African Journal of Clinical and Experimental Microbiology

A narrative review exploring phage therapy as a sustainable alternative solution to combat antimicrobial resistance in Africa: Applications, challenges and future directions

N. O. Obidi — 2025-04-04

The increasing threat of antimicrobial resistance (AMR) in Africa, coupled with limited access to advanced antibiotics and high rates of bacterial infections poses serious public health challenge. Bacteriophages, viruses that target and destroy bacteria, present a promising alternative or complementary therapy to traditional antibiotics. Phage therapy leverages its unique ability to target specific bacterial strains without affecting the host beneficial microbiota. It is an effective tool against multi-drug-resistant (MDR) microbial pathogens, particularly in resource-limited settings. This narrative review explores the potentials of phage therapy in Africa, highlighting its advantages, such as specificity, minimal side effects, and cost-effectiveness, alongside its capability to tackle biofilm-associated and AMR infections. It discusses current research and collaborations, including case studies from Nigeria, Benin, and South Africa that demonstrate the efficacy of phage therapy against bacterial pathogens such as Escherichia coli, Acinetobacter baumannii and Klebsiella pneumoniae. Furthermore, it discusses the challenges to phage therapy implementation such as regulatory hurdles, public skepticism, and infrastructure limitations, while emphasizing the importance of developing local production and awareness campaigns. The review concludes by recommending the integration of phage therapy into Africa healthcare strategies to address AMR. Through strategic partnerships, education and regulatory frameworks, phage therapy could become a transformative solution, particularly for neglected diseases and infections common in low-resource settings. As Africa seeks innovative approaches to its growing AMR crisis, phage therapy stands out as a viable and adaptable option.

The journey to institutionalising Antimicrobial Stewardship (AMS) in a resource-constrained tertiary healthcare facility in Lagos, Nigeria

O. O. Oduyebo — 2025-04-04

Background: Antimicrobial stewardship (AMS) is one of the main strategies to stem the global tide of antimicrobial resistance (AMR). While developed nations have successfully implemented antimicrobial stewardship programmes, such initiatives remain underdeveloped in many Nigerian healthcare institutions. This is a report of a project to improve the AMS programme at the Lagos University Teaching Hospital (LUTH), Nigeria, by strengthening the antimicrobial stewardship committee (AMSC) and antimicrobial stewardship team (AMST) of the hospital.
Methodology: The Commonwealth Partnerships for Antimicrobial Stewardship (CwPAMS) facility assessment tool was used to identify gaps in the AMS programme (ASP) of LUTH, and activities to address the gaps were conducted over a 3-year period (2021-2024).
Results: The results of the activities to address the identified gaps in the ASP were the expansion of AMS activities from 3 to 10 departments of the hospital, a strong management commitment and support, consistent antibiotic consumption calculations, strategic training of professionals, and increased knowledge and awareness of AMS among staff and students. However, major challenges identified included shortage of staff and lack of functional electronic medical records.
Conclusion: Continuing pre- and in-service training of staff, AMS activities and monitoring, and incorporation of AMS actions and interventions performed with the electronic medical records are recommended for sustaining AMS in the hospital.

Bacterial profile and antibiogram of clinical isolates in a tertiary healthcare facility in northeast Nigeria: Initial steps towards developing local antibiotic guidelines and antimicrobial stewardship programme

