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 - PubMed (original) (raw)

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

Ilya S Korotetskiy et al. Microorganisms. 2023.

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.

Keywords: MLST; PacBio sequencing; bacterial pathogen; genotyping; hospital infection; methylomics; virulence factor.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1

Genealogical tree of plasmids of the selected isolates.

Figure 2

(A) Clustering of GIs identified in different genomes of pathogenic isolates through similarities in their patterns of tetranucleotides. Each node on the scheme corresponds to one GI. Numbers in several nodes are the consecutive clockwise numbers of GIs identified in the genomes, starting from the replication origins. Host microorganisms are depicted using different colors, as explained in the legend. (B) The network of GIs is identical to that in part A, but recolored in a way that the darker grey color represents more recent inserts of GIs, i.e., the GIs with more dissimilar patterns of tetranucleotides compared to the patterns calculated for the host microorganisms. The gradient bar below the scheme shows the correspondence of the grey shading to the distance between patterns calculated with the SeqWord Sniffer program.

Figure 3

Atlas presentation of the circular chromosome of the strain E. coli 3/145. Locations of motifs methylated at both DNA strands are depicted with colored triangles, as explained in the legend.

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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 - PubMed (original) (raw)