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Metagenomic sequencing of clinical samples reveals a single widespread clone of Lawsonia intracellularis responsible for porcine proliferative enteropathy

Stadejek, Tomasz and Archibald, Alan L. and Bengtsson, Rebecca J. and Ait-Ali, Tahar and Wee, Bryan A. and Fitzgerald, J. Ross and Yebra, Gonzalo and Jacobson, Magdalena and Guedes, Roberto M. C. and Watson, Eleanor and Bacigalupe, Rodrigo (2020). Metagenomic sequencing of clinical samples reveals a single widespread clone of Lawsonia intracellularis responsible for porcine proliferative enteropathy. Microbial genomics. 6 , 000358 , 1-10
[Journal article]

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Abstract

Lawsonia intracellularis is a Gram-negative obligate intracellular bacterium that is the aetiological agent of proliferative enteropathy (PE), a common intestinal disease of major economic importance in pigs and other animal species. To date, progress in understanding the biology of L. intracellularis for improved disease control has been hampered by the inability to culture the organism in vitro. In particular, our understanding of the genomic diversity and population structure of clinical L. intercellularis is very limited. Here, we utilized a metagenomic shotgun approach to directly sequence and assemble 21 L. intracellularis genomes from faecal and ileum samples of infected pigs and horses across three continents. Phylogenetic analysis revealed a genetically monomorphic clonal lineage responsible for infections in pigs, with distinct subtypes associated with infections in horses. The genome was highly conserved, with 94% of genes shared by all isolates and a very small accessory genome made up of only 84 genes across all sequenced strains. In part, the accessory genome was represented by regions with a high density of SNPs, indicative of recombination events importing novel gene alleles. In summary, our analysis provides the first view of the population structure for L. intracellularis, revealing a single major lineage associated with disease of pigs. The limited diversity and broad geographical distribution suggest the recent emergence and clonal expansion of an important livestock pathogen.

Authors/Creators:Stadejek, Tomasz and Archibald, Alan L. and Bengtsson, Rebecca J. and Ait-Ali, Tahar and Wee, Bryan A. and Fitzgerald, J. Ross and Yebra, Gonzalo and Jacobson, Magdalena and Guedes, Roberto M. C. and Watson, Eleanor and Bacigalupe, Rodrigo
Title:Metagenomic sequencing of clinical samples reveals a single widespread clone of Lawsonia intracellularis responsible for porcine proliferative enteropathy
Year of publishing :2020
Volume:6
Article number:000358
Number of Pages:10
Publisher:Microbiology Society
ISSN:2057-5858
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution-Noncommercial 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109)
Keywords:Lawsonia intracellularis, proliferative enteropathy, metagenomic, phylogeny, monomorphic clonal lineage
URN:NBN:urn:nbn:se:slu:epsilon-p-105775
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-105775
Additional ID:
Type of IDID
DOI10.1099/mgen.0.000358
Web of Science (WoS)000531010100008
ID Code:17118
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Clinical Sciences
Deposited By: SLUpub Connector
Deposited On:23 Jun 2020 07:08
Metadata Last Modified:23 Jun 2020 07:08

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