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Che Hamzah AM, Chew CH, Al-Trad EI, Puah SM, Chua KH, A Rahman NI, Ismail S, Maeda T, Palittapongarnpim P, Yeo CC. Whole genome sequencing of methicillin-resistant Staphylococcus aureus clinical isolates from Terengganu, Malaysia, indicates the predominance of the EMRSA-15 (ST22-SCCmec IV) clone. Sci Rep 2024; 14:3485. [PMID: 38347106 PMCID: PMC10861583 DOI: 10.1038/s41598-024-54182-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/09/2024] [Indexed: 02/15/2024] Open
Abstract
Despite the importance of methicillin-resistant Staphylococcus aureus (MRSA) as a priority nosocomial pathogen, the genome sequences of Malaysian MRSA isolates are currently limited to a small pool of samples. Here, we present the genome sequence analyses of 88 clinical MRSA isolates obtained from the main tertiary hospital in Terengganu, Malaysia in 2016-2020, to obtain in-depth insights into their characteristics. The EMRSA-15 (ST22-SCCmec IV) clone of the clonal complex 22 (CC22) lineage was predominant with a total of 61 (69.3%) isolates. Earlier reports from other Malaysian hospitals indicated the predominance of the ST239 clone, but only two (2.3%) isolates were identified in this study. Two Indian-origin clones, the Bengal Bay clone ST772-SCCmec V (n = 2) and ST672 (n = 10) were also detected, with most of the ST672 isolates obtained in 2020 (n = 7). Two new STs were found, with one isolate each, and were designated ST7879 and ST7883. From the core genome phylogenetic tree, the HSNZ MRSA isolates could be grouped into seven clades. Antimicrobial phenotype-genotype concordance was high (> 95%), indicating the accuracy of WGS in predicting most resistances. Majority of the MRSA isolates were found to harbor more than 10 virulence genes, demonstrating their pathogenic nature.
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Affiliation(s)
- Ainal Mardziah Che Hamzah
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, 21300, Kuala Nerus, Terengganu, Malaysia.
| | - Esra'a Ibrahim Al-Trad
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, 20400, Kuala Terengganu, Terengganu, Malaysia
- Faculty of Allied Medical Sciences, Jadara University, Irbid, Jordan
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nor Iza A Rahman
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Salwani Ismail
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Toshinari Maeda
- Department of Biological Functions and Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-Ku, Kitakyushu, 808-0196, Japan
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, 20400, Kuala Terengganu, Terengganu, Malaysia.
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Al-Talib H, Samsudin S, Adnan A, Murugaiah C. Genetic Diversity among Methicillin-Resistant Staphylococcus aureus in Malaysia (2002-2020). Trop Med Infect Dis 2022; 7:360. [PMID: 36355902 PMCID: PMC9692495 DOI: 10.3390/tropicalmed7110360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023] Open
Abstract
UNLABELLED 1. BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) is a common organism seen in both healthcare-associated and community-associated infections worldwide and in Malaysia over the past two decades. The aim of this review is to provide a firsthand documentation of all MRSA strains prevalent in the Malaysian population from 2002 to present and briefly describe the changing patterns. 2. METHODS Electronic and manual intensive literature searches were conducted between 2002 and 2020, addressing issues directly related to patients and published in the English language were selected. 3. RESULTS The literature search retrieved a total of 2217 articles and abstracts of 27 articles. The search yielded a total of 24 articles on genotyping of MRSA in Malaysia. The study found that MRSA strains were mostly genetically related and resulted in the predominant MRSA clones that caused active infections. Thirty-six different sequence types (ST) were recorded. The highest rates of STs detected were ST239 (52.6%), ST1 (47.4%), and ST22 (42.1%). The majority of studies showed that both SCCmec types III and IV were the most common SCCm type in Malaysia, followed by SCCmec type V (57.9%). 4. CONCLUSIONS Both Brazilian (ST 239 IIIA) and Hungarian (ST 239-III) MRSA strains were detected in Malaysia. PFGE remains the best method for comparing MRSA strains. However, whole-genome sequencing has a promising chance to replace PFGE in the future.
