Genome based phylogeny and virulence factor analysis of mastitis causing Escherichia coli isolated from Indian cattle

MEENU CHOPRA; SAMIRAN BANDYOPADHYAY; DEBARAJ BHATTACHARYA; JAYDEEP BANERJEE; RAVI KANT SINGH; MOHIT SWARNKAR; ANIL KUMAR SINGH; SACHINANDAN DE

doi:10.56093/ijans.v90i12.113165

Authors

MEENU CHOPRA ICAR-National Dairy Research Institute, Karnal, Haryana 132 001 India
SAMIRAN BANDYOPADHYAY ICAR-National Dairy Research Institute, Karnal, Haryana 132 001 India
DEBARAJ BHATTACHARYA ICAR-National Dairy Research Institute, Karnal, Haryana 132 001 India
JAYDEEP BANERJEE ICAR-National Dairy Research Institute, Karnal, Haryana 132 001 India
RAVI KANT SINGH ICAR-National Dairy Research Institute, Karnal, Haryana 132 001 India
MOHIT SWARNKAR ICAR-National Dairy Research Institute, Karnal, Haryana 132 001 India
ANIL KUMAR SINGH ICAR-National Dairy Research Institute, Karnal, Haryana 132 001 India
SACHINANDAN DE ICAR-National Dairy Research Institute, Karnal, Haryana 132 001 India

https://doi.org/10.56093/ijans.v90i12.113165

Keywords:

Escherichia coli, Mastitis, Pangenome, Virulence genes

Abstract

Mastitis is a highly infectious disease prevalent in dairy cattle and it is majorly caused by Escherichia coli (E. coli). The objective of present study is to investigate the occurrence of virulence genes, antimicrobial susceptibility and comparative analysis of E. coli (IVRI KOL CP4 and CM IVRI KOL-1) isolates from mastitis infected animal. Whole-genome sequencing (WGS) was performed using a PacBio RS II system and de novo assembled using Hierarchical Genome Assembly Process (HGAP3). Bacterial Pan Genome Analysis Pipeline (BPGA) was used for pangenome analysis. A set of 50 E. coli isolates were used for comparative analysis (48 collected from the database and 2 reference sequences). Core genes were further concatenated for phylogenetic analyses. In silico analysis was performed for antibiotic resistance and virulence gene identification. Both of the E. coli isolates carried many resistance genes including, b-lactamase, quinolones, rifampicin, macrolide, aminoglycoside and phenicols resistance. We detected 39 virulence genes in IVRI KOL CP4 and 52 in CM IVRI KOL-1 which include toxins, adhesions, invasins, secretion machineries or iron acquisition system. High prevalence of mastitis strains belongs to phylogroups A, although few isolates were also assigned to phylogenetic groups B1 and B2. In conclusion, the present study reported the presence of genes involved in Adherence, Iron acquisition, secretion system and toxins which shown to be crucial in MPEC pathogenicity. This is the first whole genome analysis of MPEC strains to be carried out in Indian isolate to highlights the spread of resistance and virulence genes in food animals.

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References

Bhat A M, Soodan J S, Singh R, Dhobi I A, Hussain T, Dar M Y and Mir M. 2017. Incidence of bovine clinical mastitis in Jammu region and antibiogram of isolated pathogens. Veterinary World 10(8): 984–89. DOI: https://doi.org/10.14202/vetworld.2017.984-989

Bansal B K and Gupta D K. 2009. Economic analysis of bovine mastitis in India and Punjab—A review. Indian Journal of Dairy Science 62(5): 337–45.

Briñas L, Zarazaga M, Sáenz Y, Larrea F R and Torres C. 2002. Beta-lactamases in ampicillin-resistant Escherichia coli isolates from foods, humans, and healthy animals. Antimicrobial Agents Chemotherpy 46(10): 3156–63. DOI: https://doi.org/10.1128/AAC.46.10.3156-3163.2002

Bingle L E, Bailey C M and Pallen M J. 2008. Type VI secretion: a beginner’s guide. Current Opinion in Microbiology 11(1): 3–8. DOI: https://doi.org/10.1016/j.mib.2008.01.006

Blum S E, Heller E D, Sela S, Elad D, Edery N and Leitner G. 2015. Genomic and phenomic study of mammary pathogenic Escherichia coli. PLoS One 10(9): 0136387. DOI: https://doi.org/10.1371/journal.pone.0136387

Blum S E and Leitner G. 2013. Genotyping and virulence factors assessment of bovine mastitis Escherichia coli. Veterinary Microbiology 163(3–4): 305–12. DOI: https://doi.org/10.1016/j.vetmic.2012.12.037

