Analysis of Whole-Genome Sequences of Pathogenic Gram-Positive and Gram-Negative Isolates from the Same Hospital Environment to Investigate Common Evolutionary Trends Associated with Horizontal Gene Exchange, Mutations and DNA Methylation Patterning.

Hospital-acquired infections are a generally recognized problem for healthcare professionals. Clinical variants of Gram-negative and Gram-positive pathogens are characterized with enhanced antibiotic resistance and virulence due to mutations and the horizontal acquisition of respective genetic determinants. In this study, two Escherichia coli, two Klebsiella pneumoniae, three Pseudomonas aeruginosa, two Staphylococcus aureus, one Staphylococcus epidermidis and one Streptococcus pneumoniae showing broad spectra of antibiotic resistance were isolated from patients suffering from nosocomial infections in a local hospital in Almaty, Kazakhstan. The aim of the study was to compare general and species-specific pathways of the development of virulence and antibiotic resistance through opportunistic pathogens causing hospital-acquired infections. The whole-genome PacBio sequencing of the isolates allowed for the genotyping and identification of antibiotic resistance and virulence genetic determinants located in the chromosomes, plasmids and genomic islands. It was concluded that long-read sequencing is a useful tool for monitoring the epidemiological situation in hospitals. Marker antibiotic resistance mutations common for different microorganisms were identified, which were acquired due to antibiotic-selective pressure in the same clinical environment. The genotyping and identification of strain-specific DNA methylation motifs were found to be promising in estimating the risks associated with hospital infection outbreaks and monitoring the distribution and evolution of nosocomial pathogens.

Complete Genome Sequences of Gram-Positive Opportunistic Pathogens Isolated from Hospitals in Almaty, Kazakhstan.

The appearance of drug-resistant pathogens reduces the therapeutic applicability of antibiotics and increases the rate of hospital infections among patients. Complete genome sequences of four Gram-positive clinical isolates of Streptococcus and Staphylococcus were obtained and analyzed to serve as model microorganisms for further studies on drug-induced antibiotic resistance reversion.

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

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.

Complete Genome Sequences of Gram-Negative Opportunistic Pathogens Isolated in Hospitals in Almaty, Kazakhstan.

The problem of nosocomial infections is growing due to the introduction of new treatment regimens involving immunosuppressive drugs. The genomes of seven Gram-negative clinical isolates of Escherichia, Klebsiella, and Pseudomonas were sequenced and analyzed in this study to serve as model microorganisms to study drug-induced antibiotic resistance reversion.