bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraspecific Variability of the Terminal Inverted Repeats of the Linear Chromosome of
Streptomyces ambofaciens
Authors: Choulet Frédéric , Gallois Alexandre , Aigle Bertrand , Mangenot Sophie , Gerbaud Claude , Truong Chantal , Francou François-Xavier , Borges Frédéric , Fourrier Céline , Guérineau Michel , Decaris Bernard , Barbe Valérie , Pernodet Jean-Luc , Leblond Pierre 
Published: September 2006

ABSTRACT

The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two
Streptomyces ambofaciens
strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of
Streptomyces
plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.
FliT Acts as an Anti-FlhD
2
C
2
Factor in the Transcriptional Control of the Flagellar Regulon in
Salmonella enterica
Serovar Typhimurium
Authors: Yamamoto Shouji , Kutsukake Kazuhiro 
Published: September 2006

ABSTRACT

Flagellar operons are divided into three classes with respect to their transcriptional hierarchy in
Salmonella enterica
serovar Typhimurium. The class 1 gene products FlhD and FlhC act together in an FlhD
2
C
2
heterotetramer, which binds upstream of the class 2 promoters to facilitate binding of RNA polymerase. Class 2 expression is known to be enhanced by a disruption mutation in a flagellar gene,
fliT
. In this study, we purified FliT protein in a His-tagged form and showed that the protein prevented binding of FlhD
2
C
2
to the class 2 promoter and inhibited FlhD
2
C
2
-dependent transcription. Pull-down and far-Western blotting analyses revealed that the FliT protein was capable of binding to FlhD
2
C
2
and FlhC and not to FlhD alone. We conclude that FliT acts as an anti-FlhD
2
C
2
factor, which binds to FlhD
2
C
2
through interaction with the FlhC subunit and inhibits its binding to the class 2 promoter.
Signal Transduction Genes Required for Heterocyst Maturation in
Anabaena
sp. Strain PCC 7120
Authors: Fan Qing , Lechno-Yossef Sigal , Ehira Shigeki , Kaneko Takakazu , Ohmori Masayuki , Sato Naoki , Tabata Satoshi , Wolk C. Peter 
Published: September 2006

ABSTRACT
How heterocyst differentiation is regulated, once particular cells start to differentiate, remains largely unknown. Using near-saturation transposon mutagenesis and testing of transposon-tagged loci, we identified three presumptive regulatory genes not previously recognized as being required specifically for normal heterocyst maturation. One of these genes has a hitherto unreported mutant phenotype. Two previously identified regulatory genes were further characterized.
Genetic Variability in the G Protein Gene of Group A and B Respiratory Syncytial Viruses from India
Authors: Parveen Shama , Sullender Wayne M. , Fowler Karen , Lefkowitz Elliot J. , Kapoor Suresh Kumar , Broor Shobha 
Published: September 2006

ABSTRACT

Respiratory syncytial virus (RSV) is the most commonly identified viral agent of acute respiratory tract infection (ARI) of young children and causes repeat infections throughout life. Limited data are available on the molecular epidemiology of RSV from developing countries, including India. This study reports on the genetic variability in the glycoprotein G gene among RSV isolates from India. Reverse transcription-PCR for a region of the RSV G protein gene was done with nasopharyngeal aspirates (NPAs) collected in a prospective longitudinal study in two rural villages near Delhi and from children with ARI seen in an urban hospital. Nucleotide sequence comparisons among 48 samples demonstrated a higher prevalence of group A (77%) than group B (23%) RSV isolates. The level of genetic variability was higher among the group A viruses (up to 14%) than among the group B viruses (up to 2%). Phylogenetic analysis revealed that both the GA2 and GA5 group A RSV genotypes were prevalent during the 2002-2003 season and that genotype GA5 was predominant in the 2003-2004 season, whereas during the 2004-2005 season both genotype GA5 and genotype BA, a newly identified group B genotype, cocirculated in almost equal proportions. Comparison of the nonsynonymous mutation-to-synonymous mutation ratios (
dN
/
dS
) revealed greater evidence for selective pressure between the GA2 and GA5 genotypes (
dN
/
dS
, 1.78) than within the genotypes (
dN
/
dS
, 0.69). These are among the first molecular analyses of RSV strains from the second most populous country in the world and will be useful for comparisons to candidate vaccine strains.
Differential In Vitro Expression of the
brkA
Gene in
Bordetella pertussis
and
Bordetella parapertussis
Clinical Isolates
Authors: Stefanelli Paola , Sanguinetti Maurizio , Fazio Cecilia , Posteraro Brunella , Fadda Giovanni , Mastrantonio Paola 
Published: September 2006

