Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species

Functional & Integrative Genomics
André S SantosLuis G C Pacheco

Abstract

Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 recently released whole genome sequences. We used data retrieved from curated databases (MetaCyc, PathoSystems Resource Integration Center (PATRIC), The SEED, TransportDB, UniProtKB) associated with homology searches by BLAST and profile Hidden Markov...Continue Reading

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Citations

Nov 29, 2020·Genome Medicine·Melanie HennartSylvain Brisse
Dec 4, 2020·Journal of Clinical Microbiology·Justine SchaefferWerner Ruppitsch
Jun 22, 2021·Access Microbiology·Claudia M BarberisCarlos A Vay
Sep 16, 2021·Journal of Clinical Microbiology·Julien GuglielminiSylvain Brisse

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Methods Mentioned

BETA
phosphotransferase

Software Mentioned

RaptorX
makeblastdb
BLAST
tBLASTn
Modeller
PATRIC
i3Drefine
TransportDB
Bacterial Pan - Genome Analysis ( BPGA ) pipeline
Artemis

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