M. M. Manga — 2025-04-04

Background: Antibiograms and antibiotic guidelines are important tools for appropriate prescribing practices in combating the antimicrobial resistance (AMR) challenge. They serve as a prelude to an evidence-based Antimicrobial Stewardship (AMS) program, which is necessary for better Infection Prevention and Control (IPC) activities, especially in low-resource settings like Nigeria. This study determined the bacterial profile and antibiogram of clinical isolates in a tertiary healthcare facility in Gombe, northeastern Nigeria.
Methodology: This was a 4-year retrospective descriptive analysis of bacterial isolates from in and outpatient clinical specimens submitted to the Medical Microbiology Laboratory of the hospital between January 2019 to December 2022. Specimens were cultured for bacterial isolation and phenotypic identification using conventional techniques. Antibiotic susceptibility test was performed on each isolate by the Kirby Bauer disc diffusion method.
Results: A total of 15,457 bacteria were isolated over the 4-year period and include Staphylococcus aureus (6604, 42.72%), Klebsiella species (2382, 15.41%), Escherichia coli (2140, 13.84%), Pseudomonas species (1429, 9.25%), Proteus species (469, 3.03%) and Enterococcus species (215, 1.39%). The overall susceptibility (antibiogram) of all the bacterial isolates to commonly used antibiotics over the 4-year period was 59.0% for gentamicin, 54.5% for levofloxacin, 50.6% to ciprofloxacin, 48.5% to ceftriaxone, 48.5% to ceftazidime, and 41.9% to amoxicillin/clavulanate. Resistance rate was more than 50.0% for many of the tested antibiotics (ceftriaxone, ceftazidime, amoxicillin/ clavulanate, and cefoxitin).
Conclusion: There was high level of resistance to many routinely used antibiotics tested in our facility. There is need for evidence-based AMS programmes hinged on local antibiotic guidelines for better patient safety and improved healthcare quality particularly in resource poor settings.

Bacterial etiology of spreading odontogenic infection in southwest Nigeria using the 16S rRNA next generation sequencing technique

B. A. Famurewa — 2025-04-04

Background: Genomics surveillance and characterization of pathogens have enabled prompt and accurate diagnosis, for improved management and control of infectious diseases. This study aimed to identify bacteria associated with spreading odontogenic infections (SOIs) among patients visiting the Dental Center of the Obafemi Awolowo University Teaching Hospitals Complex (OAUTHC), Ile-Ife, Nigeria, by sequencing 16S rRNA gene of the bacteria.
Methodology: This was a cross-sectional study of 15 participants with clinically confirmed SOIs. Pus samples were obtained from the participants and stored at -800 C until ready for analysis. DNA was extracted from the pus samples using the Quick-DNATM Miniprep Plus Kit. Polymerase chain reaction (PCR) was used to amplify the V1-V9 regions of the 16S rRNA gene. Successfully amplified samples were cleaned up and next generation sequencing (NGS) technique was used to sequence the bacterial 16S rRNA gene. Sequence data were analyzed using Geneious Prime version 2021.2.2 which used Ribosomal Database Project Tools to assign genus and higher level taxonomy.
Results: Multiple genera of bacteria were detected in individual sample. The detected and identified bacteria belonged to Firmicutes, Bacteroidetes, Fusobacteria, Actinobacteria, Proteobacteria, Tenericutes and Spirochaetes phyla. Detected predominant bacterial genera were Streptococcus, Prevotella, Peptostreptococcus, Parvimonas and Porphyromonas. Some novel bacteria identified include Legionella, Taonella, Ferrovibro, Holdemania, and Limnobacter.
Conclusion: Bacteria detected in this study include previously reported bacteria associated with SOIs and novel bacteria, with preponderance of anaerobes.

Prevalence and aetiological agents of childhood urinary tract infections at the University Teaching Hospital (CHU) of Bouaké, Côte d'Ivoire

K. J. Gawa — 2025-04-04

Background: Urinary tract infections (UTIs) are common in paediatric environment. The microbial ecology is often modified by over-prescription of antibiotics. The aim of this study was to determine the prevalence and etiological agents responsible for paediatric UTIs, with a view to improving care for children in Bouaké, Côte d'Ivoire.
Methodology: The study was carried out in the Paediatrics Department and the Microbiology Laboratory of Bouaké University Hospital Center over a 30-month period from June 2020 to December 2022. A total of 219 children were included and urine samples were collected. Bacterial strains were identified using conventional bacteriology techniques. Antibiotic susceptibility testing was carried out using the disk diffusion method, and interpretation was made according to CASFM/EUCAST recommendations for the current year.
Results: Among the 219 children included, 28 (12.8%) cases of UTIs were diagnosed and urinary tract anomalies in 21.4% of the UTI cases (6/28). The median age of the UTI cases was 96 months, females accounted for 60.7% (17/28) with a M/F of 0.65. Fever and urinary symptoms were reported by 47.0% and 17.3% respectively. Community acquired UTIs occurred in 25.0% (7/28), while hospital acquired UTIs occurred in 75.0% (21/28). Escherichia coli (60.7%) and Klebsiella pneumoniae (17.9%) were the most frequent bacteria isolated. Resistance rates to standard beta-lactam antibiotics ranged from 56.3% to 62.3%.
Conclusion: The epidemiology of paediatric urinary tract infections was dominated by E. coli, with high rates of resistance to standard antibiotics at Bouaké University Hospital Center.

