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  • 1
    Language: English
    In: The Journal of infectious diseases, April 2013, Vol.207(7), pp.1105-14
    Description: Diabetic foot infections are a leading cause of lower extremity amputations. Our study examines the microbiota of diabetic skin prior to ulcer development or infection. In a case-control study, outpatient males were recruited at a veterans hospital. Subjects were swabbed at 4 cutaneous sites, 1 on the forearm and 3 on the foot. Quantitative polymerase chain reaction (qPCR) with primers and probes specific for bacteria, Staphylococcus species, Staphylococcus aureus, and fungi were performed on all samples. High-throughput 16S ribosomal RNA (rRNA) sequencing was performed on samples from the forearm and the plantar aspect of the foot. qPCR analysis of swab specimens from 30 diabetic subjects and 30 control subjects showed no differences in total numbers of bacteria or fungi at any sampled site. Increased log concentrations of Staphylococcus aureus, quantified by the number of nuc gene copies, were present in diabetic men on the plantar aspect of the foot. High-throughput 16S rRNA sequencing found that, on the foot, the microbiota in controls (n = 24) was dominated by Staphylococcus species, whereas the microbiota in diabetics (n = 23) was more diverse at the genus level. The forearm microbiota had similar diversity in diabetic and control groups. The feet of diabetic men had decreased populations of Staphylococcus species, increased populations of S. aureus, and increased bacterial diversity, compared with the feet of controls. These ecologic changes may affect the risk for wound infections.
    Keywords: Metagenome ; Diabetes Mellitus -- Pathology ; Diabetic Foot -- Microbiology ; Skin -- Microbiology ; Staphylococcus Aureus -- Isolation & Purification
    ISSN: 00221899
    E-ISSN: 1537-6613
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  • 2
    Language: English
    In: Lang, Gregory I., Daniel P. Rice, Mark J. Hickman, Erica Sodergren, George M. Weinstock, David Botstein, and Michael M. Desai. 2013. “Pervasive Genetic Hitchhiking and Clonal Interference in 40 Evolving Yeast Populations.” Nature 500 (7464): 571-574. doi:10.1038/nature12344. http://dx.doi.org/10.1038/nature12344.
    Description: The dynamics of adaptation determines which mutations fix in a population, and hence how reproducible evolution will be. This is central to understanding the spectra of mutations recovered in evolution of antibiotic resistance1, the response of pathogens to immune selection2,3, and the dynamics of cancer progression4,5. In laboratory evolution experiments, demonstrably beneficial mutations are found repeatedly6–8, but are often accompanied by other mutations with no obvious benefit. Here we use whole-genome whole-population sequencing to examine the dynamics of genome sequence evolution at high temporal resolution in 40 replicate Saccharomyces cerevisiae populations growing in rich medium for 1,000 generations. We find pervasive genetic hitchhiking: multiple mutations arise and move synchronously through the population as mutational “cohorts.” Multiple clonal cohorts are often present simultaneously, competing with each other in the same population. Our results show that patterns of sequence evolution are driven by a balance between these chance effects of hitchhiking and interference, which increase stochastic variation in evolutionary outcomes, and the deterministic action of selection on individual mutations, which favors parallel evolutionary solutions in replicate populations.
