bluuebunny/crossref_metadata_2025 huggingface dataset:
Respiratory Syncytial Virus Detection by Remel Xpect, Binax Now RSV, Direct Immunofluorescent Staining, and Tissue Culture
Authors: Borek Anita P. , Clemens Susan H. , Gaskins Valerie K. , Aird Deborah Z. , Valsamakis Alexandra
Published: March 2006

The performance characteristics of Xpect RSV (XP) and Binax Now RSV (BN) were compared to those of direct fluorescent-antibody staining and/or tissue culture for detection of respiratory syncytial virus (RSV) in nasopharyngeal aspirate and wash samples from children (
n
= 110) and adults (
n
= 66). The sensitivity, specificity, positive predictive value, and negative predictive value of XP were 75%, 98%, 95%, and 90%, respectively; and those of BN were 74%, 100%, 100%, and 90%, respectively. The performances of the assays were similar within a given age group and specimen type (nasopharyngeal aspirate or wash specimen). XP and BN are useful for screening for RSV in respiratory specimens when large volumes are tested or low levels of staffing occur.
Candida krusei
Transmission among Hematology Patients Resolved by Adapted Antifungal Prophylaxis and Infection Control Measures
Authors: Vos Margreet C. , Endtz Hubert P. , Horst-Kreft Deborah , Doorduijn Jeanette , Lugtenburg Elly , Verbrugh Henri A. , Löwenberg Bob , de Marie Siem , van Pelt Cindy , van Belkum Alex
Published: March 2006

A sudden increase in neutropenic hematology patients with
Candida krusei
colonization and bacteremia prompted a longitudinal epidemiological investigation. We identified 39 patients; 13 developed candidemia, and three died; 25 patients carried the same genotype. We intervened by changing antifungal prophylaxis and implementing strict infection control measures. The incidence dropped immediately.
Use of Sno Strip Filter-Paper Wicks for Collection of Genital-Tract Samples Allows Reproducible Determination of Human Immunodeficiency Virus Type 1 (HIV-1) RNA Viral Load with a Commercial HIV-1 Viral Load Assay
Authors: Sherlock Christopher H. , Lott Paula M. , Money Deborah M. , Merrick Linda , Arikan Yasemin , Remple Valencia P. , Craib Kevin , Burdge David R.
Published: March 2006

To assess the reproducibility of measurements of cervical and vaginal human immunodeficiency virus (HIV) viral load, 92 duplicate cervical and 88 duplicate vaginal samples were collected from 13 HIV-infected women using Sno Strip filter-paper wicks. RNA was eluted from the strips, extracted, and assayed using a modified protocol for the Roche Cobas Amplicor HIV-1 Monitor assay. Pearson's correlation coefficient (
R
), coefficient of determination (
D
), and Bland-Altman plots (BA) were used to compare paired log
10
-transformed viral loads. Analysis of duplicate same-site samples showed good reproducibility (cervix:
R
= 0.72,
D
= 52%, BA = 89% within range; vagina:
R
= 0.72,
D
= 51%, BA = 87% within range); paired cervix/vagina measurements showed moderate correlation only (
R
= 0.56;
D
= 31.3%). Standardized sample collection and simple modification of the Roche Cobas Amplicor HIV-1 Monitor assay allows reproducible measurement of genital viral load.
Identification of Human H1N2 and Human-Swine Reassortant H1N2 and H1N1 Influenza A Viruses among Pigs in Ontario, Canada (2003 to 2005)
Authors: Karasin Alexander I. , Carman Suzanne , Olsen Christopher W.
Published: March 2006

Since 2003, three novel genotypes of H1 influenza viruses have been recovered from Canadian pigs, including a wholly human H1N2 virus and human-swine reassortants. These isolates demonstrate that human-lineage H1N2 viruses are infectious for pigs and that viruses with a human PB1/swine PA/swine PB2 polymerase complex can replicate in pigs.
Consecutive Use of Two Multiplex PCR-Based Assays for Simultaneous Identification and Determination of Capsular Status of Nine Common
Neisseria meningitidis
Serogroups Associated with Invasive Disease
Authors: Bennett Désirée E. , Cafferkey Mary T.
Published: March 2006

We developed two
Neisseria meningitidis
multiplex PCR assays to be used consecutively that allow determination of the serogroup and capsular status of serogroup A, B, C, 29E, W135, X, and Y
cnl-3
/
cnl-1
-like-containing
N. meningitidis
isolates by direct analysis of the amplicon size. These assays offer a rapid and simple method of serogrouping
N. meningitidis
.
Emergence of Linezolid Resistance in the Vancomycin-Resistant
Enterococcus faecium
Multilocus Sequence Typing C1 Epidemic Lineage
Authors: Bonora Maria Grazia , Solbiati Maurizio , Stepan Erminia , Zorzi Antonella , Luzzani Aldo , Catania Maria Rosaria , Fontana Roberta
Published: March 2006

A relatively high rate of vancomycin-resistant
Enterococcus faecium
not susceptible to linezolid was observed in intensive care unit patients. Linezolid-resistant isolates carried the G2576T mutation in the 23S rRNA gene, belonged to different clones, and shared the same allelic profile, which clusters in the C1 multilocus sequence typing epidemic lineage.
Differentiation of Species Combined into the
Burkholderia cepacia
Complex and Related Taxa on the Basis of Their Fatty Acid Patterns
Authors: Krejčí Eva , Kroppenstedt Reiner M.
Published: March 2006

