bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex Detection of Bacteria Associated with Normal Microbiota and with Bacterial Vaginosis in Vaginal Swabs by Use of Oligonucleotide-Coupled Fluorescent Microspheres
Authors: Dumonceaux Tim J. , Schellenberg John , Goleski Vanessa , Hill Janet E. , Jaoko Walter , Kimani Joshua , Money Deborah , Ball T. Blake , Plummer Francis A. , Severini Alberto 
Published: October 2009

ABSTRACT

Bacterial vaginosis (BV) is a recurrent condition that is associated with a range of negative outcomes, including the acquisition of human immunodeficiency virus and other sexually transmitted diseases, preterm births, and pelvic inflammatory disease. In contrast to the
Lactobacillus
-dominated normal vaginal microbiota, BV is characterized by a lack of lactobacilli and an abundance of anaerobic and gram-negative organisms, including
Gardnerella vaginalis
and
Atopobium vaginae
. To date, the laboratory diagnosis of BV has relied upon the fulfillment of criteria determined by microscopic observation of Gram-stained vaginal swabs. We describe a molecular-based method for the easy determination of the species profile within the vaginal microbiota based on the amplification of the chaperonin-60 genes of all bacteria present in the swab and hybridization of the amplicon to species-specific oligonucleotide-coupled fluorescent beads that are identified by flow cytometry with a Luminex instrument. We designed a nineplex Luminex array for characterization of the vaginal microbiota and applied it to the analysis of vaginal swabs from individuals from Africa and North America. Using the presence of
A. vaginae
or
G. vaginalis
, or both, as the defining criterion for BV, we found that the method was highly specific and sensitive for the diagnosis of BV using microscopy as a gold standard.
Direct Detection of Mycobacterial Species in Pulmonary Specimens by Two Rapid Amplification Tests, the Gen-Probe Amplified
Mycobacterium tuberculosis
Direct Test and the GenoType Mycobacteria Direct Test
Authors: Syre H. , Myneedu V. P. , Arora V. K. , Grewal H. M. S. 
Published: October 2009

ABSTRACT

Nucleic acid amplification tests have improved tuberculosis diagnostics considerably. This study evaluates a new amplification test, the GenoType Mycobacteria Direct (GTMD) test, for detection of the
Mycobacterium tuberculosis
complex,
Mycobacterium avium
,
Mycobacterium intracellulare
,
Mycobacterium kansasii
, and
Mycobacterium malmoense
directly in 61 sputum samples. Thirty (49.2%) samples were auramine smear positive, and 31 (50.8%) were smear negative. The GTMD results were compared to the Gen-Probe Amplified
M. tuberculosis
Direct (MTD) test results, using culturing and sequencing of the 16S rRNA gene as reference methods. The GTMD test could identify 28 of 29 samples containing the
M. tuberculosis
complex and was negative in a sputum sample containing
M. intracellulare
. The overall sensitivity and specificity results were 93.3% and 90.0% for the GTMD test, respectively, and 93.1% and 93.5% for the MTD test, respectively. The GTMD test is rapid and can be easily included in routine clinical laboratories for the direct detection of the
M. tuberculosis
complex in smear-positive sputum samples as an adjunct to microscopy and culture. Further studies are needed to evaluate the performance of the GTMD test for the detection of atypical mycobacteria.
Analysis of Clarithromycin Resistance and CagA Status in
Helicobacter pylori
by Use of Feces from Children in Thailand
Authors: Tanuma Michiya , Rimbara Emiko , Noguchi Norihisa , Boonyaritichaikij Surasak , Kuwabara Kentaro , Fukunaga Yoshitaka , Sasatsu Masanori 
Published: October 2009

ABSTRACT

The clarithromycin resistance and CagA status of
Helicobacter pylori
in Thai children were investigated using fecal samples. Of the 284 samples,
H. pylori
was detected in 120 samples, and the clarithromycin resistance rate was 29.2%. The
cagA
gene was detected in 59 samples, and only 6.8% of these samples contained the East Asian CagA type.
Genomic Characterization of Nontypeable Rotaviruses and Detection of a Rare G8 Strain in Delhi, India
Authors: Sharma Sumit , Paul Vinod K. , Bhan Maharaj K. , Ray Pratima 
Published: October 2009

