Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 Escherichia coli to Carbapenem Exposure

Shropshire, W. C.; Song, X.; Bremer, J.; Seo, S.; Rodriguez, S.; Anand, S. S.; Dinh, A. Q.; Bhatti, M. M.; Konovalova, A.; Arias, C. A.; Kalia, A.; Shamoo, Y.; Shelburne, S. A.

doi:10.1101/2024.07.31.606066

bioRxiv · 10.1101/2024.07.31.606066

Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 Escherichia coli to Carbapenem Exposure

Shropshire, W. C.·Song, X.·Bremer, J.·Seo, S.·Rodriguez, S.·Anand, S. S.·Dinh, A. Q.·Bhatti, M. M.·Konovalova, A.·Arias, C. A.·Kalia, A.·Shamoo, Y.·Shelburne, S. A.

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Abstract

BackgroundIt remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in their progression to becoming carbapenem resistant. MethodsCarbapenem mutation frequency was measured in multiple subclades of extended-spectrum {beta}-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. ResultsAll thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P-value <1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific associations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. ConclusionsESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2/H30Rx subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.

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Shropshire, W. C., Song, X., Bremer, J., Seo, S., Rodriguez, S., Anand, S. S., Dinh, A. Q., Bhatti, M. M., Konovalova, A., Arias, C. A., Kalia, A., Shamoo, Y., Shelburne, S. A.. 2024-07-31. Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 Escherichia coli to Carbapenem Exposure. https://doi.org/10.1101/2024.07.31.606066

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