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

Abstract

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.

High genetic diversity andblaNDM-1prevalence amongAcinetobacter baumanniiin Nigerian hospitals

“…Clinical microbiology diagnostics remains a challenge in Nigeria and most developing countries. Very few patients are cultured at all and A. baumannii are particularly difficult to identify using conventional diagnostics 7,38,39 . The institution of genomic surveillance for AMR in Nigeria has been coupled with efforts to improve basic microbiology capacity, and it is expected that these measures will help plug the existing gaps in the diagnostics and surveillance of these pathogens of major public health importance 40 .…”

“…OXA-23 is the most common acquired oxacillinase in A. baumannii, and it is typically flanked by insertion elements that facilitate its effective spread through conjugative plasmids across different A. baumannii lineages 6 . The less common but significantly more potent (wider hydrolytic spectrum) New-Delhi metallobeta-lactamases (NDM), particularly NDM-1, has been reported more frequently in recent studies, including in Nigeria and other parts of Africa [7][8][9][10] . Characterisation of the genetic diversity and contexts of carbapenemase genes in various lineages would provide insights into the population dynamics of A. baumannii.…”

“…In a review of all A. baumannii genomes present in the National Center for Biotechnology Information's GenBank database in 2019, 61% were IC2, and 5% were IC1 3 . International clone 2 and, to a lesser extent, IC1 strains are also responsible for majority of the carbapenem-resistant A. baumannii outbreaks reported in hospitals throughout the world 7,[12][13][14] . However, as the success and global dissemination of these clones are associated with their propensity to carry multiple antimicrobial resistance determinants 13,15 , reports of increasing carbapenem resistance among A. baumannii isolates belonging to non-major global clones and the emergence and spread of previously uncharacterised highly resistant clones in different hospital settings is worrisome [16][17][18] .…”

Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria’s experience

“…We have similarly identified likely outbreaks of temporally and spatially connected Acinetobacter , Klebsiella and Enterobacter spp. that would have otherwise been unrecognized and have been able to confirm Acinetobacter baumanii and Serratia marcescens outbreaks that were suspected by sentinel sites based on epidemiological information [36, 38] (and Chioma Osuagwu, Oyinlola O. Oduyebo, Anderson O. Oaikhena, Erkison E. Odih and co-workers, unpublished). Serratia spp.…”

Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now?

“…145 Studies in SSA have detected CHDL genes, including blaOXA-23-like, blaOXA-24-like, blaOXA-58-like, blaOXA-143-like, and blaOXA-235-like, among others, and MBL genes (blaIMP, blaVIM, and blaNDM) in carbapenem-resistant A. baumannii. [145][146][147][148][149][150] In 2019, A. baumannii infections were the fifth most common cause of deaths attributable to antimicrobial-resistant bacteria globally, with 57,700 mortalities attributable to carbapenem-resistant A. baumannii. 151 The global percentage of resistance to carbapenems of A. baumannii varies geographically in different continents, regions, and countries.…”