Epidemiology and Overtime Genomic Evolution of Klebsiella Pneumoniae and Enterobacter Cloacae Complex (ECC) in Stools of ICU's Patients

University Hospital, Caen20 enrolled

Overview

Infections are one of the major threats for inpatients, even more for patients hospitalized in intensive care units (ICUs). They are responsible for an important increase of morbidity and mortality rates as well as a burst of medical costs since approximatively 50% of ICU patients acquire an infection during their hospitalization and 60% of attributable deaths (Vincent et al. 2009). In ICUs, patients are commonly colonized or infected by a small contingent of multidrug-resistant (MDR) isolates gathered under the acronym "ESKAPE bugs" for Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. (Pendleton et al. 2013; Rice 2010; Reardon 2014). Moreover, it is clearly established now, that epidemiological characterization in K. pneumoniae and E. cloacae isolates seemed to be an major step due to the existence of potential hyper-virulent and/or multidrug resistant strains (Lam et al. 2018; Moradigaravand et al. 2016). The aim of this study is the investigation of the overtime clonal diversity evolution of Klebsiella pneumoniae (Kpn) and Enterobacter cloacae complex (ECC) strains in long-term hospitalized patients (more than 28 days of hospitalization). To assess that objective, we will undertake a longitudinal monocentric, prospective study, based on weekly stool's samples done in ICUs patients and sent to our laboratory for MDR bacteria screening during their stay in reanimation wards and also, if possible, in their downstream wards especially in neurosurgery.

Study Type

OBSERVATIONAL

Enrollment

Conditions

Longitudinal Genomic Stability Klebsiella Infections

Eligibility

Sex: ALLMin age: 18 Years

Medical Language ↔ Plain English

Inclusion Criteria: * Patient ≥18 years old. * Hospitalization in medical and / or surgical ICU of a duration greater than or equal to 28 days and the production of 4 rectal swabs. * Absence of hospitalization in the last 4 months before inclusion * French speaking patient * Patient affiliated to the social security system * Patient having received an informed opinion on the study and collection of the non-opposition to the latter * Person of trust or family member who has received an informed opinion on the study and the collection of non-opposition to the latter when the patient is judged as incapable of expressing his non-opposition. Exclusion Criteria: * Pregnant or lactating woman * Hospitalization within 4 months before inclusion * Patient whose hospital stay is \<28 days or rectal swabs less than 4 * Absence of Kpn or ECC in the first rectal sample taken * Patient under guardianship / curatorship * Patient deprived of liberty * Patient under judicial protection * Patient not affiliated to the social security system * Refusal to participate in the study requested by the patient or the designated confidential counselor or a designated family member.

Outcomes

Primary Outcomes

Diversity and evolution

The objective is to study the diversity and the evolutionary dynamics of Kpn and / or ECC populations in the same individual hospitalized over a long period (≥ 28 days and 4 swabs) in the intensive care unit and if possible in follow-up care. First, by analysis of the genomic sequences obtained for each isolated bacterial strain, a determination of the diversity of Kpn and / or ECC strains within the digestive microbiota of patients hospitalized for the long term will be conducted by analysis of the MLST obtained during the study period.

Time frame: 1 year

Secondary Outcomes

qPCR detection of Kpn

A more technical and timely analysis will be undertaken to determine the correspondence between real-time PCR and bacterial culture on enriched agar in order to allow the implementation of a simple, efficient diagnostic tool allowing for important information rendering in the patient management.