Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

Abstract

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

Maternal Microbiota, Early Life Colonization and Breast Milk Drive Immune Development in the Newborn

“…Empirical antibiotic treatments include generally broadspectrum antibiotics, including Vancomycin and thus, the increasing prevalence of antimicrobial-resistant pathogens, such as the multidrug-resistant Staphylococcus capitis clone (NRCS-A) is alarming. Not only because NRCS-A is exceptionally disseminating in NICUs, but also due to its probable relevance in LOS pathogenesis (129,130). Approaches, such as the MinION seq platform, aim to rapidly (in less than 5 h) identify the pathogenic species and their antimicrobial-resistant genes to reduce broad-spectrum antibiotic treatment early in life and specifically target LOS in the newborn patient (131).…”

Influence of innate immune activation on endocrine and metabolic pathways in infancy

“…Widespread and prolonged use of antibiotic administration, including the use of antibiotic regimens in suspected but not confirmed cases of neonatal sepsis, is associated with the emergence of antibiotic-resistant bacteria, which is detrimental for treatment success of neonatal sepsis (18,45). For example, a multidrug-resistant Staphylococcus captitis clone has recently emerged as a major pathogen among infants in the NICU (46). These worrisome developments call for an urgent improvement in global standards for antibiotic treatment to prevent the emergence of other multidrug-resistant clones and highlight the importance of antibiotic stewardship programs.…”

Potential role of Mercury pollutants in the success of Methicillin-ResistantStaphylococcus aureusUSA300 in Latin America

“…The THD method uses pairwise genetic distances to estimate the epidemic success of each isolate in a collection, allowing comparisons of success based on various isolate characteristics. THD approaches have been successfully applied to investigate drivers of epidemic success in bacterial pathogens including Staphylococci (17,(21)(22)(23). Applied to 250 genomes of ST8 (combining those previously analyzed by (20) completed by 21 USA300-LV from our collection), the method revealed several important features: (i) the acquisition of the Panton-Valentine leucocidin gene by the ancestral ST8 clearly boosted the epidemic success of the lineage (Fig.…”