Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines.
Aged
Anti-Bacterial Agents
/ pharmacology
Child
Disease Outbreaks
Humans
Infant, Newborn
Intensive Care Units, Neonatal
Klebsiella Infections
/ drug therapy
Klebsiella pneumoniae
/ genetics
Microbial Sensitivity Tests
Multilocus Sequence Typing
Philippines
/ epidemiology
Plasmids
/ genetics
Retrospective Studies
beta-Lactamases
/ genetics
K. pneumoniae
antimicrobial resistance
outbreak detection
whole genome sequencing
Journal
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
ISSN: 1537-6591
Titre abrégé: Clin Infect Dis
Pays: United States
ID NLM: 9203213
Informations de publication
Date de publication:
01 12 2021
01 12 2021
Historique:
entrez:
1
12
2021
pubmed:
2
12
2021
medline:
16
3
2022
Statut:
ppublish
Résumé
Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied. A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data. Prevalent AMR mechanisms detected include blaCTX-M-15 (76.8%) and blaNDM-1 (37.5%). An epidemic IncFII(Yp) plasmid carrying blaNDM-1 was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year. WGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.
Sections du résumé
BACKGROUND
Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied.
METHODS
A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data.
RESULTS
Prevalent AMR mechanisms detected include blaCTX-M-15 (76.8%) and blaNDM-1 (37.5%). An epidemic IncFII(Yp) plasmid carrying blaNDM-1 was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year.
CONCLUSION
WGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.
Identifiants
pubmed: 34850834
pii: 6447008
doi: 10.1093/cid/ciab776
pmc: PMC8634409
doi:
Substances chimiques
Anti-Bacterial Agents
0
beta-Lactamases
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
S316-S324Subventions
Organisme : Wellcome Trust
ID : 206194
Pays : United Kingdom
Investigateurs
Harry Harste
(H)
Dawn Muddyman
(D)
Ben Taylor
(B)
Nicole Wheeler
(N)
Sophia David
(S)
Pilar Donado-Godoy
(P)
Johan Fabian Bernal
(JF)
Alejandra Arevalo
(A)
Maria Fernanda Valencia
(MF)
Erik C D Osma Castro
(ECD)
K L Ravikumar
(KL)
Geetha Nagaraj
(G)
Varun Shamanna
(V)
Vandana Govindan
(V)
Akshata Prabhu
(A)
D Sravani
(D)
M R Shincy
(MR)
Steffimole Rose
(S)
K N Ravishankar
(KN)
Iruka N Okeke
(IN)
Anderson O Oaikhena
(AO)
Ayorinde O Afolayan
(AO)
Jolaade J Ajiboye
(JJ)
Erkison Ewomazino Odih
(E)
Ali Molloy
(A)
Carolin Vegvari
(C)
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.
Références
Infect Immun. 2002 May;70(5):2583-90
pubmed: 11953399
mSphere. 2017 Aug 2;2(4):
pubmed: 28776045
J Clin Microbiol. 2019 Jan 2;57(1):
pubmed: 30602547
Antimicrob Agents Chemother. 2006 Jan;50(1):178-84
pubmed: 16377684
Microb Drug Resist. 2016 Oct;22(7):585-588
pubmed: 27032000
Microbiology (Reading). 2018 Oct;164(10):1213-1219
pubmed: 30052172
Euro Surveill. 2013 Jan 24;18(4):20380
pubmed: 23369389
Int J Antimicrob Agents. 2014 Mar;43(3):242-7
pubmed: 24581597
Clin Infect Dis. 2010 Aug 1;51 Suppl 1:S81-7
pubmed: 20597676
Sex Transm Dis. 2009 Dec;36(12):787-8
pubmed: 19734823
Int J Infect Dis. 2019 Aug;85:117-123
pubmed: 31129424
Epidemiol Perspect Innov. 2005 Nov 25;2:10
pubmed: 16309556
Microorganisms. 2020 Sep 11;8(9):
pubmed: 32932763
Front Microbiol. 2019 Nov 29;10:2767
pubmed: 31849904
Euro Surveill. 2017 Mar 16;22(11):
pubmed: 28333615
J Med Microbiol. 2000 Nov;49(11):1003-1010
pubmed: 11073154
Lancet Infect Dis. 2013 Feb;13(2):130-6
pubmed: 23158674
Clin Microbiol Rev. 1998 Oct;11(4):589-603
pubmed: 9767057
PLoS One. 2017 Jul 5;12(7):e0180347
pubmed: 28678874
Ups J Med Sci. 2016 Aug;121(3):159-64
pubmed: 27416324
PeerJ. 2019 May 31;7:e6995
pubmed: 31183253
J Med Microbiol. 2012 Sep;61(Pt 9):1270-1279
pubmed: 22700549
Nat Commun. 2020 Jun 1;11(1):2719
pubmed: 32483195
Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3574-81
pubmed: 26100894
PLoS Med. 2010 Feb 23;7(2):e1000238
pubmed: 20186274
MMWR Morb Mortal Wkly Rep. 2020 Jul 03;69(26):815-819
pubmed: 32614808
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Antimicrob Agents Chemother. 2014 Jul;58(7):3895-903
pubmed: 24777092
New Microbes New Infect. 2015 Feb 09;5:1-4
pubmed: 25834737
Microb Drug Resist. 2020 Jun;26(6):652-660
pubmed: 31851584
Microb Genom. 2017 Sep 4;3(10):e000131
pubmed: 29177089
Microb Genom. 2016 Nov 30;2(11):e000093
pubmed: 28348833
Microb Genom. 2016 Dec 12;2(12):e000102
pubmed: 28348840
Nat Microbiol. 2019 Nov;4(11):1919-1929
pubmed: 31358985