Immediately after birth, newborn babies experience rapid colonisation by microorganisms from their mothers and the surrounding environment 1. Diseases in childhood and later in life are potentially mediated through perturbation of the infant gut microbiota colonisations 2. However, the impact of modern clinical practices, such as caesarean section delivery and antibiotic usage, on the earliest stages of gut microbiota acquisition and development during the neonatal period (≤1 month) remains controversial 3,4. Here we report disrupted maternal transmission of Bacteroides strains and high-level colonisation by healthcare-associated opportunistic pathogens, including Enterococcus, Enterobacter and Klebsiella species, in babies delivered by caesarean section (C-section), and to a lesser extent, in those delivered vaginally with maternal antibiotic prophylaxis or not breastfed during the neonatal period. Applying longitudinal sampling and whole-genome shotgun metagenomic analysis on 1,679 gut microbiotas of 772 full term, UK-hospital born babies and mothers, we demonstrate that the mode of delivery is a significant factor impacting gut microbiota composition during the neonatal period that persists into infancy (1 month-1 year). Matched large-scale culturing and whole-genome sequencing (WGS) of over 800 bacterial strains cultured from these babies identified virulence factors and clinically relevant antimicrobial resistance (AMR) in opportunistic pathogens that may predispose to opportunistic infections. Our findings highlight the critical early roles of the local environment (i.e. mother and hospital) in establishing the gut microbiota in very early life, and identifies colonisation with AMR carrying, healthcare-associated opportunistic pathogens as a previously unappreciated risk factor.

The trials performed worldwide towards Non-Invasive Prenatal Diagnosis (NIPD) of Down syndrome (or Trisomy 21) have demonstrated the great commercial and medical potential of NIPD compared to the currently used invasive prenatal diagnostic procedures. Extensive investigation of methylation differences between the mother and the fetus has led to the identification of Differentially Methylated Regions (DMRs). In this study, we present a strategy using the Methylated DNA immunoprecipitation (MeDiP) methodology in combination with real-time qPCR to achieve fetal chromosome dosage assessment which can be performed non-invasively through the analysis of fetal-specific DMRs. We achieved non-invasive prenatal detection of trisomy 21 by determining the methylation ratio of normal and trisomy 21 cases for each tested fetal-specific DMR present in maternal peripheral blood, followed by further statistical analysis. The application of the above fetal-specific methylation ratio approach provided correct diagnosis of 14 trisomy 21 and 26 normal cases. Down Syndrome (or Trisomy 21) (OMIM190685) is considered to be the most frequent etiology of mental retardation with an incidence of 1 in 700 child births in all populations worldwide 1 . Prenatal genetic diagnosis of trisomy 21 is currently performed using conventional cytogenetic or DNA analyses, which require fetal genetic material to be obtained by amniocentesis, chorionic villus sampling or cordocentesis. However, the above procedures are invasive and are associated with a considerable risk of fetal loss 1 . Therefore, there is a need for the development of Non-Invasive Prenatal Diagnostic (NIPD) strategies.Correspondence should be addressed to P.C.P. (patsalis@cing.ac.cy). Author contributions: E.A.P. and E.T. have carried out the experiments. E.A.P. has written the manuscript. E.A.P. and A.K. performed the statistical analysis. E.T. and V.V. have collected the majority of the samples in this study. P.C.P. was the principal investigator and has supervised the project. All authors reviewed, critiqued and offered comments to the text.Competing financial interest: P.C.P. and E.A.P. declare conflict of interest as they have filed a U.S. provisional patent for the approach (Application No. 61/405,421 We have selected a subset of DMRs on chromosome 21 and we have applied the MeDiP methodology in combination with real-time qPCR in normal and trisomy 21 cases. To provide chromosome dosage information, the ffDNA has to be hypermethylated compared to the maternal DNA. This is essential to achieve fetal-specific methylation enrichment which is the key element in our study. We hypothesize that we would be able to discriminate normal from trisomy 21 cases by comparing the ratio values obtained from normal and trisomy 21 cases using fetal-specific methylated regions located on chromosome 21 (fetalspecific methylation ratio approach) ( Fig. 1). Furthermore, we hypothesize that a combination of DMRs and not a single DMR may be able to give an accurate NIPD of normal and trisomy 21...

BACKGROUND. Novel rapid diagnostics for active tuberculosis (TB) are required to overcome the time delays and inadequate sensitivity of current microbiological tests that are critically dependent on sampling the site of disease. Multiparametric blood transcriptomic signatures of TB have been described as potential diagnostic tests. We sought to identify the best transcript candidates as host biomarkers for active TB, extend the evaluation of their specificity by comparison with other infectious diseases, and to test their performance in both pulmonary and extrapulmonary TB.METHODS. Support vector machine learning, combined with feature selection, was applied to new and previously published blood transcriptional profiles in order to identify the minimal TB‑specific transcriptional signature shared by multiple patient cohorts including pulmonary and extrapulmonary TB, and individuals with and without HIV-1 coinfection.RESULTS. We identified and validated elevated blood basic leucine zipper transcription factor 2 (BATF2) transcript levels as a single sensitive biomarker that discriminated active pulmonary and extrapulmonary TB from healthy individuals, with receiver operating characteristic (ROC) area under the curve (AUC) scores of 0.93 to 0.99 in multiple cohorts of HIV-1–negative individuals, and 0.85 in HIV-1–infected individuals. In addition, we identified and validated a potentially novel 4-gene signature comprising CD177, haptoglobin, immunoglobin J chain, and galectin 10 that discriminated active pulmonary and extrapulmonary TB from other febrile infections, giving ROC AUCs of 0.94 to 1.CONCLUSIONS. Elevated blood BATF2 transcript levels provide a sensitive biomarker that discriminates active TB from healthy individuals, and a potentially novel 4-gene transcriptional signature differentiates between active TB and other infectious diseases in individuals presenting with fever.FUNDING. MRC, Wellcome Trust, Rosetrees Trust, British Lung Foundation, NIHR.