Blum S E, Goldstone R J, Connolly L P R, Ferter M R, Germon P, Inglis N F, Krifucks O, Mathur S, Manson E, Mclean K, Rainard P, Roe A J, Leitner G and Smithb D G E. 2018. Postgenomics characterization of an essential genetic determinant of mammary pathogenic Escherichia coli. mBio 9: e00423–18. DOI: https://doi.org/10.1128/mBio.00423-18

Carlos C, Pires M M, Stoppe N C, Hachich E M, Sato M I, Gomes T A, Amaral L A and Ottoboni L M. 2010. Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination. BMC Microbiology 10(1): 161. DOI: https://doi.org/10.1186/1471-2180-10-161

Castanie-Cornet M P and Foster J W. 2001. Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes. Microbiology 147(3): 709–15. DOI: https://doi.org/10.1099/00221287-147-3-709

Chaudhari N M, Gupta V K and Dutta C. 2016. BPGA- an ultrafast pan-genome analysis pipeline. Scientific Reports 6(1). DOI: https://doi.org/10.1038/srep24373

Chen L, Zou Y, She P and Wu Y. 2015. Composition, function, and regulation of T6SS in Pseudomonas aeruginosa. Microbiological Research 172: 19–25. DOI: https://doi.org/10.1016/j.micres.2015.01.004

Conesa A, Götz S, García-Gómez M J, Terol J, Talón M and Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18): 3674–76. DOI: https://doi.org/10.1093/bioinformatics/bti610

Dagan T and Martin W. 2006. The tree of one percent. Genome Biology 7(10): 118. DOI: https://doi.org/10.1186/gb-2006-7-10-118

Dogan B, Rishniw M, Bruant G, Harel J, Schukken Y H and Simpson K W. 2012. Phylogroup and lpfA influence epithelial invasion by mastitis associated Escherichia coli. Veterinary Microbiology 159(1–2): 163–70. DOI: https://doi.org/10.1016/j.vetmic.2012.03.033

Filloux A, Hachani A and Bleves S. 2008. The bacterial type VI secretion machine: yet another player for protein transport across membranes. Microbiology 154(6): 1570–83. DOI: https://doi.org/10.1099/mic.0.2008/016840-0

Fourth M. 2012. 9781936113415: Molecular Cloning: A Laboratory Manual (Fourth Edition): Three-volume set— AbeBooks - Michael R. Green; Joseph Sambrook: 1936113414.

Goebel W, Chakraborty T and Kreft J. 1988. Bacterial hemolysins as virulence factors. Antonie van Leeuwenhoek 54(5): 453– 63. DOI: https://doi.org/10.1007/BF00461864

Gómez P A J, Ríos J E G, Mendoza A R, Ramonet P D P, Albiach R G and Sainz M P R. 2004. Molecular basis of quinolone resistance in Escherichia coli from wild birds. Candanian Journal of Veterinary Research 68(3): 229–31.

Juan C, Maciá M D, Gutiérrez O, Vidal C, Pérez J L and Oliver A. 2005. Molecular mechanisms of -Lactam resistance mediated by AmpC hyperproduction in Pseudomonas aeruginosa clinical strains. Antimicrobial Agents Chemotherapy 49(11): 4733–38. DOI: https://doi.org/10.1128/AAC.49.11.4733-4738.2005

Kaas R S, Friis C, Ussery D W and Aarestrup F M. 2012. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics 13(1): 577. Kaipainen T, Pohjanvirta T, Shpigel N Y, Shwimmer A, Pyörälä S and Pelkonen S. 2002. Virulence factors of Escherichia coli isolated from bovine clinical mastitis. Veterinary Microbiology 85(1): 37–46. DOI: https://doi.org/10.1186/1471-2164-13-577

Kalita A, Hu J and Torres A G. 2014. Recent advances in adherence and invasion of pathogenic Escherichia coli. Current Opinion in Infectious Diseases 27(5): 459–64. DOI: https://doi.org/10.1097/QCO.0000000000000092

Kempf F, Slugocki C, Blum S E, Leitner G and Germon P. 2016. Genomic comparative study of bovine mastitis Escherichia coli. PLoS One 11(1): 0147954. DOI: https://doi.org/10.1371/journal.pone.0147954

Liu Y, Liu G, Liu W, Liu Y, Ali T, Chen W, Yin J and Han B. 2014. Phylogenetic group, virulence factors and antimicrobial resistance of Escherichia coli associated with bovine mastitis. Research in Microbiology 165(4): 273–77. DOI: https://doi.org/10.1016/j.resmic.2014.03.007

Medini D, Donati C, Tettelin H, Masignani V and Rappuoli R. 2005. The microbial pan-genome. Current Opinion in Genetics and Development 15(6): 589–94. DOI: https://doi.org/10.1016/j.gde.2005.09.006

