1 Vol.:(0123456789) Scientifc Reports | (2021) 11:23359 | https://doi.org/10.1038/s41598-021-02755-5 www.nature.com/scientificreports Antimicrobial resistance in commensal opportunistic pathogens isolated from non‑sterile sites can be an efective proxy for surveillance in bloodstream infections Karina‑Doris Vihta 1,2,12* , Nicola Claire Gordon 3 , Nicole Stoesser 1,2,4 , T. Phuong Quan 1,2 , Carina S. B. Tyrrell 5 , Manivanh Vongsouvath 6 , Elizabeth A. Ashley 6,7 , Vilada Chansamouth 6,7 , Paul Turner 7,8 , Clare L. Ling 7,9 , David W. Eyre 2,4,10 , Nicholas J. White 7,11 , Derrick Crook 1,2,4 , Tim E. A. Peto 1,2,4 & Ann Sarah Walker 1,2 Antimicrobial resistance (AMR) surveillance in bloodstream infections (BSIs) is challenging in low/ middle‑income countries (LMICs) given limited laboratory capacity. Other specimens are easier to collect and process and are more likely to be culture‑positive. In 8102 E. coli BSIs, 322,087 E. coli urinary tract infections, 6952 S. aureus BSIs and 112,074 S. aureus non‑sterile site cultures from Oxfordshire (1998–2018), and other (55,296 isolates) rarer commensal opportunistic pathogens, antibiotic resistance trends over time in blood were strongly associated with those in other specimens (maximum cross‑correlation per drug 0.51–0.99). Resistance prevalence was congruent across drug‑ years for each species (276/312 (88%) species‑drug‑years with prevalence within ± 10% between blood/ other isolates). Results were similar across multiple countries in high/middle/low income‑settings in the independent ATLAS dataset (103,559 isolates, 2004–2017) and three further LMIC hospitals/ programmes (6154 isolates, 2008–2019). AMR in commensal opportunistic pathogens cultured from BSIs is strongly associated with AMR in commensal opportunistic pathogens cultured from non‑sterile sites over calendar time, suggesting the latter could be used as an efective proxy for AMR surveillance in BSIs. Antimicrobial resistance (AMR) is among the top ten global health threats 1 , and is a particularly acute challenge in low- to middle-income countries (LMICs) 2–4 . Surveillance is a key tool to combat AMR, particularly in LMICs where lack of laboratory capacity prevents routine patient-level antimicrobial susceptibility testing 5 . Te lack of surveillance data contributes to a pragmatic but broad-spectrum empiric treatment approach in hospitals with limited laboratory facilities 2,6 , generally resulting in overtreatment and acting as a selective pressure for AMR 7 . To date, surveillance capacity-building programmes have generally focused on implementing blood culture surveillance due to the high mortality of bloodstream infections (BSIs); however, blood cultures are a OPEN 1 Nufeld Department of Clinical Medicine, University of Oxford, Oxford, UK. 2 National Institute for Health Research Health Protection Research Unit, Oxford, UK. 3 London School of Hygiene and Tropical Medicine, London, UK. 4 Oxford University Hospitals NHS Foundation Trust, Oxford, UK. 5 University of Cambridge, Cambridge, UK. 6 Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos. 7 Centre for Tropical Medicine & Global Health, Nufeld Department of Medicine, University of Oxford, Oxford, UK. 8 Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia. 9 Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand. 10 Big Data Institute, University of Oxford, Oxford, UK. 11 Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. 12 Microbiology Research Level 7, John Radclife Hospital, Headley Way, Oxford OX3 9DU, UK. * email: karina-doris.vihta@eng.ox.ac.uk