Using the established commercial system Sherlock (MIDI, Inc.), cellular fatty acid methyl ester analysis for differentiation among
Burkholderia cepacia
complex species was proven. The identification key based on the diagnostic fatty acids is able to discern phenotypically related
Ralstonia pickettii
and
Pandoraea
spp. and further distinguish
Burkholderia pyrrocinia
,
Burkholderia ambifaria
, and
Burkholderia vietnamiensis
.
Fatal Case of Community-Acquired Bacteremia and Necrotizing Fasciitis Caused by
Chryseobacterium meningosepticum
: Case Report and Review of the Literature
Authors: Lee Ching-Chi , Chen Po-Lin , Wang Li-Rong , Lee Hsin-Chun , Chang Chia-Ming , Lee Nan-Yao , Wu Chi-Jung , Shih Hsin-I , Ko Wen-Chien
Published: March 2006

A diabetic patient with chronic heart failure developed necrotizing fasciitis and bacteremia caused by
Chryseobacterium meningosepticum
, which rapidly evolved into death, even with fasciotomy and intensive care. A review of the English literature found 10 cases of soft tissue infection caused by
C. meningosepticum
, which is rarely acquired in the community.
Pelvic Abscess Due to
Ochrobactrum anthropi
in an Immunocompetent Host: Case Report and Review of the Literature
Authors: Vaidya Sagar A. , Citron Diane M. , Fine Marjorie B. , Murakami Georgette , Goldstein Ellie J. C.
Published: March 2006

Ochrobactrum anthropi
infection is rare in humans and is generally associated with immunocompromised hosts with indwelling foreign bodies. We report a case of pelvic abscess with
O. anthropi
after a routine appendectomy in an immunocompetent patient and review the literature on
O. anthropi
infection in patients with normal immune function.
Endocarditis Due toKytococcus schroeteri: Case Report and Review of the Literature
Authors: Mnif Basma , Boujelbène Inès , Mahjoubi Fouzia , Gdoura Radouane , Trabelsi Imen , Moalla Sana , Frikha Imed , Kammoun Samir , Hammami Adnane
Published: March 2006

We report the third case of endocarditis caused by the newly described micrococcal speciesKytococcus schroeteri. A 49-year-old woman was admitted to the hospital with suspected prosthetic valve endocarditis. Five blood cultures and prosthetic valve cultures grew the same type of organism, initially identified asMicrococcussp. Assignment to the genusKytococcuswas suggested by the arginine dihydrolase activity and resistance to oxacillin. After sequencing of the 16S rRNA genes, the isolate was recognized asK. schroeteri. The patient was treated first with vancomycin combined with gentamicin and later with pristinamycin and rifampin. Three cases ofK. schroeteriendocarditis described within a short period of time might indicate a specific pathogenicity of this new species. The isolation of kytococci from normally sterile sites should not be overlooked.
Recurrent Osteomyelitis Caused by Infection with Different Bacterial Strains without Obvious Source of Reinfection
Authors: Uçkay Ilker , Assal Mathieu , Legout Laurence , Rohner Peter , Stern Richard , Lew Daniel , Hoffmeyer Pierre , Bernard Louis
Published: March 2006

Recurrence of osteomyelitis by the same bacterial strain is well known. We report three patients with a second episode of osteomyelitis at the same site caused by different strains of bacteria from the original. Formerly infected and altered bone surface might present a region of diminished resistance for a new infection.
Identification of Medically Important Yeast Species by Sequence Analysis of the Internal Transcribed Spacer Regions
Authors: Leaw Shiang Ning , Chang Hsien Chang , Sun Hsiao Fang , Barton Richard , Bouchara Jean-Philippe , Chang Tsung Chain
Published: March 2006

Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as
Pichia
,
Rhodotorula
,
Trichosporon
, and
Saccharomyces
spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (
Rhodotorula glutinis
BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods.
Multidrug Resistance in
Salmonella enterica
Serotype Typhimurium from Humans in France (1993 to 2003)
Authors: Weill François-Xavier , Guesnier Françoise , Guibert Véronique , Timinouni Mohammed , Demartin Marie , Polomack Lucette , Grimont Patrick A. D.
Published: March 2006

The aim of this study was to determine the distribution of the antimicrobial resistance phenotypes (R types), the phage types and XbaI-pulsed-field gel electrophoresis (PFGE) types, the genes coding for resistance to β-lactams and to quinolones, and the class 1 integrons among a representative sample of
Salmonella enterica
serotype Typhimurium isolates collected from humans in 2002 through the French National Reference Center for
Salmonella
(NRC-Salm) network. The trends in the evolution of antimicrobial resistance of serotype Typhimurium were reviewed by using NRC-Salm data from 1993, 1997, 2000, and 2003. In 2002, 3,998 isolates of serotype Typhimurium were registered at the NRC-Salm among 11,775 serotyped
S. enterica
isolates (34%). The most common multiple antibiotic resistance pattern was resistance to amoxicillin, chloramphenicol, streptomycin and spectinomycin, sulfonamides, and tetracycline (ACSSpSuTe R type), with 156 isolates (48.8%). One isolate resistant to extended-spectrum cephalosporins due to the production of TEM-52 extended-spectrum β-lactamase was detected (0.3%), and one multidrug-resistant isolate was highly resistant to ciprofloxacin (MIC > 32 mg/liter). We found that 57.2% of the isolates tested belonged to the DT104 clone. The main resistance pattern of DT104 isolates was R type ACSSpSuTe (83.2%). However, evolutionary changes have occurred within DT104, involving both loss (variants of
Salmonella
genomic island 1) and acquisition of genes for drug resistance to trimethoprim or to quinolones. PFGE profile X1 was the most prevalent (74.5%) among DT104 isolates, indicating the need to use a more discriminatory subtyping method for such isolates. Global data from the NRC-Salm suggested that DT104 was the main cause of multidrug resistance in serotype Typhimurium from humans from at least 1997 to 2003, with a roughly stable prevalence during this period.
Analysis of Mutations within the 5′ Untranslated Region, Interferon Sensitivity Region, and PePHD Region as a Function of Response to Interferon Therapy in Hepatitis C Virus-Infected Patients in India
Authors: Gupta Romi , Subramani Murugan , Khaja Mohammed N. , Madhavi Chandra , Roy Swagata , Habibullah Chittoor M. , Das Saumitra
Published: March 2006