ABSTRACT
In the present investigation we molecularly characterized nontypeable rotavirus strains previously identified during surveillance in New Delhi, India. The majority of strains were demonstrated to belong to genotype G1 (54.5%) or P[8] (77.8%) on the basis of nucleotide sequencing of fragments from their VP7 and VP4 genes. The other genotypes detected included G2, G8, G9, G12, and P[4]. A G8P[6] strain, strain DS108, was detected for the first time in northern India. The VP7 gene of DS108 was most homologous with the VP7 gene of a bovine G8 strain, strain A5 (98.9%), indicating its bovine parentage. In contrast, the VP4 gene had a high degree of nucleotide sequence homology (92.9% to 99.1%) with the VP4 genes of human P[6] strains. The VP6 gene and nonstructural genes (NSP1 to NSP3 and NSP5) were most homologous with the VP6 gene and nonstructural genes of human rotaviruses belonging to the DS1 genogroup. Interestingly, the NSP4 gene of DS108 clustered within genotype E6 that until now had only two representative strains, both with G12P[6] specificity (strains RV176-00 and N26-02). Together, these results indicate that G8 strain DS108 belongs to the DS1 genogroup and could be the result of the acquisition of the VP7, VP4, and NSP4 genes by a human G2P[4] strain from more than one donor, similar to the evolution of G12P[6] strain RV176-00. The present study highlights the importance of characterizing multiple genes of nontypeable rotavirus strains to detect novel strains and get a more complete picture of rotavirus evolution.
Emergence of Hepatitis C Virus Genotype 4: Phylogenetic Analysis Reveals Three Distinct Epidemiological Profiles
Authors: de Bruijne Joep , Schinkel Janke , Prins Maria , Koekkoek Sylvie M. , Aronson Sem J. , van Ballegooijen Marijn W. , Reesink Hendrik W. , Molenkamp Richard , van de Laar Thijs J. W. 
Published: October 2009

ABSTRACTHepatitis C virus (HCV) genotype 4 (HCV-4) infection is considered to be difficult to treat and has become increasingly prevalent in European countries, including The Netherlands. Using a molecular epidemiological approach, the present study investigates the genetic diversity and evolutionary origin of HCV-4 in Amsterdam, The Netherlands. Phylogenetic analysis of the NS5B sequences (668 bp) obtained from 133 patients newly diagnosed with HCV-4 infection over the period from 1999 to 2008 revealed eight distinct HCV-4 subtypes; the majority of HCV-4 isolates were of subtypes 4d (57%) and 4a (37%). Three distinct monophyletic clusters were identified, with each one having a specific epidemiological profile: (i) Egyptian immigrants infected with HCV-4a (n= 46), (ii) Dutch patients with a history of injecting drug use infected with HCV-4d (n= 44), and (iii) Dutch human immunodeficiency virus (HIV)-positive men who have sex with men (MSM) infected with HCV-4d (n= 26). Subsequent molecular clock analyses confirmed that the emergence of HCV-4 within these three risk groups coincided with (i) the parenteral antischistosomal therapy campaigns in Egypt (1920 to 1960), (ii) the popularity of injecting drug use in The Netherlands (1960 to 1990), and (iii) the rise in high-risk sexual behavior among MSM after the introduction of highly active antiretroviral therapy (1996 onwards). Our data show that in addition to the influx of HCV-4 strains from countries where HCV-4 is endemic, the local spread of HCV-4d affecting injecting drug users and, in recent years, especially HIV-positive MSM will further increase the relative proportion of HCV-4-infected patients in The Netherlands. HCV-4-specific agents are drastically needed to improve treatment response rates and decrease the future burden of HCV-4-related disease.
Efficient Diagnosis of Vulvovaginal Candidiasis by Use of a New Rapid Immunochromatography Test
Authors: Marot-Leblond Agnes , Nail-Billaud Sandrine , Pilon Françoise , Beucher Bertrand , Poulain Daniel , Robert Raymond 
Published: October 2009

