Genomic epidemiology, antimicrobial resistance and virulence factors of Enterobacter cloacae complex causing potential community-onset bloodstream infections in a tertiary care hospital of Nepal

Manandhar, S; Nguyen, Q; Nguyen Thi Nguyen, T; Pham, DT; Rabaa, MA; Dongol, S; Basnyat, B; Dixit, SM; Baker, S; Karkey, A

Journal article

Genomic epidemiology, antimicrobial resistance and virulence factors of Enterobacter cloacae complex causing potential community-onset bloodstream infections in a tertiary care hospital of Nepal

Abstract:: Objectives
Community-onset bloodstream infections (BSIs) caused by carbapenemase-producing Enterobacter cloacae complex (ECC) species are increasing internationally. This observation suggests that ECC are emerging pathogens, requiring for detailed understanding on their genomic epidemiology including transmission dynamics and antimicrobial resistance profiles.

Patients and methods
We performed WGS on 79 Enterobacter spp. isolated from the patients with clinically significant BSIs and admitted to emergency department of a major tertiary hospital in Nepal between April 2016 and October 2017.

Results
We identified 5 species and 13 STs of ECC. Enterobacter xiangfangensis ST171, one of the globally emerging carbapenem resistant ECC clones with epidemic potential, was the most prevalent (42%). Phylogenetic analysis showed a large (>19 400 SNPs) core genome SNP distance across major STs, which was minimal (<30 SNPs) among the isolates of each prevalent ST, suggesting the relatively recent importation of major STs followed by local clonal expansions. Genomic evidence for resistance to all major antimicrobial classes except for colistin and macrolides was detected. A limited number of isolates also carried blaNDM-1 (n = 2) and blaOXA-48 (n = 1) carbapenemase genes. Virulence factors encoding siderophores (24%), T6SSD (25%) and fimbriae (54%) were detected.

Conclusions
Our study highlighted that MDR ECC clones are important pathogens of BSIs in community. Though of low prevalence, carbapenem resistance observed in our ECC isolates raised concern about further community dissemination, underscoring the need for community surveillance to identify MDR ECC clones with epidemic potential.

Publication status:: Published

Peer review status:: Peer reviewed

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APA Style

Manandhar, S., Nguyen, Q., Nguyen Thi Nguyen, T., Pham, D. T., Rabaa, M. A., Dongol, S., Basnyat, B., Dixit, S. M., Baker, S., & Karkey, A. (2022). Genomic epidemiology, antimicrobial resistance and virulence factors of Enterobacter cloacae complex causing potential community-onset bloodstream infections in a tertiary care hospital of Nepal. JAC-Antimicrobial Resistance, 4(3).

MLA Style

Manandhar, S., et al. “Genomic Epidemiology, Antimicrobial Resistance and Virulence Factors of Enterobacter Cloacae Complex Causing Potential Community-Onset Bloodstream Infections in a Tertiary Care Hospital of Nepal.” JAC-Antimicrobial Resistance, vol. 4, no. 3, Oxford University Press, 2022.

Chicago Style

Manandhar, S, Q Nguyen, T Nguyen Thi Nguyen, DT Pham, MA Rabaa, S Dongol, B Basnyat, SM Dixit, S Baker, and A Karkey. 2022. “Genomic Epidemiology, Antimicrobial Resistance and Virulence Factors of Enterobacter Cloacae Complex Causing Potential Community-Onset Bloodstream Infections in a Tertiary Care Hospital of Nepal.” JAC-Antimicrobial Resistance 4 (3).
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