    Keywords: Adaptation, Physiological–Genetics ; Cell Nucleus–Genetics ; Clone Cells–Cytology ; Clone Cells–Metabolism ; Evolution, Molecular–Genetics ; Genes, Fungal–Genetics ; Mutation–Classification ; Saccharomyces Cerevisiae–Cytology ; Saccharomyces Cerevisiae–Genetics ; Saccharomyces Cerevisiae–Growth & Development ; Saccharomyces Cerevisiae–Growth & Development ; Stochastic Processes–Growth & Development ; Time Factors–Growth & Development ; Mutation ; Yeast ; Hitchhiking ; Evolution ; Population ; Cloning ; Genomes;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 3
    Language: English
    In: PLoS ONE, 01 January 2015, Vol.10(6), p.e0130902
    Description: Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently within mucosal lesions of patients with Crohn's disease (CD). The AIEC phenotype consists of adherence and invasion of intestinal epithelial cells and survival within macrophages of these bacteria in vitro. Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth. Differential expression analysis of coding sequences (CDS) homologous to both strains demonstrated 224 and 241 genes with increased and decreased expression, respectively, in LF82 relative to HS. Transition metal transport and siderophore metabolism related pathway genes were up-regulated, while glycogen metabolic and oxidation-reduction related pathway genes were down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82 during the exponential phase, but flagellum-dependent motility pathway genes were down-regulated in LF82 during the stationary phase. CDS that mapped only to the LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics approach to identify CDS specific to AIEC by incorporating the genomes of 10 other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 genome and lacked homology to any of the 11 human NIEC strains. We compared these CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci belonging to clustered regularly interspaced short palindromic repeats region (CRISPR)--CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent from all non-pathogenic bacteria. As previously reported, AIEC strains were enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 AIEC strains. Reverse transcription quantitative polymerase chain reaction assays for 6 genes were conducted on fecal and ileal RNA samples from 22 inflammatory bowel disease (IBD), and 32 patients without IBD (non-IBD). The expression of Cas loci was detected in a higher proportion of CD than non-IBD fecal and ileal RNA samples (p 〈0.05). These results support a comparative genomic/transcriptomic approach towards identifying candidate AIEC signature transcripts.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: 2012, Vol.7(11), p.e50937
    Description: The Anelloviridae family consists of non-enveloped, circular, single-stranded DNA viruses. Three genera of anellovirus are known to infect humans, named TTV, TTMDV, and TTMV. Although anelloviruses were initially thought to cause non-A-G viral hepatitis, continued research has shown no definitive associations between anellovirus and human disease to date. Using high-throughput sequencing, we investigated the association between anelloviruses and fever in pediatric patients 2–36 months of age. We determined that although anelloviruses were present in a large number of specimens from both febrile and afebrile patients, they were more prevalent in the plasma and nasopharyngeal (NP) specimens of febrile patients compared to afebrile controls. Using PCR to detect each of the three species of anellovirus that infect humans, we found that anellovirus species TTV and TTMDV were more prevalent in the plasma and NP specimens of febrile patients compared to afebrile controls. This was not the case for species TTMV which was found in similar percentages of febrile and afebrile patient specimens. Analysis of patient age showed that the percentage of plasma and NP specimens containing anellovirus increased with age until patients were 19–24 months of age, after which the percentage of anellovirus positive patient specimens dropped. This trend was striking for TTV and TTMDV and very modest for TTMV in both plasma and NP specimens. Finally, as the temperature of febrile patients increased, so too did the frequency of TTV and TTMDV detection. Again, TTMV was equally present in both febrile and afebrile patient specimens. Taken together these data indicate that the human anellovirus species TTV and TTMDV are associated with fever in children, while the highly related human anellovirus TTMV has no association with fever.
    Keywords: Research Article ; Biology ; Medicine ; Virology ; Public Health And Epidemiology ; Infectious Diseases ; Epidemiology
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: 2012, Vol.7(11), p.e48996
    Description: Human microbiome research characterizes the microbial content of samples from human habitats to learn how interactions between bacteria and their host might impact human health. In this work a novel parametric statistical inference method based on object-oriented data analysis (OODA) for analyzing HMP data is proposed. OODA is an emerging area of statistical inference where the goal is to apply statistical methods to objects such as functions, images, and graphs or trees. The data objects that pertain to this work are taxonomic trees of bacteria built from analysis of 16S rRNA gene sequences (e.g. using RDP); there is one such object for each biological sample analyzed. Our goal is to model and formally compare a set of trees. The contribution of our work is threefold: first, a weighted tree structure to analyze RDP data is introduced; second, using a probability measure to model a set of taxonomic trees, we introduce an approximate MLE procedure for estimating model parameters and we derive LRT statistics for comparing the distributions of two metagenomic populations; and third the Jumpstart HMP data is analyzed using the proposed model providing novel insights and future directions of analysis.
    Keywords: Research Article ; Biology ; Mathematics ; Genetics And Genomics ; Microbiology ; Evolutionary Biology ; Mathematics
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: Emerging infectious diseases, November 2011, Vol.17(11), pp.2050-2
    Description: Astroviruses cause diarrhea, but it is not known whether they circulate in human plasma. Astrovirus MLB2 was recently discovered in diarrhea samples from children. We detected MLB2 in the plasma of a febrile child, which suggests that MLB2 has broader tropism than expected and disease potential beyond the gastrointestinal tract.
    Keywords: Astroviridae Infections -- Virology ; Mamastrovirus -- Isolation & Purification ; Viremia -- Virology
    ISSN: 10806040
    E-ISSN: 1080-6059
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  • 7
    In: The New England Journal of Medicine, 2011, Vol.365(10), pp.892-900
    Description: Background Daptomycin is a lipopeptide with bactericidal activity that acts on the cell membrane of enterococci and is often used off-label to treat patients infected with vancomycin-resistant enterococci. However, the emergence of resistance to daptomycin during therapy threatens its usefulness. Methods We performed whole-genome sequencing and characterization of the cell envelope of a clinical pair of vancomycin-resistant Enterococcus faecalis isolates from the blood of a patient with fatal bacteremia; one isolate (S613) was from blood drawn before treatment and the other isolate (R712) was from blood drawn after treatment with daptomycin. The minimal inhibitory concentrations (MICs) of these two isolates were 1 and 12 μg per milliliter, respectively. Gene replacements were made to exchange the alleles found in isolate S613 with those in isolate R712. Results Isolate R712 had in-frame deletions in three genes. Two genes encoded putative enzymes involved in phospholipid metabolism, GdpD (which denotes glycerophosphoryl diester phosphodiesterase) and Cls (which denotes cardiolipin synthetase), and one gene encoded a putative membrane protein, LiaF (which denotes lipid II cycle-interfering antibiotics protein but whose exact function is not known). LiaF is predicted to be a member of a three-component regulatory system (LiaFSR) involved in the stress-sensing response of the cell envelope to antibiotics. Replacement of the liaF allele of isolate S613 with the liaF allele from isolate R712 quadrupled the MIC of daptomycin, whereas replacement of the gdpD allele had no effect on MIC. Replacement of both the liaF and gdpD alleles of isolate S613 with the liaF and gdpD alleles of isolate R712 raised the daptomycin MIC for isolate S613 to 12 μg per milliliter. As compared with isolate S613, isolate R712 — the daptomycin-resistant isolate — had changes in the structure of the cell envelope and alterations in membrane permeability and membrane potential. Conclusions Mutations in genes encoding LiaF and a GdpD-family protein were necessary and sufficient for the development of resistance to daptomycin during the treatment of vancomycin-resistant enterococci. (Funded by the National Institute of Allergy and Infectious Diseases and the National Institutes of Health.) Daptomycin is a novel antimicrobial agent with activity against vancomycin-resistant enterococci. In this report, the authors elucidate the mechanism of resistance to daptomycin by vancomycin-resistant enterococci and show that it is related to genetic alterations. The treatment of enterococcal infections has become an enormous challenge for clinicians because these organisms frequently exhibit resistance to the standard drugs of choice — namely, ampicillin, vancomycin, and aminoglycosides (with high-level resistance to aminoglycosides). In addition, there has been a striking increase in the frequency of isolation and the spread of vancomycin-resistant enterococci in hospitals around the world, which has resulted in significant increases in mortality, length of hospital stay, and hospitalization costs.1 Enterococcus faecium is one of the so-called ESKAPE pathogens (E. faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and enterobacter species) flagged by . . .