Mutations in several subgenomic regions have been implicated in influencing response to interferon therapy; however, a comprehensive picture of Indian patients was lacking. Based on the viral load and clinical factors, 10 out of 15 patients were found to be complete responders, whereas 5 patients were nonresponders. The pretreatment viral RNA load of the patients was found to be between 5.20 and 6.13 log
10
IU/ml, which eventually fell to 2.77 log
10
IU/ml after 24 weeks of treatment, whereas in the case of nonresponders, the average was 5.38 log
10
IU/ml. In order to study the influence of the hepatitis C virus genotype on the response to interferon therapy, the 5′ untranslated region sequences of the samples were analyzed, which showed that genotype 3 patients responded better than genotype 1 patients. Additionally, the mutations in the interferon sensitivity-determining region (ISDR) of the NS5A protein and the double-stranded RNA-activated protein kinase-eukaryotic initiation factor 2 alpha phosphorylation homology domain (PePHD) of the E2 envelope protein, before and after treatment, were compared with nonresponder prototype J. Although, no clear correlation was found in the case of the mutated ISDR, some significant changes in residues were observed in the PePHD region, which could be helpful in understanding the molecular basis of resistance to therapy. Interestingly, analysis of the quasispecies variations showed a change in genotype in one sample during treatment, which might have contributed to the resistance. The results suggest that the mutations in different regions of the viral genome might have a concerted effect on the response to interferon therapy.
Performance Assessment of the DR. MTBC Screen Assay and the BD ProbeTec ET System for Direct Detection of
Mycobacterium tuberculosis
in Respiratory Specimens
Authors: Wang Jann-Yuan , Lee Li-Na , Hsu Hsiao-Leng , Hsueh Po-Ren , Luh Kwen-Tay
Published: March 2006

The performance of the DR. MTBC PCR-based assay and the BD ProbeTec ET
Mycobacterium tuberculosis
Complex Direct Detection (DTB) assay for the direct detection of
Mycobacterium tuberculosis
was evaluated using 1,066 consecutive clinical respiratory samples collected from 494 patients who did not have old cases of pulmonary tuberculosis and were not receiving antituberculosis treatment at National Taiwan University Hospital from January to February 2005. The results of both assays were compared to the “gold standard” of combined culture results and clinical diagnosis. The overall sensitivity and specificity of the DR. MTBC Screen assay were 56.6% and 98.9%, respectively, and of the DTB assay were 63.2% and 98.4%, respectively. The positive and negative predictive values for the DR. MTBC Screen assay were 84.5% and 95.4%, respectively, and for the DTB assay were 81.7% and 96.0%, respectively. The DR. MTBC Screen assay produced 11 false-positive results for 11 patients, including three samples yielding non-
M. tuberculosis
mycobacteria (one each for
M. abscessus
, a mixture of
M. abscessus
and
M. chelonae
, and unidentified non-tuberculosis mycobacteria). The DTB assay produced 15 false-positive results for 13 patients, including five samples from four patients yielding non-tuberculosis mycobacteria (two for
M. abscessus
, one for a mixture of
M. abscessus
and
M. chelonae
, and two for unidentified non-tuberculosis mycobacteria). This study demonstrated that the DR. MTBC Screen assay has a similar diagnostic value but fewer false-positive results than the DTB assay for respiratory specimens.
Comparison between Two Amplification Sets for Molecular Diagnosis of Toxoplasmosis by Real-Time PCR
Authors: Cassaing S. , Bessières M. H. , Berry A. , Berrebi A. , Fabre R. , Magnaval J. F.
Published: March 2006

PCR is now commonly applied to the diagnosis of toxoplasmosis. Although several methods are available, comparative studies are few, making it difficult to compare the performance of each technique. We compared the sensitivities of two real-time PCR assays through a prospective study on fetuses, neonates, and immunocompromised patients and on the ocular diagnosis of toxoplasmosis. The first system targeted the widely used B1 gene (GenBank accession number AF179871) while the second (RE) targeted a more recently described sequence repeated roughly 200 to 300 times (GenBank accession number AF146527). We demonstrated that molecular diagnosis requires the duplication of PCR assays, especially with the B1 system, as only one PCR was positive in 33.3% of cases. Our study showed that the RE target was more sensitive for all biological samples (amniotic fluid, placenta, aqueous humor, whole blood, and cerebrospinal and bronchoalveolar fluids) and significantly improved the performance of the diagnosis of toxoplasmosis. Taking into consideration all clinical samples, the mean gain in the crossing point value was 4.2 ± 1.7 cycles and was even more significant for amniotic fluid (5.8 ± 1.7 cycles).
Molecular Genotyping of
Candida parapsilosis
Group I Clinical Isolates by Analysis of Polymorphic Microsatellite Markers
Authors: Lasker Brent A. , Butler Geraldine , Lott Timothy J.
Published: March 2006

