Search

This study aimed to develop a phage-based approach against Klebsiella pneumoniae sequence type (ST16). Phages were investigated using sewage samples from Brazil, Bangladesh, Saudi Arabia, Thailand and the United Kingdom. After isolation, the bacteriophages were submitted to microbiological, structural and genomic characterisation. The best phages were selected to integrate a phage-cocktail for potential use in humans. In vitro and in vivo experiments were performed to demonstrate the efficiency of this approach using a collection of 56 clinical strains of K. pneumoniae ST16 with distinct genetic backgrounds. Anti-biofilm activity, synergism with meropenem and activity in human body fluids were also evaluated. Fourteen lytic phages were isolated, belonging to Autographiviridae, Ackermannviridae, Demerecviridae, Drexlerviridae, and Myoviridae families. The viruses demonstrated good activity against our collection of K. pneumoniae ST16 at a different range of temperatures but also against other important Klebsiella clones such as ST11, ST15, and ST258. The cocktail Katrice-16 was highly active in vitro against K. pneumoniae ST16 collection consisting of isolates from several disparate countries. It demonstrated good in vivo activity in the Galleria mellonella model, anti-biofilm and synergic activity with meropenem. In addition, we also showed the Katrice-16 activity in human body fluids. Our results reinforce how effective bacteriophages can be, supporting their capacity for human clinical use to combat prevalent antimicrobial resistance bacterial clones.

Background Carbapenemase-producing Klebsiella pneumoniae has become a global priority, not least in low- and middle-income countries. Here, we report the emergence and clinical impact of a novel Klebsiella pneumoniae carbapenemase–producing K. pneumoniae (KPC-KP) sequence type (ST) 16 clone in a clonal complex (CC) 258–endemic setting. Methods In a teaching Brazilian hospital, a retrospective cohort of adult KPC-KP bloodstream infection (BSI) cases (January 2014 to December 2016) was established to study the molecular epidemiology and its impact on outcome (30-day all-cause mortality). KPC-KP isolates underwent multilocus sequence typing. Survival analysis between ST/CC groups and risk factors for fatal outcome (logistic regression) were evaluated. Representative isolates underwent whole-genome sequencing and had their virulence tested in a Galleria larvae model. Results One hundred sixty-five unique KPC-KP BSI cases were identified. CC258 was predominant (66%), followed by ST16 (12%). The overall 30-day mortality rate was 60%; in contrast, 95% of ST16 cases were fatal. Patients’ severity scores were high and baseline clinical variables were not statistically different across STs. In multivariate analysis, ST16 (odds ratio [OR], 21.4; 95% confidence interval [CI], 2.3–202.8; P = .008) and septic shock (OR, 11.9; 95% CI, 4.2–34.1; P < .001) were independent risk factors for fatal outcome. The ST16 clone carried up to 14 resistance genes, including blaKPC-2 in an IncFIBpQIL plasmid, KL51 capsule, and yersiniabactin virulence determinants. The ST16 clone was highly pathogenic in the larvae model. Conclusions Mortality rates were high in this KPC-KP BSI cohort, where CC258 is endemic. An emerging ST16 clone was associated with high mortality. Our results suggest that even in endemic settings, highly virulent clones can rapidly emerge demanding constant monitoring., An emerging clone, Klebsiella pneumoniae carbapenemase 2–producing K. pneumoniae ST16, associated with high mortality rates in a CC258 endemic setting, was identified. This clone carried the KL51 capsule and displayed higher virulence in a Galleria larvae pathogenicity model than CC258 clones.