• Alexandra Sofia Simões, Tiago Touret, Nuno Alexandre Faria, Susana Peres Ladeiro, João Costa, Soraia Bispo, Mónica Serrano, Carlos Palos, Maria Miragaia, Ricardo Bastos Leite, and Raquel Sá-Leão.
• Laboratory of Molecular Microbiology of Human Pathogens. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras. Portugal.
• Acta Medica Port. 2022 Jan 3; 35 (1): 36-41.

IntroductionHealthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the investigation of a CRKP outbreak based on WGS, with the aim of determining, in the minimum possible time, genetic relatedness between CRKP clinical and environmental isolates.Material And MethodsTen CRKP clinical isolates routinely obtained in the hospital laboratory were used. Forty environmental samples - from sinks and sink drains of ward rooms - were collected. Environmental samples were plated on selective media and presumptive CRKP colonies were isolated. Total DNA was extracted from all putative CRKP isolates and sequenced. Clonal relatedness was determined by multi-locus sequence typing and core genome single nucleotide polymorphism analysis; the presence of carbapenemase genes was evaluated.ResultsClinical isolates were characterized in 48 hours: eight strains were confirmed as CRKP, of which six were of ST13 and carried blaKPC-3. Environmental samples results were obtained in six days: eight CRKP were isolated from which five were of ST13 and carried blaKPC-3. Clinical and environmental ST13 isolates were highly related: ten (of 11) isolates differed from each other in < 0.001% of 2 172 367 core nucleotides.DiscussionWGS can be used as a high-resolution effective tool to investigate healthcare associated infections and track routes of dissemination in real-time.ConclusionIn Portugal, routine use of WGS to improve infection control could thrive through collaborative initiatives between hospitals and research institutes.

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