1
|
Saleem M, Ahmad I, Salem AM, Almarshedy SM, Moursi SA, Syed Khaja AS, Rakha E, Azhar A, Ashammari MN, Almalaq H, Alshurtan K, Khan MS. Molecular and genetic analysis of methicillin-resistant Staphylococcus aureus (MRSA) in a tertiary care hospital in Saudi Arabia. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025; 398:7559-7569. [PMID: 39777537 DOI: 10.1007/s00210-024-03771-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Accepted: 12/27/2024] [Indexed: 01/11/2025]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) continues to pose significant challenges in healthcare settings due to its multi-drug resistance (MDR) and virulence. This retrospective study examines the molecular and resistance profiles of MRSA isolates from a tertiary care hospital in Saudi Arabia, providing valuable insights into regional epidemiology. A total of 190 MRSA strains were analysed to assess antimicrobial susceptibility, genetic diversity, and virulence factors. Antimicrobial susceptibility testing was conducted according to CLSI guidelines, while molecular characterization involved spa typing, SCCmec typing, and DNA microarray analysis to determine clonal complexes (CCs), resistance genes, and virulence determinants. The isolates showed extensive resistance to beta-lactam antibiotics, with 78% classified as MDR. Notably, resistance to fusidic acid and ciprofloxacin was detected in 70% and 55% of isolates, respectively. The most prevalent clonal complexes-CC5, CC6, and CC22-comprised over 60% of the isolates and exhibited diverse spa types. The Panton-Valentine leukocidin (PVL) gene, linked to heightened virulence, was identified in approximately 20% of isolates, particularly within CC5, CC30, and CC80. Enterotoxin genes (sea and seb) and immune evasion genes (sak, chp, and scn) were also commonly detected, reflecting the isolates' capacity to adapt and persist within the hospital environment. These findings underscore the high burden of MDR MRSA with considerable genetic diversity and virulence potential. The study highlights the urgent need for strengthened molecular surveillance and targeted infection control measures to limit MRSA transmission and effectively manage infection risks in healthcare facilities.
Collapse
Affiliation(s)
- Mohd Saleem
- Department of Pathology, College of Medicine, University of Hail, Hail, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Alharbi Mohammed Salem
- Department of Internal Medicine, College of Medicine, University of Hail, Hail, Saudi Arabia
| | | | - Soha Abdallah Moursi
- Department of Pathology, College of Medicine, University of Hail, Hail, Saudi Arabia
| | | | - Ehab Rakha
- Laboratory Department, King Khalid Hospital, Hail, Saudi Arabia
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Asim Azhar
- NAP Lifesciences, Evershine City, Vasai East, Maharashtra, 401208, India
| | | | - Homoud Almalaq
- Department of Medical Supplies, Hail Health Cluster, Hail, Saudi Arabia
| | - Kareemah Alshurtan
- Department of Internal Medicine, College of Medicine, University of Hail, Hail, Saudi Arabia
| | - Mohd Shahid Khan
- Department of Microbiology, Hind Institute of Medical Sciences, Mau, Ataria, Sitapur, Uttar Pradesh, India, 261303.
