# Transmission dynamics of Klebsiella pneumoniae in a neonatal intensive care unit in Zambia before and after an infection control bundle

## TL;DR

This study examines how Klebsiella pneumoniae spreads in a Zambian neonatal unit before and after infection control measures, showing that while some transmission is reduced, new strains continue to emerge.

## Contribution

The study uses whole genome sequencing to track K. pneumoniae transmission dynamics and the impact of an IPC bundle in a low-resource neonatal setting.

## Key findings

- Klebsiella pneumoniae ST307 was the most common strain, dominating infections during the baseline period.
- An IPC bundle reduced transmission but did not eliminate all strains, allowing some to re-emerge and new strains to establish clusters.
- Transmission clusters varied in onset timing, suggesting different contamination sources like reagents or the environment.

## Abstract

Klebsiella pneumoniae is a leading cause of neonatal sepsis in low- and middle-income countries, with antimicrobial resistance (AMR) significantly contributing to mortality. We used whole genome sequencing to explore the impact of an infection prevention and control (IPC) intervention on K. pneumoniae strains and transmission dynamics responsible for sepsis in a Zambian neonatal unit. Blood culture isolates were collected during the Sepsis Prevention in Neonates in Zambia (SPINZ) study, including a 7-month baseline period and 12 months following implementation of a low-cost IPC bundle. K. pneumoniae genomes associated with 411 neonatal infections were characterised, comprising 24 unique sequence types (STs) and dominated by ST307 (69.3%, n = 285). Nearly all isolates (99.0%) carried extended spectrum beta-lactamases, but few carried carbapenemases (2.7%). Most infections (95.6%) were associated with probable transmission clusters, ranging in size from 2–202 patients and spanning durations of 2–232 days. Most K. pneumoniae (n = 228, 70%) were isolated during the 7-month baseline period and formed six clusters, including one cluster of >200 neonates infected with ST307. Transmission of all strains was periodically suppressed by an IPC bundle; however not all strains were eliminated, and some were able to re-emerge later to re-establish infection and transmission, alongside newly introduced strains that formed additional transmission clusters. Some clusters were associated with rapid onset of disease (within 2 days of admission) and others with delayed onset, suggesting different sources of contamination (e.g., reagent vs environmental). These findings reinforce the need for sustained IPC efforts, and better understanding of environmental reservoirs of opportunistic pathogens in neonatal units to inform such efforts.