Implication of different replicons in the spread of the VIM-1-encoding integron, In110, in Enterobacterales from Czech hospitals

Ibrahim Bitar; Costas C Papagiannitsis; Lucie Kraftova; Vittoria Mattioni Marchetti; Efthymia Petinaki; Marc Finianos; Katerina Chudejova; Helena Zemlickova; Jaroslav Hrabak

doi:10.3389/fmicb.2022.993240

Implication of different replicons in the spread of the VIM-1-encoding integron, In110, in Enterobacterales from Czech hospitals

Front Microbiol. 2023 Jan 4:13:993240. doi: 10.3389/fmicb.2022.993240. eCollection 2022.

Authors

Ibrahim Bitar^{1

2}, Costas C Papagiannitsis³, Lucie Kraftova^{1

2}, Vittoria Mattioni Marchetti^{1

2}, Efthymia Petinaki³, Marc Finianos^{1

2}, Katerina Chudejova^{1

2}, Helena Zemlickova^{4

5}, Jaroslav Hrabak^{1

2}

Affiliations

¹ Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.
² Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia.
³ Department of Microbiology, University Hospital of Larissa, Larissa, Greece.
⁴ National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czechia.
⁵ Department of Medical Microbiology, 3rd Faculty of Medicine, Charles University, Prague, Czechia.

Abstract

Background: VIM metallo-β-lactamases are enzymes characterized by the ability to hydrolyze all β-lactams. Usually, bla _VIM-like genes are carried by class 1 integrons. In the Czech Republic, only sporadic cases of VIM-producing Enterobacterales have been reported in which those isolates carried the VIM-1 carbapenemase-encoding integron In110. However, during 2019-2020, an increased number was reported. Therefore, the aim of the current study was to characterize the genetic elements involved in the increased spread of bla _VIM genes.

Materials and methods: 32 VIM-producing Enterobacterales collected between 2019 and 2020 were subjected to: antimicrobial susceptibility testing, integron analysis, and short reads sequencing. Based on the results, 19 isolates were selected as representative and sequenced using Sequel I platform.

Results: The 32 VIM-producing isolates exhibited variations in the MICs of carbapenems. Based on short-read data, 26 of the 32 sequenced isolates harbored the bla _VIM-1 allele while six isolates carried the bla _VIM-4 gene. The most prevalent was the In110 integron (n = 24) and two isolates carried the In4873 class 1 integron. The bla _VIM-4 allele was identified in class 1 integrons In1174 (n = 3), In416 (n = 1), In2143 (n = 1) and In2150. Long reads sequencing revealed that the bla _VIM was carried by: pKPC-CAV1193-like (n = 6), HI1 (pNDM-CIT; n = 4), HI2 (n = 3), FIB (pECLA; n = 2) and N (n = 1) incompatibility groups. Two bla _VIM-carrying plasmids could not be typed by the database, while another one was integrated into the chromosome.

Conclusion: We observed the spread of VIM-encoding integrons, mainly of In110, among Enterobacterales isolated from Czech hospitals, but also an increased number of novel elements underlining the ongoing evolution.

Keywords: Enterobacterales; In110; blaVIM-1; blaVIM-4; integrons; plasmids; whole-genome sequencing.