In Silico Assigned Resistance Genes Confer Bifidobacterium with Partial Resistance to Aminoglycosides but Not to Β-Lactams

peer-reviewedBifidobacteria have received significant attention due to their contribution to human gut health and the use of specific strains as probiotics. It is thus not surprising that there has also been significant interest with respect to their antibiotic resistance profile. Numerous culture-based studies have demonstrated that bifidobacteria are resistant to the majority of aminoglycosides, but are sensitive to β-lactams. However, limited research exists with respect to the genetic basis for the resistance of bifidobacteria to aminoglycosides. Here we performed an in-depth in silico analysis of putative Bifidobacterium-encoded aminoglycoside resistance proteins and β-lactamases and assess the contribution of these proteins to antibiotic resistance. The in silico-based screen detected putative aminoglycoside and β-lactam resistance proteins across the Bifidobacterium genus. Laboratory-based investigations of a number of representative bifidobacteria strains confirmed that despite containing putative β-lactamases, these strains were sensitive to β-lactams. In contrast, all strains were resistant to the aminoglycosides tested. To assess the contribution of genes encoding putative aminoglycoside resistance proteins in Bifidobacterium sp. two genes, namely Bbr_0651 and Bbr_1586, were targeted for insertional inactivation in B. breve UCC2003. As compared to the wild-type, the UCC2003 insertion mutant strains exhibited decreased resistance to gentamycin, kanamycin and streptomycin. This study highlights the associated risks of relying on the in silico assignment of gene function. Although several putative β-lactam resistance proteins are located in bifidobacteria, their presence does not coincide with resistance to these antibiotics. In contrast however, this approach has resulted in the identification of two loci that contribute to the aminoglycoside resistance of B. breve UCC2003 and, potentially, many other bifidobacteria.Fiona Fouhy is in receipt of an Irish Research Council for Science, Engineering and Technology EMBARK scholarship and is a Teagasc Walsh fellow. Research in the PDC laboratory is supported by the Irish Government under the National Development Plan through the Science Foundation Ireland Investigator award 11/PI/1137. Research in the RPR, CS, PDC and DvS laboratories is also supported by the Science Foundation of Ireland-funded Centre for Science, Engineering and Technology, the Alimentary Pharmabiotic Centre (grant no.s 02/CE/B124 and 07/CE/B1368) and a HRB postdoctoral fellowship (Grant no. PDTM/20011/9) awarded to MOCM

Multiple strand displacement amplification of mitochondrial DNA from clinical samples

<p>Abstract</p> <p>Background</p> <p>Whole genome amplification (WGA) methods allow diagnostic laboratories to overcome the common problem of insufficient DNA in patient specimens. Further, body fluid samples useful for cancer early detection are often difficult to amplify with traditional PCR methods. In this first application of WGA on the entire human mitochondrial genome, we compared the accuracy of mitochondrial DNA (mtDNA) sequence analysis after WGA to that performed without genome amplification. We applied the method to a small group of cancer cases and controls and demonstrated that WGA is capable of increasing the yield of starting DNA material with identical genetic sequence.</p> <p>Methods</p> <p>DNA was isolated from clinical samples and sent to NIST. Samples were amplified by PCR and those with no visible amplification were re-amplified using the Multiple Displacement Amplificaiton technique of whole genome amplification. All samples were analyzed by mitochip for mitochondrial DNA sequence to compare sequence concordance of the WGA samples with respect to native DNA. Real-Time PCR analysis was conducted to determine the level of WGA amplification for both nuclear and mtDNA.</p> <p>Results</p> <p>In total, 19 samples were compared and the concordance rate between WGA and native mtDNA sequences was 99.995%. All of the cancer associated mutations in the native mtDNA were detected in the WGA amplified material and heteroplasmies in the native mtDNA were detected with high fidelity in the WGA material. In addition to the native mtDNA sequence present in the sample, 13 new heteroplasmies were detected in the WGA material.</p> <p>Conclusion</p> <p>Genetic screening of mtDNA amplified by WGA is applicable for the detection of cancer associated mutations. Our results show the feasibility of this method for: 1) increasing the amount of DNA available for analysis, 2) recovering the identical mtDNA sequence, 3) accurately detecting mtDNA point mutations associated with cancer.</p

