bluuebunny/crossref_metadata_2025 huggingface dataset:
Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage
Authors: Ihmels Jan , Bergmann Sven , Gerami-Nejad Maryam , Yanai Itai , McClellan Mark , Berman Judith , Barkai Naama
Published: August 2005

Recent experiments revealed large-scale differences in the transcription programs of related species, yet little is known about the genetic basis underlying the evolution of gene expression and its contribution to phenotypic diversity. Here we describe a large-scale modulation of the yeast transcription program that is connected to the emergence of the capacity for rapid anaerobic growth. Genes coding for mitochondrial and cytoplasmic ribosomal proteins display a strongly correlated expression pattern in
Candida albicans
, but this correlation is lost in the fermentative yeast
Saccharomyces cerevisiae
. We provide evidence that this change in gene expression is connected to the loss of a specific cis-regulatory element from dozens of genes following the apparent whole-genome duplication event. Our results shed new light on the genetic mechanisms underlying the large-scale evolution of transcriptional networks.
Export-Mediated Assembly of Mycobacterial Glycoproteins Parallels Eukaryotic Pathways
Authors: VanderVen Brian C. , Harder Jeffery D. , Crick Dean C. , Belisle John T.
Published: August 2005

Protein
O
-mannosylation is an essential and evolutionarily conserved post-translational modification among eukaryotes. This form of protein modification is also described in
Mycobacterium tuberculosis
; however, the mechanism of mannoprotein assembly remains unclear. Evaluation of differentially translocated chimeric proteins and mass spectrometry to monitor glycosylation demonstrated that specific translocation processes were required for protein
O
-mannosylation in
M. tuberculosis
. Additionally, Rv1002c, a
M. tuberculosis
membrane protein homolog of eukaryotic protein mannosyltransferases, was shown to catalyze the initial step of protein mannosylation. Thus, the process of protein mannosylation is conserved between
M. tuberculosis
and eukaryotic organisms.
Sumptuous Survey of Hexapod History
Authors: Jarzembowski Edmund
Published: August 2005

Evolution of the Insects
.
By David Grimaldi and Michael S. Engel
. Cambridge University Press, Cambridge, 2005. 771 pp. $75, £45. ISBN 0-521-82149-5.

In a profusely illustrated account that synthesizes data from fossil and extant taxa, the authors cover the evolution and relationships of each hexapod order.
Use of a Suspension Array for Rapid Identification of the Varieties and Genotypes of the
Cryptococcus neoformans
Species Complex
Authors: Diaz Mara R. , Fell Jack W.
Published: August 2005

Cryptococcus neoformans
is an encapsulated fungal pathogen known to cause severe disease in immunocompromised patients. The disease, cryptococcosis, is mostly acquired by inhalation and can result in a chronic meningoencephalitis, which can be fatal. Here, we describe a molecular method to identify the varieties and genotypic groups within the
C. neoformans
species complex from culture-based assays. The method employs a novel flow cytometer with a dual laser system that allows the simultaneous detection of different target sequences in a multiplex and high-throughput format. The assay uses a liquid suspension hybridization format with specific oligonucleotide probes that are covalently bound to the surface of fluorescent color-coded microspheres. Biotinylated target amplicons, which hybridized to their complementary probe sequences, are quantified by the addition of the conjugate, streptavidin R-phycoerythrin. In this study we developed and validated eight probes derived from sequence analysis of the intergenic spacer region of the rRNA gene region. The assay proved to be specific and sensitive, allowed discrimination of a 1-bp mismatch with no apparent cross-reactivity, and detected 10
1
to 10
3
genome copies. The described protocol, which can be used directly with yeast cells or isolated DNA, can be undertaken in less than 1 h following PCR amplification and permits identification of species in a multiplex format. In addition to a multiplex capability, the assay allows the simultaneous detection of target sequences in a single reaction. The accuracy, speed, flexibility, and sensitivity of this technology are a few of the advantages that will make this assay useful for the diagnosis of human cryptococcal infections and other pathogenic diseases.
Development of a New Oligonucleotide Array To Identify Staphylococcal Strains at Species Level
Authors: Giammarinaro Philippe , Leroy Sabine , Chacornac Jean-Paul , Delmas Julien , Talon Regine
Published: August 2005

The genus
Staphylococcus
is made up of 36 validated species which contain strains that are pathogenic, saprophytic, or used as starter cultures for the food industry. An oligonucleotide array targeting the manganese-dependent superoxide dismutase (
sodA
) gene was developed to overcome the drawbacks of the conventional methods of identification. Divergences of the
sodA
gene were used to design oligonucleotide probes, and we showed that each of the 36 species had a characteristic pattern of hybridization. To evaluate the array, we analyzed 38 clinical and 38 food or food plant
Staphylococcus
isolates identified by the phenotype-based system VITEK 2 (bioMérieux). This commercial kit failed to identify 8 (21%) of the clinical isolates and 32 (84%) of the food and food plant isolates. In contrast, the oligonucleotide array we designed provided an accurate and rapid method for the identification of staphylococcal strains, isolated from clinical, environmental, or food samples, at species level.
Multilocus Sequence Typing of Swedish Invasive Group B Streptococcus Isolates Indicates a Neonatally Associated Genetic Lineage and Capsule Switching
Authors: Luan Shi-Lu , Granlund Margareta , Sellin Mats , Lagergård Teresa , Spratt Brian G. , Norgren Mari
Published: August 2005