Candida parapsilosis
, a pathogenic yeast, is composed of three newly designated genomic species that are physiologically and morphologically indistinguishable. Nosocomial infections caused by group I
C. parapsilosis
are often associated with the breakdown of infection control practices and the contamination of medical devices, solutions, and indwelling catheters. Due to the low levels of nucleotide sequence variation that are observed, an investigation of the size polymorphisms in loci harboring microsatellite repeat sequences was applied for the typing of
C. parapsilosis
group I isolates. PCR primer sets that flank the microsatellite repeats for seven loci were designed. Following amplification by PCR, the size of each amplification product was determined automatically by capillary electrophoresis. A total of 42
C. parapsilosis
group I isolates were typed by microsatellite analysis, and their profiles were compared to the hybridization profiles obtained by use of the Cp3-13 DNA probe. A high degree of discrimination (discriminatory power = 0.971) was observed by microsatellite analysis. The number of different alleles per locus ranged from 14 for locus B to 5 for locus C. Microsatellite analysis detected 30 different microsatellite genotypes, with 24 genotypes represented by a single isolate. Comparison of the genotypes obtained by microsatellite analysis and those obtained by analysis of the Cp3-13 hybridization profiles showed that they were similar, and these methods were able to identify related and unrelated isolates. Some discrepancies were observed between the methods and may be due to higher mutation rates and/or homoplasy by microsatellite markers. Identical results were observed between microsatellite analysis and Cp3-13 DNA hybridization profile analysis for
C. parapsilosis
isolates obtained from two patients, demonstrating the reproducibilities of the methods in vivo. Identical microsatellite profiles were observed for isolates displaying different phenotypic switching morphologies. Indistinguishable Cp3-13 DNA hybridization profiles were observed for six epidemiologically related isolates; however, only three of six primary isolates had identical microsatellite profiles. Size variation at a single locus was observed for three of six isolates obtained either after the outbreak period or from a different body site, suggesting the potential of the method to detect microevolutionary events. Interestingly, for most loci a single allele per strain was observed; in contrast, two alleles per locus were observed for some strains, and consistent with the findings for natural isolates, some isolates may be aneuploid. Due to the potential for high throughput, reproducibility, and discrimination, microsatellite analysis may provide a robust and efficient method for the genotyping of large numbers of
C. parapsilosis
group I isolates.
Effects ofMoraxella(Branhamella)ovisCulture Filtrates on Bovine Erythrocytes, Peripheral Mononuclear Cells, and Corneal Epithelial Cells
Authors: Cerny Henry E. , Rogers Douglas G. , Gray Jeffrey T. , Smith David R. , Hinkley Susanne
Published: March 2006

Infectious bovine keratoconjunctivitis (IBK) is a highly contagious ocular disease that affects cattle of all ages and that occurs worldwide. Piliated hemolyticMoraxella bovisis recognized as the etiologic agent of IBK. According to data from the Nebraska Veterinary Diagnostic Laboratory System, however,Moraxella(Branhamella)ovishas been isolated with increasing frequency from cattle affected with IBK. The objective of this study was, therefore, to examineM. ovisfield isolates for the presence of the putative virulence factors ofM. bovis. Culture filtrates from selectedM. ovisfield isolates demonstrated hemolytic activity on bovine erythrocytes and cytotoxic activity on bovine peripheral blood mononuclear cells and corneal epithelial cells. The hemolytic activity of the culture filtrates was attenuated after heat treatment. Polyclonal antibodies raised against theM. bovishemolysin-cytotoxin also recognized a protein of approximately 98 kDa in a Western blot assay. These data indicate that theM. ovisfield isolates examined produce one or more heat-labile exotoxins and may suggest thatM. ovisplays a role in the pathogenesis of IBK.
Isolation of the Genome Sequence StrainMycobacterium avium104 from Multiple Patients over a 17-Year Period
Authors: Horan Kathleen L. , Freeman Robert , Weigel Kris , Semret Makeda , Pfaller Stacy , Covert Terry C. , van Soolingen Dick , Leão Sylvia C. , Behr Marcel A. , Cangelosi Gerard A.
Published: March 2006

The genome sequence strain 104 of the opportunistic pathogenMycobacterium aviumwas isolated from an adult AIDS patient in Southern California in 1983. Isolates of non-paratuberculosisM. aviumfrom 207 other patients in Southern California and elsewhere were examined for genotypic identity to strain 104. This process was facilitated by the use of a novel two-step approach. In the first step, all 208 strains in the sample were subjected to a high-throughput, large sequence polymorphism (LSP)-based genotyping test, in which DNA from each strain was tested by PCR for the presence or absence of 4 hypervariable genomic regions. Nineteen isolates exhibited an LSP type that resembled that of strain 104. This subset of 19 isolates was then subjected to high-resolution repetitive sequence-based PCR typing, which identified 10 isolates within the subset that were genotypically identical to strain 104. These isolates came from 10 different patients at 5 clinical sites in the western United States, and they were isolated over a 17-year time span. Therefore, the sequenced genome ofM. aviumstrain 104 has been associated with disease in multiple patients in the western United States. AlthoughM. aviumis known for its genetic plasticity, these observations also show that strains of the pathogen can be genotypically stable over extended time periods.
Genetic Heterogeneity of Shiga Toxin-Producing
Escherichia coli
Strains Isolated in São Paulo, Brazil, from 1976 through 2003, as Revealed by Pulsed-Field Gel Electrophoresis
Authors: Vaz Tânia Mara I. , Irino Kinue , Nishimura Lucilia S. , Cergole-Novella Maria Cecília , Guth Beatriz Ernestina C.
Published: March 2006

