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Diagnostics Research & Training in Zambia

Study to serotype Klebsiella pneumoniae and map markers of antimicrobial resistance in neonatal sepsis 

PI: Davidson Hamer, MD, Department of Global Health, Boston University School of Public Health, Boston, MA, USA


Matthew Bates, PhD, University of Lincoln/HerpeZ, Lincoln, UK

Franklyn Nkongho, PhD, University of Lincoln, U.K

John Tembo, PhD, University Teaching Hospital/HerpeZ, Lusaka, Zambia

Susan Coffin, MD, MPH, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

Goal:To characterize the serotypes and sequence diversity over time and across patients among Klebsiella pneumoniae isolates from bacteremic neonates hospitalized in a large neonatal intensive care unit (NICU) in Zambia.

Background:We performed a prospective cohort study, the Sepsis Prevention in Neonates in Zambia study (SPINZ), between 2015 to 2017 that enrolled 3,463 neonates who were admitted to the NICU at the largest public referral hospital, University Teaching Hospital, in Lusaka, Zambia. A full description of this cohort have been previously published (Mwananyanda et al... CID 2019) along with our previous aetiology study that informed on SPINZ (Kabwe et al... PIDJ 2016). All blood cultures were performed using the Bactec system and VITEK-2 was used for organism identification and antimicrobial susceptibility testing. Clinical isolates from the SPINZ study have been frozen in glycerol and maintained at -80°C in a monitored freezer within the UTH Clinical Microbiology Laboratory.

Enrolled neonates experienced 668 episodes of laboratory-confirmed bloodstream infections. K. pneumoniae was the most prevalent organism and was isolated from 438 cultures; E. coli was the third most commonly isolated organism (n = 16) with enterococci taking second place. Nearly all (98%) of the K. pneumoniae isolates were phenotypically identified as producing extended-spectrum beta-lactamases (ESBL); resistance to carbapenem antibiotics was rare. In contrast, 81% of the E. coliisolates were ESBL-producing.

Serotype analysis and molecular genetic characterization were not included in the original study plans due to budget constraints. Using institutional overheads, we have managed to collect some baseline data to help inform on proposals to support this work. Preliminary sequence analysis of 4 isolates performed in Dr. Matthew Bates’ laboratory at the University of Lincoln (Lincoln, UK) suggests that the isolates are all K. pneumoniae sequence type 307. An additional 270 samples have had DNA extracted and gel electrophoresis of these samples suggests high quality DNA has been recovered for sequencing. We are seeking funding to support the sequencing of all isolates in the SPINZ biobank, and would like to couple such analysis to ongoing capacity development towards sustainable molecular surveillance of infectious diseases in Zambia.

Specific objectives:

  • To characterize the (O and K types) serotypes of all K. pneumoniae bloodstream isolates from the SPINZ study
  • To sequence a biobank of 438 K. pneumoniaeisolates from neonates with suspected sepsis at UTH
    1. To define predominant sequence types
    2. To provide molecular data to inform the development of Klesbiella vaccines
    3. To define the prevalent markers of antibiotic resistance
    4. To identify molecular markers/virulence determinants associated with mortality


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