bluuebunny/crossref_metadata_2025_split huggingface dataset:
PslD Is a Secreted Protein Required for Biofilm Formation by
Pseudomonas aeruginosa
Authors: Campisano Andrea , Schroeder Christine , Schemionek Mirle , Overhage Joerg , Rehm Bernd H. A. 
Published: April 2006

ABSTRACT

The function of
pslD
, which is part of the
psl
operon from
Pseudomonas aeruginosa
, was investigated in this study. The
psl
operon is involved in exopolysaccharide biosynthesis and biofilm formation. An isogenic marker-free
pslD
deletion mutant of
P. aeruginosa
PAO1 which was deficient in the formation of differentiated biofilms was generated. Expression of only the
pslD
gene coding region restored the wild-type phenotype. A C-terminal, hexahistidine tag fusion enabled the identification of PslD. LacZ and PhoA translational fusions with PslD indicated that PslD is a secreted protein required for biofilm formation, presumably via its role in exopolysaccharide export.
Arsenic Resistance in
Campylobacter
spp. Isolated from Retail Poultry Products
Authors: Sapkota Amy R. , Price Lance B. , Silbergeld Ellen K. , Schwab Kellogg J. 
Published: April 2006

ABSTRACT

Organoarsenicals are commonly used for growth promotion in U.S. poultry production. Susceptibilities to arsenite, arsenate, and the organoarsenical roxarsone were measured in 251
Campylobacter
isolates from conventional and antimicrobial-free retail poultry products. Isolates from conventional poultry products had significantly higher roxarsone MICs (
z
= 8.22;
P
< 0.0001).
Absence of VanA- and VanB-Containing Enterococci in Poultry Raised on Nonintensive Production Farms in Brazil
Authors: Batista Xavier Diego , Moreno Bernal Francisco Ernesto , Titze-de-Almeida Ricardo 
Published: April 2006

ABSTRACT

We examined cloacal samples from poultry raised on nonintensive production farms in Brazil for the presence of vancomycin-resistant enterococci. No VanA- or VanB-containing enterococci were identified in a total of 200 cloacal swabs. The most prevalent species were
Enterococcus gallinarum
(
vanC1
; 13.0%) and
E. casseliflavus
(
vanC2/3
; 5.5%).
Potential Impact of Conjugate Vaccine on the Incidence of Invasive Pneumococcal Disease among Children in Scotland
Authors: Clarke Stuart C. , Jefferies Johanna M. , Smith Andrew J. , McMenamin Jim , Mitchell Timothy J. , Edwards Giles F. S. 
Published: April 2006

ABSTRACT
We sought to determine the potential impact of seven-valent pneumococcal conjugate vaccine on the incidence of invasive pneumococcal disease (IPD) among children in Scotland. Invasive pneumococci from blood and cerebrospinal fluid, isolated between 2000 and 2004 from all children aged less than 5 years in Scotland, were characterized by serotyping. Using reported efficacy data of the seven-valent pneumococcal conjugate vaccine (PCV7) along with likely coverage rates, we made an estimation of the potential impact on the incidence of IPD among children in Scotland. A total of 217 pneumococci were characterized into 22 different serogroups/types, the most common, in rank order, being 14, 19F, 6B, 18C, 23F, 9V, 4, 1, 19A, and 6A. Estimated serotype coverage for PCV7 was 76.5% in those aged less than 5 years of age but increased to 88.9% for those aged 1 year. By using serotype coverage and estimates of vaccine efficacy and uptake, the potential impact of the vaccine for those greater than 2 months of age, but less than 5 years, was estimated as 67.3%, leading to an average of 29 preventable cases per year. The introduction of PCV7 into the childhood immunization schedule would reduce the burden of pneumococcal disease in children, and the incidence would be particularly reduced in those children aged 1 year. Additional benefits may be gained in adults through herd protection. Continued surveillance of IPD is required before, during, and after the introduction of PCV7.
Description ofMycobacterium conceptionensesp. nov., aMycobacterium fortuitumGroup Organism Isolated from a Posttraumatic Osteitis Inflammation
Authors: Adékambi Toïdi , Stein Andréas , Carvajal Joseph , Raoult Didier , Drancourt Michel 
Published: April 2006