The pulsed-field gel electrophoresis (PFGE) patterns of 46 Shiga toxin-producing
Escherichia coli
(STEC) strains isolated in São Paulo, Brazil, during the period from 1976 to 2003 were compared with those found among 30 non-STEC strains that carried
eae
and that belonged to the same serogroups as the STEC strains. All except two of the STEC and non-STEC strains of human origin were from sporadic and unrelated cases of infection; two O111 strains originated from the same patient. Multiple PFGE patterns were found among STEC strains of distinct serotypes. Moreover, the PFGE restriction patterns of STEC strains differed substantially from those observed among non-STEC strains of the same serogroup except serotype O26 strains. Based on the indistinguishable PFGE pattern for two O157:H7 STEC strains isolated in the same geographic area at an interval of approximately 15 days and toxin profile data, the first occurrence of an O157:H7 outbreak in Brazil during that period can be suggested. In general, a close relationship between types of intimin, serotypes, and diarrheagenic groups of
E. coli
was observed. This is the first time that a large collection of STEC strains from Brazil has been analyzed, and a great genetic diversity was shown among O157:H7 and non-O157:H7 STEC strains isolated in São Paulo, Brazil.
Evaluation of MGIT 960-Based Antimicrobial Testing and Determination of Critical Concentrations of First- and Second-Line Antimicrobial Drugs with Drug-Resistant Clinical Strains of
Mycobacterium tuberculosis
Authors: Krüüner Annika , Yates Malcolm D. , Drobniewski Francis A.
Published: March 2006

The objectives of this study were to (i) compare agreement of the MGIT 960 system for first-line drugs with a methodology (the resistance ratio method [RRM]) that had been used in clinical trials, relating drug susceptibility to clinical outcome; (ii) compare the performance of the MGIT 960, RRM, and microtiter plate assay (MPA) methodologies for second-line drug testing; and (iii) define critical concentrations for ciprofloxacin and moxifloxacin for liquid-culture-based testing. The large collection of clinical isolates of
Mycobacterium tuberculosis
(
n
= 247) used included 176 (71%) multidrug-resistant isolates. The results for MGIT 960 and the RRM for rifampin and isoniazid (
n
= 200) were in excellent (99 to 100%) agreement for all strains. For streptomycin, 97% of the results at the critical concentration and 92% at high concentration, and for pyrazinamide 92% of results overall, were concordant, but for ethambutol, fewer than 85% (65% for the critical concentration and 84% for the high concentration) of the MGIT-based results were concordant with those for the RRM. The MGIT 960, RRM, and MPA assays (
n
= 133) correlated well for most second-line drugs tested. For susceptibility to ofloxacin, the MGIT 960 and MPA results were in full agreement. The amikacin and rifabutin results obtained by MGIT 960 agreed with the RRM results in 131 (99%) cases, and for capreomycin, they agreed for 129 of 133 isolates tested (97%). For prothionamide testing, only a limited number of drug-resistant isolates were available for testing and drawing definitive conclusions. We propose critical concentrations of 1.0 μg/ml and 0.125 μg/ml for ciprofloxacin and moxifloxacin, respectively, for liquid-culture-based testing.
Sequencing of the
rpoB
Gene and Flanking Spacers for Molecular Identification of
Acinetobacter
Species
Authors: La Scola Bernard , Gundi Vijay A. K. B. , Khamis Atieh , Raoult Didier
Published: March 2006

Acinetobacter
species are defined on the basis of several phenotypic characters, results of DNA-DNA homology, and more recently, similarities or dissimilarities in 16S rRNA gene sequences. However, the 16S rRNA gene is not polymorphic enough to clearly distinguish all
Acinetobacter
species. We used an RNA polymerase β-subunit gene (
rpoB
)-based identification scheme for the delineation of species within the genus
Acinetobacter
, and towards that end, we determined the complete
rpoB
gene and flanking spacer (
rplL
-
rpoB
and
rpoB
-
rpoC
) sequences of the 17 reference strains of
Acinetobacter
species and 7 unnamed genomospecies. By using complete gene sequences (4,089 bp), we clearly separated all species and grouped them into different clusters. A phylogenetic tree constructed using these sequences was supported by bootstrap values higher than those obtained with 16S rRNA or the
gyrB
or
recA
gene. Four pairs of primers enabled us to amplify and sequence two highly polymorphic partial sequences (350 and 450 bp) of the
rpoB
gene. These and flanking spacers were designed and tested for rapid identification of the 17 reference strains of
Acinetobacter
species and 7 unnamed genomospecies. Each of these four variable sequences enabled us to delineate most species. Sequences of at least two polymorphic sequences should be used to distinguish
Acinetobacter grimontii
,
Acinetobacter junii
,
Acinetobacter baylyi
, and genomic species 9 from one another. Finally, 21 clinical isolates of
Acinetobacter baumannii
were tested for intraspecies relationships and assigned correctly to the same species by comparing the partial sequences of the
rpoB
gene and its flanking spacers.
Report of Two Fatal Cases of
Mycobacterium mucogenicum
Central Nervous System Infection in Immunocompetent Patients
Authors: Adékambi Toïdi , Foucault Cedric , La Scola Bernard , Drancourt Michel
Published: March 2006