Glycoside hydrolase family 13 α-glucosidases encoded by Bifidobacterium breve UCC2003; A comparative analysis of function, structure and phylogeny

peer-reviewedBifidobacterium breve is a noted inhabitant and one of the first colonizers of the human gastro intestinal tract (GIT). The ability of this bacterium to persist in the GIT is reflected by the abundance of carbohydrate-active enzymes that are encoded by its genome. One such family of enzymes is represented by the α-glucosidases, of which three, Agl1, Agl2 and MelD, have previously been identified and characterized in the prototype B. breve strain UCC2003. In this report, we describe an additional B. breve UCC2003-encoded α-glucosidase, along with a B. breve UCC2003-encoded α-glucosidase-like protein, designated here as Agl3 and Agl4, respectively, which together with the three previously described enzymes belong to glycoside hydrolase (GH) family 13. Agl3 was shown to exhibit hydrolytic specificity towards the α-(1 → 6) linkage present in palatinose; the α-(1 → 3) linkage present in turanose; the α-(1 → 4) linkages found in maltotriose and maltose; and to a lesser degree, the α-(1 → 2) linkage found in sucrose and kojibiose; and the α-(1 → 5) linkage found in leucrose. Surprisingly, based on the substrates analyzed, Agl4 did not exhibit biologically relevant α-glucosidic activity. With the presence of four functionally active GH13 α-glucosidases, B. breve UCC2003 is capable of hydrolyzing all α-glucosidic linkages that can be expected in glycan substrates in the lower GIT. This abundance of α-glucosidases provides B. breve UCC2003 with an adaptive ability and metabolic versatility befitting the transient nature of growth substrates in the GIT.Department of Agriculture and Food's Food Institutional Research Measure (FIRM

Analysis of Factors Driving Incident and Ascending Infection and the Role of Serum Antibody in Chlamydia trachomatis Genital Tract Infection

Background. Chlamydia trachomatis genital tract infection is a major cause of female reproductive morbidity. Risk factors for ascending infection are unknown, and the role for antibody in protection is not well established

Identification of Chlamydia trachomatis Antigens Recognized by T Cells From Highly Exposed Women Who Limit or Resist Genital Tract Infection

Background. Natural infection induces partial immunity to Chlamydia trachomatis. Identification of chlamydial antigens that induce interferon γ (IFN-) secretion by T cells from immune women could advance vaccine development

Enhanced Virulence of Chlamydia muridarum Respiratory Infections in the Absence of TLR2 Activation

Chlamydia trachomatis is a common sexually transmitted pathogen and is associated with infant pneumonia. Data from the female mouse model of genital tract chlamydia infection suggests a requirement for TLR2-dependent signaling in the induction of inflammation and oviduct pathology. We hypothesized that the role of TLR2 in moderating mucosal inflammation is site specific. In order to investigate this, we infected mice via the intranasal route with C. muridarum and observed that in the absence of TLR2 activation, mice had more severe disease, higher lung cytokine levels, and an exaggerated influx of neutrophils and T-cells into the lungs. This could not be explained by impaired bacterial clearance as TLR2-deficient mice cleared the infection similar to controls. These data suggest that TLR2 has an anti-inflammatory function in the lung during Chlamydia infection, and that the role of TLR2 in mucosal inflammation varies at different mucosal surfaces

Audible Image Description as an Accommodation in Statewide Assessments for Students with Visual and Print Disabilities.

Introduction:Although image description has been identified as an accommodation for presentations conducted in the classroom, only a few U.S. states have approved it for use in high-stakes assessments. This study examined the use of audible image description as an assessment accommodation for students with visual and print disabilities by investigating student comprehension under multiple conditions. Methods: Students in three western states in grades three through eight who had visual (n= 117) or print (n= 178) disabilities participated in an abbreviated test constructed of retired assessment questions in English language arts, mathematics, and science, that were aligned with each state's instructional standards, under conditions with and without standardized description of graphic images. The study used a within-subjects block design to collect and compare comprehension data under conditions where audible image description was both used and not used in an abbreviated test. Results: Results indicated that students who read braille were more likely to respond correctly under the audible image description condition, and students with visual and print disabilities who used print were equally likely to respond correctly regardless of condition. Discussion: Braille readers were more likely to obtain a correct answer when audible image description accompanied the question. Audible image description did not affect the likelihood of a correct response from students with print disabilities or students with visual disabilities who read print. Implications for practitioners: Audible image description is an accommodation that may help braille readers perform better on tests. Although the Partnership for Assessment of Readiness for College and Careers (PARCC) and Smarter Balanced consortia are taking steps to include image (or picture) descriptions in their assessment accommodations, teachers may want to develop a standard method for describing images and familiarize their braille readers to the strategy by including it in instruction and in classroom tests. Readers are referred to the National Center on Accessible Media’s online guidelines for image description

What Can a Pilot Congestive Heart Failure Disease Management Program Tell Us about Likely Return on Investment?: A Case Study from a Program Offered to Federal Employees

