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. 2024 Sep 14;24(1):347.
doi: 10.1186/s12866-024-03491-2.

Linezolid-resistant Enterococcus faecium clinical isolates from Pakistan: a genomic analysis

Syed Ali Raza Nasir  1 , Mohammad Zeeshan  1 , Najia Ghanchi  1   2 , Noureen Saeed  1 , Hassan Ghayas  1 , Sadaf Zaka  1 , Javaria Ashraf  1 , Kauser Jabeen  1 , Joveria Farooqi  1 , Zahra Hasan  1 , Tazeen Fatima  2 , Faiza Rezwan  2 , Syed Faisal Mahmood  1 , Mehreen Arshad  1 , Erum Khan  1 , Egon A Ozer  3 , Rumina Hasan  4   5
Affiliations

Linezolid-resistant Enterococcus faecium clinical isolates from Pakistan: a genomic analysis

Syed Ali Raza Nasir et al. BMC Microbiol. .

Abstract

Background: Linezolid-resistant Enterococcus faecium (LRE) is a global priority pathogen. Thirteen LRE were reported from clinical specimens between November 2021 and April 2023 at two laboratories in Karachi, Pakistan. We aimed to investigate the strain types and genes associated with linezolid resistance among these isolates. Whole genome sequencing (WGS) was performed and analyzed by multilocus sequence typing (MLST). The presence of linezolid resistance genes was identified using ResFinder v4.1.11 and the LRE-finder tool.

Results: Twelve isolates belonged to clonal complex 17 (CC17); ST80 (n = 10), ST612 (n = 1) and ST1380 (n = 1). Six isolates showed the presence of optrA gene and G2576T mutations in the 23S rRNA gene, while six showed poxtA and cfr(D) genes. One isolate showed the combination of optrA, cfr(D) and poxtA genes.

Conclusion: Our findings show the circulation of CC17 sequence types with a known outbreak potential and we identified molecular mechanisms of resistance that were not previously reported from Pakistan.

Keywords: Linezolid resistant Enterococcus; Mechanism of resistance; Pakistan; Whole genome sequencing.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Relatedness of the fifteen Enterococcus faecium strains from Pakistan with global isolates. The phylogenetic tree of fifteen isolates from Pakistan (EFPK_1 to EFPK_15) generated with strains from three countries: India, China and USA were visualized and annotated in iTOL (https://itol.embl.de/upload.cgi). The isolates were annotated based on country, MLST, source of specimen (blood, urine and central venous catheter tip), Vancomycin resistance (resistant = purple), Linezolid resistance (resistant = blue) and presence of genes vanHAX, optrA, poxtA, cfr(D), 23S G2576T (presence is labelled as black)
Fig. 2
Fig. 2
BRIG plot of Enterococcus faecium strains. The coverage map of four Enterococcus faecium sequences (EFPK_01, EFPK_08, EFPK_10 and EFPK_13) are labelled as blue, red, green, and magenta, and are compared with the reference strain from India (VB3025, grey). All four sequences show more than 90% similarity with the reference strain. Additional GC content and GC Skew features are displayed. Antimicrobial resistance genes were annotated correspond to the reference (VB3025). The tool used to draw figure is BRIG tool (https://brig.sourceforge.net/)
See this image and copyright information in PMC

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