Characterization of typical and atypical bacteria in pediatric upper respiratory tract infections at Kisumu County Hospital

Loice Mahila Machanja; Godfrey Gitonga Mutuma; Nathan Shaviya; Eliphalet Ochieng Otunga

doi:10.51867/scimundi.6.1.40

Auteurs

Loice Mahila Machanja Masinde Muliro University of Science and Technology, Kenya https://orcid.org/0000-0001-9483-1486
Godfrey Gitonga Mutuma Masinde Muliro University of Science and Technology, Kenya https://orcid.org/0000-0003-1891-1817
Nathan Shaviya Masinde Muliro University of Science and Technology, Kenya https://orcid.org/0000-0001-7347-3130
Eliphalet Ochieng Otunga Masinde Muliro University of Science and Technology, Kenya https://orcid.org/0009-0009-9561-3638

DOI :

https://doi.org/10.51867/scimundi.6.1.40

Mots-clés :

Atypical Bacteria, Characterization, Infections, Typical, Upper Respiratory Tract

Résumé

Upper respiratory tract infections (URTIs) are among the leading causes of illness and mortality among children under five, particularly in low and middle-income countries. Management becomes complicated due to bacterial pathogens and antimicrobial resistance, particularly in areas with limited diagnostic capacity. The objective of this study was to isolate and characterize the bacteriological pathogens associated with upper respiratory tract infections among children at Kisumu County Hospital. A cross-sectional descriptive study was conducted involving 100 purposively recruited children under five years of age presenting with URTI symptoms. Throat swabs were collected between June 2025 and July 2025 and subjected to culture on blood and MacConkey agar, then incubated at 37°C for 24 hours. Bacteria were identified using morphological, Gram staining, and biochemical tests. Antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method following CLSI guidelines. Molecular characterization using the PCR technique was used to detect resistance genes. Descriptive and inferential statistics were used for analysis. The most frequently isolated bacteria were Staphylococcus aureus (40%), Streptococcus pyogenes (31%), and Enterococcus faecalis (19%). Antimicrobial sensitivity was highest in S. pyogenes (52%) and lowest in Klebsiella species (30%), which also showed the highest resistance (45%) and multidrug resistance (60%). PCR analysis confirmed high prevalence of the 16S rRNA mutation gene and MecA in all five samples tested isolates. Other AMR genes identified were TEM, TYLA, VANA/B, EF-Tu mutants, and APH(3) IIIa. Although there is no statistically significant association between bacterial species and the overall sensitivity patterns with the antibiotics (p = 0.135), there was a statistically significant association between the type of bacterial isolate and MDR (p = 0.045). These results indicate no statistically significant association between bacterial isolates and specific AMR gene profiles (p > 0.05). Bacterial pathogens, particularly Gram-positive cocci, are major contributors to URTIs among children in Kisumu. A high prevalence of antimicrobial and multidrug resistance, especially in urban areas, threatens treatment outcomes. There is a need for the ministry of health to incorporate molecular diagnostics, including PCR and metagenomics, into routine hospital laboratory workflows for early detection of resistance genes and more accurate pathogen identification in all county-level 5 hospitals for better diagnosis and management of patients. Clinicians should also consider isolating both typical and atypical bacteria present in patients with respiratory tract infections.

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