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Volume 7, Issue 7

Comparative genomic analysis of isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes Open Access

Abstract

is a major causative agent of environmental bovine mastitis and this disease causes significant economic losses for the dairy industry. There is still debate in the literature as to whether mammary pathogenic (MPEC) is indeed a unique pathotype, or whether this infection is merely an opportunistic infection caused by any isolate being displaced from the bovine gastrointestinal tract to the environment and, then, into the udder. In this study, we conducted a thorough genomic analysis of 113 novel MPEC isolates from clinical mastitis cases and 100 bovine commensal isolates. A phylogenomic analysis indicated that MPEC and commensal isolates formed clades based on common sequence types and O antigens, but did not cluster based on mammary pathogenicity. A comparative genomic analysis of MPEC and commensal isolates led to the identification of nine genes that were part of either the core or the soft-core MPEC genome, but were not found in any bovine commensal isolates. These apparent MPEC marker genes were genes involved with nutrient intake and metabolism [, adenine permease; , pyruvate-flavodoxin oxidoreductase; and , putative major facilitator superfamily (MFS)-type transporter], included fitness and virulence factors commonly seen in uropathogenic (, zinc metallopeptidase, and , intimin-like adhesin, respectively), and putative proteins [, uncharacterized helix-turn-helix-type transcriptional activator; , putative inner membrane transporter; and , putative periplasmic protein]. Further characterization of these highly conserved MPEC genes may be critical to understanding the pathobiology of MPEC.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): comparative genomics , environmental bovine mastitis , mammary pathogenic Escherichia coli and whole-genome sequencing
Funding
This study was supported by the:
  • OP+Lait
    • Principle Award Recipient: JenniferRonholm
  • Dairy Farmers of Canada (CA)
    • Principle Award Recipient: JenniferRonholm
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2021-07-06
2024-04-23
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References

  1. Gomes F, Henriques M. Control of bovine mastitis: old and recent therapeutic approaches. Curr Microbiol 2016; 72:377–382 [View Article] [PubMed]
     [Google Scholar]
  2. Aghamohammadi M, Haine D, Kelton DF, Barkema HW, Hogeveen H et al. Herd-level mastitis-associated costs on Canadian dairy farms. Front Vet Sci 2018; 5:100 [View Article] [PubMed]
     [Google Scholar]
  3. Donovan DM, Kerr DE, Wall RJ. Engineering disease resistant cattle. Transgenic Res 2005; 14:563–567 [View Article] [PubMed]
     [Google Scholar]
  4. Bradley AJ. Bovine mastitis: an evolving disease. Vet J 2002; 164:116–128 [View Article] [PubMed]
     [Google Scholar]
  5. Klaas IC, Zadoks RN. An update on environmental mastitis: challenging perceptions. Transbound Emerg Dis 2018; 65:166–185 [View Article]
     [Google Scholar]
  6. Levison LJ, Miller-Cushon EK, Tucker AL, Bergeron R, Leslie KE et al. Incidence rate of pathogen-specific clinical mastitis on conventional and organic Canadian dairy farms. J Dairy Sci 2016; 99:1341–1350 [View Article] [PubMed]
     [Google Scholar]
  7. Thompson-Crispi KA, Miglior F, Mallard BA. Incidence rates of clinical mastitis among Canadian Holsteins classified as high, average, or low immune responders. Clin Vaccine Immunol 2013; 20:106–112 [View Article] [PubMed]
     [Google Scholar]
  8. Gritsenko VA, Bukharin OV. The ecological and medical aspects of the symbiosis between Escherichia coli and man. Zh Mikrobiol Epidemiol Immunobiol 2000; 3:92–99
     [Google Scholar]
  9. Shpigel NY, Elazar S, Rosenshine I. Mammary pathogenic Escherichia coli. Curr Opin Microbiol 2008; 11:60–65 [View Article] [PubMed]
     [Google Scholar]
  10. Marrs CF, Zhang L, Foxman B. Escherichia coli mediated urinary tract infections: are there distinct uropathogenic E. coli (UPEC) pathotypes?. FEMS Microbiol Lett 2005; 252:183–190 [View Article] [PubMed]
     [Google Scholar]
  11. Foxman B, Barlow R, D’Arcy H, Gillespie B, Sobel JD. Urinary tract infection: self-reported incidence and associated costs. Ann Epidemiol 2000; 10:509–515
     [Google Scholar]
