FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / PLoS One / Molecular analysis of the chromosomal 16S rRNA gene and vapA...
PloS one2018; 13(9); e0204024; doi: 10.1371/journal.pone.0204024

Molecular analysis of the chromosomal 16S rRNA gene and vapA plasmid gene of Polish field strains of R. equi.

Abstract: Rhodococcus equi (R. hoagii) is an opportunistic pathogen commonly found in foals up to 6 months old and animal environment. The R. equi genome contains genetically stable chromosomal DNA and an 80-90 kb plasmid containing vapA gene, responsible for virulence. Most reports from around the world focus on the determination of R. equi plasmid profiles. Few studies have attempted to determine differences in nucleotide sequences between virulent strains of R. equi isolated from foals and breeding environment. The aim of the study was to perform a molecular analysis of a fragment of the chromosomal gene encoding the 16S rRNA subunit and the vapA plasmid gene of virulent R. equi strains isolated on Polish studs from foals and from the breeding environment of horses. The sequencing method was used to compare the primary structure of fragments of the chromosomal and plasmid DNA of the virulent R. equi strains. The sequences of 22 clinical and 18 environmental R. equi isolates were compared with the sequences of the gene fragments of reference strains available in the NCBI GenBank database. All sequenced 16S rRNA amplicons of Polish field strains were identical and showed 99.5% similarity to the four randomly selected sequences of this gene fragment in the GenBank database. The results confirm that fragments of the 16S rRNA gene of R. equi strains are highly conserved and do not undergo variation in field conditions. Analysis of the sequencing results for the vapA gene fragment of the strains used in our study revealed two polymorphic variants and clear differences between the sequences of strains isolated from foals and from soil samples. Presumably, R. equi strains present in the breeding environment are more exposed than clinical strains to adverse external factors. This may result in changes in the DNA sequence due to natural selection.
Get Full Text
Publication Date: 2018-09-25 PubMed ID: 30252885PubMed Central: PMC6155501DOI: 10.1371/journal.pone.0204024Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article

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 examines the genetic structure of Rhodococcus equi, a common pathogen found in young foals and their environments. It discovers that there’s a great deal of similarity in the 16S rRNA gene but noticeable variation in the vapA gene, which may be due to different environmental pressures.

Research Background

  • Rhodococcus equi, also known as R. hoagii, is a pathogen that often affects foals that are six months old or younger. It can also be present in their surroundings.
  • The genome of R. equi contains two key components: stable chromosomal DNA and an 80-90 kb plasmid that houses the vapA gene, crucial for making the organism dangerous to its hosts.
  • Previous research has mostly focused on the plasmid profile of R. equi, with fewer studies examining the nucleotide sequences of virulent strains from foals and their breeding environment.

Research Aim and Methodology

  • The researchers aimed to perform a thorough molecular analysis of the 16S rRNA chromosomal gene and vapA plasmid gene in harmful R. equi strains. These strains were isolated from Polish studs, both directly from foals and their breeding environments.
  • Sequencing methods were used to compare the primary structure of the chromosomal and plasmid DNA fragments.
  • A total of 40 sequences were compared, including 22 strains from clinical instances and 18 from environmental samples. The gene fragments of these strains were compared to reference strains obtained from the GenBank database of the National Center for Biotechnology Information (NCBI).

Results and Findings

  • All the sequenced 16S rRNA genes from the Polish field strains were identical and closely matched the sequences of the gene fragment in GenBank, with 99.5% similarity.
  • It was found that the 16S rRNA gene fragments in R.equi strains are habitually conserved and do not exhibit any variation under field circumstances.
  • The vapA gene demonstrated two polymorphic variants, with clear differences noted between the strains from foals and the strains from soil samples.

Interpretation and Conclusion

  • The authors suggest that the contrasting level of variation between the 16S rRNA and vapA genes could be due to the different environmental pressures facing the strains. The strains found in the breeding environment may encounter more adverse factors, leading to changes in the DNA sequence due to natural selection.