Neurological infections due to rapidly growing mycobacteria (RGM) have rarely been reported. We recently investigated two unrelated immunocompetent patients, one with community-acquired lymphocytic meningitis and the other with cerebral thrombophlebitis.
Mycobacterium mucogenicum
was isolated in pure culture and detected by PCR sequencing of cerebrospinal fluid samples. Both patients eventually died. The two isolates exhibited an overlapping antimicrobial susceptibility pattern. They were susceptible in vitro to tetracyclines, macrolides, quinolones, amikacin, imipenem, cefoxitin, and trimethoprim-sulfamethoxazole and resistant to ceftriaxone. They shared 100% 16S rRNA gene sequence similarity with
M. mucogenicum
ATCC 49650
T
over 1,482 bp. Their partial
rpoB
sequences shared 97.8% and 98.1% similarity with
M. mucogenicum
ATCC 49650
T
, suggesting that the two isolates were representative of two sequevars of
M. mucogenicum
species. This case report should make clinicians aware that
M. mucogenicum
, an RGM frequently isolated from tap water or from respiratory specimens and mostly without clinical significance, can even be encountered in the central nervous system of immunocompetent patients.
Clonal Relationships between Invasive and Noninvasive Lancefield Group C and G Streptococci and
emm
-Specific Differences in Invasiveness
Authors: Pinho M. D. , Melo-Cristino J. , Ramirez M. ,   the Portuguese Group for the Study of Streptococcal Infections
Published: March 2006

Lancefield group G and group C streptococci (GGS and GCS, respectively) are pathogens responsible for a number of life-threatening infections. A collection of 116 recent (1998 to 2004) invasive (
n
= 28) and noninvasive (
n
= 88) GGS and GCS clinical isolates from Portugal were characterized. All isolates were identified as
Streptococcus dysgalactiae
subsp.
equisimilis
and characterized by
emm
typing and DNA macrorestriction profiling using pulsed-field gel electrophoresis (PFGE).
emm
typing revealed the presence of 22 distinct types, including 3 novel types. PFGE identified 14 clones with more than two isolates, but over half of the isolates were concentrated in 3 large clones. Individual clones and
emm
types showed a low level of association, since the majority of the clones included more than one
emm
type and the same
emm
type was found among diverse genetic backgrounds. Two
emm
types,
stg2078
and
stg10
, were significantly more frequent among invasive isolates, and another two,
stg6792
and
stg166b
, were present only in noninvasive isolates, suggesting a correlation between
emm
type and invasive disease potential.
Sensitivity of
Escherichia coli
O157 Detection in Bovine Feces Assessed by Broth Enrichment followed by Immunomagnetic Separation and Direct Plating Methodologies
Authors: LeJeune Jeffrey T. , Hancock Dale D. , Besser Thomas E.
Published: March 2006

In order to more precisely predict food safety risks, the fecal presence of food-borne pathogens among animals at slaughter must be correctly determined. Quantification of
Escherichia coli
O157 is also desirable. In two separate experiments, detection and enumeration of a nalidixic acid-resistant strain of
E. coli
O157 in bovine feces was assessed by culture on MacConkey agar supplemented with nalidixic acid (MACnal) and compared to overnight broth enrichment followed by immunomagnetic separation (IMS) and to direct plating of dilutions of bovine feces onto sorbitol MacConkey agar containing cefixime and tellurite (SMACct). The sensitivity of detection of
E. coli
O157 by both direct plating and IMS was highly dependent upon the initial concentration of the target organism in the sample. Sensitivity of detection by IMS was poor below 100 CFU/g but was better, and not affected by initial
E. coli
O157 numbers, above this concentration. Sensitivity of detection of
E. coli
O157 in bovine feces at low initial concentrations is very poor for both direct plating and IMS. Direct plating of dilutions of bovine feces on SMACct can be used to determine the magnitude of fecal
E. coli
excretion among cattle excreting greater than 100 CFU/g. Among positive samples identified by direct plating on SMACct, the direct counts of
E. coli
O157:H7 were highly correlated with the estimates obtained with the MACnal plates (
r
= 0.88,
P
< 0.001). Because the majority of cattle excrete less than 10
2
CFU
E. coli
O157/g feces, most studies, including those using IMS methods, probably grossly underestimate the prevalence of
E. coli
O157 in cattle.
Reactivity of Antibodies from Syphilis Patients to a Protein Array Representing theTreponema pallidumProteome
Authors: Brinkman Mary Beth , McKevitt Matthew , McLoughlin Melanie , Perez Carla , Howell Jerrilyn , Weinstock George M. , Norris Steven J. , Palzkill Timothy
Published: March 2006

To identify antigens important in the human immune response to syphilis, the serum antibody reactivity of syphilitic patients was examined with 908 of the 1,039 proteins in the proteome ofTreponema pallidumsubsp.pallidumusing a protein array enzyme-linked immunosorbent assay. Thirty-four proteins exhibited significant reactivity when assayed with human sera from patients in the early latent stage of syphilis. A subset of antigens identified were further scrutinized for antibody reactivity at primary, secondary, and latent disease stages, and the results demonstrate that the humoral immune response to individualT. pallidumproteins develops at different rates during the time course of infection.
Detection of Feline Leukemia Virus RNA in Saliva from Naturally Infected Cats and Correlation of PCR Results with Those of Current Diagnostic Methods
Authors: Gomes-Keller M. A. , Gönczi E. , Tandon R. , Riondato F. , Hofmann-Lehmann R. , Meli M. L. , Lutz H.
Published: March 2006

