Biology subjects

Aboderin, A. O.

Publications and source records attributed to Aboderin, A. O..

5 recordsLinked to original sources

bioRxiv2025

Genomic epidemiology of enteropathogenic Escherichia coli (EPEC) in southwestern Nigeria

BackgroundEnteropathogenic Escherichia coli (EPEC) are etiological agents of diarrhea. We studied the genetic diversity and virulence factors of EPEC in southwestern Nigeria, where this pathotype is rarely characterized. Methodology/ Principal findingsEPEC isolates (n=96) recovered from recent southwestern Nigeria diarrhea case-control studies were whole genome-sequenced using Illumina technology. Genomes were assembled using SPAdes and quality was evaluated using QUAST. Virulencefinder, SeroTypefinder, and Resfinder were used to identify virulence genes, serotypes, and resistance genes, while multilocus sequence typing was done by STtyping. Single nucleotide polymorphisms (SNPs) were called out of whole genome alignment using SNP-sites and a phylogenetic tree was constructed using IQtree. Thirty-nine of the 96 (40.6%) EPEC isolates were from cases of diarrhea. Nine isolates from diarrhea patients and four from healthy controls were typical EPEC, harboring bundle-forming pilus (bfp) genes whilst the rest were atypical EPEC. Fifteen isolates were EPEC-EAEC hybrids. Atypical serotypes O71:H19 (16, 16.6%), O108:H21 (6, 6.3%), O157:H39 (5, 5.2%), and O165:H9 (4, 4.2%) were most prevalent; only 8(8.3%) isolates belonged to classical EPEC serovars. The largest clade comprised ST517 isolates, of O71:H19 and O165:H9 serovars harboring multiple siderophore and serine protease autotransporter genes. An O71:H19 subclade comprised isolates <10 SNPs apart, representing a likely outbreak involving 15 children, four presenting with diarrhea. Conclusion/ SignificanceLikely outbreaks, of typical O119:H6(ST28) and atypical O127:H29(ST7798) were additionally identified. EPEC circulating in southwestern Nigeria are diverse and differ substantially from well-characterized lineages seen previously elsewhere. EPEC carriage and outbreaks could be commonplace but are largely undetected, hence, unreported, and require genomic surveillance for identification.

microbiology↗

bioRxiv2024

Whole genome Sequencing Reveals Enterobacter hormaechei as a key Bloodstream Pathogen in six tertiary care hospitals in southwestern Nigeria.

Enterobacter spp. are an important cause of healthcare-associated bloodstream infections uncommonly reported in Africa. This study used whole genome sequencing (WGS) to characterise Enterobacter spp. from hospitals in Nigerias antimicrobial resistance (AMR) surveillance system. Blood-culture isolates of Enterobacter from six such tertiary-care hospitals recovered between 2014 and 2020 were re-identified and antimicrobial susceptibility-tested using VITEK2. Illumina technology provided whole genome sequences for genome nomenclature, antimicrobial resistance gene prediction, Single Nucleotide Polymorphism (SNP) phylogeny, and multi-locus sequence typing via publicly available bioinformatics pipelines. Initial biochemical delineation often misclassified Enterobacter, necessitating whole-genome sequencing for accurate classification. Among 98 Enterobacter received, Enterobacter hormaechei subspecies xiangfangensis predominated (43), followed by other E. hormachei subspecies (18), E. cloacae (26), E. roggenkampii (4), E. bugandensis (3), E. kobei (2), E. asburiae (1) and E. cancerogenous (1). Cephalosporins, aminoglycoside, chloramphenicol, macrolide, and carbapenem resistance in E. hormaechei was attributed to known resistance genes. They belonged to clusters III, IV, and VIII based on hsp60 typing and clades A, B, C, and D according to Sutton and Cos nomenclature. These isolates and other Enterobacter species recently reported from Nigeria reveal extensive E. hormaechei diversity, as well as clusters representing potential outbreaks. Enterobacter hormaechei, often misidentified and rarely reported from Nigeria, is this studys most common blood culture isolated Enterobacter spp. Uncovering underappreciated species as important bloodstream pathogens and retrospective detection of likely outbreaks emphasise the value of genomic surveillance in resource-limited settings. DATA SUMMARYAll sequence reads were submitted to the European Nucleotide Archive (ENA) under the project ID PRJEB29739 (https://www.ebi.ac.uk/ena/browser/view/PRJEB29739). Accessions can be found in Table S1. IMPACT STATEMENTAccurate identification of Enterobacter is essential in healthcare settings as misidentification can lead to selecting antimicrobials to the genus is intrinsically resistant resistant before susceptibility testing results are available. Also, misidentification can compromise microbiology support for infection prevention and control. We show that E. hormaechei, which is never reported from clinical laboratories in Nigeria, is frequently misidentified using conventional methods like tube- or strip biochemical testing and VITEK systems. Whole genome sequence data demonstrates that E. hormaechei and E. cloacae are the most common Enterobacter isolated from bloodstream infections in Nigeria. Enhanced identification methods for surveillance play pivotal roles in improving patient care, optimising antibiotic stewardship, and combating the evolving challenges posed by this pathogen. Overall, this study reveals the effectiveness of WGS in correctly identifying this important pathogen.