ABSTRACT

In this study, we set up a real-time reverse transcriptase PCR assay to measure the relative amounts of
brkA
transcripts in 50
Bordetella
isolates. The results suggested that
brkA
expression is strain dependent and its level may play a role in determining the serum resistance or susceptibility phenotype. Pertussis immunocompetent sera were unable to kill
Bordetella parapertussis
via complement deposition.
Use of the Phoenix Automated System for Identification of
Streptococcus
and
Enterococcus
spp
Authors: Brigante Gioconda , Luzzaro Francesco , Bettaccini Alessia , Lombardi Gianluigi , Meacci Francesca , Pini Beatrice , Stefani Stefania , Toniolo Antonio 
Published: September 2006

ABSTRACT

The Phoenix system (Becton Dickinson Diagnostic Systems, Sparks, MD) was evaluated for identification (ID) to the species level of streptococci and enterococci. Two hundred clinical isolates were investigated: beta-hemolytic streptococci (
n
= 50),
Streptococcus pneumoniae
organisms (
n
= 46), viridans group streptococci (
n
= 31),
Enterococcus faecium
(
n
= 36),
Enterococcus faecalis
(
n
= 25), and other catalase-negative cocci (
n
= 12). The API system (bioMérieux, Marcy l'Étoile, France) was used as a comparator. Molecular methods (sequencing of 16S rRNA and
zwf
and
gki
genes and
ddl
gene amplification) were used to investigate discordant results. Upon resolution of discrepancies, correct species ID was achieved by the Phoenix system for 121/129 (93.8%) streptococci and 63/70 (90.0%) enterococci. Excellent results were obtained for
S. pneumoniae
(45/45) and beta-hemolytic streptococci (49/50). With regard to viridans streptococci, the accuracy of the Phoenix system was 83.9%. Among the latter organisms, the best performance was obtained with isolates of the
Streptococcus sanguinis
group and
Streptococcus anginosus
group; problems were instead encountered with the
Streptococcus mitis
group. Four
E. faecium
and three
E. faecalis
isolates were misidentified as
Enterococcus casseliflavus/Enterococcus gallinarum
or
Enterococcus durans
. Thus, these isolates were identified only at the genus level. Compared with commercially available systems, the Phoenix system appears a reliable diagnostic tool for identifying clinically relevant streptococci and enterococci. The SMIC/ID-2 panel proved particularly effective for beta-hemolytic streptococci and pneumococci.
Relevance of Influenza A Virus Detection by PCR, Shell Vial Assay, and Tube Cell Culture to Rapid Reporting Procedures
Authors: Zitterkopf Nicole L. , Leekha Surbhi , Espy Mark J. , Wood Christina M. , Sampathkumar Priya , Smith Thomas F. 
Published: September 2006

ABSTRACT
Influenza A virus was detected at higher rates and for more extended time periods with real-time PCR than with cell cultures. We show here that, using the theranostic approach, rapid viral detection and reporting can provide for early implementation and assessment of available antiviral therapy.
Molecular Epidemiology of Oral Treponemes in Patients with Periodontitis and in Periodontitis-Resistant Subjects
Authors: Moter Annette , Riep Birgit , Haban Vesna , Heuner Klaus , Siebert Gerda , Berning Moritz , Wyss Chris , Ehmke Benjamin , Flemmig Thomas F. , Göbel Ulf B. 
Published: September 2006

ABSTRACT

The etiologic role of oral treponemes in human periodontitis is still under debate. Although seen by dark-field microscopy in large numbers, their possible role is still unclear since they comprise some 60 different phylotypes, most of which are still uncultured. To determine their status as mere commensals or opportunistic pathogens, molecular epidemiological studies are required that include both cultured and as-yet-uncultured organisms. Here we present such data, comparing treponemal populations from chronic periodontitis (CP) or generalized aggressive periodontitis (GAP) patients. As a periodontitis-resistant (PR) control group, we included elderly volunteers with more than 20 natural teeth and no history of periodontal treatment and no or minimal clinical signs of periodontitis. Almost every treponemal phylotype was present in all three groups. For most treponemes, the proportion of subjects positive for a certain species or phylotype was higher in both periodontitis groups than in the PR group. This difference was pronounced for treponemes of the phylogenetic groups II and IV and for
Treponema socranskii
and
Treponema lecithinolyticum
. Between the periodontitis groups the only significant differences were seen for
T. socranskii
and
T. lecithinolyticum
, which were found more often in periodontal pockets of GAP patients than of CP patients. In contrast, no difference was found for
Treponema denticola
. Our findings, however, strengthen the hypothesis of treponemes being opportunistic pathogens. It appears that
T. socranskii
,
T. lecithinolyticum
and group II and IV treponemes may represent good indicators for periodontitis and suggest the value of the respective probes for microbiological diagnosis in periodontitis subjects.
Rapid Identification of Ascomycetous Yeasts from Clinical Specimens by a Molecular Method Based on Flow Cytometry and Comparison with Identifications from Phenotypic Assays
Authors: Page Brent T. , Shields Christine E. , Merz William G. , Kurtzman Cletus P. 
Published: September 2006

