Analysis of phenotypic properties and genetic determinants of antimicrobial resistance in Klebsiella aerogenes isolates



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Abstract

Klebsiella aerogenes is an important pathogen associated with outbreaks of respiratory and urinary tract infections often associated with resistance to cephalosporins, carbapenems, and other classes of antimicrobial drugs. The aim of the study was to analyze the phenotypic properties and genetic determinants underlying antimicrobial drug resistance based on whole‑genome sequencing of K. aerogenes strains. For this, three isolates of K. aerogenes previously isolated from clinical material of children were retrieved from the collection of the Laboratory of Microbiome and Microecology. The strains were identified using conventional methods and mass spectrometry. Phenotype analysis was carried out using the Burri‑Ginsa method, the mucus production test, the SENSILATEST G‑II, the disc diffusion method, the “double discs” method, and the CIM-test. Bacterial- isolate-specific genome-wide sequencing and genotyping, search and description of plasmids, as well as resistance and virulence genes were performed. K. aerogenes isolates formed no capsules and hyperviscous mucus. According to SENSILATEST G-II and disco diffusion method, either two isolates No. 89 and 93 or all three isolates, respectively, were verified as multidrug-resistant strains. The isolates produced ESBL, but not carbapenemases. The GC composition of all three draft genomes is characteristic of the K. aerogenes species. Isolates No. 89 and 93 were assigned to ST‑389, while isolate No. 13 – to ST‑4/CC1. All isolates were characterized by detecting a wide array of determinants encoding antibiotic resistance, among which efflux systems held a lead place. The predominant virulence determinants in the studied strains were yersiniabactin, flagella, adhesins, and enterobactin. The fepC gene was a distinctive trait of strain No. 13. Each K. aerogenes isolate was found to carry one conjugative plasmid. Comparing plasmid from isolate No. 13 and plasmids from isolates No. 89 and 93 differed in size, replicon and relaxase type, as well as pilus type. A distinctive characteristic for the study K. aerogenes isolates is identifying a specific phenotype characterized by the production of extended‑spectrum β‑lactamases but not carbapenemases, as well as the presence of genetic markers thereby suggesting a potential link between pathogenic, virulent properties and antimicrobial resistance.

About the authors

Ekaterina Vladimirovna Grigorova

Scientific Centre for Family Health and Human Reproduction Problems

Email: buxarowa.ekaterina@yandex.ru
ORCID iD: 0000-0001-6588-2591
Scopus Author ID: 57199710917
ResearcherId: V-4210-2018

Candidate of biological sciences, researcher at the laboratory of microbiome and microecology

Russian Federation, Russian Federation, Irkutsk, Timiryazeva str., 16, 664003

Uliana Mikhailovna Nemchenko

Scientific Centre for Family Health and Human Reproduction Problems

Email: umnemch@mail.ru
ORCID iD: 0000-0002-7656-342X
Scopus Author ID: 51764227900
ResearcherId: AAB-4717-2020

Candidate of Biological Sciences, Senior Researcher at the Laboratory of Microbiome and Microecology

Russian Federation, Russian Federation, Irkutsk, Timiryazeva str., 16, 664003

Natalia Leonidovna Belkova

Scientific Centre for Family Health and Human Reproduction Problems

Email: nlbelkova@gmail.com
ORCID iD: 0000-0001-9720-068X
Scopus Author ID: 8373682700
ResearcherId: N-6987-2014

Candidate of Biological Sciences, Associate Professor, Leading Researcher at the Laboratory of Microbiome and Microecology

Russian Federation, Russian Federation, Irkutsk, Timiryazeva str., 16, 664003

Elizaveta Stanislavovna Klimenko

Scientific Centre for Family Health and Human Reproduction Problems

Email: klimenko.elizabet@gmail.com
ORCID iD: 0000-0003-0979-8816
Scopus Author ID: 57202131923
ResearcherId: M-5830-2018

Junior Researcher at the Laboratory of Microbiome and Microecology

Russian Federation, Russian Federation, Irkutsk, Timiryazeva str., 16, 664003

Nadezhda Evgenievna Smurova

Scientific Centre for Family Health and Human Reproduction Problems

Email: nadinasmurova@mail.ru
ORCID iD: 0009-0004-3614-6631
Scopus Author ID: 58682343800

Laboratory assistant at the Microbiome and Microecology Laboratory

Russian Federation, Russian Federation, Irkutsk, Timiryazeva str., 16, 664003

Evgeny Dmitrievich Savilov

Scientific Centre for Family Health and Human Reproduction Problems

Author for correspondence.
Email: savilov47@gmail.com
ORCID iD: 0000-0002-9217-6876
Scopus Author ID: 6602084322

MD, Professor, Chief Researcher at the Laboratory of Epidemiologically and Socially Significant Infections

Russian Federation, Russian Federation, Irkutsk, Timiryazeva str., 16, 664003

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