High-Risk International Clones of Carbapenem-Nonsusceptible Pseudomonas aeruginosa Endemic to Indonesian Intensive Care Units: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level

• Published in: mBio Vol. 10; no. 6
• Main Authors: Pelegrin, Andreu Coello, Saharman, Yulia Rosa, Griffon, Aurélien, Palmieri, Mattia, Mirande, Caroline, Karuniawati, Anis, Sedono, Rudyanto, Aditianingsih, Dita, Goessens, Wil H F, van Belkum, Alex, Verbrugh, Henri A, Klaassen, Corné H W, Severin, Juliëtte A
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 12.11.2019
• Subjects: Anti-Bacterial Agents - pharmacology; Carbapenems - pharmacology; Clinical Science and Epidemiology; Drug Resistance, Neoplasm; Humans; Indonesia; Indonesia - epidemiology; Infection Control; Intensive Care Units; microbial drug resistance; Microbial Sensitivity Tests; Pseudomonas aeruginosa; Pseudomonas aeruginosa - classification; Pseudomonas aeruginosa - drug effects; Pseudomonas aeruginosa - genetics; Pseudomonas Infections - epidemiology; Pseudomonas Infections - microbiology; Pseudomonas Infections - prevention & control; ROC Curve; single nucleotide polymorphism; Indonesia; Pseudomonas aeruginosa; microbial drug resistance; infection control; single nucleotide polymorphism; Indonesia; intensive care units
• ISSN: 2161-2129; 2150-7511; 2150-7511
• DOI: 10.1128/mBio.02384-19

Infection control effectiveness evaluations require detailed epidemiological and microbiological data. We analyzed the genomic profiles of carbapenem-nonsusceptible (CNPA) strains collected from two intensive care units (ICUs) in the national referral hospital in Jakarta, Indonesia, where a multifaceted infection control intervention was applied. We used clinical data combined with whole-genome sequencing (WGS) of systematically collected CNPA to infer the transmission dynamics of CNPA strains and to characterize their resistome. We found that the number of CNPA transmissions and acquisitions by patients was highly variable over time but that, overall, the rates were not significantly reduced by the intervention. Environmental sources were involved in these transmissions and acquisitions. Four high-risk international CNPA clones (ST235, ST823, ST357, and ST446) dominated, but the distribution of these clones changed significantly after the intervention was implemented. Using resistome analysis, carbapenem resistance was explained by the presence of various carbapenemase-encoding genes ( , , and ) and by mutations within the porin OprD. Our results reveal for the first time the dynamics of antimicrobial resistance (AMR) profiles in Indonesia and additionally show the utility of WGS in combination with clinical data to evaluate the impact of an infection control intervention. (This study has been registered at www.trialregister.nl under registration no. NTR5541). In low-to-middle-income countries such as Indonesia, work in intensive care units (ICUs) can be hampered by lack of resources. Conducting large epidemiological studies in such settings using genomic tools is rather challenging. Still, we were able to systematically study the transmissions of carbapenem-nonsusceptible strains of (CNPA) within and between ICUs, before and after an infection control intervention. Our data show the importance of the broad dissemination of the internationally recognized CNPA clones, the relevance of environmental reservoirs, and the mixed effects of the implemented intervention; it led to a profound change in the clonal make-up of CNPA, but it did not reduce the patients' risk of CNPA acquisitions. Thus, CNPA epidemiology in Indonesian ICUs is part of a global expansion of multiple CNPA clones that remains difficult to control by infection prevention measures.