ABSTRACTA nonpigmented rapidly growing mycobacterium was isolated from wound liquid outflow, bone tissue biopsy, and excised skin tissue from a 31-year-old woman who suffered an accidental open right tibia fracture and prolonged stay in a river. The three isolates grew in 3 days at 24 to 37°C. 16S rRNA sequence analyses over 1,483 bp showed that they were identical and shared 99.7% (4-bp difference) sequence similarity with that ofMycobacterium porcinum, the most closely related species. PartialrpoB(723 bp) sequence analyses showed that the isolates shared 97.0% sequence similarity with that ofM. porcinum. Further polyphasic approaches, including biochemical tests, antimicrobial susceptibility analyses, andhsp65,sodA, andrecAgene sequence analysis, as well as % G+C determination and cell wall fatty acid composition analysis supported the evidence that these isolates were representative of a new species. Phylogenetic analyses showed the close relationship withM. porcinumin theMycobacterium fortuitumgroup. The isolates were susceptible to most antibiotics and exhibited evidence for penicillinase activity, in contrast toM. porcinum. We propose the nameMycobacterium conceptionensesp. nov. for this new species associated with posttraumatic osteitis. The type strain is D16T(equivalent to CIP 108544Tand CCUG 50187T).
Identification and Quantification of Archaea Involved in Primary Endodontic Infections
Authors: Vianna M. E. , Conrads G. , Gomes B. P. F. A. , Horz H. P. 
Published: April 2006

ABSTRACT

Members of the domain
Archaea
, one of the three domains of life, are a highly diverse group of prokaryotes, distinct from bacteria and eukaryotes. Despite their abundance and ubiquity on earth, including their close association with humans, animals, and plants, so far no pathogenic archaea have been described. As some archaea live in close proximity to anaerobic bacteria, for instance, in the human gut system and in periodontal pockets, the aim of our study was to assess whether archaea might possibly be involved in human endodontic infections, which are commonly polymicrobial. We analyzed 20 necrotic uniradicular teeth with radiographic evidence of apical periodontitis and with no previous endodontic treatment. Using real-time quantitative PCR based on the functional gene
mcrA
(encoding the methyl coenzyme M reductase, specific to methanogenic archaea) and on archaeal 16S rRNA genes, we found five cases to be positive. Direct sequencing of PCR products from both genes showed that the archaeal community was dominated by a
Methanobrevibacter oralis
-like phylotype. The size of the archaeal population at the diseased sites ranged from 1.3 × 10
5
to 6.8 × 10
5
16S rRNA gene target molecule numbers and accounted for up to 2.5% of the total prokaryotic community (i.e., bacteria plus archaea). Our findings show that archaea can be intimately connected with infectious diseases and thus support the hypothesis that members of the domain
Archaea
may have a role as human pathogens.
Presence of E6 and E7 mRNA from Human Papillomavirus Types 16, 18, 31, 33, and 45 in the Majority of Cervical Carcinomas
Authors: Kraus Irene , Molden Tor , Holm Ruth , Lie A. Kathrine , Karlsen Frank , Kristensen Gunnar B. , Skomedal Hanne 
Published: April 2006

