Complete genome sequence and analysis of a ST573 multidrug-resistant methicillin-resistant Staphylococcus aureus SauR3 clinical isolate from Terengganu, Malaysia

Esra’a I. Al-Trad; Ainal Mardziah Che Hamzah; Suat Moi Puah; Kek Heng Chua; Muhamad Zarul Hanifah; Qasim Ayub; Prasit Palittapongarnpim; Stephen M. Kwong; Ching Hoong Chew; Chew Chieng Yeo

doi:10.3390/pathogens12030502

Complete genome sequence and analysis of a ST573 multidrug-resistant methicillin-resistant Staphylococcus aureus SauR3 clinical isolate from Terengganu, Malaysia

Esra’a I. Al-Trad, Ainal Mardziah Che Hamzah, Suat Moi Puah, Kek Heng Chua, Muhamad Zarul Hanifah, Qasim Ayub, Prasit Palittapongarnpim, Stephen M. Kwong, Ching Hoong Chew, Chew Chieng Yeo

Western Sydney University

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

2 Citations (Scopus)

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a World Health Organization-listed priority pathogen. Scarce genomic data are available for MRSA isolates from Malaysia. Here, we present the complete genome sequence of a multidrug-resistant MRSA strain SauR3, isolated from the blood of a 6-year-old patient hospitalized in Terengganu, Malaysia, in 2016. S. aureus SauR3 was resistant to five antimicrobial classes comprising nine antibiotics. The genome was sequenced on the Illumina and Oxford Nanopore platforms and hybrid assembly was performed to obtain its complete genome sequence. The SauR3 genome consists of a circular chromosome of 2,800,017 bp and three plasmids designated pSauR3-1 (42,928 bp), pSauR3-2 (3011 bp), and pSauR3-3 (2473 bp). SauR3 belongs to sequence type 573 (ST573), a rarely reported sequence type of the staphylococcal clonal complex 1 (CC1) lineage, and harbors a variant of the staphylococcal cassette chromosome mec (SCCmec) type V (5C2&5) element which also contains the aac(6′)-aph(2″) aminoglycoside-resistance genes. pSauR3-1 harbors several antibiotic resistance genes in a 14,095 bp genomic island (GI), previously reported in the chromosome of other staphylococci. pSauR3-2 is cryptic, whereas pSauR3-3 encodes the ermC gene that mediates inducible resistance to macrolide-lincosamide-streptogramin B (iMLS_B). The SauR3 genome can potentially be used as a reference genome for other ST573 isolates.

Original language	English
Article number	502
Number of pages	21
Journal	Pathogens
Volume	12
Issue number	3
DOIs	https://doi.org/10.3390/pathogens12030502
Publication status	Published - Mar 2023

Bibliographical note

Publisher Copyright:
© 2023 by the authors.

Open Access - Access Right Statement

© 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/).

Keywords

genomic islands
prophages
resistance genes
plasmids
SCCmec element
hybrid assembly
Staphylococcus aureus ST573

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Al-Trad, E. I., Hamzah, A. M. C., Puah, S. M., Chua, K. H., Hanifah, M. Z., Ayub, Q., Palittapongarnpim, P., Kwong, S. M., Chew, C. H., & Yeo, C. C. (2023). Complete genome sequence and analysis of a ST573 multidrug-resistant methicillin-resistant Staphylococcus aureus SauR3 clinical isolate from Terengganu, Malaysia. Pathogens, 12(3), Article 502. https://doi.org/10.3390/pathogens12030502

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abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is a World Health Organization-listed priority pathogen. Scarce genomic data are available for MRSA isolates from Malaysia. Here, we present the complete genome sequence of a multidrug-resistant MRSA strain SauR3, isolated from the blood of a 6-year-old patient hospitalized in Terengganu, Malaysia, in 2016. S. aureus SauR3 was resistant to five antimicrobial classes comprising nine antibiotics. The genome was sequenced on the Illumina and Oxford Nanopore platforms and hybrid assembly was performed to obtain its complete genome sequence. The SauR3 genome consists of a circular chromosome of 2,800,017 bp and three plasmids designated pSauR3-1 (42,928 bp), pSauR3-2 (3011 bp), and pSauR3-3 (2473 bp). SauR3 belongs to sequence type 573 (ST573), a rarely reported sequence type of the staphylococcal clonal complex 1 (CC1) lineage, and harbors a variant of the staphylococcal cassette chromosome mec (SCCmec) type V (5C2&5) element which also contains the aac(6′)-aph(2″) aminoglycoside-resistance genes. pSauR3-1 harbors several antibiotic resistance genes in a 14,095 bp genomic island (GI), previously reported in the chromosome of other staphylococci. pSauR3-2 is cryptic, whereas pSauR3-3 encodes the ermC gene that mediates inducible resistance to macrolide-lincosamide-streptogramin B (iMLSB). The SauR3 genome can potentially be used as a reference genome for other ST573 isolates.",

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T1 - Complete genome sequence and analysis of a ST573 multidrug-resistant methicillin-resistant Staphylococcus aureus SauR3 clinical isolate from Terengganu, Malaysia

AU - Al-Trad, Esra’a I.