A novel diagnostic test for feline leukemia virus (FeLV) RNA in saliva from naturally infected cats is described in this study. We evaluated different diagnostic tests and compared them with the widely used enzyme-linked immunosorbent assay (ELISA) for the detection of p27 in the diagnosis of FeLV. Blood samples from 445 cats were tested for the presence of provirus by real-time PCR and plasma and saliva specimens from those cats were tested for the presence of viral RNA by real-time reverse transcription (RT)-PCR and for the presence of p27 by ELISA. In comparison to conventional ELISA, the diagnostic sensitivity and specificity of the detection of salivary FeLV RNA by real-time RT-PCR were found to be 98.1 and 99.2%, respectively. Detection of viral RNA in saliva had a positive predictive value of 94.6% and a negative predictive value of 99.7%. The kappa value was 0.96, demonstrating an almost perfect agreement between both tests. Furthermore, we confirmed previous results showing that a number of cats which tested negative for the presence of p27 in plasma were in fact positive for the presence of DNA provirus in blood specimens (5.4%). However, 96.4% of these latently infected cats did not shed viral RNA in saliva; therefore, we assume that these cats are of relatively low clinical importance at the time of testing. This study shows considerable diagnostic value of the detection of saliva FeLV RNA in naturally infected cats. This new diagnostic method has advantages over the conventional ELISA, such as less invasive sample collection and no requirement for trained personnel.
Antigenic Properties and Diagnostic Potential of African Swine Fever Virus Protein pp62 Expressed in Insect Cells
Authors: Gallardo Carmina , Blanco Esther , Rodríguez Javier M. , Carrascosa Angel L. , Sanchez-Vizcaino Jose Manuel
Published: March 2006

African swine fever (ASF) is an infectious and economically important disease of domestic pigs. The absence of vaccine renders the diagnostic test the only tool that can be used for the control of new outbreaks of the disease. At present, the enzyme-linked immunosorbent assay (ELISA) test is the most useful method for large-scale ASF serological studies, although false positives have been detected, mainly on poorly preserved sera. In order to improve the current diagnostic test available for ASF, we have studied the antigenic properties of the ASF virus polyprotein pp62 and its suitability for use in a novel ELISA. Two well-known antigenic proteins of ASF virus, p32 and p54, were also included in this study. These proteins were expressed in the baculovirus expression system and used as antigens in ASF serological tests. Our results indicate that the use of these recombinant proteins as antigens in the ELISAs improves the sensitivity and specificity obtained with the conventional diagnosis test used to detect antibodies against ASF virus. Furthermore, the use of polyprotein pp62 in an ELISA for testing poorly preserved sera allows performance of the diagnosis of ASF without the need to confirm the results by the immunoblot test. These features make pp62 one of the most interesting viral proteins to be used for serological ASF diagnosis.
Molecular Epidemiology of Bovine Coronavirus on the Basis of Comparative Analyses of the S Gene
Authors: Liu Lihong , Hägglund Sara , Hakhverdyan Mikhayil , Alenius Stefan , Larsen Lars Erik , Belák Sándor
Published: March 2006

Bovine coronavirus (BCoV), a group 2 member of the genus
Coronavirus
in the family
Coronaviridae
, is an important pathogen in cattle worldwide. It causes diarrhea in adult animals (winter dysentery), as well as enteric and respiratory diseases in calves. The annual occurrence of BCoV epidemics in Sweden and Denmark led to this investigation, with the aim to deepen the knowledge of BCoV epidemiology at the molecular level. A total of 43 samples from outbreaks in both countries were used for PCR amplification and direct sequencing of a 624-nucleotide fragment of the BCoV S gene. Sequence comparison and phylogenetic studies were performed. The results showed (i) identical sequences from different animals in the same herds and from paired nasal and fecal samples, suggesting a dominant virus circulating in each herd at a given time; (ii) sequence differences among four outbreaks in different years in the same herd, indicating new introduction of virus; (iii) identical sequences in four different Danish herds in samples obtained within 2 months, implying virus transmission between herds; and (iv) that at least two different virus strains were involved in the outbreaks of BCoV in Denmark during the spring of 2003. This study presents molecular data of BCoV infections that will contribute to an increased understanding of BCoV epidemiology in cattle populations.
Prevalence, Risk Factor Analysis, and Follow-Up of Infections Caused by Three Feline Hemoplasma Species in Cats in Switzerland
Authors: Willi Barbara , Boretti Felicitas S. , Baumgartner Claudia , Tasker Séverine , Wenger Bettina , Cattori Valentino , Meli Marina L. , Reusch Claudia E. , Lutz Hans , Hofmann-Lehmann Regina
Published: March 2006

Recently, a third novel feline hemotropicMycoplasmasp. (aka hemoplasma), “CandidatusMycoplasma turicensis,” in a cat with hemolytic anemia has been described. This is the first study to investigate the prevalence, clinical manifestations, and risk factors for all three feline hemoplasma infections in a sample of 713 healthy and ill Swiss cats using newly designed quantitative real-time PCR assays. “CandidatusMycoplasma haemominutum” infection was detected in 7.0% and 8.7% andMycoplasma haemofeliswas detected in 2.3% and 0.2% of healthy and ill cats, respectively. “CandidatusMycoplasma turicensis” was only detected in six ill cats (1.1%); three of them were coinfected with “CandidatusMycoplasma haemominutum.” The 16S rRNA gene sequence of 12 Swiss hemoplasma isolates revealed >98% similarity with previously published sequences. Hemoplasma infection was associated with male gender, outdoor access, and old age but not with retrovirus infection and was more frequent in certain areas of Switzerland. “CandidatusMycoplasma haemominutum”-infected ill cats were more frequently diagnosed with renal insufficiency and exhibited higher renal blood parameters than uninfected ill cats. No correlation between hemoplasma load and packed cell volume was found, although several hemoplasma-infected cats, some coinfected with feline immunodeficiency virus or feline leukemia virus, showed hemolytic anemia. HighM. haemofelisloads (>9 × 105copies/ml blood) seem to lead to anemia in acutely infected cats but not in recovered long-term carriers. A repeated evaluation of 17 cats documented that the infection was acquired in one case by blood transfusion and that there were important differences among species regarding whether or not antibiotic administration led to the resolution of bacteremia.
Genotype 1 and Genotype 2 Bovine Noroviruses Are Antigenically Distinct but Share a Cross-Reactive Epitope with Human Noroviruses
Authors: Oliver S. L. , Batten C. A. , Deng Y. , Elschner M. , Otto P. , Charpilienne A. , Clarke I. N. , Bridger J. C. , Lambden P. R.
Published: March 2006