microbiology↗

bioRxiv2021

Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria

IntroductionKlebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about the population structure and evolution of Klebsiella circulating in Nigeria. MethodsWe performed whole genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing, AMR gene, virulence gene, plasmid, and K and O loci profiling, as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines. ResultsPhylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, one of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum {beta} lactamase (ESBL) gene blaCTX_M-15 was seen in 72 % of K. pneumoniae genomes, while 8% encoded a carbapenemase. Four likely outbreak clusters from one facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones. ConclusionThis study uncovered known and novel K. pneumoniae lineages circulating in Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals. summaryWe performed whole genome sequencing (WGS) of 141 Klebsiella isolated in 2016-2018 at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. This study uncovered known and novel K. pneumoniae lineages circulating in Nigeria that include multidrug-resistant ESBL producers. FUNDINGThis work was supported by Official Development Assistance (ODA) funding from the National Institute of Health Research [16/136/111: NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance]. This research was commissioned by the National Institute of Health Research using Official Development Assistance (ODA) funding. INO is an African Research Leader supported by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement that is also part of the EDCTP2 program supported by the European Union. The funders had no role in the content, crafting or submission of this paper. The views expressed in this publication are those of the authors and not necessarily those of the funders or their affiliates. CONFLICT OF INTERESTThe authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest.

genomics↗

bioRxiv2019

MULTICENTER STUDY OF THE BURDEN OF MULTIDRUG-RESISTANT BACTERIA IN THE ETIOLOGY OF INFECTED DIABETIC FOOT ULCERS

BackgroundInfected diabetic foot ulcer (IDFU) is a public health issue and a leading cause of non-traumatic limb amputation. Very few published data on IDFU is available in most West African countries. The objective of this study was to investigate the etiological agents of IDFU and the challenge of antibacterial drug resistance in the management of infections.\n\nMethodsThis was a prospective cross-sectional hospital-based study involving three tertiary healthcare facilities. Consecutive eligible patients presenting in the facilities were recruited. Tissue biopsies and/or aspirates were collected and cultured on a set of selective and non-selective media and incubated in appropriate atmospheric conditions for 24 to 72 hours. Isolates were identified by established standard methods. Antibiotic susceptibility testing was performed using modified Kirby-Bauer disc diffusion method. Specific resistance determinants were investigated by polymerase chain reaction-based protocols. Data analysis was done with SPSS version 20.\n\nResultsNinety patients with clinical diagnosis of DFI were studied between July 2016 and April 2017. A total of 218 microorganisms were isolated, comprising 129 (59.2%) Gram-negative bacilli (GNB), 59 (27.1%) Gram-positive cocci (GPC) and 29 (13.2%) anaerobic bacteria. The top five facultative/aerobic bacteria encountered were: Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae and Citrobacter spp. representing 41 (18.8%), 23 (10.5%), 20 (9.2%), 19 (8.7%) and 19 (8.7%) isolates, in that order, respectively. The commonest anaerobes were Bacteroides spp., and Peptostreptococcus anaerobius which accounted for 7 (24.1%) and 6 (20.7%), respectively. Of the 93 IDFU cases, 74 (80%) were infected by multidrug-resistant (MDR) bacteria predominantly methicillin-resistant S. aureus, extended-spectrum {beta}-lactamase-producing GNB, mainly of the CTX-M variety. Only 4 (3.1%) GNB were carbapenemase-producers encoded by blaVIM. Factors associated with presence of MDR bacteria were peripheral neuropathy (r= 4.05, P= 0.042) and duration of foot infection >1 month(r= 7.63, P= 0.015).\n\nConclusionsMDR facultative/aerobic bacteria are overrepresented amongst agents causing IDFU. A relatively low proportion of the etiological agents were anaerobic bacteria. This finding should help formulate empirical therapeutic options for managing IDFU. Furthermore, drastic reduction in inappropriate use of cocktail of antibiotics for IDFUs is advocated to combat infection by MDR bacteria in these patients.

epidemiology↗

bioRxiv2019

A large self-transmissible plasmid from Nigeria confers resistance to multiple antibacterials without a carrying cost

Antimicrobial resistance is rapidly expanding, in a large part due to mobile genetic elements. We screened 94 fecal fluoroquinolone-resistant Escherichia coli isolates from Nigeria for six plasmid-mediated quinolone resistance (PMQR) genes. Sixteen isolates harbored at least one of the PMQR genes and four were positive for aac-6-Ib-cr. In one strain, aac-6-Ib-cr was mapped to a 125 Kb self-transmissible IncFII plasmid, pMB2, which also bears blaCTX-M-15, seven other functional resistance genes and multiple resistance pseudogenes. We hypothesized that pMB2 had been selected by antimicrobials and that its large size would confer a growth disadvantage. However, laboratory strains carrying pMB2 grew at least as fast as isogenic strains lacking the plasmid in both rich and minimal media. We excised a 32 Kb fragment containing the sitABCD and another putative transporter, pefB, a papB homolog, and several open-reading frames of unknown function. The resulting 93 Kb mini-plasmid conferred slower growth rates and lower fitness than wildtype pMB2. Trans-complementing the deletion with the cloned sitABCD genes confirmed that they accounted for the growth advantage conferred by pMB2 in iron-depleted media. The mini-plasmid additionally conferred autoaggregation and was less transmissible and both phenotypes could be complemented with a pefB clone. pMB2 is a large plasmid with a flexible resistance region that contains multiple loci that can account for evolutionary success in the absence of antimicrobials. Ancillary functions conferred by resistance plasmids can mediate their retention and transmissibility, worsening the trajectory for antimicrobial resistance and potentially circumventing efforts to contain resistance through restricted use.

microbiology↗