1. Molecular epidemiology of clinically high‐riskPseudomonas aeruginosastrains: Practical overview
- Author
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Mao Kinoshita, Kyoko Momiyama, Teiji Sawa, Kiyoshi Moriyama, Toshihito Mihara, and Atsushi Kainuma
- 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 - 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.
- Published
- 2020