Co-existence of Plasmid-encoded blaVIM-4 and Chromosomal blaNDM-1 in a Carbapenem-Resistant Pseudomonas guariconensis clinical isolate from Ethiopia: Comparative Genomic and Phylogenetic Analysis

2025 · doi:10.1099/acmi.0.001133.v1
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This study reports the first detection of a carbapenem-resistant *Pseudomonas guariconensis* clinical isolate from Ethiopia, carrying both plasmid-encoded *bla*VIM-4 and chromosomal *bla*NDM-1 genes.

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This study investigated a rare clinical isolate, Pseudomonas guariconensis strain PM99, from a patient hospitalized at Tikur Anbessa Specialized Hospital in Ethiopia, using phenotypic testing and long-read whole-genome sequencing with comparative genomic and phylogenetic analyses. The authors found a plasmid carrying blaVIM-4 embedded in a class 1 integron and flanked by transposase elements consistent with a putative composite transposon, alongside sul1 and qnrVC6; the isolate was susceptible to colistin and resistant to carbapenems. They also detected multiple carbapenem resistance genes on the chromosome, including blaNDM-1 and blaOXA-10, and reported that pairwise SNP comparisons showed >700 SNP differences from all publicly available P. guariconensis genomes, indicating no close relatedness. This paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

Pseudomonas guariconensis is a rare clinical isolate. This paper reports the first detection of a plasmid harboring carbapenem-resistant P. guariconensis strain, PM99, isolated from a patient admitted at Tikur Anbessa Specialized Hospital in Ethiopia. The isolate was phenotypically susceptible to colistin and resistant to carbapenems. Whole genome sequencing was performed using long read sequencing. The isolate carried a plasmid-encoded blaVIM-4 gene embedded within a class 1 integron, alongside sul1 and qnrVC6 genes. The blaVIM-4 gene was flanked upstream by a DDE-Tn3 family transposase and downstream by IS91 family transposases, forming a putative composite transposon. This plasmid configuration suggests a mobile genetic structure capable of facilitating horizontal gene transfer and contributing to the dissemination of carbapenem resistance. The isolate also carried chromosomal blaNDM-1,blaOXA-10, sul1, aph(3')-VIa, aac(6')-Ib, and ant(3'')-Ia) genes. Pairwise SNP analysis showed that all publicly available P. guariconensis genomes differed from PM99 by > 700 SNPs, suggesting no close genetic relatedness. Although P. guariconensis is a rare clinical isolate, its capacity to harbor resistance determinants in both stable and mobile genetic contexts raises concern about its potential role as a reservoir for antimicrobial resistance. Furthermore, its potential to survive in different environments warrant further genomic monitoring.
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Full text loading... Abstract Pseudomonas guariconensis is a rare clinical isolate. This paper reports the first detection of a plasmid harboring carbapenem-resistant P. guariconensis strain, PM99, isolated from a patient admitted at Tikur Anbessa Specialized Hospital in Ethiopia. The isolate was phenotypically susceptible to colistin and resistant to carbapenems. Whole genome sequencing was performed using long read sequencing. The isolate carried a plasmid-encoded blaVIM-4 gene embedded within a class 1 integron, alongside sul1 and qnrVC6 genes. The blaVIM-4 gene was flanked upstream by a DDE-Tn3 family transposase and downstream by IS91 family transposases, forming a putative composite transposon. This plasmid configuration suggests a mobile genetic structure capable of facilitating horizontal gene transfer and contributing to the dissemination of carbapenem resistance. The isolate also carried chromosomal blaNDM-1,blaOXA-10, sul1, aph(3')-VIa, aac(6')-Ib, and ant(3'')-Ia) genes. Pairwise SNP analysis showed that all publicly available P. guariconensis genomes differed from PM99 by > 700 SNPs, suggesting no close genetic relatedness. Although P. guariconensis is a rare clinical isolate, its capacity to harbor resistance determinants in both stable and mobile genetic contexts raises concern about its potential role as a reservoir for antimicrobial resistance. Furthermore, its potential to survive in different environments warrant further genomic monitoring. - Received: - Version Posted: Funding - Addis Ababa University - Principal Award Recipient: Matifan Dereje Olana - Styrelsen för Internationellt Utvecklingssamarbete - Principal Award Recipient: Matifan Dereje Olana

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