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Case Reports
. 2023 Jul 21;12(7):961.
doi: 10.3390/pathogens12070961.

Novel Metallo-β-Lactamase blaCVI-1 Isolated from a Chromobaterium violaceum Clinical Strain Resistant to Colistin

Sonia A Gomez  1   2 , María Belén Sanz  1 , Melina Rapoport  1 , Graciela Sucin  3 , Teresa A Corallo  3 , Tomás Poklepovich  4 , Josefina Campos  4 , Paola Ceriana  1 , Juan Manuel de Mendieta  1 , Mónica Prieto  5 , Fernando Pasteran  1 , Alejandra Corso  1
Affiliations
Case Reports

Novel Metallo-β-Lactamase blaCVI-1 Isolated from a Chromobaterium violaceum Clinical Strain Resistant to Colistin

Sonia A Gomez et al. Pathogens. .

Abstract

Objective: We aimed to describe a colistin (COL)-resistant (R) Chromobacterium violaceum (Cvi) isolate from a septic patient in Argentina expressing a previously unknown gene, blaCVI-1.

Methods: In 2019, a 12 year old child was injured with a thorn in a lagoon. The child was hospitalized due to sepsis and multiple abscesses. Cvi was isolated from skin and soft tissue and tracheal aspirate. The patient was successfully treated with imipenem (IMI) plus amikacin. Antimicrobial susceptibility was assessed by disk diffusion, broth microdilution, and the E-test. Carbapenemase activity was assayed by double-disk synergy and microbiological tests. Resistance, virulence, and additional gene searches were performed by in silico analysis of sequences obtained by whole-genome sequencing (WGS). A maximum likelihood phylogenetic tree was built with public Cvi genomes.

Results: R was seen for IMI and COL. Expression of a metallo-β-lactamase was confirmed. Genome analysis revealed blaCVI-1, a subclass B2 metallo-β-lactamase with 62.66% ID with CphA from A. hydrophila (WP081086394). R to COL could be attributed to the arnC and arnT genes. Virulence factors required for invasion and toxicity were also found. No plasmids were detected. The phylogeny tree showed two main clades with geographical distinction, and the isolate studied here stands alone in a branch closely related to two clinical isolates from the USA.

Conclusions: This is the second report of infection by Cvi in Argentina. This pathogen carried a new gene, blaCVI-1, a metallo-β-lactamase that can be detected by routine methods. Prompt suspicion of C. violaceum infection is crucial to treating this rare pathogen rapidly and properly.

Keywords: CVI-1; Chomobacterium violaceum; carbapenemase; colistin resistance; metallo-beta-lactamase.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Pan-genome analysis of C. violaceum. Tree construction details and analysis are described in the text. Branch tips are color-coded according to the country of isolation, as indicated by the lateral-colored bar. The circled leaf node represents the isolate studied here (Cvi_M23796). Country and isolation sites are labeled with a color code, as shown in the figure. Clusters were determined using FastBAPS based on an alignment of core genes. The scale bar represents the number of mutations per variable site. Full metadata of the isolates can be viewed at (https://microreact.org/project/qyijLM4sQvt5jDLP9gWfah-raxml-cvim23976, accessed on 13 June 2023). “nd” indicates “not determined”.
Figure 2
Figure 2
A phylogenetic tree showing the evolutionary relationship between CVI-1 and known Ambler class B β-lactamases is shown. The tree was drawn to scale, and the evolutionary distances are in units of arnC amino acid substitutions per site.
See this image and copyright information in PMC

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