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Comparison of de-duplication methods used by WHO Global Antimicrobial Resistance Surveillance System (GLASS) and Japan Nosocomial Infections Surveillance (JANIS) in the surveillance of antimicrobial resistance [article]

Toshiki Kajihara, Koji Yahara, John Stelling, Sergey Romualdovich Eremin, Barbara Tornimbene, Visanu Thamlikitkul, Aki Hirabayashi, Eiko Anzai, Tomoyo Wakai, Nobuaki Matsunaga, Kayoko Hayakawa, Norio Ohmagari (+2 others)
2020 bioRxiv   pre-print

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https://web.archive.org/web/20200325012224/https://www.biorxiv.org/content/biorxiv/early/2020/01/13/2020.01.13.904136.full.pdf

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A major issue in the surveillance of antimicrobial resistance (AMR) is "de-duplication" or removal of repeated isolates, for which there exist multiple methods. The World Health Organization (WHO) Global Antimicrobial Resistance Surveillance System (GLASS) requires de-duplication by selecting only the first isolate of a given bacterial species per patient per surveillance period per specimen type per age group, gender, and infection origin stratification. However, no study on the comparative
more » ... lication of this method has been reported. The objective of this study was to evaluate differences in data tabulation between the WHO GLASS and the Japan Nosocomial Infections Surveillance (JANIS) system, which counts both patients and isolates after removing repeated isolates of the same bacterial species per multiresistance phenotype isolated from a patient within 30 days, regardless of specimen type. All bacterial data, consisting of approximately 8 million samples from 1795 Japanese hospitals in 2017 were exported from the JANIS database, and were tabulated using either the de-duplication algorithm of GLASS, or JANIS. We compared the tabulated results of the total number of patients whose blood and urine cultures were taken and of the percentage of resistant isolates of Escherichia coli for each priority antibiotic. The number of patients per specimen type tabulated by the JANIS method was always smaller than that of GLASS. There was a small (< 3%) difference in the percentage of resistance of E. coli for any antibiotic between the two methods in both out- and inpatient settings and blood and urine isolates. The two tabulation methods did not show considerable differences in terms of the tabulated percentages of resistance for E. coli . We further discuss how the use of GLASS tabulations to create a public software and website that could help to facilitate the understanding of and treatment against AMR.
doi:10.1101/2020.01.13.904136 fatcat:4alhp73lybg3xb24urr52prnba
Citation

Toshiki Kajihara, Koji Yahara, John Stelling, Sergey Romualdovich Eremin, Barbara Tornimbene, Visanu Thamlikitkul, Aki Hirabayashi, Eiko Anzai, Tomoyo Wakai, Nobuaki Matsunaga, Kayoko Hayakawa, Norio Ohmagari, Motoyuki Sugai, Keigo Shibayama. "Comparison of de-duplication methods used by WHO Global Antimicrobial Resistance Surveillance System (GLASS) and Japan Nosocomial Infections Surveillance (JANIS) in the surveillance of antimicrobial resistance." bioRxiv (2020)