Prevalence, molecular characteristics and antibiotic susceptibility of clinical isolates of Clostridioides difficile in southeastern Nigeria

E. I. Oghonyon — 2025-04-04

Background: Clostridioides difficile is a major contributor to healthcare-associated infections, exhibiting global variations in its prevalence and resistance. There is an absence of data on its molecular characteristics and antibiotic susceptibility of C. difficile in southeastern Nigeria. This study aims to evaluate its prevalence, molecular features, and resistance patterns to enhance treatment and control strategies.
Methodology: Stool samples were collected from 450 hospitalized adult patients with persistent diarrhoea and prolonged antibiotic use from selected public and private healthcare facilities across the five States of southeastern Nigeria. The total anaerobes were enumerated using standard bacteriological methods. Clostridioides difficile was cultured on Clostridium difficile differential agar with selective supplements, followed by biochemical testing including catalase, oxidase, and reverse CAMP tests. Genomic bacterial DNA was extracted, purified, and amplified by polymerase chain reaction (PCR) assay. Sequencing of the DNA amplicon was performed and results were blasted on the NCBI database. Virulence (tcdA, tcdB, cdtA, and cdtB) and resistance (tetS, tetA, and ermB) genes were detected by conventional PCR assay. Antibiotic susceptibility of each isolate was determined using the Kirby-Bauer disc diffusion method.
Results: The mean anaerobe counts ranged from 5.61±0.11 log10 CFU/g (Ebonyi) to 5.65±0.07 log10 CFU/g (Enugu). Antibiotic susceptibility test revealed sensitivity to gentamicin, meropenem, and amoxicillin-clavulanic acid, while resistance was observed to tetracycline and erythromycin. The multiple antibiotic resistance (MAR) index of isolates was 0.44. All isolates (100%) harbored tcdB gene while 69.56% harbored tcdA gene. Additionally, 4.34% of isolates contained cdtA and cdtB genes.
Conclusions: This study highlights significant antibiotic resistance and presence of virulence genes in C. difficile isolates in southeastern Nigeria, emphasizing the need for monitoring and tailored treatment strategies.

Biochemical evaluation of liver function enzymes in Lassa fever patients

A. A. Anjorin — 2025-04-04

Background: Lassa fever (LF) is a zoonotic acute viral hemorrhagic disease caused by the Lassa virus (LV). It has a high case fatality rate of about 5,000 deaths in humans from 300,000-500,000 cases each year globally. The high mortality rate from Lassa fever has been associated with abnormal liver enzyme production due to LV infiltration of the liver. However, data are sparse on the different enzymes and their proportions associated with LF. This study aims to evaluate the effect of LF on the levels of selected liver enzymes.
Methodology: This was a case-control epidemiological study of 100 participants comprising 70 participants with LF attending Federal Medical Centre, Owo between May and September 2023, and 30 healthy controls randomly selected within the hospital environs. Demographic information (age and gender) was collected from the participants with data collection form. Venous blood samples were collected from the participants into appropriate sample bottles and centrifuged to separate plasma for laboratory analyses. Lassa fever was confirmed by amplification of LV RNA using reverse transcriptase-polymerase chain reaction (RT-PCR) technique. Specific liver enzymes, including alanine transaminase (ALT), aspartate transaminase (AST), and alkaline phosphatase (ALP), were assayed from the plasma using Mindray chemistry system with Architect c8000 and Roche Cobas c501 chemistry analyzers. Data were analysed using SPSS version 20.0. software. Mean values were compared using the t-test while categorical variables were compared using the Chi-square test. Statistical significance was set at p<0.05 with 95% confidence interval.
Results: The results showed that among the study participants, the age group 20-39 years had the highest frequency of LF (37.1%, 26/70), with a slightly higher frequency in the females (51.4%, 36/70), compared to the males (48.6%, 34/70). The mean plasma ALP level of 263.84±50.73 U/L in LF patients was significantly higher than 46.80±1.85 U/L in the controls (t=35.740, p<0.0001). Similarly, the mean plasma ALT level of 158.96±11.46 U/L in LF patients was significantly higher than 10.67±8.55 U/L in the control (t=71.405,
p<0.0001), and the mean plasma AST level of 283.0±15.71 U/L in LF patients was significantly higher than 19.26±9.02 U/L in the control (t=105.60, p<0.0001). Elevated plasma levels of ALP, ALT and AST were recorded in 45.7%, 70.0% and 85.7% of LF patients, compared to 0%, 6.7% and 6.7% in the controls respectively (p<0.0001).
Conclusion: The study found significantly elevated liver enzymes in LF patients, providing insights into the pathological effects of the LV virus on the liver.

