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Research article - Peer-reviewed, 2020

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

Bengtsson, Rebecca J.; Wee, Bryan A.; Yebra, Gonzalo; Bacigalupe, Rodrigo; Watson, Eleanor; Guedes, Roberto M. C.; Jacobson, Magdalena; Stadejek, Tomasz; Archibald, Alan L.; Fitzgerald, J. Ross; Ait-Ali, Tahar


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.


Lawsonia intracellularis; proliferative enteropathy; metagenomic; phylogeny; monomorphic clonal lineage

Published in

Microbial genomics
2020, volume: 6, number: 4, article number: 000358

Authors' information

Stadejek, Tomasz
Warsaw Univ Life Sci
Archibald, Alan L.
Univ Edinburgh
Bengtsson, Rebecca J.
Univ Edinburgh
Ait-Ali, Tahar
Univ Edinburgh
Wee, Bryan A.
Univ Edinburgh
Fitzgerald, J. Ross
Univ Edinburgh
Yebra, Gonzalo
Univ Edinburgh
Swedish University of Agricultural Sciences, Department of Clinical Sciences
Guedes, Roberto M. C.
Univ Fed Minas Gerais
Watson, Eleanor
Moredun Res Inst
Bacigalupe, Rodrigo
Katholieke Univ Leuven

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