An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals

A review of antimicrobial resistance challenges in Nigeria: The need for a one health approach

The discovery of penicillin and other antibiotics has revolutionized modern medicine. However, overreliance on antibiotics has led to a global antimicrobial resistance (AMR) crisis, jeopardizing progress made over the past decades. Antimicrobial resistance poses a critical public health challenge, affecting humans, animals, and the environment. The AMR challenge is particularly dire in Nigeria owing to the extensive antibiotic use across various sectors and ineffective antimicrobial stewardship programs. This narrative review summarizes the literature from January 2018 to December 2023, focusing on the current trends in AMR in Nigeria, including knowledge of antimicrobial usage, prescription patterns, and adherence to guidelines for humans, animals, and their shared environments. High antibiotic resistance patterns were detected in isolates recovered from healthcare settings, food supply chains, companion animals, wildlife, and the environment. Factors exacerbating the AMR crisis in Nigeria include poor regulation of antimicrobial agents, improper empirical prescriptions, inadequate infection prevention practices, arbitrary and prophylactic use of antibiotics in food-producing animals, environmental contamination, and insufficient surveillance programs. To effectively mitigate this crisis, it is essential to adopt the One Health approach, which prioritizes collaborative efforts among stakeholders, including governmental agencies, healthcare institutions, veterinary experts, farmers, and the scientific community, to address the convergence of human, animal, and environmental health. These efforts will promote transdisciplinary surveillance approaches and the establishment of policies aimed at ameliorating the impact of AMR on the Nigerian economy, the well-being of its population, and diverse ecosystems.

Molecular characterization of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement, Nairobi, Kenya, based on whole-genome sequencing analysis

High genomic plasticity within Escherichia coli enables it to acquire and accumulate genetic material through horizontal gene transfer. In this study, we sought to investigate the virulence genes, phylogroups, antibiotic resistance genes, plasmid replicons, multilocus sequence types (MLST), and core genome MLST of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement in Nairobi, Kenya. A total of 39 multidrug-resistant (MDR) strains had their DNA extracted, and whole-genome sequencing was done using the Illumina HiSeq 2000 platform. Twenty-six E. coli assemblies were analyzed using web-based bioinformatics tools available at the Centre for Genomic Epidemiology and EnteroBase. The isolates were categorized into four main phylogroups, where 10/26 (38.5%) belonged to the B2 phylogroup, 4/26 (15.4%) belonged to D, 3/26 (11.5%) belonged to A, 1/26 (3.8%) belonged to B1, while 8/26 (30.8%) were not determined. FimH30 was predominantly found in the most frequent phylogroup B2 and sequence type (ST) 131. The most common beta-lactam resistance genes were bla TEM-1B and blaCTXM 15, followed by three fluoroquinolone resistance genes [qnrS1 6/26 (23.1%), qnrB4 2/26 (7.7%), and aac(6')-Ib-cr, 8/26 (30.8%)]. Of 26 isolates, 15 had at least one amino acid substitution in the housekeeping genes gyrA (p.S83L), gyrA (p.D87N), parC (p.S80I), parC (p.E84V), parC (p.S57T), and parE (p.I529L), associated with resistance to fluoroquinolones. A total of 40 diverse virulence genes were detected among the isolates. Thirteen different STs were isolated from the E. coli genomes, which included ST 131, ST 3036, ST 38, ST 10, ST 12569, ST 15271, ST 2076, ST 311, ST 3572, ST 394, ST 453, ST 46, and ST 1722. Only two isolates (2/26, 7.7%) from the Municipal City Council clinic were genetically related. Additionally, the most abundant plasmid replicon identified belonged to the IncF family, IncFII(pRSB107), in particular, followed by the Col family. The study highlighted the first E. coli ST46 to harbor the bla NDM5 gene encoded in Col(BS512), IncFII(pRSB107), and IncFIB(AP001918) plasmid replicons in Kenya. We further demonstrated the diversity of MDR E. coli associated with diarrhea in an endemic setting in Kenya.

IMPORTANCE

This study investigated the molecular characterization of multidrug-resistant Escherichia coli isolated from diarrheagenic children under 5 years of age in Mukuru Informal Settlement in Nairobi, Kenya. This is an important addition to the genomic analysis data of multi-drug resistant diarrheal Escherichia coli in Kenya. The use of whole-genome sequencing to identify and characterize these isolates is valuable and provides valuable insights into the molecular epidemiology of E. coli in the region.