Streptococcus agalactiae
, also designated group B streptococcus (GBS), is an important pathogen in neonates, pregnant women, and nonpregnant adults with predisposing conditions. We used multilocus sequence typing (MLST) to characterize 158 GBS isolates that were associated with neonatal and adult invasive disease and that were collected in northern and western Sweden from 1988 to 1997. Five major genetic lineages (sequence type [ST] 19, ST-17, ST-1, ST-23, and ST-9 complexes) were identified among the isolates, including serotype Ia, Ib, and II to V isolates, indicating a highly clonal population structure among invasive GBS isolates. A number of STs were found to contain isolates of different serotypes, which indicates that capsule switching occurred rather frequently. Two distantly related genetic lineages were identified among isolates of serotype III, namely, clonal complex 19 (CC19), and CC17. CC19 was equally common among isolates from adult and neonatal disease (accounting for 10.3% of GBS isolates from adult disease and 18.7% from neonatal disease), whereas CC17 significantly appeared to be associated with neonatal invasive disease (isolated from 21.9% of neonatal isolates but only 2.6% of adult isolates). The distribution of the mobile elements GBSi1 and IS
1548
reveals that they can act as genetic markers for lineages CC17 and CC19, respectively.
Ability of the Vector Tick
Boophilus microplus
To Acquire and Transmit
Babesia equi
following Feeding on Chronically Infected Horses with Low-Level Parasitemia
Authors: Ueti Massaro W. , Palmer Guy H. , Kappmeyer Lowell S. , Statdfield Mary , Scoles Glen A. , Knowles Donald P.
Published: August 2005

The protozoan parasite
Babesia equi
replicates within erythrocytes. During the acute phase of infection,
B. equi
can reach high levels of parasitemia, resulting in a hemolytic crisis. Horses that recover from the acute phase of the disease remain chronically infected. Subsequent transmission is dependent upon the ability of vector ticks to acquire
B. equi
and, following development and replication, establishment of
B. equi
in the salivary glands. Although restriction of the movement of chronically infected horses with
B. equi
is based on the presumption that ticks can acquire and transmit the parasite at low levels of long-term infection, parasitemia levels during the chronic phase of infection have never been quantified, nor has transmission been demonstrated. To address these epidemiologically significant questions, we established long-term
B. equi
infections (>1 year), measured parasitemia levels over time, and tested whether nymphal
Boophilus microplus
ticks could acquire and, after molting to the adult stage, transmit
B. equi
to naive horses.
B. equi
levels during the chronic phase of infection ranged from 10
3.3
to 10
6.0
/ml of blood, with fluctuation over time within individual horses.
B. microplus
ticks fed on chronically infected horses with mean parasite levels of 10
5.5
± 10
0.48
/ml of blood acquired
B. equi
, with detection of
B. equi
in the salivary glands of 7 to 50% of fed ticks, a range encompassing the percentage of positive ticks that had been identically fed on a horse in the acute phase of infection with high parasitemia levels. Ticks that acquired
B. equi
from chronically infected horses, as well as those fed during the acute phase of infection, successfully transmitted the parasite to naive horses. The results unequivocally demonstrated that chronically infected horses with low-level parasitemia are competent mammalian reservoirs for tick transmission of
B. equi
.
Identification of Medically Important Molds by an Oligonucleotide Array
Authors: Hsiao Chen Ren , Huang Liyin , Bouchara Jean-Philippe , Barton Richard , Li Hsin Chieh , Chang Tsung Chain
Published: August 2005

Infections caused by fungi have increased in recent years. Accurate and rapid identification of fungal pathogens is important for appropriate treatment with antifungal agents. On the basis of the internal transcribed spacer 1 (ITS 1) and ITS 2 sequences of the rRNA genes, an oligonucleotide array was developed to identify 64 species (32 genera) of clinically important filamentous (or dimorphic) fungi. These 64 species included fungi causing superficial, cutaneous, subcutaneous, and invasive infections. The method consisted of PCR amplification of the ITS regions using a pair of universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of species- or group-specific oligonucleotides immobilized on a nylon membrane. Of 397 fungal strains (290 target and 107 nontarget strains) tested, the sensitivity and specificity of the array was 98.3% (285/290) and 98.1% (105/107), respectively. Misidentified strains were usually those belonging to the same genus of the target species or having partial homology with oligonucleotide probes on the membrane. The whole procedure can be finished within 24 h starting from isolated colonies; reproductive structures, which are essential for the conventional identification methods, are not needed. In conclusion, the present array is a powerful tool for identification of clinically important filamentous fungi and may have the potential to be continually extended by adding further oligonucleotides to the array without significantly increasing the cost or complexity.
Broadly Reactive Nested Reverse Transcription-PCR Using an Internal RNA Standard Control for Detection of Noroviruses in Stool Samples
Authors: Medici Maria Cristina , Martinelli Monica , Ruggeri Franco Maria , Abelli Laura Anna , Bosco Simona , Arcangeletti Maria Cristina , Pinardi Federica , De Conto Flora , Calderaro Adriana , Chezzi Carlo , Dettori Giuseppe
Published: August 2005