ABSTRACT

This study was designed to compare the identification of ascomycetous yeasts recovered from clinical specimens by using phenotypic assays (PA) and a molecular flow cytometric (FC) method. Large-subunit rRNA domains 1 and 2 (D1/D2) gene sequence analysis was also performed and served as the reference for correct strain identification. A panel of 88 clinical isolates was tested that included representatives of nine commonly encountered species and six infrequently encountered species. The PA included germ tube production, fermentation of seven carbohydrates, morphology on corn meal agar, urease and phenoloxidase activities, and carbohydrate assimilation tests when needed. The FC method (Luminex) employed species-specific oligonucleotides attached to polystyrene beads, which were hybridized with D1/D2 amplicons from the unidentified isolates. The PA identified 81 of 88 strains correctly but misidentified 4 of
Candida dubliniensis
, 1 of
C. bovina
, 1 of
C. palmioleophila
, and 1 of
C. bracarensis
. The FC method correctly identified 79 of 88 strains and did not misidentify any isolate but did not identify nine isolates because oligonucleotide probes were not available in the current library. The FC assay takes approximately 5 h, whereas the PA takes from 2 h to 5 days for identification. In conclusion, PA did well with the commonly encountered species, was not accurate for uncommon species, and takes significantly longer than the FC method. These data strongly support the potential of FC technology for rapid and accurate identification of medically important yeasts. With the introduction of new antifungals, rapid, accurate identification of pathogenic yeasts is more important than ever for guiding antifungal chemotherapy.
Abdominal Aortic Aneurysm Infected by
Yersinia pseudotuberculosis
Authors: Hadou Tahar , Elfarra Mazen , Alauzet Corentine , Guinet Françoise , Lozniewski Alain , Lion Christine 
Published: September 2006

ABSTRACT

Infected aneurysms caused by
Yersinia
are very uncommon and are principally due to
Yersinia enterocolitica
. We describe the first case of an infected aneurysm caused by
Yersinia pseudotuberculosis
in an elderly patient with a history of atherosclerotic cardiovascular disease.
Diagnostic Value of Reverse Transcription-PCR for Detection of Cytomegalovirus pp67 in Samples from Solid-Organ Transplant Recipients
Authors: Meyer-Koenig Ursula , Romberg Ilona , Schneider Kerstin , Weidmann Manfred , Kern Winfried V. , Hufert Frank T. 
Published: September 2006

ABSTRACT
We evaluated a highly sensitive quantitative real-time one-step reverse transcription-PCR (RT-PCR) for detection of human cytomegalovirus pp67 transcripts in monitoring of solid-organ transplant recipients. Results were compared with those of pp65 antigen testing and quantitative DNA-PCR. Due to a low clinical sensitivity, the pp67 RT-PCR was not able to replace these assays.
rpoB
Gene Mutations and Molecular Characterization of Rifampin-Resistant
Mycobacterium tuberculosis
Isolates from Shandong Province, China
Authors: Ma Xin , Wang Haiying , Deng Yunfeng , Liu Zhimin , Xu Yong , Pan Xi , Musser James M. , Graviss Edward A. 
Published: September 2006

ABSTRACT

Sixty rifampin (RIF)-resistant and 75 RIF-susceptible
Mycobacterium tuberculosis
isolates from Shandong Province, China, were analyzed for
rpoB
gene mutations and genotyped. Mycobacterial interspersed repetitive unit (MIRU) genotype 223325173533 was overrepresented among RIF-resistant isolates. MIRU combined with IS
6110
restriction fragment length polymorphism analysis as the second-line genotyping method may reflect epidemiologic links more reliably than each method alone.
Evaluation of the SPF
10
-INNO LiPA Human Papillomavirus (HPV) Genotyping Test and the Roche Linear Array HPV Genotyping Test
Authors: van Hamont Dennis , van Ham Maaike A. P. C. , Bakkers Judith M. J. E. , Massuger Leon F. A. G. , Melchers Willem J. G. 
Published: September 2006