ABSTRACT
The oncogenic potential of the human papillomavirus (HPV) early genes E6 and E7 is well established and a source of interest with regard to HPV testing for cervical carcinoma. Here we present a study performed with 204 histologically confirmed invasive cervical squamous cell carcinomas (SCCs) in which we evaluated the HPV E6 and E7 mRNA detection assay PreTect HPV-Proofer for detection of high-risk HPV types 16, 18, 31, 33, and 45. For further evaluation, detection of E6 and E7 mRNA from HPV types 35, 52, and 58 by real-time multiplex nucleic acid sequence-based amplification was also included. For comparison and to assess the overall prevalence of various HPV types, samples were also tested for HPV DNA by both consensus and type-specific PCR, reverse line blotting, sequencing, and in situ hybridization. The overall prevalence of HPV was 97%. HPV E6 and E7 transcripts were detected in 188 of 204 (92%) biopsy specimens, of which 181 contained one of the following HPV types: 16, 18, 31, 33, or 45. Consensus PCR and type-specific PCR detected HPV in 187 of 204 and 188 of 204 (92%) specimens, respectively. In conclusion, this study verifies the presence of HPV E6 and E7 mRNA in SCCs and demonstrates that HPV infections among Norwegian women with SCCs are limited mainly to the five high-risk types, 16, 18, 31, 33, and 45. This, together with the fact that PreTect HPV-Proofer detects the HPV oncogenic transcripts, suggests that the assay is a valuable approach in the field of HPV detection in cervical carcinoma.
Occurrence of Overlooked Zoonotic Tuberculosis: Detection of
Mycobacterium bovis
in Human Cerebrospinal Fluid
Authors: Shah N. P. , Singhal A. , Jain A. , Kumar P. , Uppal S. S. , Srivatsava M. V. P. , Prasad H. K. 
Published: April 2006

ABSTRACT

The paucibacillary nature of the cerebrospinal fluid (CSF) has been a major obstacle in the diagnosis of human tuberculous meningitis (TBM). This study shows that with molecular techniques direct precise determination to the species level of mycobacterial pathogens can be made. The present report describes the utility of a nested PCR (N-PCR) assay (A. Mishra, A. Singhal, D. S. Chauhan, V. M. Katoch, K. Srivastava, S. S. Thakral, S. S. Bharadwaj, V. Sreenivas, and H. K. Prasad, J. Clin. Microbiol. 43:5670-5678, 2005) in detecting
M. tuberculosis
and
M. bovis
in human CSF. In 2.8% (6/212) of the samples,
M. tuberculosis
was detected, and in 17% (36/212),
M. bovis
was detected. Mixed infection was observed in 22 samples. Comparative analysis of clinical diagnosis, smear microscopy, and N-PCR in 69 patients (TBM, 25; non-TBM, 44) showed that the sensitivity of N-PCR (61.5%) was greater than that of smear microscopy (38.4%). Determination to the species level is important from the viewpoint of determining the prevalence of these mycobacteria in a community and would influence strategies currently adopted for the prevention of tuberculosis.
Rapid Detection of Norovirus from Fecal Specimens by Real-Time Reverse Transcription-Loop-Mediated Isothermal Amplification Assay
Authors: Fukuda Shinji , Takao Shinichi , Kuwayama Masaru , Shimazu Yukie , Miyazaki Kazuo 
Published: April 2006

ABSTRACT

In this study, we developed a one-step, single-tube genogroup-specific reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of norovirus (NoV) genomes targeting from the C terminus of the RNA-dependent RNA polymerase gene to the capsid N-terminal/shell domain region. This is the first report on the development of an RT-LAMP assay for the detection of NoV genomes. Because of the diversity of NoV genotypes, we used 9 and 13 specially designed primers containing mixed bases for genogroup I (GI) and II (GII), respectively. The RT-LAMP assay had the advantages of rapidity, simplicity, specificity, and selectively and could obtain results within 90 min, generally even within 60 min, under isothermal conditions at 62°C. The detection limits for NoV genomes were between 10
2
and 10
3
copies/tube for GI and GII with differentiation by genotype, and no cross-reactions among NoV GI and GII and other gastroenteritis viruses, such as sapovirus, human astrovirus, adenovirus type 40 and 41, and group A and C rotavirus, were found. In the evaluation tests with fecal specimens obtained from gastroenteritis outbreaks, the sensitivity and specificity of the RT-LAMP assay with regard to RT-PCR were 100 and 94% for GI and 100 and 100% for GII, respectively. These findings establish that the RT-LAMP assay is potentially useful for the rapid detection of NoV genomes from fecal specimens in outbreaks of food-borne and person-to-person-transmitted gastroenteritis.
Use of PCR and Reverse Line Blot Hybridization Assay for Rapid Simultaneous Detection and Serovar Identification of
Chlamydia trachomatis
Authors: Xiong Likuan , Kong Fanrong , Zhou Hua , Gilbert Gwendolyn L. 
Published: April 2006

