South Asian Journal of Research in Microbiology

Beyond the Antibiogram: The Significance and Advantages of WHONET-Driven AST Analysis in the Modern Food Microbiology Laboratory

L. C. Nnodim, E. B. Enaregha, F. O. Osakuade — Sat, 08 Aug 2026 00:00:00 +0000

Food microbiology laboratories generate large volumes of antimicrobial susceptibility testing data, yet the analytical conventions they apply were largely inherited from clinical bacteriology. The cumulative antibiogram, designed to inform empirical therapy for hospital patients, remains the dominant summary artefact in many food-sector laboratories, although its assumptions about patients, specimens and treatment decisions align poorly with commodity chains, regulatory monitoring and microbiological rather than clinical definitions of resistance. WHONET, free software distributed since 1989 for the management and analysis of microbiological laboratory data, has been taken up in more than one hundred countries, but its documented application to food isolates remains sparse relative to human clinical use. This critical narrative review evaluates what WHONET-driven analysis can and cannot contribute to food microbiology laboratories, and distinguishes claims supported by evidence from those resting on plausibility alone. Literature was identified through structured searching of publicly accessible scholarly indexes and citation registries, supplemented by backward and forward citation tracking and by examination of authoritative institutional sources, then appraised for design adequacy, transparency and topical relevance rather than pooled quantitatively. Four propositions are examined: that retention of quantitative test measurements permits interpretation against epidemiological cut-off values and retrospective reinterpretation as guidance changes; that structured extraction from laboratory information systems reduces transcription burden and supports international reporting; that resistance-profile analysis offers a phenotypic signal useful for detecting unusual clusters; and that internal consistency checks improve data quality. The evidence supporting the first and second propositions is reasonably firm and is corroborated by the design of European harmonised monitoring; evidence for the third derives almost entirely from clinical and public health settings and has not been demonstrated for food matrices; evidence for the fourth is largely descriptive. Reported food-sector applications are few, geographically uneven and frequently opaque about isolate selection, guideline version and denominators. Software adoption is treated in much of the literature as an outcome rather than as a means to analytical improvement, and this conflation obscures whether analytical quality has actually improved.

Molecular Detection of Tetracycline Resistance Genes in Escherichia coli Isolated from Urine Samples in Michael Okpara University of Agriculture Clinic, Umudike

Perfect Victory Nwakwuruibe, Immaculata Ugochi Nwankwo — Sat, 01 Aug 2026 00:00:00 +0000

Background: Antimicrobial resistance among urinary Escherichia coli isolates can reduce the effectiveness of commonly used antibacterial agents.

Aims: This study examined antibiotic susceptibility and the presence of tetracycline-resistance genes in E. coli recovered from urine samples at Michael Okpara University of Agriculture, Umudike, Nigeria.

Methods: One hundred midstream urine samples were examined using cultural, morphological and biochemical methods. Six presumptive E. coli isolates were subjected to disc-diffusion susceptibility testing against ampicillin, ceftazidime, ciprofloxacin, gentamicin, amoxicillin–clavulanate, tetracycline and cefuroxime. Three tetracycline-resistant isolates were selected for 16S rRNA gene analysis and polymerase chain reaction screening for tetA and tetB.

Results: Six E. coli isolates were recovered, representing 6.0% of the samples examined. Three of the six isolates were resistant to tetracycline. Resistance to ampicillin, ciprofloxacin and amoxicillin–clavulanate was detected in two isolates each, while one isolate each was resistant to ceftazidime, gentamicin and cefuroxime. The three isolates selected for molecular analysis produced 16S rRNA amplicons. Among these three isolates, one carried both tetA and tetB, corresponding to 33.3% of the molecularly screened isolates and 16.7% of all six E. coli isolates.

Conclusion: Tetracycline resistance and associated efflux-mediated resistance genes were detected among a small number of urinary E. coli isolates. Larger studies using complete clinical data, validated molecular controls and broader resistance-gene panels are required to determine the local epidemiological significance of these findings.

Molecular Detection of Quinolone and Aminoglycoside-Resistant Genes in Multidrug-Resistant Uropathogenic Escherichia coli Isolated from Diabetic Patients with Urinary Tract Infection in Bauchi Metropolis

S. Isma’il, T. Inusa, M. Y. Iliyasu, A. F. Umar — Thu, 06 Aug 2026 00:00:00 +0000

Background: Urinary tract infection (UTI) is one of the most common medical conditions associated with diabetes mellitus across all age groups. Most cases are caused by uropathogenic E. coli (UPEC). Inappropriate antibiotic use has contributed to the emergence of multidrug-resistant strains. The increasing emergence of multidrug-resistant uropathogenic E. coli, particularly strains resistant to quinolones and aminoglycosides, poses a significant public health concern.

Aims: This study aimed to investigate the molecular characterisation of quinolone- and aminoglycoside-resistance genes in MDR UPEC isolates from diabetic patients with urinary tract infections in Bauchi metropolis.