ABSTRACT

The need for accurate genotyping of human papillomavirus (HPV) infections is becoming increasingly important, since (i) the oncogenic potential among the high-risk HPV genotypes varies in the pathogenesis of cervical cancer, (ii) monitoring multivalent HPV vaccines is essential to investigate the efficiency of the vaccines, and (iii) genotyping is crucial in epidemiologic studies evaluating HPV infections worldwide. Various genotyping assays have been developed to meet this demand. Comparison of different studies that use various HPV genotyping tests is possible only after a performance assessment of the different assays. In the present study, the SPF
10
LiPA version 1 and the recently launched Roche Linear Array HPV genotyping assays are compared. A total of 573 liquid-based cytology samples were tested for the presence of HPV by a DNA enzyme immunoassay; 210 were found to be positive for HPV DNA and were evaluated using both genotyping assays (163 with normal cytology, 22 with atypical squamous cells of undetermined significance, 20 with mild/moderate dysplasia, and 5 with severe dysplasia). Comparison analysis was limited to the HPV genotype probes common to both assays. Of the 160 samples used for comparison analysis, 129 (80.6%) showed absolute agreement between the assays (concordant), 18 (11.2%) showed correspondence for some but not all genotypes detected on both strips (compatible), and the remaining 13 (8.2%) samples did not show any similarity between the tests (discordant). The overall intertest comparison agreement for all individually detectable genotypes was considered very good (κ value, 0.79). The genotyping assays were therefore highly comparable and reproducible.
Molecular Characterization of Non-Penicillin-Susceptible
Streptococcus pneumoniae
in Norway
Authors: Sogstad Maren K. R. , Høiby E. Arne , Caugant Dominique A. 
Published: September 2006

ABSTRACT

A total of 125 non-penicillin-susceptible
Streptococcus pneumoniae
isolates were received at the Norwegian Institute of Public Health in the period from 1995 to 2001. The strains were tested for antimicrobial susceptibility, serotyped, and genotyped by multilocus sequence typing (MLST); and their penicillin-binding proteins (PBPs) were typed by restriction fragment length polymorphism analysis of their
pbp
genes. Of the 125 strains, 48 (38%) were fully resistant to penicillin and 77 (62%) were intermediately resistant to penicillin. Most of the strains resistant to penicillin were also resistant to one or several additional antibiotics. The most frequent serotypes among the non-penicillin-susceptible strains were 14, 9V, 19F, 23F, and 6B. MLST analysis showed a high degree of genetic diversity among the 119 strains tested, with a total of 74 different sequence types. Six of the 26 internationally known resistant clones were present; the Spain
9V
-3 clone was the most frequent, with 19 isolates. A total of 74 (62%) of the isolates were related to 1 of the 26 international clones. Restriction enzyme analyses of the
pbp1a
,
pbp2b
, and
pbp2x
genes revealed 12, 12, and 19 different patterns, respectively; and a total of 43 different PBPs types were demonstrated. Our data indicate that the non-penicillin-susceptible strains in Norway are highly diverse genetically and that limited spread of the internationally known resistant strains occurred in the country in the period examined.
Highly Effective Detection of Human Papillomavirus 16 and 18 DNA by a Testing Algorithm Combining Broad-Spectrum and Type-Specific PCR
Authors: van Doorn Leen-Jan , Molijn Anco , Kleter Bernhard , Quint Wim , Colau Brigitte 
Published: September 2006

