Biology subjects

Eze, P. M.

Publications and source records attributed to Eze, P. M..

3 recordsLinked to original sources

bioRxiv2025

Whole-Genome Sequencing Uncovers Chromosomal and Plasmid-Borne Multidrug Resistance and Virulence Genes in Poultry-Associated Escherichia coli from Nigeria

BackgroundUnregulated antibiotic use in poultry farming drives the emergence of multidrug-resistant (MDR) bacteria, which can spread to humans through the food chain and environment, posing serious public health risks. Whole-genome sequencing (WGS), combined with antimicrobial susceptibility testing (AST), enables detailed characterization of resistance mechanisms and supports antimicrobial stewardship. This study investigated the phenotypic and genotypic antimicrobial resistance (AMR), plasmid content, and virulence factors of an MDR Escherichia coli strain isolated from chicken droppings in Enugu State, Nigeria. ResultsDisk diffusion AST showed resistance to six of seven antibiotics tested (cefotaxime, ampicillin, erythromycin, gentamicin, ciprofloxacin, and doxycycline). Broth microdilution confirmed elevated minimum inhibitory concentrations across multiple classes, indicating an MDR phenotype. Hybrid WGS (Illumina and Nanopore) produced a 5.33 Mb genome comprising one chromosome and four plasmid-associated contigs. Chromosomal antimicrobial resistance genes (ARGs), including aac(6)-Ib-cr, blaCTX-M-15, and blaOXA-1, conferred resistance to aminoglycosides, fluoroquinolones, cephalosporins, and penicillins. Additional resistance determinants included efflux pumps, transport-associated genes, regulatory elements, and membrane modification genes. Plasmid-borne ARGs conferring resistance to aminoglycosides, trimethoprim, macrolides, sulfonamides, penicillins, and tetracyclines were also identified. The presence of Col156 and IncF-type plasmids indicates strong potential for horizontal gene transfer. Virulence profiling revealed numerous chromosomally encoded factors related to adhesion, iron acquisition, and toxin production. These included the pap gene cluster encoding P fimbriae; adhesion-associated genes (yagW/ecpD, ykgK/ecpR); multiple iron acquisition systems (enterobactin, yersiniabactin, aerobactin, and heme uptake); and sat, which encodes an autotransporter toxin. Additionally, the plasmid-borne gene senB encodes an enterotoxin that induces intestinal fluid secretion and contributes to diarrheal disease. Multilocus sequence typing identified the strain as ST131, a globally disseminated high-risk lineage. ConclusionsThis study provides a comprehensive genomic characterization of an MDR E. coli strain from poultry, revealing multiple chromosomal and plasmid-borne ARGs, and a diverse virulence gene repertoire. The detection of ST131 in poultry waste highlights a complex public health issue involving zoonotic transmission, veterinary impact, and environmental spread of AMR. These findings underscore the need for prudent antibiotic use, continuous monitoring, and integrated genomic surveillance across agricultural and environmental sectors, alongside improved antimicrobial stewardship and strengthened farm biosecurity measures.

microbiology↗

bioRxiv2025

Whole-Genome Sequencing, Annotation and Taxonomic Confirmation of a Multidrug-Resistant Escherichia coli Isolated from the Blood of a Sepsis Patient