  12. Wiles TJ, Kulesus RR, Mulvey MA. Origins and virulence mechanisms of uropathogenic Escherichia coli. Exp Mol Pathol 2008; 85:11–19 [View Article] [PubMed]
     [Google Scholar]
  13. Bien J, Sokolova O, Bozko P. Role of uropathogenic Escherichia coli virulence factors in development of urinary tract infection and kidney damage. Int J Nephrol 2012; 2012:681473 [View Article] [PubMed]
     [Google Scholar]
  14. Karami N, Wold AE, Adlerberth I. Antibiotic resistance is linked to carriage of papC and iutA virulence genes and phylogenetic group D background in commensal and uropathogenic Escherichia coli from infants and young children. Eur J Clin Microbiol Infect Dis 2017; 36:721–729 [View Article] [PubMed]
     [Google Scholar]
  15. Ostblom A, Adlerberth I, Wold AE, Nowrouzian FL. Pathogenicity island markers, virulence determinants malX and usp, and the capacity of Escherichia coli to persist in infants’ commensal microbiotas. Appl Environ Microbiol 2011; 77:2303–2308 [View Article] [PubMed]
     [Google Scholar]
  16. Reidl J, Boos W. The malX malY operon of Escherichia coli encodes a novel enzyme II of the phosphotransferase system recognizing glucose and maltose and an enzyme abolishing the endogenous induction of the maltose system. J Bacteriol 1991; 173:4862–4876 [View Article] [PubMed]
     [Google Scholar]
  17. Yazdanpour Z, Tadjrobehkar O, Shahkhah M. Significant association between genes encoding virulence factors with antibiotic resistance and phylogenetic groups in community acquired uropathogenic Escherichia coli isolates. BMC Microbiol 2020; 20:241 [View Article] [PubMed]
     [Google Scholar]
  18. Leimbach A, Poehlein A, Vollmers J, Görlich D, Daniel R et al. No evidence for a bovine mastitis Escherichia coli pathotype. BMC Genomics 2017; 18:359 [View Article] [PubMed]
     [Google Scholar]
  19. Blum SE, Heller ED, Sela S, Elad D, Edery N et al. Genomic and phenomic study of mammary pathogenic Escherichia coli. PLoS One 2015; 10:e0136387 [View Article] [PubMed]
     [Google Scholar]
  20. Goldstone RJ, Harris S, Smith DGE. Genomic content typifying a prevalent clade of bovine mastitis-associated Escherichia coli. Sci Rep 2016; 6:30115 [View Article] [PubMed]
     [Google Scholar]
  21. Kempf F, Slugocki C, Blum SE, Leitner G, Germon P. Genomic comparative studyic of bovine mastitis Escherichia coli. PLoS One 2016; 11:e0147954 [View Article] [PubMed]
     [Google Scholar]
  22. Richards VP, Lefébure T, Pavinski Bitar PD, Dogan B, Simpson KW et al. Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli. PLoS One 2015; 10:e0119799 [View Article]
     [Google Scholar]
  23. Wenz JR, Barrington GM, Garry FB, Ellis RP, Magnuson RJ. Escherichia coli isolates’ serotypes, genotypes, and virulence genes and clinical coliform mastitis severity. J Dairy Sci 2006; 89:3408–3412 [View Article] [PubMed]
     [Google Scholar]
  24. Burvenich C, Merris V, Mehrzad J, Diez-Fraile A, Duchateau L. Severity of E. coli mastitis is mainly determined by cow factors. Vet Res 2003; 34:521–564 [View Article]
     [Google Scholar]
  25. Blum SE, Heller ED, Jacoby S, Krifucks O, Leitner G. Comparison of the immune responses associated with experimental bovine mastitis caused by different strains of Escherichia coli. J Dairy Res 2017; 84:190–197 [View Article]
     [Google Scholar]
  26. Blum SE, Goldstone RJ, Connolly JPR, Répérant-Ferter M, Germon P et al. Postgenomics characterization of an essential genetic determinant of mammary pathogenic Escherichia coli. mBio 2018; 9:e00423–18 [View Article] [PubMed]
     [Google Scholar]
  27. Olson MA, Siebach TW, Griffitts JS, Wilson E, Erickson DL. Genome-wide identification of fitness factors in mastitis-associated Escherichia coli. Appl Environ Microbiol 2018; 84:e02190–17 [View Article] [PubMed]
     [Google Scholar]
  28. Dufour S, Labrie J, Jacques M. The mastitis pathogens culture collection. Microbiol Resour Announc 2019; 8:e00133–19 [View Article]
     [Google Scholar]
  29. Fairbrother J-H, Dufour S, Fairbrother JM, Francoz D, Nadeau É et al. Characterization of persistent and transient Escherichia coli isolates recovered from clinical mastitis episodes in dairy cows. Vet Microbiol 2015; 176:126–133 [View Article]
     [Google Scholar]
  30. Sears PM, McCarthy KK. Diagnosis of mastitis for therapy decisions. Vet Clin North Am Small Anim Pract 2003; 19:93–108
     [Google Scholar]
  31. Arimizu Y, Kirino Y, Sato MP, Uno K, Sato T et al. Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains. Genome Res 2019; 29:1495–1505 [View Article] [PubMed]
