Draft Genome Sequence of Turicella otitidis TD1, Isolated from a Patient with Bacteremia

Abstract

T uricella otitidis is a nonfermenting Gram-positive non-sporeforming rod usually isolated from ear exudates. The bacterium was described originally in 1994 from acute and chronic otitis media and has since been isolated from a posterior auricular abscess, mastoiditis, and blood (1-3). To date, only one case of bacteremia due to T. otitidis has ever been reported (3). Its association with otitis media is controversial, as it has been isolated from the external auditory canal of healthy subjects at ratios comparable to those noted when T. otitidis otitis media was diagnosed (4-6). Most isolates demonstrate high resistance to macrolides and lincosamides with associated 23S rRNA mutations (4, 7).As only one whole genome of T. otitidis had been sequenced previously, we sequenced the draft genome of T. otitidis strain TD1, isolated from a central line catheter tip culture. The isolate, and another one on the same patient, from the same source, that was submitted 3 months before, had previously been identified in our laboratory by biochemical and cellular fatty acid analysis.DNA from strain TD1 was extracted using the Promega Genomic DNA Wizard kit, and paired-end libraries were constructed using the Nextera XT kit. Sequences were adapted and quality (Q30) trimmed using Cutadapt, de novo assembled using SPAdes version 3.5, metagenomically screened with SURPI, and annotated via Prokka version 1.1, as described previously (8-12). A total of 739, 492 paired-end reads with an average length of 173 nucleotides were recovered after trimming. De novo assembly yielded 160 contigs covering a total of 2,150,112 bp with an N 50 of 24,176 bp, a GC content of 71.2%, an average coverage of 54ϫ, and a total of 1,866 annotated coding sequences.BLASTn of the assembled 16S sequence from strain TD1 against the NCBI WGS database aligned 99.35% to T. otiditis ATCC 51513 and had an average nucleotide identity of 98.75% to ATCC 51513, confirming the identity of the strain (13). Direct mapping of TD1 reads to ATCC 51513 revealed 20,176 variants between the two strains. De novo assembly of reads that failed to map to ATCC 51513 revealed a total of 85.4 kb unique sequence, including a locus of 50 kb containing Ͼ60 hypothetical proteincoding sequences with no nucleotide homology to the NT database that aligned Ͻ35% amino acid by BLASTx and HHPred to various mycobacterium phage protein sequences (14). Genes in the remaining loci not present in ATCC 51513 included an arylsulfatase, a cadmium-cobalt antiporter, a phosphate/phosphonate transporter operon, and a unique ABC transporter, with all predicted proteins having Ͻ65% amino acid identity to the closest species, Corynebacterium glycinophilum AJ 3170. Antibiotic resistance genes annotated by the Comprehensive Antibiotic Resistance Database included a cfrA 50S methyltransferase (99% amino acid to T. otitidis ATCC 51513) and two major facilitator superfamily-type drug-resistance transporters (99% amino acid T. otitidis ATCC 51513 and 57 to 59% amino acid to Corynebacterium spp.) (15). In addition...

Metabolism and gene sequence variation in Turicella otitidis implies its adaptability and pathogenicity in extra-otic infection: a systematic review

“…Both TD1 and ATC5153 possess the gene responsible for converting histidine to glutamate, enabling pathogenic T. otitidis to overcome the limiting factor as well as a stress response. This supports the colonization of Turicella otitidis in the middle ear, leading to otitis media, whereas other bacteria are unable to colonize and cause infection [ 44 ].…”

“…We herein provide a summary of the genome and cellular fatty acid analysis of T. otitidis draft strain (TD1) isolated from a central line catheter tip culture in a patient with a history of bowel obstruction and ATCC 51,513 strain from the ear [ 35 , 44 ]. Comparative studies were conducted to investigate the changes in the genome and metabolic pathways of both strains.…”

“…These findings imply a potential role in the survival and adaptation of T. otitidis to diverse niches. Also, TD1 strain has antibiotic resistance genes, including a cfrA 50 S methyltransferase that shares 99% amino acid similarity with T. otitidis ATCC 51,513, as well as two major facilitator superfamily–type drug-resistance transporters that exhibit 99% amino acid similarity to T. otitidis ATCC 51,513 and 57–59% amino acid similarity to Corynebacterium species [ 35 , 44 ].…”

Reviewing the Pathogenic Potential of the Otitis-Associated Bacteria Alloiococcus otitidis and Turicella otitidis

“…It has also been isolated in pure culture from a posterior auricular abscess (Reynolds et al, 2001) and a case of mastoiditis (Dana et al, 2001), both in young children. The T. otitidis strain TD1, whose genome was recently sequenced (Greninger et al, 2015), was isolated from a venous catheter. It is therefore plausible that the genomic contents of this strain are not representative of strains involved in OM.…”

Turicella otitidis central venous-related bacteremia during pediatric acute lymphoblastic leukemia

“…T. otitidis is a non-fermenting Gram-positive rod isolated almost exclusively from ear exudate fluids, although its clinical significance in both acute and chronic otitis is still controversial [ 2 - 5 ]. Isolated since two decades [ 2 ], its genoma has been sequenced [ 3 ]. T. otitidis habitat seems limited to the ear and surrounding areas, but it has been retrieved as an infrequent cause of bacteremia [ 2 - 5 ], especially in children with hemato-logic malignancies [ 2 , 4 ].…”