A Potential New Human Pathogen Belonging to Helicobacter Genus, Identified in a Bloodstream Infection

Abstract

We isolated from aerobic and anaerobic blood culture bottles from a febrile patient, a Helicobacter-like Gram negative, rod-shaped bacterium that MALDI-TOF MS failed to identify. Blood agar cultures incubated in a microaerobic atmosphere revealed a motile Gram negative rod, which was oxidase, catalase, nitrate reductase, esterase, and alkaline phosphatase positive. It grew at 42°C with no detectable urease activity. Antimicrobial susceptibility testing showed that the organism was susceptible to beta-lactams, gentamicin, erythromycin, and tetracycline but resistant to ciprofloxacin. Electronic microscopy analysis revealed a 3 × 0.5 μm curved rod bacterium harboring two sheathed amphitrichous flagella. Whole genome sequencing revealed a genome 1,708,265 base-pairs long with a GC content of 37.80% and a total of 1,697 coding sequences. The genomic analyses using the nucleotide sequences of the 16S rRNA gene, hsp60 and gyrB genes, as well as the GyrA protein sequence, and the results of Average Nucleotide Identity and in silico DNA-DNA hybridization suggest evidence for a novel Helicobacter species close to Helicobacter equorum and belonging to the group of enterohepatic Helicobacter species. As soon as the particular peptide mass fingerprint of this pathogen is added to the spectral databases, MALDI-TOF MS technology will improve its identification from clinical specimens, especially in case of "sterile infection". We propose to associate the present strain with the Latin name of the place of isolation; Caesarodunum (Tours, France) and suggest "Helicobacter caesarodunensis" for further description of this new bacterium.

Keywords: Helicobacter sp.; electron microscopy; genome content; human infection; phylogeny.

Figure 1

Aspect of S15 colonies on trypcase soy agar. Culture of an identified organism on trypcase soy agar enriched with 5% horse blood for 2–3 days at 37°C.

Figure 2

Electron microscopy pictures of strain S15. Microscopic examinations revealed a rod-shaped bacterium 3 μm in length and 0.5 μm width (A). Pictures show amphitrichous sheathed flagella with a diameter around 60 nm (B).

Figure 3

Phylogenetic trees. Evolutionary relationships of Helicobacter taxa based on the 16S rRNA gene (A) and GyrA protein encoded gene (B). The phylogeny presented is based on the alignment of approximately 1,400 nucleotides of the 16S rRNA gene and 700 residues of the GyrA protein. The phylogenetic analyses were generated with the neighbor-joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) is shown next to the branches. The trees are not rooted and drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Kimura 2-parameter method for 16S rRNA gene, the Poisson correction method for GyrA and are represented in the units of the number of base substitutions per site. The analysis included 34 sequences. All ambiguous positions were removed for each sequence pair. Evolutionary analyses were conducted using MEGA6. All sequences are labeled according to species, strain name, collection number in brackets. Mycobacterium tuberculosis was used as the outgroup sequence. All accession numbers are provided in Supplementary Table S2.