     [Google Scholar]
  32. Madoshi BP, Kudirkiene E, Mtambo MMA, Muhairwa AP, Lupindu AM et al. Characterisation of commensal Escherichia coli isolated from apparently healthy cattle and their attendants in Tanzania. PLoS One 2016; 11:e0168160 [View Article] [PubMed]
     [Google Scholar]
  33. Bushnell B. Bbtools Software PackageBBTools software package 2014
     [Google Scholar]
  34. Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 2018; 19:153 [View Article] [PubMed]
     [Google Scholar]
  35. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
     [Google Scholar]
  36. Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics 2016; 32:292–294 [View Article] [PubMed]
     [Google Scholar]
  37. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  38. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–D36 [View Article] [PubMed]
     [Google Scholar]
  39. UniProt Consortium UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 2019; 47:D506–D515 [View Article] [PubMed]
     [Google Scholar]
  40. Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011; 7:e1002195 [View Article] [PubMed]
     [Google Scholar]
  41. Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK et al. TIGRFAMs and genome properties in 2013. Nucleic Acids Res 2013; 41:D387–D395 [View Article] [PubMed]
     [Google Scholar]
  42. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J et al. The Pfam protein families database. Nucleic Acids Res 2012; 40:D290–D301 [View Article] [PubMed]
     [Google Scholar]
  43. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  44. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 2017; 34:2115–2122 [View Article] [PubMed]
     [Google Scholar]
  45. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
     [Google Scholar]
  46. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
     [Google Scholar]
  47. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  48. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article] [PubMed]
     [Google Scholar]
  49. Oliveros JC. Venny: an Interactive Tool for Comparing Lists with Venn Diagrams ( https://bioinfogp.cnb.csic.es/tools/venny/index.html) 2015
     [Google Scholar]
  50. Hall T. Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  51. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S et al. NCBI Blastblast: A better web interface. Nucleic Acids Res 2008; 36:W5–W9 [View Article]
     [Google Scholar]
  52. Jolley KA, Maiden MCJ. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11:595 [View Article] [PubMed]
     [Google Scholar]
  53. Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M et al. In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. Microb Genom 2016; 2:e000064 [View Article] [PubMed]
     [Google Scholar]
  54. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  55. Bertelli C, Laird MR, Williams KP. Simon Fraser University Research Computing Group Lau BY et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article]
     [Google Scholar]
  56. Segura A, Auffret P, Klopp C, Bertin Y, Forano E et al. Draft genome sequence and characterization of commensal Escherichia coli strain bg1 isolated from bovine gastro-intestinal tract. Stand Genomic Sci 2017; 12:61 [View Article] [PubMed]
     [Google Scholar]
  57. Sartori L, Fernandes MR, Ienne S, de Souza TA, Gregory L et al. Draft genome sequences of two fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST90 (ST23 complex) isolated from a calf and a dairy cow in South America. J Glob Antimicrob Resist 2017; 11:145–147 [View Article] [PubMed]
     [Google Scholar]
  58. Papakostas K, Botou M, Frillingos S. Functional identification of the hypoxanthine/guanine transporters YjcD and YgfQ and the adenine transporters PurP and YicO of Escherichia coli K-12. J Biol Chem 2013; 288:36827–36840 [View Article] [PubMed]
     [Google Scholar]
  59. Yang J, Xie X, Wang X, Dixon R, Wang Y-P et al. reconstruction and minimal gene requirements for the alternative iron-only nitrogenase in Escherichia coli. Proc Natl Acad Sci USA 2014; 111:E3718–E3725
     [Google Scholar]
  60. Vicente EJ, Dean DR. Keeping the nitrogen-fixation dream alive. Proc Natl Acad Sci USA 2017; 114:3009–3011 [View Article] [PubMed]
     [Google Scholar]
  61. Carroll SM, DePeters EJ, Taylor SJ, Rosenberg M, Perez-Monti H et al. Milk composition of Holstein, Jersey, and brown Swiss cows in response to increasing levels of dietary fat. Anim Feed Sci Tech 2006; 131:451–473 [View Article]