We developed a nested reverse transcription-PCR (nRT-PCR) for the detection of noroviruses in stools, using random primers for RT, the JV12/JV13 primer pair in the first round of nPCR, and a set of nine inner primers for the second, comprising the reverse sequences of primers SR46, SR48, SR50, and SR52, and five novel oligonucleotide sequences (113-1, 113-2, 115-1, 115-2, and 115-3). The specificity of the nRT-PCR was confirmed by testing 61 stools containing enteric viruses other than noroviruses. In comparative assays on either stools or RNA dilutions from two genogroup I and three genogroup II (GII) norovirus-positive samples, nRT-PCR was always at least as sensitive as RT-PCR and Southern hybridization. With some of the samples tested, the increase in sensitivity was 10-fold or higher. For GII viruses, the detectable range of nRT-PCR was estimated to be 8.4 × 10
4
to 2 RNA viral particles. When used on 85 stools from pediatric patients with acute gastroenteritis negative for viruses by electron microscopy and cell culture, the nRT-PCR detected norovirus in 19 samples (22.3%), while it failed to detect one reference RT-PCR-positive sample containing a Desert Shield strain. Sixteen of the 19 nRT-PCR-positive samples gave concordant results with reference RT-PCR and Southern hybridization, and all with sequence analysis. Partial sequencing of the polymerase region revealed that from January to April 2000 all GII strains except two (Rotterdam- and Leeds-like viruses) formed a tight cluster related to Hawaii virus. The nRT-PCR described could prove suitable for large epidemiological studies and for specialized clinical laboratories performing routine molecular testing.
DNA Probe Array for the Simultaneous Identification of Herpesviruses, Enteroviruses, and Flaviviruses
Authors: Korimbocus Jehanara , Scaramozzino Noël , Lacroix Bruno , Crance Jean Marc , Garin Daniel , Vernet Guy
Published: August 2005

Viral infections of the central nervous system (CNS) are caused by a variety of viruses, namely, herpesviruses, enteroviruses, and flaviviruses. The similar clinical signs provoked by these viruses make the diagnosis difficult. We report on the simultaneous detection of these major CNS pathogens using amplification by PCR and detection of amplified products using DNA microarray technology. Consensus primers were used for the amplification of all members of each genus. Sequences specific for the identification of each virus species were selected from the sequence alignments of each target gene and were synthesized on a high-density microarray. The amplified products were pooled, labeled, and cleaved, followed by hybridization on a single array. This method was successfully used to identify herpesviruses, namely, herpes simplex virus type 1 (HSV-1), HSV-2, and cytomegalovirus; all serotypes of human enteroviruses; and five flaviviruses (West Nile virus, dengue viruses, and Langat virus). This approach, which used highly conserved consensus primers for amplification and specific sequences for identification, would be extremely useful for the detection of variants and would probably help solve some unexplained cases of encephalitis. The analytical sensitivity of the method was shown to be 500 genome equivalents ml
−1
for HSV-1, 0.3 50% tissue culture infectious doses (TCID
50
s) ml
−1
for the enterovirus coxsackievirus A9, and 200 TCID
50
s ml
−1
for West Nile virus. The clinical sensitivity of this method must now be evaluated.
Analysis of the Comparative Workflow and Performance Characteristics of the VITEK 2 and Phoenix Systems
Authors: Eigner U. , Schmid A. , Wild U. , Bertsch D. , Fahr A.-M.
Published: August 2005

The VITEK 2 (bioMérieux, Marcy L′Ètoile, France) and the Phoenix systems (BD Diagnostic Systems, Sparks, Md.) are automated instruments for rapid organism identification and susceptibility testing. We evaluated the workflow, the time to result, and the performance of identification and susceptibility testing of both instruments. A total of 307 fresh clinical isolates were tested: 141
Enterobacteriaceae
, 22 nonfermenters, 93
Staphylococcus
spp., and 51
Enterococcus
spp. Manipulation time was measured in batches, each with seven isolates, for a total of 39 batches. The mean (± standard deviation [SD]) manipulation time per batch was 20.9 ± 1.8 min for Phoenix and 10.6 ± 1.0 min for VITEK 2 (
P
< 0.001). Mean (±SD) time to result for all bacterial groups was 727 ± 162 min for Phoenix and 506 ± 120 min for VITEK 2 (
P
< 0.001). Concerning identification, Phoenix and VITEK 2 yielded the same results for nonfermenters (100%), staphylococci (97%), and enterococci (100%). For 140
Enterobacteriaceae
strains evaluated, 135 (96%) were correctly identified by Phoenix and 137 (98%) by VITEK 2 (
P
= 0.72). The overall category agreement for all isolates was 97.0% for both instruments. The minor error rate, major error rate, and very major error rate for all bacterial isolates tested were 3.0, 0.3, and 0.6 and 2.8, 0.2, and 1.7 for Phoenix and VITEK 2, respectively (
P
values of 0.76, 0.75, and 0.09). The VITEK 2 system required less manual manipulation time and less time than the Phoenix system to yield results.
Identification of Four Fimbria-Encoding Genomic Islands That Are Highly Specific for Verocytotoxin-Producing
Escherichia coli
Serotype O157 Strains
Authors: Shen Songhai , Mascarenhas Mariola , Morgan Robyn , Rahn Kris , Karmali Mohamed A.
Published: August 2005

Verocytotoxin-producing
Escherichia coli
causes zoonotic food- or waterborne infection that may be associated with massive outbreaks and with the serious complication of hemolytic uremic syndrome (HUS). Serotypes O157:H7 and O157:NM are more commonly associated with HUS and outbreaks than other serotypes, such as O26:H11. To determine whether a genetic basis exists for why serotype O157:H7/NM causes HUS and outbreaks more often than other serotypes, such as O26:H11, we conducted suppression subtractive hybridization (SSH) between the genomes of the sequenced O157:H7 strain EDL933 and CL1, a clinical serotype O26:H11 isolate. Genes from four EDL933 fimbria-encoding genomic O islands (OIs) (OI-1, -47, -141, and -154) were identified in the SSH library. OI-47 encodes several additional putative virulence factors, including secreted and signaling proteins, a hemolysin locus, a lipoprotein, an ABC transport system, and a lipid biosynthesis locus. The distribution of the OIs was investigated by PCR and Southern hybridization (when PCR was negative) with 69 VTEC strains belonging to 39 different serotypes corresponding to 5 seropathotypes that differ in their disease and epidemic potential. The four OIs described here were distributed almost exclusively in serotypes O157:H7 and O157:NM, which indicates that they may be associated with the ability of these strains to colonize human and/or animal intestinal tracts and to cause epidemic and serious disease more frequently than other serotypes. The occurrence of the four OIs in enteropathogenic
E. coli
O55:H7 strains is consistent with their vertical inheritance by VTEC O157:H7/NM from this clonally related ancestor.
Phylogenetic Analysis of the SpirochetesBorrelia parkeriandBorrelia turicataeand the Potential for Tick-Borne Relapsing Fever in Florida
Authors: Schwan Tom G. , Raffel Sandra J. , Schrumpf Merry E. , Policastro Paul F. , Rawlings Julie A. , Lane Robert S. , Breitschwerdt Edward B. , Porcella Stephen F.
Published: August 2005

