bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Identification of Zygomycetes from Culture and Experimentally Infected Tissues
Authors: Schwarz Patrick , Bretagne Stéphane , Gantier Jean-Charles , Garcia-Hermoso Dea , Lortholary Olivier , Dromer Françoise , Dannaoui Eric 
Published: February 2006

ABSTRACT

Mucormycosis is an emerging infection associated with a high mortality rate. Identification of the causative agents remains difficult and time-consuming by standard mycological procedures. In this study, internal transcribed spacer (ITS) sequencing was validated as a reliable technique for identification of Zygomycetes to the species level. Furthermore, species identification directly from infected tissues was evaluated in experimentally infected mice. Fifty-four Zygomycetes strains belonging to 16 species, including the most common pathogenic species of
Rhizopus
spp.,
Absidia
spp.,
Mucor
spp., and
Rhizomucor
spp., were used to assess intra- and interspecies variability. Ribosomal DNA including the complete ITS1-5.8S-ITS2 region was amplified with fungal universal primers, sequenced, and compared. Overall, for a given species, sequence similarities between isolates were >98%. In contrast, ITS sequences were very different between species, allowing an accurate identification of Zygomycetes to the species level in most cases. Six species (
Rhizopus oryzae
,
Rhizopus microsporus
,
Rhizomucor pusillus
,
Mucor circinelloides
, and
Mucor indicus
) were also used to induce disseminated mucormycosis in mice and to demonstrate that DNA extraction, amplification of fungal DNA, sequencing, and molecular identification were possible directly from frozen tissues.
Correlation of Disease Severity with Fecal Toxin Levels in Patients with
Clostridium difficile
-Associated Diarrhea and Distribution of PCR Ribotypes and Toxin Yields In Vitro of Corresponding Isolates
Authors: Åkerlund Thomas , Svenungsson Bo , Lagergren Åsa , Burman Lars G. 
Published: February 2006

ABSTRACT

We investigated in vivo and in vitro yields of toxins A and B from and PCR ribotypes of
Clostridium difficile
isolates from 164 patients with differing severities of
C. difficile
-associated diarrhea (CDAD) (patients were grouped as follows: <3 loose stools per day,
n
= 45; 3 to 10 per day,
n
= 97; >10 per day,
n
= 22). The median fecal toxin levels in each group were 0.5, 6.8, and 149 U/g feces (
P
< 0.001), respectively. Patients with severe diarrhea also had more-frequent occurrence of blood in stool and vomiting, but there was no association with fecal toxin levels per se. There was no correlation between fecal toxin level and toxin yield in vitro for the corresponding
C. difficile
isolate or between its PCR ribotype and disease severity. A broad range of toxin yields among isolates belonging to major PCR ribotypes indicated a presence of many subtypes. We hypothesize that bacterial and host factors that affect
C. difficile
toxin levels in feces are important determinants of symptoms in CDAD patients. An inverse correlation between toxin yield and spore count (
r
= 0.66) in stationary-phase cultures supported the notion that toxin production and sporulation represent opposite alternative survival strategies for
C. difficile
cells facing nutrient shortage.
Epidemiological and Genetic Correlates of Severe Acute Respiratory Syndrome Coronavirus Infection in the Hospital with the Highest Nosocomial Infection Rate in Taiwan in 2003
Authors: Chen Yi-Ming Arthur , Liang Shu-Yuan , Shih Yi-Ping , Chen Chia-Yen , Lee Yuan-Ming , Chang Ling , Jung Shiao-Ying , Ho Mei-Shang , Liang Kung-Yee , Chen Hour-Young , Chan Yu-Jiun , Chu Da-Chen 
Published: February 2006

ABSTRACT

Taiwan experienced a series of outbreaks of nosocomial severe acute respiratory syndrome (SARS) infections in 2003. Two months after the final outbreak, we recruited 658 employees from the hospital that suffered the first and most severe SARS infections to help us investigate epidemiological and genetic factors associated with the SARS coronavirus (SARS-CoV). SARS-CoV infections were detected by using enzyme immunoassays and confirmed by a combination of Western blot assays, neutralizing antibody tests, and commercial SARS tests. Risk factors were analyzed via questionnaire responses and sequence-specific oligonucleotide probes of human leukocyte antigen (HLA) alleles. Our results indicate that 3% (20/658) of the study participants were seropositive, with one female nurse identified as a subclinical case. Identified SARS-CoV infection risk factors include working in the same building as the hospital's emergency room and infection ward, providing direct care to SARS patients, and carrying a Cw*0801 HLA allele. The odds ratio for contracting a SARS-CoV infection among persons with either a homozygous or a heterozygous Cw*0801 genotype was 4.4 (95% confidence interval, 1.5 to 12.9;
P
= 0.007).
Use of an Adaptation of a Commercially Available PCR Assay Aimed at Diagnosis of Chlamydia and Gonorrhea To Detect
Trichomonas vaginalis
in Urogenital Specimens
Authors: Van Der Pol Barbara , Kraft Colleen S. , Williams James A. 
Published: February 2006

