Abstract:
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.
