Prolonged survival of a patient with active MDR-TB HIV co-morbidity: insights from a Mycobacterium tuberculosis strain with a unique genomic deletion

Abstract

Coinfection of HIV and multidrug-resistant tuberculosis (MDR-TB) presents significant challenges in terms of the treatment and prognosis of tuberculosis, leading to complexities in managing the disease and impacting the overall outcome for TB patients. This study presents a remarkable case of a patient with MDR-TB and HIV coinfection who survived for over 8 years, despite poor treatment adherence and comorbidities. Whole genome sequencing (WGS) of the infecting Mycobacterium tuberculosis (Mtb) strain revealed a unique genomic deletion, spanning 18 genes, including key genes involved in hypoxia response, intracellular survival, immunodominant antigens, and dormancy. This deletion, that we have called "Del-X," potentially exerts a profound influence on the bacterial physiology and its virulence. Only few similar deletions were detected in other non-related Mtb genomes worldwide. In vivo evolution analysis identified drug resistance and metabolic adaptation mutations and their temporal dynamics during the patient's treatment course.

Keywords: HspX; Mycobacterium tuberculosis (MTB); acquired immunodeficiency syndrome (AIDS); dormancy; human immunodeficiency virus (HIV); in vivo evolution; multidrug-resistant tuberculosis (MDR-TB); whole genome sequencing (WGS).

Figure 1

Timeline medical history of Mr. X. Colored dots represent susceptibility to antibiotics of the isolates. Yellow rectangles show the duration of antimicrobial treatment with a specific antibiotic. The ticks on the right side indicate the sequenced samples.

Figure 2

Del-X genes and coverage. On the top: a genomic map of the Del-X region according to the Mtb H37Rv reference genome. Genes in red are immunogenic. Symbols represent gene functions of interest. On the bottom: coverage of the Del-X region with short Illumina reads of sample “Mr.X 10–10”; combined coverage of all Nanopore long reads from Mr. X’s samples except for “Mr.X 02–19”; coverage of the isolate that is most closely related to Mr. X’s samples, according to Pathogen Detection. Dashed lines represent deletion borders, and left labels on ticks show coverage depth. BWA-MEM (21) was used to map short reads, and minimap2 v2.24-r1122 (22) was used to map long reads.

Figure 3

Minimum spanning tree of Mr. X isolates and other closely related genomes: Minimum spanning tree of 11 Mr. X’s samples and 13 closest samples from the Pathogen detection cluster PDS000010075.9. Numbers on branches represent the distance between nodes in SNPs, while nodes present a distance of zero SNPs. Nodes are colored according to their countries of origin. For visual purposes, the SAMN23441947-SAMEA1403736 branch has been shortened.

Figure 4

Deletions overlapping Del-X in other Mtb genomes: On the top: a genomic map of the Del-X region according to the H37Rv reference genome. Genes in red are immunogenic. Symbols represent gene functions of interest. On the bottom: Samples from the NCBI RefSeq containing a genomic deletion of at least 5 kb that overlaps the Del-X region. The deletions are shown as orange rectangles. Ticks on the right display country of origin and lineage. The left ticks indicate the BioSample accession number, and the asterisk denotes that the deletion was confirmed using the sequencing data from the SRA database. Bars to the left of BioSample IDs indicate identical deletions. Pathogen detection was used to find the number of SNP between samples with identical deletions. The turquoise bar shows the parent–child pair with one SNP difference. The samples marked with the red bar have zero distance between them. The brown bar shows two samples with 16 SNPs difference.

Figure 5

In vivo evolution: Genes determined to undergo non-synonymous mutations during the infection of Mr. The left column includes genes determined as adaptive in Mtb by Gatt and Margalit (15) and the right column includes additional genes. Functional categories of the are denoted next to the table. Genes undergoing mutations in mechanisms predicted to lead to loss of function are marked in red, and genes undergoing other non-synonymous mutations are marked in gray.