Specimen-Stratified Bacterial Epidemiology and Antimicrobial Resistance in a Rural South African District: A Seven-Year Retrospective Analysis
1
Pharmacy, University of Limpopo, Polokwane, South Africa
Popul. Med. 2026;8(Supplement Supplement 1):A228
ABSTRACT
BACKGROUND:
Antimicrobial resistance (AMR) surveillance in low- and middle-income countries frequently relies on aggregated antibiograms that obscure clinically relevant heterogeneity across infection sites. This limitation is particularly consequential in resource-limited settings, where empiric therapy often depends on routine laboratory data.
METHODS:
We conducted a retrospective analysis of routine antimicrobial susceptibility testing data generated by the National Health Laboratory Service in the Capricorn District, Limpopo Province, South Africa, from 2016 to 2022. A total of 59,478 clinical isolates from blood, urine, respiratory, wound, device-associated, and superficial specimens were analysed. Pathogen distribution, demographic patterns, and antimicrobial resistance profiles were evaluated using specimen-stratified epidemiological, ecological, and statistical analyses, including diversity indices and multivariate community comparisons.
RESULTS:
Gram-positive (40.6%) and Gram-negative (38.6%) bacteria contributed comparably to the overall isolate burden. Coagulase-negative staphylococci, Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus accounted for nearly half of all isolates. Marked ecological and resistance heterogeneity was observed across specimen types. Invasive and device-associated specimens exhibited reduced microbial diversity and substantially higher resistance burdens, including elevated resistance to third-generation cephalosporins, fluoroquinolones, and carbapenems among Gram-negative isolates, and high cefoxitin resistance among Gram-positive bloodstream isolates. Urinary isolates showed lower carbapenem resistance but persistently high resistance to commonly used oral agents. Multivariate analyses confirmed specimen type as a major determinant of pathogen community structure and resistance profiles.
CONCLUSIONS:
Antimicrobial resistance in the Capricorn District is strongly shaped by infection site, healthcare exposure, and pathogen ecology. Aggregated antibiograms substantially underestimate resistance in invasive and device-associated infections. These findings provide robust empirical support for specimen-stratified AMR surveillance as a pragmatic and clinically relevant approach to guide empiric therapy and strengthen antimicrobial stewardship in resource-limited healthcare systems.
Antimicrobial resistance (AMR) surveillance in low- and middle-income countries frequently relies on aggregated antibiograms that obscure clinically relevant heterogeneity across infection sites. This limitation is particularly consequential in resource-limited settings, where empiric therapy often depends on routine laboratory data.
METHODS:
We conducted a retrospective analysis of routine antimicrobial susceptibility testing data generated by the National Health Laboratory Service in the Capricorn District, Limpopo Province, South Africa, from 2016 to 2022. A total of 59,478 clinical isolates from blood, urine, respiratory, wound, device-associated, and superficial specimens were analysed. Pathogen distribution, demographic patterns, and antimicrobial resistance profiles were evaluated using specimen-stratified epidemiological, ecological, and statistical analyses, including diversity indices and multivariate community comparisons.
RESULTS:
Gram-positive (40.6%) and Gram-negative (38.6%) bacteria contributed comparably to the overall isolate burden. Coagulase-negative staphylococci, Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus accounted for nearly half of all isolates. Marked ecological and resistance heterogeneity was observed across specimen types. Invasive and device-associated specimens exhibited reduced microbial diversity and substantially higher resistance burdens, including elevated resistance to third-generation cephalosporins, fluoroquinolones, and carbapenems among Gram-negative isolates, and high cefoxitin resistance among Gram-positive bloodstream isolates. Urinary isolates showed lower carbapenem resistance but persistently high resistance to commonly used oral agents. Multivariate analyses confirmed specimen type as a major determinant of pathogen community structure and resistance profiles.
CONCLUSIONS:
Antimicrobial resistance in the Capricorn District is strongly shaped by infection site, healthcare exposure, and pathogen ecology. Aggregated antibiograms substantially underestimate resistance in invasive and device-associated infections. These findings provide robust empirical support for specimen-stratified AMR surveillance as a pragmatic and clinically relevant approach to guide empiric therapy and strengthen antimicrobial stewardship in resource-limited healthcare systems.
| eISSN: | 2654-1459 |
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