Skip to main content
SpringerLink
Log in

Multilocus Sequence Typing (MLST) of Chlamydiales

  • Protocol
  • First Online:
Chlamydia trachomatis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2042))

Abstract

Developed two decades ago as a molecular method to provide definite characterization of a bacterial isolate, Multilocus Sequence Typing (MLST) is today globally adopted as a universal fine-detailed molecular typing tool and has been applied to numerous pathogenic and nonpathogenic bacterial as well eukaryotic organisms. MLST utilizes DNA sequence of several conserved housekeeping (HK) genes which are assigned an allelic number, which then collectively constitute an allelic profile or sequence type (ST), a “molecular barcode” of the interrogated bacterial strain or a eukaryotic organism. Here, we describe the principles and molecular approaches for generating MLST data for an analysis of a bacteria in the order Chlamydiales, using a Chlamydia pecorum-specific MLST scheme as an example.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Taylor-Brown A, Vaughan L, Greub G, Timms P, Polkinghorne A (2015) Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae. Path Dis 73:1–15

    Article  CAS  Google Scholar 

  2. Pillonel T, Bertelli C, Greub G (2018) Environmental metagenomic assemblies reveal seven new highly divergent chlamydial lineages and hallmarks of a conserved intracellular lifestyle. Front Microbiol 9:79

    Article  Google Scholar 

  3. Staub E, Marti H, Biondi R, Levi A, Donati M, Leonard CA et al (2018) Novel Chlamydia species isolated from snakes are temperature-sensitive and exhibit decreased susceptibility to azithromycin. Sci Rep 8:5660

    Article  Google Scholar 

  4. Bachmann NL, Polkinghorne A, Timms P (2014) Chlamydia genomics: providing novel insights into chlamydial biology. Trends Microbiol 22:464–472

    Article  CAS  Google Scholar 

  5. Ziklo N, Huston WM, Hocking JS, Timms P (2016) Chlamydia trachomatis genital tract infections: when host immune response and the microbiome collide. Trends Microbiol 24:750–765

    Article  CAS  Google Scholar 

  6. Taylor HR, Burton MJ, Haddad D, West S, Wright H (2014) Trachoma. Lancet 384:2142–2152

    Article  Google Scholar 

  7. Roulis E, Polkinghorne A, Timms P (2013) Chlamydia pneumoniae: modern insights into an ancient pathogen. Trends Microbiol 21:120–128

    Article  CAS  Google Scholar 

  8. Rodolakis A, Laroucau K (2015) Chlamydiaceae and chlamydial infections in sheep or goats. Vet Microbiol 181:107–118

    Article  CAS  Google Scholar 

  9. Knittler MR, Sachse K (2015) Chlamydia psittaci: update on an underestimated zoonotic agent. Path Dis 73:1–15

    Article  CAS  Google Scholar 

  10. Jelocnik M, Branley J, Heller J, Raidal S, Alderson S, Galea F et al (2017) Multilocus sequence typing identifies an avian-like Chlamydia psittaci strain involved in equine placentitis and associated with subsequent human psittacosis. Emerg Microbes Infect 6:e7

    Article  CAS  Google Scholar 

  11. Polkinghorne A, Hanger J, Timms P (2013) Recent advances in understanding the biology, epidemiology and control of chlamydial infections in koalas. Vet Microbiol 165:214–223

    Article  Google Scholar 

  12. Walker E, Lee EJ, Timms P, Polkinghorne A (2015) Chlamydia pecorum infections in sheep and cattle: A common and under-recognised infectious disease with significant impact on animal health. Vet J 206:252–260

    Article  Google Scholar 

  13. Sachse K, Laroucau K, Riege K, Wehner S, Dilcher M, Creasy HH et al (2014) Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov. Syst Appl Microbiol 37:79–88

    Article  Google Scholar 

  14. Taylor-Brown A, Polkinghorne A (2017) New and emerging chlamydial infections of creatures great and small. New Microbes New Infect 18:28–33

    Article  CAS  Google Scholar 

  15. Taylor-Brown A, Spang L, Borel N, Polkinghorne A (2017) Culture-independent metagenomics supports discovery of uncultivable bacteria within the genus Chlamydia. Sci Rep 7:10661

    Article  Google Scholar 

  16. Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R et al (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–3145

    Article  CAS  Google Scholar 

  17. Maiden MCJ (2006) Multilocus sequence typing of bacteria. Annu Rev Microbiol 60:561–588

    Article  CAS  Google Scholar 

  18. Maiden MCJ, van Rensburg MJJ, Bray JE, Earle SG, Ford SA, Jolley KA et al (2013) MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 11:728–736

    Article  CAS  Google Scholar 

  19. Pérez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA (2013) Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect Genet Evol 16:38–53

