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Summary Background Enterobacter cloacae complex contains nosocomial pathogens responsible for infection outbreaks. Identification at the species level within the E cloacae complex remains difficult. Using whole genome sequencing, our aim was to decipher the transmission routes that led to the death of six of seven neonates who had bacteraemia caused by E cloacae complex isolates in a neonatal intensive care unit (NICU) over a 13 month period. Methods In this cohort study, E cloacae complex isolates were taken from 186 newborns in an NICU: 14 were clinical samples (eg, blood cultures), 728 rectal swab samples, and 38 environmental samples (20 from siphons, 18 from incubators, and one from a mattress). The samples were analysed to decipher the possible role of manual cross transmission or environmental source in an outbreak of fatal septic shocks related to E cloacae complex bacteraemia. After the replacement of the incubators suspected to be the reservoir of some outbreak-related isolates on Feb 1, 2018, E cloacae complex strains were screened again for 10 months (503 rectal swab samples from 163 newborns). The 71 E cloacae complex isolates recovered from screening, clinical, and environmental samples across both study periods were compared by whole genome sequencing. The pathogenicity of E cloacae complex isolates responsible for fatal septic shocks was assessed using a Galleria mellonella in-vivo model. Findings From Dec 9, 2016, to Jan 31, 2018, 249 (34%) of 728 rectal swab samples were positive for E cloacae complex, with 66 (35%) of 186 newborns colonised. E cloacae complex were also recovered from four (20%) of 20 siphons and 11 (61%) of 18 incubators. During this period, whole genome sequencing identified that the isolates responsible for the six fatal septic shocks were all Enterobacter bugandensis. A G mellonella infection model showed a higher virulence of E bugandensis. Genomic analysis highlighted the role of incubators as a long-term reservoir and source of cross contamination, leading to their replacement on Feb 1, 2018. Following incubator replacement, a 10-month follow-up investigation identified a physiological gut colonisation with polyclonal E cloacae complex in 52 (34%) of 163 neonates within a median of 9 days (5–14), but no E cloacae complex-related septic shocks. Interpretation Despite around 30% of neonates being physiologically colonised with E cloacae complex, fatal sepsis was systematically linked with bacteraemia caused by E bugandensis. Our findings highlight the need for accurate identification methods to detect the hypervirulent species within the E cloacae complex recovered in neonates. Funding Assistance Publique–Hopitaux de Paris.

Infections caused by extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) are constantly rising worldwide and are often reported as causative agent of outbreaks in intensive care units (ICUs). During the first wave of the COVID-19 pandemic, bacterial cross-transmission was thought unlikely to occur due to the reinforcement of hygiene measures and prevention control. However, we report here an ESBL-producing K. pneumoniae (ST394) isolate responsible for a nosocomial outbreak in an ICU dedicated to COVID-19 patients.

The FecalSwab® displays high performances for stool culture, but it was not assessed for carbapenemase-producing Enterobacterales (CPE) screening. We assess the performances of the Xpert Carba-R v2® with the FecalSwab®. Using a collection of 12 CPE strains, the limit of detection was assessed at 158 CFU/swab [interquartile range 93-589]. In 2019, 1540 swabs were included by 4 hospital laboratories, of which 39 (2.5%) yield an invalid result. Among the 1501 valid, 87 (5.8%) were positives by culture and PCR and 25 (1.7%) were discrepant: 7 PCR-negative culture-positive, and 18 PCR-positive culture-negative. Two PCR-positive culture-negative results involved non-Enterobacterales strains: a KPC-producing Acinetobacter baumannii and a KPC-producing Aeromonas spp. The overall percent agreement was 98.3% and the Kappa value was 0.88. FecalSwab® is an accurate sampling device for CPE screening. It allows performing all eXDR screening using a single swab, simplifying the sample collection, and improving the patient comfort. Regarding discrepant, we suggest combining a CPE screening by both culture and Xpert Carba-R v2® methods.

Early detection of patients colonised with carbapenemase-producing Enterobacteriaceae (CPE) is crucial for implementing proper infection control measures. Here we evaluated the biological performance of the Xpert® Carba-R v2 (Cepheid) in the daily workflow of a hygiene unit in a country with a low CPE prevalence. Patients repatriated from countries known for high CPE prevalence or contact patients of a known CPE carrier were targeted as being ‘high-risk patients’ for CPE carriage. Between September 2015 and March 2016, 241 ‘high-risk patients’ for CPE carriage were screened using the Xpert® Carba-R v2 and by plating on chromID® CARBA Smart medium (bioMerieux) with and without ertapenem-containing enrichment culture for 24 h. Of these patients, 81.7% were previously hospitalised abroad and 18.3% were contact patients of known CPE carriers. The Xpert® Carba-R v2 was able to detect 12 OXA-48-like, 1 KPC and 1 OXA-48-like/NDM carriers. For 2 of the 14 Xpert® Carba-R v2-positive samples, cultures remained negative even on two additional screenings (performed at Days 4 and 7). The Xpert® Carba-R v2 presents 100% sensitivity, 99.13% specificity, 85.71% positive predictive value and 100% negative predictive value. This study demonstrated that the Xpert® Carba-R v2 kit is well adapted for rapid screening of high-risk patients even in low prevalence regions (in

An OXA-181 producing Escherichia coli isolate that went recurrently undetected directly from rectal swab sample using Xpert® Carba-R, was successfully detected using ertapenem supplemented broth enrichment followed by culture-based method. Our data suggest that implementation of culture-based methods plus enrichment might be crucial for the efficient screening of patients considered to be at “high-risk” of colonization with carbapenemase producers and who are colonized at low level.