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Whole-Genome Sequencing and Comparative Genomics Analysis of a Newly Emerged Multidrug-Resistant Klebsiella pneumoniae Isolate of ST967
10.1128/spectrum.04011-22
Jie Sheng
Rory Cave
Mary M. Ter-Stepanyan
Nune Kotsinyan
Jiazhen Chen
Li Zhang
Taijiao Jiang
Hermine V. Mkrtchyan
Research Article
Research Article
Klebsiella pneumoniae
whole-genome sequencing
multidrug resistance
phylogenetic analysis
American Society for Microbiology
Sheng et al.
Copyright © 2023 Sheng et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
20230406
2023
ABSTRACT
Klebsiella pneumoniae is a common cause of hospital- and community-acquired infections globally, yet its population structure remains unknown for many regions, particularly in low- and middle-income countries (LMICs). Here, we report for the first-time whole-genome sequencing (WGS) of a multidrug-resistant K. pneumoniae isolate, ARM01, recovered from a patient in Armenia. Antibiotic susceptibility testing revealed that ARM01 was resistant to ampicillin, amoxicillin-clavulanic acid, ceftazidime, cefepime, norfloxacin, levofloxacin, and chloramphenicol. Genome sequencing analysis revealed that ARM01 belonged to sequence type 967 (ST967), capsule type K18, and antigen type O1. ARM01 carried 13 antimicrobial resistance (AMR) genes, including blaSHV-27, dfrA12, tet(A), sul1, sul2, catII.2, mphA, qnrS1, aadA2, aph3-Ia, strA, and strB and the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-15, but only one known virulence factor gene, yagZ/ecpA, and one plasmid replicon, IncFIB(K)(pCAV1099-114), were detected. The plasmid profile, AMR genes, virulence factors, accessory gene profile, and evolutionary analyses of ARM01 showed high similarity to isolates recovered from Qatar (SRR11267909 and SRR11267906). The date of the most recent common ancestor (MRCA) of ARM01 was estimated to be around 2017 (95% confidence interval [CI], 2017 to 2018). Although in this study, we report the comparative genomics analysis of only one isolate, it emphasizes the importance of genomic surveillance for emerging pathogens, urging the need for implementation of more effective infection prevention and control practices.
IMPORTANCE Whole-genome sequencing and population genetics analysis of K. pneumoniae are scarce from LMICs, and none has been reported for Armenia. Multilevel comparative analysis revealed that ARM01 (an isolate belonging to a newly emerged K. pneumoniae ST967 lineage) was genetically similar to two isolates recovered from Qatar. ARM01 was resistant to a wide range of antibiotics, reflecting the unregulated usage of antibiotics (in most LMICs, antibiotic use is typically unregulated.) Understanding the genetic makeup of these newly emerging lineages will aid in optimizing antibiotic use for patient treatment and contribute to the worldwide efforts of pathogen and AMR surveillance and implementation of more effective infection prevention and control strategies.
20221002
20230316
2165-0497
Adobe LiveCycle PDF Generator; modified using iText® 5.5.13.2 ©2000-2020 iText Group NV (AGPL-version)2023-04-13T08:55:32-07:00
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