Nocardia species epidemiology and susceptibility profiles from 2019 to 2022 in South Africa

Background. Nocardia species cause infections in humans, from localised to disseminated disease. They constitute a public health threat owing to the lack of sufficient information about them. In South Africa (SA), the last publication on this organism was in 2010. Predominant species types and antibiotic susceptibilities may have changed over this period. Objective. To address the knowledge gap surrounding Nocardia species and their antibiotic susceptibilities in SA. Methods. This was a retrospective and cross-sectional study. Data were collected from the Central Data Warehouse (CDW) of the National Health Laboratory Service (NHLS) on suspected Nocardia species from 1 January 2019 to 31 December 2022. Organism speciation was performed using 16S rRNA sequencing and antibiotic susceptibility testing (AST) by the broth microdilution (BMD) method. Data analysis included patient age, sample types from which the organism was cultured, distribution in the various SA provinces, species types and species AST profiles, including a record of trimethoprim-sulfamethoxazole (TMP/SMX) non-susceptibility. Results. One hundred and sixty-five positive culture results were analysed. The majority of positive cultures (28%, n=46) were from the 30 - 39-year age group. The organism was predominantly cultured from pus samples (31%, n=51). The top two provinces from which the largest numbers of isolates were submitted were Gauteng (69%, n=114) and Western Cape (18%, n=30) provinces. Two percent (n=4) of isolates were not sequenced, and 18% (n=30) of isolates lacked AST results. Twenty-nine percent (n=47) of the Nocardia species that were sequenced could not be speciated using 16S rRNA sequencing. The top two species country-wide were N. abscessus complex (25%, n=42) and N. cyriacigeorgica (18%, n=29). Approximately 90% (n=121) of all isolates tested were TMP/SMX susceptible. Conclusion. The predominant isolation of Nocardia species from pus samples suggests that the majority were deep-seated infections. The most common Nocardia species types and the AST profiles have changed over time. The study highlights the need for alternative methods for the speciation of this organism.