An unusual genetic switch controls Mycobacterium avium pathogenesis, antibiotic resistance and colony morphology

Nilsson, H. J.; Netter, Z.; Tuncel, M.; Garelis, N. E.; Siddiqui, N.; Semaan, M.; McCall, R. M.; Dangerfield, K.; Cox, E. K.; Britt, L.; Voorhies, M.; Roberts, A. W.; Mitchell, G.; Cangelosi, G. A.; Jacobs, W. R.; Sil, A.; Budzik, J. M.; Cox, J. S.

doi:10.1101/2025.07.28.667291

bioRxiv · 10.1101/2025.07.28.667291

An unusual genetic switch controls Mycobacterium avium pathogenesis, antibiotic resistance and colony morphology

Nilsson, H. J.·Netter, Z.·Tuncel, M.·Garelis, N. E.·Siddiqui, N.·Semaan, M.·McCall, R. M.·Dangerfield, K.·Cox, E. K.·Britt, L.·Voorhies, M.·Roberts, A. W.·Mitchell, G.·Cangelosi, G. A.·Jacobs, W. R.·Sil, A.·Budzik, J. M.·Cox, J. S.

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Abstract

Mycobacterium avium subspecies hominissuis (Mah) is an emerging environmental pathogen highly adapted to a wide range of niches, from treated water systems to mammalian tissues. On solid media, Mah forms two distinct colony morphologies, smooth transparent (SmT) and smooth opaque (SmO). These colony morphologies are representative of broader differential phenotypic states in which SmT cells are virulent and have high resistance to antibiotics while SmO cells are avirulent, antibiotic-sensitive and grow faster than SmT cells in culture. Importantly, Mah interconverts between these two morphotypes but the mechanism of SmT-SmO switching is unknown. Here we show that SmT-SmO switching is governed by a reversible transposition event that regulates expression of a periplasmic lipoprotein, Erp (extracellular repetitive protein). We found that transposition of IS1245, an endogenous insertion sequence, into the erp gene correlated with the SmT-SmO transition, and its precise removal coincided with the switch back to SmT. Genetic analyses showed that erp is required for maintenance of the SmT state and sufficient to drive the switch from SmO to SmT. We also identified a mutation in a periplasmic protease, MarP, that locks Mah in the SmO state and blocks erp-mediated switching to SmT. Our results indicate that Erp and MarP function in a signal transduction pathway that regulates a broad transcriptional response to periplasmic stress. Moreover, identification of components that control Mah colony morphology switching has revealed a potential new strategy for combating the inherent antibiotic resistance of Mycobacterium avium infections.

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Nilsson, H. J., Netter, Z., Tuncel, M., Garelis, N. E., Siddiqui, N., Semaan, M., McCall, R. M., Dangerfield, K., Cox, E. K., Britt, L., Voorhies, M., Roberts, A. W., Mitchell, G., Cangelosi, G. A., Jacobs, W. R., Sil, A., Budzik, J. M., Cox, J. S.. 2025-07-28. An unusual genetic switch controls Mycobacterium avium pathogenesis, antibiotic resistance and colony morphology. https://doi.org/10.1101/2025.07.28.667291

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