Streptococcal taxonomy based on genome sequence analyses

F1000Research
Cristiane C ThompsonAna Carolina P Vicente

Abstract

The identification of the clinically relevant viridans streptococci group, at species level, is still problematic. The aim of this study was to extract taxonomic information from the complete genome sequences of 67 streptococci, comprising 19 species, by means of genomic analyses, multilocus sequence analysis (MLSA), average amino acid identity (AAI), genomic signatures, genome-to-genome distances (GGD) and codon usage bias. We then attempted to determine the usefulness of these genomic tools for species identification in streptococci. Our results showed that MLSA, AAI and GGD analyses are robust markers to identify streptococci at the species level, for instance, S. pneumoniae, S. mitis, and S. oralis. A Streptococcus species can be defined as a group of strains that share ≥ 95% DNA similarity in MLSA and AAI, and > 70% DNA identity in GGD. This approach allows an advanced understanding of bacterial diversity.

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Citations

Jan 21, 2016·Antonie van Leeuwenhoek·Luciana R AppolinarioCristiane C Thompson
Aug 4, 2015·Diagnostic Microbiology and Infectious Disease·Katarzyna ObszańskaIzabela Sitkiewicz
Dec 24, 2014·Archives of Microbiology·Cristiane C ThompsonFabiano L Thompson
Jun 22, 2016·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·L H RasmussenX C Nielsen
Mar 14, 2018·International Journal of Systematic and Evolutionary Microbiology·Maria Soledad Morales-CovarrubiasBruno Gomez-Gil
Aug 22, 2013·Microbial Ecology·Cristiane C ThompsonFabiano L Thompson
Feb 8, 2014·International Journal of Systematic and Evolutionary Microbiology·Gilda Rose S AmaralCristiane C Thompson
Dec 4, 2019·Antimicrobial Resistance and Infection Control·Maja Kosecka-StrojekAlexander W Friedrich
Jul 10, 2021·BMC Genomics·Dhiraj SinhaPierre-Edouard Fournier
Aug 24, 2021·Frontiers in Cellular and Infection Microbiology·Mohamed M H AbdelbaryGeorg Conrads

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Software Mentioned

MLSA
MEGA5
ClustalX
BLAST
BLASTp

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