4.6 Article

Long-Read Whole Genome Sequencing Elucidates the Mechanisms of Amikacin Resistance in Multidrug-Resistant Klebsiella pneumoniae Isolates Obtained from COVID-19 Patients

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ANTIBIOTICS-BASEL
卷 11, 期 10, 页码 -

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MDPI
DOI: 10.3390/antibiotics11101364

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antimicrobial resistance; Klebsiella pneumoniae; COVID-19; plasmids; multidrug resistance; genomic epidemiology; whole genome sequencing

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Klebsiella pneumoniae is a major cause of healthcare-associated infections globally, and its antibiotic resistance has increased in recent years, especially during the COVID-19 pandemic. Whole genome sequencing is a promising approach to understanding the mechanisms of resistance, particularly in relation to mobile genetic elements like plasmids. This study sequenced three carbapenem-resistant K. pneumoniae isolates from COVID-19 patients, identifying a small plasmid carrying a resistance gene. These findings contribute to our understanding of antibiotic resistance mechanisms in this important pathogen and highlight the importance of ongoing genomic epidemiology surveillance of clinical isolates.
Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile bacterium, which represents a global challenge to public health as one of the major causes of healthcare-associated infections worldwide. In the recent decade, the World Health Organization (WHO) noticed a critically increasing rate of carbapenem-resistant K. pneumoniae occurrence in hospitals. The situation with extended-spectrum beta-lactamase (ESBL) producing bacteria further worsened during the COVID-19 pandemic, due to an increasing number of patients in intensive care units (ICU) and extensive, while often inappropriate, use of antibiotics including carbapenems. In order to elucidate the ways and mechanisms of antibiotic resistance spreading within the K. pneumoniae population, whole genome sequencing (WGS) seems to be a promising approach, and long-read sequencing is especially useful for the investigation of mobile genetic elements carrying antibiotic resistance genes, such as plasmids. We have performed short- and long read sequencing of three carbapenem-resistant K. pneumoniae isolates obtained from COVID-19 patients in a dedicated ICU of a multipurpose medical center, which belonged to the same clone according to cgMLST analysis, in order to understand the differences in their resistance profiles. We have revealed the presence of a small plasmid carrying aph(3 ')-VIa gene providing resistance to amikacin in one of these isolates, which corresponded perfectly to its phenotypic resistance profile. We believe that the results obtained will facilitate further elucidating of antibiotic resistance mechanisms for this important pathogen, and highlight the need for continuous genomic epidemiology surveillance of clinical K. pneumoniae isolates.

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