Isolates ofBorrelia turicatae,Borrelia parkeri, and the Florida canine borrelia (FCB) were examined to further phylogenetically characterize the identities of these spirochetes in the United States. DNA sequences of four chromosomal loci (the 16S rRNA gene,flaB,gyrB, andglpQ) were determined for eight isolates ofB. turicataeand six isolates ofB. parkeri, which grouped the spirochetes into two distinct but closely related taxa (>98% sequence identity) separate fromBorrelia hermsii. The FCB was clearly separated with the group identified asB. turicatae, confirming this bacterium as a relapsing fever spirochete. Therefore, the potential for tick-borne relapsing fever in humans and other animals exists in Florida and future efforts are needed to determine the enzootic hosts and distribution of this spirochete in the southeastern United States. Analysis of plasmids demonstrated both linear and circular forms inB. turicataebut only linear plasmids inB. parkeri, which should be of interest to investigators concerned with plasmid diversity and evolution within this group of spirochetes.
Simultaneous Detection of Hepatitis C Virus (HCV) Core Antigen and Anti-HCV Antibodies Improves the Early Detection of HCV Infection
Authors: Laperche Syria , Le Marrec Nadine , Girault Annie , Bouchardeau Françoise , Servant-Delmas Annabelle , Maniez-Montreuil Michèle , Gallian Pierre , Levayer Thierry , Morel Pascal , Simon Nicole
Published: August 2005

To evaluate whether a new enzyme immunoassay developed for the simultaneous detection of hepatitis C virus (HCV) core antigen (Ag) and anti-HCV antibodies (anti-HCV Ab) (Monolisa HCV Ag/Ab ULTRA; Bio-Rad) could improve the early detection of HCV infection, we compared its sensitivity to that of anti-HCV, HCV core Ag, and HCV RNA assays. The populations studied included 12 blood donor samples positive for HCV RNA and HCV core Ag but negative for anti-HCV antibodies and 23 hemodialysis patients who developed anti-HCV Ab (seroconversion) during the follow-up. From these 23 individuals, 83 samples sequentially collected prior to seroconversion and 108 samples collected after seroconversion were tested. Six of 12 blood donations were positive by the HCV Ag/Ab assay. In the hemodialysis cohort, the 24 HCV RNA-negative samples were negative by the HCV Ag/Ab assay and 23 of the 59 HCV RNA-positive samples (39%) were positive. The HCV Ag/Ab assay detected HCV infection on average 21.6 days before the most sensitive antibody assay. The HCV Ag/Ab assay did not detect HCV infection as early as the HCV RNA assay (mean delay, 30.3 days) or HCV Ag assay (mean delays, 27.9, and 16.3 days by the HCV core Ag quantification assay and the HCV Ag blood screening assay, respectively). This new assay provides a notable improvement for the early detection of HCV infection during the so-called window period compared with anti-HCV Ab assays and could be a useful alternative to HCV RNA detection or HCV core Ag assays for diagnosis or blood screening when nucleic acid technologies or HCV core Ag detection are not implemented.
Use of a Heminested Reverse Transcriptase PCR Assay for Detection of Astrovirus in Environmental Swabs from an Outbreak of Gastroenteritis in a Pediatric Primary Immunodeficiency Unit
Authors: Gallimore Chris I. , Taylor Clive , Gennery Andrew R. , Cant Andrew J. , Galloway Angela , Lewis David , Gray Jim J.
Published: August 2005

An outbreak of astrovirus gastroenteritis occurred in the Primary Immunodeficiency Unit at Newcastle General Hospital in March 2004. Environmental swabbing of the unit was undertaken after the outbreak, with multiple sites swabbed pre- and postcleaning. Astroviruses were detected in four environmental swabs and from two patient fecal samples using heminested reverse transcriptase PCR. An astrovirus genotype 3 strain was identified in both environmental swabs and fecal specimens and was the strain identified as being responsible for the outbreak. Environmental transmission of the virus was thought to have occurred by contamination of a syringe pump outside the laminar-flow curtain of a patient who was admitted with astrovirus gastroenteritis. This was subsequently transmitted to a cubicle next door and to a television/games console in a parents' room in the ward. Environmental monitoring of surfaces/equipment, using PCR assays for gastroenteric viruses in hospital situations where infection can give rise to serious clinical complications, may have a role in controlling and monitoring cleaning and the subsequent prevention of nosocomial transmission of gastroenteritis.
Association of Tumor Necrosis Factora-2anda-8Microsatellite Alleles with Human Papillomavirus and Squamous Intraepithelial Lesions among Women in Brazil
Authors: Simões R. T. , Gonçalves M. A. G. , Donadi E. A. , Simões A. L. , Bettini J. S. R. , Duarte G. , Quintana S. M. , Carvalho M. W. P. , Soares E. G.
Published: August 2005

