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

Korotetskiy, Ilya S.; Jumagaziyeva, Ardak B.; Kerimzhanova, Bahkytzhan; Reva, Oleg N.; Shilov, Sergey V.; Kuznetsova, Tatyana; Ivanova, Ludmila; Korotetskaya, N. V.; Bekmukhamedova, Aimana; Satylgankyzy, Ganiya; КЛИВЛЕЕВА, Н.Г.

doi:10.1128/mra.00093-22

Cited by 2 publications

(3 citation statements)

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“…This study was approved by the Committee of Institutional Animal Care and Use in the Scientific Center for Anti-Infectious Drugs (SCAID), Almaty (REF: #2 from 16 September 2020). The strains collected during this study were obtained using selective media, as described previously [ 20 , 21 ]. A routine confirmation of species’ identities was performed using the NEFERM test kit (Erba Lachema s.r.o., Brno, Czech Republic).…”

Section: Methodsmentioning

confidence: 99%

“…The DNA libraries were sequenced in Macrogen using the PacBio Sequel-I (Pacific Biosciences, Menlo Park, CA, USA) sequencing platform, exploiting the circular consensus sequencing (CCS) system producing HiFi (high-fidelity) DNA reads ensuring a 99.5% base call accuracy suitable for genome assembly and calling polymorphic sites [ 23 ]. The average coverage of reads per one nucleotide in different genomes was 150–200 [ 21 ]. A further processing of the DNA reads was performed using software tools, as described below, with default parameter settings if not indicated otherwise.…”

Section: Methodsmentioning

confidence: 99%

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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

Korotetskiy¹,

Shilov²,

Kuznetsova³

et al. 2023

Microorganisms

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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.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

Korotetskiy¹,

Shilov²,

Kuznetsova³

et al. 2023

Microorganisms

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show abstract

“…The DNA library was sequenced using the PacBio Sequel-I (Pacific Biosciences) sequencing platform by Macrogen (Seoul, Korea) as described before [4] . Further processing of the DNA reads was performed using software tools as described below with default parameter settings if not indicated otherwise.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

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

Korotetskiy¹,

Jumagaziyeva²,

Kerimzhanova³

et al. 2022

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

Cited by 2 publications

References 10 publications

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

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

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

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