1887

Abstract

We report here the complete genome sequence of the widely studied serovar 8 reference strain 405, generated using the Pacific Biosciences (PacBio) RS II platform. Furthermore, we compared draft sequences generated by Illumina sequencing of six stocks of this strain, including the same original stock used to generate the PacBio sequence, held in different countries and found little genetic variation, with only three SNPs identified, all within the gene. However, sequences of two small plasmids, pARD3079 and p405tetH, detected by Illumina sequencing of the draft genomes were not identified in the PacBio sequence of the reference strain.

Funding
This study was supported by the:
  • Wellcome Trust (Award 098051)
    • Principle Award Recipient: MatthewT.G. Holden
  • National Natural Science Foundation of China (Award 31520103917)
    • Principle Award Recipient: LianchengLei
  • Biotechnology and Biological Sciences Research Council (Award BB/S005897/1)
    • Principle Award Recipient: PaulR. Langford
  • Biotechnology and Biological Sciences Research Council (Award BB/S002103/1)
    • Principle Award Recipient: PaulR. Langford
  • Biotechnology and Biological Sciences Research Council (Award BB/G020744/1)
    • Principle Award Recipient: AndrewN. Rycroft
  • Biotechnology and Biological Sciences Research Council (Award BB/G018553/1)
    • Principle Award Recipient: PaulR. Langford
  • Biotechnology and Biological Sciences Research Council (Award BB/G019274/1)
    • Principle Award Recipient: DuncanJ. Maskell
  • Biotechnology and Biological Sciences Research Council (Award BB/G019177/1)
    • Principle Award Recipient: BrendanW. Wren
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000687
2021-11-24
2024-05-29
Loading full text...

Full text loading...

/deliver/fulltext/mgen/7/11/mgen000687.html?itemId=/content/journal/mgen/10.1099/mgen.0.000687&mimeType=html&fmt=ahah