Pathogenicity of filamentous fungi isolated from poultry farms on gastrointestinal system of day-old chicks in Anambra State, Nigeria

Anthonia Nkiruka Mba — 2025-04-04

Background: The pervasive presence of filamentous fungi in poultry farming environments has a profound impact on the bird health, leading to reduced growth rates, increased mortality, and decreased egg production. The objective of this study was to use an avian model to determine the pathogenicity of some filamentous fungal isolates from litter, feed, and fecal samples on day-old birds.
Methodology: A total of 300 environmental samples (feed, litter, and droppings) were collected from 10 selected poultry farms in six local government areas (LGAs) in Anambra State, and cultured for fungi isolation by phenotypic (macroscopic and microscopic) and genotypic methods. Five of the fungi isolates were used for pathogenicity study on day-old chicks. A total of 25 day-old-chicks, randomly divided into 5 groups of 5 each, were orally infected with 1 ml of the different fungal conidia. A 6th group served as the control and was inoculated with the same volume of phosphate-buffered saline. All the birds were observed twice daily for appearance of clinical signs for 10 days. Histological examination of the intestinal tissues and stomach of infected birds was done. Data were analysed using one-way ANOVA on SPSS version 21.0, with p<0.05 considered significant.
Results: The pathogenic effects of the 5 fungi isolates (Curvularia verruculosa, Aspergillus tubingensis, Cunninghamella bertholletiae, Fusarium oxysporum and Aspergillus fumigatus) used for the pathogenicity study on the birds include symptoms such as; (i) reduction in food and water intake, fraying of feathers and loss of reflex within 5 days of exposure to C. verruculosa, and (ii) discolored and enlarged bursa of Fabricius, obstructed, dark, and slightly sloughed intestine, reduction in the sizes of livers and gizzards, and swelling of the rectum with exposure to F. oxysporum and A. fumigatus. Histological examination revealed severe destruction of the intestinal villi, distortion of the intestinal mucosa, and haemorrhage in all the groups of birds exposed to the 5 fungi isolates. Mortality in the groups of birds infected with C. verruculosa and C. bertholletiae (80.0%, 4/5) was significantly higher (p<0.001) than in other groups.
Conclusion: This study showed that the poultry farms were highly laddened with a variety of filamentous fungi, which have a lot of detrimental effects on the health of bird and needs to be controlled through proper hygiene practices and the provision of biosecurity for the birds.

Antimicrobial susceptibility pattern of Salmonella isolates from clinical, environmental and food sources in Lagos, Nigeria

S. O. Ajoseh — 2025-04-04

Background: Salmonellosis persists in Lagos, Nigeria, despite interventions. This study investigated antimicrobial resistance patterns of Salmonella species from clinical, food, and environmental samples in Lagos.
Methodology: From June to December 2018, 276 samples (86 blood, 80 stool, 40 hospital effluents, and 70 food) were collected for microbiological analysis. Clinical samples (blood and stool) were collected from patients in General Hospital Igando and Lagos State University Teaching Hospital Ikeja. Food samples were collected from food vendors in the urban periphery of Lagos State, and hospital effluents were collected from Gbagada General Hospital and Ojo Health Centre. The samples were processed using standard microbiological procedures. Antimicrobial susceptibility of isolated bacteria was done using the Kirby-Bauer disk diffusion method.
Results: Of the 276 samples, an overall prevalence of Salmonella spp from all sources was 9.1% (25/276), with 7.0% from blood, 17.5% from stool, 10.0% from hospital effluents, and 1.4% from food samples. Salmonella strains showed multidrug resistance (MDR) to at least four of nine antibiotics, with 98.0% resistance to ampicillin, nitrofurantoin and augmentin, and 99.0% sensitivity to imipenem. Five unique resistance patterns (A1-A5) were identified, with pattern A1 (AMP AUG GEN OFX CXM CTZ CIP NIT) observed in 72.0% of the Salmonella isolates, followed by A5 (AMP AUG GEN CXM CTZ NIT) in 8.0% of the isolates from two sources (stool and hospital effluent). The remaining patterns (A2, A3, and A4) were exhibited by Salmonella isolates from a single source.
Conclusion: The findings of this study suggest potential multi-source transmission dynamics of the investigated Salmonella species. It highlights the circulation of MDR Salmonella species from food and environmental sources with possible transmission to humans, emphasizing the need for continuous surveillance and control strategies. The persistence of Salmonella species and antimicrobial resistance in Lagos underscores the importance of targeted public health interventions to mitigate this public health threat.