Nemeth J, Muckle C A and Gyles C L. 1994. In vitro comparison of bovine mastitis and fecal Escherichia coli isolates. Veterinary Microbiology 40(3–4): 231–38. DOI: https://doi.org/10.1016/0378-1135(94)90112-0

Poirel L, Goutines J, Aires-De-Sousa M and Nordmann P. 2018. High rate of association of 16S rRNA methylases and carbapenemases in Enterobacteriaceae recovered from hospitalized children in Angola. Antimicrobial Agents Chemotherapy 62: e00021–18. DOI: https://doi.org/10.1128/AAC.00021-18

Pukatzki S, Ma A T, Revel A T, Sturtevant D and Mekalanos J J. 2007. Type VI secretion system translocates a phage tail spikelike protein into target cells where it cross-links actin. Proceedings of the National Academy of Sciences 104(39): 15508–13. DOI: https://doi.org/10.1073/pnas.0706532104

Ragupathi N K D, Veeraraghavan B, Sethuvel D P M, Anandan S, Vasudevan K, Neeravi A R, Daniel J L K, Sathyendra S, Iyadurai R and Mutreja A. 2020. First Indian report on genomewide comparison of multidrug-resistant Escherichia coli from blood stream infections. PLoS One 15(2): e0220428. DOI: https://doi.org/10.1371/journal.pone.0220428

Reingold J, Starr N, Maurer J and Lee M D. 1999. Identification of a new Escherichia coli She haemolysin homolog in avian E. coli. Veterinary Microbiology 66(2): 125–34. DOI: https://doi.org/10.1016/S0378-1135(98)00310-1

Richards V P, Lefébure T, Pavinski Bitar P D, Dogan B, Simpson K W, Schukken Y H and Stanhope M J. 2015. Genome based phylogeny and comparative genomic analysis of intramammary pathogenic Escherichia coli. PLoS One 10(3): 0119799. DOI: https://doi.org/10.1371/journal.pone.0119799

Rouli L, Merhej V, Fournier P E and Raoult D. 2015. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes and New Infections 7: 72–85. DOI: https://doi.org/10.1016/j.nmni.2015.06.005

Sanchez-Carlo V, Wilson R A, McDonald J S and Packer R A. 1984. Biochemical and serologic properties of Escherichia coli isolated from cows with acute mastitis. American Journal Of Veterinary Research 45(9): 1771–74.

Shrivastava S and Mande S S. 2008. Identification and functional characterization of gene components of Type VI Secretion system in bacterial genomes. PLoS One 3(8): e2955. DOI: https://doi.org/10.1371/journal.pone.0002955

Snipen L, Almøy T and Ussery D W. 2009. Microbial comparative pan-genomics using binomial mixture models. BMC Genomics 10(1): 385. DOI: https://doi.org/10.1186/1471-2164-10-385

Song W, Thomas T and Edwards R J. 2019. Complete genome sequences of pooled genomic DNA from 10 marine bacteria using PacBio long-read sequencing. Marine Genomics 48: 100687. DOI: https://doi.org/10.1016/j.margen.2019.05.002

Sugumar M, Kumar K M, Manoharan A, Anbarasu A and Ramaiah, S. 2014. Detection of OXA 1 -Lactamase Gene of Klebsiella pneumoniae from blood stream infections (BSI) by conventional PCR and in-silico analysis to understand the mechanism of OXA mediated resistance. PLoS One 9: e91800. DOI: https://doi.org/10.1371/journal.pone.0091800

Taylor E, Sriskandan S, Woodford N and Hopkins K L. 2018. High prevalence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacteriaceae in the UK and Ireland. International Journal Antimicrobial Agents 52(2): 278–82. DOI: https://doi.org/10.1016/j.ijantimicag.2018.03.016

Tchesnokova V, Aprikian P, Kisiela D, Gowey S, Korotkova N, Thomas W and Sokurenko E. 2011. Type 1 Fimbrial Adhesin FimH elicits an immune response that enhances cell adhesion of Escherichia coli. Infectious Immunology 79(10): 3895– 3904. DOI: https://doi.org/10.1128/IAI.05169-11

White D G and Mcdermott P F. 2001. Emergence and transfer of antibiotic resistance. Journal of Dairy Science 84: 151–55. DOI: https://doi.org/10.3168/jds.S0022-0302(01)70209-3

Zadoks R N, Middleton J R, McDougall S, Katholm J and Schukken Y H. 2011. Molecular epidemiology of mastitis pathogens of dairy cattle and comparative relevance to humans. Journal of Mammary Gland Biology Neoplasia 16(4): 357– 72. DOI: https://doi.org/10.1007/s10911-011-9236-y

Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup F M and Larsen M V. 2012. Identification of acquired antimicrobial resistance genes. Journal of Antimicrobial Chemotherapy 67(11): 2640–44. DOI: https://doi.org/10.1093/jac/dks261