Infection with oncogenic human papillomavirus (HPV) is considered to be the major risk factor for cervical cancer. Tumor necrosis factor (TNF) is a pluripotent cytokine that plays an important role in inhibiting the action of microbial agents, andTNFmicrosatellite polymorphisms have been associated with several diseases, including cancer and viral infections. This study analyzed the associations betweenTNFato -emicrosatellite polymorphisms and the severity of squamous intraepithelial lesions (SIL), according to the presence of the oncogenic HPV16 and HPV18 types. Samples from 146 HPV-positive women with low-grade SIL (LSIL) and high-grade SIL (HSIL) and samples from 101 healthy women were studied.TNFmicrosatellite polymorphism typing and HPV detection and typing were performed using PCR-amplified DNA hybridized with sequence-specific primers. Data were analyzed by Fisher's exact test using the GENEPOP software. Significant associations were observed between LSIL and theTNFa-8allele (4/166;P= 0.04), as well as betweenTNFa-2with HPV18 only (16/44;P= 0.002) andTNFa-2with HPV18 coinfection with HPV16 (16/44;P= 0.001). Patients exhibiting theTNFa-2allele and harboring HPV18, in the presence or absence of coinfection with HPV16, had an increased risk of HSIL occurrence (13/38;P= 0.04; 5/10;P= 0.04) compared to patients with other HPV types. These results suggest that theTNFa-8allele is associated with increased susceptibility to the occurrence of LSIL and that despite the presence of a high TNF-α production allele, the ability of HPV18 to resist the inhibitory effects of TNF-α may contribute to the occurrence of infection and consequently to HSIL in women with cervical HPV18 infection.
Clinical and Microbiological Features ofInquilinussp. Isolates from Five Patients with Cystic Fibrosis
Authors: Chiron Raphaël , Marchandin Hélène , Counil François , Jumas-Bilak Estelle , Freydière Anne-Marie , Bellon Gabriel , Husson Marie-Odile , Turck Dominique , Brémont François , Chabanon Gérard , Segonds Christine
Published: August 2005

Patients with cystic fibrosis (CF) may be colonized with unusual gram-negative bacilli whose identification is difficult and clinical impact unclear. We describe the clinical and microbiological features of five colonizations with organisms belonging to the recently described genusInquilinusin CF patients. Isolates were identified fromBurkholderia cepaciaselective medium by means of 16S rRNA analysis. All of them were resistant to colistin, penicillins, cephalosporins, and monobactams but exhibited a remarkable susceptibility to imipenem. One of the five patients was transiently colonized with a nonmucoid isolate, whereas the four other patients were persistently colonized over the period of follow-up (8 to 21 months) with mucoid isolates. Pulsed-field gel electrophoresis of SpeI-digested genomic DNA was powerful for strain genotyping and demonstrated the clonality ofInquilinussp. colonization for the two patients tested. Clinical evolution after the onset ofInquilinuswas heterogeneous, but for at least one patient the lung function worsened and eradication ofInquilinussp. was unsuccessful despite several imipenem courses. Finally,Inquilinusspp. may represent a new threat for CF patients due to their mucoid characteristic, their multiresistant pattern to antibiotics, and their ability to persist in the respiratory tract.
Early Immune Response to the Components of the Type III System of
Pseudomonas aeruginosa
in Children with Cystic Fibrosis
Authors: Corech R. , Rao A. , Laxova A. , Moss J. , Rock M. J. , Li Z. , Kosorok M. R. , Splaingard M. L. , Farrell P. M. , Barbieri J. T.
Published: August 2005

The lungs of patients with cystic fibrosis (CF) are colonized initially by
Pseudomonas aeruginosa
, which is associated with progressive lung destruction and increased mortality. The pathogenicity of
P. aeruginosa
is caused by a number of virulence factors, including exotoxin A (ETA) and the type III cytotoxins (ExoS, ExoT, ExoU, and ExoY).
P. aeruginosa
contacts the plasma membrane to deliver type III cytotoxins through a channel formed by PopB, PopD, and PcrV; ETA enters mammalian cells via receptor-mediated endocytosis. The Wisconsin CF Neonatal Screening Project is a longitudinal investigation to assess the potential benefits and risks of newborn screening for CF; the project was the source of serum samples used in this study. Past studies evaluated the longitudinal appearance of antibodies to ETA and elastase and
P. aeruginosa
infections in patients with CF. The current study characterized the longitudinal appearance of antibodies to components of the type III system in children with CF. Western blot analyses showed that serum antibodies to PopB, PcrV, and ExoS were common. Longitudinal enzyme-linked immunosorbent assays determined that the first detection of antibodies to pooled ExoS/PopB occurred at a time similar to those of detection of antibodies to a
P. aeruginosa
cell lysate and the identification of oropharyngeal cultures positive for
P. aeruginosa
. This indicates that children with CF are colonized early with
P. aeruginosa
expressing the type III system, implicating it in early pathogenesis, and implies that surveillance of clinical symptoms, oropharyngeal cultures, and seroconversion to type III antigens may facilitate early detection of
P. aeruginosa
infections.
Detection of
Streptococcus pneumoniae
Antigen in Bronchoalveolar Lavage Fluid Samples by a Rapid Immunochromatographic Membrane Assay
Authors: Jacobs Jan A. , Stobberingh Ellen E. , Cornelissen Elisa I. M. , Drent Marjolein
Published: August 2005