ABSTRACT

The clinical symptoms of vulvovaginal candidiasis (VVC) are nonspecific, and misdiagnosis is common, leading to a delay in the initiation of antifungal treatment. We evaluated a new immunochromatography test (ICT), the CandiVagi assay (SR2B, Avrille, France), for the rapid diagnosis of VVC. This test, which employs an immunoglobulin M antibody directed against the β-1,2-mannopyranosyl epitopes found in the yeast cell wall, was compared with direct microscopic examination and culture of vaginal swabs. Two-hundred five women were investigated, including 130 women with symptomatic vaginitis and 75 asymptomatic controls. Two vaginal swabs were obtained from each woman: one was used to prepare a wet mount and Gram-stained preparations for direct microscopic examination and was also cultured on Sabouraud dextrose agar for the isolation of
Candida
spp., and the second swab was used for ICT. The sensitivities of microscopic examination, culture, and ICT for the diagnosis of VVC were 61%, 100%, and 96.6%, respectively, while the specificities of the three methods were 100%, 82%, and 98.6%, respectively. ICT had a negative predictive value of 98.6%, a positive predictive value of 96.6%, and an efficiency of 98%. ICT provided a rapid result and a better compromise between sensitivity and specificity than conventional microscopy and culture for the diagnosis of VVC. This easy-to-perform diagnostic test will be useful to practitioners treating women with symptoms of vaginitis.
Implementation of a Universal Admission Surveillance and Decolonization Program for Methicillin-Resistant
Staphylococcus aureus
(MRSA) Reduces the Number of MRSA and Total Number of
S. aureus
Isolates Reported by the Clinical Laboratory
Authors: Hacek Donna M. , Paule Suzanne M. , Thomson Richard B. , Robicsek Ari , Peterson Lance R. 
Published: October 2009

ABSTRACT

Our three-hospital system began active surveillance for methicillin-resistant
Staphylococcus aureus
(MRSA) nasal colonization, with decolonization of positive patients, on all admissions starting 1 August 2005. A question not previously addressed is whether reduction of the incidence of MRSA disease would lower the total number of
S. aureus
clinical isolates recovered by the microbiology laboratory that are reported to health care providers. The decreases in the numbers of MRSA and total
S. aureus
clinical isolates for each year after August 2005 were highly statistically significant compared to the numbers in each of the prior 3 years (
P
< 0.0001).
First
Neisseria gonorrhoeae
Genotyping Analysis in France: Identification of a Strain Cluster with Reduced Susceptibility to Ceftriaxone
Authors: Monfort Laura , Caro Valérie , Devaux Zaelle , Delannoy Anne-Sophie , Brisse Sylvain , Sednaoui Patrice 
Published: October 2009

ABSTRACT

Sexually transmitted infections are a major public health problem in France and other European countries. Particularly, surveillance data about
Neisseria gonorrhoeae
infections have clearly indicated an increase in the incidence of gonorrhoea in France in 2006. The French laboratories participated on voluntary basis in the RENAGO (Réseau National du Gonocoque) network and sent all of their collected strains to the National Reference Center for
Neisseria gonorrhoeae
. In this first French molecular epidemiological study, 93 isolates collected in 2006 and representative of the French gonorrhoea epidemiology were selected. Antibiotic susceptibility to six antibiotics was determined, and serotyping and
N. gonorrhoeae
multiantigen sequence typing (NG-MAST) were performed. NG-MAST identified 53 sequence types (STs), of which 13 STs contained 2 to 16 isolates. The major STs identified in France were previously described elsewhere. However, two newly described STs, ST1479 and ST1987, had only been found in France until now. ST1479 was characterized by a multiple-resistance phenotype, whereas ST1987 presented a susceptibility phenotype. Moreover, among the predominant French STs, ST225, which had already been described in many countries, comprised isolates (14/16) resistant to ciprofloxacin and with reduced susceptibility to ceftriaxone. Thus, the surveillance of resistance to antibiotics is a priority in order to adapt treatment and decrease the transmission of resistant strains. Of note, no predominant ST was identified among rectal isolates from men who have sex with men.
Actinomyces neuii
subsp.
neuii
Associated with Periprosthetic Infection in Total Hip Arthroplasty as Causative Agent
Authors: Rieber Heime , Schwarz Roman , Krämer Oliver , Cordier Wolfgang , Frommelt Lars 
Published: October 2009

ABSTRACT

Actinomyces neuii
has until now not been described as a pathogen associated with periprosthetic infection in total joint replacement. The case presented here suggests that
A. neuii
subsp.
neuii
is a causative pathogen. The discussion and review of the literature indicate the impact that detection of
Actinomyces
species could have.
Switching Gears for an Influenza Pandemic: Validation of a Duplex Reverse Transcriptase PCR Assay for Simultaneous Detection and Confirmatory Identification of Pandemic (H1N1) 2009 Influenza Virus
Authors: LeBlanc Jason J. , Li Yan , Bastien Nathalie , Forward Kevin R. , Davidson Ross J. , Hatchette Todd F. 
Published: October 2009