| |
Collapse
|
2
|
Hotz JF, Staudacher M, Schefberger K, Spettel K, Schmid K, Kriz R, Schneider L, Hagemann JB, Cyran N, Schmidt K, Starzengruber P, Lötsch F, Leutzendorff A, Daller S, Ramharter M, Burgmann H, Lagler H. Unraveling novel mutation patterns and morphological variations in two dalbavancin-resistant MRSA strains in Austria using whole genome sequencing and transmission electron microscopy. BMC Infect Dis 2024; 24:899. [PMID: 39223565 PMCID: PMC11367932 DOI: 10.1186/s12879-024-09797-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains resistant to non-beta-lactam antimicrobials poses a significant challenge in treating severe MRSA bloodstream infections. This study explores resistance development and mechanisms in MRSA isolates, especially after the first dalbavancin-resistant MRSA strain in our hospital in 2016. METHODS This study investigated 55 MRSA bloodstream isolates (02/2015-02/2021) from the University Hospital of the Medical University of Vienna, Austria. The MICs of dalbavancin, linezolid, and daptomycin were assessed. Two isolates (16-33 and 19-362) resistant to dalbavancin were analyzed via whole-genome sequencing, with morphology evaluated using transmission electron microscopy (TEM). RESULTS S.aureus BSI strain 19-362 had two novel missense mutations (p.I515M and p.A606D) in the pbp2 gene. Isolate 16-33 had a 534 bp deletion in the DHH domain of GdpP and a SNV in pbp2 (p.G146R). Both strains had mutations in the rpoB gene, but at different positions. TEM revealed significantly thicker cell walls in 16-33 (p < 0.05) compared to 19-362 and dalbavancin-susceptible strains. None of the MRSA isolates showed resistance to linezolid or daptomycin. CONCLUSION In light of increasing vancomycin resistance reports, continuous surveillance is essential to comprehend the molecular mechanisms of resistance in alternative MRSA treatment options. In this work, two novel missense mutations (p.I515M and p.A606D) in the pbp2 gene were newly identified as possible causes of dalbavancin resistance.
Collapse
Affiliation(s)
- Julian Frederic Hotz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria
- Department of Internal Medicine III, Division of Infectious Diseases, University Hospital of Ulm, Ulm, 89081, Germany
- Department of Neurology, Hospital St. John's of God, Vienna, 1020, Austria
| | - Moritz Staudacher
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria
- Department of Angiology, Medical University of Vienna, Vienna, 1090, Austria
| | - Katharina Schefberger
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | - Kathrin Spettel
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, 1090, Austria
| | - Katharina Schmid
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | - Richard Kriz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | - Lisa Schneider
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | | | - Norbert Cyran
- Faculty of Life Sciences, Research Support Facilities UBB, University of Vienna, Vienna, 1030, Austria
| | - Katy Schmidt
- Faculty of Life Sciences, Research Support Facilities UBB, University of Vienna, Vienna, 1030, Austria
| | - Peter Starzengruber
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, 1090, Austria
| | - Felix Lötsch
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, 1090, Austria
| | - Amelie Leutzendorff
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, 1090, Austria
| | - Simon Daller
- Department of Respiratory and Lung Diseases, Klinik Penzing, Vienna, 1140, Austria
| | - Michael Ramharter
- Center for Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20359, Germany
| | - Heinz Burgmann
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | - Heimo Lagler
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, 1090, Austria.
| |
Collapse
|
3
|
Mogoi NN, Sifuna AW, Okoth PK, Reva O, Malaba R, Negesa R, Nyongesa KP, Osoro KE, Welch M. Staphylococcus aureus associated with surgical site infections in Western Kenya reveals genomic hotspots for pathogen evolution. Access Microbiol 2024; 6:000734.v4. [PMID: 39045253 PMCID: PMC11261728 DOI: 10.1099/acmi.0.000734.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/03/2024] [Indexed: 07/25/2024] Open
Abstract
Objectives. Staphylococcus aureus is one of the most common pathogens attributed to hospital infections. Although S. aureus infections have been well studied in developed countries, far less is known about the biology of the pathogen in sub-Saharan Africa. Methods. Here, we report on the isolation, antibiotic resistance profiling, whole genome sequencing, and genome comparison of six multi-drug resistant isolates of S. aureus obtained from a referral hospital in Kakamega, Western Kenya. Results. Five of the six isolates contained a 20.7 kb circular plasmid carrying blaZ (associated with resistance to β-lactam antibiotics). These five strains all belonged to the same sequence type, ST152. Despite the similarity of the plasmid in these isolates, whole genome sequencing revealed that the strains differed, depending on whether they were associated with hospital-acquired or community-acquired infections. Conclusion. The intriguing finding is that the hospital-acquired and the community-acquired isolates of S. aureus belonging to the same genotype, ST152, formed two separate sub-clusters in the phylogenetic tree and differed by the repertoire of accessory virulence genes. These data suggest ongoing adaptive evolution and significant genomic plasticity.