ABSTRACT

The use of a single broad-spectrum human papillomavirus (HPV) DNA-based PCR test may fail to detect lower concentrations of HPV DNA due to competition between different genotypes in mixed infections. To improve HPV detection by PCR, broad-spectrum and type-specific (TS) PCRs were combined, with a focus on HPV-16 and HPV-18. Cervical and cervicovaginal cell samples were obtained from 1,113 healthy women (age range, 15 to 25 years) participating in an HPV-16/HPV-18 candidate vaccine efficacy trial. These samples were tested by a broad-spectrum SPF
10
PCR-DNA enzyme immunoassay, followed by a primer SPF
10
-based line probe assay (SPF
10
LiPA), and HPV-16- and HPV-18-TS PCRs. The results for the majority of the HPV-16/18 SPF
10
LiPA-positive samples were confirmed by TS-PCR (kappa values, 0.775 for HPV-16 and 0.785 for HPV-18). However, TS PCR revealed additional positive samples among those that contained other HPV genotypes due to competition. Conversely, SPF
10
LiPA identified HPV-16 or -18 in samples that remained negative by TS PCR as a result of sampling variation. Analysis of follow-up samples from more than 1,000 women confirmed that the combination of SPF
10
-LiPA with additional HPV-16- and HPV-18-TS PCR diminishes the rate of false-negative diagnosis. The combination of broad-spectrum and TS PCRs resulted in a novel testing algorithm. This combination of assays is more accurate than either method alone, and the novel algorithm offers a highly accurate and effective method for the analysis of HPV infections.
Characterization of
Bacillus cereus
Isolates Associated with Fatal Pneumonias: Strains Are Closely Related to
Bacillus anthracis
and Harbor
B. anthracis
Virulence Genes
Authors: Hoffmaster Alex R. , Hill Karen K. , Gee Jay E. , Marston Chung K. , De Barun K. , Popovic Tanja , Sue David , Wilkins Patricia P. , Avashia Swati B. , Drumgoole Rahsaan , Helma Charles H. , Ticknor Lawrence O. , Okinaka Richard T. , Jackson Paul J. 
Published: September 2006

ABSTRACT

Bacillus cereus
is ubiquitous in nature, and while most isolates appear to be harmless, some are associated with food-borne illnesses, periodontal diseases, and other more serious infections. In one such infection,
B. cereus
G9241 was identified as the causative agent of a severe pneumonia in a Louisiana welder in 1994. This isolate was found to harbor most of the
B. anthracis
virulence plasmid pXO1 (13). Here we report the characterization of two clinical and one environmental
B. cereus
isolate collected during an investigation of two fatal pneumonia cases in Texas metal workers. Molecular subtyping revealed that the two cases were not caused by the same strain. However, one of the three isolates was indistinguishable from
B. cereus
G9241. PCR analysis demonstrated that both clinical isolates contained
B. anthracis
pXO1 toxin genes. One clinical isolate and the environmental isolate collected from that victim's worksite contained the
cap A
,
B
, and
C
genes required for capsule biosynthesis in
B. anthracis
. Both clinical isolates expressed a capsule; however, neither was composed of poly-
d
-glutamic acid. Although most
B. cereus
isolates are not opportunistic pathogens and only a limited number cause food-borne illnesses, these results demonstrate that some
B. cereus
strains can cause severe and even fatal infections in patients who appear to be otherwise healthy.
Clonal Relationship among
Vibrio cholerae
O1 El Tor Strains Causing the Largest Cholera Epidemic in Kenya in the Late 1990s
Authors: Scrascia M. , Maimone F. , Mohamud K. A. , Materu S. F. , Grimont F. , Grimont P. A. D. , Pazzani C. 
Published: September 2006

ABSTRACT

Eighty
Vibrio cholerae
O1 strains selected to represent the 1998-to-1999 history of the largest cholera epidemic in Kenya were characterized by ribotyping, antimicrobial susceptibility, and random amplified polymorphic DNA patterns. Except for 19 strains from 4 local outbreaks in North Eastern Province along the Somalia border, the other 61 strains from 25 outbreaks occurring in districts scattered around the country were all ribotype B27 and resistant to chloramphenicol, spectinomycin, streptomycin, sulfamethoxazole, and trimethoprim. The 61 strains showed similar and specific amplified DNA patterns. These findings indicate that the predominant strains that caused the Kenyan epidemic had a clonal origin and suggest that ribotype B27 strains, which first appeared in West Africa in 1994, have had a rapid spread to eastern Africa.
Spread of Cholera with Newer Clones of
Vibrio cholerae
O1 El Tor, Serotype Inaba, in India
Authors: Dutta B. , Ghosh R. , Sharma N. C. , Pazhani G. P. , Taneja N. , Raychowdhuri A. , Sarkar B. L. , Mondal S. K. , Mukhopadhyay A. K. , Nandy R. K. , Bhattacharya M. K. , Bhattacharya S. K. , Ramamurthy T. 
Published: September 2006

ABSTRACT

During 2004 and 2005, cholera was recorded in 15 states of India, with 7 outbreaks. The newly emerged
Vibrio cholerae
O1 Inaba had a different antibiogram and ribotype, different pulsotypes, and different mutations in the
wbeT
gene. Due to the absence of serogroup O139, the Inaba serotype may have acquired the potential to affect the population at large.