The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli.
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% CO2or 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.
Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA.
Sylvia
S
Omulo
Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA.
Eric T
ET
Lofgren
Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
Maina
M
Mugoh
Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
Moshe
M
Alando
Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
Joshua
J
Obiya
Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
Korir
K
Kipyegon
Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
Gilbert
G
Kikwai
Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
Wilson
W
Gumbi
Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.
Samuel
S
Kariuki
Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA; The Nelson Mandela African Institute for Science and Technology, Arusha, Tanzania. Electronic address: drcall@wsu.edu.
Douglas R
DR
Call
D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D015169:Colony Count, Microbial; D003470:Culture Media; D024881:Drug Resistance, Bacterial; D004352:Drug Resistance, Microbial; D004926:Escherichia coli / Q000187:drug effects / Q000302:isolation & purification* / Q000472:pathogenicity; D004927:Escherichia coli Infections / Q000175:diagnosis / Q000453:epidemiology; D005243:Feces / Q000382:microbiology*; D006801:Humans; D007630:Kenya / Q000453:epidemiology; D008826:Microbial Sensitivity Tests; D015995:Prevalence; D018401:Sample Size
D000900:Anti-Bacterial Agents; D003470:Culture Media
Antibiotic resistance prevalence; E. coli; Re-plating; Storage