Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates.
Anti-Bacterial Agents
/ therapeutic use
Bacterial Proteins
/ genetics
Carbapenem-Resistant Enterobacteriaceae
/ drug effects
Carbapenems
/ therapeutic use
Disease Outbreaks
Humans
Klebsiella Infections
/ drug therapy
Klebsiella pneumoniae
/ drug effects
Microbial Sensitivity Tests
/ methods
Multilocus Sequence Typing
/ methods
Plasmids
/ genetics
Slovenia
Whole Genome Sequencing
/ methods
beta-Lactamases
/ genetics
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
19
11
2019
accepted:
24
03
2020
entrez:
14
4
2020
pubmed:
14
4
2020
medline:
14
7
2020
Statut:
epublish
Résumé
The first hospital outbreak of carbapenemase-producing Enterobacteriaceae in Slovenia occurred in 2014-2016. Whole genome sequencing was used to analyse the population of carbapenem-resistant Klebsiella pneumoniae collected in Slovenia in 2014-2017, including OXA-48 and/or NDM-1 producing strains from the outbreak. A total of 32 K. pneumoniae isolates were analysed using short-read sequencing. Multi-locus sequence typing and core genome multi-locus sequence typing were used to infer genetic relatedness. Antimicrobial resistance markers, virulence factors, plasmid content and wzi types were determined. Long-read sequencing was used for six isolates for detailed analysis of plasmids and their possible transmission. Overall, we detected 10 different sequence types (STs), the most common being ST437 (40.6%). Isolates from the initial outbreak belonged to ST437 (12/16) and ST147 (4/16). A second outbreak of four ST15 isolates was discovered. A new ST (ST3390) and two new wzi types (wzi-556, wzi-559) were identified. blaOXA-48 was found in 17 (53.1%) isolates, blaNDM-1 in five (15.6%), and a combination of blaOXA-48/NDM-1 in seven (21.9%) isolates. Identical plasmids carrying blaOXA-48 were found in outbreak isolates sequenced with long-read sequencing technology. Whole genome sequencing of Slovenian carbapenem-resistant K. pneumoniae isolates revealed multiple clusters of STs, two of which were involved in the first hospital outbreak of carbapenem producing K. pneumoniae in Slovenia. Transmission of the plasmid carrying blaOXA-48 between two STs was likely to have occurred. A previously unidentified second outbreak was also discovered, highlighting the importance of whole genome sequencing in detection and/or characterization of hospital outbreaks and surveillance of drug-resistant bacterial clones.
Identifiants
pubmed: 32282829
doi: 10.1371/journal.pone.0231503
pii: PONE-D-19-32138
pmc: PMC7153892
doi:
Substances chimiques
Anti-Bacterial Agents
0
Bacterial Proteins
0
Carbapenems
0
beta-Lactamases
EC 3.5.2.6
beta-lactamase NDM-1
EC 3.5.2.6
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0231503Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Bioinformatics. 2015 Oct 15;31(20):3350-2
pubmed: 26099265
Antimicrob Agents Chemother. 2015 Oct;59(10):5873-84
pubmed: 26169401
Int J Med Microbiol. 2013 Aug;303(6-7):298-304
pubmed: 23499304
Clin Microbiol Infect. 2014 Feb;20(2):O132-4
pubmed: 24033741
J Antimicrob Chemother. 2012 Nov;67(11):2640-4
pubmed: 22782487
Antimicrob Agents Chemother. 2017 Jan 24;61(2):
pubmed: 27872077
Infect Immun. 2011 Aug;79(8):3309-16
pubmed: 21576334
BMC Genomics. 2011 Aug 08;12:402
pubmed: 21824423
Trends Microbiol. 2016 Dec;24(12):944-956
pubmed: 27742466
Euro Surveill. 2016 Sep 15;21(37):
pubmed: 27685838
PLoS One. 2009;4(3):e4982
pubmed: 19319196
J Antimicrob Chemother. 2017 Jan;72(1):315-316
pubmed: 27659734
Clin Microbiol Infect. 2014 Jan;20(1):O27-9
pubmed: 23809141
Genome Med. 2018 Oct 29;10(1):77
pubmed: 30371343
J Clin Microbiol. 2013 Dec;51(12):4073-8
pubmed: 24088853
J Infect Dis. 2017 Dec 27;217(1):82-92
pubmed: 29029188
Front Microbiol. 2016 Jun 13;7:895
pubmed: 27379038
Clin Microbiol Infect. 2018 Apr;24(4):355-360
pubmed: 29117578
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
FEMS Microbiol Rev. 2017 May 1;41(3):252-275
pubmed: 28521338
Genome Biol Evol. 2015 Apr 10;7(5):1267-79
pubmed: 25861820
PLoS Comput Biol. 2017 Jun 8;13(6):e1005595
pubmed: 28594827
J Antimicrob Chemother. 2019 Mar 1;74(3):577-581
pubmed: 30517666
J Hosp Infect. 2019 Feb;101(2):142-149
pubmed: 30399389
Genome Res. 2008 May;18(5):821-9
pubmed: 18349386
J Clin Microbiol. 2005 Aug;43(8):4178-82
pubmed: 16081970
Antimicrob Agents Chemother. 2017 Apr 24;61(5):
pubmed: 28242665
J Clin Microbiol. 2015 Sep;53(9):2861-8
pubmed: 26135860
Euro Surveill. 2019 Feb;24(9):
pubmed: 30862330
Pathogens. 2014 Apr 15;3(2):356-76
pubmed: 25437804
Antimicrob Agents Chemother. 2004 Jan;48(1):15-22
pubmed: 14693513
Diagn Microbiol Infect Dis. 2011 Jun;70(2):274-7
pubmed: 21397425
Biomol Detect Quantif. 2017 Oct 23;14:1-6
pubmed: 29255684
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Antimicrob Agents Chemother. 2014 Jul;58(7):3895-903
pubmed: 24777092
Microb Genom. 2017 Aug 18;3(10):e000128
pubmed: 29177087
Antimicrob Agents Chemother. 2014 Aug;58(8):4961-5
pubmed: 24913165
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Emerg Infect Dis. 2014 Nov;20(11):1812-20
pubmed: 25341126
Antimicrob Agents Chemother. 2012 Jan;56(1):559-62
pubmed: 22083465
Microb Drug Resist. 2018 Sep;24(7):973-979
pubmed: 29267137
Lancet Infect Dis. 2017 Feb;17(2):153-163
pubmed: 27866944
EMBO Mol Med. 2015 Feb 20;7(3):227-39
pubmed: 25712531
Antimicrob Resist Infect Control. 2018 May 2;7:62
pubmed: 29744043
Eur J Clin Microbiol Infect Dis. 2016 Mar;35(3):333-41
pubmed: 26718943
Bioinformatics. 2011 Apr 1;27(7):1009-10
pubmed: 21278367
Nat Microbiol. 2019 Nov;4(11):1919-1929
pubmed: 31358985
J Antimicrob Chemother. 2019 Mar 1;74(3):582-593
pubmed: 30445429
Int J Antimicrob Agents. 2018 Sep;52(3):331-337
pubmed: 29654892