Moser, Aline I; Campos-Madueno, Edgar I; Perreten, Vincent; Endimiani, Andrea (2022). Genome stability during serial sub-culturing in hyperepidemic multidrug-resistant Klebsiella pneumoniae and Escherichia coli. Journal of global antimicrobial resistance, 31, pp. 152-161. Elsevier 10.1016/j.jgar.2022.08.014
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1-s2.0-S2213716522002041-main.pdf - Accepted Version Available under License Creative Commons: Attribution-Noncommercial-No Derivative Works (CC-BY-NC-ND). Download (1MB) | Preview |
BACKGROUND
Core-genome single-nucleotide variant (cgSNV) analysis represents a powerful tool for epidemiological investigations of multidrug-resistant (MDR) bacteria. However, cgSNV thresholds to confirm whether isolates are the same clone are not formally defined.
METHODS
We implemented hybrid whole-genome sequencing to study the genomic changes of 4 MDR isolates belonging to hyperepidemic sequence types (STs) during 20 propagation steps (T20) on MacConkey and CHROMID ESBL plates. The following strains were analyzed: K. pneumoniae AE-2247421 (OXA-48/NDM-1-producing, ST101), K. pneumoniae MCL-2017-2 (CTX-M-15-producing, ST307), E. coli Ec-042 (OXA-181-producing, ST410), and E. coli Ec-050 (NDM-5-producing, ST167). The genome assembly at T5 and T20 was compared to that at time point zero (T0) and to two reference genomes.
RESULTS
At T20, AE-2247421 lost the IncL blaOXA-48-carrying plasmid when grown on CHROMID ESBL plates, while a large fragment encompassing blaNDM-1 was lost from its IncC plasmid when grown on both plates. In contrast, no structural changes were noted for the other 3 strains. With regard to the cgSNVs, the following results were obtained at T5 and T20 (ranges considering the different agar plates and reference genomes): AE-2247421 (1-8 and 2-12 cgSNVs), MCL-2017-2 (both 1-2 cgSNVs), Ec-042 (both 0 cgSNVs), and Ec-050 (0-6 and 0-9 cgSNVs).
CONCLUSIONS
We showed that structural changes and accumulation of cgSNVs can occur in few propagation steps under laboratory conditions. These changes might also arise in the clinical context in a short time, especially under antibiotics treatment. This phenomenon should be carefully considered because it might affect the final interpretation of epidemiological genomic analyses.
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