The Rhône-Loire metropolitan areas’ 2020/21 respiratory syncytial virus (RSV) epidemic was delayed following the implementation of non-pharmaceutical interventions (NPI), compared with previous seasons. Very severe lower respiratory tract infection incidence among infants ≤ 3 months decreased twofold, the proportion of cases among children aged > 3 months to 5 years increased, and cases among adults > 65 years were markedly reduced. NPI appeared to reduce the RSV burden among at-risk groups, and should be promoted to minimise impact of future RSV outbreaks.

The effect of natural sunlight on culturability and persistence of pathogenicity of Escherichia coli was examined in the field, i.e., in the Morlaix Estuary, France, using an enterotoxigenic strain of Escherichia coli H10407. Results showed that E. coli responds to the estuarine diurnal solar cycle by entering the viable but nonculturable state upon exposure to sunlight. That is, direct counts of viable cells remained stable without significant change, but E. coli cells remained fully culturable only when exposed to seawater in control chambers in the dark, i.e., without solar irradiation. The effect of sunlight on the pathogenicity of E. coli H10407 was studied, using both the rabbit intestinal loop assay and ganglioside-enzyme-linked immunosorbent assay (GM1-ELISA), a sensitive procedure for testing for production of enterotoxin. Results of the GM1-ELISA demonstrated that strains of E. coli, after exposure to sunlight and entering the viable but nonculturable state, as well as culturable E. coli, retained pathogenicity, i.e., produced enterotoxin. The GM1-ELISA is concluded to be more sensitive than the rabbit intestinal loop assay for analysis of enterotoxin in natural water samples.

first aligned the genome sequences of the 250 isolates against the NRCS-A reference genome CR01, resulting in a total of 22,621 single nucleotide polymorphisms (SNPs). To quantify recombination, we used ClonalFrameML 12 , which is specifically aimed at analysing whole-genome sequence data (see Supplementary Information). The results indicated that the impact of recombination (r) on the genome-wide substitution rate in S. capitis overall is almost equal to the impact of mutation (m), with r/m = 0.85. ClonalFrameML identified 190 recombination events in the global genealogy (Extended Data Fig. 1). The largest detected events (up to 26 kb) are probably products of horizontal gene transfer, some of which correspond to the insertion of pathogenicity islands. Clonal specialization and geographical dispersion of NRCS-A.The reconstructed maximum-likelihood tree (Fig. 1a) enabled us to draw a clear distinction between NRCS-A isolates that harbour the previously described specific NRCS-A pulsed-field gel electrophoresis pattern 8 (n = 197) and all the other strains found in basal positions (n = 53; hereafter 'basal'). These reconstructions revealed that this NRCS-A population is composed of at least three sublineages, which we named in chronological order of divergence on the basis of the observed branching order in the tree: 'proto-outbreak 1' (n = 18), 'proto-outbreak 2' (n = 17) and 'outbreak' (n = 162) (Fig. 1a,b). These three clades are supported both by bootstrap values greater than 95% and by the trimodal distribution of the

Key Points Question What are the long-term outcomes associated with dysbiosis of gut microbiota in very preterm newborns? Findings In this cohort study of 577 very preterm newborns across 24 neonatal intensive care units from a French nationwide cohort, gut microbiota at week 4 after birth showed 6 bacterial patterns that varied according to gestational age, perinatal characteristics, individual treatments, and neonatal intensive care unit strategies. Three clusters were associated with 2-year outcomes after adjustment for these confounders. Meaning Modifying strategies associated with alterations in microbiota, such as promoting enteral nutrition, reducing sedation use, promoting early extubation, or skin-to-skin practice, may be correlated with outcomes in preterm newborns.

Nosocomial late-onset sepsis represents a frequent cause of morbidity and mortality in preterm neonates. The Staphylococcus capitis clone NRCS-A has been previously described as an emerging cause of nosocomial bacteraemia in French neonatal intensive-care units (NICUs). In this study, we aimed to explore the possible unrecognized dissemination of this clone on a larger geographical scale. One hundred methicillin-resistant S. capitis strains isolated from neonates (n = 86) and adult patients (n = 14) between 2000 and 2013 in four different countries (France, Belgium, the UK, and Australia) were analysed with SmaI pulsed-field gel electrophoresis (PFGE) and dru typing. The vast majority of NICU strains showed the NRCS-A pulsotype and the dt11c type (96%). We then randomly selected 14 isolates (from neonates, n = 12, three per country; from adult patients, n = 2), considered to be a subset of representative isolates, and performed further molecular typing (SacII PFGE, SCCmec typing, and multilocus sequence typing-like analysis), confirming the clonality of the S. capitis strains isolated from neonates, despite their distant geographical origin. Whole genome single-nucleotide polymorphism-based phylogenetic analysis of five NICU isolates (from the different countries) attested to high genetic relatedness within the NRCS-A clone. Finally, all of the NRCS-A strains showed multidrug resistance (e.g. methicillin and aminoglycoside resistance, and decreased vancomycin susceptibility), with potential therapeutic implications for infected neonates. In conclusion, this study represents the first report of clonal dissemination of methicillin-resistant coagulase-negative Staphylococcus clone on a large geographical scale. Questions remain regarding the origin and means of international spread, and the reasons for this clone's apparent predilection for neonates.