Prospective genomic and epidemiologic surveillance of Klebsiella pneumoniae in a tertiary NICU

Abstract Background Klebsiella pneumoniae complex (Kp) is a relevant neonatal pathogen colonizing preterm infants. While outbreak investigations often focus on multidrug-resistant strains, the epidemiology and genomic dynamics of wild-type Kp in nonoutbreak neonatal intensive care unit (NICU) settings remain elusive. Methods We conducted a 30-month (October 2021 to March 2024) cohort study with weekly active, unselective colonization surveillance of all NICU patients to identify risk factors for nosocomial Kp acquisition and drivers of transmission in a tertiary 21-bed NICU/intermediate care unit (IMC) in Germany. Results Among 936 patients, 8.7% carried Kp, of which 70.4% were nosocomial. Very low birth weight (VLBW; < 1500 g) was the only independent risk factor for nosocomial acquisition (adjusted odds ratio [aOR], 3.42; 95% CI, 1.29–9.32). Kp infections occurred in three Kp carriers (3.7%). Genomic analyses of at least the first isolate per patient (83 in total) revealed an oligoclonal population structure, with ten distinct sequence types (STs) underlying temporally overlapping clusters. Ten genomic clusters (median size, four patients) were identified, with markedly higher odds in VLBW infants (aOR, 8.76; 95% CI, 2.45–34.16). Nosocomial cluster-assigned cases had higher rates and longer durations of noninvasive ventilation and peripheral venous catheter use. Cluster prevalence showed climate-associated variation, with a six-feature extreme gradient boosting (XGBoost) model identifying temperature and humidity among the strongest predictors. Conclusions Patient- and climate-associated parameters are main drivers of nosocomial wild-type Kp acquisition and cluster occurrence. Comprehensive surveillance and risk-adapted infection prevention and control support sustainable Kp control in VLBW infants.