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Serratia sp. dominates the lung microbiome of patients with tuberculosis and non-tuberculous mycobacterial lung diseases

M Belheouane(1) B Kalsdorf(1) S Niemann(1,2) K I Gaede(1,3,4) C Lange(1,2,5,7) J Heyckendorf(1,6) M Merker(1)

1:Research Center Borstel, Borstel; 2:German Center for Infection Research (DZIF), Partner site Hamburg, Lübeck, Borstel, Riems, Borstel, Germany; 3:German Centre for Lung Research (DZL), Airway Research Centre North (ARCN), 22927 Großhansdorf, Germany; 4:PopGen 2.0 Biobanking Network (P2N), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; 5:Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany; 6:Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany; 7:Baylor College of Medicine and Texas Children´s Hospital, Global TB Program, Houston, TX, USA

Pathogenic mycobacteria, such as the Mycobacterium tuberculosis complex (Mtbc), and few non-tuberculous mycobacteria (NTMs) can cause severe chronic pulmonary infections. However, not all infected patients develop active disease. Yet, it is unclear whether certain key taxa in the lung microbiome play a role in the pathogenesis of tuberculosis (TB) and NTM lung disease (LD).

We employed 16S rRNA amplicon sequencing (V3-V4) to characterize the baseline microbiome in bronchoalveolar lavage fluid (BALF) from patients diagnosed with TB (n=23), NTM-LD (n=19), or non-infectious inflammatory disease (n=4) prior to the initiation of therapy. The analysis included the depletion of human cells, removal of extracellular DNA, implementation of a decontamination strategy, and exploratory whole-metagenome sequencing (WMS) of selected specimens.

The genera Serratia and unclassified Yersiniaceae dominated the lung microbiome of all patients with a mean relative abundance of >15% and >70%, respectively. However, at the sub-genus level, as determined by amplicon sequence variants (ASVs), TB-patients exhibited increased community diversity, and TB specific ASV_7 (unclassified Yersiniaceae), and ASV_21 (Serratia) signatures. Exploratory analysis by WMS and ASV similarity analysis suggested the presence of Serratia liquefaciens, Serratia grimesii, Serratia myotis and/or Serratia quinivorans in both TB and NTM-LD patients. Overall, presence/absence of certain Serratia ASVs was significantly associated with disease state.

The lung microbiome of TB-patients harbors a distinct, and heterogenous microbiome structure with specific occurrences of certain Serratia traits. Serratia sp. plays a pivotal role in our understanding of microbial interactions in the lung microbiome of patients infected with Mtbc.

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