Integrating multi-wet laboratory diagnostics to study staphylococci in animals in Uganda.

BACKGROUND: Several diagnostic environments in Uganda lack real-time, robust and high-throughput technologies for comprehensive typing of microbes, which is a setback to infectious disease surveillance. This study combined various wet laboratory diagnostics to understand the epidemiology of pathogenic staphylococci isolated from animals in Uganda and the implications for global health security priorities. METHODS: A retrospective study was conducted employing records and pathogenic staphylococci (from animals) archived at the Central Diagnostic Laboratory (CDL), Makerere University, Uganda, between January 2012 and December 2019. The bacteria were speciated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and tested for virulence factors [beta lactamases, lecithinase, deoxyribonuclease (DNase), haemolysins] and resistance to ten antimicrobials of clinical and veterinary relevance. Tetracycline and methicillin resistance genes were also tested. RESULTS: The prevalent diseases were mastitis in cattle and skin infections in dogs. Of the 111 staphylococci tested by MALDI-TOF MS, 79 (71.2%) were Staphylococcus aureus, 27 (24.3%) were Staphylococcus pseudintermedius and 5 (4.5%) were Staphylococcus schleiferi. All these strains expressed haemolysins. The prevalence of strains with lecithinase, penicillinase, cephalosporinase and DNase was 35.9% (14/39), 89.7% (35/39), 0.0% (0/39) and 87.2% (34/39), respectively. Staphylococci were primarily resistant to early penicillins (over 80%), tetracycline (57.7%), and chloramphenicol (46.2%). Minimal resistance was noted with cloxacillin (0.0%), ciprofloxacin (9.6%), and cefoxitin (3.8%). The prevalence of multidrug resistance (MDR) was 78.8% for general staphylococci, 82.2% for S. aureus, 73.1% for S. pseudintermedius, and 60.0% for S. schleiferi. Multidrug resistant staphylococci were significantly more prevalent in the cattle isolates than in the dog isolates (P < 0.05). The prevalence of methicillin-resistant staphylococci (MRS) tested by resistance to cefoxitin and mecA carriage was 3.8%. These four strains were all isolated from dog skin infections. The tetK gene was the most predominant (35.4%), followed by tetM (25.0%). CONCLUSION: In resource-constrained settings, the approach of integrated diagnostics promises sustainable disease surveillance and the addressing of current capacity gaps. The emergence of MRS (zoonotic bacteria) in companion animals creates a likelihood of reduced treatment options for related human infections, a threat to global health.

Reflections on Drivers for the Emergence and Spread of Antimicrobial Resistant Bacteria Detected from Chickens reared on Commercial Layer Farms in Mukono District, Uganda.

Purpose: We investigated the fecal carriage of antimicrobial resistant Escherichia coli and potential practices influencing antimicrobial resistance (AMR) dynamics among poultry farm settings in Mukono District, Uganda. Methods: Twenty-nine commercial layer farms were visited and samples collected from 10 birds. The samples were then subjected to culture and sensitivity testing. The investigative framework for antimicrobial stewardship practices (IFAP) was used as a participatory tool to generate data through interviews and observations on antimicrobial use, drivers for use, players, and actions following non-responsive treatment outcomes. Results: The cultures done on 290 cloacal swabs yielded a total of 273 Escherichia coli isolates (94.1% recovery rate) which were tested in vitro for their sensitivity to different antibiotics. The prevalence of multi-drug resistant E. coli was 59.3% (162/273). A high prevalence of resistance to tetracycline (91.6%, n = 250) and trimethoprim sulphamethoxazole (70.3%, n = 192) was noted. In this collection of isolates, the prevalence of molecular determinants associated with the predominant phenotypes was; tetA (79.3%; 138/174), tetB (17.2%; 30/174), tetC (7.5%; 13/174), sul1 (11.5%; 20/174), and sul2 (60.3%; 105/174). Responses derived using the IFAP revealed several vices related to misuse and overuse of antibiotics, a threat to the poultry industry. The farmers also reported habits of selling off sick birds for slaughter when treatment outcomes were non-responsive. Such a practice could drive dissemination of antimicrobial resistant organisms and antibiotic residues to the consumers of those poultry products. Conclusion: The IFAP tool was useful and can be modified, and adopted for use in engaging agricultural communities in participatory AMR surveillance. A high carriage of multi-drug resistant E. coli was detected in the birds. On these farms, the worrying antimicrobial stewardship practices discovered could be sponsoring the emergence and spread of antimicrobial resistant bacteria in the Ugandan context.