     [Google Scholar]
  62. Miyake Y, Inaba T, Watanabe H, Teramoto J, Yamamoto K et al. Regulatory roles of pyruvate-sensing two-component system PyrSR (YpdAB) in Escherichia coli K-12. FEMS Microbiol Lett 2019; 366:fnz009 [View Article] [PubMed]
     [Google Scholar]
  63. Kristoficova I, Vilhena C, Behr S, Jung K. BTST, a novel and specific pyruvate/H+ symporter in Escherichia coli. J Bacteriol 2018; 200:e00599–17 [View Article]
     [Google Scholar]
  64. Subashchandrabose S, Smith SN, Spurbeck RR, Kole MM, Mobley HLT. Genome-wide detection of fitness genes in uropathogenic Escherichia coli during systemic infection. PLoS Pathog 2013; 9:e1003788 [View Article] [PubMed]
     [Google Scholar]
  65. Nesta B, Spraggon G, Alteri C, Moriel DG, Rosini R et al. FdeC, a novel broadly conserved Escherichia coli adhesin eliciting protection against urinary tract infections. mBio 2012; 3:e00010–12 [View Article] [PubMed]
     [Google Scholar]
  66. Grinter R, Leung PM, Wijeyewickrema LC, Littler D, Beckham S et al. Protease-associated import systems are widespread in gram-negative bacteria. PLoS Genet 2019; 15:e1008435 [View Article] [PubMed]
     [Google Scholar]
  67. Ziegler EE. Consumption of cow’s milk as a cause of iron deficiency in infants and toddlers. Nutrition Reviews 2011; 69:S37–S42
     [Google Scholar]
  68. Chen Q, Savarino SJ, Venkatesan MM. Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12. Microbiology (Reading) 2006; 152:1041–1054 [View Article] [PubMed]
     [Google Scholar]
  69. Moriel DG, Bertoldi I, Spagnuolo A, Marchi S, Rosini R et al. Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli. Proc Natl Acad Sci USA 2010; 107:9072–9077 [View Article]
     [Google Scholar]
  70. Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 2008; 190:6881–6893 [View Article] [PubMed]
     [Google Scholar]
  71. Oshima K, Toh H, Ogura Y, Sasamoto H, Morita H et al. Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res 2008; 15:375–386 [View Article] [PubMed]
     [Google Scholar]
  72. Easton DM, Allsopp LP, Phan M-D, Moriel DG, Goh GK et al. The intimin-like protein FdeC is regulated by H-NS and temperature in enterohemorrhagic Escherichia coli. Appl Environ Microbiol 2014; 80:7337–7347 [View Article] [PubMed]
     [Google Scholar]
  73. Sathiyabarathi M, Jeyakumar S, Manimaran A, Pushpadass HA, Sivaram M et al. Investigation of body and udder skin surface temperature differentials as an early indicator of mastitis in Holstein Friesian crossbred cows using digital infrared thermography technique. Vet World 2016; 9:1386–1391 [View Article] [PubMed]
     [Google Scholar]
  74. Flores-Bautista E, Cronick CL, Fersaca AR, Martinez-Nuñez MA, Perez-Rueda E. Functional prediction of hypothetical transcription factors of Escherichia coli K-12 based on expression data. Comput Struct Biotechnol J 2018; 16:157–166 [View Article] [PubMed]
     [Google Scholar]
  75. Hall BG, Malik HS. Determining the evolutionary potential of a gene. Mol Biol Evol 1998; 15:1055–1061 [View Article] [PubMed]
     [Google Scholar]
  76. Rudd KE. EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 2000; 28:60–64 [View Article] [PubMed]
     [Google Scholar]
  77. Boehmer T, Vogler AJ, Thomas A, Sauer S, Hergenroether M et al. Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany. PLoS One 2018; 13:e0206252 [View Article] [PubMed]
     [Google Scholar]
  78. Nanayakkara BS, O’Brien CL, Gordon DM. Diversity and distribution of Klebsiella capsules in Escherichia coli. Environ Microbiol Rep 2019; 11:107–117
     [Google Scholar]
  79. Cao J, Woodhall MR, Alvarez J, Cartron ML, Andrews SC. EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in E. coli O157:H7. Mol Microbiol 2007; 65:857–875 [View Article] [PubMed]
     [Google Scholar]
  80. Leimbach A, Poehlein A, Witten A, Scheutz F, Schukken Y et al. Complete genome sequences of Escherichia coli strains 1303 and ECC-1470 isolated from bovine mastitis. Genome Announc 2015; 3:e00182–15 [View Article] [PubMed]
     [Google Scholar]
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Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes
M Gen 7, 000597 (2021); https://doi.org/10.1099/mgen.0.000597
/content/journal/mgen/10.1099/mgen.0.000597
/content/journal/mgen/10.1099/mgen.0.000597
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