Increased knowledge of Francisella genus diversity highlights the benefits of optimised DNA-based assays

Ahlinder, Jon; Öhrman, Caroline; Svensson, Kerstin; Lindgren, Petter; Johansson, Anders; Forsman, Mats; Larsson, Pär; Sjödin, Andreas

doi:10.1186/1471-2180-12-220

Cited by 15 publications

(12 citation statements)

References 69 publications

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“…species (closest to). Recent attempts to conduct comparative genomic studies among members of the Francisella genus either have been conducted on only a few representatives (32,33,59), have focused on subspecies within F. tularensis (60,61), or have been conducted on incomplete, lower-quality draft genomes (62,63), where interpretation of relationships may be confounded by missing genetic features in the incomplete genomes.…”

mentioning

confidence: 99%

Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection

Challacombe

Petersen

Gallegos‐Graves

et al. 2017

Appl Environ Microbiol

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Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features-for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria.IMPORTANCE DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisella organisms identified in clinical samples or environmental surveys.

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confidence: 99%

Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection

Challacombe

Petersen

Gallegos‐Graves

et al. 2017

Appl Environ Microbiol

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“…During recent years, polymerase chain reaction (PCR)based methods have been successfully used for the rapid identification and classification of Francisella isolates, with increased sensitivity and specificity [54,78]. However, false positive results related to non-pathogenic closely related Francisella subspecies, occurring naturally in the environment, may hamper species and subspecies identification [78].…”

Section: Molecular Methodsmentioning

confidence: 99%

Tularaemia: A challenging zoonosis

Carvalho

Zé-Zé

et al. 2014

Comparative Immunology, Microbiology and Infectious Diseases

109

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a b s t r a c tIn recent years, several emerging zoonotic vector-borne infections with potential impact on human health have been identified in Europe, including tularaemia, caused by Francisella tularensis. This remarkable pathogen, one of the most virulent microorganisms currently known, has been detected in increasingly new settings and in a wide range of wild species, including lagomorphs, rodents, carnivores, fish and invertebrate arthropods. Also, a renewed concern has arisen with regard to F. tularensis: its potential use by bioterrorists. Based on the information published concerning the latest outbreaks, the aim of this paper is to review the main features of the agent, its biology, immunology and epidemiology. Moreover, special focus will be given to zoonotic aspects of the disease, as tularaemia outbreaks in human populations have been frequently associated with disease in animals.

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“…Members of the Francisella genus range from intracellular pathogens with different host preferences (F. tularensis, F. noatunensis, and F. halioticida) to specialized endosymbionts (Francisella-like endosymbionts) to generalists believed capable of a free-living existence (F. philomiragia and F. novicida) (8), with only a subset of Francisella spp. linked to human illness.…”

Section: Case Reportmentioning

confidence: 99%

Cutaneous Infection Caused by a Novel Francisella sp

et al. 2013

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A 69-year-old patient presented with a tender, thickly crusted skin lesion of 1 week's duration. A bacterial culture swab taken from the underlying granular tissue yielded a pure isolate of a Gram-negative coccobacillus, presumptively identified as a novel Francisella species via 16S rRNA and multilocus gene sequence analysis. CASE REPORTO n 5 January 2011, a 69-year-old white male presented to a dermatology clinic with a tender lesion on his left ankle. The patient had been well until the previous week when he cut down an Arizona ash tree near his home in southern Louisiana, close to the Mississippi River. Branches from the tree scratched his legs and abraded his left ankle. He applied mupirocin ointment to the ankle lesion, but it became increasingly tender and erythematous. His underlying medical conditions included non-insulin-dependent diabetes, hypertension, hyperlipidemia, and a history of a squamous cell carcinoma excised from his right arm in March 2010. The patient denied fever, chills, or other systemic symptoms.On initial examination, the patient was afebrile with a 4-by 6-cm thickly crusted erythematous nodule on the medial aspect of the left ankle, with surrounding erythema and tenderness to palpation (Fig. 1A). Incision and drainage of the nodule was attempted; however, no pus or purulent drainage was noted. Tissue underlying the eschar was pink and granular. A biopsy specimen of the underlying granular tissue was submitted for histopathology, deep fungal culture, and atypical mycobacterial culture; a swab was also taken for routine bacterial culture.Initial histopathology of the biopsied tissue was interpreted as squamous cell carcinoma. The patient was referred to a general surgeon for excision of the lesion but, because of the surrounding erythema, was also prescribed 500 mg ciprofloxacin twice daily (BID) for 7 days. The patient noted improvement in the lesion after 24 h. Deep fungal and atypical mycobacterial cultures were both negative. A Gram-negative coccobacillus grew from the bacterial swab taken from the underlying granular tissue and was presumptively identified as Francisella tularensis (described below). Based on the isolation of a Francisella species from the lesion, an additional 7 days of ciprofloxacin was prescribed, and the pathologist who performed histopathology was contacted to review the initial biopsy specimen. The pathologist's amended report noted probable pseudoepitheliomatous hyperplasia overlying a dense suppurative granulomatous dermatitis, rather than squamous cell carcinoma. However, significant atypia was noted, and the remaining lesion was excised in the operating room on 4 March 2011. The area healed well without further sequelae. Subsequent independent histopathology of the biopsy tissue similarly indicated no evidence of squamous cell carcinoma but rather marked inflammation and pseudoepitheliomatous epidermal hyperplasia with a dense, mixed dermal infiltrate including scattered small neutrophilic microabscesses, histiocytes, lymphocytes, and plasma cells (Fig....

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Increased knowledge of Francisella genus diversity highlights the benefits of optimised DNA-based assays

Cited by 15 publications

References 69 publications

Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection

Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection

Tularaemia: A challenging zoonosis

Cutaneous Infection Caused by a Novel Francisella sp

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