We conducted a retrospective study to evaluate an immunochromatographic membrane test (ICT), applied to bronchoalveolar lavage (BAL) fluid samples obtained in patients with suspected pneumonia, for the detection of
Streptococcus pneumoniae
antigen. The NOW
Streptococcus pneumoniae
test was assessed on 96 BAL fluid samples. Sensitivity was tested in 20 samples obtained from patients diagnosed as having pneumococcal pneumonia (growth of
S. pneumoniae
in blood cultures and/or in BAL fluid samples of ≥10
4
CFU/ml). Specificity was tested in BAL fluid samples of nonpneumococcal etiology (
n
= 41) and in samples with no respiratory pathogen and a total bacterial count of <10
4
CFU/ml (
n
= 35). Using the ICT, pneumococcal antigen was detected in 29 (30.2%) BAL fluid samples, with a sensitivity of 95.0% (95% confidence interval [CI], 90.6% to 99.4%) and a specificity of 86.8% (95% CI, 80.1% to 93.8%). The ICT was easy to perform and revealed unequivocal and reproducible results. No interference was observed with high cell counts, red blood cells, or elevated protein levels. Four out of 10 false-positive readings occurred in samples with
S. pneumoniae
counts below the 10
4
CFU/ml threshold limit of pneumonia. In BAL fluid samples obtained after pneumococcal bacteremia, positive test results were found for up to 35 days after bacteremia. The ICT test applied to BAL fluid specimens is reproducible and accurate in the diagnosis of pneumococcal antigen. Further studies are required to establish the impact of the ICT on patient care.
Predominance of Rotavirus Genotype G9 during the 1999, 2000, and 2002 Seasons among Hospitalized Children in the City of Salvador, Bahia, Brazil: Implications for Future Vaccine Strategies
Authors: Santos Norma , Volotão Eduardo M. , Soares Caroline C. , Campos Gúbio S. , Sardi Silvia Ines , Hoshino Yasutaka
Published: August 2005

Two hundred eight of 648 (32%) diarrheal stool samples collected from hospitalized children under 5 years of age during a 3-year period (1999, 2000, and 2002) in the city of Salvador, in the state of Bahia, Brazil, were rotavirus positive. One hundred sixty-four of 208 (78.8%) rotavirus-positive samples had genotype G9 specificity, predominantly in association with P[8]. Other specificities detected were G1 (12.0%) and G4 (1.4%). Viruses with G2, G3, or P[4] specificity were not detected. Rotavirus genotype G9 predominated during each of the three seasons studied; it represented 89.2% of rotavirus strains detected in 1999, 85.3% in 2000, and 74.5% in 2002. G1 viruses (the globally most common G type) have a unique epidemiological characteristic of maintaining predominance during multiple consecutive rotavirus seasons. We have shown in this study for the first time that the G9 viruses also have a similar epidemiological characteristic, albeit for a shorter period of surveillance. The next generation of rotavirus vaccines will need to provide adequate protection against disease caused by G9 viruses.
Distribution of the Serine Protease Autotransporters of the
Enterobacteriaceae
among Extraintestinal Clinical Isolates of
Escherichia coli
Authors: Parham Nick J. , Pollard Samantha J. , Desvaux Mickaël , Scott-Tucker Anthony , Liu Chengjie , Fivian Amanda , Henderson Ian R.
Published: August 2005

Urinary tract infections continue to be among the most common extraintestinal diseases. Cystitis in women is by far the most common urinary tract infection; pyelonephritis in both sexes and prostatitis in men are more severe but less frequent complaints.
Escherichia coli
is by far the most common cause of urinary tract infection. It is believed that uropathogenic
E. coli
is adept at colonizing the urinary tract via the production of specific virulence factors. Recently, a novel virulence determinant, Vat, was described for the prototypical uropathogenic
E. coli
strain CFT073. Vat is a member of the SPATE (serine protease autotransporters of the
Enterobacteriaceae
) subfamily of the autotransporters. Previously, SPATEs have been described for all pathovars of
E. coli
, but until recently their presence had been noticeably absent in nonpathogenic
E. coli
. In this report we describe the prevalence and phylogenetic distribution of the SPATEs among uropathogenic
E. coli
and the ECOR collection, demonstrating an association between the presence of the SPATEs, including Vat, and uropathogenic
E. coli
phylogroups. In addition, we describe the distribution of SPATEs among nonpathogenic
E. coli
.
Genetic Diversity among Type
emm28
Group A
Streptococcus
Strains Causing Invasive Infections and Pharyngitis
Authors: Green Nicole M. , Beres Stephen B. , Graviss Edward A. , Allison James E. , McGeer Allison J. , Vuopio-Varkila Jaana , LeFebvre Rance B. , Musser James M.
Published: August 2005

Genome sequencing of group A
Streptococcus
(GAS) has revealed that prophages account for the vast majority of gene content differences between strains. Serotype M28 strains are a leading cause of pharyngitis and invasive infections, but little is known about genetic diversity present in natural populations of these organisms. To study this issue, population-based samples of 568 strains from Ontario, Canada; Finland; and Houston, Texas, were analyzed. Special attention was given to analysis of variation in prophage-encoded virulence gene content by a PCR-based method. Thirty and 29 distinct prophage-encoded virulence gene profiles were identified among pharyngitis and invasive infection isolates. Thirteen profiles, representing the majority of the strains, were shared between these two classes of isolates. Significant differences were observed in the frequency of occurrence of certain prophage toxin gene profiles and infection type. M28 strains are highly diverse in prophage-encoded virulence gene content and integration site, supporting the key concept that prophages are critical contributors to GAS genetic diversity and population biology. Nucleotide sequence variation in the
emm
gene (encodes M protein) was also examined. Only three allelic variants were identified in the hypervariable portion of the
emm28
gene. All but one strain had the same inferred amino acid sequence in the first 100 amino acids of the mature M28 protein. In contrast, size differences in the
emm28
gene and inferred protein due to variable numbers of C-terminal repeats were common. The presence of macrolide resistance genes (
mefA
,
ermB
, and
ermTR
) was analyzed by PCR, and less than 2% of the strains were positive.
Pilot Study To Evaluate Microarray Hybridization as a Tool forSalmonella entericaSerovar Typhimurium StrainDifferentiation
Authors: Pelludat C. , Prager R. , Tschäpe H. , Rabsch W. , Schuchhardt J. , Hardt W.-D.
Published: August 2005