References

  1. Pattison IH, Howell DG, Elliot J. A Haemophilus-like organism isolated from pig lung and the associated pneumonic lesions. J Comp Pathol Ther 1957; 67:320–IN37 [View Article]
    [Google Scholar]
  2. Shope RE. Porcine contagious pleuropneumonia. I. Experimental transmission, etiology, and pathology. J Exp Med 1964; 119:357–368 [View Article] [PubMed]
    [Google Scholar]
  3. Kilian M, Nicolet J, Biberstein EL. Biochemical and serological characterization of Haemophilus pleuropneumoniae (Matthews and Pattison 1961) Shope 1964 and proposal of a neotype strain. Int J Syst Bacteriol 1978; 28:20–26 [View Article]
    [Google Scholar]
  4. Pohl S, Bertschinger HU, Frederiksen W, Mannheim W. Transfer of Haemophilus pleuropneumoniae and the Pasteurella haemolytica-Like organism causing porcine necrotic pleuropneumonia to the genus Actinobacillus (Actinobacillus pleuropneumoniae comb. nov.) on the basis of phenotypic and deoxyribonucleic acid relatedness. Int J Syst Bacteriol 1983; 33:510–514 [View Article]
    [Google Scholar]
  5. Bossé JT, Li Y, Sárközi R, Fodor L, Lacouture S et al. Proposal of serovars 17 and 18 of Actinobacillus pleuropneumoniae based on serological and genotypic analysis. Vet Microbiol 2018; 217:1–6 [View Article] [PubMed]
    [Google Scholar]
  6. Stringer OW, Bossé JT, Lacouture S, Gottschalk M, Fodor L. Proposal of Actinobacillus pleuropneumoniae serovar 19, and reformulation of previous multiplex PCRs for capsule-specific typing of all known serovars. Vet Microbiol 2021; 255:109021 [View Article] [PubMed]
    [Google Scholar]
  7. Sassu EL, Bossé JT, Tobias TJ, Gottschalk M, Langford PR. Update on Actinobacillus pleuropneumoniae-knowledge, gaps and challenges. Transbound Emerg Dis 2018; 65 Suppl 1:72–90 [View Article] [PubMed]
    [Google Scholar]
  8. Kim B, Hur J, Lee JY, Choi Y, Lee JH. Molecular serotyping and antimicrobial resistance profiles of Actinobacillus pleuropneumoniae isolated from pigs in South Korea. Vet Q 2016; 36:137–144 [View Article]
    [Google Scholar]
  9. Gottschalk M. The challenge of detecting herds sub-clinically infected with Actinobacillus pleuropneumoniae. Vet J 2015; 206:30–38 [View Article] [PubMed]
    [Google Scholar]
  10. Perry MB, Altman E, Brisson J-R, Beynon LM, Richards JC. Structural characteristics of the antigenic capsular polysaccharides and lipopolysaccharides involved in the serological classification of Actinobacillus (Haemophilus) pleuropneumoniae strains. Serodiagnosis and Immunotherapy in Infectious Disease 1990; 4:299–308 [View Article]
    [Google Scholar]
  11. Bossé JT, Li Y, Fernandez Crespo R, Lacouture S, Gottschalk M et al. Comparative sequence analysis of the capsular polysaccharide loci of Actinobacillus pleuropneumoniae serovars 1-18, and development of two multiplex PCRs for comprehensive capsule typing. Vet Microbiol 2018; 220:83–89 [View Article] [PubMed]
    [Google Scholar]
  12. Thomson J. Diagnostic tests for pleuropneumonia (Actinobacillus pleuropneumoniae); 2010 https://www.pig333.com/articles/diagnostic-tests-for-pleuropneumonia-actinobacillus-pleuropneumoniae_2497/
  13. Nielsen R, O’Connor PJ. Serological characterization of 8 Haemophilus pleuropneumoniae strains and proposal of a new serotype: serotype 8. Acta Vet Scand 1984; 25:96–106 [View Article] [PubMed]
    [Google Scholar]
  14. O’Neill C, Jones SCP, Bossé JT, Watson CM, Williamson SM et al. Prevalence of Actinobacillus pleuropneumoniae serovars in England and Wales. Vet Rec 2010; 167:661–662 [View Article] [PubMed]
    [Google Scholar]
  15. Li Y, Bossé JT, Williamson SM, Maskell DJ, Tucker AW et al. Actinobacillus pleuropneumoniae serovar 8 predominates in England and Wales. Vet Rec 2016; 179: [View Article] [PubMed]
    [Google Scholar]
  16. Cohen LM, Grøntvedt CA, Klem TB, Gulliksen SM, Ranheim B. A descriptive study of acute outbreaks of respiratory disease in Norwegian fattening pig herds. Acta Vet Scand 2020; 62:1–13 [View Article] [PubMed]
    [Google Scholar]
