Comparative genome analysis of Pasteurella multocida strains of porcine origin
Abstract
Pasteurella multocida causes acute/chronic pasteurellosis in porcine, resulting in considerable economic losses globally. The draft genomes of two Indian strains NIVEDIPm17 (serogroup D) and NIVEDIPm36 (serogroup A) were sequenced. A total of 2182–2284 coding sequences (CDSs) were predicted along with 5–6 rRNA and 45–46 tRNA genes in the genomes. Multilocus sequence analysis and LPS genotyping showed the presence of ST50: genotype 07 and ST74: genotype 06 in NIVEDIPm17 and NIVEDIPm36, respectively. Pangenome analysis of 61 strains showed the presence of 1653 core genes, 167 soft core genes, 750 shell genes, and 1820 cloud genes. Analysis of virulence-associated genes in 61 genomes indicated the presence of nanB, exbB, exbD, ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB, and omp87 in all strains. The 61 genomes contained genes encoding tetracycline (54%), streptomycin (48%), sulphonamide (28%), tigecycline (25%), chloramphenicol (21%), amikacin (7%), cephalosporin (5%), and trimethoprim (5%) resistance. Multilocus sequence type revealed that ST50 was the most common (34%), followed by ST74 (26%), ST13 (24%), ST287 (5%), ST09 (5%), ST122 (3%), and ST07 (2%). Single-nucleotide polymorphism and core genome-based phylogenetic analysis clustered the strains into three major clusters. In conclusion, we described the various virulence factors, mobile genetic elements, and antimicrobial resistance genes in the pangenome of P. multocida of porcine origin, besides the rare presence of LPS genotype 7 in serogroup D.
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Information & Authors
Information
Published In
Genome
Volume 67 • Number 1 • January 2024
Pages: 13 - 23
History
Received: 31 March 2023
Accepted: 22 August 2023
Accepted manuscript online: 28 August 2023
Version of record online: 28 September 2023
Copyright
© 2023 The Author(s). Permission for reuse (free in most cases) can be obtained from copyright.com.
Data Availability Statement
Genome sequences of NIVEDIPm17 and NIVEDIPm36 have been deposited in the National Center for Biotechnology Information (NCBI) Sequence genome submission portal and have been assigned the accession ID of JAKNTU00000000 and JAKNTV000000000, respectively. Further, raw Illumina sequence read data have been deposited in the NCBI sequence read archive [SRA (https://www.ncbi.nlm.nih.gov/sra)] under the accession numbers PRJNA804361 and PRJNA804365, respectively.
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Authors
Author Contributions
Conceptualization: AP
Data curation: AP, SKM
Formal analysis: AP, MMC
Funding acquisition: SBS
Investigation: AP, RY, NNM
Methodology: AP, RY, SKM, MMC, SS
Project administration: SBS
Resources: RY, NNM, SBS
Software: SKM, MMC
Supervision: SBS
Validation: SS
Visualization: AP
Writing – original draft: AP
Writing – review & editing: RY, MMC, SS, SBS
Competing Interests
The authors declare no competing interests.
Funding Information
Indian Council of Agricultural Research: IXX12176
This study was a part of doctoral research carried out by AP under the institute project (Code: IXX12176) entitled “Epidemiology of haemorrhagic septicaemia (HS) in India” granted to SBS.
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Awadhesh Prajapati, Revanaiah Yogisharadhya, Nihar Nalini Mohanty, Suresh Kumar Mendem, Mohammed Mudassar Chanda, Shivakumara Siddaramappa, and Sathish Bhadravati Shivachandra. 2024. Comparative genome analysis of Pasteurella multocida strains of porcine origin. Genome.
67(1): 13-23. https://doi.org/10.1139/gen-2023-0021
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