Diagnostic specimens from all dogs (N = 167) housed at the animal shelter were collected on the 27th June 2015 in Nairobi, Kenya by veterinarians using the TRANSWAB® Amies swabs. Nasal specimens were collected by inserting the swabs up to 10 cm into the nasal cavity of the animals, which were restrained without sedation for the procedure. Wound infections were also swabbed when present. The Staphylococcaceae strains were isolated at the laboratories of the International Livestock Research Institute (ILRI) using standard methods without selective enrichment (44 ). Briefly, each swab was streaked on Baird Parker Agar (Carl Roth) plates and incubated at 37°C overnight. One to two suspicious colonies per plate were picked, expanded in LB media (Carl Roth), and stored as glycerol stocks at −80°C before being shipped for further characterization to the Institute of Veterinary Bacteriology (IVB) in Switzerland. Strains were streaked onto Trypticase Soy Agar (TSA-B; Becton Dickinson) with 5% sheep blood (TSA-B; Becton Dickinson) and incubated at 37°C overnight. Species designation was assigned using MALDI-TOF MS (Bruker) as previously reported (30 (link)) followed by metabolic phenotyping (see below). Data on strains investigated in this study are provided in Dataset S1.
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