and contamination of preevisceration beef carcasses. J Food Prot. 2010;73(6):1030–7. doi: 10.4315/0362-028x-73.6.1030 20537257.

14. Noll LW, Shridhar PB, Dewsbury DM, Shi X, Cernicchiaro N, Renter DG, et al. A comparison of culture- and PCR-based methods to detect six major non-O157 serogroups of Shiga toxin-producing Escherichia coli in cattle feces. PLoS One. 2015;10(8):e0135446. doi: 10.1371/journal.pone.0135446 26270482.

15. Cull CA, Renter DG, Dewsbury DM, Noll LW, Shridhar PB, Ives SE, et al. Feedlot- and pen-level prevalence of enterohemorrhagic Escherichia coli in feces of commercial feedlot cattle in two major U.S. cattle feeding areas. Foodborne Pathog Dis. 2017;14(6):309–17. Epub 2017/03/11. doi: 10.1089/fpd.2016.2227 28281781.

16. Noll LW, Shridhar PB, Ives SE, Cha E, Nagaraja TG, Renter DG. Detection and Quantification of seven major serogroups of Shiga toxin–producing Escherichia coli on hides of cull dairy, cull beef, and fed beef cattle at slaughter. Journal of Food Protection. 2018;81(8):1236–44. doi: 10.4315/0362-028X.JFP-17-497 29969294.

17. Bai J, Paddock ZD, Shi X, Li S, An B, Nagaraja TG. Applicability of a multiplex PCR to detect the seven major Shiga toxin-producing Escherichia coli based on genes that code for serogroup-specific O-antigens and major virulence factors in cattle feces. Foodborne Pathog Dis. 2012;9(6):541–8. doi: 10.1089/fpd.2011.1082 22568751.

18. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. JComputBiol. 2012;19.

19. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9. doi: 10.1186/1471-2164-9-75 18261238

20. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, et al. Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli. Journal of clinical microbiology. 2014;52(5):1501–10. doi: 10.1128/JCM.03617-13 24574290

21. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–4. Epub 2012/07/12. doi: 10.1093/jac/dks261 22782487.

22. Zhang Q, Ye Y. Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics. 2017;18:92. doi: 10.1186/s12859-017-1512-4 28166719

23. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol. 2006;60. doi: 10.1111/j.1365-2958.2006.05172.x 16689791

24. Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, Guigon G, et al. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics. 2008;9(1):560. doi: 10.1186/1471-2164-9-560 19036134

25. Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15(11):524. Epub 2014/11/21. doi: 10.1186/s13059-014-0524-x 25410596.

26. Lorenz SC, Gonzalez-Escalona N, Kotewicz ML, Fischer M, Kase JA. Genome sequencing and comparative genomics of enterohemorrhagic Escherichia coli O145:H25 and O145:H28 reveal distinct evolutionary paths and marked variations in traits associated with virulence & colonization. BMC Microbiology. 2017;17:183. doi: 10.1186/s12866-017-1094-3 28830351

27. Fan R, Shao K, Yang X, Bai X, Fu S, Sun H, et al. High prevalence of non-O157 Shiga toxin-producing Escherichia coli in beef cattle detected by combining four selective agars. BMC Microbiology. 2019;19(1):213. doi: 10.1186/s12866-019-1582-8 31488047

28. Jajarmi M, Imani Fooladi AA, Badouei MA, Ahmadi A. Virulence genes, Shiga toxin subtypes, major O-serogroups, and phylogenetic background of Shiga toxin-producing Escherichia coli strains isolated from cattle in Iran. Microb Pathog. 2017;109:274–9. Epub 2017/06/05. doi: 10.1016/j.micpath.2017.05.041 28578089.

29. Friedrich AW, Bielaszewska M, Zhang W-L, Pulz M, Kuczius T, Ammon A, et al. Escherichia coli harboring Shiga toxin 2 gene variants: frequency and association with clinical symptoms. J Infect Dis. 2002;185(1):74–84. doi: 10.1086/338115 11756984.

30. Persson S, Olsen KEP, Ethelberg S, Scheutz F. Subtyping Method for Escherichia coli Shiga Toxin (Verocytotoxin) 2 Variants and Correlations to Clinical Manifestations. Journal of Clinical Microbiology. 2007;45(6):2020–4. doi: 10.1128/JCM.02591-06 17446326

31. Iyoda S, Manning SD, Seto K, Kimata K, Isobe J, Etoh Y, et al. Phylogenetic Clades 6 and 8 of Enterohemorrhagic Escherichia coli O157:H7 With Particular stx Subtypes are More Frequently Found in Isolates From Hemolytic Uremic Syndrome Patients Than From Asymptomatic Carriers. Open Forum Infect Dis. 2014;1(2):ofu061. doi: 10.1093/ofid/ofu061 25734131.

32. McDaniel TK, Jarvis KG, Donnenberg MS, Kaper JB. A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens. Proc Natl Acad Sci U S A. 1995;92(5):1664–8. Epub 1995/02/28. doi: 10.1073/pnas.92.5.1664 7878036.

