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Microbial genomics2020; 6(4); doi: 10.1099/mgen.0.000358

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

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.
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Publication Date: 2020-04-02 PubMed ID: 32238228PubMed Central: PMC7276710DOI: 10.1099/mgen.0.000358Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research identifies a single widespread strain of Lawsonia intracellularis responsible for a common intestinal disease in pigs and other animals. The study used metagenomic sequencing of clinical samples from different regions to uncover the bacterium’s population structure and genomic diversity.

Method and Data Collection

  • The researchers utilized a method called a metagenomic shotgun approach to sequence and assemble 21 genomes of Lawsonia intracellularis. These were sourced from faecal and ileum samples collected from infected pigs and horses across three continents.
  • The method allowed them to bypass the challenges being faced in prior studies where it was hard to culture the bacterium thus impeding progress in understanding its biology and finding improved disease control systems.

Analyses and Findings

  • Upon performing a phylogenetic analysis of the sequenced genomes, they discovered a genetically monomorphic clonal lineage of Lawsonia intracellularis that was responsible for infections in pigs.
  • Interestingly, there were distinct subtypes of the bacteria associated with infections in horses, indicating variation according to species.
  • The genome of the bacterium was found to be highly conserved, with 94% of the genes being shared between all the isolates.

Population Structure–Diversity and Genetics

  • The researchers also noted a very small accessory genome made up of only 84 genes across all the sequenced strains, speaking to the limited diversity of Gilbert’s bacterium.
  • Within the accessory genome, regions with high densities of SNPs (Single Nucleotide Polymorphisms) were observed. These are indicative of recombination events that import novel gene alleles, likely contributing to how the bacterium adapts and evolves.
  • The population structure revealed from the research showed a single major lineage associated with pig diseases. This lineage had a broad geographical distribution, suggesting its recent emergence and clonal expansion as an important livestock pathogen.
  • The limited diversity in the genome of Lawsonia intracellularis suggests that it is a young species, and this fact could have contributed to its success as a widespread pathogen.

Cite This Article

APA
Bengtsson RJ, Wee BA, Yebra G, Bacigalupe R, Watson E, Guedes RMC, Jacobson M, Stadejek T, Archibald AL, Fitzgerald JR, Ait-Ali T. (2020). Metagenomic sequencing of clinical samples reveals a single widespread clone of Lawsonia intracellularis responsible for porcine proliferative enteropathy. Microb Genom, 6(4). https://doi.org/10.1099/mgen.0.000358

Publication

Microbial genomics
ISSN: 2057-5858
NlmUniqueID: 101671820
Country: England
Language: English
Volume: 6
Issue: 4

Researcher Affiliations

Bengtsson, Rebecca J
  • Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK.
  • Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
Wee, Bryan A
  • Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK.
  • Usher Institute, University of Edinburgh, Edinburgh, UK.
Yebra, Gonzalo
  • Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK.
Bacigalupe, Rodrigo
  • Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK.
  • Laboratory of Molecular Biology, Rega Institute for Medical Research, KU Leuven, Belgium.
Watson, Eleanor
  • Moredun Research Institute, Penicuik, UK.
Guedes, Roberto M C
  • Veterinary School, Department of Clinic and Surgery, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Jacobson, Magdalena
  • Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Stadejek, Tomasz
  • Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland.
  • ANSES Fougères Laboratory, 10B rue Claude Bourgelat, Javené CS 40608, BP 90203, 35306 FOUGÈRES, France.
Archibald, Alan L
  • Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK.
Fitzgerald, J Ross
  • Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK.
Ait-Ali, Tahar
  • Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK.

MeSH Terms

  • Animals
  • Feces / microbiology
  • High-Throughput Nucleotide Sequencing
  • Horse Diseases / microbiology
  • Horses
  • Ileum / microbiology
  • Intestinal Diseases / microbiology
  • Intestinal Diseases / veterinary
  • Lawsonia Bacteria / classification
  • Lawsonia Bacteria / genetics
  • Metagenomics / methods
  • Phylogeny
  • Sequence Analysis, DNA
  • Swine
  • Swine Diseases / microbiology

Grant Funding

  • BB/L01680X/1 / Biotechnology and Biological Sciences Research Council
  • BB/J004227/1 / Biotechnology and Biological Sciences Research Council
  • BB/P013740/1 / Biotechnology and Biological Sciences Research Council

Conflict of Interest Statement

The authors declare that there are no conflicts of interest.

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