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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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  • 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.

References

This article includes 46 references
  1. Gebhart CJ, Barns SM, Mcorist S, Lin G-F, Lawson GH. Ileal symbiont intracellularis, an obligate intracellular bacterium of porcine intestines showing a relationship to Desulfovibrio species.. International Journal of Systematic and Evolutionary Microbiology 1993;43:533–538.
    pubmed: 8347512
  2. Klein EC, Gebhart CJ, Duhamel GE. Fatal outbreaks of proliferative enteritis caused by Lawsonia intracellularis in young colony-raised rhesus macaques.. J Med Primatol 1999;28:11.
    doi: 10.1111/j.1600-0684.1999.tb00084.xpubmed: 10372536google scholar: lookup
  3. Lawson GHK, Gebhart CJ. Proliferative enteropathy.. J Comp Pathol 2000;122:77–100.
    doi: 10.1053/jcpa.1999.0347pubmed: 10684678google scholar: lookup
  4. Pusterla N, Mapes S, Rejmanek D, Gebhart C. Detection of Lawsonia intracellularis by real-time PCR in the feces of free-living animals from equine farms with documented occurrence of equine proliferative enteropathy.. J Wildl Dis 2008;44:992.
    doi: 10.7589/0090-3558-44.4.992pubmed: 18957657google scholar: lookup
  5. Murakata K, Sato A, Yoshiya M, Kim S, Watarai M. Infection of different strains of mice with Lawsonia intracellularis derived from rabbit or porcine proliferative enteropathy.. J Comp Pathol 2008;139:8–15.
    doi: 10.1016/j.jcpa.2008.03.001pubmed: 18479698google scholar: lookup
  6. Rowland A, Rowntree P. A haemorrhagic bowel syndrome associated with intestinal adenomatosis in the pig.. Veterinary Record 1972;91:235–241.
    doi: 10.1136/vr.91.10.235pubmed: 4538678google scholar: lookup
  7. Shimizu C, Shibahara T, Takai S, Kasuya K, Chikuba T. Lawsonia intracellularis and virulent Rhodococcus equi infection in a thoroughbred Colt.. J Comp Pathol 2010;143:303–308.
    doi: 10.1016/j.jcpa.2010.03.005pubmed: 20471028google scholar: lookup
  8. Van Den Wollenberg L, Butler C, Houwers D, de Grootv M, Panhuijzen H. Lawsonia intracellularis-associated proliferative enteritis in weanling foals in the Netherlands.. Tijdschr Diergeneeskd 2011;136:565–570.
    pubmed: 22111417
  9. Pusterla N, Gebhart CJ. Equine proliferative enteropathy - a review of recent developments.. Equine Vet J 2013;45:403–409.
    doi: 10.1111/evj.12075pmc: PMC7163532pubmed: 23662705google scholar: lookup
  10. Pusterla N, Gebhart C. Equine proliferative enteropathy caused by Lawsonia intracellularis .. Equine Vet Educ 2009;21:415–419.
    doi: 10.2746/095777309X453119pmc: PMC7163693pubmed: 32313386google scholar: lookup
  11. Lavoie JP, Drolet R, Parsons D, Leguillette R, Sauvageau R. Equine proliferative enteropathy: a cause of weight loss, colic, diarrhoea and hypoproteinaemia in foals on three breeding farms in Canada.. Equine Vet J 2000;32:418–425.
    doi: 10.2746/042516400777591110pubmed: 11037264google scholar: lookup
  12. Pusterla N, Wattanaphansak S, Mapes S, Collier J, Hill J. Oral infection of weanling foals with an equine isolate of Lawsonia intracellularis, agent of equine proliferative enteropathy.. J Vet Intern Med 2010;24:622–627.
    doi: 10.1111/j.1939-1676.2010.0482.xpubmed: 20337907google scholar: lookup
  13. Vannucci FA, Pusterla N, Mapes SM, Gebhart C. Evidence of host adaptation in Lawsonia intracellularis infections.. Vet Res 2012;43:53.
    doi: 10.1186/1297-9716-43-53pmc: PMC3443049pubmed: 22715937google scholar: lookup
  14. Sampieri F, Vannucci FA, Allen AL, Pusterla N, Antonopoulos AJ. Species-Specificity of equine and porcine Lawsonia intracellularis isolates in laboratory animals.. Canadian Journal of Veterinary Research 2013;77:261–272.
    pmc: PMC3788657pubmed: 24124268
  15. Lawson GH, McOrist S, Jasni S, Mackie RA. Intracellular bacteria of porcine proliferative enteropathy: cultivation and maintenance in vitro .. J Clin Microbiol 1993;31:1136–1142.
