Objectives Co-trimoxazole (trimethoprim/sulfamethoxazole) is clinically valuable in treating skin and soft tissue infections (SSTIs) caused by community-associated methicillin-resistant Staphylococcus aureus (MRSA). The genetic basis of emerging trimethoprim/sulfamethoxazole resistance in S. aureus from Africa is unknown. Such knowledge is essential to anticipate its further spread. We investigated the molecular epidemiology of trimethoprim resistance in S. aureus collected in and imported from Africa. Methods Five hundred and ninety-eight human S. aureus isolates collected at five locations across sub-Saharan Africa [Gabon, Namibia, Nigeria (two) and Tanzania] and 47 isolates from travellers treated at six clinics in Europe because of SSTIs on return from Africa were tested for susceptibility to trimethoprim, sulfamethoxazole and trimethoprim/sulfamethoxazole, screened for genes mediating trimethoprim resistance in staphylococci [dfrA (dfrS1), dfrB, dfrG and dfrK] and assigned to spa genotypes and clonal complexes. Results In 313 clinical and 285 colonizing S. aureus from Africa, 54% of isolates were resistant to trimethoprim, 21% to sulfamethoxazole and 19% to trimethoprim/sulfamethoxazole. We found that 94% of trimethoprim resistance was mediated by the dfrG gene. Of the 47 S. aureus isolates from travellers with SSTIs, 27 (57%) were trimethoprim resistant and carried dfrG. Markers of trimethoprim resistance other than dfrG were rare. The presence of dfrG genes in S. aureus was neither geographically nor clonally restricted. Conclusions dfrG, previously perceived to be an uncommon cause of trimethoprim resistance in human S. aureus, is widespread in Africa and abundant in imported S. aureus from ill returning travellers. These findings may foreshadow the loss of trimethoprim/sulfamethoxazole for the empirical treatment of SSTIs caused by community-associated MRSA.

Background: There is a concern with the growing use of antimicrobials across countries increasing antimicrobial resistance (AMR) rates. A key area within hospitals is their use for the prevention of surgical site infections (SSI) with concerns with timing of the first dose, which can appreciably impact on effectiveness, as well as duration with extended prophylaxis common among low- and middle-income countries (LMICs). This is a concern as extended duration increases utilization rates and AMR as well as adverse events. Consequently, there is a need to document issues of timing and duration of surgical antibiotic prophylaxis (SAP) among LMICs together with potential ways forward to address current concerns. Methods: Narrative review of timings and duration of SAP among LMICs combined with publications documenting successful approaches to improve SAP to provide future direction to all key stakeholder groups. Results: There were documented concerns with the timing of the first dose of antibiotics, with appropriate timing as low as 6.7% in Egypt, although as high as 81.9% in Turkey. There was also an extensive duration of SAP, ranging from long duration times in all patients in a study in Nigeria with a mean of 8.7 days and 97% of patients in Egypt to 42.9% of patients in Pakistan and 35% in Turkey. Successful interventions to improve SAP typically involved multiple approaches including education of all key stakeholder groups, monitoring of usage against agreed guidelines,as well as quality targets. Multiple approaches typically improved timing and duration as well as reduced costs. For instance, in one study appropriateness increased from 30.1% to 91.4%, prolonged duration reduced to 5.7% of patients, and mean costs of antibiotics decreased 11-fold. Conclusion: There are considerable concerns with the timing and duration of SAP among LMICs. Multiple interventions among LMICs can address this providing future directions.

Carbapenem-resistant Enterobacterales are a global problem, however little is known about the burden and origin of carbapenem resistance in Africa. The objectives of this study were to determine the proportion of carbapenem-resistant isolates among extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), to identify the underlying mechanisms of resistance and to assess the population structure of carbapenem-resistant isolates from Nigeria. ESBL-E isolates (n = 175) from infections were collected at four hospitals in Lagos, Nigeria, from July 2016 to January 2018 and were screened for carbapenem resistance using a VITEK®2 automated system. All carbapenem-resistant ESBL-E (CRE) were screened for blaKPC, blaCTX-M, blaCMY-2, blaNDM, blaVIM, blaIMP, blaOXA-181 and blaOXA-48 genes. Genotyping of randomly selected isolates was performed by whole-genome sequencing. The isolates included Escherichia coli (n = 113; 64.6%) and Klebsiella pneumoniae (n = 62; 35.4%). Of the 175 ESBL-E isolates, 48 (27.4%) were resistant to carbapenems (15 E. coli and 33 K. pneumoniae). CRE isolates carried blaNDM (n = 30; 62.5%), blaNDM + blaOXA-181 (n = 10; 20.8%), blaOXA-181 (n = 2; 4.2%) and blaNDM + blaOXA-48 (n = 1; 2.1%); no carbapenemase gene was detected in 5 isolates (10.4%). The isolates showed low diversity and were mainly associated with multilocus sequence typing (MLST) sequence types ST410 for E. coli and ST395 and ST147 for K. pneumoniae. Carbapenem resistance is frequent among ESBL-E in Nigeria and is mainly associated with blaNDM. Genotyping suggested that the observed clones possibly originated from Southeast Asia.

The African Journal of Laboratory Medicine focuses on the role of the laboratory and its professionals in the clinical and public healthcare sectors, and is specifically based on an African frame of reference.

Carbapenem-resistant Pseudomonas aeruginosa strains are on the rise worldwide. This study characterized clinical isolates of P. aeruginosa from three Nigerian hospitals for carbapenem resistance. Strains isolated from wounds (n = 88), urine/catheter tips (n = 25), sputum/tracheotomy aspirates (n = 5), ear swabs (n = 4) and vaginal swabs (n = 1) were identified by MALDI-TOF and antibiotic susceptibility testing was performed using the VITEK 2 system. The genomic DNA of each isolate was subject to sequencing using Illumina and Oxford nanopore technology. Bioinformatics analyses were performed to detect antimicrobial resistance genes, clonal affiliations and phylogenetic relations of 123 non-duplicate P. aeruginosa isolates, whereas assembly of the nanopore reads using the plasmIDent pipeline enabled the identification of plasmids. Forty-three percent of the isolates were resistant to all antibiotic categories tested. More than 40% of the isolates were resistant to the carbapenems imipenem and/or meropenem (39% and 44%, respectively). Among the meropenem-resistant isolates, 48 (89%) carried at least one carbapenemase gene. The predominant one was bla_NDM-₁ (n = 34), which conferred resistance to all five antibiotic categories and highly increased the MICs of both meropenem and imipenem. The other recurrent carbapenemase genes were bla_VIM-2 (n = 4), and bla_VIM-5-like (n = 11), which co-existed with bla_NDM-1 in two isolates. The study revealed a high rate of carbapenem resistance and conjugative, broad host range plasmids carrying carbapenemase-encoding genes, especially the NDM-1 type, among isolates of P. aeruginosa. This may forebode the emergency of ubiquitous carbapenem resistance urging the implementation of infection control and antimicrobial stewardship strategies in Nigerian hospitals.