Sampling strategies in antimicrobial resistance monitoring: evaluating how precision and sensitivity vary with the number of animals sampled per farm.
Because antimicrobial resistance in food-producing animals is a major public health concern, many countries have implemented antimicrobial monitoring systems at a national level. When designing a sampling scheme for antimicrobial resistance monitoring, it is necessary to consider both cost effectiveness and statistical plausibility. In this study, we examined how sampling scheme precision and sensitivity can vary with the number of animals sampled from each farm, while keeping the overall sample size constant to avoid additional sampling costs. Five sampling strategies were investigated. These employed 1, 2, 3, 4 or 6 animal samples per farm, with a total of 12 animals sampled in each strategy. A total of 1,500 Escherichia coli isolates from 300 fattening pigs on 30 farms were tested for resistance against 12 antimicrobials. The performance of each sampling strategy was evaluated by bootstrap resampling from the observational data. In the bootstrapping procedure, farms, animals, and isolates were selected randomly with replacement, and a total of 10,000 replications were conducted. For each antimicrobial, we observed that the standard deviation and 2.5-97.5 percentile interval of resistance prevalence were smallest in the sampling strategy that employed 1 animal per farm. The proportion of bootstrap samples that included at least 1 isolate with resistance was also evaluated as an indicator of the sensitivity of the sampling strategy to previously unidentified antimicrobial resistance. The proportion was greatest with 1 sample per farm and decreased with larger samples per farm. We concluded that when the total number of samples is pre-specified, the most precise and sensitive sampling strategy involves collecting 1 sample per farm.
Viral Disease and Epidemiology Research Division, National Institute of Animal Health, Kannondai, Tsukuba, Ibaraki, Japan.
Takehisa
T
Yamamoto
Viral Disease and Epidemiology Research Division, National Institute of Animal Health, Kannondai, Tsukuba, Ibaraki, Japan.
Yoko
Y
Hayama
Viral Disease and Epidemiology Research Division, National Institute of Animal Health, Kannondai, Tsukuba, Ibaraki, Japan.
Arata
A
Hidano
Viral Disease and Epidemiology Research Division, National Institute of Animal Health, Kannondai, Tsukuba, Ibaraki, Japan.
Sota
S
Kobayashi
Viral Disease and Epidemiology Research Division, National Institute of Animal Health, Kannondai, Tsukuba, Ibaraki, Japan.
Norihiko
N
Muroga
Animal Products Safety Division, Food Safety and Consumer Affairs Bureau, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo Japan.
Kiyoyasu
K
Ishikawa
Animal Products Safety Division, Food Safety and Consumer Affairs Bureau, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo Japan.
Aki
A
Ogura
Viral Disease and Epidemiology Research Division, National Institute of Animal Health, Kannondai, Tsukuba, Ibaraki, Japan.
Toshiyuki
T
Tsutsui
D000822:Animal Husbandry; D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D024901:Drug Resistance, Multiple, Bacterial; D004926:Escherichia coli / Q000187:drug effects* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000188:drug therapy / Q000382:microbiology / Q000662:veterinary*; D005243:Feces / Q000737:chemistry* / Q000382:microbiology*; D007564:Japan / Q000453:epidemiology; D008826:Microbial Sensitivity Tests; D015995:Prevalence; D018401:Sample Size; D013552:Swine; D013553:Swine Diseases / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology
D000900:Anti-Bacterial Agents