  17. Gottschalk M, Lacouture S. Actinobacillus pleuropneumoniae serotypes 3, 6, 8 and 15 isolated from diseased pigs in North America. Vet Rec 2014; 174:452 [View Article] [PubMed]
    [Google Scholar]
  18. Laboratório de Genética Molecular de Microrganismos, BIOAGRO, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil Rossi CC, Vicente AM, Guimarães WV, Fernandes de Araújo E. Face to face with Actinobacillus pleuropneumoniae: Landscape of the distribution of clinical isolates in Southeastern Brazil. Afr J Microbiol Res 2013; 7:2916–2924 [View Article]
    [Google Scholar]
  19. Gram T, Ahrens P. Improved diagnostic PCR assay for Actinobacillus pleuropneumoniae based on the nucleotide sequence of an outer membrane lipoprotein. J Clin Microbiol 1998; 36:443–448 [View Article] [PubMed]
    [Google Scholar]
  20. Bossé JT, Chaudhuri RR, Li Y, Leanse LG, Fernandez Crespo R. Complete genome sequence of MIDG2331, a genetically tractable serovar 8 clinical isolate of Actinobacillus pleuropneumoniae. Genome Announc 2016; 4:e01667-15 [View Article] [PubMed]
    [Google Scholar]
  21. Bossé JT, Li Y, Fernandez Crespo R, Chaudhuri RR, Rogers J. ICEApl1, an integrative conjugative element related to ICEHin1056, identified in the pig pathogen Actinobacillus pleuropneumoniae. Front Microbiol 2016; 7:810 [View Article] [PubMed]
    [Google Scholar]
  22. Foote SJ, Bossé JT, Bouevitch AB, Langford PR, Young NM. The complete genome sequence of Actinobacillus pleuropneumoniae L20 (serotype 5b). J Bacteriol 2008; 190:1495–1496 [View Article] [PubMed]
    [Google Scholar]
  23. Xu Z, Chen X, Li L, Li T, Wang S. Comparative genomic characterization of Actinobacillus pleuropneumoniae. J Bacteriol 2010; 192:5625–5636 [View Article] [PubMed]
    [Google Scholar]
  24. Zhan B, Angen Ø, Hedegaard J, Bendixen C, Panitz F. Draft genome sequences of Actinobacillus pleuropneumoniae serotypes 2 and 6. J Bacteriol 2010; 192:5846–5847 [View Article] [PubMed]
    [Google Scholar]
  25. Gram T, Ahrens P, Angen O. Two Actinobacillus pleuropneumoniae serotype 8 reference strains in circulation. J Clin Microbiol 2000; 38:468 [View Article] [PubMed]
    [Google Scholar]
  26. Cross LJ, Russell JE, Desai M. Examining the genetic variation of reference microbial cultures used within food and environmental laboratories using fluorescent amplified fragment length polymorphism analysis. FEMS Microbiol Lett 2011; 321:100–106 [View Article] [PubMed]
    [Google Scholar]
  27. Freddolino PL, Amini S, Tavazoie S. Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. J Bacteriol 2012; 194:303–306 [View Article] [PubMed]
    [Google Scholar]
  28. Bæk KT, Frees D, Renzoni A, Barras C, Rodriguez N. Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing. PLoS ONE 2013; 8:e77122 [View Article] [PubMed]
    [Google Scholar]
  29. Pascoe B, Williams LK, Calland JK, Meric G, Hitchings MD. Domestication of Campylobacter jejuni NCTC 11168. Microb Genom 2019; 5:e000279 [View Article] [PubMed]
    [Google Scholar]
  30. Spira B, de Almeida Toledo R, Maharjan RP, Ferenci T. The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example. BMC Microbiol 2011; 11:1–9 [View Article] [PubMed]
    [Google Scholar]
  31. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ et al. A large genome center’s improvements to the Illumina sequencing system. Nat Methods 2008; 5:1005–1010 [View Article] [PubMed]
    [Google Scholar]
  32. Howell KJ, Weinert LA, Luan S-L, Peters SE, Chaudhuri RR et al. Gene content and diversity of the loci encoding biosynthesis of capsular polysaccharides of the 15 serovar reference strains of Haemophilus parasuis. J Bacteriol 2013; 195:4264–4273 [View Article] [PubMed]
    [Google Scholar]
  33. Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 2018; 19:153 [View Article] [PubMed]
    [Google Scholar]
  34. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
    [Google Scholar]
  35. Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol 2015; 16:294 [View Article] [PubMed]
    [Google Scholar]