Cite This Article

APA
Kalinowski M, Grądzki Z, Jarosz Ł, Adaszek Ł. (2018). Molecular analysis of the chromosomal 16S rRNA gene and vapA plasmid gene of Polish field strains of R. equi. PLoS One, 13(9), e0204024. https://doi.org/10.1371/journal.pone.0204024

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 13
Issue: 9
Pages: e0204024
PII: e0204024

Researcher Affiliations

Kalinowski, Marcin
  • Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland.
Grądzki, Zbigniew
  • Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland.
Jarosz, Łukasz
  • Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland.
Adaszek, Łukasz
  • Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland.

MeSH Terms

  • Actinomycetales Infections / microbiology
  • Actinomycetales Infections / veterinary
  • Animals
  • Chromosomes, Bacterial / genetics
  • Genes, Bacterial / genetics
  • Horse Diseases / microbiology
  • Horses
  • Plasmids / genetics
  • Poland
  • Polymerase Chain Reaction / veterinary
  • RNA, Ribosomal, 16S / genetics
  • Rhodococcus equi / genetics
  • Rhodococcus equi / isolation & purification
  • Sequence Analysis, DNA / veterinary

Conflict of Interest Statement

The authors have declared that no competing interests exist.

References

This article includes 40 references
  1. Kämpfer P, Dott W, Martin K, Glaeser SP. Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov.. Int J Syst Evol Microbiol 2014 Mar;64(Pt 3):755-761.
    doi: 10.1099/ijs.0.053322-0pubmed: 24198057google scholar: lookup
  2. von Bargen K, Haas A. Molecular and infection biology of the horse pathogen Rhodococcus equi.. FEMS Microbiol Rev 2009 Sep;33(5):870-91.
    doi: 10.1111/j.1574-6976.2009.00181.xpubmed: 19453748google scholar: lookup
  3. Duquesne F, Hébert L, Sévin C, Breuil MF, Tapprest J, Laugier C, Petry S. Analysis of plasmid diversity in 96 Rhodococcus equi strains isolated in Normandy (France) and sequencing of the 87-kb type I virulence plasmid.. FEMS Microbiol Lett 2010 Oct;311(1):76-81.
    doi: 10.1111/j.1574-6968.2010.02070.xpubmed: 20707817google scholar: lookup
  4. Giguère S, Cohen ND, Chaffin MK, Hines SA, Hondalus MK, Prescott JF, Slovis NM. Rhodococcus equi: clinical manifestations, virulence, and immunity.. J Vet Intern Med 2011 Nov-Dec;25(6):1221-30.
    doi: 10.1111/j.1939-1676.2011.00804.xpubmed: 22092609google scholar: lookup
  5. Muscatello G, Leadon DP, Klayt M, Ocampo-Sosa A, Lewis DA, Fogarty U, Buckley T, Gilkerson JR, Meijer WG, Vazquez-Boland JA. Rhodococcus equi infection in foals: the science of 'rattles'.. Equine Vet J 2007 Sep;39(5):470-8.
    pubmed: 17910275doi: 10.2746/042516407x209217google scholar: lookup
  6. Prescott JF. Rhodococcus equi: an animal and human pathogen.. Clin Microbiol Rev 1991 Jan;4(1):20-34.
    pmc: PMC358176pubmed: 2004346doi: 10.1128/cmr.4.1.20google scholar: lookup
  7. Darraj M, Fainstein R, Kasper K, Keynan Y. Immune Reconstitution Syndrome secondary to Rhodococcus equi infection in a patient with HIV and Burkitt's lymphoma.. J Infect Public Health 2017 Mar-Apr;10(2):224-227.
    doi: 10.1016/j.jiph.2016.05.001pubmed: 27373968google scholar: lookup
  8. Kalinowski M, Grądzki Z, Jarosz Ł, Adaszek Ł. Rodokokoza jako zoonoza. Med Weter 2013;69: 139–144.