ABSTRACT

The aim of this study was to develop and evaluate multiplex and nested PCR-reverse line blot (RLB) hybridization assays for detection and serovar identification of
Chlamydia trachomatis
. Two sets of primers targeting the VD2 region of the
omp1
gene and one set targeting the cryptic plasmid were designed for use in multiplex (both targets) and nested PCR (
omp1
only). For the RLB assay, labeled
omp1
amplicons were hybridized to a membrane containing probes specific for 15
C. trachomatis
serovars. The assays were used to test 429 clinical specimens, which had been previously tested for
C. trachomatis
using the COBAS AMPLICOR system. Specimens were tested without knowledge of the COBAS AMPLICOR result. Of 205 specimens that were positive by COBAS AMPLICOR, 201 (98%) were positive by multiplex PCR-RLB and 188 (92%) were also positive by
omp1
nested PCR-RLB. In addition, three of 224 COBAS AMPLICOR-negative specimens were positive by
omp1
nested PCR-RLB. One hundred sixty-six of 191 (87%) specimens in which
C. trachomatis
serovars were identified contained only one serovar and 25 (13%) contained two or three serovars. Serovars D, E, and F were found in 31 (16%), 83 (43%), and 51 (27%) specimens, respectively. Serovar E (41%) was the most commonly identified single serovar. Serovars J and K were found alone uncommonly (<2% each), but 18 of 25 (72%) specimens with multiple
C. trachomatis
serovars contained one or both (10 specimens) of these serovars. The nested (
ompI
) PCR-RLB is a specific and sensitive method for simultaneous detection and serovar identification of
C. trachomatis
, which can reliably identify mixed
C. trachomatis
serovars. It is suitable for use in epidemiological studies.
Use of a Serotype-Specific DNA Microarray for Identification of Group B
Streptococcus
(
Streptococcus agalactiae
)
Authors: Wen Linyan , Wang Quan , Li Yayue , Kong Fanrong , Gilbert Gwendolyn L. , Cao Boyang , Wang Lei , Feng Lu 
Published: April 2006

ABSTRACT

Group B
Streptococcus
(GBS;
Streptococcus agalactiae
) is an important cause of sepsis and meningitis. Nine GBS serotypes, based on capsular polysaccharide (CPS) antigens, have been described. Their distribution varies worldwide and needs to be monitored to understand the epidemiology of GBS disease and inform the development of vaccines. In this study, we sequenced
cpsH
of GBS serotype II (
cpsHII
) and compared it with that of the other eight serotypes to identify serotype-specific regions. We then developed a DNA microarray based on the
cpsH
gene and used it to test 88 GBS isolates—9 serotype reference strains and 79 clinical isolates—and 7 other bacterial and fungal species which are commonly present in the vagina flora. The microarray was shown to be specific and reproducible. This is the first report of a microarray which can identify the nine GBS serotypes. The use of a microarray has advantages over traditional serotyping methods and will be of practical value in both reference and diagnostic laboratories.
Can the
fliC
PCR-Restriction Fragment Length Polymorphism Technique Replace Classic Serotyping Methods for Characterizing the H Antigen of Enterotoxigenic
Escherichia coli
Strains?
Authors: Ramos Moreno Ana Carolina , Cabilio Guth Beatriz Ernestina , Baquerizo Martinez Marina 
Published: April 2006

