Draft Whole-Genome Sequence of a Catalase-Negative Staphylococcus aureus subsp. aureus (Sequence Type 25) Strain Isolated from a Patient with Endocarditis and Septic Arthritis.

Staphylococcus aureus strains without catalase activity are rare, challenging to identify with conventional biochemical methods, and, despite a supposed decreased pathogenicity, can still cause disease. The first whole-genome sequence of a catalase-negative S. aureus isolate causing severe recurrent invasive infection with two novel missense mutations in the katA gene is reported here. © Crown copyright 2016.

GENOME ANNOUNCEMENT

Catalase protects bacteria from hydrogen peroxide and is used in the phenotypic identification of Staphylococcus aureus (1, 2). Despite a potential role in pathogenicity, catalase-negative isolates can cause infections (3–5). Sequencing of the katA gene has revealed multiple mutations/deletions responsible for this phenotype (6–8), but no whole-genome sequence has been performed on catalase-negative isolates of this important pathogen.

A catalase-negative (3% H2O2), methicillin-susceptible S. aureus subsp. aureus (CN-MSSA) was isolated from a patient with bacteremia, native aortic valve endocarditis, and bilateral knee native joint septic arthritis. The patient’s past medical history included diabetes and hypertension. CN-MSSA was isolated from blood, the aortic valve, and knee synovial fluid; the bacterium grew well in air at 35°C in 24 h, with golden-pigmented, beta-hemolytic colonies which were tube- and slide-coagulase positive (9). Identification (Vitek MS and Vitek 2; bioMérieux) and cefazolin disk susceptibility testing on Mueller-Hinton agar (Oxoid) were done in a CAP-accredited laboratory following CLSI guidelines. The isolate was susceptible to all other antibiotics tested, except for penicillin (data not shown). The patient received knee washouts on post-admission day (PAD) 3 (growth) and PAD 17 (no growth) and a bioprosthetic aortic valve replacement on PAD 9. Blood cultures remained positive until PAD 12 despite high-dose cloxacillin therapy. The patient received a six-week course of cloxacillin (2 g IV q4h) and rifampin post-surgery. Five days after completing the antibiotic course, the patient presented with relapsed CN-MSSA bacteremia, development of an aortic root abscess, and new mitral and tricuspid valve vegetations. This required a homograft replacement of the aortic root and valve and repair of the tricuspid and mitral valves. There was no evidence of metastic infection at that time. The CN-MSSA grew again from blood and the excised bioprosthetic valve tissue. After the second surgery the patient was treated with cefazolin and rifampin for 10 weeks. An isolate from the aortic valve removed during the first surgery was used for whole-genome shotgun sequencing.

A whole-genome shotgun paired-end library was prepared, sequenced, and assembled as previously described (10). This generated 1,221,050 reads with a total of 366,411,852 bp on a MiSeq sequencer (Illumina) and produced a draft genome of 2,782,699 bp in eight contigs (>1,000 bp) with 142-fold coverage and a 32.68% G+C content. Annotation of the genome using Prokka (11) revealed 2,599 coding sequences, 58 tRNA genes, and nine rRNA sequences. The isolate was sequence type 25, based on in silico multilocus sequence type analysis (pubmlst.org).

The catalase gene and protein sequence from National Microbiology Laboratory (NML) identifier 151290 were compared to S. aureus NCTC 8532T using BLAST. Two silent mutations were identified at C1146T and C1239T, and two novel missense point mutations were identified at T490C (Y164R) and T549A (D183E). The Y164R mutation may interfere in the tetramer binding capacity as it is situated between two amino acid residues (162 and 165) that are essential for this functional domain of the protein (12). The second point mutation (D183E) is in the NADPH-binding domain and could also contribute to the inactivation of the enzyme.

Accession number(s).

The draft genome of strain NML 151290 has been deposited at DDBJ/EMBL/GenBank under the accession number MEGZ00000000. The S. aureus NCTC 8532T accession number used was WP_000082539.1.