  9. Topino S, Galati V, Grilli E, Petrosillo N. Rhodococcus equi infection in HIV-infected individuals: case reports and review of the literature.. AIDS Patient Care STDS 2010 Apr;24(4):211-22.
    doi: 10.1089/apc.2009.0248pubmed: 20377432google scholar: lookup
  10. Vázquez-Boland JA, Giguère S, Hapeshi A, MacArthur I, Anastasi E, Valero-Rello A. Rhodococcus equi: the many facets of a pathogenic actinomycete.. Vet Microbiol 2013 Nov 29;167(1-2):9-33.
    doi: 10.1016/j.vetmic.2013.06.016pubmed: 23993705google scholar: lookup
  11. Yamshchikov AV, Schuetz A, Lyon GM. Rhodococcus equi infection.. Lancet Infect Dis 2010 May;10(5):350-9.
    doi: 10.1016/S1473-3099(10)70068-2pubmed: 20417417google scholar: lookup
  12. Letek M, González P, Macarthur I, Rodríguez H, Freeman TC, Valero-Rello A, Blanco M, Buckley T, Cherevach I, Fahey R, Hapeshi A, Holdstock J, Leadon D, Navas J, Ocampo A, Quail MA, Sanders M, Scortti MM, Prescott JF, Fogarty U, Meijer WG, Parkhill J, Bentley SD, Vázquez-Boland JA. The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.. PLoS Genet 2010 Sep 30;6(9):e1001145.
    doi: 10.1371/journal.pgen.1001145pmc: PMC2947987pubmed: 20941392google scholar: lookup
  13. Takai S, Koike K, Ohbushi S, Izumi C, Tsubaki S. Identification of 15- to 17-kilodalton antigens associated with virulent Rhodococcus equi.. J Clin Microbiol 1991 Mar;29(3):439-43.
    pmc: PMC269796pubmed: 2037660doi: 10.1128/jcm.29.3.439-443.1991google scholar: lookup
  14. Takai S, Sekizaki T, Ozawa T, Sugawara T, Watanabe Y, Tsubaki S. Association between a large plasmid and 15- to 17-kilodalton antigens in virulent Rhodococcus equi.. Infect Immun 1991 Nov;59(11):4056-60.
    pmc: PMC258996pubmed: 1937765doi: 10.1128/iai.59.11.4056-4060.1991google scholar: lookup
  15. Letek M, Ocampo-Sosa AA, Sanders M, Fogarty U, Buckley T, Leadon DP, González P, Scortti M, Meijer WG, Parkhill J, Bentley S, Vázquez-Boland JA. Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids.. J Bacteriol 2008 Sep;190(17):5797-805.
    doi: 10.1128/JB.00468-08pmc: PMC2519538pubmed: 18606735google scholar: lookup
  16. Bell KS, Philp JC, Christofi N, Aw DW. Identification of Rhodococcus equi using the polymerase chain reaction.. Lett Appl Microbiol 1996 Aug;23(2):72-4.
    pubmed: 8987445doi: 10.1111/j.1472-765x.1996.tb00033.xgoogle scholar: lookup
  17. Grądzki Z, Ziętek-Barszcz A. Suitability of PCR and culture for antemortem diagnosis of rhodococcosis in foals. Med Weter 2011;67: 327–331.
  18. Sellon DC, Walker K, Suyemoto M, Altier C. Nucleic acid amplification for rapid detection of Rhodococcus equi in equine blood and tracheal wash fluids.. Am J Vet Res 1997 Nov;58(11):1232-7.
    pubmed: 9361884
  19. Sellon DC, Besser TE, Vivrette SL, McConnico RS. Comparison of nucleic acid amplification, serology, and microbiologic culture for diagnosis of Rhodococcus equi pneumonia in foals.. J Clin Microbiol 2001 Apr;39(4):1289-93.
    doi: 10.1128/JCM.39.4.1289-1293.2001pmc: PMC87926pubmed: 11283043google scholar: lookup
  20. Meijer WG, Prescott JF. Rhodococcus equi.. Vet Res 2004 Jul-Aug;35(4):383-96.
    doi: 10.1051/vetres:2004024pubmed: 15236672google scholar: lookup
  21. Rofe AP, Davis LJ, Whittingham JL, Latimer-Bowman EC, Wilkinson AJ, Pryor PR. The Rhodococcus equi virulence protein VapA disrupts endolysosome function and stimulates lysosome biogenesis.. Microbiologyopen 2017 Apr;6(2).
