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Genomic analysis of a Mycobacterium intracellulare subsp. chimaera variant cluster in a German hospital

M Diricks(1,2,3) P Böhmer(4) J Kompenhans(5) J Dreesman(5) M Bach(5) C Wiesener(5) J Biniek(5) U Schlotthauer(6) D Hillemann(3) S Haller(7) W Haas(8) F Szabados(9) N Wetzstein(10) S Niemann(1,2,3) I Friesen(3)

1:Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, 23845, Germany; 2:German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Germany; 3:National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, 23845, Germany; 4:Bonifatius Hospital Lingen gGmbH, Wilhelmstr. 13 49808 Lingen, Germany; 5:Governmental Institute of Public Health of Lower Saxony, Roesebeckstr. 4-6; D - 30449 Hannover; Germany; 6:Institute of Medical Microbiology and Hygiene, Saarland University, 66424 Homburg/Saar, Germany; 7:Fachgebiet 37, Robert Koch-Institut, Seestr. 10, 13353 Berlin, Germany; 8:Fachgebiet 36, Robert Koch-Institut, Seestr. 10, 13353 Berlin, Germany; 9:Laborarztpraxis Osnabrück, Rostockerstrasse 5-7, 49124 Georgsmarienhütte, Germany; 10:Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, Frankfurt am Main, Germany

Between 2020 and 2023, lower respiratory tract samples from 63 patients staying in a hospital in West-Germany were tested positive for mycobacteria. The organisms were initially identified as Mycobacterium vulneris by 16S rRNA sequencing, and could not be differentiated at the species level by the routinely used GenoType Mycobacterium CM-v2.0 diagnostic test. Due to this unusual high number of cases an investigation with extensive environmental sampling was initiated. Water samples and swabs were collected in the hospital from bronchoscopes, disinfection equipment, drinking water fountains, showers and sinks for further investigation. Whole genome sequencing analysis identified all isolates as belonging to Mycobacterium intracellulare subsp. chimaera. Subsequent core genome multi-locus sequence typing (based on 3719 genes) showed that the 29 available patient isolates were closely related to each other (1-30 alleles difference; median distance: 9) and to an isolate from a water related source inside the hospital (min. 1 allele difference). When compared to 600 publicly available M. chimaera group 1 isolates, they constituted a distinct clade unrelated to the M. chimaera strains which caused the global cardiac surgery-related outbreak. However, this separate clade also included 6 closely related isolates from other sites in Germany (min. 3 alleles). The closest non-German isolate was obtained from the United Kingdom (23 alleles distance). After implementing prevention measures, no additional patient isolates were found positive with the clone. Altogether, this suggests the existence of a widespread clone but whether the patients are truly infected, colonized temporarily or samples are merely contaminated is still under investigation.

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