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Affiliation(s)
- Hassanain Al-Talib
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh 47000, Malaysia
| | - Syahirah Samsudin
- Institute for Medical and Molecular Biotechnology, Universiti Teknologi MARA (UiTM), Sungai Buloh 47000, Malaysia
| | - Ariza Adnan
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh 47000, Malaysia
| | - Chandrika Murugaiah
- Department of Biomedical Sciences and Therapeutics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Malaysia
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Che Hamzah AM, Yeo CC, Puah SM, Chua KH, Chew CH. Staphylococcus aureus Infections in Malaysia: A Review of Antimicrobial Resistance and Characteristics of the Clinical Isolates, 1990-2017. Antibiotics (Basel) 2019; 8:E128. [PMID: 31454985 PMCID: PMC6784215 DOI: 10.3390/antibiotics8030128] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus aureus is an important nosocomial pathogen and its multidrug resistant strains, particularly methicillin-resistant S. aureus (MRSA), poses a serious threat to public health due to its limited therapeutic options. The increasing MRSA resistance towards vancomycin, which is the current drug of last resort, gives a great challenge to the treatment and management of MRSA infections. While vancomycin resistance among Malaysian MRSA isolates has yet to be documented, a case of vancomycin resistant S. aureus has been reported in our neighboring country, Indonesia. In this review, we present the antimicrobial resistance profiles of S. aureus clinical isolates in Malaysia with data obtained from the Malaysian National Surveillance on Antimicrobial Resistance (NSAR) reports as well as various peer-reviewed published records spanning a period of nearly three decades (1990-2017). We also review the clonal types and characteristics of Malaysian S. aureus isolates, where hospital-associated (HA) MRSA isolates tend to carry staphylococcal cassette chromosome mec (SCCmec) type III and were of sequence type (ST)239, whereas community-associated (CA) isolates are mostly SCCmec type IV/V and ST30. More comprehensive surveillance data that include molecular epidemiological data would enable further in-depth understanding of Malaysian S. aureus isolates.
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Affiliation(s)
- Ainal Mardziah Che Hamzah
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Nerus 21300, Terengganu, Malaysia
| | - Chew Chieng Yeo
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Terengganu, Malaysia
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Nerus 21300, Terengganu, Malaysia.
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Ho WY, Choo QC, Chew CH. Predominance of Three Closely Related Methicillin-ResistantStaphylococcus aureusClones Carrying a UniqueccrC-Positive SCCmectype III and the Emergence ofspa t304andt690SCCmectype IVpvl+MRSA Isolates in Kinta Valley, Malaysia. Microb Drug Resist 2017; 23:215-223. [DOI: 10.1089/mdr.2015.0250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Wai-Yew Ho
- Centre for Foundation Studies, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| | - Quok-Cheong Choo
- Departments of Biological Sciences, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| | - Choy-Hoong Chew
- Biomedical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar, Malaysia
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Steinig EJ, Andersson P, Harris SR, Sarovich DS, Manoharan A, Coupland P, Holden MTG, Parkhill J, Bentley SD, Robinson DA, Tong SYC. Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus. BMC Genomics 2015; 16:388. [PMID: 25981586 PMCID: PMC4432960 DOI: 10.1186/s12864-015-1599-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/28/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-associated infection, but there is growing awareness of the emergence of multidrug-resistant lineages in community settings around the world. One such lineage is ST772-MRSA-V, which has disseminated globally and is increasingly prevalent in India. Here, we present the complete genome sequence of DAR4145, a strain of the ST772-MRSA-V lineage from India, and investigate its genomic characteristics in regards to antibiotic resistance and virulence factors. RESULTS Sequencing using single-molecule real-time technology resulted in the assembly of a single continuous chromosomal sequence, which was error-corrected, annotated and compared to nine draft genome assemblies of ST772-MRSA-V from Australia, Malaysia and India. We discovered numerous and redundant resistance genes associated with mobile genetic elements (MGEs) and known core genome mutations that explain the highly antibiotic resistant phenotype of DAR4145. Staphylococcal toxins and superantigens, including the leukotoxin Panton-Valentinin Leukocidin, were predominantly associated with genomic islands and the phage φ-IND772PVL. Some of these mobile resistance and virulence factors were variably present in other strains of the ST772-MRSA-V lineage. CONCLUSIONS The genomic characteristics presented here emphasize the contribution of MGEs to the emergence of multidrug-resistant and highly virulent strains of community-associated MRSA. Antibiotic resistance was further augmented by chromosomal mutations and redundancy of resistance genes. The complete genome of DAR4145 provides a valuable resource for future investigations into the global dissemination and phylogeography of ST772-MRSA-V.
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Affiliation(s)
- Eike J Steinig
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
| | - Patiyan Andersson
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Derek S Sarovich
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
| | - Anand Manoharan
- Pushpagiri Research Center, Pushpagiri Institute of Medical Sciences and Research Center, Thiruvalla, India.
| | - Paul Coupland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | | | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Stephen D Bentley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - D Ashley Robinson
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS, USA.
| | - Steven Y C Tong
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
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