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Jiang S, Matuszewska M, Chen M, Hong Y, Chen Y, Wang Z, Zhuang H, Sun L, Zhu F, Wang H, Wu X, Ji S, Holmes MA, Ba X, Chen Y, Yu Y. Emergence and spread of ST5 methicillin-resistant Staphylococcus aureus with accessory gene regulator dysfunction: genomic insights and antibiotic resistance. Microbiol Res 2025; 297:128196. [PMID: 40311457 DOI: 10.1016/j.micres.2025.128196] [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: 02/20/2025] [Revised: 04/23/2025] [Accepted: 04/24/2025] [Indexed: 05/03/2025]
Abstract
The globally disseminated Staphylococcus aureus ST5 clone poses a major public health threat due to its multidrug resistance and virulence. Here, we identified an agr-dysfunctional (agrA-I238K) ST5 MRSA clone that has spread across East and Southeast Asia, with recent increases in China since its emergence in the 1970s. Comparative genomic analyses identified distinct single-nucleotide polymorphisms and mobile genetic elements linked to enhanced resistance and virulence. This clone exhibits resistance to seven antimicrobial classes, including third-generation tetracyclines and fusidic acid, and shares phenotypic and genetic similarities with the vancomycin-intermediate S. aureus Mu50 strain, including reduced susceptibility to vancomycin, teicoplanin, and daptomycin. The agrA-I238K mutation attenuates hemolytic activity, increases biofilm formation, and reduces daptomycin susceptibility, suggesting a key role in the clone's success. Our results demonstrate the important role of agrA-I238K mutation in the widespread distribution of agr-dysfunctional MRSA and highlight the importance of genomic surveillance in tracking the spread of agr-dysfunctional ST5 MRSA.
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Affiliation(s)
- Shengnan Jiang
- Centre of Laboratory Medicine, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China; Zhejiang University School of Medicine, Hangzhou, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, University of Cambridge, Cambridge, UK
| | - Mengzhen Chen
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Yueqin Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yiyi Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhengan Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hemu Zhuang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lu Sun
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feiteng Zhu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haiping Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xueqing Wu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shujuan Ji
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Yan Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Yunsong Yu
- Centre of Laboratory Medicine, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Girma A. Staphylococcus aureus: Current perspectives on molecular pathogenesis and virulence. Cell Surf 2025; 13:100137. [PMID: 39758277 PMCID: PMC11699754 DOI: 10.1016/j.tcsw.2024.100137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 12/04/2024] [Accepted: 12/07/2024] [Indexed: 01/07/2025] Open
Abstract
Staphylococcus aureus has evolved a sophisticated regulatory system to control its virulence. One of the main roles of this interconnected network is to sense and respond to diverse environmental signals by altering the synthesis of virulence components required for survival in the host, including cell surface adhesins, extracellular enzymes and toxins. The accessory gene regulator (agr), a quorum sensing system that detects the local concentration of a cyclic peptide signaling molecule, is one of the well-studied of these S. aureus regulatory mechanisms. By using this system, S. aureus is able to sense its own population density and translate this information into a specific pattern of gene expression. In addition to Agr, this pathogen senses specific stimuli through various two-component systems and synchronizes responses with alternative sigma factors and cytoplasmic regulators of the SarA protein family. These different regulatory mechanisms combine host and environmental information into a network that guarantees the best possible response of pathogens to changing circumstances. In this article, an overview of the most significant and thoroughly studied regulatory systems of S. aureus is provided, along with a summary of their roles in host interactions.
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Affiliation(s)
- Abayeneh Girma
- Department of Biology, College of Natural and Computational Science, Mekdela Amba University, P.O. Box 32, Tulu Awuliya, Ethiopia
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3
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Muteeb G, Kazi RNA, Aatif M, Azhar A, Oirdi ME, Farhan M. Antimicrobial resistance: Linking molecular mechanisms to public health impact. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2025; 33:100232. [PMID: 40216324 DOI: 10.1016/j.slasd.2025.100232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2025] [Revised: 03/20/2025] [Accepted: 04/08/2025] [Indexed: 04/21/2025]
Abstract
BACKGROUND Antimicrobial resistance (AMR) develops into a worldwide health emergency through genetic and biochemical adaptations which enable microorganisms to resist antimicrobial treatment. β-lactamases (blaNDM, blaKPC) and efflux pumps (MexAB-OprM) working with mobile genetic elements facilitate fast proliferation of multidrug-resistant (MDR) and exttreme drug-resistant (XDR) phenotypes thus creating major concerns for healthcare systems and community health as well as the agricultural sector. OBJECTIVES The review dissimilarly unifies molecular resistance pathways with public health implications through the study of epidemiological data and monitoring approaches and innovative therapeutic solutions. Previous studies separating their attention between molecular genetics and clinical outcomes have been combined into our approach which delivers an all-encompassing analysis of AMR. KEY INSIGHTS The report investigates the resistance mechanisms which feature enzymatic degradation and efflux pump overexpression together with target modification and horizontal gene transfer because these factors represent important contributors to present-day AMR developments. This review investigates AMR effects on hospital and community environments where it affects pathogens including MRSA, carbapenem-resistant Klebsiella pneumoniae, and drug-resistant Pseudomonas aeruginosa. This document explores modern AMR management methods that comprise WHO GLASS molecular surveillance systems and three innovative strategies such as CRISPR-modified genome editing and bacteriophage treatments along with antimicrobial peptides and artificial intelligence diagnostic tools. CONCLUSION The resolution of AMR needs complete scientific and global operational methods alongside state-of-the-art therapeutic approaches. Worldwide management of drug-resistant infection burden requires both enhanced infection prevention procedures with next-generation antimicrobial strategies to reduce cases effectively.
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Affiliation(s)
- Ghazala Muteeb
- Department of Nursing, College of Applied Medical Science, King Faisal University, Al-Ahsa, Saudi Arabia.
| | - Raisa Nazir Ahmed Kazi
- Department of Respiratory Therapy, College of Applied Medical Science, King Faisal, University, Al-Ahsa, Saudi Arabia
| | - Mohammad Aatif
- Department of Public Health, College of Applied Medical Science, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Asim Azhar
- NAP Life Sciences; Metropolitan Region, Maharashtra 401208, India
| | - Mohamed El Oirdi
- Department of Biological Sciences, College of Science, King Faisal University, Al Ahsa, Saudi Arabia; Department of Basic Sciences, Preparatory Year, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mohd Farhan
- Department of Basic Sciences, Preparatory Year, King Faisal University, Al-Ahsa, Saudi Arabia; Department of Chemistry, College of Science, King Faisal University, Al Ahsa, Saudi Arabia.
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García-Cobos S, Seco Alberca N, Bravo-Queipo-de-Llano B, Casquero-García V, Ramírez de Arellano E, Calvo C, Ruíz-Carrascoso G, Falces-Romero I, Larrosa Escartín N, Viñado-Perez B, Martínez-López MÁ, Melendo Pérez S, Ruíz de Gopegui E, Pérez Vázquez S, Carrasco-Colom J, Aracil García B, Pérez-Vázquez M, Méndez-Echevarría A, Oteo Iglesias J. Genomic analysis of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) causing infections in children-a Spanish multicenter study. Front Microbiol 2025; 16:1534840. [PMID: 40415924 PMCID: PMC12098397 DOI: 10.3389/fmicb.2025.1534840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 04/14/2025] [Indexed: 05/27/2025] Open
Abstract
Objectives Staphylococcus aureus is one of the most common human pathogens causing skin and soft tissue infections (SSTIs) among children. This study investigated the molecular traits of community-associated methicillin-resistant S. aureus (CA-MRSA) isolates causing infections in children in Spain. Methods Antibiotic susceptibility testing and whole-genome sequencing were performed in 98 CA-MRSA isolates (4.2 median age, 52% males). The phylogenetic relationship, antibiotic resistance, virulence, and plasmid replicon genes content were investigated. Results Resistance rates were found as follows: Erythromycin, 42.9%, which could be explained due to the presence of erm(C), mph(C), and msr(A) genes; tobramycin, 27.5%, which could be explained due to the presence of aac(6')-Ie/aph(2″)-Ia and aadD1 genes; tetracycline, 25.5%, which could be explained mainly due to the presence of tet(K) genes; levofloxacin and moxifloxacin, 19.4%, which could be explained primarily due to the mutations in gyrA and parC genes; and gentamicin, 15.3%, which could be explained due to the presence of aac(6')-Ie/aph(2″)-Ia gene. The most prevalent lineage was ST8-IVc and t008. Most isolates were genetically diverse, except for three groups of isolates from the same hospital and one group of isolates from different hospitals. These had less than or equal to 5 allele differences by core-genome multilocus sequence typing (cgMLST) analysis or 0-6 core single-nucleotide polymorphisms (SNPs) by core-genome SNP-based analysis. Phage-encoded Panton-Valentine leukocidin (PVL) genes were found in 75.5% of the isolates. Other common virulence genes were related to adhesion (capA and capP), lipid degradation (geh), hemolysis (hlb, hld, hlgABC, and hly/hla), and tissue destruction (sspAB). Conclusion This study observed a high genetic diversity among CA-MRSA isolates causing community-acquired infections in children in Spain, with ST8-IVc as the most prevalent lineage. Nevertheless, genetic relatedness of some isolates from the same as well as different hospitals suggests the dissemination of CA-MRSA among children by contact.
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Affiliation(s)
- Silvia García-Cobos
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Natalia Seco Alberca
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Blanca Bravo-Queipo-de-Llano
- Servicio de Pediatría y Enfermedades Infecciosas, Hospital Universitario La Paz, Fundación IdiPaz, Madrid, Spain; Universidad Autónoma de Madrid, Red de Investigación Traslación en Infectología Pediátrica (RITIP), Madrid, Spain
| | - Verónica Casquero-García
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Eva Ramírez de Arellano
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Calvo
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Pediatría y Enfermedades Infecciosas, Hospital Universitario La Paz, Fundación IdiPaz, Madrid, Spain; Universidad Autónoma de Madrid, Red de Investigación Traslación en Infectología Pediátrica (RITIP), Madrid, Spain
| | - Guillermo Ruíz-Carrascoso
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario La Paz, Fundación IdiPaz, Madrid, Spain
| | - Iker Falces-Romero
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario La Paz, Fundación IdiPaz, Madrid, Spain
| | - Nieves Larrosa Escartín
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Vall d’Hebron, Barcelona, Spain
- Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Belén Viñado-Perez
- Servicio de Microbiología, Hospital Universitario Vall d’Hebron, Barcelona, Spain
- Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | | | - Enrique Ruíz de Gopegui
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Son Espases, Mallorca, Spain
| | | | | | - Belén Aracil García
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Méndez-Echevarría
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Pediatría y Enfermedades Infecciosas, Hospital Universitario La Paz, Fundación IdiPaz, Madrid, Spain; Universidad Autónoma de Madrid, Red de Investigación Traslación en Infectología Pediátrica (RITIP), Madrid, Spain
| | - Jesús Oteo Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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Wassanarungroj P, Nobthai P, Ruekit S, Srijan A, Sukhchat P, Serichantalergs O, Crawford JM, Swierczewski BE, Chaudhury S, Lertsethtakarn P. Molecular Characterization of Clinical Isolates of Methicillin-Resistant Staphylococcus aureus from Chonburi, Thailand. Pathogens 2025; 14:406. [PMID: 40430727 PMCID: PMC12114143 DOI: 10.3390/pathogens14050406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 05/29/2025] Open
Abstract
Staphylococcus aureus (S. aureus), especially methicillin-resistant S. aureus (MRSA), remains a major public health concern. This study reports the antimicrobial resistance profiles and molecular characteristics of 31 S. aureus isolated during 2017-2018 from inpatient and outpatient clinical specimens from Queen Sirikit Naval Hospital (QSH) in Chonburi province, Thailand. All isolates were tested for antimicrobial susceptibility. Staphylococcal cassette chromosome mec (SCCmec) typing, Panton-Valentine leukocidin (pvl) toxin, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and staphylococcal protein A (spa) typing were performed. Twenty-seven isolates were confirmed to be MRSA and exhibited resistance to up to seven antibiotics classes. The main MLST type was SCCmec type II (51.9%) and ST764 (55.6%). Five spa types were identified with t045 (55.6%) as the major type. All 31 S. aureus isolates were grouped into seven types using PFGE with the SCCmecII-ST764-t045 clone being the most prevalent. Overall, our findings reveal that the S. aureus isolates in this study differ from previous reports in Thailand, indicating a potential shift in local strains, highlighting the need for ongoing molecular surveillance of multidrug resistance patterns of MRSA in Southeast Asia.
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Affiliation(s)
- Patcharawalai Wassanarungroj
- Department of Bacterial and Parasitic Diseases, Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences (WRAIR-AFRIMS), 315/6 Rajvithi Rd., Bangkok 10400, Thailand; (P.W.); (P.N.); (S.R.); (A.S.); (S.C.)
| | - Panida Nobthai
- Department of Bacterial and Parasitic Diseases, Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences (WRAIR-AFRIMS), 315/6 Rajvithi Rd., Bangkok 10400, Thailand; (P.W.); (P.N.); (S.R.); (A.S.); (S.C.)
| | - Sirigade Ruekit
- Department of Bacterial and Parasitic Diseases, Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences (WRAIR-AFRIMS), 315/6 Rajvithi Rd., Bangkok 10400, Thailand; (P.W.); (P.N.); (S.R.); (A.S.); (S.C.)
| | - Apichai Srijan
- Department of Bacterial and Parasitic Diseases, Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences (WRAIR-AFRIMS), 315/6 Rajvithi Rd., Bangkok 10400, Thailand; (P.W.); (P.N.); (S.R.); (A.S.); (S.C.)
| | | | - Oralak Serichantalergs
- Department of Bacterial and Parasitic Diseases, Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences (WRAIR-AFRIMS), 315/6 Rajvithi Rd., Bangkok 10400, Thailand; (P.W.); (P.N.); (S.R.); (A.S.); (S.C.)
| | - John M. Crawford
- US Army Research Institute of Chemical Defense, Gunpowder, MA 21010, USA;
| | - Brett E. Swierczewski
- US Army Medical Research Institute of Infectious Diseases, Frederick, MA 21702, USA;
| | - Sidhartha Chaudhury
- Department of Bacterial and Parasitic Diseases, Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences (WRAIR-AFRIMS), 315/6 Rajvithi Rd., Bangkok 10400, Thailand; (P.W.); (P.N.); (S.R.); (A.S.); (S.C.)
| | - Paphavee Lertsethtakarn
- Department of Bacterial and Parasitic Diseases, Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences (WRAIR-AFRIMS), 315/6 Rajvithi Rd., Bangkok 10400, Thailand; (P.W.); (P.N.); (S.R.); (A.S.); (S.C.)
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6
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Kizziah JL, Mukherjee A, Parker LK, Dokland T. Structure of the Staphylococcus aureus bacteriophage 80α neck shows details of the DNA, tail completion protein, and tape measure protein. Structure 2025:S0969-2126(25)00104-2. [PMID: 40174589 DOI: 10.1016/j.str.2025.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 02/21/2025] [Accepted: 03/06/2025] [Indexed: 04/04/2025]
Abstract
The Staphylococcus aureus pathogenicity islands (SaPIs), including SaPI1, are a type of mobile genetic elements (MGEs) that are mobilized at high frequency by "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from helper-encoded structural proteins. 80α and SaPI1 virions consist of an icosahedral head connected via a portal vertex to a long, non-contractile tail. A connector or "neck" forms the interface between the tail and the head. Here, we have determined the high-resolution structure of the neck section of SaPI1 virions, including the dodecameric portal and head-tail-connector proteins, and the hexameric head-tail joining, tail terminator and major tail proteins. We also resolved the DNA, the tail completion protein (TCP), and the tape measure protein (TMP) inside the tail, features that have not previously been observed at high resolution. Our study provides insights into the assembly and infection process in this important group of MGEs.
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Affiliation(s)
- James L Kizziah
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amarshi Mukherjee
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura K Parker
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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7
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Periferakis A, Periferakis AT, Troumpata L, Periferakis K, Georgatos-Garcia S, Touriki G, Dragosloveanu CDM, Caruntu A, Savulescu-Fiedler I, Dragosloveanu S, Scheau AE, Badarau IA, Caruntu C, Scheau C. Pinosylvin: A Multifunctional Stilbenoid with Antimicrobial, Antioxidant, and Anti-Inflammatory Potential. Curr Issues Mol Biol 2025; 47:204. [PMID: 40136458 PMCID: PMC11941527 DOI: 10.3390/cimb47030204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 03/13/2025] [Accepted: 03/15/2025] [Indexed: 03/27/2025] Open
Abstract
Stilbenoids are a category of plant compounds exhibiting notable health-related benefits. After resveratrol, perhaps the most well-known stilbenoid is pinosylvin, a major phytochemical constituent of most plants characterised by the pine spines among others. Pinosylvin and its derivatives have been found to exert potent antibacterial and antifungal effects, while their antiparasitic and antiviral properties are still a subject of ongoing research. The antioxidant properties of pinosylvin are mostly based on its scavenging of free radicals, inhibition of iNOS and protein kinase C, and promotion of HO-1 expression. Its anti-inflammatory properties are based on a variety of mechanisms, such as COX-2 inhibition, NF-κB and TRPA1 activation inhibition, and reduction in IL-6 levels. Its anticancer properties are partly associated with its antioxidant and anti-inflammatory potential, although a number of other mechanisms are described, such as apoptosis induction and matrix metalloproteinase inhibition. A couple of experiments have also suggested a neuroprotective potential. A multitude of ethnomedical and ethnobotanical effects of pinosylvin-containing plants are reported, like antimicrobial, antioxidant, anti-inflammatory, hepatoprotective, and prokinetic actions; many of these are corroborated by recent research. The advent of novel methods of artificial pinosylvin synthesis may facilitate its mass production and adoption as a medical compound. Finally, pinosylvin may be a tool in promoting environmentally friendly pesticide and insecticide policies and be used in land remediation schemes.
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Affiliation(s)
- Argyrios Periferakis
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Akadimia of Ancient Greek and Traditional Chinese Medicine, 16675 Athens, Greece
- Elkyda, Research & Education Centre of Charismatheia, 17675 Athens, Greece
| | - Aristodemos-Theodoros Periferakis
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Elkyda, Research & Education Centre of Charismatheia, 17675 Athens, Greece
| | - Lamprini Troumpata
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Konstantinos Periferakis
- Akadimia of Ancient Greek and Traditional Chinese Medicine, 16675 Athens, Greece
- Pan-Hellenic Organization of Educational Programs (P.O.E.P.), 17236 Athens, Greece
| | - Spyrangelos Georgatos-Garcia
- Tilburg Institute for Law, Technology, and Society (TILT), Tilburg University, 5037 DE Tilburg, The Netherlands
- Corvers Greece IKE, 15124 Athens, Greece
| | - Georgia Touriki
- Faculty of Law, Democritus University of Thrace, 69100 Komotini, Greece
| | - Christiana Diana Maria Dragosloveanu
- Department of Ophthalmology, Faculty of Dentistry, The “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Department of Ophthalmology, Clinical Hospital for Ophthalmological Emergencies, 010464 Bucharest, Romania
| | - Ana Caruntu
- Department of Oral and Maxillofacial Surgery, “Carol Davila” Central Military Emergency Hospital, 010825 Bucharest, Romania
- Department of Oral and Maxillofacial Surgery, Faculty of Dental Medicine, Titu Maiorescu University, 031593 Bucharest, Romania
| | - Ilinca Savulescu-Fiedler
- Department of Internal Medicine, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Internal Medicine and Cardiology, Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Serban Dragosloveanu
- Department of Orthopaedics and Traumatology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Orthopaedics, “Foisor” Clinical Hospital of Orthopaedics, Traumatology and Osteoarticular TB, 021382 Bucharest, Romania
| | - Andreea-Elena Scheau
- Department of Radiology and Medical Imaging, “Foisor” Clinical Hospital of Orthopaedics, Traumatology and Osteoarticular TB, 021382 Bucharest, Romania
| | - Ioana Anca Badarau
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Constantin Caruntu
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Dermatology, “Prof. N.C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 011233 Bucharest, Romania
| | - Cristian Scheau
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Radiology and Medical Imaging, “Foisor” Clinical Hospital of Orthopaedics, Traumatology and Osteoarticular TB, 021382 Bucharest, Romania
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Kovács L, Szabó Á, Barnácz F, Csirmaz B, Jerzsele Á, Kerek Á. Antimicrobial Susceptibility Profiles of Commensal Staphylococcus spp. Isolates from Turkeys in Hungarian Poultry Farms Between 2022 and 2023. Antibiotics (Basel) 2025; 14:200. [PMID: 40001443 PMCID: PMC11851855 DOI: 10.3390/antibiotics14020200] [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: 01/16/2025] [Revised: 02/12/2025] [Accepted: 02/12/2025] [Indexed: 02/27/2025] Open
Abstract
Background: The poultry industry is one of the most rapidly growing sectors, producing the highest amount of animal-derived protein per unit time while also being the second-largest consumer of antibiotics. The widespread and accelerating spread of antimicrobial resistance (AMR) underscores the necessity of regular monitoring studies. Periodic assessments, especially focusing on commensal strains, can serve as indicators of emerging resistance patterns. Methods: This study assesses the antimicrobial susceptibility profiles of putative commensal Staphylococcus strains (n = 166) isolated from large-scale turkey flocks in Hungary using minimal inhibitory concentration (MIC) determination. The isolated strains were tested against antibiotics of veterinary and public health importance. The results were analyzed using the Kruskal-Wallis test and the Mann-Whitney U test, as well as t-tests. Additionally, correlation analysis and principal component analysis were performed. Results: Our findings revealed the highest resistance rates to tiamulin (90.4%), doxycycline (79.5%), and enrofloxacin (68.7%). Conclusions: These results reflect the extensive antibiotic use in the poultry sector, which contributes to the widespread presence of antimicrobial resistance. As regular monitoring and the identification of trends can aid in mitigating the spread of resistance, these findings should be complemented by data on antibiotic usage at the surveyed farms in further studies. The observed resistance rate of 18.1% to vancomycin is particularly concerning from a public health perspective, given that comparative human data show only a 0.05% resistance rate. Additionally, for multidrug-resistant strains, next-generation sequencing should be utilized to elucidate the genetic mechanisms underlying resistance, particularly in strains exhibiting high levels of resistance to vancomycin, which is of critical importance in human medicine, as well as to the critically important enrofloxacin and the widely used doxycycline and tiamulin. However, the limitations of the study should also be acknowledged, including the relatively small sample size, which is significantly lower than that of available human data, as well as the spatial distribution of the samples.
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Affiliation(s)
- László Kovács
- Department of Animal Hygiene, Herd Health and Mobile Clinic, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary;
- Poultry-Care Kft., H-5052 Újszász, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary;
| | - Ábel Szabó
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (Á.S.); (F.B.); (B.C.)
| | - Franciska Barnácz
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (Á.S.); (F.B.); (B.C.)
| | - Bence Csirmaz
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (Á.S.); (F.B.); (B.C.)
| | - Ákos Jerzsele
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary;
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (Á.S.); (F.B.); (B.C.)
| | - Ádám Kerek
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary;
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (Á.S.); (F.B.); (B.C.)
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9
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Li Y, Berti AD, Abdelhady W, Xiong YQ. Prophage ϕSA169 Enhances Vancomycin Persistence in Methicillin-Resistant Staphylococcus aureus (MRSA). Antibiotics (Basel) 2025; 14:191. [PMID: 40001434 PMCID: PMC11852059 DOI: 10.3390/antibiotics14020191] [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: 12/19/2024] [Revised: 01/25/2025] [Accepted: 02/11/2025] [Indexed: 02/27/2025] Open
Abstract
Background: Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections present a significant clinical therapeutic challenge. Prophages are increasingly recognized as important genetic factors influencing the pathogenicity of S. aureus, yet their role in antibiotic persistence in MRSA remains underexplored. Our previous work demonstrated that prophage ϕSA169 promotes vancomycin (VAN) persistence in an experimental model of endocarditis caused by MRSA strains with a clonal complex (CC) 45 genetic background. However, it is unknown whether this persistence-promoting effect of ϕSA169 extends to other clinically relevant MRSA lineages. This study aims to elucidate the role of ϕSA169 in influencing VAN persistence across diverse MRSA genetic backgrounds. Methods: A pilot analysis of clinical data suggested that patients infected by MRSA containing ϕSA169-like prophage appear to have worse clinical outcomes. Thus, we lysogenized representative clinical resolving bacteremia (RB) MRSA strains with ϕSA169 and evaluated phenotypes closely associated with VAN persistence, including VAN susceptibility, biofilm formation, and the efficacy of VAN treatment in an experimental infective endocarditis (IE) model. Each ϕSA169 lysogenic strain was compared to its isogenic MRSA parental counterpart. Results: ϕSA169 lysogeny significantly promotes biofilm formation and enhances survival to VAN exposure under human-mimicking conditions for RB strains from CC5 and CC30. ϕSA169 lysogeny significantly reduces VAN effectiveness in the IE model due to RB lysogen from CC5 despite no detectable impact on VAN MICs. Conclusions: These results indicate that ϕSA169 promotes VAN persistence across clonal backgrounds, likely through biofilm formation and VAN tolerance. Targeting prophage could provide new strategies to combat persistent MRSA infections.
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Affiliation(s)
- Yi Li
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (Y.L.); (W.A.)
| | - Andrew D. Berti
- Department of Pharmacy Practice, Wayne State University College of Pharmacy and Health Sciences, Detroit, MI 48201, USA;
| | - Wessam Abdelhady
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (Y.L.); (W.A.)
| | - Yan Q. Xiong
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (Y.L.); (W.A.)
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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10
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Rallis D, Atzemoglou N, Kapetaniou K, Giaprou LE, Baltogianni M, Giapros V. Molecular Epidemiology Clinical Manifestations, Decolonization Strategies, and Treatment Options of Methicillin-Resistant Staphylococcus aureus Infection in Neonates. Pathogens 2025; 14:155. [PMID: 40005530 PMCID: PMC11858580 DOI: 10.3390/pathogens14020155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 01/23/2025] [Accepted: 02/03/2025] [Indexed: 02/27/2025] Open
Abstract
Preterm and low-birth-weight neonates are particularly susceptible to methicillin-resistant Staphylococcus aureus (MRSA) colonization, whereas MRSA infection is associated with significant neonatal morbidity and mortality globally. The objective of our study was to examine the current body of knowledge about molecular traits, epidemiology, risk factors, clinical presentation, decolonization techniques, and available treatments for MRSA infection in neonates. MRSA strains that predominate in neonatal units, namely healthcare-associated (HA)-MRSA, differ from community-acquired (CA)-MRSA strains in molecular characteristics, toxin synthesis, including Panton-Valentine leukocidin, and resistance to antibiotics. Colonization with MRSA predisposes neonates to infection. The clinical impact of MRSA infection includes bacteremia, sepsis, pneumonia, endocarditis, osteomyelitis, septic arthritis, skin and soft tissue infections, and toxic shock syndrome. To reduce MRSA transmission, colonization, and infection, customized approaches are required, including continuous surveillance of MRSA epidemiology, new techniques for detecting MRSA resistance, and the application of basic preventive measures. Antimicrobial susceptibility monitoring is essential to identify the best empirical antimicrobial treatments. The growing antibiotic resistance of MRSA remains challenging, and vancomycin is still the best option. Further extensive research and surveillance are warranted to explore the genetic diversity and prevalence of MRSA.
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Affiliation(s)
- Dimitrios Rallis
- Neonatal Intensive Care Unit, School of Medicine, University of Ioannina, 45110 Ioannina, Greece; (D.R.); (N.A.); (L.-E.G.); (M.B.)
| | - Natalia Atzemoglou
- Neonatal Intensive Care Unit, School of Medicine, University of Ioannina, 45110 Ioannina, Greece; (D.R.); (N.A.); (L.-E.G.); (M.B.)
| | - Konstantina Kapetaniou
- Department of Pediatrics, School of Medicine, University of Ioannina, 45110 Ioannina, Greece;
| | - Lida-Eleni Giaprou
- Neonatal Intensive Care Unit, School of Medicine, University of Ioannina, 45110 Ioannina, Greece; (D.R.); (N.A.); (L.-E.G.); (M.B.)
| | - Maria Baltogianni
- Neonatal Intensive Care Unit, School of Medicine, University of Ioannina, 45110 Ioannina, Greece; (D.R.); (N.A.); (L.-E.G.); (M.B.)
| | - Vasileios Giapros
- Neonatal Intensive Care Unit, School of Medicine, University of Ioannina, 45110 Ioannina, Greece; (D.R.); (N.A.); (L.-E.G.); (M.B.)
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11
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Acharyya S, Majumder S, Nandi S, Ghosh A, Saha S, Bhattacharya M. Uncovering mercury accumulation and the potential for bacterial bioremediation in response to contamination in the Singalila National Park. Sci Rep 2025; 15:3664. [PMID: 39881141 PMCID: PMC11779926 DOI: 10.1038/s41598-024-81927-5] [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: 10/16/2024] [Accepted: 11/30/2024] [Indexed: 01/31/2025] Open
Abstract
Several recent investigations into montane regions have reported on excess mercury accumulation in high-altitude forest ecosystems. This study explored the Singalila National Park, located on the Singalila ridge of the Eastern Himalayas, revealing substantial mercury contamination. Particular focus was on Sandakphu (3636 m), the highest peak in West Bengal, India. It harboured 6.77 ± 0.01 mg/kg of total mercury in its topsoil. Further evidence was provided by accumulation in leaves (0.040 ± 0.01 mg/kg), and roots (0.150 ± 0.008 mg/kg) of local vegetation, litterfall (0.234 ± 0.019 mg/kg), mosses (0.367 ± 0.043 mg/kg), surface water from local lakes and waterbodies (0.010 ± 0.005 mg/l), fresh snow (0.014 ± 0.004 mg/l), and sleet (0.019 ± 0.009 mg/l). Samples from other points of varying elevation in the park also demonstrated contamination. The soil displayed a range of 0.068-5.28 mg/kg, while the mean concentration in leaves was 0.153 ± 0.105 mg/kg, roots was 0.106 ± 0.054 mg/kg, and leaf litter was 0.240 ± 0.112 mg/kg. Additionally, the microbial consortia isolated from the contaminated soil displayed a high tolerance to mercuric chloride, presumably gained through repeated and consistent exposure. Four high tolerance bacterial strains, MTS2C, MTS3A, MTS4B and MTS6A, were further characterized for potential use in bioremediation strategies. Their mercury removal capacities were determined to be 82.35%, 75.21%, 61.95%, and 37.47%, respectively. Overall, the findings presented provide evidence for a highly contaminated environment in the Singalila National Park, that poses significant ecological risk to the flora, fauna and local inhabitants of this biodiversity hotspot. This research also highlights the need for further exploration and monitoring of the Eastern Himalayas for its role as a sink for atmospheric mercury.
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Affiliation(s)
- Sukanya Acharyya
- Molecular Biology and Tissue Culture Laboratory, Department of Tea Science, University of North Bengal, Siliguri, West Bengal, India
| | - Soumya Majumder
- Molecular Biology and Tissue Culture Laboratory, Department of Tea Science, University of North Bengal, Siliguri, West Bengal, India
| | - Sudeshna Nandi
- Molecular Biology and Tissue Culture Laboratory, Department of Tea Science, University of North Bengal, Siliguri, West Bengal, India
| | - Arindam Ghosh
- Molecular Biology and Tissue Culture Laboratory, Department of Tea Science, University of North Bengal, Siliguri, West Bengal, India
| | - Sumedha Saha
- Molecular Biology and Tissue Culture Laboratory, Department of Tea Science, University of North Bengal, Siliguri, West Bengal, India
| | - Malay Bhattacharya
- Molecular Biology and Tissue Culture Laboratory, Department of Tea Science, University of North Bengal, Siliguri, West Bengal, India.
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12
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Faraj R, Ramadan H, Bentum KE, Alkaraghulli B, Woube Y, Hassan Z, Samuel T, Adesiyun A, Jackson CR, Abebe W. Antimicrobial Resistance, Virulence Gene Profiling, and Spa Typing of Staphylococcus aureus Isolated from Retail Chicken Meat in Alabama, USA. Pathogens 2025; 14:107. [PMID: 40005484 PMCID: PMC11858072 DOI: 10.3390/pathogens14020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 01/13/2025] [Accepted: 01/20/2025] [Indexed: 02/27/2025] Open
Abstract
Antibiotic-resistant Staphylococcus aureus (S. aureus) in retail meat poses a public health threat requiring continuous surveillance. This study investigated the frequency of isolation, toxin genes, and antibiotic resistance profile of S. aureus recovered from retail poultry meat samples and presented results beneficial to public health interventions. Of 200 samples collected, 16% (32/200) tested positive for S. aureus, and these were recovered from thigh 37.5% (12/32), wing 34.4% (11/32), gizzard (15.6% (5/32), and liver 12.5% (4/32) samples. Findings of spa typing analysis revealed that 68.8% (22/32), 18.8% (6/32), 9.4% (3/32), and 3.0% (1/32) of the isolates belonged to the spa types t267, t160, t548, and t008, respectively. For antibiotic susceptibility testing, 12.5% (4/32) of the isolates were resistant to only penicillin, but one isolate (1/32; 3%) showed resistance to the antibiotics penicillin, erythromycin, ampicillin, and oxacillin. PCR analysis revealed that 9.4% (3/32) of the isolates carried the mecA gene associated with methicillin-resistant Staphylococcus aureus (MRSA) isolates. One MRSA isolate was identified as a t008 spa type, and harbored a 26,974 bp-sized plasmid, which was the source of its resistance to penicillin, ampicillin, erythromycin, and oxacillin. The staphylococcal enterotoxin (SE) genes seg, sei, sek, seb, selm, and seln were also identified among the isolates, and mostly the antimicrobial and enterotoxin genes were carried on plasmids of the isolates. This study raises awareness on the continuous circulation of pathogenic microbes like S. aureus in retail poultry meat.
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Affiliation(s)
- Rawah Faraj
- Center for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA; (R.F.); (K.E.B.); (B.A.); (Y.W.); (Z.H.); (T.S.)
| | - Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt;
| | - Kingsley E. Bentum
- Center for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA; (R.F.); (K.E.B.); (B.A.); (Y.W.); (Z.H.); (T.S.)
| | - Bilal Alkaraghulli
- Center for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA; (R.F.); (K.E.B.); (B.A.); (Y.W.); (Z.H.); (T.S.)
| | - Yilkal Woube
- Center for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA; (R.F.); (K.E.B.); (B.A.); (Y.W.); (Z.H.); (T.S.)
| | - Zakaria Hassan
- Center for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA; (R.F.); (K.E.B.); (B.A.); (Y.W.); (Z.H.); (T.S.)
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Temesgen Samuel
- Center for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA; (R.F.); (K.E.B.); (B.A.); (Y.W.); (Z.H.); (T.S.)
| | - Abiodun Adesiyun
- Faculty of Medical Sciences, School of Veterinary Medicine, University of the West Indies, St. Augustine 999183, Trinidad and Tobago;
| | - Charlene R. Jackson
- Poultry Microbiological Safety and Processing Research Unit USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA;
| | - Woubit Abebe
- Center for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA; (R.F.); (K.E.B.); (B.A.); (Y.W.); (Z.H.); (T.S.)
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13
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Chopjitt P, Tangthong P, Kongkaem J, Wonkyai P, Charoenwattanamaneechai A, Khankhum S, Sunthamala P, Kerdsin A, Sunthamala N. Molecular characterization and genotype of multi-drug resistant Staphylococcus epidermidis in nasal carriage of young population, Mahasarakham, Thailand. BIOMOLECULES & BIOMEDICINE 2025; 25:461-471. [PMID: 39388710 PMCID: PMC11734814 DOI: 10.17305/bb.2024.11116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 10/07/2024] [Accepted: 10/07/2024] [Indexed: 10/12/2024]
Abstract
Staphylococcus epidermidis, a coagulase-negative staphylococcus, is a prevalent skin commensal that has increasingly been recognized as a significant pathogen, particularly in hospital environments, where it is associated with device-related infections. The emergence of multi-drug resistance and its ability to form biofilms complicate the clinical management of infections caused by this organism, posing a growing public health concern. This study aimed to investigate the nasal carriage of S. epidermidis among healthy young individuals and to analyze its antibiotic resistance patterns, resistance genes, and biofilm formation capabilities. Nasal swabs were collected from 40 undergraduate students at Mahasarakham University, Thailand, aged between 20 and 22 years. A total of 38 isolates were confirmed as S. epidermidis through both phenotypic and molecular characterization. Antibiotic susceptibility testing demonstrated resistance to various classes of antimicrobials, including beta-lactams, macrolides, and tetracyclines. Notably, five isolates exhibited methicillin resistance S. epidermidis (MRSE). Resistance genes, such as mecA, ermA, tetM, tetL, and tetK, were identified across the isolates, contributing to the observed resistance profiles. Biofilm formation assays revealed that most isolates displayed weak to moderate biofilm formation, with only one isolate demonstrating strong biofilm-forming capacity. Genetic analysis indicated a significant correlation between biofilm formation and the presence of the icaA gene, which is crucial for biofilm production. This study suggests the necessity for ongoing surveillance of nasal carriage of S. epidermidis to enhance understanding of its role in the dissemination of antimicrobial resistance and biofilm-associated infections, particularly within healthcare settings.
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Affiliation(s)
- Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat, Sakon Nakhon Campus, Sakon Nakhon, Thailand
| | - Panita Tangthong
- Department of Biology, Faculty of Science, Mahasarakham University, Mahasarakham, Thailand
| | - Jiranuch Kongkaem
- Mahasarakham University Demonstration School (Secondary), Mahasarakham University, Mahasarakham, Thailand
| | - Pritprapoan Wonkyai
- Mahasarakham University Demonstration School (Secondary), Mahasarakham University, Mahasarakham, Thailand
| | | | - Surasak Khankhum
- Department of Biology, Faculty of Science, Mahasarakham University, Mahasarakham, Thailand
| | - Phitcharat Sunthamala
- Department of Biotechnology, Faculty of Technology, Mahasarakham University, Mahasarakham, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat, Sakon Nakhon Campus, Sakon Nakhon, Thailand
| | - Nuchsupha Sunthamala
- Department of Biology, Faculty of Science, Mahasarakham University, Mahasarakham, Thailand
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14
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Horsman S, Zaugg J, Meler E, Mikkelsen D, Soares Magalhães RJ, Gibson JS. Molecular Epidemiological Characteristics of Staphylococcus pseudintermedius, Staphylococcus coagulans, and Coagulase-Negative Staphylococci Cultured from Clinical Canine Skin and Ear Samples in Queensland. Antibiotics (Basel) 2025; 14:80. [PMID: 39858366 PMCID: PMC11761246 DOI: 10.3390/antibiotics14010080] [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: 12/14/2024] [Revised: 01/08/2025] [Accepted: 01/10/2025] [Indexed: 01/27/2025] Open
Abstract
Background/Objectives: Infections in dogs caused by methicillin-resistant staphylococci (MRS) present limited treatment options. This study's objective was to investigate the molecular epidemiology of Staphylococcus spp. cultured exclusively from clinical canine skin and ear samples in Queensland, Australia, using whole-genome sequencing (WGS). Methods: Forty-two Staphylococcus spp. isolated from clinical canine skin and ear samples, from an unknown number of dogs, were sourced from two veterinary diagnostic laboratories between January 2022 and May 2023. These isolates underwent matrix-assisted laser desorption ionisation- time of flight bacterial identification, minimum inhibitory concentration testing using SensititreTM plates and WGS. Phylogenetic trees and core genome multilocus sequence typing (cgMLST) minimum spanning trees (MSTs) were constructed. Results: The isolates included methicillin-resistant and -sensitive S. pseudintermedius (MRSP: 57.1%, 24/42; and MSSP: 19.1%, 8/42), methicillin-resistant and -sensitive S. coagulans (MRSC: 14.3%, 6/42; and MSSC: 2.4%, 1/42) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS: 7.1%, 3/42). Thirty-nine isolates were included after WGS, where all MRS harboured the mecA gene. Eighteen sequence types (STs) were identified, including three novel MRSP and six novel MSSP STs. MRSP ST496-V-VII (23%; 9/39) and MRSP ST749-IV-(IVg) (12.8%; 5/39) were commonly isolated. Phylogenetic analysis of single nucleotide polymorphisms showed that MRSP, MRSC and MSSC were similar to globally isolated staphylococci from canine skin and ear infections. Using cgMLST MSTs, MRSP isolates were not closely related to global strains. Conclusions: Our findings revealed a genotypically diverse geographical distribution and phylogenetic relatedness of staphylococci cultured from clinical canine skin and ear samples across Queensland. This highlights the importance of ongoing surveillance to aid in evidence-based treatment decisions and antimicrobial stewardship.
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Affiliation(s)
- Sara Horsman
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (E.M.); (J.S.G.)
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Erika Meler
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (E.M.); (J.S.G.)
| | - Deirdre Mikkelsen
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD 4072, Australia;
| | | | - Justine S. Gibson
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (E.M.); (J.S.G.)
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15
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Kizziah JL, Mukherjee A, Parker LK, Dokland T. Structure of the Staphylococcus aureus bacteriophage 80α neck shows the interactions between DNA, tail completion protein and tape measure protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.10.627806. [PMID: 39713459 PMCID: PMC11661146 DOI: 10.1101/2024.12.10.627806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Tailed bacteriophages with double-stranded DNA genomes (class Caudoviricetes) play an important role in the evolution of bacterial pathogenicity, both as carriers of genes encoding virulence factors and as the main means of horizontal transfer of mobile genetic elements (MGEs) in many bacteria, such as Staphylococcus aureus. The S. aureus pathogenicity islands (SaPIs), including SaPI1, are a type of MGEs are that carry a variable complement of genes encoding virulence factors. SaPI1 is mobilized at high frequency by "helper" bacteriophages, such as 80α, leading to packaging of the SaPI1 genome into virions made from structural proteins supplied by the helper. 80α and SaPI1 virions consist of an icosahedral head (capsid) connected via a unique vertex to a long, non-contractile tail. At one end of the tail, proteins associated with the baseplate recognize and bind to the host. At the other end, a connector or "neck" forms the interface between the tail and the head. The neck consists of several specialized proteins with specific roles in DNA packaging, phage assembly, and DNA ejection. Using cryo-electron microscopy and three-dimensional reconstruction, we have determined the high-resolution structure of the neck section of SaPI1 virions made in the presence of phage 80α, including the dodecameric portal (80α gene product (gp) 42) and head-tail-connector (gp49) proteins, the hexameric head-tail joining (gp50) and tail terminator (gp52) proteins, and the major tail protein (gp53) itself. We were also able to resolve the DNA, the tail completion protein (gp51) and the tape measure protein (gp56) inside the tail. This is the first detailed structural description of these features in a bacteriophage, providing insights into the assembly and infection process in this important group of MGEs and their helper bacteriophages.
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Affiliation(s)
- James L. Kizziah
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amarshi Mukherjee
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura K. Parker
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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16
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Straub C, Taylor W, French NP, Murdoch DR, Priest P, Anderson T, Scott P. Zoonotic transmission of asymptomatic carriage Staphylococcus aureus on dairy farms in Canterbury, New Zealand. Microb Genom 2024; 10:001318. [PMID: 39630492 PMCID: PMC11616781 DOI: 10.1099/mgen.0.001318] [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: 04/17/2024] [Accepted: 10/03/2024] [Indexed: 12/07/2024] Open
Abstract
Zoonotic pathogen transmission is of growing concern globally, with agricultural intensification facilitating interactions between humans, livestock and wild animals. Staphylococcus aureus is a major human pathogen, but it also causes mastitis in dairy cattle, leading to an economic burden on the dairy industry. Here, we investigated transmission within and between cattle and humans, including potential zoonotic transmission of S. aureus isolated from cattle and humans from three dairy farms and an associated primary school in New Zealand. Nasal swabs (N=170) were taken from healthy humans. Inguinal and combined nasal/inguinal swabs were taken from healthy cattle (N=1163). Whole-genome sequencing was performed for 96 S. aureus isolates (44 human and 52 cattle). Multilocus sequence typing and assessments of antimicrobial resistance and virulence were carried out. Potential within- and across-species transmission events were determined based on single nucleotide polymorphisms (SNPs). Thirteen potential transmission clusters were detected, with 12 clusters restricted to within-species and one potential zoonotic transmission cluster (ST5). Potential transmission among cattle was mostly limited to single age groups, likely because different age groups are managed separately on farms. While the prevalence of antimicrobial resistance (AMR) was low among both bovine and human isolates, the discovery of an extended-spectrum beta-lactamase gene (bla TEM-116) in a bovine isolate was concerning. This study provides evidence around frequency and patterns of potential transmission of S. aureus on dairy farms and highlights the AMR and virulence profile of asymptomatic carriage S. aureus isolates.
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Affiliation(s)
- Christina Straub
- The Institute of Environmental Science and Research, Auckland, New Zealand
- Genomics Aotearoa, Dunedin, New Zealand
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - William Taylor
- The Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Nigel P. French
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David R. Murdoch
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Patricia Priest
- Department of Preventive and Social Medicine, University of Otago, Dunedin, New Zealand
| | - Trevor Anderson
- Microbiology Department, Canterbury Health Laboratories, Te Whatu Ora – Health New Zealand Waitaha, Christchurch, New Zealand
| | - Pippa Scott
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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Contarin R, Drapeau A, François P, Madec JY, Haenni M, Dordet-Frisoni E. The interplay between mobilome and resistome in Staphylococcus aureus. mBio 2024; 15:e0242824. [PMID: 39287446 PMCID: PMC11481524 DOI: 10.1128/mbio.02428-24] [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: 08/08/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024] Open
Abstract
Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.
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Affiliation(s)
- Rachel Contarin
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Antoine Drapeau
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pauline François
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Jean-Yves Madec
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
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Ashraf MA, Irfan S, Baig A, Zeeshan SM, Khan H, Ahmed I, Virani N, Roshan R. Role of Xpert PCR kit in assessing MRSA colonization in medical and surgical units of a tertiary care teaching hospital. BMC Infect Dis 2024; 24:1096. [PMID: 39358697 PMCID: PMC11448093 DOI: 10.1186/s12879-024-09710-5] [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: 02/09/2024] [Accepted: 08/02/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND AND RATIONALE Methicillin resistant Staphylococcus aureus (MRSA) colonization increases the risk of MRSA infection. Detecting MRSA colonization can influence postoperative outcomes and prolong hospital stay. The conventional standard culture method for detecting MRSA colonization has limitations in terms of sensitivity and turnaround time. Hence, we sought out use of Xpert PCR kit for prompt evaluation of MRSA colonization to support MRSA prevention in a tertiary care hospital in Karachi, Pakistan. MATERIALS AND METHODS During 1st April-31st December 2022, 290 nasal and skin swab samples were collected from 257 patients and processed using routine culture (as gold standard method) and PCR-based MRSA detection assay (MRSA Xpert). RESULTS A total of two hundred and ninety (290) swab samples from 257 patients were obtained, 33 of which were paired. The overall prevalence of MRSA colonization was 12% by both methods, with 90% of cases classified as community-associated (CA-MRSA) whereas 10% as hospital-acquired (HA-MRSA). The colonized group showed a higher subsequent MRSA infection rate (11% vs. 3.5%) compared to the noncolonized group. Culture identified 11% of screening samples as MRSA positive, Xpert MRSA assay showed 100% sensitivity and 95% specificity. The cost of a single MRSA Xpert assay was $50 while MRSA culture cost around $7.50. CONCLUSION Our study findings suggest that the presence of MRSA colonization in our cohort of patients is consistent with the existing trends in hospital epidemiology. Both conventional culture and Xpert MRSA methods showed comparable efficacy for detection of MRSA colonization. Larger-scale studies are recommended to validate these findings conclusively.
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Affiliation(s)
- Muhammad Arsalan Ashraf
- Section Microbiology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Seema Irfan
- Section Microbiology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan.
| | - Ammarah Baig
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Syed Mohammad Zeeshan
- Section Microbiology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Hira Khan
- Aga Khan Medical College and University, Karachi, Pakistan
| | - Israr Ahmed
- Section Microbiology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Nazleen Virani
- Department of Infection Prevention and Hospital Epidemiology, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Rozina Roshan
- Department of Infection Prevention and Hospital Epidemiology, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
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Anjum A, Tabassum J, Islam S, Hassan AKMI, Jabeen I, Shuvo SR. Deciphering the genomic character of the multidrug-resistant Staphylococcus aureus from Dhaka, Bangladesh. AIMS Microbiol 2024; 10:833-858. [PMID: 39628721 PMCID: PMC11609420 DOI: 10.3934/microbiol.2024036] [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: 04/05/2024] [Revised: 09/02/2024] [Accepted: 09/20/2024] [Indexed: 12/06/2024] Open
Abstract
Staphylococcus aureus is one of the leading agents of nosocomial and community-acquired infections. In this study, we explored the genomic characterization of eight methicillin-resistant clinical isolates of S. aureus from Dhaka, Bangladesh. Notably, all strains were resistant to penicillin, cephalosporins, and monobactams, with partial susceptibility to meropenem and complete susceptibility to amikacin, vancomycin, and tigecycline antibiotics. The strains were found to have an average genome size of 2.73 Mbp and an average of 32.64% GC content. Multi-locus sequence typing analysis characterized the most predominant sequence type as ST361, which belongs to the clonal complex CC361. All isolates harbored the mecA gene, often linked to SCCmec_type IV variants. Multidrug resistance was attributed to efflux pumps NorA, NorC, SdrM, and LmrS alongside genes encoding beta-lactamase BlaZ and factors like ErmC and MepA. Additionally, virulence factors including adsA, sdrC, cap8D, harA, esaA, essC, isdB, geh, and lip were commonly identified. Furthermore, genes associated with heme uptake and clumping were present, highlighting their roles in S. aureus colonization and pathogenesis. Nine secondary metabolite biosynthetic gene clusters were found, of which six were common in all the strains. Numerous toxin-antitoxin systems were predicted, with ParE and ParB-like nuclease domains found to be the most prevalent toxin and antitoxin, respectively. Pan-genome analysis revealed 2007 core genes and 229 unique genes in the studied strains. Finally, the phylogenomic analysis showed that most Bangladeshi strains were grouped into two unique clades. This study provides a genomic and comparative insight into the multidrug resistance and pathogenicity of S. aureus strains, which will play a crucial role in the future antibiotic stewardship of Bangladesh.
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Affiliation(s)
| | | | | | | | | | - Sabbir R. Shuvo
- Department of Biochemistry & Microbiology, North South University, Dhaka, Bangladesh
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20
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Ndhlovu GON, Javkar KG, Matuvhunye T, Ngondoh F, Jamrozy D, Bentley S, Shittu AO, Dube FS. Investigating genomic diversity of Staphylococcus aureus associated with pediatric atopic dermatitis in South Africa. Front Microbiol 2024; 15:1422902. [PMID: 39224215 PMCID: PMC11366657 DOI: 10.3389/fmicb.2024.1422902] [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: 04/24/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Importance Staphylococcus aureus frequently colonizes the skin and nose of patients with atopic dermatitis (AD), a disease associated with skin barrier dysfunction and chronic cutaneous inflammation. Published genomic studies on AD-associated S. aureus in pediatric populations in sub-Saharan Africa are limited. Objectives To investigate the phenotypic and genomic diversity of S. aureus in children with and without AD during early childhood. Data setting and participants A cross-sectional study of 220 children (aged 9-38 months) with AD (cases) and without AD (controls) from Cape Town and Umtata, South Africa. Main outcomes and measures S. aureus phenotypic and genomic diversity were investigated using whole-genome sequencing, antibiotic susceptibility testing and biofilm microtiter assay. Results Of the 124 S. aureus isolates recovered from 220 children, 96 isolates (79 cases and 17 controls) with high-quality sequences were analyzed. Isolates from cases showed greater phenotypic resistance to gentamicin (10%), rifampicin (4%), chloramphenicol (4%), and exhibited multidrug resistance (9%) than in controls. Furthermore, the isolates from cases formed stronger biofilms than those from controls (76% vs. 35%, p = 0.001), but showed no dominance of any virulence factor gene or mobile genetic elements. There was no significant difference in the distribution of immune evasion cluster types between cases and controls. However, IEC type G was identified only among cases. Conclusion and relevance AD-associated S. aureus has phenotypic and genetic features that are important for successful pathogenic colonization and survival. Further studies are needed to assess the pathological implications of colonization of various S. aureus lineages in vivo to elucidate their pathological contribution to AD pathogenesis and pathophysiology.
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Affiliation(s)
- Gillian O. N. Ndhlovu
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Kiran G. Javkar
- Department of Computer Science, University of Maryland, College Park, MD, United States
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, United States
| | - Takudzwa Matuvhunye
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Froodia Ngondoh
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Dorota Jamrozy
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Stephen Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adebayo O. Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
- Institute of Medical Microbiology, University Hospital Munster, Munster, Germany
| | - Felix S. Dube
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
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21
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Al-Zuhairi ZA, Muslim ET, Faja OM, Alkhozai ZM, Mohammed BJ. Molecular identification of Staphylococcus aureus-related enterotoxin genes in cheese samples. Open Vet J 2024; 14:2073-2078. [PMID: 39308717 PMCID: PMC11415922 DOI: 10.5455/ovj.2024.v14.i8.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 07/20/2024] [Indexed: 09/25/2024] Open
Abstract
Background Dairy products are considered some important sources of various nutritional compounds; however, pathogenic bacterial growth is a critical destructive factor to these products leading to consumer health and system financial crises. Aim The current study was carried out to identify if there is any presence of Staphylococcus aureus-related enterotoxin genes in cheese samples. Methods The research included the collection of 35 samples. The samples passed through conventional cultivation processes and a PCR method to detect the presence of icaA, sea, hla, and fnbA enterotoxin genes in these samples. Results The conventional identification revealed the growth of S. aureus from the cheese samples. The PCR findings recorded the presence of the icaA, sea, hla, and fnbA in 31 (88.5%), 27 (77%), 19 (54%), and 12 (34%), respectively, of cheese samples. The sequencing revealed close similarities with global isolates, which reached up to 98.5% of identity. Conclusion The current results indicate the presence of enterotoxin genes of S. aureus in high rates in the dairy products examined, which reveals critical problems of food safety due to the possible presence of enterotoxins in consumer dairy products.
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Affiliation(s)
| | - Esraa Taher Muslim
- Collage of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah City, Iraq
| | - Orooba Meteab Faja
- Collage of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah City, Iraq
| | - Ziad M. Alkhozai
- Collage of Biotechnology, University of Al-Qadisiyah, Al-Diwaniyah City, Iraq
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Mauffrey F, Bertelli C, Greub G, Senn L, Blanc DS. Genomic evolution of ST228 SCCmec-I MRSA 10 years after a major nosocomial outbreak. J Clin Microbiol 2024; 62:e0020324. [PMID: 38934681 PMCID: PMC11250417 DOI: 10.1128/jcm.00203-24] [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: 02/12/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, we investigated the genomic changes in a major methicillin-resistant Staphylococcus aureus (MRSA) clone following a significant outbreak at a hospital. Whole-genome sequencing of MRSA isolates was utilized to explore the genomic evolution of post-outbreak MRSA strains. The epidemicity of the clone declined over time, coinciding with the introduction of multimodal infection control measures. A genome-wide association study (GWAS) identified multiple genes significantly associated with either high or low epidemic success, indicating alterations in mobilome, virulence, and defense mechanisms. Random Forest models pinpointed a gene related to fibrinogen binding as the most influential predictor of epidemicity. The decline of the MRSA clone may be attributed to various factors, including the implementation of new infection control measures, single nucleotide polymorphisms accumulation, and the genetic drift of a given clone. This research underscores the complex dynamics of MRSA clones, emphasizing the multifactorial nature of their evolution. The decline in epidemicity seems linked to alterations in the clone's genetic profile, with a probable shift towards decreased virulence and adaptation to long-term carriage. Understanding the genomic basis for the decline of epidemic clones is crucial to develop effective strategies for their surveillance and management, as well as to gain insights into the evolutionary dynamics of pathogen genomes.
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Affiliation(s)
- Florian Mauffrey
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurence Senn
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S. Blanc
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Qi J, Zhang X, Guo X, Yang Y, Fan X, Han Y, Liu Y. Evaluation of the in vitro and in vivo antimicrobial activity of alkaloids prepared from Chelidonium majus L. using MRSA- infected C. elegans as a model host. Fitoterapia 2024; 175:105944. [PMID: 38580033 DOI: 10.1016/j.fitote.2024.105944] [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: 01/12/2024] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
Chelidonium majus L. contained alkaloids as its main component, exhibiting various biological activities, particularly antibacterial activity. This study aimed to extract alkaloids from C. majus L. (total alkaloids) and evaluate their antibacterial activity both in vitro and in vivo. Reflux extraction was carried out on C. majus L., and the extract was purified with HPD-600 macroporous resin and 732 cation exchange resin columns. Infection modeling of Caenorhabditis elegans (C. elegans) was established to investigate the impact of Methicillin-resistant Staphylococcus aureus (MRSA) and Methicillin-sensitive Staphylococcus aureus (MSSA) on the motility, longevity, and reactive oxygen species (ROS) levels of wild-type worms (N2 strain). The effects of total alkaloids on longevity and ROS were further evaluated in infected N2 worms. Additionally, the effect of total alkaloids on the stress resistance of C. elegans and the mechanism of action were investigated. By utilizing CB1370, DR26 and CF1038 transgenic strains of C. elegans to identify whether the antibacterial activity of total alkaloids was dependent on DAF-2/DAF-16 pathway. The results showed that total alkaloids exhibited a significant antibacterial activity against both MRSA and MSSA (MIC 31.25 μg/mL). Compared with MSSA, the MRSA exhibited a stronger inhibitory effect on the movement behavior and development of worms, along with faster pathogenicity and unique virulence factors. Total alkaloids also displayed the ability to extend the lifespan of C. elegans under oxidative stress and heat stress, and reduce the expression of ROS. The antibacterial activity of total alkaloids was primarily dependent on the DAF-2/DAF-16 pathway, and the presence of functional DAF-2 was deemed essential in total alkaloids mediated immune response against MRSA. Moreover, the antibacterial and anti-infection effects of total alkaloids were found to be associated with the daf-16 gene fragment.
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Affiliation(s)
- Jinchai Qi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xinyun Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xiaochen Guo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yuping Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xiaoxiao Fan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yunfeng Han
- Peking University Third Hospital, Beijing 102488, China.
| | - Yonggang Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
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Mouhammed K, Gdoura R. Study of the Genomic Characterization of Antibiotic-Resistant Escherichia Coli Isolated From Iraqi Patients with Urinary Tract Infections. Indian J Microbiol 2024; 64:457-466. [PMID: 39011020 PMCID: PMC11246310 DOI: 10.1007/s12088-023-01123-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/16/2023] [Indexed: 07/17/2024] Open
Abstract
Urinary tract infection is one of the last diseases prevalent in humans, with various causative agents affecting 250 million people annually, This study analyzed UTIs in Iraqi patients caused by Escherichia coli. ESBL enzymes contribute to antibiotic resistance. The research aimed to analyze ESBL gene frequency, resistance patterns, and genetic diversity of E. coli strains; Between Dec 2020 and May 2021, 200 urine samples were collected, cultured on blood agar, EMB, and MacConkey's plates, samples incubated at 37 °C for 24 h. Positive samples (> 100 cfu/ml) underwent Kirby-Bauer and CLSI antibiotic susceptibility testing. PCR detected virulence genes, Beta-lactamase coding genes, and biofilm-associated resistance genes in E. coli isolates; Out of 200 isolates, 80% comprised Gram-positive and Gram-negative bacteria. Specifically, 120 isolates (60%) were Gram-negative, while 40 isolates (20%) were Gram-positive. Among Gram-negative isolates, 20% were identified as E. coli. Remarkably, all E. coli strains showed resistance to all tested antibiotics, ranging from 80 to 95% resistance. The E. coli isolates harbored three identified resistance genes: blaTEM, blaSHV, and blaCTXM. Regarding biofilm production, 10% showed no formation, 12% weak formation, 62% moderate formation, and 16% strong formation; our study found that pathogenic E. coli caused 20% of UTIs. The majority of studied E. coli strains from UTI patients carried the identified virulence genes, which are vital for infection development and persistence.
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Affiliation(s)
- Kareem Mouhammed
- Faculty of Sciences, Research Laboratory of Environmental Toxicology Microbiology and Health (LR17ES06), Sfax University, BP 1171, 3000 Sfax, Tunisia
| | - Radhouane Gdoura
- Faculty of Sciences, Research Laboratory of Environmental Toxicology Microbiology and Health (LR17ES06), Sfax University, BP 1171, 3000 Sfax, Tunisia
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25
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Bak YS, Park JY, Kim JB, Cho SH. Molecular characterization and antibiotic resistance of Staphylococcus aureus strains isolated from patients with diarrhea in Korea between the years 2007 and 2022. Food Sci Biotechnol 2024; 33:1965-1974. [PMID: 38752118 PMCID: PMC11091020 DOI: 10.1007/s10068-023-01478-9] [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: 08/20/2023] [Revised: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 05/18/2024] Open
Abstract
To investigate the molecular characteristics and antibiotic resistance of Staphylococcus aureus isolates from patients with diarrhea in Korea, 327 S. aureus strains were collected between 2007 and 2022. The presence of staphylococcal enterotoxin (SE) and toxic shock syndrome toxin-1 (TSST-1) genes in S. aureus isolates was determined by PCR. The highest expression of the TSST-1 gene was found in the GIMNO type (43.1% of GIMNO type). GIMNO type (Type I) refers to each staphylococcal enterotoxin (SE) gene gene (initials of genes): G = seg; I = sei; M = selm; N = seln; O = selo. Moreover, Type I isolates showed a significantly higher resistance to most antibiotics. A total of 195 GIMNO-type S. aureus strains were analyzed using multilocus sequence typing (MLST), and 18 unique sequence types (STs) were identified. The most frequent sequence type was ST72 (36.9%), followed by ST5 (22.1%) and ST30 (16.9%). Interestingly, ST72 strains showed a higher prevalence of MRSA than the other STs. In conclusion, our results were the first reported for S. aureus strains in Korea, which significantly expanded S. aureus genotype information for the surveillance of pathogenic S. aureus and may provide important epidemiological information to resolve several infectious diseases caused by S. aureus. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-023-01478-9.
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Affiliation(s)
- Young-Seok Bak
- Department of Emergency Medical Services, Sun Moon University, Asan-si, Chungcheongnam-do 31460 Korea
| | - Jun-Young Park
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jung-Beom Kim
- Department of Food Science and Technology, Suncheon National University, Suncheon, 57922 Korea
| | - Seung-Hak Cho
- Department of Emergency Medical Services, Sun Moon University, Asan-si, Chungcheongnam-do 31460 Korea
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Heungdeok-Gu, Cheongju, 363-951 Republic of Korea
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26
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Ramos B, Cunha MV. The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124241. [PMID: 38825220 DOI: 10.1016/j.envpol.2024.124241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/28/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.
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Affiliation(s)
- Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal.
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Souza SSR, Smith JT, Marcovici MM, Eckhardt EM, Hansel NB, Martin IW, Andam CP. Demographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:14. [PMID: 38725655 PMCID: PMC11076216 DOI: 10.1038/s44259-024-00032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/08/2024] [Indexed: 05/12/2024]
Abstract
Staphylococcus aureus in the bloodstream causes high morbidity and mortality, exacerbated by the spread of multidrug-resistant and methicillin-resistant S. aureus (MRSA). We aimed to characterize the circulating lineages of S. aureus from bloodstream infections and the contribution of individual lineages to resistance over time. Here, we generated 852 high-quality short-read draft genome sequences of S. aureus isolates from patient blood cultures in a single hospital from 2010 to 2022. A total of 80 previously recognized sequence types (ST) and five major clonal complexes are present in the population. Two frequently detected lineages, ST5 and ST8 exhibited fluctuating demographic structures throughout their histories. The rise and fall in their population growth coincided with the acquisition of antimicrobial resistance, mobile genetic elements, and superantigen genes, thus shaping the accessory genome structure across the entire population. These results reflect undetected selective events and changing ecology of multidrug-resistant S. aureus in the bloodstream.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
| | - Joshua T. Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Michael M. Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
| | - Elissa M. Eckhardt
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Nicole B. Hansel
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
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Bang J, Park J, Lee SH, Jang J, Hwang J, Kamarov O, Park HJ, Lee SJ, Seo MD, Won HS, Seok SH, Kim JH. Nontraditional Roles of Magnesium Ions in Modulating Sav2152: Insight from a Haloacid Dehalogenase-like Superfamily Phosphatase from Staphylococcus aureus. Int J Mol Sci 2024; 25:5021. [PMID: 38732240 PMCID: PMC11084212 DOI: 10.3390/ijms25095021] [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: 04/01/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infection has rapidly spread through various routes. A genomic analysis of clinical MRSA samples revealed an unknown protein, Sav2152, predicted to be a haloacid dehalogenase (HAD)-like hydrolase, making it a potential candidate for a novel drug target. In this study, we determined the crystal structure of Sav2152, which consists of a C2-type cap domain and a core domain. The core domain contains four motifs involved in phosphatase activity that depend on the presence of Mg2+ ions. Specifically, residues D10, D12, and D233, which closely correspond to key residues in structurally homolog proteins, are responsible for binding to the metal ion and are known to play critical roles in phosphatase activity. Our findings indicate that the Mg2+ ion known to stabilize local regions surrounding it, however, paradoxically, destabilizes the local region. Through mutant screening, we identified D10 and D12 as crucial residues for metal binding and maintaining structural stability via various uncharacterized intra-protein interactions, respectively. Substituting D10 with Ala effectively prevents the interaction with Mg2+ ions. The mutation of D12 disrupts important structural associations mediated by D12, leading to a decrease in the stability of Sav2152 and an enhancement in binding affinity to Mg2+ ions. Additionally, our study revealed that D237 can replace D12 and retain phosphatase activity. In summary, our work uncovers the novel role of metal ions in HAD-like phosphatase activity.
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Affiliation(s)
- Jaeseok Bang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Jaehui Park
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Sung-Hee Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Jinhwa Jang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Junwoo Hwang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Otabek Kamarov
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Hae-Joon Park
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Soo-Jae Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea;
- College of Pharmacy, Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon 16499, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea;
- BK21 Project Team, Department of Applied Life Science, Graduate School, Konkuk University, Chungju 27478, Republic of Korea
| | - Seung-Hyeon Seok
- College of Pharmacy, Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 632433, Republic of Korea
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
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Bashabsheh RH, AL-Fawares O, Natsheh I, Bdeir R, Al-Khreshieh RO, Bashabsheh HH. Staphylococcus aureus epidemiology, pathophysiology, clinical manifestations and application of nano-therapeutics as a promising approach to combat methicillin resistant Staphylococcus aureus. Pathog Glob Health 2024; 118:209-231. [PMID: 38006316 PMCID: PMC11221481 DOI: 10.1080/20477724.2023.2285187] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023] Open
Abstract
Staphylococcus aureus is a Gram-positive bacterium and one of the most prevalent infectious disease-related causes of morbidity and mortality in adults. This pathogen can trigger a broad spectrum of diseases, from sepsis and pneumonia to severe skin infections that can be fatal. In this review, we will provide an overview of S. aureus and discuss the extensive literature on epidemiology, transmission, genetic diversity, evolution and antibiotic resistance strains, particularly methicillin resistant S. aureus (MRSA). While many different virulence factors that S. aureus produces have been investigated as therapeutic targets, this review examines recent nanotechnology approaches, which employ materials with atomic or molecular dimensions and are being used to diagnose, treat, or eliminate the activity of S. aureus. Finally, having a deeper understanding and clearer grasp of the roles and contributions of S. aureus determinants, antibiotic resistance, and nanotechnology will aid us in developing anti-virulence strategies to combat the growing scarcity of effective antibiotics against S. aureus.
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Affiliation(s)
- Raghad H.F. Bashabsheh
- Department of Medical Laboratory Analysis, Faculty of Science, Al-Balqa Applied University, Al-salt, Jordan
| | - O’la AL-Fawares
- Department of Medical Laboratory Analysis, Faculty of Science, Al-Balqa Applied University, Al-salt, Jordan
| | - Iyad Natsheh
- Department of Allied Medical Sciences, Zarqa College, Al-Balqa Applied University, Zarqa, Jordan
| | - Roba Bdeir
- Department of Allied Health Sciences, Faculty of Nursing, Al-Balqa Applied University, Al-salt, Jordan
| | - Rozan O. Al-Khreshieh
- Department of Medical Laboratory Analysis, Faculty of Science, Al-Balqa Applied University, Al-salt, Jordan
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Gopikrishnan M, Haryini S, C GPD. Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review. J Basic Microbiol 2024; 64:e2300579. [PMID: 38308076 DOI: 10.1002/jobm.202300579] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/04/2024]
Abstract
In recent years, antibiotic therapy has encountered significant challenges due to the rapid emergence of multidrug resistance among bacteria responsible for life-threatening illnesses, creating uncertainty about the future management of infectious diseases. The escalation of antimicrobial resistance in the post-COVID era compared to the pre-COVID era has raised global concern. The prevalence of nosocomial-related infections, especially outbreaks of drug-resistant strains of Staphylococcus aureus, have been reported worldwide, with India being a notable hotspot for such occurrences. Various virulence factors and mutations characterize nosocomial infections involving S. aureus. The lack of proper alternative treatments leading to increased drug resistance emphasizes the need to investigate and examine recent research to combat future pandemics. In the current genomics era, the application of advanced technologies such as next-generation sequencing (NGS), machine learning (ML), and quantum computing (QC) for genomic analysis and resistance prediction has significantly increased the pace of diagnosing drug-resistant pathogens and insights into genetic intricacies. Despite prompt diagnosis, the elimination of drug-resistant infections remains unattainable in the absence of effective alternative therapies. Researchers are exploring various alternative therapeutic approaches, including phage therapy, antimicrobial peptides, photodynamic therapy, vaccines, host-directed therapies, and more. The proposed review mainly focuses on the resistance journey of S. aureus over the past decade, detailing its resistance mechanisms, prevalence in the subcontinent, innovations in rapid diagnosis of the drug-resistant strains, including the applicants of NGS and ML application along with QC, it helps to design alternative novel therapeutics approaches against S. aureus infection.
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Affiliation(s)
- Mohanraj Gopikrishnan
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sree Haryini
- Department of Biomedical Sciences, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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31
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Guillén-Chable F, Valdez Iuit JO, Avila Castro LA, Rosas C, Merino E, Rodríguez-Escamilla Z, Martínez-Núñez MA. Geographical distribution of mobile genetic elements in microbial communities along the Yucatan coast. PLoS One 2024; 19:e0301642. [PMID: 38683832 PMCID: PMC11057721 DOI: 10.1371/journal.pone.0301642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024] Open
Abstract
Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan's microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It's important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.
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Affiliation(s)
- Francisco Guillén-Chable
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Johnny Omar Valdez Iuit
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | | | - Carlos Rosas
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Zuemy Rodríguez-Escamilla
- Facultad de Sistemas Biológicos e Innovación Tecnológica, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca de Juárez, Oaxaca, México
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32
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Ulrich RJ, Podkowik M, Tierce R, Irnov I, Putzel G, Samhadaneh N, Lacey KA, Boff D, Morales SM, Makita S, Karagounis TK, Zwack EE, Zhou C, Kim R, Drlica K, Pironti A, van Bakel H, Torres VJ, Shopsin B. Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589803. [PMID: 38659881 PMCID: PMC11042277 DOI: 10.1101/2024.04.17.589803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We recently described the evolution of a community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 variant responsible for an outbreak of skin and soft tissue infections. Acquisition of a mosaic version of the Φ11 prophage (mΦ11) that increases skin abscess size was an early step in CA-MRSA adaptation that primed the successful spread of the clone. The present report shows how prophage mΦ11 exerts its effect on virulence for skin infection without encoding a known toxin or fitness genes. Abscess size and skin inflammation were associated with DNA methylase activity of an mΦ11-encoded adenine methyltransferase (designated pamA). pamA increased expression of fibronectin-binding protein A (fnbA; FnBPA), and inactivation of fnbA eliminated the effect of pamA on abscess virulence without affecting strains lacking pamA. Thus, fnbA is a pamA-specific virulence factor. Mechanistically, pamA was shown to promote biofilm formation in vivo in skin abscesses, a phenotype linked to FnBPA's role in biofilm formation. Collectively, these data reveal a novel mechanism-epigenetic regulation of staphylococcal gene expression-by which phage can regulate virulence to drive adaptive leaps by S. aureus.
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Affiliation(s)
- Robert J. Ulrich
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Magdalena Podkowik
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
| | - Rebecca Tierce
- Division of Comparative Medicine, NYU Langone Health, New York, NY, USA
| | - Irnov Irnov
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Gregory Putzel
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Nora Samhadaneh
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Keenan A. Lacey
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Daiane Boff
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Sabrina M. Morales
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Sohei Makita
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Theodora K. Karagounis
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Erin E. Zwack
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Chunyi Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Randie Kim
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Karl Drlica
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Alejandro Pironti
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Victor J. Torres
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Bo Shopsin
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
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Fernandes AS, Campos KF, de Assis JCS, Gonçalves OS, Queiroz MVD, Bazzolli DMS, Santana MF. Investigating the impact of insertion sequences and transposons in the genomes of the most significant phytopathogenic bacteria. Microb Genom 2024; 10. [PMID: 38568199 DOI: 10.1099/mgen.0.001219] [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] [Indexed: 04/05/2024] Open
Abstract
Genetic variability in phytopathogens is one of the main problems encountered for effective plant disease control. This fact may be related to the presence of transposable elements (TEs), but little is known about their role in host genomes. Here, we performed the most comprehensive analysis of insertion sequences (ISs) and transposons (Tns) in the genomes of the most important bacterial plant pathogens. A total of 35 692 ISs and 71 transposons were identified in 270 complete genomes. The level of pathogen-host specialization was found to be a significant determinant of the element distribution among the species. Some Tns were identified as carrying virulence factors, such as genes encoding effector proteins of the type III secretion system and resistance genes for the antimicrobial streptomycin. Evidence for IS-mediated ectopic recombination was identified in Xanthomonas genomes. Moreover, we found that IS elements tend to be inserted in regions near virulence and fitness genes, such ISs disrupting avirulence genes in X. oryzae genomes. In addition, transcriptome analysis under different stress conditions revealed differences in the expression of genes encoding transposases in the Ralstonia solanacearum, X. oryzae, and P. syringae species. Lastly, we also investigated the role of Tns in regulation via small noncoding regulatory RNAs and found these elements may target plant-cell transcriptional activators. Taken together, the results indicate that TEs may have a fundamental role in variability and virulence in plant pathogenic bacteria.
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Verma AK, Jaiswal G, Sultana KN, Srivastava SK. 'Computational studies on coumestrol-ArlR interaction to target ArlRS signaling cascade involved in MRSA virulence'. J Biomol Struct Dyn 2024; 42:3712-3730. [PMID: 37293938 DOI: 10.1080/07391102.2023.2220028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Two component signaling system ArlRS (Autolysis-related locus) regulates adhesion, biofilm formation and virulence in methicillin resistant Staphylococcus aureus. It consists of a histidine kinase ArlS and response regulator ArlR. ArlR is composed of a N-terminal receiver domain and DNA-binding effector domain at C-terminal. ArlR receiver domain dimerizes upon signal recognition and activates DNA binding by effector domain and subsequent virulence expression. In silico simulation and structural data suggest that coumestrol, a phytochemical found in Pueraria montana, forges a strong intermolecular interaction with residues involved in dimer formation and destabilizes ArlR dimerization, an essential conformational switch required for downstream effector domain to bind to virulent loci. Structural and energy profiles of simulated ArlR-coumestrol complexes suggest lower affinity between ArlR monomers due to structural rigidity at the dimer interface hindering the conformational rearrangements relevant for dimer formation. These analyses could be an attractive strategy to develop therapeutics and potent leads molecules response regulators of two component systems in which are involved in MRSA virulence as well as other drug-resistant pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhishek Kumar Verma
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Grijesh Jaiswal
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Kazi Nasrin Sultana
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Sandeep Kumar Srivastava
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
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Rosa DS, Oliveira SADS, Souza RDFS, de França CA, Pires IC, Tavares MRS, de Oliveira HP, da Silva Júnior FAG, Moreira MAS, de Barros M, de Menezes GB, Antunes MM, Azevedo VADC, Naue CR, da Costa MM. Antimicrobial and antibiofilm activity of highly soluble polypyrrole against methicillin-resistant Staphylococcus aureus. J Appl Microbiol 2024; 135:lxae072. [PMID: 38503568 DOI: 10.1093/jambio/lxae072] [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: 11/13/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 03/21/2024]
Abstract
AIMS The purpose was to evaluate the antimicrobial activity of highly soluble polypyrrole (Hs-PPy), alone or combined with oxacillin, as well as its antibiofilm potential against methicillin-resistant Staphylococcus aureus strains. Furthermore, the in silico inhibitory mechanism in efflux pumps was also investigated. METHODS AND RESULTS Ten clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and two reference strains were used. Antimicrobial activity was determined by broth microdilution, and the combination effect with oxacillin was evaluated by the checkerboard assay. The biofilm formation capacity of MRSA and the interference of Hs-PPy were evaluated. The inhibitory action of Hs-PPy on the efflux pump was evaluated in silico through molecular docking. Hs-PPy showed activity against the isolates, with inhibitory action between 62.5 and 125 µg ml-1 and bactericidal action at 62.5 µg ml-1, as well as synergism in association with oxacillin. The isolates ranged from moderate to strong biofilm producers, and Hs-PPy interfered with the formation of this structure, but not with mature biofilm. There was no in silico interaction with the efflux protein EmrD, the closest homolog to NorA. CONCLUSIONS Hs-PPy interferes with biofilm formation by MRSA, has synergistic potential, and is an efflux pump inhibitor.
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Affiliation(s)
- Danillo Sales Rosa
- Universidade Federal do Vale do São Francisco, Petrolina, Pernambuco 56300-000, Brazil
| | | | | | | | | | | | | | | | | | - Mariana de Barros
- Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | | | - Maísa Mota Antunes
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | | | - Carine Rosa Naue
- Hospital Universitário da Universidade Federal do Vale do São Francisco, Petrolina, Pernambuco 56304-205, Brazil
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Liu Z, Wang L, Sun J, Zhang Q, Peng Y, Tang S, Zhang L, Li X, Yu Z, Zhang T. Whole Genome Sequence Analysis of Two Oxacillin-Resistant and mecA-Positive Strains of Staphylococcus haemolyticus Isolated from Ear Swab Samples of Patients with Otitis Media. Infect Drug Resist 2024; 17:1291-1301. [PMID: 38576824 PMCID: PMC10992674 DOI: 10.2147/idr.s455051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024] Open
Abstract
Objective Staphylococcus haemolyticus can cause a series of infections including otitis media (OM), and the oxacillin-resistant S. haemolyticus has become a serious health concern. This study aimed to investigate the genomic characteristics of two strains of oxacillin-resistant and mecA-positive S. haemolyticus isolated from the samples of ear swabs from patients with OM and explore their acquired antibiotic resistance genes (ARGs) and the mobile genetic elements (MGEs). Methods Two oxacillin-resistant S. haemolyticus strains, isolated from ear swab samples of patients with OM, underwent antimicrobial susceptibility evaluation, followed by whole-genome sequencing. The acquired ARGs and the MGEs carried by the ARGs, harbored by the genomes of two strains of S. haemolyticus were identified. Results The two strains of oxacillin-resistant S. haemolyticus (strain SH1275 and strain SH9361) both carried the genetic contexts of mecA with high similarity with the SCCmec type V(5C2&5) subtype c. Surprisingly, the chromosomal aminoglycoside resistance gene aac(6')-aph(2") harbored by S. haemolyticus strain SH936 was flanked by two copies of IS256, forming the IS256-element (IS256-GNAT-[aac(6')-aph(2")]-IS256), which was widely present in strains of both Staphylococcus and Enterococcus genus. Furthermore, the two strains of oxacillin-resistant and MDR S. haemolyticus were found to harbor antimicrobial resistance plasmids, including one 26.9-kb plasmid (pSH1275-2) containing msr(A)-mph(C)) and qacA, one mobilizable plasmid pSH1275-3 harboring vga(A)LC, one plasmid (pSH9361-1) carrying erm(C), and one plasmid (pSH9361-2) carrying qacJ. Conclusion The systematic analysis of whole-genome sequences provided insights into the mobile genetic elements responsible for multi-drug resistance in these two strains of oxacillin-resistant and mecA-positive S. haemolyticus, which will assist clinicians in devising precise, personalized, and clinical therapeutic strategies for treating otitis media caused by multi-drug resistant S. haemolyticus.
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Affiliation(s)
- Zhao Liu
- Department of Otolaryngology, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, People’s Republic of China
| | - Ling Wang
- Department of Obstetrics, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Jiabing Sun
- Department of Otolaryngology, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, People’s Republic of China
| | - Qinghuan Zhang
- Department of Clinical Laboratory, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Yue Peng
- Department of Otolaryngology, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, People’s Republic of China
| | - Susu Tang
- Department of Otolaryngology, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, People’s Republic of China
| | - Limei Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, People’s Republic of China
| | - Xiaobin Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, People’s Republic of China
- Zhuhai Precision Medical Center, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, People’s Republic of China
| | - Zhijian Yu
- Department of Otolaryngology, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, People’s Republic of China
| | - Tao Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Jinan University, Guangzhou, People’s Republic of China
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Røken M, Iakhno S, Haaland AH, Bjelland AM, Wasteson Y. The Home Environment Is a Reservoir for Methicillin-Resistant Coagulase-Negative Staphylococci and Mammaliicocci. Antibiotics (Basel) 2024; 13:279. [PMID: 38534714 DOI: 10.3390/antibiotics13030279] [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: 02/13/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Coagulase-negative staphylococci (CoNS) and mammaliicocci are opportunistic human and animal pathogens, often resistant to multiple antimicrobials, including methicillin. Methicillin-resistant CoNS (MRCoNS) have traditionally been linked to hospitals and healthcare facilities, where they are significant contributors to nosocomial infections. However, screenings of non-hospital environments have linked MRCoNS and methicillin-resistant mammaliicocci (MRM) to other ecological niches. The aim of this study was to explore the home environment as a reservoir for MRCoNS and MRM. A total of 33 households, including households with a dog with a methicillin-resistant staphylococcal infection, households with healthy dogs or cats and households without pets, were screened for MRCoNS and MRM by sampling one human, one pet (if present) and the environment. Samples were analyzed by a selective culture-based method, and bacterial species were identified by MALDI-TOF MS and tested for antibiotic susceptibility by the agar disk diffusion method. Following whole-genome sequencing, a large diversity of SCCmec elements and sequence types was revealed, which did not indicate any clonal dissemination of specific strains. Virulome and mobilome analyses indicated a high degree of species specificity. Altogether, this study documents that the home environment is a reservoir for a variety of MRCoNS and MRM regardless of the type of household.
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Affiliation(s)
- Mari Røken
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Institute of Microbiology, Norwegian Armed Forces Joint Medical Services, 2027 Kjeller, Norway
| | | | - Anita Haug Haaland
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Regulations and Control Department, Animal Health, 0304 Oslo, Norway
| | - Ane Mohn Bjelland
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Department of Bacteriology, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Yngvild Wasteson
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
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Moragues-Solanas L, Le-Viet T, McSorley E, Halford C, Lockhart DS, Aydin A, Kay GL, Elumogo N, Mullen W, O'Grady J, Gilmour MW. Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection. BMC Med Genomics 2024; 17:71. [PMID: 38443925 PMCID: PMC10916079 DOI: 10.1186/s12920-024-01835-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory illness, and modified approaches may address two requisite factors for metagenomics to be used as a BSI diagnostic: depletion of the high level of host DNA to then detect the low abundance of microbes in blood. METHODS Blood samples from healthy donors were spiked with different concentrations of four prevalent causative species of BSI. All samples were then subjected to a modified saponin-based host DNA depletion protocol and optimised DNA extraction, whole genome amplification and debranching steps in preparation for sequencing, followed by bioinformatical analyses. Two related variants of the protocol are presented: 1mL of blood processed without bacterial enrichment, and 5mL of blood processed following a rapid bacterial enrichment protocol-SepsiPURE. RESULTS After first identifying that a large proportion of host mitochondrial DNA remained, the host depletion process was optimised by increasing saponin concentration to 3% and scaling the reaction to allow more sample volume. Compared to non-depleted controls, the 3% saponin-based depletion protocol reduced the presence of host chromosomal and mitochondrial DNA < 106 and < 103 fold respectively. When the modified depletion method was further combined with a rapid bacterial enrichment method (SepsiPURE; with 5mL blood samples) the depletion of mitochondrial DNA improved by a further > 10X while also increasing detectable bacteria by > 10X. Parameters during DNA extraction, whole genome amplification and long-read sequencing were also adjusted, and subsequently amplicons were detected for each input bacterial species at each of the spiked concentrations, ranging from 50-100 colony forming units (CFU)/mL to 1-5 CFU/mL. CONCLUSION In this proof-of-concept study, four prevalent BSI causative species were detected in under 12 h to species level (with antimicrobial resistance determinants) at concentrations relevant to clinical blood samples. The use of a rapid and precise metagenomic protocols has the potential to advance the diagnosis of BSI.
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Affiliation(s)
- Lluis Moragues-Solanas
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- University of East Anglia, Norwich, Norfolk, UK
| | - Thanh Le-Viet
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
| | - Elinor McSorley
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Carl Halford
- University of East Anglia, Norwich, Norfolk, UK
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, UK
| | - Daniel S Lockhart
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Alp Aydin
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Gemma L Kay
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Ngozi Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, UK
| | - William Mullen
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Justin O'Grady
- University of East Anglia, Norwich, Norfolk, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK.
- University of East Anglia, Norwich, Norfolk, UK.
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Buytaers FE, Verhaegen B, Van Nieuwenhuysen T, Roosens NHC, Vanneste K, Marchal K, De Keersmaecker SCJ. Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling. Front Microbiol 2024; 15:1330814. [PMID: 38495515 PMCID: PMC10940517 DOI: 10.3389/fmicb.2024.1330814] [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: 10/31/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction Shotgun metagenomics has previously proven effective in the investigation of foodborne outbreaks by providing rapid and comprehensive insights into the microbial contaminant. However, culture enrichment of the sample has remained a prerequisite, despite the potential impact on pathogen detection resulting from the growth competition. To circumvent the need for culture enrichment, we explored the use of adaptive sampling using various databases for a targeted nanopore sequencing, compared to shotgun metagenomics alone. Methods The adaptive sampling method was first tested on DNA of mashed potatoes mixed with DNA of a Staphylococcus aureus strain previously associated with a foodborne outbreak. The selective sequencing was used to either deplete the potato sequencing reads or enrich for the pathogen sequencing reads, and compared to a shotgun sequencing. Then, living S. aureus were spiked at 105 CFU into 25 g of mashed potatoes. Three DNA extraction kits were tested, in combination with enrichment using adaptive sampling, following whole genome amplification. After data analysis, the possibility to characterize the contaminant with the different sequencing and extraction methods, without culture enrichment, was assessed. Results Overall, the adaptive sampling outperformed the shotgun sequencing. While the use of a host removal DNA extraction kit and targeted sequencing using a database of foodborne pathogens allowed rapid detection of the pathogen, the most complete characterization was achieved when using solely a database of S. aureus combined with a conventional DNA extraction kit, enabling accurate placement of the strain on a phylogenetic tree alongside outbreak cases. Discussion This method shows great potential for strain-level analysis of foodborne outbreaks without the need for culture enrichment, thereby enabling faster investigations and facilitating precise pathogen characterization. The integration of adaptive sampling with metagenomics presents a valuable strategy for more efficient and targeted analysis of microbial communities in foodborne outbreaks, contributing to improved food safety and public health.
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Affiliation(s)
- Florence E. Buytaers
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Tom Van Nieuwenhuysen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDlab, IMEC, Ghent University, Ghent, Belgium
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Mukherjee A, Kizziah JL, Hawkins NC, Nasef MO, Parker LK, Dokland T. Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation. J Mol Biol 2024; 436:168415. [PMID: 38135177 PMCID: PMC10923094 DOI: 10.1016/j.jmb.2023.168415] [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] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.
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Affiliation(s)
- Amarshi Mukherjee
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - James L Kizziah
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - N'Toia C Hawkins
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mohamed O Nasef
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura K Parker
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Terje Dokland
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Benvenga V, Cuénod A, Purushothaman S, Dasen G, Weisser M, Bassetti S, Roloff T, Siegemund M, Heininger U, Bielicki J, Wehrli M, Friderich P, Frei R, Widmer A, Herzog K, Fankhauser H, Nolte O, Bodmer T, Risch M, Dubuis O, Pranghofer S, Calligaris-Maibach R, Graf S, Perreten V, Seth-Smith HMB, Egli A. Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection. Genome Med 2024; 16:23. [PMID: 38317199 PMCID: PMC10840241 DOI: 10.1186/s13073-024-01292-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: 05/30/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes. METHODS We accessed 451 historic (1965-1987) MRSA isolates stored in the Culture Collection of Switzerland, mostly collected from the Zurich region. We determined phenotypic antimicrobial resistance (AMR) and performed whole genome sequencing (WGS) using Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international assemblies from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes. RESULTS Among the 451 historic Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-III. Early MRSA were predominantly from clonal complex (CC)8. From 1980 to the end of the twentieth century, we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally. CONCLUSIONS The combined analysis of 1761 historic and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss-German and international MRSA across time.
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Affiliation(s)
- Vanni Benvenga
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
| | - Srinithi Purushothaman
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
| | | | - Maja Weisser
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Stefano Bassetti
- Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
- Swiss Institute of Bioinformatics, University of Basel, Lausanne, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Martin Siegemund
- Intensive Care Medicine, University Hospital Basel, Basel, Switzerland
| | - Ulrich Heininger
- Infectious Diseases and Hospital Epidemiology, University of Basel Children's Hospital, Basel, Switzerland
| | - Julia Bielicki
- Infectious Diseases and Hospital Epidemiology, University of Basel Children's Hospital, Basel, Switzerland
| | - Marianne Wehrli
- Microbiology Department, Hospital of Schaffhausen, Schaffhausen, Switzerland
| | - Paul Friderich
- Medicinal microbiology department, Hospital of Lucerne, Lucerne, Switzerland
| | - Reno Frei
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Andreas Widmer
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Kathrin Herzog
- Clinical Microbiology, Cantonal Hospital Thurgau, Münsterlingen, Switzerland
| | - Hans Fankhauser
- Clinical Microbiology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Oliver Nolte
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
- Clinical Microbiology, Zentrum für Labormedizin St, Gallen, St. Gallen, Switzerland
| | | | | | - Olivier Dubuis
- Clinical Microbiology, Viollier AG, Allschwil, Switzerland
| | | | | | - Susanne Graf
- Clinical Microbiology, Cantonal Hospital Basellandschaft, Liestal, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
- Swiss Pathogen Surveillance Platform (SPSP), Lausanne, Switzerland
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
- Swiss Institute of Bioinformatics, University of Basel, Lausanne, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland.
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.
- Swiss Pathogen Surveillance Platform (SPSP), Lausanne, Switzerland.
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Yi EJ, Nguyen TTM, Jin X, Bellere AD, Kim MJ, Yi TH. Human Milk-Derived Enterococcus faecalis HM20: A Potential Alternative Agent of Antimicrobial Effect against Methicillin-Resistant Staphylococcus aureus (MRSA). Microorganisms 2024; 12:306. [PMID: 38399710 PMCID: PMC10892211 DOI: 10.3390/microorganisms12020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
The increasing global impact of skin diseases, fueled by methicillin-resistant Staphylococcus aureus (MRSA), emphasizes the necessity for alternative therapies with lower toxicity, such as lactic acid bacteria (LAB). This study aims to isolate potential LAB from human milk and evaluate their efficacy against MRSA using various methods, including well diffusion, microdilution, crystal violet assay, enzymatic characterization, SDS-PAGE, and scanning electron microscopy (SEM). Among the 26 LAB screened, the human milk-derived strain HM20 exhibited significant antimicrobial activity against S. aureus CCARM 3089 (MRSA), which is a highly resistant skin pathogen. Through 16S rRNA sequencing, strain HM20 was identified as closely related to Enterococcus faecalis ATCC 19433T, which was subsequently designated as Enterococcus faecalis HM20. The minimum inhibitory concentration (MIC) of the cell-free supernatant (CFS) of HM20 against S. aureus KCTC 3881 and S. aureus CCARM 3089 was determined to be 6.25% and 12.5%, respectively. Furthermore, the effective inhibition of biofilm formation in S. aureus KCTC 3881 and S. aureus CCARM 3089 was observed at concentrations of 12.5% and 25% or higher, respectively. The antibacterial effect of the CFS was attributed to the presence of organic acids, hydrogen peroxide, and bacteriocins. Additionally, the antimicrobial peptides produced by HM20 were found to be stable under heat treatment and analyzed to have a size below 5 kDa. SEM image observations confirmed that the CFS of HM20 caused damage to the cell wall, forming pores and wrinkles on S. aureus KCTC 3881 and S. aureus CCARM 3089. This comprehensive investigation on strain HM20 conducted in this study provides foundational data for potential developments in functional materials aimed at addressing skin infections and antibiotic-resistant strains in the future.
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Affiliation(s)
- Eun-Ji Yi
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (E.-J.Y.); (T.T.M.N.); (A.D.B.)
| | - Trang Thi Minh Nguyen
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (E.-J.Y.); (T.T.M.N.); (A.D.B.)
| | - Xiangji Jin
- Department of Dermatology, School of Medicine, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dong-daemun, Seoul 02447, Republic of Korea;
| | - Arce Defeo Bellere
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (E.-J.Y.); (T.T.M.N.); (A.D.B.)
| | - Mi-Ju Kim
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Tae-Hoo Yi
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (E.-J.Y.); (T.T.M.N.); (A.D.B.)
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Boroujeni MB, Mohebi S, Malekian A, Shahraeini SS, Gharagheizi Z, Shahkolahi S, Sadeghi RV, Naderifar M, Akbarizadeh MR, Soltaninejad S, Moghadam ZT, Moghadam MT, Mirzadeh F. The therapeutic effect of engineered phage, derived protein and enzymes against superbug bacteria. Biotechnol Bioeng 2024; 121:82-99. [PMID: 37881139 DOI: 10.1002/bit.28581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/18/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Defending against antibiotic-resistant infections is similar to fighting a war with limited ammunition. As the new century unfolded, antibiotic resistance became a significant concern. In spite of the fact that phage treatment has been used as an effective means of fighting infections for more than a century, researchers have had to overcome many challenges of superbug bacteria by manipulating phages and producing engineered enzymes. New enzymes and phages with enhanced properties have a significant impact on the ability to fight antibiotic-resistant infections, which is considered a window of hope for the future. This review, therefore, illustrates not only the challenges caused by antibiotic resistance and superbug bacteria but also the engineered enzymes and phages that are being developed to solve these issues. Our study found that engineered phages, phage proteins, and enzymes can be effective in treating superbug bacteria and destroying the biofilm caused by them. Combining these engineered compounds with other antimicrobial substances can increase their effectiveness against antibiotic-resistant bacteria. Therefore, engineered phages, proteins, and enzymes can be used as a substitute for antibiotics or in combination with antibiotics to treat patients with superbug infections in the future.
