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

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

doi:10.1128/mra.00974-21

Cited by 5 publications

(3 citation statements)

References 13 publications

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“…Whole-genome sequencing (WGS) was performed using the Illumina-NovaSeq 6000 platform with 2 × 150-bp paired-end reads for the 199 isolates from hospital C. Short-read sequence data of 71 local bla NDM-1 -positive ST308 isolates originating from hospital As and B, as well as 85 global bla NDM-1 -negative ST308 isolates, were downloaded from publicly available sequence databases (the NCBI Sequence Read Archive [SRA] and European Nucleotide Archive [ENA]) ( 5 , 6 , 18 – 22 ). Of these 85 isolates, 79 isolates were sequenced using Illumina, 4 were sequenced using both Illumina and Nanopore, and 2 were sequenced using Pacific Biosciences sequencing platforms.…”

Section: Methodsmentioning

confidence: 99%

Dissemination of Pseudomonas aeruginosa bla _NDM-1 -Positive ST308 Clone in Singapore

et al. 2023

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P. aeruginosa is a Gram-negative opportunistic pathogen ubiquitously found in the environment and a major cause of nosocomial infections. While the P. aeruginosa ST308 clone has been known to bear bla IMP and bla VIM among global isolates, reports of bla NDM-1 -positive P. aeruginosa ST308 are rare.

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Section: Methodsmentioning

confidence: 99%

Dissemination of Pseudomonas aeruginosa bla _NDM-1 -Positive ST308 Clone in Singapore

et al. 2023

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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%

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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“…Isolates were obtained by plating from biological material on selective and differential-diagnostic media ( Table 1 ). This study was approved by the Committee of Institutional Animal Care and Use of the Scientific Center for Anti-Infectious Drugs (SCAID), Almaty, Kazakhstan ( 2 ). For more details on the isolates, see NCBI BioProject number PRJNA754843 .…”

Section: Announcementmentioning

confidence: 99%

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

Korotetskiy¹,

Jumagaziyeva²,

Kerimzhanova³

et al. 2022

Microbiol Resour Announc

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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.

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

Cited by 5 publications

References 13 publications

Dissemination of Pseudomonas aeruginosa bla _NDM-1 -Positive ST308 Clone in Singapore

Dissemination of Pseudomonas aeruginosa bla _NDM-1 -Positive ST308 Clone in Singapore

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

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

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

Cited by 5 publications

References 13 publications

Dissemination of Pseudomonas aeruginosa bla NDM-1 -Positive ST308 Clone in Singapore

Dissemination of Pseudomonas aeruginosa bla NDM-1 -Positive ST308 Clone in Singapore

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

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

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Dissemination of Pseudomonas aeruginosa bla _NDM-1 -Positive ST308 Clone in Singapore

Dissemination of Pseudomonas aeruginosa bla _NDM-1 -Positive ST308 Clone in Singapore