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Mustafa AS. Whole Genome Sequencing: Applications in Clinical Bacteriology. Med Princ Pract 2024; 33:185-197. [PMID: 38402870 DOI: 10.1159/000538002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/22/2024] [Indexed: 02/27/2024] Open
Abstract
The success in determining the whole genome sequence of a bacterial pathogen was first achieved in 1995 by determining the complete nucleotide sequence of Haemophilus influenzae Rd using the chain-termination method established by Sanger et al. in 1977 and automated by Hood et al. in 1987. However, this technology was laborious, costly, and time-consuming. Since 2004, high-throughput next-generation sequencing technologies have been developed, which are highly efficient, require less time, and are cost-effective for whole genome sequencing (WGS) of all organisms, including bacterial pathogens. In recent years, the data obtained using WGS technologies coupled with bioinformatics analyses of the sequenced genomes have been projected to revolutionize clinical bacteriology. WGS technologies have been used in the identification of bacterial species, strains, and genotypes from cultured organisms and directly from clinical specimens. WGS has also helped in determining resistance to antibiotics by the detection of antimicrobial resistance genes and point mutations. Furthermore, WGS data have helped in the epidemiological tracking and surveillance of pathogenic bacteria in healthcare settings as well as in communities. This review focuses on the applications of WGS in clinical bacteriology.
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Affiliation(s)
- Abu Salim Mustafa
- Department of Microbiology, College of Medicine, Kuwait University, Kuwait City, Kuwait
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Zaghen F, Sora VM, Meroni G, Laterza G, Martino PA, Soggiu A, Bonizzi L, Zecconi A. Epidemiology of Antimicrobial Resistance Genes in Staphylococcus aureus Isolates from a Public Database from a One Health Perspective-Sample Origin and Geographical Distribution of Isolates. Antibiotics (Basel) 2023; 12:1654. [PMID: 38136688 PMCID: PMC10740469 DOI: 10.3390/antibiotics12121654] [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: 10/12/2023] [Revised: 11/14/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Staphylococcus aureus are commensal bacteria that are found in food, water, and a variety of settings in addition to being present on the skin and mucosae of both humans and animals. They are regarded as a significant pathogen as well, with a high morbidity that can cause a variety of illnesses. The Centers for Disease Control and Prevention (CDC) has listed them among the most virulent and resistant to antibiotics bacterial pathogens, along with Escherichia coli, Staphylococcus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium. Additionally, S. aureus is a part of the global threat posed by the existence of antimicrobial resistance (AMR). Using 26,430 S. aureus isolates from a global public database (NPDIB; NCBI Pathogen Detection Isolate Browser), epidemiological research was conducted. The results corroborate the evidence of notable variations in isolate distribution and ARG (Antimicrobial Resistance Gene) clusters between isolate sources and geographic origins. Furthermore, a link between the isolates from human and animal populations is suggested by the ARG cluster patterns. This result and the widespread dissemination of the pathogens among animal and human populations highlight how crucial it is to learn more about the epidemiology of these antibiotic-resistance-related infections using a One Health approach.
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Affiliation(s)
- Francesca Zaghen
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
- Department of Clinical and Community Sciences, School of Medicine, University of Milan, Via Celoria 22, 20133 Milan, Italy
| | - Valerio Massimo Sora
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
- Department of Clinical and Community Sciences, School of Medicine, University of Milan, Via Celoria 22, 20133 Milan, Italy
| | - Gabriele Meroni
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Giulia Laterza
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
- Department of Clinical and Community Sciences, School of Medicine, University of Milan, Via Celoria 22, 20133 Milan, Italy
| | - Piera Anna Martino
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Alessio Soggiu
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Luigi Bonizzi
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Alfonso Zecconi
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
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