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Affiliation(s)
| | - Samane Mohebi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Azam Malekian
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Sadegh Shahraeini
- Department of Medical Biotechnology, Drug Design and Bioinformatics Unit, Biotechnology Research Centre, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Gharagheizi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Shaghayegh Shahkolahi
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Rezvaneh Vahedian Sadeghi
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mahin Naderifar
- School of Nursing & Midwifery, Zabol University of Medical Sciences, Zabol, Iran
| | | | | | - Zahra Taati Moghadam
- School of Nursing and Midwifery, Guilan University of Medical Sciences, Rasht, Iran
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Vasconcelos PC, Leite EL, Saraiva MMS, Ferrari RG, Cibulski SP, Silva NMV, Freitas Neto OC, Givisiez PEN, Vieira RFC, Oliveira CJB. Genomic Analysis of a Community-Acquired Methicillin-Resistant Staphylococcus aureus Sequence Type 1 Associated with Caprine Mastitis. Pathogens 2023; 13:23. [PMID: 38251331 PMCID: PMC10819347 DOI: 10.3390/pathogens13010023] [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: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
This study aimed to investigate the genomic and epidemiological features of a methicillin-resistant Staphylococcus aureus sequence type 1 (MRSA ST1) strain associated with caprine subclinical mastitis. An S. aureus strain was isolated from goat's milk with subclinical mastitis in Paraiba, Northeastern Brazil, by means of aseptic procedures and tested for antimicrobial susceptibility using the disk-diffusion method. Whole genome sequencing was performed using the Illumina MiSeq platform. After genome assembly and annotation, in silico analyses, including multilocus sequence typing (MLST), antimicrobial resistance and stress-response genes, virulence factors, and plasmids detection were performed. A comparative SNP-based phylogenetic analysis was performed using publicly available MRSA genomes. The strain showed phenotypic resistance to cefoxitin, penicillin, and tetracycline and was identified as sequence type 1 (ST1) and spa type 128 (t128). It harbored the SCCmec type IVa (2B), as well as the lukF-PV and lukS-PV genes. The strain was phylogenetically related to six community-acquired MRSA isolates (CA-MRSA) strains associated with human clinical disease in North America, Europe, and Australia. This is the first report of a CA-MRSA strain associated with milk in the Americas. The structural and epidemiologic features reported in the MRSA ST1 carrying a mecA-SCCmec type IVa suggest highly complex mechanisms of horizontal gene transfer in MRSA. The SNP-based phylogenetic analysis suggests a zooanthroponotic transmission, i.e., a strain of human origin.
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Affiliation(s)
- Priscylla C. Vasconcelos
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
| | - Elma L. Leite
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
| | - Mauro M. S. Saraiva
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
- School of Agricultural and Veterinarian Sciences, Department of Pathology, Reproduction, and One Health, São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil
| | - Rafaela G. Ferrari
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
| | - Samuel P. Cibulski
- Center for Biotechnology (CBiotec), Federal University of Paraiba (CBiotec/UFPB), João Pessoa 58051-900, PB, Brazil;
| | - Nubia M. V. Silva
- Animal Production Center, National Institute of Semiarid (INSA), Campina Grande 58434-700, PB, Brazil;
| | - Oliveiro C. Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil;
| | - Patrícia E. N. Givisiez
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
| | - Rafael F. C. Vieira
- Department of Public Health Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Celso J. B. Oliveira
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
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45
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Jiang JH, Cameron DR, Nethercott C, Aires-de-Sousa M, Peleg AY. Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin Microbiol Rev 2023; 36:e0014822. [PMID: 37982596 PMCID: PMC10732075 DOI: 10.1128/cmr.00148-22] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.
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Affiliation(s)
- Jhih-Hang Jiang
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - David R Cameron
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Cara Nethercott
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Genetics, Institutode Tecnologia Químicae Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisbon, Portugal
| | - Anton Y Peleg
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton, Melbourne, Victoria, Australia
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46
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Abebe AA, Birhanu AG. Methicillin Resistant Staphylococcus aureus: Molecular Mechanisms Underlying Drug Resistance Development and Novel Strategies to Combat. Infect Drug Resist 2023; 16:7641-7662. [PMID: 38111667 PMCID: PMC10726795 DOI: 10.2147/idr.s428103] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023] Open
Abstract
Antimicrobial resistance (AMR) represents a major threat to global health. Infection caused by Methicillin-resistant Staphylococcus aureus (MRSA) is one of the well-recognized global public health problem globally. In some regions, as many as 90% of S. aureus infections are reported to be MRSA, which cannot be treated with standard antibiotics. WHO reports indicated that MRSA is circulating in every province worldwide, significantly increasing the risk of death by 64% compared to drug-sensitive forms of the infection which is attributed to its antibiotic resistance. The emergence and spread of antibiotic-resistant MRSA strains have contributed to its increased prevalence in both healthcare and community settings. The resistance of S. aureus to methicillin is due to expression of penicillin-binding protein 2a (PBP2a), which renders it impervious to the action of β-lactam antibiotics including methicillin. The other is through the production of beta-lactamases. Although the treatment options for MRSA are limited, there are promising alternatives to antibiotics to combat the infections. Innovative therapeutic strategies with wide range of activity and modes of action are yet to be explored. The review highlights the global challenges posed by MRSA, elucidates the mechanisms underlying its resistance development, and explores mitigation strategies. Furthermore, it focuses on alternative therapies such as bacteriophages, immunotherapy, nanobiotics, and antimicrobial peptides, emphasizing their synergistic effects and efficacy against MRSA. By examining these alternative approaches, this review provides insights into the potential strategies for tackling MRSA infections and combatting the escalating threat of AMR. Ultimately, a multifaceted approach encompassing both conventional and novel interventions is imperative to mitigate the impact of MRSA and ensure a sustainable future for global healthcare.
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Affiliation(s)
- Assefa Asnakew Abebe
- Department of Molecular Biology, Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medical laboratory Sciences, Institute of Health, Bule Hora University, Bule Hora, Ethiopia
| | - Alemayehu Godana Birhanu
- Department of Molecular Biology, Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
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47
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Taha AE, Alduraywish AS, Alanazi AA, Alruwaili AH, Alruwaili AL, Alrais MM, Alyousef AA, Alrais AA, Alanazi MA, Alhudaib SN, Alazmi BM. High Bacterial Contamination Load of Self-Service Facilities in Sakaka City, Aljouf, Saudi Arabia, with Reduced Sensitivity to Some Antimicrobials. Microorganisms 2023; 11:2937. [PMID: 38138082 PMCID: PMC10745763 DOI: 10.3390/microorganisms11122937] [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: 10/22/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Although self-service facilities (SSFs) have been used on a large scale worldwide, they can be easily contaminated by microorganisms from the hands of their sequential users. This research aimed to study the prevalence and antimicrobial susceptibility/resistance of bacteria contaminating SSFs in Sakaka, Aljouf, Saudi Arabia. We randomly swabbed the surfaces of 200 SSFs, then used the suitable culture media, standard microbiological methods, and the MicroScan WalkAway Microbiology System, including the identification/antimicrobial susceptibility testing-combo panels. A high SSFs' bacterial contamination load was detected (78.00%). Ninety percent of the samples collected in the afternoon, during the maximum workload of the SSFs, yielded bacterial growth (p < 0.001 *). Most of the contaminated SSFs were supermarket payment machines, self-pumping equipment at gas stations (p = 0.004 *), online banking service machines (p = 0.026 *), and barcode scanners in supermarkets. In the antiseptic-deficient areas, 55.1% of the contaminated SSFs were detected (p = 0.008 *). Fifty percent of the contaminated SSFs were not decontaminated. The most common bacterial contaminants were Escherichia coli (70 isolates), Klebsiella pneumoniae (66 isolates), Staphylococcus epidermidis (34 isolates), methicillin-resistant Staphylococcus aureus (18 isolates), and methicillin-sensitive Staphylococcus aureus (14 isolates), representing 31.53%, 29.73%, 15.32%, 8.11%, and 6.31% of the isolates, respectively. Variable degrees of reduced sensitivity to some antimicrobials were detected among the bacterial isolates. The SSFs represent potential risks for the exchange of antimicrobial-resistant bacteria between the out-hospital environment and the hospitals through the hands of the public. As technology and science advance, there is an urgent need to deploy creative and automated techniques for decontaminating SSFs and make use of recent advancements in materials science for producing antibacterial surfaces.
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Affiliation(s)
- Ahmed E. Taha
- Microbiology and Immunology Unit, Department of Pathology, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
| | | | - Ali A. Alanazi
- College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
| | | | | | - Mmdoh M. Alrais
- College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
| | | | | | | | | | - Bandar M. Alazmi
- College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
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48
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Houtak G, Bouras G, Nepal R, Shaghayegh G, Cooksley C, Psaltis AJ, Wormald PJ, Vreugde S. The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis. Microb Genom 2023; 9:001128. [PMID: 38010322 PMCID: PMC10711304 DOI: 10.1099/mgen.0.001128] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/23/2023] [Indexed: 11/29/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus paired isolates (34 pairs) were sourced from 34 CRS patients at least 6 months apart. Isolates were grown into 48 h biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41 % (14/34 pairs) of S. aureus isolates were persistent, while 59 % (20/34 pairs) were non-persistent. Persistent isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. Furthermore, a significant increase in the copy number of conserved plasmids of persistent strains was observed. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics, which was linked to a significant increase in biofilm biomass over time, indicating a potential biofilm pathoadaptive process in persistent isolates. In conclusion, our study provides important insights into the mutational changes during S. aureus persistence in CRS patients highlighting potential pathoadaptive mechanisms in S. aureus persistent isolates culminating in increased biofilm biomass.
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Affiliation(s)
- Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Roshan Nepal
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Gohar Shaghayegh
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Clare Cooksley
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Alkis James Psaltis
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Peter-John Wormald
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
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49
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Agyirifo DS, Mensah TA, Senya ASY, Hounkpe A, Dornyoh CD, Otwe EP. Dynamics of antimicrobial resistance and virulence of staphylococcal species isolated from foods traded in the Cape Coast metropolitan and Elmina municipality of Ghana. Heliyon 2023; 9:e21584. [PMID: 38027608 PMCID: PMC10663863 DOI: 10.1016/j.heliyon.2023.e21584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
The impact of staphylococci on food poisoning and infections could be higher than previously reported. In this study, we characterised the occurrence and coexistence of antimicrobial resistance and virulence genes of staphylococci isolates in foods. Staphylococci were isolated from 236 samples of selected street-vended foods and identified. The pattern of antimicrobial resistance and virulence genes in the staphylococci were assessed using disc diffusion, PCR and analysis of next-generation sequencing data. The food samples (70.76 %) showed a high prevalence of staphylococci and differed among the food categories. Forty-five Staphylococcus species were identified and comprised coagulase-negative and positive species. Staphylococcus sciuri (now Mammaliicoccus sciuri), S. aureus, S. kloosii, S. xylosus, S. saprophyticus, S. haemolyticus and S. succinus were the most abundant species. The staphylococcal isolates exhibited resistance to tetracycline, levofloxacin, ciprofloxacin, norfloxacin, gentamicin and amikacin and susceptibility to nitrofurantoin. Antimicrobial susceptibilities were also reported for cefoperazone, ceftriaxone, cefotaxime, nalidixic acid and piperacillin-tazobactam. The antimicrobial resistance and virulence genes commonly detected consisted of tet, arl, macB, van, gyr, nor, optrA, bcrA, blaZ, taeA and S. aureus lmrS. The isolates frequently exhibited multiple resistance (30.42 %) of up to eight antimicrobial drug classes. The isolates predominantly harboured genes that express efflux pump proteins (50.53 %) for antibiotic resistance compared with inactivation (10.05 %), target alteration (26.72 %), protection (7.67 %) and replacement (3.17 %). The virulence determinants comprised genes of pyrogenic toxin superantigens (eta, etb, tst), adhesions (clf, fnbA, fnbB, cna, map, ebp, spA, vWbp, coa) and genes that express exoproteins (nuclease, metalloprotease, γ-hemolysin, hyaluronate lyase). There was a statistically significant difference in the prevalence of staphylococci isolates and their antimicrobial resistance and virulence profile as revealed by the phenotypic, PCR and next-generation sequencing techniques. The findings suggest a higher health risk for consumers. We recommend a critical need for awareness and antimicrobial susceptibility and anti-virulence strategies to ensure food safety and counteract the spread of this clinically relevant genus.
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Affiliation(s)
- Daniel Sakyi Agyirifo
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Theophilus Abonyi Mensah
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Andrews Senyenam Yao Senya
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Alphonse Hounkpe
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Cindy Deladem Dornyoh
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Emmanuel Plas Otwe
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
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50
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Rodríguez MF, Gomez AP, Ceballos-Garzon A. Antimicrobial Resistance Profiles of Staphylococcus Isolated from Cows with Subclinical Mastitis: Do Strains from the Environment and from Humans Contribute to the Dissemination of Resistance among Bacteria on Dairy Farms in Colombia? Antibiotics (Basel) 2023; 12:1574. [PMID: 37998777 PMCID: PMC10668774 DOI: 10.3390/antibiotics12111574] [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: 08/06/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Staphylococcus is a very prevalent etiologic agent of bovine mastitis, and antibiotic resistance contributes to the successful colonization and dissemination of these bacteria in different environments and hosts on dairy farms. This study aimed to identify the antimicrobial resistance (AMR) genotypes and phenotypes of Staphylococcus spp. isolates from different sources on dairy farms and their relationship with the use of antibiotics. An antimicrobial susceptibility test was performed on 349 Staphylococcus strains (S. aureus, n = 152; non-aureus staphylococci (NAS), n = 197) isolated from quarter milk samples (QMSs) from cows with subclinical mastitis (176), the teats of cows (116), the milking parlor environment (32), and the nasal cavities of milk workers (25). Resistance and multidrug resistance percentages found for S. aureus and NAS were (S. aureus = 63.2%, NAS = 55.8%) and (S. aureus = 4.6%, NAS = 11.7%), respectively. S. aureus and NAS isolates showed resistance mainly to penicillin (10 IU) (54.1% and 32.4%) and ampicillin (10 mg) (50.3% and 27.0%) drugs. The prevalence of AMR Staphylococcus was higher in environmental samples (81.3%) compared to other sources (52.6-76.0%). In S. aureus isolates, the identification of the blaZ (83.9%), aacAaphD (48.6%), ermC (23.5%), tetK (12.9%), and mecA (12.1%) genes did not entirely agree with the AMR phenotype. We conclude that the use of β-lactam antibiotics influences the expression of AMR in Staphylococcus circulating on dairy farms and that S. aureus isolates from the environment and humans may be reservoirs of AMR for other bacteria on dairy farms.
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Affiliation(s)
| | - Arlen Patricia Gomez
- Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Sede Bogotá, Bogotá 111321, Colombia;
| | - Andres Ceballos-Garzon
- Proteomics and Human Mycosis Unit, Infectious Diseases Group, Microbiology Department, School of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
- BIOASTER, Institut de Recherche Technologique, 40 Avenue Tony Garnier, 69007 Lyon, France
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