    Article  Google Scholar 

  20. Jolley K, Maiden M (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595

    Article  Google Scholar 

  21. Maiden MCJ, Harrison OB (2016) Population and functional genomics of the Neisseria revealed with gene-by-gene approaches. J Clin Microbiol 54:1949–1955

    Article  CAS  Google Scholar 

  22. Pannekoek Y, Morelli G, Kusecek B, Morre S, Ossewaarde J, Langerak A et al (2008) Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis. BMC Microbiol 8:42

    Article  Google Scholar 

  23. Pannekoek Y, Dickx V, Beeckman DSA, Jolley KA, Keijzers WC, Vretou E et al (2010) Multi Locus sequence typing of Chlamydia reveals an association between Chlamydia psittaci genotypes and host species. PLoS One 5:e14179

    Article  CAS  Google Scholar 

  24. Jelocnik M, Frentiu FD, Timms P, Polkinghorne A (2013) Multi-locus sequence analysis provides insights into the molecular epidemiology of Chlamydia pecorum infections in Australian sheep, cattle and koalas. J Clin Microbiol 51:2625–2632

    Article  CAS  Google Scholar 

  25. Guo W, Jelocnik M, Li J, Sachse K, Polkinghorne A, Pannekoek Y et al (2017) From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen. BMC Genomics 18:949

    Article  Google Scholar 

  26. Versteeg B, Bruisten SM, Pannekoek Y, Jolley KA, Maiden MCJ, van der Ende A, Harrison OB (2018) Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease. BMC Genomics 19(1):130

    Article  Google Scholar 

  27. Li M, Jelocnik M, Yang F, Gong J, Kaltenboeck B, Polkinghorne A et al (2017) Asymptomatic infections with highly polymorphic Chlamydia suis are ubiquitous in pigs. BMC Vet Res 13:370

    Article  Google Scholar 

  28. Jelocnik M, Walker E, Pannekoek Y, Ellem J, Timms P, Polkinghorne A (2014) Evaluation of the relationship between Chlamydia pecorum sequence types and disease using a species-specific multi-locus sequence typing scheme (MLST). Vet Microbiol 174:214–222

    Article  CAS  Google Scholar 

  29. Jelocnik M, Self R, Timms P, Borel N, Polkinghorne A (2015) Novel sequence types of Chlamydia pecorum infect free-ranging Alpine ibex (Capra ibex) and red deer (Cervus elaphus) in Switzerland. J Wildl Dis 51:479–483

    Article  Google Scholar 

  30. Lorenz TC (2012) Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies. J Vis Exp 63:3998

    Google Scholar 

  31. Lee PY, Costumbrado J, Hsu C-Y, Kim YH (2012) Agarose gel electrophoresis for the separation of DNA fragments. J Vis Exp 62:3923

    Google Scholar 

  32. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S et al (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

    Article  Google Scholar 

  33. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739

    Article  CAS  Google Scholar 

  34. Sanchez-Villeda H, Schroeder S, Flint-Garcia S, Guill KE, Yamasaki M, McMullen MD (2008) DNAAlignEditor: DNA alignment editor tool. BMC Bioinformatics 9:154–154

    Article  Google Scholar 

  35. Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ, Tomita T et al (2014) SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 6:90

    Article  Google Scholar 

  36. Jolley KA, Maiden MCJ (2013) Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar. Euro Surveill 18:20379–20379

    Article  CAS  Google Scholar 

  37. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  Google Scholar 

  38. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113

    Article  Google Scholar 

  39. Librado P, Rozas J (2009) Dna SP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  CAS  Google Scholar 

  40. Francisco A, Bugalho M, Ramirez M, Carrico J (2009) Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics 10:152

    Article  Google Scholar 

  41. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772–772

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia

    Martina Jelocnik

  2. Department of Microbiology and Infectious Diseases, Nepean Hospital, NSW Health Pathology, Penrith, NSW, Australia

    Adam Polkinghorne

  3. Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands

    Yvonne Pannekoek

Authors
  1. Martina Jelocnik
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Adam Polkinghorne
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yvonne Pannekoek
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yvonne Pannekoek .

Editor information

Editors and Affiliations

  1. Department of Microbiology and Immunology, Vet School, Cornell University, Ithaca, NY, USA

    Amanda Claire Brown

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Jelocnik, M., Polkinghorne, A., Pannekoek, Y. (2019). Multilocus Sequence Typing (MLST) of Chlamydiales. In: Brown, A. (eds) Chlamydia trachomatis. Methods in Molecular Biology, vol 2042. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9694-0_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9694-0_7

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9693-3

  • Online ISBN: 978-1-4939-9694-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation