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Abusheraida NSA, AlBaker AAH, Aljabri ASA, Abdelrahman HA, Al-Mana H, Wilson GJ, Anan KA, Eltai NO. Rapid Visual Detection of Methicillin-Resistant Staphylococcus aureus in Human Clinical Samples via Closed LAMP Assay Targeting mecA and spa Genes. Microorganisms 2024; 12:157. [PMID: 38257983 PMCID: PMC10819026 DOI: 10.3390/microorganisms12010157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
The emergence of antimicrobial resistance (AMR), particularly methicillin-resistant Staphylococcus aureus (MRSA), poses a significant global health threat as these bacteria increasingly become resistant to the most available therapeutic options. Thus, developing an efficient approach to rapidly screen MRSA directly from clinical specimens has become vital. In this study, we establish a closed-tube loop-mediated isothermal amplification (LAMP) method incorporating hydroxy-naphthol blue (HNB) colorimetric dye assay to directly detect MRSA from clinical samples based on the presence of mecA and spa genes. In total, 125 preidentified S. aureus isolates and 93 clinical samples containing S. aureus were sourced from the microbiology laboratory at Hamad General Hospital (HGH). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were computed based on conventional PCR. The assay demonstrated 100% specificity, 91.23% sensitivity, 0.90 Cohen Kappa (CK), 100% PPV, and 87.8% NPV for the clinical samples, while clinical isolates exhibited 100% specificity, 97% sensitivity, 0.926 CK, 100% PPV, and 88.89% NPV. Compared to cefoxitin disk diffusion, LAMP provided 100% specificity and sensitivity, 1.00 CK, and 100% for PPV and NPV. The study revealed that the closed-tube LAMP incorporating (HNB) dye is a rapid technique with a turnaround time of less than 1 h and high specificity and sensitivity.
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Affiliation(s)
- Noora S. A. Abusheraida
- College of Health Science, Qatar University, Doha P.O. Box 2713, Qatar; (N.S.A.A.); (A.A.H.A.); (A.S.A.A.)
| | - Asraa A. H. AlBaker
- College of Health Science, Qatar University, Doha P.O. Box 2713, Qatar; (N.S.A.A.); (A.A.H.A.); (A.S.A.A.)
| | - Asmaa S. A. Aljabri
- College of Health Science, Qatar University, Doha P.O. Box 2713, Qatar; (N.S.A.A.); (A.A.H.A.); (A.S.A.A.)
| | - Hana A. Abdelrahman
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.A.); (H.A.-M.)
| | - Hassan Al-Mana
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.A.); (H.A.-M.)
| | - Godwin J. Wilson
- Laboratory Medicine and Pathology, Hamad General Hospital, Doha P.O. Box 3050, Qatar;
| | | | - Nahla O. Eltai
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.A.); (H.A.-M.)
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Silvola J, Gröndahl-Yli-Hannuksela K, Hirvioja T, Rantakokko-Jalava K, Rintala E, Auranen K, Junnila J, Marttila H, Lindholm L, Vuopio J. Whole genome sequencing reveals new links between spa t172/CC59 methicillin-resistant Staphylococcus aureus cases in low-endemicity region of Southwest Finland, 2007‒2016. Sci Rep 2022; 12:21326. [PMID: 36494398 PMCID: PMC9734107 DOI: 10.1038/s41598-022-25556-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) rates have remained relatively low in Finland. In Southwest Finland, however, annual MRSA incidence increased from 12 to 25/100,000 between 2007 and 2016 with spa t172 strain causing one fourth (237/983) of all cases. This provoked us to study the molecular epidemiology of t172-MRSA, aiming to better understand the transmission of this strain type. We combined epidemiological data and whole genome sequencing (WGS) of a set of 64 (27%, 64/237) t172-MRSA isolates covering 10 years. Isolates represented sporadic and index cases of all identified healthcare-associated outbreaks (HAOs) and family clusters (FCs). Among the included 62 isolates, core-genome MLST analysis revealed eight genomic clusters comprising 24 (38.7%) isolates and 38 (61.3%) non-clustered isolates. Cluster 1 comprised ten and the remaining seven clusters two isolates each, respectively. Two epidemiologically distinct HAOs were linked in cluster 1. FCs were involved in all clusters. All strains were associated with epidemic clonal complex CC59. We were able to confirm the spread of several successful t172-MRSA subclones in regional healthcare and the community. WGS complemented routine surveillance by revealing undetected links between t172-MRSA cases. Targeted, WGS-based typing could enhance MRSA surveillance without the need for routine WGS diagnostics.