33. McDaniel TK, Kaper JB. A cloned pathogenicity island from enteropathogenic Escherichia coli confers the attaching and effacing phenotype on E. coli K-12. Molecular microbiology. 1997;23(2):399–407. Epub 1997/01/01. doi: 10.1046/j.1365-2958.1997.2311591.x 9044273.

34. Bugarel M, Beutin L, Fach P. Low-density macroarray targeting non-locus of enterocyte effacement effectors (nle genes) and major virulence factors of Shiga toxin-producing Escherichia coli (STEC): a new approach for molecular risk assessment of STEC isolates. Appl Environ Microbiol. 2010;76(1):203–11. Epub 2009/11/03. doi: 10.1128/AEM.01921-09 19880649.

35. Karmali MA, Mascarenhas M, Shen S, Ziebell K, Johnson S, Reid-Smith R, et al. Association of genomic O island 122 of Escherichia coli EDL 933 with verocytotoxin-producing Escherichia coli seropathotypes that are linked to epidemic and/or serious disease. J Clin Microbiol. 2003;41(11):4930–40. Epub 2003/11/08. doi: 10.1128/JCM.41.11.4930-4940.2003 14605120.

36. Oswald E, Schmidt H, Morabito S, Karch H, Marches O, Caprioli A. Typing of intimin genes in human and animal enterohemorrhagic and enteropathogenic Escherichia coli: characterization of a new intimin variant. Infection and immunity. 2000;68. doi: 10.1128/iai.68.1.64-71.2000

37. Zhang X, Cheng Y, Xiong Y, Ye C, Zheng H, Sun H, et al. Enterohemorrhagic Escherichia coli Specific Enterohemolysin Induced IL-1β in Human Macrophages and EHEC-Induced IL-1β Required Activation of NLRP3 Inflammasome. PLOS ONE. 2012;7(11):e50288. doi: 10.1371/journal.pone.0050288 23209696

38. Schmidt H, Karch H. Enterohemolytic phenotypes and genotypes of Shiga toxin-producing Escherichia coli O111 strains from patients with diarrhea and hemolytic-uremic syndrome. Journal of clinical microbiology. 1996;34(10):2364–7. 8880480.

39. Brunder W, Schmidt H, Karch H. EspP, a novel extracellular serine protease of enterohaemorrhagic Escherichia coli O157: H7 cleaves human coagulation factor V. Mol Microbiol. 1997;24. doi: 10.1046/j.1365-2958.1997.3871751.x 9194704

40. Silva LE, Souza TB, Silva NP, Scaletsky IC. Detection and genetic analysis of the enteroaggregative Escherichia coli heat-stable enterotoxin (EAST1) gene in clinical isolates of enteropathogenic Escherichia coli (EPEC) strains. BMC Microbiology. 2014;14(1):135. doi: 10.1186/1471-2180-14-135 24884767

41. Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, et al. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proceedings of the National Academy of Sciences. 2009;106(42):17939–44. doi: 10.1073/pnas.0903585106 19815525

42. Mshana SE, Imirzalioglu C, Hossain H, Hain T, Domann E, Chakraborty T. Conjugative IncFI plasmids carrying CTX-M-15 among Escherichia coli ESBL producing isolates at a University hospital in Germany. BMC Infectious Diseases. 2009;9(1):97. doi: 10.1186/1471-2334-9-97 19534775

43. Lyimo B, Buza J, Subbiah M, Temba S, Kipasika H, Smith W, et al. IncF Plasmids Are Commonly Carried by Antibiotic Resistant Escherichia coli Isolated from Drinking Water Sources in Northern Tanzania. International Journal of Microbiology. 2016;2016:7. doi: 10.1155/2016/3103672 27110245

44. Johnson TJ, Nolan LK. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol Rev. 2009;73. doi: 10.1128/mmbr.00015-09 19946140

45. Kozyreva VK, Jospin G, Greninger AL, Watt JP, Eisen JA, Chaturvedi V. Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone Resistance. mSphere. 2016;1(6). doi: 10.1128/mSphere.00344-16 28028547

46. Folster JP, Pecic G, Taylor E, Whichard J. Characterization of isolates from an outbreak of multidrug-resistant, Shiga toxin-producing Escherichia coli O145 in the United States. Antimicrob Agents Chemother. 2011;55. doi: 10.1128/aac.05545-11 21930875

47. Tobe T, Beatson SA, Taniguchi H, Abe H, Bailey CM, Fivian A, et al. An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proceedings of the National Academy of Sciences of the United States of America. 2006;103(40):14941–6. doi: 10.1073/pnas.0604891103 16990433

Analysis of virulence potential of Escherichia coli O145 isolated from cattle feces and hide samples based on whole genome sequencing

Souhrn

Klíčová slova:

Zdroje

PLOS One

Aktuální možnosti diagnostiky a léčby litiáz