Studies On The In Vitro Transposition Of Bacteriophage Mu Dna

The early steps in the transposition of Mu DNA have been examined in vitro using purified Mu A, Mu B and E. coli HU proteins, a mini-Mu donor plasmid and target DNA. Two stable protein-DNA complexes, or transpososomes, have been characterized. Type 1 complex formation requires a supercoiled mini-Mu donor plasmid, Mu A and HU protein. In the Type 1 complex the two ends of Mu are held together, creating two independent topological domains; a supercoiled Mu domain and a relaxed vector domain (due to nicking at the Mu ends). In the presence of Mu B protein, ATP, and target DNA, the Type 1 complex is converted into a Type 2 complex which is the protein associated product of the strand transfer reaction.;Type 1 complex formation with a mini-Mu plasmid with in vivo level of supercoiling ({dollar}\sigma{dollar} = {dollar}-{dollar}0.025) was dependent on an additional E. coli protein factor which we named supercoiling relief factor (SRF). This protein was shown to be integration host factor (IHF). Low levels of IHF also reduce the amount of HU and Mu A required for the reaction and at high concentrations of IHF, HU is not required. The SRF activity of IHF is mediated through an IHF binding site in the Mu early promoter region. This site is part of a larger enhancer-like element which stimulates the initial rate of the in vitro reaction 100-fold.;Point mutations at the terminal nucleotide of the Mu ends in a mini-Mu plasmid inhibit the introduction of nicks at the Mu ends in a reaction with Mu A, HU and IHF proteins. Addition of Mu B and ATP, however, dramatically stimulates the reaction of mutant mini-Mu plasmids carrying the mutation at one end. Two products are observed; a normal Type 1 complex which contains nicks at both Mu ends, and free relaxed plasmid which is nicked only at the wild type end. Stable protein-DNA complexes characteristic of the first step in the in vitro transposition reaction require the introduction of nicks at both Mu ends

Culture Enriched Molecular Profiling of the Cystic Fibrosis Airway Microbiome

The microbiome of the respiratory tract, including the nasopharyngeal and oropharyngeal microbiota, is a dynamic community of microorganisms that is highly diverse. The cystic fibrosis (CF) airway microbiome refers to the polymicrobial communities present in the lower airways of CF patients. It is comprised of chronic opportunistic pathogens (such as Pseudomonas aeruginosa) and a variety of organisms derived mostly from the normal microbiota of the upper respiratory tract. The complexity of these communities has been inferred primarily from culture independent molecular profiling. As with most microbial communities it is generally assumed that most of the organisms present are not readily cultured. Our culture collection generated using more extensive cultivation approaches, reveals a more complex microbial community than that obtained by conventional CF culture methods. To directly evaluate the cultivability of the airway microbiome, we examined six samples in depth using culture-enriched molecular profiling which combines culture-based methods with the molecular profiling methods of terminal restriction fragment length polymorphisms and 16S rRNA gene sequencing. We demonstrate that combining culture-dependent and culture-independent approaches enhances the sensitivity of either approach alone. Our techniques were able to cultivate 43 of the 48 families detected by deep sequencing; the five families recovered solely by culture-independent approaches were all present at very low abundance (<0.002% total reads). 46% of the molecular signatures detected by culture from the six patients were only identified in an anaerobic environment, suggesting that a large proportion of the cultured airway community is composed of obligate anaerobes. Most significantly, using 20 growth conditions per specimen, half of which included anaerobic cultivation and extended incubation times we demonstrate that the majority of bacteria present can be cultured

Bacterial DNA patterns identified using paired-end Illumina sequencing of 16S rRNA genes from whole blood samples of septic patients in the emergency room and intensive care unit

Abstract Background Sepsis refers to clinical presentations ranging from mild body dysfunction to multiple organ failure. These clinical symptoms result from a systemic inflammatory response to pathogenic or potentially pathogenic microorganisms present systemically in the bloodstream. Current clinical diagnostics rely on culture enrichment techniques to identify bloodstream infections. However, a positive result is obtained in a minority of cases thereby limiting our knowledge of sepsis microbiology. Previously, a method of saponin treatment of human whole blood combined with a comprehensive bacterial DNA extraction protocol was developed. The results indicated that viable bacteria could be recovered down to 10 CFU/ml using this method. Paired-end Illumina sequencing of the 16S rRNA gene also indicated that the bacterial DNA extraction method enabled recovery of bacterial DNA from spiked blood. This manuscript outlines the application of this method to whole blood samples collected from patients with the clinical presentation of sepsis. Results Blood samples from clinically septic patients were obtained with informed consent. Application of the paired-end Illumina 16S rRNA sequencing to saponin treated blood from intensive care unit (ICU) and emergency department (ED) patients indicated that bacterial DNA was present in whole blood. There were three clusters of bacterial DNA profiles which were distinguished based on the distribution of Streptococcus, Staphylococcus, and Gram-negative DNA. The profiles were examined alongside the patient’s clinical data and indicated molecular profiling patterns from blood samples had good concordance with the primary source of infection. Conclusions Overall this study identified common bacterial DNA profiles in the blood of septic patients which were often associated with the patients’ primary source of infection. These results indicated molecular bacterial DNA profiling could be further developed as a tool for clinical diagnostics for bloodstream infections

