Whole genome sequencing and molecular epidemiology of clinical isolates of Staphylococcus aureus from Algeria

Rachida Namoune; Abla Djebbar; Rebecca Mekler; Martin Patrick McHugh; Mohammed El Amine Bekara; Arun Decano; Matthew Holden; Mohammed Sebaihia

doi:10.3390/microorganisms11082047

Whole genome sequencing and molecular epidemiology of clinical isolates of Staphylococcus aureus from Algeria

Rachida Namoune, Abla Djebbar, Rebecca Mekler, Martin Patrick McHugh, Mohammed El Amine Bekara, Arun Decano, Matthew Holden^*, Mohammed Sebaihia^*

^*Corresponding author for this work

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

Abstract

Staphylococcus aureus is an important pathogen responsible for various healthcare- and community-acquired infections. In this study, whole genome sequencing (WGS) was used to genotype S. aureus clinical isolates from two hospitals in Algeria and to characterize their genetic determinants of antimicrobial resistance. Seventeen S. aureus isolates were included in this study. WGS, single-nucleotide polymorphism (SNP)-based phylogenetic analysis, in silico multilocus sequence typing (MLST), spa and staphylococcal cassette chromosome mec (SCCmec) typing and in silico antimicrobial resistance profiling were performed. Phenotypic antibiotic susceptibility testing was performed using the Vitek 2 system and the disk diffusion method. The isolates were separated into sequence types (STs), with ST80 being predominant; five clonal complexes (CCs); four spa types (t044, t127, t368, t386); and two SCCmec types (IVc and IVa). Whole genome analysis revealed the presence of the resistance genes mecA, blaZ, ermC, fusB, fusC, tetK, aph(3′)-IIIa and aad(6) and mutations conferring resistance in the genes parC and fusA. The rate of multidrug resistance (MDR) was 64%. This work provides a high-resolution characterization of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates and emphasizes the importance of continuous surveillance to monitor the spread of S. aureus in healthcare settings in the country.

Original language	English
Article number	2047
Number of pages	11
Journal	Microorganisms
Volume	11
Issue number	8
DOIs	https://doi.org/10.3390/microorganisms11082047
Publication status	Published - 9 Aug 2023

Keywords

Staphylococcus aureus
MRSA
WGS
MLST
Antibiotic resistance
Algeria

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.3390/microorganisms11082047Licence: CC BY

Namoune-2023-Whole-genome-sequencing-Microorganisms-11-02047-CCBY
Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/4.0/).
Final published version, 605 KBLicence: CC BY

Prof M Holden MRC: Holistic approach to unravel antibacterial resistance in East Africa (HATUA)
Holden, M. (PI), Gillespie, S. H. (CoI), Keenan, K. L. (CoI), Kesby, M. (CoI), Lynch, A. (CoI), Sabiiti, W. (CoI), Sloan, D. J. (CoI) & Smith, V. A. (CoI)
Medical Research Council
1/05/18 → 30/04/21
Project: Standard

Staphylococcus aureus: Whole genome sequencing and molecular epidemiology of clinical isolates of Staphylococcus aureus from Algeria (dataset)
Holden, M. (Creator), NCBI GenBank, 2023
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA930663
Dataset

Cite this

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title = "Whole genome sequencing and molecular epidemiology of clinical isolates of Staphylococcus aureus from Algeria",

abstract = "Staphylococcus aureus is an important pathogen responsible for various healthcare- and community-acquired infections. In this study, whole genome sequencing (WGS) was used to genotype S. aureus clinical isolates from two hospitals in Algeria and to characterize their genetic determinants of antimicrobial resistance. Seventeen S. aureus isolates were included in this study. WGS, single-nucleotide polymorphism (SNP)-based phylogenetic analysis, in silico multilocus sequence typing (MLST), spa and staphylococcal cassette chromosome mec (SCCmec) typing and in silico antimicrobial resistance profiling were performed. Phenotypic antibiotic susceptibility testing was performed using the Vitek 2 system and the disk diffusion method. The isolates were separated into sequence types (STs), with ST80 being predominant; five clonal complexes (CCs); four spa types (t044, t127, t368, t386); and two SCCmec types (IVc and IVa). Whole genome analysis revealed the presence of the resistance genes mecA, blaZ, ermC, fusB, fusC, tetK, aph(3′)-IIIa and aad(6) and mutations conferring resistance in the genes parC and fusA. The rate of multidrug resistance (MDR) was 64%. This work provides a high-resolution characterization of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates and emphasizes the importance of continuous surveillance to monitor the spread of S. aureus in healthcare settings in the country.",

keywords = "Staphylococcus aureus, MRSA, WGS, MLST, Antibiotic resistance, Algeria",

author = "Rachida Namoune and Abla Djebbar and Rebecca Mekler and McHugh, {Martin Patrick} and {El Amine Bekara}, Mohammed and Arun Decano and Matthew Holden and Mohammed Sebaihia",

