Genetic relatedness of serial rectal isolates of Acinetobacter baumannii in an adult intensive care unit of a tertiary hospital in Kuwait

Al-Hashem, Ghayda; Rotimi, Vincent O.; Albert, M. John

doi:10.1371/journal.pone.0230976

Cited by 4 publications

(7 citation statements)

References 37 publications

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“…Our isolates originated in the intestinal tracts of a group of patients who were sampled multiple times over a 15-month period. Two isolates each from 8 patients and three isolates each from 2 patients were identical by pulsed field-gel electrophoresis as analyzed by bionumerics [14], thus constituting a total of 22 identical isolates. Thus, of the 269 isolates subjected to the gyrB PCR assay, 247 isolates were non-identical from individual patients.…”

Section: Discussionmentioning

confidence: 99%

“…The relevant details have been published previously [14, 15]. Briefly, the study consisted of 32 adult patients.…”

Section: Methodsmentioning

confidence: 99%

“…We conducted a study on the sequential rectal colonization of adult patients with A. baumannii in the Intensive Care Unit of Mubarak Al Kabeer Hospital, Kuwait, the partial results of which have been published [14, 15]. We utilized this opportunity to evaluate the multiplex gyrB PCR assay with the whole-genome sequence-based Kraken 2 taxonomy for the identification of A. baumannii, and ANI.…”

Section: Introductionmentioning

confidence: 99%

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Multiplex gyrB PCR Assay for Identification of Acinetobacter baumannii Is Validated by Whole Genome Sequence-Based Assays

Albert¹,

Hashem²,

Rotimi³

2022

Med Princ Pract

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Objective: A multiplex gyrB PCR assay has been used to diagnose Acinetobacter baumannii. However, this assay has not been validated against the gold standard DNA-DNA hybridization assay, which is a laborious method. DNA-DNA hybridization assay is now replaced by whole genome sequence (WGS)-based methods. Two such methods are a k-mer-based search of sequence reads using the Kraken 2 program and average nucleotide identity (ANI). The objective was to validate the gyrB PCR assay with WGS methods. Subjects and Methods: We cultured 270 sequential A. baumannii isolates from the rectal swabs of 32 adult patients. The identity of the isolates was determined by gyrB PCR. The sequences of 269 isolates were determined by Illumina sequencing and the taxonomy was inferred by the Kraken 2 program and ANI. Results: All the 269 isolates were confirmed as A. baumannii by Kraken 2 and ANI. Conclusion: gyrB PCR assay is now a validated assay for easy identification of A. baumannii in comparison with gold standard whole genome sequence-based assays.

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Section: Discussionmentioning

confidence: 99%

“…The relevant details have been published previously [14, 15]. Briefly, the study consisted of 32 adult patients.…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Multiplex gyrB PCR Assay for Identification of Acinetobacter baumannii Is Validated by Whole Genome Sequence-Based Assays

Albert¹,

Hashem²,

Rotimi³

2022

Med Princ Pract

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“…The same cohort of patients used in the previous two studies has been used in the current study. The relevant details have already been published ( 17 , 18 ). Briefly, the study consisted of 32 adult patients admitted to the ICU of Mubarak Al Kabeer Hospital, Jabriya, Kuwait, all of whom were identified as having gastrointestinal tracts colonized long term with A. baumannii .…”

Section: Methodsmentioning

confidence: 99%

The whole-genome molecular epidemiology of sequential isolates of Acinetobacter baumannii colonizing the rectum of patients in an adult intensive care unit of a tertiary hospital