Collapse
Affiliation(s)
- Nyabera Nicholas Mogoi
- Department of Biological sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Anthony Wawire Sifuna
- Department of Medical Biochemistry, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Patrick Kirsteen Okoth
- Department of Biological sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Centre For Bioinformatics And Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Rose Malaba
- Kakamega County General Teaching and Referral Hospital, Kakamega, Kenya
| | - Ruth Negesa
- Kakamega County General Teaching and Referral Hospital, Kakamega, Kenya
| | - Kuloba Peter Nyongesa
- Department of Medical Microbiology and Parasitology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Kombo Ezra Osoro
- Department of Medical Biochemistry, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
4
|
Nyasinga J, Munshi Z, Kigen C, Nyerere A, Musila L, Whitelaw A, Ziebuhr W, Revathi G. Displacement of Hospital-Acquired, Methicillin-Resistant Staphylococcus aureus Clones by Heterogeneous Community Strains in Kenya over a 13-Year Period. Microorganisms 2024; 12:1171. [PMID: 38930553 PMCID: PMC11205442 DOI: 10.3390/microorganisms12061171] [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: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/28/2024] Open
Abstract
We determined antibiotic susceptibility and employed Oxford Nanopore whole-genome sequencing to explore strain diversity, resistance, and virulence gene carriage among methicillin-resistant Staphylococcus aureus (MRSA) strains from different infection sites and timepoints in a tertiary Kenyan hospital. Ninety-six nonduplicate clinical isolates recovered between 2010 and 2023, identified and tested for antibiotic susceptibility on the VITEK ID/AST platform, were sequenced. Molecular typing, antibiotic resistance, and virulence determinant screening were performed using the relevant bioinformatics tools. The strains, alongside those from previous studies, were stratified into two periods covering 2010-2017 and 2018-2023 and comparisons were made. Mirroring phenotypic profiles, aac(6')-aph(2″) [aminoglycosides]; gyrA (S84L) and grlA (S80Y) [fluoroquinolones]; dfrG [anti-folates]; and tet(K) [tetracycline] resistance determinants dominated the collection. While the proportion of ST239/241-t037-SCCmec III among MRSA reduced from 37.7% to 0% over the investigated period, ST4803-t1476-SCCmec IV and ST152-t355-SCCmec IV were pre-eminent. The prevalence of Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) genes was 38% (33/87) and 6.8% (6/87), respectively. We observed the displacement of HA-MRSA ST239/241-t037-SCCmec III with the emergence of ST152-t355-SCCmec IV and a greater clonal heterogeneity. The occurrence of PVL+/ACME+ CA-MRSA in recent years warrants further investigations into their role in the CA-MRSA virulence landscape, in a setting of high PVL prevalence.
Collapse
Affiliation(s)
- Justin Nyasinga
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
- Department of Biomedical Sciences and Technology, Technical University of Kenya, Nairobi P.O. Box 52428-00200, Kenya
- Institute of Science, Technology & Innovation, Pan-African University, Nairobi P.O. Box 62000-00200, Kenya;
| | - Zubair Munshi
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
| | - Collins Kigen
- Walter Reed Army Institute of Research—Africa, Kericho P.O. Box 1357-20200, Kenya; (C.K.); (L.M.)
| | - Andrew Nyerere
- Institute of Science, Technology & Innovation, Pan-African University, Nairobi P.O. Box 62000-00200, Kenya;
| | - Lillian Musila
- Walter Reed Army Institute of Research—Africa, Kericho P.O. Box 1357-20200, Kenya; (C.K.); (L.M.)
| | - Andrew Whitelaw
- Division of Medical Microbiology and Immunology, Stellenbosch University, Matieland, Stellenbosch 7602, South Africa;
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, Josef-Schneider Str. 2D/15, D-97080 Wurzburg, Germany;
| | - Gunturu Revathi
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
| |
Collapse
|