Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations

Eleonora Cella,Alessia Conti,Raffaele Antonelli Incalzi,Taj Azarian,Marta Fogolari,Massimo Ciccozzi,Mattia Prosperi,Francesca Antonelli,Alessandra Lo Presti,Marina De Cesaris,Michele Equestre,Marco Salemi,Silvia Spoto,Silvia Angeletti,Roberto Coppola,Giordano Dicuonzo

doi:10.1038/s41598-017-03581-4

Abstract

Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-drug resistant nosocomial pathogens. Between January 2012 and February 2013, twenty-one multi-drug resistant K. pneumoniae strains, were collected from patients hospitalized among different wards of the University Hospital Campus Bio-Medico. Epidemiological contact tracing of patients and Bayesian phylogenetic analysis of bacterial WGS data were used to investigate the evolution and spatial dispersion of K. pneumoniae in support of hospital infection control. The epidemic curve of incident K. pneumoniae cases showed a bimodal distribution of cases with two peaks separated by 46 days between November 2012 and January 2013. The time-scaled phylogeny suggested that K. pneumoniae strains isolated during the study period may have been introduced into the hospital setting as early as 2007. Moreover, the phylogeny showed two different epidemic introductions in 2008 and 2009. Bayesian genomic epidemiology is a powerful tool that promises to improve the surveillance and control of multi-drug resistant pathogens in an effort to develop effective infection prevention in healthcare settings or constant strains reintroduction.

Highlights

Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem
Analyses of bacterical whole genome sequencing (WGS) data has been applied to methicillin resistant S. aureus (MRSA) nosocomial infections demonstrating improved discriminatory power compared to other typing techniques, such as Multi-Locus Sequence Typing (MLST), even in this genetically homogenous group[8, 9]
The epidemic curve based on the number of isolates collected during the study period (Fig. 1b) showed two discrete consecutive periods of infections (November 2012 and January 2013) separated by 46 days

Summary

Introduction

Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. Carbapenems resistance in Klebsiella pneumoniae strains, often results from the presence of plasmid-encoded K. pneumoniae carbapenemase (KPC)[2,3,4], is one of the leading causes of hospital-acquired infections (HAIs), characterized by high rate of morbidity and mortality[3, 4] Despite this emerging health threat, little is known about the genetic diversity of K. pneumoniae strains circulating in hospital settings. Whole genome sequencing was used to study a hospital outbreak of multidrug-resistant Acinetobacter baumannii in England combining WGS information with classical epidemiological data By these means, the transmission events were reconstructed and adequate measure for hospital infection control improved[6]. Roch et al performed a prospective study applying WGS to all bacterial isolates obtained from a tertiary care hospital’s intensive care units and demonstrated that the genomic surveillance of clinical isolates provides a useful tool to highlight important differences among bacterial strains encouraging the introduction of microbial genome sequencing into routine clinical care[10]

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Results

Conclusion