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Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
Published on: December 23, 2022
Whole genome sequence data of Stenotrophomonas maltophilia SCAID WND1-2022 (370)
Ilya Korotetskiy1, Ardak Jumagaziyeva1, Bahkytzhan Kerimzhanova1
1JSC Scientific Center for Anti-Infectious Drugs, Almaty, Kazakhstan.
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.
Insights
The whole genome of the hospital pathogen Stenotrophomonas maltophilia SCAID WND1-2022 was sequenced, revealing antibiotic resistance and virulence genes. A unique plasmid may contribute to pathogenicity but not drug resistance.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Stenotrophomonas maltophilia is an opportunistic pathogen frequently associated with hospital-acquired infections.
- Understanding the genomic basis of its virulence and antibiotic resistance is crucial for effective treatment and control.
Purpose of the Study:
- To report the complete genome sequence of Stenotrophomonas maltophilia SCAID WND1-2022, a hospital infection agent.
- To identify genes associated with antibiotic resistance and virulence within this strain.
- To characterize the genetic elements, including plasmids, that contribute to the pathogen's characteristics.
Main Methods:
- Whole genome sequencing using PacBio technology.
- Bioinformatic analysis for genome assembly and annotation.
- Comparative genomics to determine taxonomic provenance and identify specific genes.
Main Results:
- The genome consists of a 4.88 Mb chromosome and a 38.6 Kb plasmid.
- Identified numerous antibiotic resistance genes (efflux pumps, beta-lactamases) and virulence factors (biofilm formation) on the chromosome.
- The plasmid is novel and appears to contribute to virulence but not antibiotic resistance.
Conclusions:
- The genome sequence provides a valuable resource for studying Stenotrophomonas maltophilia.
- The identified resistance and virulence genes highlight potential therapeutic targets.
- The unique plasmid may represent a novel factor in pathogen evolution and host interaction.