ABSTRACT
Rapid methods for the detection and confirmatory identification of pandemic influenza A virus (also known as pandemic [H1N1] 2009) are of utmost importance. In this study, a conventional reverse transcriptase PCR (RT-PCR) assay for the detection of influenza A virus and the hemagglutinin of swine lineage H1 (swH1) was designed, optimized, and validated. Nucleic acids were extracted from 198 consecutive nasopharyngeal, nasal, or throat swab specimens collected early in the outbreak (127 negative specimens, 66 specimens with pandemic [H1N1] 2009 influenza virus, 3 specimens with seasonal [H1N1] influenza A virus, and 2 specimens with seasonal [H3N2] influenza A virus). The performance characteristics of the duplex RT-PCR assay were assessed and compared to those of various detection methods: a monoplex RT-PCR assay at the National Microbiology Laboratory, a real-time RT-PCR assay using a Centers for Disease Control and Prevention protocol, an in-house multiplex RT-PCR assay (targeting influenza A virus, influenza B virus, and respiratory syncytial virus), and a rapid antigen test (the Binax Now Influenza A & B assay). The sensitivity of the duplex RT-PCR assay for influenza A virus detection was 97.2%, whereas the sensitivities were 74.6%, 71.8%, 47.8%, and 12.7% for the other four assays, respectively. The duplex RT-PCR assay was also able to identify swH1 in 94% of the cases, thereby reducing the number of specimens forwarded to reference laboratories for confirmatory identification. Only a limited number of specimens that contained influenza A virus had amounts of virus that fell below the limit of detection of the assay with the swH1 primers. Overall, the duplex RT-PCR assay is a reliable method for the simultaneous detection and confirmatory identification of pandemic (H1N1) 2009 influenza virus and would be particularly attractive to laboratories without real-time RT-PCR capabilities.
Characteristics of
Candida albicans
Biofilms Grown in a Synthetic Urine Medium
Authors: Uppuluri Priya , Dinakaran Hemamalini , Thomas Derek P. , Chaturvedi Ashok K. , Lopez-Ribot Jose L. 
Published: October 2009

ABSTRACT

Urinary tract infections (UTIs) are the most common type of nosocomial infection, and
Candida albicans
is the most frequent organism causing fungal UTIs. Presence of an indwelling urinary catheter represents a significant risk factor for UTIs. Furthermore, these infections are frequently associated with the formation of biofilms on the surface of these catheters. Here, we describe the characterization of
C. albicans
biofilms formed in vitro using synthetic urine (SU) medium and the frequently used RPMI medium and compare the results. Biofilms of
C. albicans
strain SC5314 were formed in 96-well microtiter plates and on silicon elastomer pieces using both SU and RPMI media. Biofilm formation was monitored by microscopy and a colorimetric XTT [2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] reduction assay. As in biofilms grown in RPMI medium, time course studies revealed that biofilm formation using SU medium occurred after an initial adherence phase, followed by growth, proliferation, and maturation. However, microscopy techniques revealed that the architectural complexity of biofilms formed in SU medium was lower than that observed for those formed using RPMI medium. In particular, the level of filamentation of cells within the biofilms formed in SU medium was diminished compared to those in the biofilms grown in RPMI medium. This observation was also corroborated by expression profiling of five filamentation-associated genes using quantitative real-time reverse transcriptase PCR. Sessile
C. albicans
cells were resistant to fluconazole and amphotericin B, irrespective of the medium used to form the biofilms. However, caspofungin exhibited potent in vitro activity at therapeutic levels against
C. albicans
biofilms grown in both SU and RPMI media.
Moraxella lacunata
Septic Arthritis in a Patient with Lupus Nephritis
Authors: Woodbury Anna , Jorgensen James , Owens Aaron , Henao-Martinez Andres 
Published: October 2009

ABSTRACT

Moraxella lacunata
is a rare, usually commensal gram-negative rod most commonly associated with eye infections. We report a unique case of noniatrogenic
M
.
l
acunata
bacteremia and septic knee arthritis in a patient with class III-IV lupus nephritis and speculate on the association between invasive
Moraxella
infection and renal impairment.
Effects of Volume and Site of Blood Draw on Blood Culture Results
Authors: Gonsalves Wilson I. , Cornish Nancy , Moore Michael , Chen Aimin , Varman Meera 
Published: October 2009