  36. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
    [Google Scholar]
  37. Sahl JW, Lemmer D, Travis J, Schupp JM, Gillece JD. NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb Genom 2016; 2:e000074 [View Article] [PubMed]
    [Google Scholar]
  38. Matter D, Rossano A, Sieber S, Perreten V. Small multidrug resistance plasmids in Actinobacillus porcitonsillarum. Plasmid 2008; 59:144–152 [View Article] [PubMed]
    [Google Scholar]
  39. Blanco M, Kadlec K, Gutiérrez Martín CB, de la Fuente AJM, Schwarz S. Nucleotide sequence and transfer properties of two novel types of Actinobacillus pleuropneumoniae plasmids carrying the tetracycline resistance gene tet(H). J Antimicrob Chemother 2007; 60:864–867 [View Article] [PubMed]
    [Google Scholar]
  40. Michael GB, Bossé JT, Schwarz S, Aarestrup FM, Schwarz S et al. Antimicrobial resistance in Pasteurellaceae of veterinary origin. Microbiol Spectr 2018; 6:1–33 [View Article]
    [Google Scholar]
  41. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V. The complete genome sequence of Escherichia coli K-12. Science 1997; 277:1453–1462 [View Article] [PubMed]
    [Google Scholar]
  42. Sakurai K, Kawasaki H. Genetic variation during long-term preservation of bacteria in public culture collections. Int J Syst Evol Microbiol 2018; 68:1815–1821 [View Article] [PubMed]
    [Google Scholar]
  43. Liu B, Eydallin G, Maharjan RP, Feng L, Wang L. Natural Escherichia coli isolates rapidly acquire genetic changes upon laboratory domestication. Microbiology 2017; 163:22–30 [View Article] [PubMed]
    [Google Scholar]
  44. Christensen H, Kuhnert P. International Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of Pasteurellaceae: minutes of the meetings, 25 August 2011, Elsinore, Denmark. Int J Syst Evol Microbiol 2012; 62:257–258 [View Article] [PubMed]
    [Google Scholar]
  45. Walsh NP, Alba BM, Bose B, Gross CA, Sauer RT. OMP peptide signals initiate the envelope-stress response by activating DegS protease via relief of inhibition mediated by its PDZ domain. Cell 2003; 113:61–71 [View Article] [PubMed]
    [Google Scholar]
  46. Sheehan BJ, Bossé JT, Beddek AJ, Rycroft AN, Kroll JS. Identification of Actinobacillus pleuropneumoniae genes important for survival during infection in its natural host. Infect Immun 2003; 71:3960–3970 [View Article] [PubMed]
    [Google Scholar]
  47. Bossé JT, Sinha S, Li M-S, O’Dwyer CA, Nash JHE. Regulation of pga operon expression and biofilm formation in Actinobacillus pleuropneumoniae by sigmaE and H-NS. J Bacteriol 2010; 192:2414–2423 [View Article] [PubMed]
    [Google Scholar]
  48. Antenucci F, Fougeroux C, Bossé JT, Magnowska Z, Roesch C. Identification and characterization of serovar-independent immunogens in Actinobacillus pleuropneumoniae. Vet Res 2017; 48:74 [View Article] [PubMed]
    [Google Scholar]
  49. Zeth K. Structural analysis of DegS, a stress sensor of the bacterial periplasm. FEBS Lett 2004; 569:351–358 [View Article] [PubMed]
    [Google Scholar]
  50. Quail MA, Smith M, Coupland P, Otto TD, Harris SR. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012; 13:1–13 [View Article] [PubMed]
    [Google Scholar]
  51. Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME. Opportunities and challenges in long-read sequencing data analysis. Genome Biol 2020; 21:30 [View Article] [PubMed]
    [Google Scholar]
  52. Juraschek K, Borowiak M, Tausch SH, Malorny B, Käsbohrer A. Outcome of different sequencing and assembly approaches on the detection of plasmids and localization of antimicrobial resistance genes in commensal Escherichia coli. Microorganisms 2021; 9:598 [View Article] [PubMed]
    [Google Scholar]
  53. Arredondo-Alonso S, Willems RJ, van Schaik W, Schürch AC. On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data. Microb Genom 2017; 3:e000128 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000687
Loading
/content/journal/mgen/10.1099/mgen.0.000687
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error