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Diagn Microbiol Infect Dis. 2018 Apr;90(4):241-247. doi: 10.1016/j.diagmicrobio.2017.11.023. Epub 2017 Dec 6.

Challenges of Francisella classification exemplified by an atypical clinical isolate.

Author information

1
Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA. Electronic address: lisa.matz@alumni.bcm.edu.
2
Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA.
3
Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
4
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
5
Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
6
Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology, Texas Children's Hospital, Houston, TX, USA.

Abstract

The accumulation of sequenced Francisella strains has made it increasingly apparent that the 16S rRNA gene alone is not enough to stratify the Francisella genus into precise and clinically useful classifications. Continued whole-genome sequencing of isolates will provide a larger base of knowledge for targeted approaches with broad applicability. Additionally, examination of genomic information on a case-by-case basis will help resolve outstanding questions regarding strain stratification. We report the complete genome sequence of a clinical isolate, designated here as F. novicida-like strain TCH2015, acquired from the lymph node of a 6-year-old male. Two features were atypical for F. novicida: exhibition of functional oxidase activity and additional gene content, including proposed virulence determinants. These differences, which could potentially impact virulence and clinical diagnosis, emphasize the need for more comprehensive methods to profile Francisella isolates. This study highlights the value of whole-genome sequencing, which will lead to a more robust database of environmental and clinical genomes and inform strategies to improve detection and classification of Francisella strains.

KEYWORDS:

Clinical microbiology; Comparative genomics; Whole genome sequencing

PMID:
29329757
PMCID:
PMC5857240
[Available on 2019-04-01]
DOI:
10.1016/j.diagmicrobio.2017.11.023
[Indexed for MEDLINE]

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