A genomic surveillance study identified several multidrug-resistant (MDR), high-risk clones of Escherichia coli and Klebsiella pneumoniae in Kenya, Uganda, and Jordan, researchers reported this week in Emerging Infectious Diseases.
Using an antimicrobial resistance (AMR) surveillance program run by the US Armed Forces Health Surveillance Division, researchers analyzed MDR E coli and K pneumoniae isolates collected from patients with healthcare-associated and community-acquired infections in the three countries from 2012 through 2022. A total of 758 E coli and 378 K pneumoniae isolates were tested for susceptibility to a panel of different classes of antibiotics and subjected to whole-genome sequencing (WGS).
Genetically diverse, high-risk MDR clones
Among the E coli isolates, there were 124 sequence types (STs), 20 of which were shared among the three countries. The dominant ST was ST131, which has emerged as a major cause of MDR urinary tract infections worldwide, followed by ST1193, a high-risk clone that recently diverged from ST131. Three potential zoonotic E coli STs (ST10, ST95, and ST117) that are common in food animals and have pathogenic potential were also identified. Among K pneumoniae isolates, there were 123 STs, with ST14, ST147, ST307, and ST258 identified as the most concerning.
WGS revealed acquired extended-spectrum beta-lactamase (ESBL) genes in 50.8% of E coli isolates and 68.8% of K pneumoniae isolates, while carbapenemase genes were detected in 1% of E coli and 12% of K pneumoniae isolates. Mobile colistin-resistance (MCR) genes were found in 2 E coli isolates (MCR-1.1) and 5 K pneumoniae isolates (MCR-8.1 and MCR-9).
"Overall, our study highlights the emergence and threat of genetically diverse high-risk MDR clones of 2 of the most critical groups of MDR bacteria causing severe infections with limited treatment options," the study authors wrote. "The abundance of global high-risk STs bearing resistance genes indicates their effective dissemination, the potential for intraspecies and interspecies transmission of resistance genes, and emergence of new high-risk clones."