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Case Reports
. 2016 Apr 14:11:31.
doi: 10.1186/s40793-016-0150-1. eCollection 2016.

High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov

Cheikh Ibrahima Lo  1 , Senthil Alias Sankar  2 , Bécaye Fall  3 , Bissoume Sambe-Ba  3 , Silman Diawara  3 , Mamadou Wague Gueye  3 , Oleg Mediannikov  1 , Caroline Blanc-Tailleur  2 , Boubacar Wade  3 , Didier Raoult  4 , Pierre-Edouard Fournier  2 , Florence Fenollar  1
Affiliations
Case Reports

High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov

Cheikh Ibrahima Lo et al. Stand Genomic Sci. .

Retraction in

Abstract

Strain FF7(T) was isolated from the peritoneal fluid of a 44-year-old woman who suffered from pelvic peritonitis. This strain exhibited a 16S rRNA sequence similarity of 94.8 % 16S rRNA sequence identity with Haemophilus parasuis, the phylogenetically closest species with a name with standing in nomenclature and a poor MALDI-TOF MS score (1.32 to 1.56) that does not allow any reliable identification. Using a polyphasic study made of phenotypic and genomic analyses, strain FF7(T) was a Gram-negative, facultatively anaerobic rod and member of the family Pasteurellaceae. It exhibited a genome of 2,442,548 bp long genome (one chromosome but no plasmid) contains 2,319 protein-coding and 67 RNA genes, including 6 rRNA operons. On the basis of these data, we propose the creation of Haemophilus massiliensis sp. nov. with strain FF7(T) (= CSUR P859 = DSM 28247) as the type strain.

Keywords: Culturomics; Genome; Haemophilus massiliensis; Taxono-genomics.

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Figures

Fig. 1
Fig. 1
Phylogenetic tree showing the position of Haemophilus massiliensis strain FF7T relative to the most closely related type strains other type strains (type = T) within the genus Haemophilus. The GenBank accession numbers for 16S rRNA genes are indicated in parentheses. An asterisk marks strains that have a genome sequence in the NCBI database. Sequences were aligned using MUSCLE [35], and a phylogenetic tree inferred using the Maximum Likelihood method with Kimura 2-parameter model using the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. Only bootstrap values equal to or greater than 70 % are displayed. The scale bar represents a rate of substitution per site of 1 %. Escherichia coli strain ATCC 11775T was used as outgroup
Fig. 2
Fig. 2
Morphology of Haemophilus massiliensis sp. nov. strain FF7T. a: Gram staining. b: Transmission electron microscopy. The scale bar represents 500 nm
Fig. 3
Fig. 3
Graphical circular map of the Haemophilus massiliensis strain FF7T chromosome. From the outside in, the outer two circles show open reading frames oriented in the forward (colored by COG categories) and reverse (colored by COG categories) directions, respectively. The third circle marks the tRNA genes (green). The fourth circle shows the G + C% content plot. The inner-most circle shows GC skew, purple indicating negative values whereas olive for positive values
Fig. 4
Fig. 4
Distribution of functional classes of predicted genes in the genomes from Haemophilus massiliensis (HM) strain FF7T, H. parasuis (HPA) strain ATCC 19417T, Aggregatibacter segnis (AE) strain ATCC 33393T, H. aegyptius (HA) strain ATCC 11116T, H. ducreyi (HD) strain CIP 54.2, H. haemolyticus (HH) strain ATCC 33390T, H. influenzae (HI) strain ATCC 33391T, H. parahaemolyticus (HP), H. parainfluenzae (HPI) strain ATCC 10014T, H. pittmaniae (HPT) strain HK 85T, and H. sputorum (HS) strain CCUG 13788T chromosomes according to the clusters of orthologous groups of proteins
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