High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020

Odih, Erkison Ewomazino; Oaikhena, Anderson O; Underwood, Anthony; Hounmanou, Yaovi Mahuton Gildas; Oduyebo, OO; Fadeyi, Abayomi; Aboderin, AO; Ogunleye, Veronica O.; Argimón, Silvia; Akpunonu, Vitus Nnaemeka; Oshun, Phillip O; Egwuenu, Abiodun; Okwor, Tochi; Ihekweazu, Chikwe; Aanensen, David M.; Dalsgaard, Anders; Okeke, Iruka N.

doi:10.1128/msphere.00098-23

Cited by 9 publications

(8 citation statements)

References 65 publications

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“…A few STs belonged to the major international clones IC1, IC6, and IC9, but the majority were either singletons or belonged to none of the globally disseminated clones. Despite the recovery of A. baumannii complex isolates in all but 1 of the 12 sampling months, specific A. baumannii sequence types were only detected transiently throughout the study, suggesting the absence of a reservoir for these STs in the hospital environment and reflecting the previously identified diversity of A. baumannii lineages in clinical settings in southwestern Nigeria ( 19 ). Interestingly, no strain belonging to IC2, which is the most predominant clinical A. baumannii lineage in Nigeria ( 19 ) and has been previously reported in hospital wastewater in Germany ( 25 ), was detected throughout the 12 months.…”

Section: Discussionmentioning

confidence: 80%

“…The low numbers of these clusters may be due to the preponderance of novel STs among the wastewater isolates and the fact that Acinetobacter spp. causing clinical infections are likely under-detected in our setting ( 19 ). Importantly, the clustering and close phylogenetic relationships between the clinical and wastewater isolates, including those from the final treated effluent, illustrate the presence of possible transmission chains from the hospital environment or even patients to the environment receiving the final treated wastewater.…”

Section: Discussionmentioning

confidence: 98%

“…These included the genomes of 86 A . baumannii isolates characterized in our previous study ( 19 ) and 3 other additional isolates obtained from UCH, Ibadan. In total, 21 of the clinical isolates (including 18 previously characterized isolates) were from the UCH health facility, where the wastewater samples were collected, while the remaining 68 were from other healthcare facilities in different states within the same southwestern region of Nigeria.…”

Section: Methodsmentioning

confidence: 98%

“…The intrinsic bla OXA-51 -like and bla ADC -like genes were also not reported. To determine the genetic contexts of the detected carbapenem resistance genes, we mapped both the assemblies and the reads of the wastewater isolates to previously characterized mobile genetic elements carrying acquired carbapenem resistance genes in A. baumannii ( 16 , 19 , 54 – 56 ) using Gview server ( https://server.gview.ca/ ) with default parameters (for the assemblies) and BWA MEM ( 57 ) version 0.7.17 (for the reads). Duplicate reads were marked and removed using Picard version 3.0.0 ( http://broadinstitute.github.io/picard ).…”

Section: Methodsmentioning

confidence: 99%

“…Recent evidence has also revealed an increase in the prevalence of bla NDM-1 genes, which have a wider and more potent hydrolytic spectrum, among A. baumannii ( 14 , 17 , 18 ). Our previous study characterizing clinical A. baumannii isolates in the southwestern region of Nigeria showed a local bla NDM-1 prevalence of 27.9% compared to a 34.9% prevalence of bla OXA-23 ( 19 ). These high antimicrobial resistance rates and potential for continued spread is a significant public health concern as treatment options for infections caused by carbapenem-resistant A. baumannii are severely limited ( 11 , 20 , 21 ).…”

Section: Introductionmentioning

confidence: 97%

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NDM-1- and OXA-23-producing Acinetobacter baumannii in wastewater of a Nigerian hospital

Odih,

Sunmonu,

Okeke

et al. 2023

Microbiol Spectr

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Carbapenem-resistant Acinetobacter baumannii spp. are increasingly important pathogens with limited treatment options, and there is limited knowledge on the environmental factors contributing to their spread. We determined the occurrence of carbapenem-resistant A. baumannii in hospital wastewater and their phylogenetic relationships with clinical A. baumannii isolates. Grab samples of raw and treated hospital wastewater were collected monthly at the University College Hospital, Ibadan, Nigeria, between March 2021 and February 2022. Acinetobacter baumannii strains were selectively isolated and identified using VITEK2, and their whole genomes were sequenced on an Illumina platform. We performed antimicrobial susceptibility testing and in silico genomic characterization of the strains and determined their phylogenetic relationships to previously characterized clinical A. baumannii strains from Nigeria. A. baumannii complex isolates were recovered from wastewater throughout the study. Of the 82 isolates identified based on whole-genome sequences, 77 were A. baumannii. A. baumannii isolates had high resistance rates (≥48.1%) to 10 of 12 antimicrobials tested, and majority (42/77, 54.5%) were resistant to carbapenems, with bla NDM-1 being the most common (24/77, 31.2%) carbapenem resistance gene detected, followed by bla OXA-23 ( n = 22, 28.6%). There was no statistically significant difference in carbapenem resistance rates or carbapenem gene carriage between the raw and treated wastewater isolates. Most of the isolates belonged to novel or sparsely described lineages, some of which were closely related to clinical isolates. The release of inadequately treated hospital wastewater into the environment may contribute to the increased spread of carbapenem-resistant and clinically important A. baumannii lineages in Ibadan, Nigeria. IMPORTANCE Acinetobacter baumannii is a leading cause of hospital-associated infections globally. A. baumannii reservoirs outside hospital settings are still unknown, and their occurrence in the environment is linked to clinical and anthropogenic activities. Although the risk of transmission of A. baumannii from environmental sources to humans is not fully understood, these sources pose significant risks for the continued dissemination of A. baumannii and their resistance traits. This study provides evidence that diverse and clinically relevant A. baumannii strains, many of which are resistant to carbapenems, are constantly being discharged into the environment through inadequately treated hospital wastewater. We further elucidate potential transmission routes between the environment and clinical infections and demonstrate the high prevalence of carbapenem resistance genes on highly mobile transposons among these strains. Our findings highlight the pressing need to address hospital wastewater as a crucial factor in curtailing the spread of carbapenem-resistant A. baumannii .

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Section: Discussionmentioning

confidence: 80%

Section: Discussionmentioning

confidence: 98%

Section: Methodsmentioning

confidence: 98%