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. 2022 Oct 26:45:108694.
doi: 10.1016/j.dib.2022.108694. eCollection 2022 Dec.

Whole genome sequence data of Stenotrophomonas maltophilia SCAID WND1-2022 (370)

Ilya Korotetskiy  1 , Ardak Jumagaziyeva  1 , Bahkytzhan Kerimzhanova  1 , Oleg Reva  2 , Tatyana Kuznetsova  1 , Sergey Shilov  1 , Ludmila Ivanova  1 , Natalya Zubenko  1 , Raikhan Parenova  1 , Zhanar Iskakbayeva  1 , Bolatbek Baimakhanov  3 , Aimana Bekmuhamedova  3
Affiliations

Whole genome sequence data of Stenotrophomonas maltophilia SCAID WND1-2022 (370)

Ilya Korotetskiy et al. Data Brief. .

Abstract

The whole genome sequence of a hospital infection agent, Stenotrophomonas maltophilia SCAID WND1-2022 (370), is reported. Raw PacBio generated reads and the genome sequence were deposited at NCBI under BioProject PRJNA754843. The genome comprises two replicons: 4,880,425 bp long chromosome comprising 4524 proteins and functional RNA coding genes and 38,606 bp long plasmid containing 40 CDS. Both replicons were methylated at third cytosine residues of ACCTC motifs. The taxonomic provenance of SCAID WND1-2022 (370) was determined by calculating sequence similarity to the reference genomes at NCBI that showed the highest 97.35% identity to S. maltophilia ISMMS4. Many antibiotic resistance and virulence genes were identified on the chromosome of S. maltophilia SCAID WND1-2022 (370), which include multiple efflux pumps, beta-lactamases, and genes involved in biofilm formation. The plasmid sequence was dissimilar to any known plasmid and seemingly was acquired from a distant microorganism. Plasmid-born genes possibly contributed to the virulence of the pathogens, but not to its drug resistance.

Keywords: Antimicrobial resistance; Hospital-associated pathogen; Methylation; Multidrug-resistant; Sequencing.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Image, graphical abstract
Graphical abstract
Fig 1
Fig. 1
Phylogenetic relations of the strain SCAID WND1-2022 (370) with the selected reference Stenotrophomonas strains available from the GenBank database. Calculated pair-wise OrthoANI values are shown in the distance matrix.
Fig 2
Fig. 2
Atlas representation of the chromosome of S. maltophilia SCAID WND1-2022 (370). Replication origin is marked as Ori. Colored histograms from the uppermost (black) to the innermost (red) show respectively fluctuations of GC-content, GC-skew and deviations of frequencies of tetranucleotide of 5 kbp sliding windows from the whole genome pattern of tetranucleotides. Pink and red blocks depict locations of identified horizontally acquired genomic islands (GIs). Red GIs comprise virulence and/or drug resistance genes.
Fig 3
Fig. 3
Alignment of sequences of the plasmid found in S. maltophilia SCAID WND1-2022 (370) on the top and the plasmid pMRAD02 from Methylobacterium radiotolerans JCM 2831 selected as the closest relative found in the NCBI database by a BLASTN search. Histograms show the level of nucleotide sequence similarity between homologous fragments of the plasmids. Boxes below the histograms show gene locations. Genes encoding the T4SS system are shown in blue.
See this image and copyright information in PMC

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