ABSTRACT

Blood culture contamination greatly affects clinical decisions. Hence, it is of interest to assess the influence of factors such as the volume of blood drawn and the site of blood draw on the rates of blood culture contamination. In a retrospective study, blood cultures from infants and children up to 18 years of age who had at least one positive blood culture during the year 2006 were analyzed for their volume of blood drawn, patient's weight, site of blood draw used, and blood culture results. Blood cultures were deemed adequate collections if they contained an appropriate weight-related volume of blood. Moreover, blood culture results were categorized as true pathogens, contaminants, and negative cultures; these were then compared and analyzed with respect to their volume and site of blood draw. A total of 5,023 blood cultures were collected during 2006, of which 843 were analyzed. There were 306 (36%) positive cultures among the 843 cultures analyzed. Of the 306 positive cultures, 98 (32%) were contaminants and 208 (68%) cultures grew significant pathogens. Thirty-five percent of the contaminant cultures had adequate volume compared to 60% in the true bacteremia group (
P
< 0.001). Also, of the 843 cultures, the rates of contamination among the different sites of blood draw were as follows: peripheral venipuncture, 36%; arterial, 10%; and central venous access, 7% (
P
= 0.155). The rate of contamination was higher with lower blood volumes, and there was no significant difference in the rates of contamination among the different sites of blood draw.
The Cytoplasmic Domain of Human Immunodeficiency Virus Type 1 Transmembrane Protein gp41 Harbors Lipid Raft Association Determinants
Authors: Yang Polung , Ai Li-Shuang , Huang Shu-Chen , Li Hsiao-Fen , Chan Woan-Eng , Chang Chih-Wei , Ko Chiung-Yuan , Chen Steve S.-L. 
Published: October 2009

ABSTRACTThe molecular basis for localization of the human immunodeficiency virus type 1 envelope glycoprotein (Env) in detergent-resistant membranes (DRMs), also called lipid rafts, still remains unclear. The C-terminal cytoplasmic tail of gp41 contains three membrane-interacting, amphipathic α-helical sequences, termed lentivirus lytic peptide 2 (LLP-2), LLP-3, and LLP-1, in that order. Here we identify determinants in the cytoplasmic tail which are crucial for Env's association with Triton X-100-resistant rafts. Truncations of LLP-1 greatly reduced Env localization in lipid rafts, and the property of Gag-independent gp41 localization in rafts was conserved among different strains. Analyses of mutants containing single deletions or substitutions in LLP-1 showed that the α-helical structure of the LLP-1 hydrophobic face has a more-critical role in Env-raft associations than that of the hydrophilic face. With the exception of a Pro substitution for Val-833, all Pro substitution and charge-inverting mutants showed wild-type virus-like one-cycle viral infectivity, replication kinetics, and Env incorporation into the virus. The intracellular localization and cell surface expression of mutants not localized in lipid rafts, such as the TM844, TM813, 829P, and 843P mutants, were apparently normal compared to those of wild-type Env. Cytoplasmic subdomain targeting analyses revealed that the sequence spanning LLP-3 and LLP-1 could target a cytoplasmic reporter protein to DRMs. Mutations of LLP-1 that affected Env association with lipid rafts also disrupted the DRM-targeting ability of the LLP-3/LLP-1 sequence. Our results clearly demonstrate that LLP motifs located in the C-terminal cytoplasmic tail of gp41 harbor Triton X-100-resistant raft association determinants.
Evasion of the Mucosal Innate Immune System by Herpes Simplex Virus Type 2
Authors: Peng Tao , Zhu Jia , Klock Alexis , Phasouk Khamsone , Huang Meei-Li , Koelle David M. , Wald Anna , Corey Lawrence 
Published: October 2009

ABSTRACT
Understanding the mechanisms by which herpes simplex virus (HSV) evades host immune defenses is critical to defining new approaches for therapy and prevention. We performed transcriptional analyses and immunocytochemistry on sequential biopsy specimens of lesional tissue from the acute through the posthealing phases of recurrent mucocutaneous HSV-2 infection. Histological analysis of these biopsy specimens during the acute stage revealed a massive infiltration of T cells, as well as monocytes/macrophages, a large amount of myeloid, and a small number of plasmacytoid dendritic cells, in the dermis of these lesional biopsy specimens. Type I interferon (IFN-β and IFN-α) was poorly expressed and gamma IFN (IFN-γ) potently induced during time periods in which we detected abundant amounts of HSV-2 antigens and HSV-2 RNA. IFN-stimulated genes were also markedly upregulated, with expression patterns that more closely matched those in primary human fibroblasts treated by IFN-γ than those in fibroblasts treated by IFN-β. Transcriptional arrays of the same lesional biopsy sites during healing and at 2 and 4 weeks posthealing revealed no HSV nucleic acids or antigen; however, there was persistent expression of IFN-γ, with very low levels of IFN-β and IFN-α. The findings of extremely low levels of IFN-α and IFN-β, despite the presence of a large number of cells capable of synthesizing these substances, suggest a potent alteration in host defense during HSV-2 infection in vivo. HSV-2's blockade of the innate immune system's production of type I IFN may be a major factor in allowing the virus to break through host mucosal defenses.