ABSTRACT

In this study, we performed
fliC
PCR-restriction fragment length polymorphism (RFLP) to investigate whether this technique would be better than classic serotyping for the characterization of the H antigen in enterotoxigenic
Escherichia coli
(ETEC) strains. We showed that the
fliC
genes from ETEC strains can be characterized by restriction analysis of their polymorphism. Only one allele of the
fliC
gene from ETEC strains was found for each flagellar antigen, with the exception of H21. Nonmotile strains could also be characterized using this molecular technique. Moreover, determination of the somatic antigen was guided by the identification of the flagellar antigen from previously unknown serotypes of ETEC strains by PCR-RFLP, thus reducing the number of anti-antigen O sera used. The PCR-RFLP technique proved to be faster than classic serotyping for the characterization of the
E. coli
H antigen, taking 2 days to complete instead of the 7 or more days using classic serotyping. In conclusion, the H molecular typing for
Enterobacteriaceae
members may become an important epidemiological tool for the characterization of the H antigen of
E. coli
pathotypes. The PCR-RFLP technique is capable of guiding the determination of the H antigen and could partially replace seroagglutination. With the determination of the molecular profiles of alleles from strains obtained in epidemiological studies, new patterns will be described for ETEC strains or other
E. coli
pathotypes, thus permitting widespread use of this technique to characterize
fliC
genes and determine the H antigen of
E. coli
strains.
Characterization of Human Metapneumovirus Infections in Israel
Authors: Regev Liora , Hindiyeh Musa , Shulman Lester M. , Barak Asher , Levy Virginia , Azar Roberto , Shalev Yael , Grossman Zehava , Mendelson Ella 
Published: April 2006

ABSTRACT
Respiratory tract infections are a leading cause of morbidity and mortality worldwide. Even with the advancement of diagnostic tools, the causative agent of 20 to 30% of upper respiratory tract infections go undiagnosed. Recently, a newly identified human respiratory virus, human metapneumovirus (hMPV), was discovered in young children in The Netherlands. To study the prevalence of hMPV infections in Israeli children, respiratory specimens from 388 hospitalized children less than 5 years of age were evaluated for the presence of hMPV RNA, which was present in 42 (10.8%) of these samples. All hMPV-positive samples were negative for respiratory syncytial virus (RSV), influenza viruses (Flu) A and B, adenovirus, and parainfluenza viruses 1, 2, and 3. Conversely, hMPV RNA was not detected in 76 RSV-positive and 38 Flu A- or B-positive samples. Most hMPV activity was between the months February and April. Sequence analysis of 20 positive samples revealed that both of the hMPV genotypes (groups 1 and 2) have circulated in central Israel during the study period. Moreover, three of the four known hMPV subgroups (1A, 1B, and 2B) were detected among the tested samples. Seroprevalence of hMPV in 204 patients from the central part of Israel revealed that 100% of the children are hMPV seropositive by the age of 5 years old. We conclude that hMPV is a common respiratory pathogen in Israel, while mixed infections of hMPV with RSV or Flu in hospitalized children are apparently rare.
Quantification of Hepatitis B Virus (HBV) DNA with a TaqMan HBV Analyte-Specific Reagent following Sample Processing with the MagNA Pure LC Instrument
Authors: Germer Jeffrey J. , Qutub Mohammed O. , Mandrekar Jayawant N. , Mitchell P. Shawn , Yao Joseph D. C. 
Published: April 2006

