Phiri, N. | Search bioRxiv

bioRxiv2020

Antibiotic-resistant Salmonella species and Escherichia coli in broiler chickens from farms, abattoirs and open markets in selected districts of Zambia

Salmonella species and Escherichia coli are major bacterial enteropathogens of global public health importance that cause foodborne diseases, thereby contributing to increased human morbidity and mortality. Both pathogens have also been found to contribute towards the spread of antimicrobial resistance through the food chain, especially in poultry. The aim of this study was to determine the occurrence of antibiotic-resistant Salmonella sp. and E. coli in broiler chickens at farm level, abattoirs and open markets in selected districts of Zambia. A cross-sectional study was undertaken in seven districts of Zambia to determine the resistance profiles of Salmonella sp. and E. coli obtained from broiler chickens at farms, abattoirs and open markets. A total of 470 samples were collected, including litter, cloacal swabs and carcass swabs. Samples were inoculated into buffered peptone water, sub-cultured onto MacConkey and Xylose Lysine Deoxycholate agar plates. Identification of Salmonella sp. and E. coli was done using the API-20E kit and confirmation by 16S rDNA sequencing. Confirmed isolates were tested against a panel of 10 antibiotics using the Kirby-Bauer disc-diffusion method and interpreted according to the Clinical Laboratory Standards Institute guidelines. Analysis of the antibiotic susceptibility test results was done using WHONET 2018 software. Overall, 4 Salmonella spp. and 280 E. coli were isolated. One of the Salmonella sp. was resistant to ampicillin (25%), amoxicillin/clavulanic acid (25%) and cefotaxime (25%). E. coli antibiotic resistance was highest to tetracycline (81.4%) and lowest to imipenem (0.7%). The antibiotic susceptibility profile revealed 55% (154/280) multidrug resistant E. coli, with the highest multidrug resistance profile (20.7%) in the ampicillin-tetracycline-trimethoprim/sulfamethoxazole drug combination. Furthermore, 4.3% (12/280) of the isolates showed Extensive Drug resistance. The levels of antimicrobial resistance to E. coli and Salmonella observed in market-ready chickens is of public health concern.View Full Text

scientific communication and education↗

bioRxiv2017

Characterising maize viruses associated with maize lethal necrosis symptoms in sub Saharan Africa

Maize lethal necrosis disease (MLN) is an emerging disease in East Africa caused by the introduction of Maize chlorotic mottle virus (MCMV). Recent activity seeking to limit spread of the disease is reliant on effective diagnostics. Traditional diagnostics applied on samples with typical field symptoms of MLN have often given negative results using ELISA or PCR for MCMV and Sugarcane mosaic virus (SCMV). Samples collected in the field with typical MLN symptoms were examined using next generation sequencing (NGS). SCMV was found to be more prevalent than suggested by targeted diagnostics. Additionally, the panel of samples were found to be infected with a range of other viruses, seven of which are described here for the first time. Although not previously identified in the region, Maize yellow mosaic virus (MYMV) was the most prevalent virus after MCMV. The development of targeted diagnostics for emerging viruses is complicated when the extent of field variation is unknown, something that can be negated by using NGS methods. As a result we explored MinION technology which may be more readily deployable in resource poor settings. The results show that this sequencer can diagnose known viruses and future iterations have the potential to identify novel viruses.

microbiology↗