First detection and origin of multi-drug resistant Klebsiella pneumoniae ST15 harboring OXA-48 in South America

Abstract

Objectives: The emergence and spread of carbapenem resistant clones is of major concern for global health. This study aimed to characterize the first detected Klebsiella pneumoniae ST15 harboring the epi- demic carbapenemase OXA-48 in South America. Methods: During a routine colonization screening with carbapenem-resistant bacteria, one K. pneumoniae strain (CGHM01) was isolated from the urine of a hospitalized patient suffering from a neurodegenera- tive disease in Uruguay. We used long-read whole-genome sequencing and a phylogenomic approach to characterize the emergence of K. pneumoniae CGHM01. Results: K. pneumoniae CGHM01 is a multi-drug resistant strain carrying an IncL/M plasmid that encodes the carbapenemase gene bla OXA-48 within the Tn1999.2 transposon. Also, it carries an IncR plasmid har- boring a class I integron with an array of antibiotic resistance genes including the extended-spectrum beta-lactamase bla CTX-M-15 . Two copies of bla CTX-M-15 were also inserted in different positions of the chro- mosome. CGHM01 belongs to a ST15 sublineage that likely originated in continental Spain around 2012. Conclusions: The asymptomatic carriage of this strain in the urinary tract warns of difficulties for detec- tion and reporting of emerging carbapenem-resistant clones in new geographic areas where these are not endemic.