Objective:

To characterize the epidemiology and antimicrobial resistance trends of invasive bacterial pathogens at the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine from 2019 through 2024 and identify demographic and seasonal predictors of infection.

Approach:

• Study Design: Researchers conducted a 6-year retrospective, cross-sectional study of clinical specimens processed at the Clinical Microbiology Laboratory of the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine from 2019 through 2024.
• Data Collection: A total of 7,496 clinical specimen records were reviewed. After noninvasive specimens, duplicate isolates, contaminated samples, and incomplete records were excluded, 423 invasive isolates were included in the analysis.
• Laboratory Methods: Bacterial identification and antimicrobial susceptibility testing were performed using conventional microbiological methods and interpreted according to Clinical and Laboratory Standards Institute guidelines. Multivariable logistic regression was used to assess demographic and seasonal predictors of infection.
• Genomic Analysis: A subset of 40 Staphylococcus aureus isolates with available whole-genome sequencing data was evaluated for phylogenetic relationships and mecA gene carriage.

Key Findings:

• Staphylococcus aureus was the most common invasive bacterial pathogen, accounting for 32.9% of isolates, followed by Escherichia coli at 17.5%, Streptococcus pyogenes at 9.9%, Streptococcus pneumoniae at 9.7%, and Klebsiella pneumoniae at 8.5%.
• S. aureus showed approximately 92% resistance to penicillin, and methicillin-resistant S. aureus accounted for 10.0% of isolates.
• E. coli showed 92.0% resistance to ampicillin and 44.2% resistance to ciprofloxacin. S. pneumoniae showed approximately 97% resistance to cotrimoxazole.
• Adults aged 60 years or older had greater odds of Enterobacterales infection. S. pneumoniae was more common during the dry season, whereas K. pneumoniae was more common during the wet season.
• Whole-genome sequencing showed that mecA-positive S. aureus isolates were distributed across multiple phylogenetic clades rather than forming a single dominant cluster.

Interpretation:

The findings show substantial antimicrobial resistance among common invasive bacterial pathogens at the study institution, along with age- and season-related differences in pathogen distribution. The genomic findings suggest polyclonal rather than single-strain emergence of methicillin-resistant S. aureus.

Limitations:

• The analysis was based on surveillance data from a single research-affiliated diagnostic laboratory and may not represent the national epidemiology of invasive bacterial pathogens in The Gambia.
• Whole-genome sequencing was limited to 40 S. aureus isolates.
• Unmeasured factors, including comorbidities and previous antimicrobial treatment, may have influenced the results.

Conclusion:

The findings support the use of updated institution-level surveillance to guide empirical treatment and antimicrobial stewardship at the study institution. The authors also call for coordinated multisite surveillance to develop a more representative national picture of antimicrobial resistance in The Gambia.