Probiotics: Prevention of Severe Pneumonia and Endotracheal Colonization Trial—PROSPECT: a pilot trial

Background: Probiotics are live microorganisms that may confer health benefits when ingested. Randomized trials suggest that probiotics significantly decrease the incidence of ventilator-associated pneumonia (VAP) and the overall incidence of infection in critically ill patients. However, these studies are small, largely single-center, and at risk of bias. The aim of the PROSPECT pilot trial was to determine the feasibility of conducting a larger trial of probiotics to prevent VAP in mechanically ventilated patients in the intensive care unit (ICU). Methods: In a randomized blinded trial, patients expected to be mechanically ventilated for ≥72 hours were allocated to receive either 1 × 1010 colony-forming units of Lactobacillus rhamnosus GG or placebo, twice daily. Patients were excluded if they were at increased risk of L. rhamnosus GG infection or had contraindications to enteral medication. Feasibility objectives were: (1) timely recruitment; (2) maximal protocol adherence; (3) minimal contamination; and (4) estimated VAP rate ≥10 %. We also measured other infections, diarrhea, ICU and hospital length of stay, and mortality. Results: Overall, in 14 centers in Canada and the USA, all feasibility goals were met: (1) 150 patients were randomized in 1 year; (2) protocol adherence was 97 %; (3) no patients received open-label probiotics; and (4) the VAP rate was 19 %. Other infections included: bloodstream infection (19.3 %), urinary tract infections (12.7 %), and skin and soft tissue infections (4.0 %). Diarrhea, defined as Bristol type 6 or 7 stools, occurred in 133 (88.7 %) of patients, the median length of stay in ICU was 12 days (quartile 1 to quartile 3, 7–18 days), and in hospital was 26 days (quartile 1 to quartile 3, 14–44 days); 23 patients (15.3 %) died in the ICU. Conclusions: The PROSPECT pilot trial supports the feasibility of a larger trial to investigate the effect of L. rhamnosus GG on VAP and other nosocomial infections in critically ill patients. Trial registration: Clinicaltrials.gov NCT01782755 . Registered on 29 January 2013.Medicine, Faculty ofOther UBCNon UBCCritical Care Medicine, Division ofMedicine, Department ofReviewedFacult

Probiotics: Prevention of Severe Pneumonia and Endotracheal Colonization Trial—PROSPECT: a pilot trial

Abstract Background Probiotics are live microorganisms that may confer health benefits when ingested. Randomized trials suggest that probiotics significantly decrease the incidence of ventilator-associated pneumonia (VAP) and the overall incidence of infection in critically ill patients. However, these studies are small, largely single-center, and at risk of bias. The aim of the PROSPECT pilot trial was to determine the feasibility of conducting a larger trial of probiotics to prevent VAP in mechanically ventilated patients in the intensive care unit (ICU). Methods In a randomized blinded trial, patients expected to be mechanically ventilated for ≥72 hours were allocated to receive either 1 × 1010 colony-forming units of Lactobacillus rhamnosus GG or placebo, twice daily. Patients were excluded if they were at increased risk of L. rhamnosus GG infection or had contraindications to enteral medication. Feasibility objectives were: (1) timely recruitment; (2) maximal protocol adherence; (3) minimal contamination; and (4) estimated VAP rate ≥10 %. We also measured other infections, diarrhea, ICU and hospital length of stay, and mortality. Results Overall, in 14 centers in Canada and the USA, all feasibility goals were met: (1) 150 patients were randomized in 1 year; (2) protocol adherence was 97 %; (3) no patients received open-label probiotics; and (4) the VAP rate was 19 %. Other infections included: bloodstream infection (19.3 %), urinary tract infections (12.7 %), and skin and soft tissue infections (4.0 %). Diarrhea, defined as Bristol type 6 or 7 stools, occurred in 133 (88.7 %) of patients, the median length of stay in ICU was 12 days (quartile 1 to quartile 3, 7–18 days), and in hospital was 26 days (quartile 1 to quartile 3, 14–44 days); 23 patients (15.3 %) died in the ICU. Conclusions The PROSPECT pilot trial supports the feasibility of a larger trial to investigate the effect of L. rhamnosus GG on VAP and other nosocomial infections in critically ill patients. Trial registration Clinicaltrials.gov NCT01782755 . Registered on 29 January 2013

Additional file 1: of Probiotics: Prevention of Severe Pneumonia and Endotracheal Colonization Trial—PROSPECT: a pilot trial

PROSPECT pilot center research ethics board information. (DOCX 14 kb

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts