Tissue specific diversification, virulence and immune response to Mycobacterium bovis BCG in a patient with an IFN-γ R1 deficiency

ABSTRACT

Summary: We characterized Mycobacterium bovis BCG isolates found in lung and brain samples from a previously vaccinated patient with IFNγR1 deficiency. The isolates collected displayed distinct genomic and phenotypic features consistent with host adaptation and associated changes in antibiotic susceptibility and virulence traits.

Background: We report a case of a patient with partial recessive IFNγR1 deficiency who developed disseminated BCG infection after neonatal vaccination (BCG-vaccine). Distinct M. bovis BCG-vaccine derived clinical strains were recovered from the patient’s lungs and brain.

Methods: BCG strains were phenotypically (growth, antibiotic susceptibility, lipid) and genetically (whole genome sequencing) characterized. Mycobacteria cell infection models were used to assess apoptosis, necrosis, cytokine release, autophagy, and JAK-STAT signaling.

Results: Clinical isolates BCG-brain and BCG-lung showed distinct Rv0667 rpoB mutations conferring high- and low-level rifampin resistance; the latter displayed clofazimine resistance through Rv0678 gene (MarR-like transcriptional regulator) mutations. BCG-brain and BCG-lung showed mutations in fadA2, fadE5, and mymA operon genes, respectively. Lipid profiles revealed reduced levels of PDIM in BCG-brain and BCG-lung and increased TAGs and Mycolic acid components in BCG-lung, compared to parent BCG-vaccine. In vitro infected cells showed that the BCG-lung induced a higher cytokine release, necrosis, and cell-associated bacterial load effect when compared to BCG-brain; conversely, both strains inhibited apoptosis and altered JAK-STAT signaling.

Conclusions: During a chronic-disseminated BCG infection, BCG strains can evolve independently at different sites likely due to particular microenvironment features leading to differential antibiotic resistance, virulence traits resulting in dissimilar responses in different host tissues.

KEYWORDS:

• Tuberculosis
• BCG
• antibiotic resistance
• immunodeficiency
• Mendelian susceptibility to mycobacterial diseases
• interferon-γ

Acknowledgments

We thank the patient and the patient’s family for their contributions to the study. We thank Lisa Sadzewicz, Luke J. Tallon and members of the Institute for Genome Sciences Genomics Resource Center for help with genome sequencing. This work was supported by the Intramural Research Program, NIH Clinical Center, US National Institutes of Health (NIH). The content of this article does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. government.

Disclosure statement

The authors declare no conflict of interest.

This work was partially presented as a poster at the American Society of Microbiology meeting in 2018.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

The Intramural Research Program of the NIH, the NIH Clinical Center, and the National Institute of Allergy and Infectious Diseases supported this research.