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An Emerging Clone, Klebsiellapneumoniae Carbapenemase 2-Producing K. pneumoniae Sequence Type 16, Associated With High Mortality Rates in a CC258-Endemic Setting.

  • Andrey, Diego O1, 2
  • Pereira Dantas, Priscila3
  • Martins, Willames B S1, 4
  • Marques De Carvalho, Fabíola5
  • Almeida, Luiz Gonzaga Paula5
  • Sands, Kirsty1
  • Portal, Edward1
  • Sauser, Julien6
  • Cayô, Rodrigo4
  • Nicolas, Marisa F5
  • Vasconcelos, Ana Tereza R5
  • Medeiros, Eduardo A3
  • Walsh, Timothy R1
  • Gales, Ana C4
  • 1 Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom. , (United Kingdom)
  • 2 Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland. , (Switzerland)
  • 3 Universidade Federal de São Paulo, Hospital Epidemiology Committee, Hospital São Paulo, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, São Paulo, Brazil. , (Brazil)
  • 4 Universidade Federal de São Paulo, Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina, São Paulo, Brazil. , (Brazil)
  • 5 National Laboratory for Scientific Computing, Petrópolis, Rio de Janeiro, Brazil. , (Brazil)
  • 6 Infection Control Program, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland. , (Switzerland)
Published Article
Clinical Infectious Diseases
Oxford University Press
Publication Date
Oct 23, 2020
DOI: 10.1093/cid/ciz1095
PMID: 31712802


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. 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. 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. 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. © The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America.

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