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

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

doi:10.1186/s12866-024-03491-2

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

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

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	347
Journal	BMC Microbiology
Volume	24
Issue number	1
DOIs	https://doi.org/10.1186/s12866-024-03491-2
Publication status	Published - Dec 2024

Keywords

Linezolid resistant Enterococcus
Mechanism of resistance
Pakistan
Whole genome sequencing

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Nasir, S. A. R., Zeeshan, M., Ghanchi, N., Saeed, N., Ghayas, H., Zaka, S., Ashraf, J., Jabeen, K., Farooqi, J., Hasan, Z., Fatima, T., Rezwan, F., Mahmood, S. F., Arshad, M., Khan, E., Ozer, E. A., & Hasan, R. (2024). Linezolid-resistant Enterococcus faecium clinical isolates from Pakistan: a genomic analysis. BMC Microbiology, 24(1), Article 347. https://doi.org/10.1186/s12866-024-03491-2

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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",

author = "Nasir, {Syed Ali Raza} and Mohammad Zeeshan and Najia Ghanchi and Noureen Saeed and Hassan Ghayas and Sadaf Zaka and Javaria Ashraf and Kauser Jabeen and Joveria Farooqi and Zahra Hasan and Tazeen Fatima and Faiza Rezwan and Mahmood, {Syed Faisal} and Mehreen Arshad and Erum Khan and Ozer, {Egon A.} and Rumina Hasan",

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doi = "10.1186/s12866-024-03491-2",

language = "English",

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journal = "BMC Microbiology",

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T1 - Linezolid-resistant Enterococcus faecium clinical isolates from Pakistan

T2 - a genomic analysis

AU - Nasir, Syed Ali Raza

AU - Zeeshan, Mohammad

AU - Ghanchi, Najia

AU - Saeed, Noureen

AU - Ghayas, Hassan

AU - Zaka, Sadaf

AU - Ashraf, Javaria

AU - Jabeen, Kauser

AU - Farooqi, Joveria

AU - Hasan, Zahra

AU - Fatima, Tazeen

AU - Rezwan, Faiza

AU - Mahmood, Syed Faisal

AU - Arshad, Mehreen

AU - Khan, Erum

AU - Ozer, Egon A.

AU - Hasan, Rumina

PY - 2024/12

Y1 - 2024/12

N2 - 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.

AB - 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.

KW - Linezolid resistant Enterococcus

KW - Mechanism of resistance

KW - Pakistan

KW - Whole genome sequencing

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U2 - 10.1186/s12866-024-03491-2

DO - 10.1186/s12866-024-03491-2

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AN - SCOPUS:85204137817

SN - 1471-2180

VL - 24

JO - BMC Microbiology

JF - BMC Microbiology

IS - 1

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ER -

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

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Keywords

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