The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli

• Published in: Journal of microbiological methods Vol. 136; pp. 71 - 77
• Main Authors: Omulo, Sylvia, Lofgren, Eric T., Mugoh, Maina, Alando, Moshe, Obiya, Joshua, Kipyegon, Korir, Kikwai, Gilbert, Gumbi, Wilson, Kariuki, Samuel, Call, Douglas R.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2017
• Subjects: Anti-Bacterial Agents - pharmacology; Antibiotic resistance prevalence; Colony Count, Microbial; Culture Media; Drug Resistance, Bacterial; Drug Resistance, Microbial; E. coli; Escherichia coli - drug effects; Escherichia coli - isolation & purification; Escherichia coli - pathogenicity; Escherichia coli Infections - diagnosis; Escherichia coli Infections - epidemiology; Feces - microbiology; Humans; Kenya - epidemiology; Microbial Sensitivity Tests; Prevalence; Re-plating; Sample Size; Storage; Antibiotic resistance prevalence; Storage; Re-plating; E. coli
• ISSN: 0167-7012; 1872-8359
• DOI: 10.1016/j.mimet.2017.03.006

Investigators often rely on studies of Escherichia coli to characterize the burden of antibiotic resistance in a clinical or community setting. To determine if prevalence estimates for antibiotic resistance are sensitive to sample handling and interpretive criteria, we collected presumptive E. coli isolates (24 or 95 per stool sample) from a community in an urban informal settlement in Kenya. Isolates were tested for susceptibility to nine antibiotics using agar breakpoint assays and results were analyzed using generalized linear mixed models. We observed a <3-fold difference between prevalence estimates based on freshly isolated bacteria when compared to isolates collected from unprocessed fecal samples or fecal slurries that had been stored at 4°C for up to 7days. No time-dependence was evident (P>0.1). Prevalence estimates did not differ for five distinct E. coli colony morphologies on MacConkey agar plates (P>0.2). Successive re-plating of samples for up to five consecutive days had little to no impact on prevalence estimates. Finally, culturing E. coli under different conditions (with 5% CO2 or micro-aerobic) did not affect estimates of prevalence. For the conditions tested in these experiments, minor modifications in sample processing protocols are unlikely to bias estimates of the prevalence of antibiotic-resistance for fecal E. coli. •Explores how protocol drift might impact prevalence estimates for antibiotic-resistance.•Conditions tested: storage, replating, colony morphology and culture conditions•No impact on antimicrobial-resistance prevalence estimates and diversity observed•Minor protocol adjustments unlikely to severely impact resistance estimates.