Draft Genome Sequence of the Multidrug-Resistant Strain Stenotrophomonas maltophilia N0320, Isolated from a Commercial Nanoparticle Product

ABSTRACT

Stenotrophomonas maltophilia is an emerging opportunistic pathogen that is frequently associated with hospital infections. We report the 4.8-Mbp draft genome sequence of the oxidase-positive S. maltophilia strain N0320, an isolate from a commercial hydroxyapatite nanoparticle product.

ANNOUNCEMENT

Stenotrophomonas maltophilia is a nonfermentative, obligate aerobic Gram-negative bacterium found in clinical and nonclinical environments (1). Although S. maltophilia is not considered to be a virulent pathogen, it has become one of the most common opportunistic nosocomial pathogens associated with significant mortality in immunocompromised or cystic fibrosis patients (2). S. maltophilia carries intrinsic and acquired multiple-drug-resistant genes among its clinical and nonclinical isolates (3).

Hydroxyapatite (HA) has been most extensively used as a synthetic bone graft substitute based on its functional property of encouraging bone growth (4). However, bacterial adherence to the surface of HA in dental and orthopedic applications consequently leads to serious medical complications, including implant failure, hospitalization, and surgical intervention (5). A commercial HA product was gently mixed by inversion, and 100 ml of the dispersed suspension was spread onto tryptic soy agar (TSA) supplemented with 5% sheep blood (Remel) and aerobically cultured at 37°C for 24 h. A single colony was selected from a blood agar plate, and repeated subculturing was performed to obtain a pure culture. The isolate, a Gram-negative rod-shaped aerobic bacterium, was identified as S. maltophilia using matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (Bruker). The multidrug resistance and cytochrome oxidase expression of this isolate were determined as previously reported (6).

DNA was extracted from several colonies grown overnight on a TSA blood agar plate at 37°C using the DNeasy blood and tissue kit, following the manufacturer’s instructions (Qiagen). The DNA was quantified using a Qubit fluorometer (Thermo Fisher Scientific). Libraries were prepared using the Nextera XT library prep kit, and sequencing was performed using the MiSeq v2 reagent kit in 250-bp paired-end mode on a MiSeq instrument (Illumina). Default parameters were used for all software unless otherwise noted. A total of 1.97 million raw reads were obtained; the reads were quality checked, and low-quality reads and adapter sequences were trimmed using the Fastq Utilities Service in PATRIC (6). The filtered reads were assembled using SPAdes v3.12.0 in PATRIC (7). The draft genome sequence of strain N0320 is 4,814,846 bp long with an N₅₀ value of 108,307 bp, a G+C content of 66.35%, and 57× coverage in 79 contigs. The S. maltophilia N0320 genome sequence was annotated using the NCBI Prokaryotic Genome Pipeline (PGAP) v4.11 (8). The annotated genome sequence contains 4,328 proteins with functional assignments, 64 hypothetical proteins, 71 tRNAs, and 7 rRNAs. The genome of S. maltophilia N0320 shares an average nucleotide identity of 98.1% with the reference genome of S. maltophilia K279a (GenBank accession number NC_010943.1), determined using the Similar Genome Finder in PATRIC (6). S. maltophilia N0320 does not harbor noticeable drug resistance genes, except multiple efflux pump-associated genes, though the strain is phenotypically multidrug resistant. The efflux pump genes (smeABC, smeDEF, smeR, and smeS) may be responsible for multidrug resistance in S. maltophilia N0320, as reported for other S. maltophilia strains (9, 10).

Data availability.

The genome sequence has been deposited in GenBank under the accession number JABAGX000000000.1. The raw reads have been deposited in the Sequence Read Archive (SRA) under the accession number SRX11509207.