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Water supply and air-conditioner cooling towers (ACCT) are potential sources of infection in people. During outbreaks, traditional typing methods cannot sufficiently segregate strains to reliably trace back transmissions to these artificial water systems. Moreover, because multiple strains may be present within these systems, methods to adequately distinguish strains are needed. Whole genome sequencing (WGS) and core genome multilocus sequence typing (cgMLST), with their higher resolution are helpful in this respect. In summer 2017, the health administration of the city of Basel detected an increase of infections compared with previous months, signalling an outbreak.


We aimed to identify strains populating suspected environmental sources of the outbreak, and to assess the relations between these strains and clinical outbreak strains.


An epidemiological and WGS-based microbiological investigation was performed, involving isolates from the local water supply and two ACCTs (n = 60), clinical outbreak and non-outbreak related isolates from 2017 (n = 8) and historic isolates from 2003–2016 (n = 26).


In both ACCTs, multiple strains were found. Phylogenetic analysis of the ACCT isolates showed a diversity of a few hundred allelic differences in cgMLST. Furthermore, two isolates from one ACCT showed no allelic differences to three clinical isolates from 2017. Five clinical isolates collected in the Basel area in the last decade were also identical in cgMLST to recent isolates from the two ACCTs.


Current outbreak-related and historic isolates were linked to ACCTs, which form a complex environmental habitat where strains are conserved over years.


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