In 1999, the Blue Cross and Blue Shield Federal Employee Program (FEP) implemented a pilot disease management program to manage congestive heart failure (CHF) among members. The purpose of this project was to estimate the financial return on investment in the pilot CHF program, prior to a full program rollout. A cohort of 457 participants from the state of Maryland was matched to a cohort of 803 nonparticipants from a neighboring state where the CHF program was not offered. Each cohort was followed for 12 months before the program began and 12 months afterward. The outcome measures of primary interest were the differences over time in medical care expenditures paid by FEP and by all payers. Independent variables included indicators of program participation, type of heart disease, comorbidity measures, and demographics. From the perspective of the funding organization (FEP), the estimated return on investment for the pilot CHF disease management program was a savings of $1.08 in medical expenditure for every dollar spent on the program. Adding savings to other payers as well, the return on investment was a savings of$1.15 in medical expenditures per dollar spent on the program. The amount of savings depended upon CHF risk levels. The value of a pilot initiative and evaluation is that lessons for larger-scale efforts can be learned prior to full-scale rollout. (Disease Management 2005;8:346-360)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63402/1/dis.2005.8.346.pd

Plasmid-Cured Chlamydia caviae Activates TLR2-Dependent Signaling and Retains Virulence in the Guinea Pig Model of Genital Tract Infection

Loss of the conserved “cryptic” plasmid from C. trachomatis and C. muridarum is pleiotropic, resulting in reduced innate inflammatory activation via TLR2, glycogen accumulation and infectivity. The more genetically distant C. caviae GPIC is a natural pathogen of guinea pigs and induces upper genital tract pathology when inoculated intravaginally, modeling human disease. To examine the contribution of pCpGP1 to C. caviae pathogenesis, a cured derivative of GPIC, strain CC13, was derived and evaluated in vitro and in vivo. Transcriptional profiling of CC13 revealed only partial conservation of previously identified plasmid-responsive chromosomal loci (PRCL) in C. caviae. However, 2-deoxyglucose (2DG) treatment of GPIC and CC13 resulted in reduced transcription of all identified PRCL, including glgA, indicating the presence of a plasmid-independent glucose response in this species. In contrast to plasmid-cured C. muridarum and C. trachomatis, plasmid-cured C. caviae strain CC13 signaled via TLR2 in vitro and elicited cytokine production in vivo similar to wild-type C. caviae. Furthermore, inflammatory pathology induced by infection of guinea pigs with CC13 was similar to that induced by GPIC, although we observed more rapid resolution of CC13 infection in estrogen-treated guinea pigs. These data indicate that either the plasmid is not involved in expression or regulation of virulence in C. caviae or that redundant effectors prevent these phenotypic changes from being observed in C. caviae plasmid-cured strains

Elemental Composition and Chemical Evolution of Geologic Materials in Gale Crater, Mars: APXS Results From Bradbury Landing to the Vera Rubin Ridge

The Alpha Particle X-ray Spectrometer (APXS) on the rover Curiosity has analyzed the composition of geologic materials along a >20-km traverse in Gale crater on Mars. The APXS dataset after 6.5 Earth years (2,301 sols) includes 712 analyses of soil, sand, float, bedrock, and drilled/scooped fines. We present the APXS results over this duration and provide stratigraphic context for each target. We identify the best APXS measurement of each of the 22 drilled and scooped samples that were delivered to the instruments Chemistry and Mineralogy (CheMin; X-ray diffractometer) and Sample Analysis at Mars (SAM; mass spectrometer and gas chromatograph) during this period. The APXS results demonstrate that the basaltic and alkali-rich units in the Bradbury group (sols 0-750) show minimal alteration indicating an arid climate. In contrast, the Murray formation of the Mount Sharp group (sols ∼750-2,301) has compositions indicating pervasive alteration. Diagenetic features are common and show fluid interaction with the sediment after (and possibly during) lithification. A sandstone unit, the Stimson formation, overlies part of the Murray formation. This has a composition similar to the basaltic sand and soil, suggesting a shared source. Cross-cutting, fracture-associated haloes are evidence of late-stage fluid alteration after lithification of the sediment. The APXS dataset, evaluated in concert with the full science payload of Curiosity, indicates that Gale crater was habitable, and that liquid water was stable for extended periods.We are indebted to NASA-JPL, the Canadian Space Agency, and Australian Research Council (DP150104604) for supporting our work and the MSL mission. A portion of this study was conducted at the Jet Propulsion Laboratory, California Institute of Technology under a contract with the National Aeronautics and Space Administration