Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes

Hisham N. Altayb, Salman Hosawi, Othman Baothman, Imran Kazmi, Kamel Chaieb, Isam M. Abu Zeid, Hana S. Elbadawi, Bruno Silvester Lopes, Ehssan Moglad

Research output: Contribution to journalArticlepeer-review


Introduction: The emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of K. quasipneumoniae using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be K. pneumoniae. Methods: Whole-genome sequencing was performed using the Illumina platform, and the generated raw reads were de novo assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools. Results: Six strains were identified as K. quasipneumoniae subsp similipneumoniae and one as K. quasipneumoniae subsp. quasipneumoniae. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the fosA, blaOKP types, oqxB, and oqxA genes. One isolate additionally harbored a gene cassettes consisting of blaSHV−1, blaOXA−1, aac(6′)-Ib-cr, catB genes. The aminoglycoside-modifying enzyme gene aph(3”)-Ia was bracketed by two insertion elements. Plasmid analyses showed that IncFIBK was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, adherence, and biofilm formation (mrkA, mrkB, mrkC, mrkD, mrkF, and mrkH). Conclusion: Our study highlights the ecology and transmission of K. quasipneumoniae (which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.

Original languageEnglish
Article number1068888
JournalFrontiers in Public Health
Publication statusPublished - 12 Jan 2023

Bibliographical note

Funding Information:
This research work was funded by Institutional Fund Projects under grant no. (IFPIP: 263-130-1443). The authors gratefully acknowledge the technical and financial support provided by the Ministry of Education and King Abdulaziz University, DSR, Jeddah, Saudi Arabia.

Publisher Copyright:
Copyright © 2023 Altayb, Hosawi, Baothman, Kazmi, Chaieb, Abu Zeid, Elbadawi, Lopes and Moglad.


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