Ochoa S, Xicohtencatl-Cortes J. Pathogenesis and Immunomodulation of Urinary Tract Infections Caused by Uropathogenic Escherichia coli

Urinary tract infections (UTIs) are a leading cause of illness in children and adults of all ages, with uropathogenic Escherichia coli (UPEC) being the primary agent responsible. During colonization and subsequent infection of the urinary tract (UT), UPEC requires the expression of genes associated with virulence, such as those that encode the fimbrial adhesins FimH, PapG, and CsgA, as well as the presence of the TosA protein and the flagellar appendages of the bacteria. However, for colonization and infection to be successful, UPEC must overcome the host's immunological barriers, such as physical barriers, expressed peptides and proteins, and immune cells found in the UT. In this context, the UT functions as an integral system where these factors act to prevent the colonization of uropathogens. Significant genetic diversity exists among UPEC strains, and the clonal complex ST131 represents one of the key lineages. This lineage has a high content of virulence genes, multiple mechanisms of antibiotic resistance, and a high frequency of extended-spectrum β-lactamases (ESBLs). New knowledge regarding protein structures known as adhesins and their role in the infection process can help identify therapeutic targets and aid in the design of vaccines. These vaccines could be based on the development of chimeric fusion proteins (FimH + CsgA + PapG), which may significantly reduce the incidence of UTIs in pediatric and adult patients.

Clostridioides difficile recovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences

Genomic data on Clostridioides difficile from the African continent are currently lacking, resulting in the region being under-represented in global analyses of C. difficile infection (CDI) epidemiology. For the first time in Nigeria, we utilized whole-genome sequencing and phylogenetic tools to compare C. difficile isolates from diarrhoeic human patients (n=142), livestock (n=38), poultry manure (n=5) and dogs (n=9) in the same geographic area (Makurdi, north-central Nigeria) and relate them to the global C. difficile population. In addition, selected isolates were tested for antimicrobial susceptibility (n=33) and characterized by PCR ribotyping (n=53). Hierarchical clustering of core-genome multilocus sequence typing (cgMLST) allelic profiles revealed large diversity at the level HC150 (i.e. clusters of related genomes with maximally 150 pairwise allelic differences), which was previously shown to correlate with PCR ribotypes (RT). While several globally disseminated strains were detected, including HC150_1 (associated with RT078), HC150_3 (RT001) and HC150_3622 (RT014), 42 HC150 clusters (79%) represented unique genotypes that were new to the public genomic record, and 16 (30%) of these were novel PCR ribotypes. Considerable proportions of the C. difficile isolates displayed resistance to fluoroquinolones, macrolides and linezolid, potentially reflecting human and animal antibiotic consumption patterns in the region. Notably, our comparative phylogenomic analyses revealed human-human, human-livestock and farm-farm sharing of near-identical C. difficile genomes (≤2 core-genome allelic differences), suggesting the continued spread of multiple strains across human and animal (pig, poultry, cattle and dog) host populations. Our findings highlight the interconnectivity between livestock production and the epidemiology of human CDI and inform the need for increased CDI awareness among clinicians in this region. A large proportion of C. difficile strains appeared to be unique to the region, reflecting both the significant geographic patterning present in the C. difficile population and a general need for additional pathogen sequencing data from Africa.

Generalizability of machine learning in predicting antimicrobial resistance in E. coli: a multi-country case study in Africa

BACKGROUND

Antimicrobial resistance (AMR) remains a significant global health threat particularly impacting low- and middle-income countries (LMICs). These regions often grapple with limited healthcare resources and access to advanced diagnostic tools. Consequently, there is a pressing need for innovative approaches that can enhance AMR surveillance and management. Machine learning (ML) though underutilized in these settings, presents a promising avenue. This study leverages ML models trained on whole-genome sequencing data from England, where such data is more readily available, to predict AMR in E. coli, targeting key antibiotics such as ciprofloxacin, ampicillin, and cefotaxime. A crucial part of our work involved the validation of these models using an independent dataset from Africa, specifically from Uganda, Nigeria, and Tanzania, to ascertain their applicability and effectiveness in LMICs.