    Keywords: Medicine ; Biology ; Pharmacy, Therapeutics, & Pharmacology;
    ISSN: 0028-4793
    ISSN: 10986596
    E-ISSN: 1533-4406
    E-ISSN: 10986596
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  • 8
    Language: English
    In: PLoS ONE, March 5, 2015, Vol.10(3)
    Description: Necrotizing enterocolitis (NEC) is an inflammatory disease of the newborn bowel, primarily affecting premature infants. Early intestinal colonization has been implicated in the pathogenesis of NEC. The objective of this prospective case-control study was to evaluate differences in the intestinal microbiota between infants who developed NEC and unaffected controls prior to disease onset. We conducted longitudinal analysis of the 16S rRNA genes of 312 samples obtained from 12 NEC cases and 26 age-matched controls with a median frequency of 7 samples per subject and median sampling interval of 3 days. We found that the microbiome undergoes dynamic development during the first two months of life with day of life being the major factor contributing to the colonization process. Depending on when the infant was diagnosed with NEC (i.e. early vs. late onset), the pattern of microbial progression was different for cases and controls. The difference in the microbiota was most overt in early onset NEC cases and controls. In proximity to NEC onset, the abundances of Clostridium sensu stricto from Clostridia class were significantly higher in early onset NEC subjects comparing to controls. In late onset NEC, Escherichia/Shigella among Gammaproteobacteria, showed an increasing pattern prior to disease onset, and was significantly higher in cases than controls six days before NEC onset. Cronobacter from Gammaproteobacteria was also significantly higher in late onset NEC cases than controls 1-3 days prior to NEC onset. Thus, the specific infectious agent associated with NEC may vary by the age of infant at disease onset. We found that intravenously administered antibiotics may have an impact on the microbial diversity present in fecal material. Longitudinal analysis at multiple time points was an important strategy utilized in this study, allowing us to appreciate the dynamics of the premature infant intestinal microbiome while approaching NEC at various points.
    Keywords: Necrotizing Enterocolitis -- Risk Factors ; Necrotizing Enterocolitis -- Research ; Premature Infants -- Health Aspects ; Premature Infants -- Research ; Microbiota (Symbiotic Organisms) -- Health Aspects ; Microbiota (Symbiotic Organisms) -- Research
    ISSN: 1932-6203
    Source: Cengage Learning, Inc.
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  • 9
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article on the resequencing of Treponema pallidum ssp. pallidum strains nichols and SS14 and how the correction of sequencing errors resulted in increased separation of syphilis treponeme subclusters.
    Keywords: Treponema Pallidum Ssp. Pallidum ; Syphilis ; Genome Sequences
    ISSN: 19326203
    E-ISSN: 19326203
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  • 10
    Language: English
    In: PLoS ONE, March 5, 2015, Vol.10(3)
    Description: Necrotizing enterocolitis (NEC) is an inflammatory disease of the newborn bowel, primarily affecting premature infants. Early intestinal colonization has been implicated in the pathogenesis of NEC. The objective of this prospective case-control study was to evaluate differences in the intestinal microbiota between infants who developed NEC and unaffected controls prior to disease onset. We conducted longitudinal analysis of the 16S rRNA genes of 312 samples obtained from 12 NEC cases and 26 age-matched controls with a median frequency of 7 samples per subject and median sampling interval of 3 days. We found that the microbiome undergoes dynamic development during the first two months of life with day of life being the major factor contributing to the colonization process. Depending on when the infant was diagnosed with NEC (i.e. early vs. late onset), the pattern of microbial progression was different for cases and controls. The difference in the microbiota was most overt in early onset NEC cases and controls. In proximity to NEC onset, the abundances of Clostridium sensu stricto from Clostridia class were significantly higher in early onset NEC subjects comparing to controls. In late onset NEC, Escherichia/Shigella among Gammaproteobacteria, showed an increasing pattern prior to disease onset, and was significantly higher in cases than controls six days before NEC onset. Cronobacter from Gammaproteobacteria was also significantly higher in late onset NEC cases than controls 1-3 days prior to NEC onset. Thus, the specific infectious agent associated with NEC may vary by the age of infant at disease onset. We found that intravenously administered antibiotics may have an impact on the microbial diversity present in fecal material. Longitudinal analysis at multiple time points was an important strategy utilized in this study, allowing us to appreciate the dynamics of the premature infant intestinal microbiome while approaching NEC at various points.
    Keywords: Necrotizing Enterocolitis – Risk Factors ; Necrotizing Enterocolitis – Research ; Premature Infants – Health Aspects ; Premature Infants – Research ; Microbiota (Symbiotic Organisms) – Health Aspects ; Microbiota (Symbiotic Organisms) – Research
    ISSN: 1932-6203
    Source: Cengage Learning, Inc.
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