Data on whole genome shotgun sequencing report of clinical S. maltophilia strains from India

Stenotrophomonas maltophilia is an important emerging nosocomial pathogen with broad level multi-drug resistance. There is a lack of genomic information on S. maltophilia to understand the antimicrobial resistance (AMR) mechanism behind. The data article reports on whole genome sequence information of 9 clinical S. maltophilia strains isolated from a tertiary care hospital in India. Isolates were sequenced using Ion Torrent PGM platform. Raw reads were assembled and annotated, where the genome size ranged from ~ 3.2 to ~ 4.5 Mb with average 57.6× coverage. AMR genes blaL1, blaL2, Smqnr, aac(6׳)-lz and aph(3׳)-llc were observed among the isolates in addition to multiple virulence factors. Five isolates were identified to be ST15, ST283, ST284, ST285 and ST286.


a b s t r a c t
Stenotrophomonas maltophilia is an important emerging nosocomial pathogen with broad level multi-drug resistance. There is a lack of genomic information on S. maltophilia to understand the antimicrobial resistance (AMR) mechanism behind. The data article reports on whole genome sequence information of 9 clinical S. maltophilia strains isolated from a tertiary care hospital in India. Isolates were sequenced using Ion Torrent PGM platform. Raw reads were assembled and annotated, where the genome size ranged from $ 3.2 to $ 4.5 Mb with average 57.6 Â coverage. AMR genes blaL1, blaL2, Smqnr, aac(6')-lz and aph(3')-llc were observed among the isolates in addition to multiple virulence factors. Five isolates were identified to be ST15, ST283, ST284, ST285

Data
The data presented is on genome sequences of S. maltophilia strains from clinical nosocomial infections. The data in Table 1 represents genome annotation summary, including genome size and coverage of each S. maltophilia genome. Table 1 also describes the number of tRNA, rRNA, virulence factors from victors and virulence factors database, number of genetic resistance determinants from PATRIC, The Comprehensive Antibiotic Resistance Database and National Database of Antibiotic Resistant Organisms. Table 2 represents various genetic factors responsible for virulence of S. maltophilia strains. Multiple antimicrobial resistance (AMR) genes were identified responsible for aminoglycosides, beta-lactams and fluoroquinolones resistance in addition to efflux genes. goeBURST analysis of the study isolates exhibited the clonal relation between the clinical study isolates to the global strains as depicted in Fig. 1.

Study isolates
S. maltophilia clinical strains were isolated from blood and sputum specimens, collected between May 2017 and October 2017 in the Department of Clinical Microbiology, Christian Medical College, Vellore, India.
The S. maltophilia genomes ranged in sizes from $ 3.2 to $ 4.5 Mb. The genomes had a coverage ranging from 17 Â to 153 Â ( Table 1). The Coding DNA sequences (CDS) per genome were between 4547 and 7275, while the tRNA were from 42 to 88, and rRNA from 4 to 12.The number of virulence genes identified as per Victor's database were 1-13, and as per VFDB were 1-4. The AMR genes identified ranged from 17 to 36, 8 to 24 and 3 to 7 as per PATRIC, CARD and NDARO databases respectively. The draft genome sequences have been deposited in GenBank under the accession numbers provided in Table 1. The version described in this manuscript is version 1.

Transparency document. Supplementary material
Transparency data associated with this article can be found in the online version at https://doi.org/ 10.1016/j.dib.2018.10.005.