Bacteriological quality of Datura stramonium cocktail (‘gegemu’) and antimicrobial susceptibility of isolated bacterial pathogens

J. A. Onipede — 2025-04-04

Background: Datura stramonium, commonly known as Jimson weed, is widely recognized in traditional medicine, and is a key ingredient in various herbal concoctions. Aside from the well-known herbal formulation, a cocktail made from Datura stramonium, known locally as ‘gegemu’, has become increasingly popular among students in our environment, raising concerns about its microbial quality. The fact that this cocktail is not commercially available raises the possibility of contamination by pathogenic microorganisms during preparation or storage, posing significant health risk. The objective of this study was to assess the microbial quality of this cocktail drink and determine the antimicrobial susceptibility of the bacteria isolates.
Methodology: Because this cocktail is not commercially available, a purposive sampling technique was adopted to collect 10 samples of the ‘gegemu’ cocktail from students in three selected tertiary institutions within Abeokuta metropolis, Nigeria. The samples were transported in ice packs to the biology laboratory of the Federal College of Education, Abeokuta, Nigeria for microbial analysis. The pH of the samples was determined using pH meter. Samples were cultured on plate count, nutrient, Salmonella-Shigella, Eosin Methylene Blue (EMB) and MacConkey agar plates using pour plate method for heterotrophic count. Isolated bacteria were identified by conventional methods as described in Bergey’s Manual of Systematic Bacteriology. Antimicrobial susceptibility test (AST) was performed against 9 antibiotics using the Kirby-Bauer disk diffusion method.
Results: The mean pH of the samples was 3.705±0.005 with a range of 3.25±0.02 to 4.11±0.02. All samples were contaminated, with heterotrophic count ranging from mean value of 5.8±0.09x10⁵ for sample G4 to 7.9±0.24x10⁶ CFU/ml for sample G8, which exceed the acceptable limit of bacteria content of drinks safe for consumption. A total of 30 bacteria isolates were recovered from the samples, and this includes Staphylococcus aureus (n=6), Staphylococcus epidermidis (n=2), Bacillus cereus (n=3), Shigella flexneri (n=3), Salmonella Typhi (n=4), Pseudomonas aeruginosa (n=3), Escherichia coli (n=4), Klebsiella pneumoniae (n=3) and Vibrio cholerae (n=2). The AST results indicated that E. coli was 99.4% sensitive to cefixime but only 10.7% to tetracycline, S. flexneri was 91.7% sensitive to gentamicin but only 21.6% to cefuroxime, S. Typhi was 100.0% sensitive to cefixime but only 19.1% to tetracycline, V. cholerae was 88.3% sensitive to cefixime but only 32.6% to ampicillin, S. aureus was 85.9% sensitive to cotrimoxazole but only 16.4% to tetracycline, and S. epidermidis was 92.4% sensitive to cotrimoxazole but only 23.7% to tetracycline. Other isolates such as K. pneumoniae, P. aeruginosa and B. cereus displayed varying levels of resistance to tetracycline and ampicillin.
Conclusion: Our study indicates that in spite of the acidity of the ‘gegemu’ cocktail, it contains pathogenic bacteria that exceeded the acceptable microbial thresholds, rendering it unsafe for consumption. Additionally, some of the isolated bacteria showed resistance to tetracycline and ampicillin, which are common antibiotics used in our environment. It is essential to enhance public health awareness to address and reduce these risks.