Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase producing Enterobacterales

Graf, F. E.; Goodman, R. N.; Gallichan, S.; Forrest, S.; Picton-Barlow, E.; Fraser, A. J.; Phan, M.-D.; Mphasa, M.; Hubbard, A. T.; Musicha, P.; Schembri, M. A.; Roberts, A. P.; Edwards, T.; Lewis, J. M.; Feasey, N. A.

doi:10.1101/2023.11.16.567242

bioRxiv · 10.1101/2023.11.16.567242

Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase producing Enterobacterales

Graf, F. E.·Goodman, R. N.·Gallichan, S.·Forrest, S.·Picton-Barlow, E.·Fraser, A. J.·Phan, M.-D.·Mphasa, M.·Hubbard, A. T.·Musicha, P.·Schembri, M. A.·Roberts, A. P.·Edwards, T.·Lewis, J. M.·Feasey, N. A.

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Abstract

Infections with Enterobacterales (E) are increasingly difficult to treat due to antimicrobial resistance. After ceftriaxone replaced chloramphenicol (CHL) as empiric therapy for suspected sepsis in Malawi in 2004, ESBL-E rapidly emerged. Concurrently, resistance to CHL in Escherichia coli and Klebsiella spp. decreased, raising the possibility of CHL re-introduction. However, many phenotypically susceptible isolates still carry CHL acetyltransferase (CAT) genes. We used a combination of genomics, phenotypic susceptibility assays, experimental evolution and functional assays for CAT activity to understand the molecular mechanisms and stability of this re-emerging CHL susceptibility. Of 840 Malawian isolates, 31% had discordant CHL susceptibility genotype-phenotype, and we selected 42 isolates for in-depth analysis. Stable degradation of cat genes by insertion sequences led to re-emergence of CHL susceptibility. Our study suggests CHL could be reintroduced as reserve agent for critically ill patients with ESBL-E infections in Malawi and similar settings and highlights the ongoing challenges in inferring antimicrobial resistance from sequence data.

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Graf, F. E., Goodman, R. N., Gallichan, S., Forrest, S., Picton-Barlow, E., Fraser, A. J., Phan, M.-D., Mphasa, M., Hubbard, A. T., Musicha, P., Schembri, M. A., Roberts, A. P., Edwards, T., Lewis, J. M., Feasey, N. A.. 2023-11-16. Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase producing Enterobacterales. https://doi.org/10.1101/2023.11.16.567242

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