Description of Bacterial RNA Transcripts Detected in Mycobacterium tuberculosis – Infected Cells from Peripheral Human Granulomas using Single Cell RNA Sequencing

Next-gen sequencing has facilitated studies of bacterial genomes and uncovered pathogen variants associated with clinically relevant phenotypes such as antibiotic resistance. However, these studies are primarily focused on bacteria cultured from patient tissues, and thus, viable but non-cultivable bacteria are not assessed. This yields an incomplete genetic state of bacteria during infection. Nevertheless, it is possible to capture bacterial transcripts in libraries designed to amplify eukaryotic mRNA. These reads are often considered spurious or nuisance and are rarely investigated. Here we demonstrate that Mycobacterium tuberculosis (Mtb) ribosomal RNA sequences are detected in host human cells obtained from peripheral lymph node aspirates from patients infected with Mtb. Fine needle aspirates from periferal lymphadenopathies were collected from concenting patients arriving at the Port Moresby General Hospital (POMGH) Tuberculosis Clinic, Papua New Guinea, processed to collect the single cells, and fixed and sterilized with MeOH before returning to the University of Utah for processing for single-cell RNA sequencing using the 10X Genomics system.