Challenges of Francisella classification exemplified by an atypical clinical isolate

Matz, Lisa M.; Kamdar, KY; Holder, ME; Ga, Metcalf; Weissenberger, GM; Meng, Qingchang; Vee, Vanesa; Han, Yi; Dm, Muzny; Gibbs, RA; Johnson, Catherine L.; Revell, P. A.; Petrosino, Joe

doi:10.1016/j.diagmicrobio.2017.11.023

“…novicida sdhA sequences from these 13 air filters were identical or highly similar to each other and to those from three F . novicida isolates obtained in or near Houston from humans (Fx1, Fx2, TCH2015) [ 7 , 60 , 61 ], but were more distantly related to four F . novicida sdhA sequences (015.A01, 027.B01, 039.D01, 045.E01) generated from soil samples collected in Houston in 2003 [ 6 ].…”

Section: Resultsmentioning

confidence: 99%

Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples

Wagner

¹

,

Birdsell

²

,

McDonough

³

et al. 2022

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Francisella tularensis, the bacterium that causes the zoonosis tularemia, and its genetic near neighbor species, can be difficult or impossible to cultivate from complex samples. Thus, there is a lack of genomic information for these species that has, among other things, limited the development of robust detection assays for F. tularensis that are both specific and sensitive. The objective of this study was to develop and validate approaches to capture, enrich, sequence, and analyze Francisella DNA present in DNA extracts generated from complex samples. RNA capture probes were designed based upon the known pan genome of F. tularensis and other diverse species in the family Francisellaceae. Probes that targeted genomic regions also present in non-Francisellaceae species were excluded, and probes specific to particular Francisella species or phylogenetic clades were identified. The capture-enrichment system was then applied to diverse, complex DNA extracts containing low-level Francisella DNA, including human clinical tularemia samples, environmental samples (i.e., animal tissue and air filters), and whole ticks/tick cell lines, which was followed by sequencing of the enriched samples. Analysis of the resulting data facilitated rigorous and unambiguous confirmation of the detection of F. tularensis or other Francisella species in complex samples, identification of mixtures of different Francisella species in the same sample, analysis of gene content (e.g., known virulence and antimicrobial resistance loci), and high-resolution whole genome-based genotyping. The benefits of this capture-enrichment system include: even very low target DNA can be amplified; it is culture-independent, reducing exposure for research and/or clinical personnel and allowing genomic information to be obtained from samples that do not yield isolates; and the resulting comprehensive data not only provide robust means to confirm the presence of a target species in a sample, but also can provide data useful for source attribution, which is important from a genomic epidemiology perspective.

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“…F. tularensis nearest neighbor is Francisella novicida, with ANI values above 97.7% [12,13,14]. F. novicida has been isolated from environmental samples and its evolution is not clonal [12,15,16]. The ratio of non synonymous versus synonymous genetic variations was shown to be strikingly different in F. novicida compared to F. tularensis [12].…”

Section: Whole-genome Sequencing (Wgs) and Phylogenetic Analysismentioning

confidence: 97%

The First Finding of <em>Francisella Tularensis</em> Subsp. <em>Mediasiatica</em> in Krasnoyarsk Territory, Siberia and an Update of the Subspecies Genetic Diversity

Timofeev¹,

Бахтеева²,

Мокриевич³

et al. 2022

Preprint

0

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Tularemia is a severe infectious disease caused by the Gram-negative bacteria Francisella tularensis. F. tularensis is currently divided into three subspecies, holarctica, tularensis and mediasiatica which differ in their virulence and geographic distribution. Subspecies mediasiatica is the least studied because of its very low documented virulence for humans and limited geographic distribution. It was discovered in sparsely populated regions of Central Asia. Since 2011, a new subsp. mediasiatica lineage was identified in Altai (Russia). In 2021, we isolated one subsp. mediasiatica strain in Krasnoyarsk Territory. In spite of its geographic origin, 500 km east from Altai, this strain belongs to the Altai lineage and contributes surprisingly little genetic diversity to previous knowledge. This improved knowledge of the phylogeography of subsp. mediasiatica led us to propose a scenario in which the two zoonotic lineages, holarctica and tularensis, independently emerged from the mediasiatica lineage in Siberia or Central Asia, and make predictions which will allow to challenge this hypothesis

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“…Within the sdhA phylogeny (Fig 3), the F. novicida sdhA sequences from these 13 air filters were identical or highly similar to each other and to those from three F. novicida isolates obtained in or near Houston from humans (Fx1, Fx2, TCH2015) [7,60,61], but were more distantly related to four F. novicida sdhA sequences (015.A01, 027.B01, 039.D01, 045.E01) generated from soil samples collected in Houston in 2003 [6]. A F. novicida MAG was only assembled from sequence reads from one air filter, Air1; a F. philomiragia MAG also was assembled from this sample (S3 novicida and mechanisms of transmission to humans are poorly understood [62].…”

Section: Francisella-positive Air Filter Samplesmentioning

confidence: 99%

Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples

Wagner

¹

,

Birdsell

²

,

McDonough

³

et al. 2022

Preprint

1

0

View full text Add to dashboard Cite

Francisella tularensis, the bacterium that causes the zoonosis tularemia, and its genetic near neighbor species, can be difficult or impossible to cultivate from complex samples. Thus, there is a lack of genomic information for these species that has, among other things, limited the development of robust detection assays for F. tularensis that are both specific and sensitive. The objective of this study was to develop and validate approaches to capture, enrich, sequence, and analyze Francisella DNA present in DNA extracts generated from complex samples. RNA capture probes were designed based upon the known pan genome of F. tularensis and other diverse species in the family Francisellaceae. Probes that targeted genomic regions also present in non-Francisellaceae species were excluded, and probes specific to particular Francisella species or phylogenetic clades were identified. The capture-enrichment system was then applied to diverse, complex DNA extracts containing low-level Francisella DNA, including human clinical tularemia samples, environmental samples (i.e., animal tissue and air filters), and whole ticks/tick cell lines, which was followed by sequencing of the enriched samples. Analysis of the resulting data facilitated rigorous and unambiguous confirmation of the detection of F. tularensis or other Francisella species in complex samples, identification of mixtures of different Francisella species in the same sample, analysis of gene content (e.g., known virulence and antimicrobial resistance loci), and high-resolution whole genome-based genotyping. The benefits of this capture-enrichment system include: even very low target DNA can be amplified; it is culture-independent, reducing exposure for research and/or clinical personnel and allowing genomic information to be obtained from samples that do not yield isolates; and the resulting comprehensive data not only provide robust means to confirm the presence of a target species in a sample, but also can provide data useful for source attribution, which is important from a genomic epidemiology perspective.

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Challenges of Francisella classification exemplified by an atypical clinical isolate

Cited by 4 publications

References 42 publications

Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples

Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples

The First Finding of <em>Francisella Tularensis</em> Subsp. <em>Mediasiatica</em> in Krasnoyarsk Territory, Siberia and an Update of the Subspecies Genetic Diversity

Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples

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