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Affiliation(s)
- Jaakko Silvola
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Tiina Hirvioja
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Kaisu Rantakokko-Jalava
- grid.410552.70000 0004 0628 215XClinical Microbiology Laboratory, Turku University Hospital, Turku, Finland
| | - Esa Rintala
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Kari Auranen
- grid.1374.10000 0001 2097 1371Department of Mathematics and Statistics and Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Jenna Junnila
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Marttila
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Laura Lindholm
- grid.14758.3f0000 0001 1013 0499Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jaana Vuopio
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XClinical Microbiology Laboratory, Turku University Hospital, Turku, Finland ,grid.14758.3f0000 0001 1013 0499Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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Jones SU, Chua KH, Chew CH, Yeo CC, Abdullah FH, Othman N, Kee BP, Puah SM. spa diversity of methicillin-resistant and -susceptible Staphylococcus aureus in clinical strains from Malaysia: a high prevalence of invasive European spa-type t032. PeerJ 2021; 9:e11195. [PMID: 33889447 PMCID: PMC8038637 DOI: 10.7717/peerj.11195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/09/2021] [Indexed: 12/30/2022] Open
Abstract
Background Staphylococcus aureus is one of the important pathogens causing nosocomial infection. spa typing allows identification of S. aureus clones in hospital isolates and is useful for epidemiological studies and nosocomial infection control. This study aims to investigate the spa types in Malaysian S. aureus isolates obtained from various clinical specimens. Method A total of 89 methicillin-resistant S. aureus (MRSA) [pus (n = 55), blood (n = 27), respiratory (n = 5), eye (n = 2)] isolates and 109 methicillin-susceptible S. aureus (MSSA) [pus (n = 79), blood (n = 24), respiratory (n = 3), eye (n = 2) and urine (n = 1)] isolates were subjected to spa typing with sequences analysed using BioNumerics version 7. Results The spa sequence was successfully amplified from 77.8% of the strains (154/198) and 47 known spa types were detected. The distribution of known spa types in MRSA (36.2%, 17/47) was less diverse than in MSSA (70.2%, 33/47). The most predominant spa types were t032 (50%) in MRSA, and t127 (19%) and t091 (16.7%) in MSSA, respectively. spa type t091 in MSSA was significantly associated with skin and soft tissue infections (p = 0.0199). Conclusion The previously uncommon spa type t032 was detected in the Malaysian MRSA strains, which also corresponded to the most common spa type in Europe and Australia, and has replaced the dominant spa type t037 which was reported in Malaysia in 2010.
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Affiliation(s)
- Sherry Usun Jones
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Nerus, Terengganu, Malaysia
| | - Chew Chieng Yeo
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengganu, Malaysia
| | | | - Norlela Othman
- Department of Pathology, Hospital Sultanah Nur Zahirah, Kuala Terengganu, Terengganu, Malaysia
| | - Boon Pin Kee
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Genetic Characterization of Methicillin-Resistant Staphylococcus aureus Isolates from Human Bloodstream Infections: Detection of MLS B Resistance. Antibiotics (Basel) 2020; 9:antibiotics9070375. [PMID: 32635147 PMCID: PMC7400445 DOI: 10.3390/antibiotics9070375] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022] Open
Abstract
In this study we aimed to characterize antimicrobial resistance in methicillin-resistant Staphylococcus aureus (MRSA) isolated from bloodstream infections as well as the associated genetic lineages of the isolates. Sixteen MRSA isolates were recovered from bacteremia samples from inpatients between 2016 and 2019. The antimicrobial susceptibility of these isolates was tested by the Kirby–Bauer disk diffusion method against 14 antimicrobial agents. To determine the macrolide–lincosamide–streptogramin B (MLSB) resistance phenotype of the isolates, erythromycin-resistant isolates were assessed by double-disk diffusion (D-test). The resistance and virulence genes were screened by polymerase chain reaction (PCR). All isolates were characterized by multilocus sequence typing (MLST), spa typing, staphylococcal chromosomal cassette mec (SCCmec) typing, and accessory gene regulator (agr) typing. Isolates showed resistance to cefoxitin, penicillin, ciprofloxacin, erythromycin, fusidic acid, clindamycin, and aminoglycosides, confirmed by the presence of the blaZ, ermA, ermC, mphC, msrA/B, aac(6’)-Ie-aph(2’’)-Ia, and ant(4’)-Ia genes. Three isolates were Panton–Valentine-leukocidin-positive. Most strains (n = 12) presented an inducible MLSB phenotype. The isolates were ascribed to eight spa-types (t747, t002, t020, t1084, t008, t10682, t18526, and t1370) and four MLSTs (ST22, ST5, ST105, and ST8). Overall, most (n = 12) MRSA isolates had a multidrug-resistance profile with inducible MLSB phenotypes and belonged to epidemic MRSA clones.
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