    doi: 10.1128/JCM.31.5.1136-1142.1993pmc: PMC262892pubmed: 8501214google scholar: lookup
  16. Vannucci FA, Wattanaphansak S, Gebhart CJ. An alternative method for cultivation of Lawsonia intracellularis .. J Clin Microbiol 2012;50:1070–1072.
    doi: 10.1128/JCM.05976-11pmc: PMC3295169pubmed: 22219308google scholar: lookup
  17. Sait M, Aitchison K, Wheelhouse N, Wilson K, Lainson FA. Genome sequence of Lawsonia intracellularis strain N343, isolated from a sow with hemorrhagic proliferative enteropathy.. Genome Announc 2013;1:e00027–13.
    doi: 10.1128/genomeA.00027-13pmc: PMC3587925pubmed: 23472224google scholar: lookup
  18. Jacobson M, Aspan A, Königsson MH, Segerstad CHaf, Wallgren P. Routine diagnostics of Lawsonia intracellularis performed by PCR, serological and post mortem examination, with special emphasis on sample preparation methods for PCR.. Vet Microbiol 2004;102:189–201.
    doi: 10.1016/j.vetmic.2004.04.014pubmed: 15327794google scholar: lookup
  19. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data.. Bioinformatics 2014;30:2114–2120.
    doi: 10.1093/bioinformatics/btu170pmc: PMC4103590pubmed: 24695404google scholar: lookup
  20. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments.. Genome Biol 2014;15:R46.
    doi: 10.1186/gb-2014-15-3-r46pmc: PMC4053813pubmed: 24580807google scholar: lookup
  21. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.. Bioinformatics 2015;31:1674–1676.
    doi: 10.1093/bioinformatics/btv033pubmed: 25609793google scholar: lookup
  22. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.. Bioinformatics 2009;25:1754–1760.
    doi: 10.1093/bioinformatics/btp324pmc: PMC2705234pubmed: 19451168google scholar: lookup
  23. Kang DD, Froula J, Egan R, Wang Z, MetaBAT WZ. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.. PeerJ 2015;3:e1165.
    doi: 10.7717/peerj.1165pmc: PMC4556158pubmed: 26336640google scholar: lookup
  24. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.. Genome Res 2015;25:1043–1055.
    doi: 10.1101/gr.186072.114pmc: PMC4484387pubmed: 25977477google scholar: lookup
  25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.. Journal of Computational Biology 2012;19:455–477.
    doi: 10.1089/cmb.2012.0021pmc: PMC3342519pubmed: 22506599google scholar: lookup
  26. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies.. Bioinformatics 2013;29:1072–1075.
    doi: 10.1093/bioinformatics/btt086pmc: PMC3624806pubmed: 23422339google scholar: lookup
  27. Seemann T. Prokka: rapid prokaryotic genome annotation.. Bioinformatics 2014;30:2068–2069.
    doi: 10.1093/bioinformatics/btu153pubmed: 24642063google scholar: lookup
  28. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S. Roary: rapid large-scale prokaryote pan genome analysis.. Bioinformatics 2015;31:3691–3693.
    doi: 10.1093/bioinformatics/btv421pmc: PMC4817141pubmed: 26198102google scholar: lookup
  29. Seemann T. snippy: fast bacterial variant calling from NGS reads.. 2015.
  30. Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.. Bioinformatics 2015;32:btv566–4.
    doi: 10.1093/bioinformatics/btv566pmc: PMC4708105pubmed: 26428292google scholar: lookup
  31. Treangen TJ, Ondov BD, Koren S, Phillippy AM. The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.. Genome Biol 2014;15:524.
    doi: 10.1186/s13059-014-0524-xpmc: PMC4262987pubmed: 25410596google scholar: lookup
  32. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.. Bioinformatics 2012;28:464–469.
    doi: 10.1093/bioinformatics/btr703pmc: PMC3278759pubmed: 22199388google scholar: lookup
  33. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.. Nucleic Acids Res 2015;43:e15–e...
    doi: 10.1093/nar/gkᆖpmc: PMC4330336pubmed: 25414349google scholar: lookup
  34. Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM. Phandango: an interactive viewer for bacterial population genomics.. Bioinformatics 2018;34:292–293.
    doi: 10.1093/bioinformatics/btx610pmc: PMC5860215pubmed: 29028899google scholar: lookup
  35. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.. Mol Biol Evol 2015;32:268–274.
    doi: 10.1093/molbev/msu300pmc: PMC4271533pubmed: 25371430google scholar: lookup
  36. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates.. Nat Methods 2017;14:587.
    doi: 10.1038/nmeth.4285pmc: PMC5453245pubmed: 28481363google scholar: lookup
  37. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler.. Genome Res 2017;27:824–834.