ABSTRACT

TaqMan hepatitis B virus (HBV) analyte-specific reagent (ASR; Roche Molecular Systems, Inc., Branchburg, NJ) is designed for the quantification of HBV DNA in serum or plasma. The performance characteristics of TaqMan HBV ASR following automated sample processing with the MagNA Pure LC instrument (MP; Roche Applied Science, Indianapolis, IN) were evaluated in this study. Analytical sensitivity and precision were assessed with commercially available HBV standards, while clinical serum specimens from HBsAg-seropositive patients and healthy blood donors were used to determine clinical sensitivity, specificity, and correlation with other commercially available assays. Analytical studies yielded a limit of detection of 2.4 IU/ml, with good linearity and correlation (
R
2
= 0.9958) with expected HBV DNA titers over a wide range (6.0 × 10
0
to 2.1 × 10
8
IU/ml). Clinical sensitivity and specificity of the assay combined with automated sample processing were both 100%. Comparison of TaqMan HBV ASR and VERSANT HBV DNA 3.0 assay (bDNA; Bayer HealthCare LLC, Tarrytown, NY) results among clinical specimens yielded good correlation (
R
2
= 0.9237), with a mean difference in titer of −0.213 log
10
IU/ml (95% confidence interval, −0.678 to 1.10 log
10
IU/ml). The overall test failure rate was 2.0% among 204 clinical serum specimens tested. Total time required for MP sample processing and automated postelution handling of 24 samples was 224 min, with 57 min of actual hands-on time. MP is a reliable, labor-saving platform suitable for use with TaqMan HBV ASR, providing sensitive and accurate quantification of HBV DNA levels over a range of 8 log
10
IU/ml.
Differentiation of
Escherichia coli
Pathotypes by Oligonucleotide Spotted Array
Authors: Palaniappan Raghavan U. M. , Zhang Yu , Chiu David , Torres Alfonso , DebRoy Chobi , Whittam Thomas S. , Chang Yung-Fu 
Published: April 2006

ABSTRACT

To accurately determine the pathotypes of
Escherichia coli
strains, a comprehensive assessment of each strain that targets multiple genes is required. A new approach to the identification and characterization of
E. coli
pathotypes was developed by constructing gene-specific probes (70-mers) for not only the virulence genes associated with each
E. coli
pathotype but also the O157-, CFT073-, and K-12-specific and common genes of each pathotype. Analysis of oligonucleotide probes with reference and clinical isolates of
E. coli
pathotypes indicated that the array could differentiate the pathotypes on the basis of their virulence and specific gene patterns. Probes targeting common genes of
E. coli
were present in all the reference and clinical strains.
Salmonella enterica
subsp.
enterica
-specific genes and
Salmonella
core genes were used as negative controls. The entire
E. coli
pathotype showed reactivity to only 4 of the 81
Salmonella
-specific gene probes. Characterization of the genetic and virulence profiles of a single strain by using probes for virulence factors and specific and common genes in the spotted array is an ideal diagnostic tool for determination of
E. coli
pathotypes and could also have a significant impact on the epidemiological analysis of
E. coli
infections.
A Sensor To Detect the Early Stages in the Development of CrystallineProteus mirabilisBiofilm on Indwelling Bladder Catheters
Authors: Stickler D. J. , Jones S. M. , Adusei G. O. , Waters M. G. 
Published: April 2006

ABSTRACTA simple sensor has been developed to detect the early stages of urinary catheter encrustation and avoid the clinical crises induced by catheter blockage. In laboratory models of colonization byProteus mirabilis, the sensor signaled encrustation at an average time of 43 h before catheters were blocked with crystalline biofilm.
Molecular Investigation of Human Immunodeficiency Virus Type 2 Subtype A Cases in South Korea
Authors: Nam Jeong-Gu , Kim Gab Jung , Baek Jin Young , Suh Soon Duck , Kee Mee Kyung , Lee Joo-Shil , Kim Sung Soon 
Published: April 2006

ABSTRACT
We investigated the molecular characteristics of human immunodeficiency virus type 2 (HIV-2) subtype A isolates to clarify the transmission mode of HIV-2 within Korea. These findings indicated that the viruses from the six patients infected within Korea formed a distinct subcluster in the phylogenetic tree and might have been transmitted from one source.