note = "Funding: This research was funded by the Algerian Ministry of Higher Education and Scientific Research (DGRSDT/MESRS), and by grants from the Wellcome Trust (098731/z/11/z to St Andrews University Bioinformatics Unit) and to the Chief Scientists Office (SIRN10 to M.T.G.H.), and the National Institute for Health Research, Medical Research Council and the Department of Health and Social Care (MR/S004785/1 to M.T.G.H.); this award is also part of the EDCTP2 program supported by the European Union.",

year = "2023",

month = aug,

day = "9",

doi = "10.3390/microorganisms11082047",

language = "English",

volume = "11",

journal = "Microorganisms",

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T1 - Whole genome sequencing and molecular epidemiology of clinical isolates of Staphylococcus aureus from Algeria

AU - Namoune, Rachida

AU - Djebbar, Abla

AU - Mekler, Rebecca

AU - McHugh, Martin Patrick

AU - El Amine Bekara, Mohammed

AU - Decano, Arun

AU - Holden, Matthew

AU - Sebaihia, Mohammed

N1 - Funding: This research was funded by the Algerian Ministry of Higher Education and Scientific Research (DGRSDT/MESRS), and by grants from the Wellcome Trust (098731/z/11/z to St Andrews University Bioinformatics Unit) and to the Chief Scientists Office (SIRN10 to M.T.G.H.), and the National Institute for Health Research, Medical Research Council and the Department of Health and Social Care (MR/S004785/1 to M.T.G.H.); this award is also part of the EDCTP2 program supported by the European Union.

PY - 2023/8/9

Y1 - 2023/8/9

N2 - Staphylococcus aureus is an important pathogen responsible for various healthcare- and community-acquired infections. In this study, whole genome sequencing (WGS) was used to genotype S. aureus clinical isolates from two hospitals in Algeria and to characterize their genetic determinants of antimicrobial resistance. Seventeen S. aureus isolates were included in this study. WGS, single-nucleotide polymorphism (SNP)-based phylogenetic analysis, in silico multilocus sequence typing (MLST), spa and staphylococcal cassette chromosome mec (SCCmec) typing and in silico antimicrobial resistance profiling were performed. Phenotypic antibiotic susceptibility testing was performed using the Vitek 2 system and the disk diffusion method. The isolates were separated into sequence types (STs), with ST80 being predominant; five clonal complexes (CCs); four spa types (t044, t127, t368, t386); and two SCCmec types (IVc and IVa). Whole genome analysis revealed the presence of the resistance genes mecA, blaZ, ermC, fusB, fusC, tetK, aph(3′)-IIIa and aad(6) and mutations conferring resistance in the genes parC and fusA. The rate of multidrug resistance (MDR) was 64%. This work provides a high-resolution characterization of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates and emphasizes the importance of continuous surveillance to monitor the spread of S. aureus in healthcare settings in the country.

AB - Staphylococcus aureus is an important pathogen responsible for various healthcare- and community-acquired infections. In this study, whole genome sequencing (WGS) was used to genotype S. aureus clinical isolates from two hospitals in Algeria and to characterize their genetic determinants of antimicrobial resistance. Seventeen S. aureus isolates were included in this study. WGS, single-nucleotide polymorphism (SNP)-based phylogenetic analysis, in silico multilocus sequence typing (MLST), spa and staphylococcal cassette chromosome mec (SCCmec) typing and in silico antimicrobial resistance profiling were performed. Phenotypic antibiotic susceptibility testing was performed using the Vitek 2 system and the disk diffusion method. The isolates were separated into sequence types (STs), with ST80 being predominant; five clonal complexes (CCs); four spa types (t044, t127, t368, t386); and two SCCmec types (IVc and IVa). Whole genome analysis revealed the presence of the resistance genes mecA, blaZ, ermC, fusB, fusC, tetK, aph(3′)-IIIa and aad(6) and mutations conferring resistance in the genes parC and fusA. The rate of multidrug resistance (MDR) was 64%. This work provides a high-resolution characterization of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates and emphasizes the importance of continuous surveillance to monitor the spread of S. aureus in healthcare settings in the country.

KW - Staphylococcus aureus

KW - MRSA

KW - WGS

KW - MLST

KW - Antibiotic resistance

KW - Algeria

U2 - 10.3390/microorganisms11082047

DO - 10.3390/microorganisms11082047

M3 - Article

C2 - 37630607

SN - 2076-2607

VL - 11

JO - Microorganisms

JF - Microorganisms

IS - 8

M1 - 2047

ER -

Whole genome sequencing and molecular epidemiology of clinical isolates of Staphylococcus aureus from Algeria

Abstract

Keywords

UN SDGs

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Projects

Prof M Holden MRC: Holistic approach to unravel antibacterial resistance in East Africa (HATUA)

Datasets

Staphylococcus aureus: Whole genome sequencing and molecular epidemiology of clinical isolates of Staphylococcus aureus from Algeria (dataset)

Cite this