ABSTRACT

Trichomonas vaginalis
PCR using reagents from a commercially available assay for
Chlamydia trachomatis
and
Neisseria gonorrhoeae
was evaluated for detection of infection in women and men attending a sexually transmitted disease clinic. Evaluations included three primer sets, endocervical swabs, vaginal swabs and urine, and various storage conditions. The TVK3/TVK7 primer set was optimal in our hands with sensitivities ranging from 69.5 to 96.8%. In all comparisons,
T. vaginalis
PCR performed better than routine diagnostics using microscopy for women and culture for men (
P
> 0.05). The assay performed well for all sample types tested, and vaginal swabs were stable for up to 7 days at ambient temperature. Using samples prepared for, and reagents from, the
C. trachomatis-N. gonorrhoeae
PCR assay allowed incorporation of
T. vaginalis
PCR diagnosis into routine clinical testing.
Locus-Specific Mutational Events in a Multilocus Variable-Number Tandem Repeat Analysis of
Escherichia coli
O157:H7
Authors: Noller Anna C. , McEllistrem M. Catherine , Shutt Kathleen A. , Harrison Lee H. 
Published: February 2006

ABSTRACT

Multilocus variable-number tandem repeat analysis (MLVA) is a validated molecular subtyping method for detecting and evaluating
Escherichia coli
O157:H7 outbreaks. In a previous study, five outbreaks with a total of 21 isolates were examined by MLVA. Nearly 20% of the epidemiologically linked strains were single-locus variants (SLV) of their respective predominant outbreak clone. This result prompted an investigation into the mutation rates of the seven MLVA loci (TR1 to TR7). With an outbreak strain that was an SLV at the TR1 locus of the predominant clone, parallel and serial batch culture experiments were performed. In a parallel experiment, none (0/384) of the strains analyzed had mutations at the seven MLVA loci. In contrast, in the two 5-day serial experiments, 4.3% (41/960) of the strains analyzed had a significant variation in at least one of these loci (
P
< 0.001). The TR2 locus accounted for 85.3% (35/41) of the mutations, with an average mutation rate of 3.5 × 10
−3
; the mutations rates for TR1 and TR5 were 10-fold lower. Single additions accounted for 77.1% (27/35) of the mutation events in TR2 and all (6/6) of the additions in TR1 and TR5. The remaining four loci had no slippage events detected. The mutation rates were locus specific and may impact the interpretation of MLVA data for epidemiologic investigations.
Validation of a Multiplex Pneumococcal Serotyping Assay with Clinical Samples
Authors: Lin Jisheng , Kaltoft Margit S. , Brandao Angela P. , Echaniz-Aviles Gabriela , Brandileone M. Cristina C. , Hollingshead Susan K. , Benjamin William H. , Nahm Moon H. 
Published: February 2006