Study design: This was a cross-sectional, laboratory-based study conducted on clinical isolates of aminoglycoside- and quinolone-resistant uropathogenic E. coli obtained from diabetic patients in Bauchi metropolis.

Place and Duration of Study: The study was conducted at Abubakar Tafawa Balewa University, Bauchi (ATBU), from November 2025 to May 2026.

Methodology: Ten (10) MDR uropathogenic E. coli isolates resistant to two or more aminoglycoside and quinolone antibiotics were included. Genotypic detection was performed to confirm aminoglycoside- and quinolone-resistance genes among the isolates. The MDR isolates were subjected to polymerase chain reaction (PCR) to detect the aminoglycoside-resistance genes aph(2″)-Ib and aph(3′)-IIIa and the quinolone-resistance genes qnrS and qnrD.

Results: PCR analysis revealed that aph(2″)-Ib was the most prevalent aminoglycoside-resistance gene and was detected in all isolates; the coexistence of aph(3′)-IIIa and aph(2″)-Ib was detected in one isolate. Among the quinolone-resistance genes, qnrD was present in all isolates, whereas the coexistence of qnrS and qnrD was detected in one isolate.

Conclusion: The presence and coexistence of aminoglycoside- and quinolone-resistance genes were identified in this study. These findings suggest that the detected resistance genes may contribute to the dissemination of antibiotic resistance among MDR UPEC isolates resistant to aminoglycosides and quinolones, highlighting the potential role of horizontal gene transfer in the spread of antimicrobial resistance among bacteria.

Isolation and Identification of Dermatophytic and Non-dermatophytic Fungi among Almajiri School Children in Kano State, Nigeria

Wed, 12 Aug 2026 00:00:00 +0000

Dermatophytosis and non-dermatophytosis remain significant public health concerns because of their high prevalence, increasing antifungal resistance, and the limitations of conventional antifungal drugs. This study aimed to determine the dermatophytic and non-dermatophytic organisms associated with skin infections among Almajiri schoolchildren aged 10–15 years. Fungal isolates were obtained from skin scrapings and identified using cultural, microscopic, and molecular techniques, including PCR amplification and sequencing of the 18S rRNA gene. A total of 14 fungal isolates, representing three fungal genera, were recovered. The genera isolated were Rhizoctonia, Aspergillus, and Trichophyton, with Aspergillus occurring most frequently. The fungal species isolated were Aspergillus fumigatus (42.85%), Trichophyton interdigitale (21.43%), Aspergillus niger (14.29%), Rhizoctonia spp. (14.29%), and Aspergillus flavus (7.14%). Molecular identification confirmed A. fumigatus, T. interdigitale, and A. niger with sequence identities of 98.69%, 99.54%, and 99.80%, respectively. These findings indicate the presence of dermatophytic and non-dermatophytic fungi among the sampled children and support the need for improved hygiene and laboratory-based diagnosis in Almajiri schools. The study concluded that non-dermatophytes were associated with skin infections among Almajiri schoolchildren aged 10–15 years.

Antibiogram and Some Genetic Markers of Resistance in Coagulase Negative Staphylococci and Mammaliicoccus (Staphylococcus) Sciuri from Veterinary Sources in Rivers State, Nigeria

Victoria Ivuoma Emelu, Tombari Pius Monsi, Easter Godwin Nwokah — Thu, 20 Aug 2026 00:00:00 +0000

Coagulase-negative Staphylococci (CoNS) are important reservoirs of antibiotic-resistance genes and associated mobile genetic elements, with potential relevance to the emergence of methicillin-resistant staphylococcal clones. This study determined antibiotic resistance and molecular resistance markers among coagulase-negative Staphylococcus isolates from livestock in Port Harcourt, Rivers State, Nigeria. During a four-month study, 422 samples were collected from the ears, fur, noses and mouths of rams, goats, cows and sheep and processed using standard microbiological methods. Antimicrobial susceptibility testing was performed by disc diffusion against oxacillin, cefoxitin, erythromycin, gentamicin, clindamycin, amoxicillin, vancomycin, ciprofloxacin, ofloxacin and cefuroxime. Polymerase chain reaction was used to detect mecA, ermA, ermC and SCCmec. Ninety-four coagulase-negative isolates were recovered from the sampled anatomical sites and animal species, and the majority showed resistance to several antimicrobial agents tested. Four genera, Enterococcus, Mammaliicoccus, Staphylococcus and Micrococcus, were identified. Mammaliicoccus (Staphylococcus) sciuri was the most frequent, whereas Enterococcus gallinarum, Staphylococcus aureus and Micrococcus aloeverae were evenly represented. Of 15 representative isolates analysed by PCR, 11 harboured one or more resistance markers: six carried ermA, three ermC, one mecA and nine SCCmec. The detection of these resistance markers, together with multidrug-resistant Mammaliicoccus (Staphylococcus) sciuri, indicates that livestock in the study area may harbour coagulase-negative Staphylococci with antimicrobial-resistance determinants of veterinary and public health relevance.