    doi: 10.1101/gr.213959.116pmc: PMC5411777pubmed: 28298430google scholar: lookup
  38. Nishikawa S, Ogawa Y, Eguchi M, Rambukkana A, Shimoji Y. Draft genome sequences of Lawsonia intracellularis swine strains causing proliferative enteropathy in Japan.. Microbiol Resour Announc 2018;7:e01021–18.
    doi: 10.1128/MRA.01021-18pmc: PMC6256519pubmed: 30533927google scholar: lookup
  39. Vannucci FA, Kelley MR, Gebhart CJ. Comparative genome sequencing identifies a prophage-associated genomic island linked to host adaptation of Lawsonia intracellularis infections.. Vet Res 2013;44:49.
    doi: 10.1186/1297-9716-44-49pmc: PMC3716683pubmed: 23826661google scholar: lookup
  40. Vannucci FA, Foster DN, Gebhart CJ. Laser microdissection coupled with RNA-seq analysis of porcine enterocytes infected with an obligate intracellular pathogen (Lawsonia intracellularis). BMC Genomics 2013;14:421.
    doi: 10.1186/1471-2164-14-421pmc: PMC3718617pubmed: 23800029google scholar: lookup
  41. Achtman M, Wagner M. Microbial diversity and the genetic nature of microbial species.. Nat Rev Microbiol 2008;6:431.
    doi: 10.1038/nrmicro1872pubmed: 18461076google scholar: lookup
  42. Smith NH, Gordon SV, de la Rua-Domenech R, Clifton-Hadley RS, Hewinson RG. Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis .. Nat Rev Microbiol 2006;4:670.
    doi: 10.1038/nrmicro1472pubmed: 16912712google scholar: lookup
  43. Fèvre EM, Bronsvoort BMdeC, Hamilton KA, Cleaveland S. Animal movements and the spread of infectious diseases.. Trends Microbiol 2006;14:125–131.
    doi: 10.1016/j.tim.2006.01.004pmc: PMC7119069pubmed: 16460942google scholar: lookup
  44. Balka G, Podgórska K, Brar MS, Bálint Ádám, Cadar D. Genetic diversity of PRRSV 1 in central eastern Europe in 1994–2014: origin and evolution of the virus in the region.. Sci Rep 2018;8:7811.
    doi: 10.1038/s41598-018-26036-wpmc: PMC5958080pubmed: 29773820google scholar: lookup
  45. Gibbens JC, Wilesmith JW, Sharpe CE, Mansley LM, Michalopoulou E. Descriptive epidemiology of the 2001 foot-and-mouth disease epidemic in Great Britain: the first five months.. Veterinary Record 2001;149:729–743.
    doi: 10.1136/vr.149.24.729pubmed: 11808655google scholar: lookup
  46. Brown VR, Bevins SN. A review of classical swine fever virus and routes of introduction into the United States and the potential for virus establishment.. Frontiers in Veterinary Science 2018;5:31.
    doi: 10.3389/fvets.2018.00031pmc: PMC5844918pubmed: 29556501google scholar: lookup

Citations

This article has been cited 5 times.
  1. Hu Z, Lai R, Xu W, Guan R, Zhang Z, Yan G, Hao G. Establishment of a TaqMan Quantitative Real-Time PCR for Detecting Lawsonia intracellularis. Vet Sci 2025 May 8;12(5).
    doi: 10.3390/vetsci12050450pubmed: 40431543google scholar: lookup
  2. Yang HW, Hu T, Ait-Ali T. Lawsonia intracellularis regulates nuclear factor-κB signalling pathway during infection. PLoS One 2024;19(9):e0310804.
    doi: 10.1371/journal.pone.0310804pubmed: 39325775google scholar: lookup
  3. Suarez-Duarte ME, Santos RL, Pereira CER, Resende TP, Araujo MD, Correia PA, Barbosa JCR, Laub RP, Rodrigues DLN, Aburjaile FF, Guedes RMC. In Silico Evaluation of Lawsonia intracellularis Genes Orthologous to Genes Associated with Pathogenesis in Other Intracellular Bacteria. Microorganisms 2024 Aug 6;12(8).
    doi: 10.3390/microorganisms12081596pubmed: 39203437google scholar: lookup
  4. Wang L, Wu W, Zhao L, Zhu Z, Yao X, Fan J, Chen H, Song W, Huang X, Hua L, Qian P, Chen H, Peng Z, Wu B. Fecal PCR survey and genome analysis of Lawsonia intracellularis in China. Front Vet Sci 2024;11:1324768.
    doi: 10.3389/fvets.2024.1324768pubmed: 38384951google scholar: lookup
  5. Wencel P, Smith SH, Couck L, Hellebuyck T, Scott PC, McOrist S. Infection of juvenile falcons (Falco spp.) with intestinal Lawsonia intracellularis. Vet Med Sci 2023 Mar;9(2):744-747.
    doi: 10.1002/vms3.1063pubmed: 36639945google scholar: lookup
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