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Molecular epidemiology of clinically highâriskPseudomonas aeruginosastrains: Practical overview
- Source :
- Microbiology and Immunology. 64:331-344
- Publication Year :
- 2020
- Publisher :
- Wiley, 2020.
-
Abstract
- In recent years, numerous outbreaks of multidrug-resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing pulsed-field gel electrophoresis DNA fingerprinting are faster, easier-to-use, and less expensive polymerase chain reaction (PCR)-based methods for characterizing hospital isolates. P. aeruginosa possesses a mosaic genome structure and a highly conserved core genome displaying low sequence diversity and a highly variable accessory genome that communicates with other Pseudomonas species via horizontal gene transfer. Multiple-locus variable-number tandem-repeat analysis and multilocus sequence typing methods allow for phylogenetic analysis of isolates by PCR amplification of target genes with the support of Internet-based services. The target genes located in the core genome regions usually contain low-frequency mutations, allowing the resulting phylogenetic trees to infer evolutionary processes. The multiplex PCR-based open reading frame typing (POT) method, integron PCR, and exoenzyme genotyping can determine a genotype by PCR amplifying a specific insertion gene in the accessory genome region using a single or a multiple primer set. Thus, analyzing P. aeruginosa isolates for their clonality, virulence factors, and resistance characteristics is achievable by combining the clonality evaluation of the core genome based on multiple-locus targeting methods with other methods that can identify specific virulence and antimicrobial genes. Software packages such as eBURST, R, and Dendroscope, which are powerful tools for phylogenetic analyses, enable researchers and clinicians to visualize clonality associations in clinical isolates.
- Subjects :
- DNA, Bacterial
Immunology
Multiple Loci VNTR Analysis
Biology
Microbiology
Genome
Disease Outbreaks
03 medical and health sciences
Drug Resistance, Multiple, Bacterial
Virology
Multiplex polymerase chain reaction
Humans
Pseudomonas Infections
Genotyping
Gene
Phylogeny
030304 developmental biology
Genetics
Molecular Epidemiology
0303 health sciences
030306 microbiology
Bacterial Typing Techniques
DNA profiling
Pseudomonas aeruginosa
Horizontal gene transfer
Multilocus sequence typing
Multiplex Polymerase Chain Reaction
Software
Multilocus Sequence Typing
Subjects
Details
- ISSN :
- 13480421 and 03855600
- Volume :
- 64
- Database :
- OpenAIRE
- Journal :
- Microbiology and Immunology
- Accession number :
- edsair.doi.dedup.....b89d88d70b663cc91bbb5a9aab338cbf