Molecular dissection of carbapenem-resistant <i>Acinetobacter baumannii</i> circulating in Indian hospitals using Whole Genome Sequencing

Rose, Steffimol; Shamanna, Varun; Underwood, Anthony; Nagaraj, Geetha; Prasanna, Akshatha; Govindan, Velu; Sravani, D; Shincy, M R; Argimón, Silvia; Abrudan, Monica; Aanensen, David M.; Ravikumar, K L

doi:10.1101/2021.07.30.454432

Cited by 5 publications

(5 citation statements)

References 42 publications

(24 reference statements)

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“…The major genetic determinant of carbapenem resistance among our isolates was the bla OXA-23-like gene followed by bla NDM-1 . A similar trend has been reported among CRAB isolates in many previous studies from India [9–11, 31–33]. OXA-23 group was the first group of carbapenem-hydrolysing oxacillinases to be identified in A.…”

Section: Discussionsupporting

confidence: 85%

Genotyping of Acinetobacter baumannii isolates from a tertiary care hospital in Cochin, South India

Rajan,

Vijayan,

Puthiyottu Methal

et al. 2023

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Acinetobacter baumannii poses a significant challenge in healthcare settings across the globe, with isolates exhibiting carbapenem resistance at unprecedented rates. Here, we characterized a collection of A. baumannii isolates (n=64) recovered during the period September 2020 – November 2021 at a teaching hospital in Cochin, South India. The species identity of the isolates was confirmed with bla OXA-51-like PCR. The major carbapenemase determinants identified were bla OXA-23-like (45, 70.3 %) and bla NDM-1 (31, 48.4 %); co-occurrence of these genes was also observed in 27 (42.2 %) isolates. Other resistance genes identified included bla PER (34, 53.1 %), aac(6')-Ib-cr (42, 65.6 %), qnrS (25, 39.1 %), sul1 (32, 50 %), sul2 (33, 51.6 %), strA/strB (36, 56.3 %), aphA1-Iab (35, 54.7 %) and tetB (32, 50 %). Mapping PCR revealed the insertion element, ISAbaI upstream of bla OXA-23-like in all isolates possessing this gene. Concerning disinfectant resistance, all isolates carried the quaternary ammonium compound (QAC) resistance gene, qacEΔ1. Minimal inhibitory concentration (MIC) of benzalkonium chloride was high among the isolates and ranged from 8 to 128 µg ml−1. However, low MICs were observed for chlorhexidine and triclosan, with the majority (54, 80.6 %) of isolates showing an MIC of 2 µg ml−1 for chlorhexidine and all isolates exhibiting MICs of ≤0.125 µg ml−1 for triclosan. Further, all isolates were strong biofilm-producers, as assessed by the crystal violet-based microtitre plate assay. The ApaI-pulsed-field gel electrophoresis (PFGE) revealed the multi-clonal nature of the isolates, with 16 clusters and 16 unique pulsotypes identified at a cut-off of 80 %. In short, this study provides useful data on the molecular features of A. baumannii from this region, which could be helpful to assess the local epidemiology of this pathogen and also to devise infection control strategies.

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Section: Discussionsupporting

confidence: 85%

Genotyping of Acinetobacter baumannii isolates from a tertiary care hospital in Cochin, South India

Rajan,

Vijayan,

Puthiyottu Methal

et al. 2023

Access Microbiology

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“…Among Acinetobacter spp., the presence of the bla GES–11 (ESBL-genotype and weak carbapenemase) and the OXA-51-like ( bla OXA–66 and bla OXA–69 ) carbapenemases encoding genes is a serious threat. The OXA-51-like intrinsic carbapenemase encoding ST1 A. baumannii Isolates were reported from India ( Rose et al, 2021 ), but isolates from the present study encoded additionally the weakly carbapenem hydrolyzing bla GES–11 gene. The bla GES–11 ESBL-genotypes, and the bla OXA–51 -like carbapenemases have not been previously reported from Ethiopia, and the present study is to our knowledge the first report of bla OXA–51 like and bla GES–11 from Ethiopia.…”

Section: Discussionmentioning

confidence: 55%

Molecular epidemiology and antimicrobial susceptibility of Pseudomonas spp. and Acinetobacter spp. from clinical samples at Jimma medical center, Ethiopia

Sewunet

Asrat²,

Woldeamanuel³

et al. 2022

Front. Microbiol.