    doi: 10.1002/mbo3.416pmc: PMC5387311pubmed: 27762083google scholar: lookup
  22. Coulson GB, Miranda-CasoLuengo AA, Miranda-CasoLuengo R, Wang X, Oliver J, Willingham-Lane JM, Meijer WG, Hondalus MK. Transcriptome reprogramming by plasmid-encoded transcriptional regulators is required for host niche adaption of a macrophage pathogen.. Infect Immun 2015 Aug;83(8):3137-45.
    doi: 10.1128/IAI.00230-15pmc: PMC4496601pubmed: 26015480google scholar: lookup
  23. Sanz MG, Villarino N, Ferreira-Oliveira A, Horohov DW. VapA-specific IgG and IgG subclasses responses after natural infection and experimental challenge of foals with Rhodococcus equi.. Vet Immunol Immunopathol 2015 Mar 15;164(1-2):10-5.
    doi: 10.1016/j.vetimm.2015.01.004pubmed: 25681111google scholar: lookup
  24. Willingham-Lane JM, Berghaus LJ, Giguère S, Hondalus MK. Influence of Plasmid Type on the Replication of Rhodococcus equi in Host Macrophages.. mSphere 2016 Sep-Oct;1(5).
    doi: 10.1128/mSphere.00186-16pmc: PMC5061997pubmed: 27747295google scholar: lookup
  25. Coulson GB, Agarwal S, Hondalus MK. Characterization of the role of the pathogenicity island and vapG in the virulence of the intracellular actinomycete pathogen Rhodococcus equi.. Infect Immun 2010 Aug;78(8):3323-34.
    doi: 10.1128/IAI.00081-10pmc: PMC2916281pubmed: 20439471google scholar: lookup
  26. Giguère S, Hondalus MK, Yager JA, Darrah P, Mosser DM, Prescott JF. Role of the 85-kilobase plasmid and plasmid-encoded virulence-associated protein A in intracellular survival and virulence of Rhodococcus equi.. Infect Immun 1999 Jul;67(7):3548-57.
    pmc: PMC116543pubmed: 10377138doi: 10.1128/iai.67.7.3548-3557.1999google scholar: lookup
  27. Son WG, Lee DS, Yamatoda N, Hatori F, Shimizu N, Kakuda T, Sasaki Y, Tsubaki S, Takai S. Molecular typing of VapA-positive Rhodococcus equi isolates from Jeju native horses, Korea.. J Vet Med Sci 2006 Mar;68(3):249-53.
    pubmed: 16598168doi: 10.1292/jvms.68.249google scholar: lookup
  28. Takai S, Shoda M, Sasaki Y, Tsubaki S, Fortier G, Pronost S, Rahal K, Becu T, Begg A, Browning G, Nicholson VM, Prescott JF. Restriction fragment length polymorphisms of virulence plasmids in Rhodococcus equi.. J Clin Microbiol 1999 Oct;37(10):3417-20.
    pmc: PMC85590pubmed: 10488224doi: 10.1128/jcm.37.10.3417-3420.1999google scholar: lookup
  29. Takai S, Chaffin MK, Cohen ND, Hara M, Nakamura M, Kakuda T, Sasaki Y, Tsubaki S, Martens RJ. Prevalence of virulent Rhodococcus equi in soil from five R. equi-endemic horse-breeding farms and restriction fragment length polymorphisms of virulence plasmids in isolates from soil and infected foals in Texas.. J Vet Diagn Invest 2001 Nov;13(6):489-94.
    doi: 10.1177/104063870101300606pubmed: 11724139google scholar: lookup
  30. Takai S, Henton MM, Picard JA, Guthrie AJ, Fukushi H, Sugimoto C. Prevalence of virulent Rhodococcus equi in isolates from soil collected from two horse farms in South Africa and restriction fragment length polymorphisms of virulence plasmids in the isolates from infected foals, a dog and a monkey.. Onderstepoort J Vet Res 2001 Jun;68(2):105-10.
    pubmed: 11585087
