Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis.

Microbial Genomics
Floriana GonaDaniela Maria Cirillo

Abstract

In this work we compared the most frequently used Klebsiella pneumoniae typing methods: PFGE, cgMLST and coreSNP. We evaluated the discriminatory power of the three methods to confirm or exclude nosocomial transmission on K. pneumoniae strains isolated from January to December 2017, in the framework of the routine surveillance for multidrug-resistant organisms at the San Raffaele Hospital, in Milan. We compared the results of the different methods to the results of epidemiological investigation. Our results showed that cgMLST and coreSNP are more discriminant than PFGE, and that both approaches are suitable for transmission analyses. cgMLST appeared to be inferior to coreSNP in the K. pneumoniae CG258 phylogenetic reconstruction. Indeed, we found that the phylogenetic reconstruction based on cgMLST genes wrongly clustered ST258 clade1 and clade2 strains, conversely properly assigned by coreSNP approach. In conclusion, this study provides evidences supporting the reliability of both cgMLST and coreSNP for hospital surveillance programs and highlights the limits of cgMLST scheme genes for phylogenetic reconstructions.

References

Nov 27, 1998·Memórias do Instituto Oswaldo Cruz·M J Struelens
Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Aug 6, 2005·Journal of Clinical Microbiology·Laure DiancourtSylvain Brisse
Sep 18, 2009·Journal of Clinical Microbiology·Tommaso GianiGian Maria Rossolini
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
May 15, 2013·The Journal of Antimicrobial Chemotherapy·Maria Lina MezzatestaStefania Stefani
Aug 24, 2013·The Lancet Infectious Diseases·L Silvia Munoz-PriceJohn P Quinn
Aug 28, 2013·Nature Reviews. Microbiology·Martin C J MaidenNoel D McCarthy
Oct 8, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sergey NurkPavel A Pevzner
Mar 19, 2014·Proceedings of the National Academy of Sciences of the United States of America·Frank R DeleoBarry N Kreiswirth
May 3, 2014·Journal of Clinical Microbiology·Thomas A KohlStefan Niemann
Jun 11, 2014·Antimicrobial Agents and Chemotherapy·Meredith S WrightMark D Adams
Jun 26, 2014·MBio·Liang ChenBarry N Kreiswirth
Oct 12, 2014·Trends in Microbiology·Liang ChenBarry N Kreiswirth
Oct 24, 2014·Emerging Infectious Diseases·Suzanne Bialek-DavenetSylvain Brisse
Apr 23, 2015·The Journal of Antimicrobial Chemotherapy·Mario TumbarelloUNKNOWN ISGRI-SITA (Italian Study Group on Resistant Infections of the Società Italiana Terapia Antinfettiva)
Jun 24, 2015·Proceedings of the National Academy of Sciences of the United States of America·Kathryn E HoltNicholas R Thomson
Jul 15, 2015·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·Y JiangY Yu
Jul 15, 2015·Antimicrobial Agents and Chemotherapy·Johann D D PitoutLaurent Poirel
Jul 23, 2015·MBio·Carsten StruveKaren A Krogfelt
Sep 25, 2015·Journal of Clinical Microbiology·Mark de BeenRob J L Willems
Jun 22, 2016·Genome Biology·Brian D OndovAdam M Phillippy
Aug 12, 2016·Journal of Clinical Microbiology·Jolene R BowersPaul Keim
Aug 26, 2016·Journal of Clinical Microbiology·Alexander MellmannDag Harmsen
Dec 3, 2016·Nucleic Acids Research·Alice R WattamRick L Stevens
Feb 6, 2017·American Journal of Infection Control·Patrick TangLinda M Hoang
Apr 5, 2017·The Journal of Infectious Diseases·Latania K Logan, Robert A Weinstein
May 19, 2017·FEMS Microbiology Reviews·Shiri Navon-VeneziaAlessandra Carattoli
Jul 1, 2017·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Celine NadonUNKNOWN FWD-NEXT Expert Panel
Aug 12, 2017·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Tommaso GianiGian Maria Rossolini
Dec 15, 2017·Frontiers in Microbiology·Clémentine HenriRené S Hendriksen
Jul 18, 2018·Bioinformatics·Emmanuel Paradis, Klaus Schliep
Oct 6, 2018·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·A Nutman, D Marchaim

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Datasets Mentioned

BETA
PRJNA564099

Software Mentioned

BWA
MUMmer
Seqsphere
SeqSphere +
cgMLST SeqSphere +
PATRIC
Mash
ModelTest
SeqSphere + tool
phiSpy

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