Background SABATO (Staphylococcus aureus bacteremia antibiotic treatment options) is a randomized, parallel-group, clinical non-inferiority trial designed to examine the efficacy and safety of early oral switch therapy in low-risk Staphylococcus aureus infection. The original trial protocol was published in Trials (accessible at 10.1186/s13063-015-0973-x). Here we describe final amendments to the study protocol and discuss the underlying rationale. Methods/design Three major changes were introduced into the study protocol: (1) the inclusion and exclusion criteria were refined so that patients with certain comorbidities (end-stage renal disease, severe liver disease) and uninfected foreign bodies (orthopedic prosthesis, pacemaker, implanted cardiac cardioverter-defibrillator) became eligible for enrollment under certain conditions; (2) the target sample size was decreased by choosing a conventional non-inferiority margin of 10% and converting the interim analysis (215 patients) into the final analysis; and (3) an additional follow-up visit after 30 days was introduced to allow for a closer follow-up of patients. Conclusion Changes to the study protocol were introduced to improve the enrollment and follow-up of patients. Furthermore, the decrease of the sample size will facilitate completion of the trial. Trial registration ClinicalTrials.gov, NCT01792804. Registered on 13 February 2013. German Clinical trials register, DRKS00004741. Registered on 4 October 2013, EudraCT 2013-000577-77

Background: Staphylococcus aureus bloodstream infection (SAB) is treated with at least 14 days of intravenously administered antimicrobials. We assessed the efficacy and safety of an early oral switch therapy in patients at low risk for SAB-related complications. Methods: In an international non-inferiority trial, we randomized patients with SAB after 5 to 7 days of intravenous antimicrobial therapy to either switch to an oral antimicrobial or to continue with intravenous standard therapy. Main exclusion criteria were signs and symptoms of complicated SAB, non-removable foreign devices, and severe comorbidity. Composite primary endpoint was the occurrence of any SAB-related complication (relapsing SAB, deep-seated infection, and mortality attributable to SAB) within 90 days. Results: 213 patients were randomized into the intention-to-treat population. In the oral switch group, 14/108 (13%) participants reached the primary endpoint versus 13/105 (12%) in the standard therapy group (adjusted difference 0.7%, 95% confidence interval [CI] -7.8% to 9.1%). Participants in the oral switch group were discharged earlier (median hospital stay from SAB onset of 12 days versus 16 days; adjusted difference -3.1 days [95% CI -7.5 to 1.4]). There was no statistical difference in 30-day survival and complications of intravenous administration. More participants in the oral group experienced at least one serious adverse event (34% versus 26%, p=0.292). Conclusion: Oral switch was non-inferior to intravenous standard therapy in participants with low-risk SAB. However, a careful assessment of patients for signs and symptoms of complicated SAB at time of presentation and thereafter is necessary before considering early oral switch therapy.

The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Up to recently, exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members was limited due to 16S rDNA sequencing. Here, we developed MetaGut, a method enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using MetaGut we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, associated with Bacteroides/Phocaeicola, mixed composition and Enterococcus abundances. MetaGut revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples (up to >50% and >20%, respectively). After leukopenia, strains were stable or newly acquired. Our results demonstrate the disruptive effect of alloHSCT on the gut microbiome and pave the way for future studies based on long-read metagenomics.