In developed countries,Salmonella entericasubspecies 1 serovars Enteritidis and Typhimurium range among the most common causes of bacterial food-borne infections. The surveillance and typing of epidemicSalmonellastrains are important tools in epidemiology. Usually,Salmonella entericasubspecies 1 serovars are differentiated by serotyping for diagnostic purposes. Further differentiation is done by phage typing as well as molecular typing techniques. Here we have designed and evaluated a prototype DNA microarray as a tool for serovar Typhimurium strain differentiation. It harbors 83 serovar Typhimurium probes obtained by differential subtractive hybridization and from the public database. The microarray yielded reproducible hybridization patterns in repeated hybridizations with chromosomal DNA of the same strain and could differentiate five serovar Typhimurium reference strains (DT204, DT104, DT208, DT36, and LT2). Furthermore, the microarray identified two distinct groups among 13 serovar Typhimurium DT104 strains. This correlated with observations from pulsed-field gel electrophoresis analysis. Twenty-three further serovar Typhimurium strains were analyzed to explore future directions for optimization of the simple 83-probe DNA microarray. The data presented here demonstrate that DNA microarrays harboring small numbers of selected probes are promising tools for serovar Typhimurium strain typing.
OralCandidaIsolates Colonizing or Infecting Human Immunodeficiency Virus-Infected and Healthy Persons in Mexico
Authors: Sánchez-Vargas Luis Octavio , Ortiz-López Natalia Guadalupe , Villar María , Moragues María Dolores , Aguirre José Manuel , Cashat-Cruz Miguel , Lopez-Ribot Jose Luis , Gaitán-Cepeda Luis Alberto , Quindós Guillermo
Published: August 2005

Oral yeast carriage was studied in 312 Mexican subjects.Candida albicanswas the most frequent species, but otherCandidaspp. were isolated from 16.5 to 38.5% of patients. Colonization did not correlate with CD4+number or viral load, but highly active antiretroviral therapy reduced the frequency of candidiasis. Most isolates were susceptible to fluconazole, but 10.8% were resistant to one or more azoles.
Prevalence of Herpes Simplex Virus (Types 1 and 2), Varicella-Zoster Virus, Cytomegalovirus, and Human Herpesvirus 6 and 7 DNA in Cerebrospinal Fluid of Middle Eastern Patients with Encephalitis
Authors: Ibrahim Ali I. , Obeid Michel T. , Jouma Muhidien J. , Roemer Klaus , Mueller-Lantzsch Nikolaus , Gärtner Barbara C.
Published: August 2005

HSV-1 DNA was detected in 32 (30%) of 106 cerebrospinal fluid samples from patients with encephalitis. Cytomegalovirus, varicella-zoster virus, and human herpesvirus 6 (HHV-6) DNAs were each detected in three patients (3%); herpes simplex virus type 2 (HSV-2) and HHV-7 PCRs were negative. HSV detection was associated with seizure (P= 0.02), especially focal seizure (P= 0.0002), and pathological computed tomography (P= 0.02) with focal lesions (P= 0.0004).
Multilocus Sequence Typing of
Klebsiella pneumoniae
Nosocomial Isolates
Authors: Diancourt Laure , Passet Virginie , Verhoef Jan , Grimont Patrick A. D. , Brisse Sylvain
Published: August 2005

A multilocus sequence typing (MLST) scheme was developed for
Klebsiella pneumoniae
. Sequences of seven housekeeping genes were obtained for 67
K. pneumoniae
strains, including 19 ceftazidime- and ciprofloxacin-resistant isolates. Forty distinct allelic profiles were identified. MLST data were validated against ribotyping and showed high (96%) discriminatory power. The MLST approach provides unambiguous data useful for the epidemiology of
K. pneumoniae
isolates.
Dissemination of CTX-M-Type Extended-Spectrum β-Lactamase Genes to Unusual Hosts
Authors: Mugnaioli Claudia , Luzzaro Francesco , De Luca Filomena , Brigante Gioconda , Amicosante Gianfranco , Rossolini Gian Maria
Published: August 2005

A
Citrobacter amalonaticus
and a
Morganella morganii
producing the CTX-M-1 extended-spectrum β-lactamase (ESBL) were isolated from an area where this enzyme is now widespread in
Escherichia coli
. This is the first report of CTX-M-1 in the former species. In both cases the ESBL determinant was possibly acquired by these unusual hosts in vivo, after coinfection with
E. coli
strains carrying conjugative plasmids encoding CTX-M-1.
Comparison between Sequence Analysis and a Line Probe Assay for Testing Genotypic Resistance of Human Immunodeficiency Virus Type 1 to Antiretroviral Drugs
Authors: García-Bujalance S. , de Guevara C. Ladrón , González-García J. , Arribas J. R. , Gutiérrez A.
Published: August 2005

The purpose of this study was to compare a line probe assay (LiPA) with sequence analysis for the detection of mutations conferring resistance to nucleoside and non-nucleoside inhibitors in human immunodeficiency reverse transcriptase and protease inhibitors. The limitations for interpreting LiPA make it unacceptable for routine clinical practice.
Characterization of Prolyl Iminopeptidase-Deficient
Neisseria gonorrhoeae
Authors: Blackmore T. , Hererra G. , Shi S. , Bridgewater P. , Wheeler L. , Byrne J.
Published: August 2005