Sepsis (blood stream infection) caused by multidrug-resistant (MDR) bacteria, particularly Escherichia coli, represents a significant global health threat due to high morbidity, mortality, and limited treatment options. E. coli, a major causative agent of bloodstream infections, has evolved highly virulent and MDR strains, which contribute to the increasing burden of antimicrobial resistance (AMR), complicating clinical management and reducing the efficacy of conventional antibiotic therapies. In this study, we characterised the genomic and phenotypic drug resistance mechanism of E. coli 266631E isolated from a sepsis patient, highlighting the negative implications of MDR E. coli in sepsis. Antimicrobial susceptibility testing and minimum inhibitory concentration analysis revealed resistance to multiple antibiotics, including amoxicillin, cefotaxime, ciprofloxacin, gentamicin, and tobramycin. Whole genome sequencing identified a broad array of AMR genes encoding resistance to various antibiotic classes, such as macrolides, fluoroquinolones, aminoglycosides, carbapenems, and cephalosporins. Notably, the CTX-M-15 gene, a key extended-spectrum {beta}-lactamase determinant, was found in both the bacterial chromosome and an IncF-type plasmid, emphasizing the potential for horizontal gene transfer and rapid dissemination of resistance. Confirming the taxonomy of the novel and unidentified bacterial strain through querying its 16S rRNA sequence and genome in recognised bacterial taxonomic databases presented a challenge. The isolate showed genetic similarity to E. coli, E. fergusonii, and Shigella species despite their phenotypic differences and variations in their pathogenic traits. However, a simple phenotypic laboratory procedure, based on the biochemical and cultural differences among these bacteria in Coliform ChromoSelect Agar, confirmed the isolate as E. coli. This study underscores the critical importance of integrating phenotypic methods with genomic tools for the accurate identification of clinically significant bacteria. It also highlights the need for both phenotypic and genetic surveillance of key MDR variants in healthcare settings to enable timely, precise diagnosis and targeted treatment of life-threatening infections such as sepsis. DATA SUMMARYThe outputs of the MALDI-TOF analysis, AMR analysis using AMRFinderPlus, starAMR, and RGI, the query of bacterial 16S rRNA in the NCBI, Greengenes2, and SILVA databases, as well as Sourmash and pangenome analyses, are available in the supplementary material. The bacterial 16S rRNA gene sequence has been deposited in the NCBI GenBank database under accession number PQ871642. The isolates complete genome sequence has been submitted to the NCBI Genome database under BioProject accession PRJNA1220687 and BioSample accession SAMN46722626. The chromosome is available under GenBank accession number CP183489, while plasmids and other contigs are available under accession numbers CP183490-CP183498. The scripts used in the following bioinformatics analysis - Sourmash, Roary, and Prokka (for pangenome analysis) are available at: https://github.com/LucyDillon/MDR_isolate. IMPACT STATEMENTThis study presents a comprehensive genomic and phenotypic characterization of a multidrug-resistant Escherichia coli strain implicated in sepsis, uncovering extensive antimicrobial resistance genes across both the chromosome and plasmids. It exposes taxonomic ambiguity with closely related species such as E. coli, Shigella, and E. fergusonii, underscoring gaps in current genomic databases and reinforcing the necessity of phenotypic testing. By integrating whole-genome sequencing with biochemical differentiation, the research strengthens diagnostic precision and informs clinical decision-making for life-threatening infections. Overall, it advances AMR and bacterial taxonomy research by demonstrating the value of an integrated genomic-phenotypic framework to accurately identify and guide the treatment and surveillance of emerging MDR pathogens in clinical settings.

genomics↗

bioRxiv2025

Investigating the factors influencing antibiotic use practices and their association with antimicrobial resistance awareness among poultry farmers in Enugu State, Nigeria

BackgroundThe irrational use of antibiotics in poultry production has far-reaching consequences and continues to impact the fight against antimicrobial resistance (AMR) in Africa. In Nigeria, antibiotics are available over-the-counter and are widely used in food animal production for various reasons, including prophylaxis and growth promotion. While this practice may support animal production, it also drives the spread of AMR, posing serious health challenges due to close human-livestock interactions and the countrys high disease burden. This study examined poultry farmers knowledge, attitudes, and practices (KAP) regarding antibiotic use and AMR, aiming to highlight the public health risks and challenges in combating AMR in Nigeria. MethodsA cross-sectional survey of 200 poultry farms in Enugu State, Southeast Nigeria, was conducted to evaluate farmers KAP towards antibiotic usage and AMR. Using a validated, standardized, and self-administered questionnaire, data were collected from farmers responsible for key farm decisions, including input and feed management. The questionnaire comprised three sections: socio-demographic data, knowledge of AMR, and knowledge and practices regarding antibiotic use. Ethical approval was obtained, and participants gave oral consent based on their professional capacity. ResultsThe evaluation of poultrys farmers KAP regarding antibiotic usage and AMR revealed that the majority of farmers (90.5%) reported using antibiotics, primarily for treating infections (80.5%) or for feed enhancement, growth promotion, and prophylaxis (61%). Ampicillin (75%), ciprofloxacin (71.5%), and doxycycline (71%) were the most commonly administered antibiotics. Monthly administration was the most common (48%), and 89% of respondents believed that antibiotics promote poultry growth. Interestingly, a substantial proportion of respondents (65%) were unaware of AMR, highlighting a significant knowledge gap, with only 16% recognizing the risk of AMR infections. ConclusionOur study revealed that the surveyed poultry farmers heavily rely on antibiotics, primarily for treating infections and, to a significant extent, for growth promotion, despite their limited awareness of AMR. Ampicillin was identified as the most commonly used antibiotic, raising concerns due to its potential link to beta-lactamase selection amid the countrys carbapenem resistance issues. These findings underscore the urgent need for targeted education to address the AMR knowledge gap and reduce the misuse of antibiotics in poultry farming settings in Nigeria.

scientific communication and education↗