Bulach,

Carter,

et al. 2023

Microbiol Spectr

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Acinetobacter baumannii is a nosocomial multidrug-resistant pathogen that specifically colonizes and infects patients in intensive care units (ICUs). Genome plasticity of A. baumannii may contribute to the rapid development of A. baumannii resistance during patient treatment. There is little clarity on the dynamics of colonization of A. baumannii in humans. We studied 269 serial isolates of A. baumannii colonizing the rectum of 32 adult patients in an ICU; 5 to 16 isolates were obtained from each patient over a period of weeks to months. The isolates were sequenced using the Illumina platform. Multi-locus sequence typing revealed genetic diversity with 13 sequence types (STs); the dominant ST2 accounted for 202 of the 269 isolates and was isolated from each patient. A core genome comparison of isolates was used to elucidate a detailed understanding of the relationship among isolates within an ST and the genomic relationship among STs. One to three STs were observed in the isolates from each patient. Instances of unchanged colonization, sequential lineage colonization, and colonization with multiple lineages of A. baumannii were seen. The number of resistance genes carried by the isolates varied from 2 to 17. The predominant genes corresponded to those encoding resistance to β-lactam and aminoglycoside antibiotics. Generally, there was a strong correlation between ST and a particular antimicrobial resistance gene profile. This study makes an important baseline contribution to information that will help us understand the role of A. baumannii colonization in the development of opportunistic infections in ICU patients. IMPORTANCE Acinetobacter baumannii is a multidrug-resistant nosocomial pathogen that colonizes and infects debilitated patients in the ICU. There is very little information on the genomic characteristics of colonizing strains. This information is important to understand the evolution of lineages of A. baumannii that develop resistance while patients receive antibiotic treatment in the ICU. Our study demonstrated different patterns of colonization of the rectum of ICU patients with different STs of A. baumannii while one ST colonized all patients. Some STs carried more antibiotic resistance genes compared to others. However, there was a correlation between ST and a particular resistance gene profile. Our results further elucidate the dynamics of enteric colonization of this opportunistic pathogen.

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“…A. baumannii has the tendency for gaining multiple resistance genes with phenotypic expression of multidrug-resistant (MDR) features. Extensively drugresistant (XDR) strains display resistance to all but two antimicrobial drug classes [5][6][7] . The production of βlactamases is the main mechanism of Acinetobacter spp.…”

Section: Introductionmentioning

confidence: 99%

Hospital-Acquired Infection by Carbapenem-Resistant Acinetobacter Species in ICUs in Assiut, Egypt

Ibrahim

Abdallah

Soliman

et al. 2023

Egyptian Journal of Medical Microbiology

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The genus Acinetobacter is one of the main fears of hospital-acquired infection (HAI) wide-reaching mostly in ICUs. Objectives: This study aimed to identify the incidence of carbapenem-resistant Acinetobacter (CRA) HAI in Assiut University Hospitals ICU and determine their antimicrobial susceptibility profile. Methodology:The study included 1204 clinical samples from 928 patients with HAI and 625 environmental samples. Carbapenemase production was detected phenotypically by MIC determination using imipenem, meropenem and doripenem E-test, modified Hodge test, combined disc test and double disc synergy test (DDST). OXA genes (bla OXA-51 , bla OXA-23 , bla OXA-24 , and bla OXA-58 ) and MβL genes (bla SIM-1 , bla VIM , and bla IMP-1 ) were investigated genotypically by PCR. Results: Out of total 60 Acinetobacter isolates, 55 (91.7%) were extensively drug-resistant (XDR) and 5 (8.3%) were multi-drug resistant (MDR). 93.3% of Acinetobacter isolates were resistant to imipenem and meropenem, and 90% were resistant to doripenem. The prevalence of bla genes in isolates were bla OXA-51 (93.3%), bla , bla , bla OXA-58 (10%), bla SIM-1 (46.7%), and bla VIM (8.3%). bla IMP-1 was not detected in any isolate. Conclusion: CRA infections were considerable in our ICUs. The high prevalence of XDR Acinetobacter spp. observed in our study was very alarming and requires critical intervention. METHODOLOGY Specimen collection:This study was conducted on 1204 clinical samples obtained from 928 patients with HAI who were hospitalized in different ICUs of Assiut University Hospitals. Samples included endotracheal aspirates (n= 546), sputum (n= 218), blood (n= 217), urine (n= 161), throat swabs (n= 35), wound swabs (n= 24), ear swab

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Genetic relatedness of serial rectal isolates of Acinetobacter baumannii in an adult intensive care unit of a tertiary hospital in Kuwait

Cited by 4 publications

References 37 publications

Multiplex <b><i>gyrB</i></b> PCR Assay for Identification of <b><i>Acinetobacter baumannii</i></b> Is Validated by Whole Genome Sequence-Based Assays

Multiplex <b><i>gyrB</i></b> PCR Assay for Identification of <b><i>Acinetobacter baumannii</i></b> Is Validated by Whole Genome Sequence-Based Assays

The whole-genome molecular epidemiology of sequential isolates of Acinetobacter baumannii colonizing the rectum of patients in an adult intensive care unit of a tertiary hospital

Hospital-Acquired Infection by Carbapenem-Resistant Acinetobacter Species in ICUs in Assiut, Egypt

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