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IntroductionPseudomonas aeruginosa (P. aeruginosa) and Acinetobacter baumannii (A. baumannii) can cause difficult-to-treat infections. We characterized molecular epidemiology of ceftazidime-resistant P. aeruginosa and carbapenem-resistant A. baumannii at a tertiary hospital in Ethiopia.Materials and methodsNon-fermenting gram-negative bacilli (n = 80) isolated from admitted patients were subjected for species identification by MALDI-TOF. Pseudomonas species resistant to ceftazidime or meropenem, and Acinetobacter species resistant to meropenem, or imipenem were selected for whole genome sequencing. DNA extracted with EZ1 Advanced XL instrument (Qiagen, Hilden, Germany) was sequenced on Illumina (HiSeq2500) using libraries prepared by NEXTRA-kits (Illumina). Raw reads were assembled using SPAdes 3.13.0, and assembled genomes were used to query databases for resistome profile and sequence types.ResultAmong Pseudomonas species isolated, 31.7% (13/41), and 7.3% (3/41) were non-susceptible to ceftazidime, and meropenem, respectively. Carbapenem-resistance was 56.4% (22/39) among Acinetobacter species. Moreover, 92% (12/13) of Pseudomonas species non-susceptible to ceftazidime and/or meropenem, and 89.4% (17/19) of Acinetobacter species encoded multiple resistance genes for at least three classes of antimicrobials. The prevalent β - lactamase genes were blaOXA–486 (53.8%, 7/13), blaCTX–M–15 (23.0%, 3/13) among Pseudomonas, and blaGES–11 (57.8%, 11/19) among Acinetobacter. The blaOXA–51-like β - lactamase, blaOXA–69 (63.1%, 12/19) was the most prevalent carbapenemase gene among Acinetobacter isolates. Single isolates from both P. aeruginosa, and A. baumannii were detected with the blaNDM–1. Sequence type (ST)1 A. baumannii and ST274 P. aeruginosa were the prevalent sequence types. A cgMLST analysis of the ST1 A. baumannii isolates showed that they were closely related and belonged to the international clonal complex one (ICC1). Similarly, ST274 P. aeruginosa isolates were clonally related.ConclusionThe prevalence of MDR isolates of Pseudomonas and Acinetobacter spp. was high. A. baumannii isolates were clonally spreading in the admission wards at the hospital. Emergence of blaNDM–1 in the intensive care, and surgical wards of the hospital is a severe threat that requires urgent intervention.

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“…The ST1089 (IC9) strains were the second most common lineage in this study. These strains have been isolated from clinical samples and hospital environments, particularly from studies in Northern Africa and in the Middle East, and are frequently reported to carry blaNDM-1 and blaOXA-94 carbapenem resistance genes (32,(33)(34)(35)(36)(37)(38)(39). An ST1089 strain carrying blaNDM-1 was also isolated from raw milk in a dairy farm in Algeria (40).…”

Section: Discussionmentioning

confidence: 99%

Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria

et al. 2022

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BackgroundAcinetobacter baumannii are of major human health importance because they cause life-threatening nosocomial infections and often are highly resistant to antimicrobials. Specific multidrug-resistant A. baumannii lineages are implicated in hospital outbreaks globally. We retrospectively investigated a suspected outbreak of carbapenem-resistant A. baumannii (CRAB) colonizing patients in an intensive care unit (ICU) of a tertiary hospital in Southwest Nigeria where genomic surveillance of Acinetobacter has hitherto not been conducted.MethodsA prospective observational study was conducted among all patients admitted to the ICU between August 2017 and June 2018. Acinetobacter species were isolated from rectal swabs and verified phenotypically with the Biomerieux Vitek 2 system. Whole genome sequencing (WGS) was performed on the Illumina platform to characterize isolates from a suspected outbreak during the study period. Phylogenetic analysis, multilocus sequence typing, and antimicrobial resistance gene prediction were carried out in silico.ResultsAcinetobacter isolates belonging to the A. baumannii complex were recovered from 20 (18.5%) ICU patients. Single nucleotide polymorphism (SNP) analysis and epidemiological information revealed a putative outbreak clone comprising seven CRAB strains belonging to the globally disseminated international clone (IC) 2. These isolates had ≤2 SNP differences, identical antimicrobial resistance and virulence genes, and were all ST1114/1841.ConclusionWe report a carbapenem-resistant IC2 A. baumannii clone causing an outbreak in an ICU in Nigeria. The study findings underscore the need to strengthen the capacity to detect A. baumannii in human clinical samples in Nigeria and assess which interventions can effectively mitigate CRAB transmission in Nigerian hospital settings.

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Molecular dissection of carbapenem-resistant Acinetobacter baumannii circulating in Indian hospitals using Whole Genome Sequencing

Cited by 5 publications

References 42 publications

Genotyping of Acinetobacter baumannii isolates from a tertiary care hospital in Cochin, South India

Genotyping of Acinetobacter baumannii isolates from a tertiary care hospital in Cochin, South India

Molecular epidemiology and antimicrobial susceptibility of Pseudomonas spp. and Acinetobacter spp. from clinical samples at Jimma medical center, Ethiopia

Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria

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