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

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.

Figure 1

Distribution of the different integrons across the cities in the Czech Republic.

Figure 2

Distribution of the different plasmid types across the cities in the Czech Republic.

Figure 3

Sankey diagram showing the distribution of different integrons linking to the plasmid types (left) and to the bacterial species detected (right).

Figure 4

Linear comparisons of (A) VIM-1- (B) VIM-4- encoding MDR regions characterized from Enterobacterales isolated from Czech hospitals, during 2019–2020. Arrows show the direction of transcription of open reading frames (ORFs). Resistance genes are shown in red. IS elements and transposases are shown in yellow and aqua, respectively. intI1 genes are shaded orange. The remaining genes are shown in gray. Homologous segments (representing ≥99% sequence identity) are indicated by light gray shading, while pink shading shows inverted homologous segments.