RESULTS

Model performance varied across antibiotics. The Support Vector Machine excelled in predicting ciprofloxacin resistance (87% accuracy, F1 Score: 0.57), Light Gradient Boosting Machine for cefotaxime (92% accuracy, F1 Score: 0.42), and Gradient Boosting for ampicillin (58% accuracy, F1 Score: 0.66). In validation with data from Africa, Logistic Regression showed high accuracy for ampicillin (94%, F1 Score: 0.97), while Random Forest and Light Gradient Boosting Machine were effective for ciprofloxacin (50% accuracy, F1 Score: 0.56) and cefotaxime (45% accuracy, F1 Score:0.54), respectively. Key mutations associated with AMR were identified for these antibiotics.

CONCLUSION

As the threat of AMR continues to rise, the successful application of these models, particularly on genomic datasets from LMICs, signals a promising avenue for improving AMR prediction to support large AMR surveillance programs. This work thus not only expands our current understanding of the genetic underpinnings of AMR but also provides a robust methodological framework that can guide future research and applications in the fight against AMR.

Antimicrobial resistance containment in Africa: Moving beyond surveillance

Worldwide, infections caused by drug-resistant pathogens constitute a significant challenge threatening therapeutic efforts. According to the World Health Organization (WHO), antimicrobial resistance (AMR) ranks among the top 10 global public health threats. Organisms with a high rate of multiple host adaptivity, significant genetic diversity (multiple lineages), high virulence factors, and genetic exchange have been isolated from various sources (humans, animals, and the environment) even without exposure to prior antibiotics. Till now, the source of AMR and how resistant clones are selected in the environment remain largely elusive, and potential anthropogenic transmission has been reported in different studies. Various drug-resistant pathogens, lineages, resistant clones, outbreak clusters, plasmid replicates, and genes that play a critical role in resistance dissemination have been identified. Maintenance of certain multidrug-resistant (MDR) determinants has also been shown to enhance or support the propagation of MDR. So far, significant advances have been made in understanding the burden of AMR. However, overcoming AMR requires a holistic approach, as there is no single approach with sufficient precision to curb the threat. While strengthening AMR surveillance efforts is essential, as we have shown, there is also a need to intensify efforts to strengthen therapeutic interventions, especially in priority regions such as Africa. Herein, we discussed the burden of AMR and the dissemination of AMR in humans, animals, and the environment (non-medical drivers). We further delved into the big questions on Africa and discussed how therapeutic interventions involving vaccines and other viable biomaterials could be pivotal in reducing the burden of AMR to the barest minimum.

Multidrug-resistant extended spectrum β-lactamase (ESBL)-producing Escherichia coli from farm produce and agricultural environments in Edo State, Nigeria

Antimicrobial resistance (AMR) is a major public health concern, especially the extended-spectrum β-lactamase-producing (ESBL) Escherichia coli bacteria are emerging as a global human health hazard. This study characterized extended-spectrum β-lactamase Escherichia coli (ESBL-E. coli) isolates from farm sources and open markets in Edo State, Nigeria. A total of 254 samples were obtained in Edo State and included representatives from agricultural farms (soil, manure, irrigation water) and vegetables from open markets, which included ready-to-eat (RTE) salads and vegetables which could potentially be consumed uncooked. Samples were culturally tested for the ESBL phenotype using ESBL selective media, and isolates were further identified and characterized via polymerase chain reaction (PCR) for β-lactamase and other antibiotic resistance determinants. ESBL E. coli strains isolated from agricultural farms included 68% (17/25) from the soil, 84% (21/25) from manure and 28% (7/25) from irrigation water and 24.4% (19/78) from vegetables. ESBL E. coli were also isolated from RTE salads at 20% (12/60) and vegetables obtained from vendors and open markets at 36.6% (15/41). A total of 64 E. coli isolates were identified using PCR. Upon further characterization, 85.9% (55/64) of the isolates were resistant to ≥ 3 and ≤ 7 antimicrobial classes, which allows for characterizing these as being multidrug-resistant. The MDR isolates from this study harboured ≥1 and ≤5 AMR determinants. The MDR isolates also harboured ≥1 and ≤3 beta-lactamase genes. Findings from this study showed that fresh vegetables and salads could be contaminated with ESBL-E. coli, particularly fresh produce from farms that use untreated water for irrigation. Appropriate measures, including improving irrigation water quality and agricultural practices, need to be implemented, and global regulatory guiding principles are crucial to ensure public health and consumer safety.