AU - Hamzah, Ainal Mardziah Che

AU - Puah, Suat Moi

AU - Chua, Kek Heng

AU - Hanifah, Muhamad Zarul

AU - Ayub, Qasim

AU - Palittapongarnpim, Prasit

AU - Kwong, Stephen M.

AU - Chew, Ching Hoong

AU - Yeo, Chew Chieng

PY - 2023/3

Y1 - 2023/3

N2 - Methicillin-resistant Staphylococcus aureus (MRSA) is a World Health Organization-listed priority pathogen. Scarce genomic data are available for MRSA isolates from Malaysia. Here, we present the complete genome sequence of a multidrug-resistant MRSA strain SauR3, isolated from the blood of a 6-year-old patient hospitalized in Terengganu, Malaysia, in 2016. S. aureus SauR3 was resistant to five antimicrobial classes comprising nine antibiotics. The genome was sequenced on the Illumina and Oxford Nanopore platforms and hybrid assembly was performed to obtain its complete genome sequence. The SauR3 genome consists of a circular chromosome of 2,800,017 bp and three plasmids designated pSauR3-1 (42,928 bp), pSauR3-2 (3011 bp), and pSauR3-3 (2473 bp). SauR3 belongs to sequence type 573 (ST573), a rarely reported sequence type of the staphylococcal clonal complex 1 (CC1) lineage, and harbors a variant of the staphylococcal cassette chromosome mec (SCCmec) type V (5C2&5) element which also contains the aac(6′)-aph(2″) aminoglycoside-resistance genes. pSauR3-1 harbors several antibiotic resistance genes in a 14,095 bp genomic island (GI), previously reported in the chromosome of other staphylococci. pSauR3-2 is cryptic, whereas pSauR3-3 encodes the ermC gene that mediates inducible resistance to macrolide-lincosamide-streptogramin B (iMLSB). The SauR3 genome can potentially be used as a reference genome for other ST573 isolates.

AB - Methicillin-resistant Staphylococcus aureus (MRSA) is a World Health Organization-listed priority pathogen. Scarce genomic data are available for MRSA isolates from Malaysia. Here, we present the complete genome sequence of a multidrug-resistant MRSA strain SauR3, isolated from the blood of a 6-year-old patient hospitalized in Terengganu, Malaysia, in 2016. S. aureus SauR3 was resistant to five antimicrobial classes comprising nine antibiotics. The genome was sequenced on the Illumina and Oxford Nanopore platforms and hybrid assembly was performed to obtain its complete genome sequence. The SauR3 genome consists of a circular chromosome of 2,800,017 bp and three plasmids designated pSauR3-1 (42,928 bp), pSauR3-2 (3011 bp), and pSauR3-3 (2473 bp). SauR3 belongs to sequence type 573 (ST573), a rarely reported sequence type of the staphylococcal clonal complex 1 (CC1) lineage, and harbors a variant of the staphylococcal cassette chromosome mec (SCCmec) type V (5C2&5) element which also contains the aac(6′)-aph(2″) aminoglycoside-resistance genes. pSauR3-1 harbors several antibiotic resistance genes in a 14,095 bp genomic island (GI), previously reported in the chromosome of other staphylococci. pSauR3-2 is cryptic, whereas pSauR3-3 encodes the ermC gene that mediates inducible resistance to macrolide-lincosamide-streptogramin B (iMLSB). The SauR3 genome can potentially be used as a reference genome for other ST573 isolates.

KW - genomic islands

KW - prophages

KW - resistance genes

KW - plasmids

KW - SCCmec element

KW - hybrid assembly

KW - Staphylococcus aureus ST573

UR - https://hdl.handle.net/1959.7/uws:69550

UR - http://www.scopus.com/inward/record.url?scp=85151438099&partnerID=8YFLogxK

U2 - 10.3390/pathogens12030502

DO - 10.3390/pathogens12030502

M3 - Article

SN - 2076-0817

VL - 12

JO - Pathogens

JF - Pathogens

IS - 3

M1 - 502

ER -

Complete genome sequence and analysis of a ST573 multidrug-resistant methicillin-resistant Staphylococcus aureus SauR3 clinical isolate from Terengganu, Malaysia

Abstract

Bibliographical note

Open Access - Access Right Statement

Keywords

UN SDGs

Access to Document

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