The bovine enteric caliciviruses Bo/Jena/1980/DE and Bo/Newbury2/1976/UK represent two distinct genotypes within a new genogroup, genogroup III, in the genus
Norovirus
of the family
Caliciviridae
. In the present study, the antigenic relatedness of these two genotypes was determined for the first time to enable the development of tests to detect and differentiate between both genotypes. Two approaches were used. First, cross-reactivity was examined by enzyme-linked immunosorbent assay (ELISA) using recombinant virus-like particles (VLPs) and convalescent-phase sera from calves infected with either Jena (genotype 1) or Newbury2 (genotype 2). Second, cross-reactivity was examined between the two genotypes with a monoclonal antibody, CM39, derived using Jena VLPs. The two genotypes, Jena and Newbury2, were antigenically distinct with little or no cross-reactivity by ELISA to the heterologous VLPs using convalescent calf sera that had homologous immunoglobulin G titers of log
10
3.1 to 3.3. CM39 reacted with both Jena and heterologous Newbury2 VLPs. The CM39 epitope was mapped to nine amino acids (
31
PTAGAQIAA
39
) in the Jena capsid protein, which was not fully conserved for Newbury2 (
31
PTAGAPVAA
39
). Molecular modeling showed that the CM39 epitope was located within the NH
2
-terminal arm inside the virus capsid. Surprisingly, CM39 also reacted with VLPs from two genogroup II/3 human noroviruses by ELISA and Western blotting. Thus, although the bovine noroviruses Jena and Newbury2 corresponded to two distinct antigenic types or serotypes, they shared at least one cross-reactive epitope. These findings have relevance for epidemiological studies to determine the prevalence of bovine norovirus serotypes and to develop vaccines to bovine noroviruses.
Nutritional support in the premature newborn
Authors: Puntis J W L
Published: March 2006

The theory and practice of nutritional support in the premature newborn has assumed increasing importance with survival of greater numbers of very immature infants. After birth, many do not tolerate full enteral feeding until gastrointestinal motor function has matured. During this process some will develop necrotising enterocolitis (NEC), a devastating failure of adaptation to postnatal life that may result in death, or severe complications. The feeding strategy that minimises the risk of NEC remains to be defined. In addition, promoting growth rates and nutrient accretion equivalent to those achieved during fetal development while optimising neurodevelopmental and long term health outcomes represents an important challenge for neonatologists. This review will focus on the problems associated with enteral nutrition, the requirement for parenteral nutrition, and the long term consequences of early nutritional interventions, underlining the need for prolonged follow up in assessing the potential benefits of different approaches to feeding.
Video assisted thoracic surgery in the management of spontaneous pneumothorax: the current status
Authors: Ng C S H , Lee T W , Wan S , Yim A P C
Published: March 2006

Over the past decade, video assisted thoracic surgery (VATS) has changed the way spontaneous pneumothorax (SP) is managed. Benefits of VATS include less postoperative pain, shorter hospital stay, and attenuated postoperative inflammatory response are evident compared with open thoracic procedures. Furthermore, the increasing acceptance by patients and referring physicians is testament to its success. Recent studies and the authors decade of experience in management of SP by VATS show that it is quick, safe, and effective, with recurrence rates generally comparable to open procedures, with some exceptions. However, selecting the correct procedure and patient, as well as knowing the limitations of the surgeons and techniques are paramount for success. Even to this day, there are considerable variations in the treatment of SP and large scale controlled studies are needed to better define timing of surgery and the role of the different procedures in the treatment and prevention of SP.
Paediatric acute peritoneal dialysis in southern Nigeria
Authors: Anochie I C , Eke F U
Published: March 2006

Background

Acute peritoneal dialysis (APD) is the preferred treatment for isolated failure of the kidney. The authors reviewed children with acute renal failure (ARF) who had APD in Port Harcourt, Nigeria.

Results

221 patients, 147 boys and 74 girls (M: F, 1.99:1), mean (SD) age 5.4 (4.9) years had ARF. Dialysis was indicated in 112 cases. The main clinical indication being convulsion/uraemia 30 (26.8%) Only 27 patients (21 boys and 6 girls) had APD, giving an access rate of 24.1%. The commonest dialysis related complication was catheter malfunction 12 (44.4%). The mortality rate among the dialysed patients was 22.2%. Lack of dialysis and intractable hypertension significantly increased mortality (χ2 = 7.13, p<0.01) and (χ2 = 14.9, p<0.001) respectively.

Conclusion

APD is effective in reducing mortality of children with ARF. However, there were low dialysis access rate and few complications.