Prolyl iminopeptidase (PIP) is an enzyme produced by
Neisseria gonorrhoeae
, the detection of which is incorporated into several commercial test panels. In this report we describe two distinct mutations in the
pip
gene which account for the loss of PIP activity.
Isolation and Molecular Typing of
Naegleria fowleri
from the Brain of a Cow That Died of Primary Amebic Meningoencephalitis
Authors: Visvesvara Govinda S. , De Jonckheere Johan F. , Sriram Rama , Daft Barbara
Published: August 2005

Naegleria fowleri
causes an acute and rapidly fatal central nervous system infection called primary amebic meningoencephalitis (PAM) in healthy children and young adults. We describe here the identification of
N. fowleri
isolated from the brain of one of several cows that died of PAM based on sequencing of the internal transcribed spacers, including the 5.8S rRNA genes.
High Seroprevalence of Herpes Simplex Virus Type 2 Infection in French Human Immunodeficiency Virus Type 1-Infected Outpatients
Authors: Andréoletti Laurent , Piednoir Emmanuel , Legoff Jérôme , Brodard Véronique , Beguinot Isabelle , Strady Christophe , Rouger Christine , Piketty Christophe , Si-Mohamed Ali , Kazatchkine Michel Daniel , Malkin Jean-Elie , Bélec Laurent
Published: August 2005

Using commercially available herpes simplex virus (HSV) type-specific serological diagnostic tests, HSV type 2 (HSV-2) antibody prevalence was assessed in two parallel prospective studies including 534 human immunodeficiency virus type 1 (HIV-1)-infected outpatients living in two areas of northern France. In the first cohort of 434 subjects, 223 (51%) individuals demonstrated a positive HSV-2 serological status while 66 (66%) of 100 subjects in the second cohort were seropositive for HSV-2 (51 versus 66%;
P
= 0.08). Among the 223 HSV-2-seropositive subjects identified in the first study cohort, only 22 (10%) had suffered from recurrent anogenital lesions during the past 12 months while 154 (69%) had no clinical history of herpesvirus infection. Our findings demonstrate high proportions of subclinical and undiagnosed HSV-2 infection in HIV-1-infected individuals and suggest that HSV type-specific serological testing in the French HIV-1-infected subpopulation could be an efficient strategy to diagnose clinically asymptomatic HSV-2 infections.
Improved Sensitivity of Human Immunodeficiency Virus Type 2 Subtype B Plasma Viral Load Assay
Authors: Damond Florence , Collin Gilles , Descamps Diane , Matheron Sophie , Pueyo Sophie , Taieb Audrey , Campa Pauline , Benard Antoine , Chêne Geneviève , Brun-Vezinet Francoise
Published: August 2005

We developed a new assay for human immunodeficiency virus type 2 plasma RNA quantification based on a previous format. The new version performed significantly better than the original regarding the detection of subtype B, allowing the detection of 14 out of 36 plasma RNAs in the subtype B-infected patients not detected with the original version.
Long-Term Respiratory Tract Infection with Canine-Associated
Pasteurella dagmatis
and
Neisseria canis
in a Patient with Chronic Bronchiectasis
Authors: Allison Kim , Clarridge Jill E.
Published: August 2005

Pasteurella dagmatis
and
Neisseria canis
were repeatedly isolated from the sputum of a poodle-owning patient with chronic bronchiectasis. Commercially available systems failed to identify these unusual organisms: identification was made by 16S rRNA gene sequencing. Difficulties identifying these and five other canine-associated isolates (
P. dagmatis
[
n
= 2],
Pasteurella canis
[
n
= 2], and
N. canis
[
n
= 1]) are discussed.
Pulmonary
Mycobacterium sherrisii
Infection in a Human Immunodeficiency Virus Type 1-Infected Patient
Authors: Gämperli Andrea , Bosshard Philipp P. , Sigrist Thomas , Brändli Otto , Wildermuth Simon , Weber Rainer , Mueller Nicolas J.
Published: August 2005

We report the first case of a pulmonary infection with
Mycobacterium sherrisii
in a patient with advanced human immunodeficiency virus infection.
Mycobacterium sherrisii
is a newly described nontuberculous mycobacterium related to
Mycobacterium simiae
. Sequencing of the 16S rRNA gene was used for species identification. Treatment and antibiotic susceptibilities are described.
Recurrent early childhood injuries among disadvantaged children in primary care settings
Authors: Braun P A , Beaty B L , DiGuiseppi C , Steiner J F
Published: August 2005

Objective:To examine differences in social risk factors and health care use between young children with and without recurrent injuries.

Design:Retrospective cohort study using administrative claims and medical records. Children with no, one, or more than one injury were compared.

Setting:Integrated public healthcare system.

Subjects:All children born at Denver Health Medical Center (DHMC) in 1993 who continued care there beyond 15 months of age. Children were followed to 36 months.

Outcome measures:Sociodemographic information, service use, injury episodes, cause of injury, and social risk factors.

Results:371 injury episodes occurred among 817 children. In the study cohort, 7% had >1 injury episode, 26% had one injury, and 67% had none. Among children with >1 injury episode, 78% had at least one social risk factor compared with 63% of children with one injury and 52% of children with none (p<0.0001). Risk factors for >1 injury included maternal substance abuse (p = 0.0003), maternal age under 18 years (p = 0.04), a primary caregiver who was single (p<0.0001) or mentally ill (p = 0.03), and a history of family violence (p = 0.01). Multiple injury episodes were associated with increased non-injury service use, including primary care visits (p<0.0001), emergency department visits (p<0.0001), and total non-injury encounters (p<0.0001).

Conclusions:Children with recurrent injury were more likely to have social risk factors, and used DHMC more frequently, than children with one or no injuries. Children with risk factors for recurrent injury can be identified and injury prevention counseling can be delivered to their families at their multiple visits to the system.