  31. Takai S, Son WG, Lee DS, Madarame H, Seki I, Yamatoda N, Kimura A, Kakuda T, Sasaki Y, Tsubaki S, Lim YK. Rhodococcus equi virulence plasmids recovered from horses and their environment in Jeju, Korea: 90-kb type II and a new variant, 90-kb type V.. J Vet Med Sci 2003 Dec;65(12):1313-7.
    pubmed: 14709819doi: 10.1292/jvms.65.1313google scholar: lookup
  32. Rahal K, Kodjo A, Gretzel D, Richard Y. Isolation of a new type of virulence plasmid DNA in Rhodococcus equi strains from horses and equine environments in France. Rev Med Vet 1999;150: 349–352.
  33. Kalinowski M, Grądzki Z, Jarosz Ł, Kato K, Hieda Y, Kakuda T, Takai S. Plasmid Profiles of Virulent Rhodococcus equi Strains Isolated from Infected Foals in Poland.. PLoS One 2016;11(4):e0152887.
    doi: 10.1371/journal.pone.0152887pmc: PMC4830601pubmed: 27074033google scholar: lookup
  34. Witkowski L, Rzewuska M, Takai S, Chrobak-Chmiel D, Kizerwetter-Świda M, Feret M, Gawryś M, Witkowski M, Kita J. Molecular characterization of Rhodococcus equi isolates from horses in Poland: pVapA characteristics and plasmid new variant, 85-kb type V.. BMC Vet Res 2017 Jan 26;13(1):35.
    doi: 10.1186/s12917-017-0954-2pmc: PMC5267371pubmed: 28122544google scholar: lookup
  35. Ziętek-Barszcz A, Grądzki Z. Optimisation of the DNA extraction method from foal faeces for the diagnosis of Rhodococcus equi infections using PCR. Bull Vet Inst Pulawy 2009;53: 345–349.
  36. Grądzki Z, Ziętek-Barszcz A. Detection of Rhodococcus equi in tracheobronchial aspirate of foals in enzootic farms depending on age and season. Bull Vet Inst Pulawy 2011;55: 619–624.
  37. Pilares L, Agüero J, Vázquez-Boland JA, Martínez-Martínez L, Navas J. Identification of atypical Rhodococcus-like clinical isolates as Dietzia spp. by 16S rRNA gene sequencing.. J Clin Microbiol 2010 May;48(5):1904-7.
    doi: 10.1128/JCM.01730-09pmc: PMC2863862pubmed: 20220156google scholar: lookup
  38. Coenye T, Vandamme P. Diversity and significance of Burkholderia species occupying diverse ecological niches.. Environ Microbiol 2003 Sep;5(9):719-29.
    pubmed: 12919407doi: 10.1046/j.1462-2920.2003.00471.xgoogle scholar: lookup
  39. Makrai L, Takai S, Tamura M, Tsukamoto A, Sekimoto R, Sasaki Y, Kakuda T, Tsubaki S, Varga J, Fodor L, Solymosi N, Major A. Characterization of virulence plasmid types in Rhodococcus equi isolates from foals, pigs, humans and soil in Hungary.. Vet Microbiol 2002 Sep 24;88(4):377-84.
    pubmed: 12220812doi: 10.1016/s0378-1135(02)00157-8google scholar: lookup
  40. Takai S, Hines SA, Sekizaki T, Nicholson VM, Alperin DA, Osaki M, Takamatsu D, Nakamura M, Suzuki K, Ogino N, Kakuda T, Dan H, Prescott JF. DNA sequence and comparison of virulence plasmids from Rhodococcus equi ATCC 33701 and 103.. Infect Immun 2000 Dec;68(12):6840-7.
    pmc: PMC97788pubmed: 11083803doi: 10.1128/iai.68.12.6840-6847.2000google scholar: lookup

Citations

This article has been cited 1 times.
  1. Khan N, Martínez-Hidalgo P, Humm EA, Maymon M, Kaplan D, Hirsch AM. Inoculation With a Microbe Isolated From the Negev Desert Enhances Corn Growth. Front Microbiol 2020;11:1149.
    doi: 10.3389/fmicb.2020.01149pubmed: 32636811google scholar: lookup
Subscribe to our newsletter
Join 99,357 horse owners like you who receive our email updates on horse health and nutrition.