ABSTRACT

We have recently developed a rapid pneumococcal serotyping method called “multibead assay” (J. Yu et al., J. Clin. Microbiol.
43:
156-162, 2005) based on a multiplexed immunoassay for capsular polysaccharides in lysates of pneumococcal cultures. The multibead assay can identify 36 serotypes (1, 2, 3, 4, 5, 6A, 6B, 7A/7F, 8, 9L/9N, 9V, 10A/10B/39/33C, 11A/11D/11F, 12A/12B/12F, 14, 15B/5C, 17F, 18C, 19A, 19F, 20, 22A/22F, 23F, and 33A/33F). More than 90% of the U.S. isolates express one of these serotypes (J. B. Robbins et al., J. Infect. Dis.
148:
1136-1159, 1983). To validate the new assay, we examined 495 clinical isolates of pneumococci obtained in Brazil, Denmark, and Mexico. Pneumococci were serotyped by the Neufeld test in their countries of origin, and lysates of each strain were coded and mailed to the United States for the multibead assay at ambient temperature without any thermal protection. After breaking the code, 54 discrepancies (11% of samples) were noted, but 46 were due to nonreproducible technical problems or insufficient growth of the pneumococci. All of the isolates grew well for a second test, and therefore, the culture medium used for the multibead assay is adequate. The discrepancies persisted for eight isolates, involving the 6A, 11A, and 18C serotypes. Additional studies of the eight isolates showed that the discrepancies were due to differences in the reagents used in the multibead or Neufeld tests for these three serotypes. For instance, five isolates were typed as 6A with the Neufeld test but as nontypeable by the multibead assay. Selection of another new monoclonal antibody (Hyp6AG1) for the multibead assay resulted in all five discrepant isolates typing as 6A. This finding indicates the validity of the multibead assay and emphasizes the need to validate any new pneumococcal serotyping assay with a large number of clinical isolates from different locations. It also suggests the presence of serological subtypes among isolates expressing the 6A serotype.
Occurrence and Kinetics of False-PositiveAspergillusGalactomannan Test Results following Treatment with β-Lactam Antibiotics in Patients with Hematological Disorders
Authors: Aubry Alban , Porcher Raphael , Bottero Julie , Touratier Sophie , Leblanc Thierry , Brethon Benoît , Rousselot Philippe , Raffoux Emmanuel , Menotti Jean , Derouin Francis , Ribaud Patricia , Sulahian Annie 
Published: February 2006

ABSTRACTSeveral reports have described a high rate of false-positiveAspergillusgalactomannan (GM) test results for patients treated with piperacillin-tazobactam. In this retrospective study, we first examined the relationships between intravenous administration of three β-lactam antibiotics and the occurrence of false-positive GM test results in hematology patients. We then estimated the kinetics of clearance of GM after the cessation of treatment. Sequential serum samples from 69 patients that had received β-lactams were analyzed by using a PlateliaAspergillustest. A significant association was found between GM positivity (≥0.5) and the administration of β-lactams (P< 0.0001). The direct role of β-lactams in patients' serum positivity was assessed by testing 39 batches of β-lactams, of which 27 were positive for GM. None of the latter were positive according to a fungus- andAspergillus-specific PCR. The kinetics of the decrease of GM was analyzed on sequential serum samples obtained after treatment. By use of a nonlinear regression model, the average time to negative antigen was assessed to be 5.5 days (95% confidence interval [CI], 4.1 to [7.0]), with a half-life of elimination of GM of 2.4 days (95% CI, 1.8 to 3.0). This study confirms that the administration of β-lactams containing GM is responsible for false-positive diagnostic results, even up to 5 days after the cessation of treatment.
Environmental Monitoring for Gastroenteric Viruses in a Pediatric Primary Immunodeficiency Unit
Authors: Gallimore Chris I. , Taylor Clive , Gennery Andrew R. , Cant Andrew J. , Galloway Angela , Iturriza-Gomara Miren , Gray Jim J. 
Published: February 2006

ABSTRACT
The aim of this study was to determine if gastroenteric viruses were present on surfaces and equipment in a pediatric primary immunodeficiency unit (PPIU) by environmental sampling using swabs and subsequent nucleic acid extraction and reverse transcriptase PCR assays. A PPIU was chosen, and 11 swabs were taken at the same sites every 2 weeks for 6 months. Nested/heminested PCR assays were used to screen for astroviruses (AsV), noroviruses (NoV), and rotaviruses (RV). AsV, NoV, and RV were detected at multiple swab sites during the study period. NoV was the most frequently detected virus on environmental surfaces; however, RV was detected on 79% and NoV on 50% of swabbing dates during the study period. Toilet taps were the most contaminated sites. Fecal samples from selected patients in the unit were also screened during the study period, and patients excreted AsV, NoV, and RV at times during the study. New cleaning schedules and changes in some of the PPIU sanitary furniture have been suggested as a means of reducing environmental contamination.
High Analytical Sensitivity and Low Rates of Inhibition May Contribute to Detection of
Chlamydia trachomatis
in Significantly More Women by the APTIMA Combo 2 Assay
Authors: Chernesky Max , Jang Dan , Luinstra Kathy , Chong Sylvia , Smieja Marek , Cai Wenjie , Hayhoe Beth , Portillo Eder , MacRitchie Cindy , Main Cheryl , Ewert Ruth 
Published: February 2006

ABSTRACT

The clinical sensitivity of nucleic acid amplification tests may be determined by analytical sensitivity and inhibitors in patient samples. We established endpoints for detection of propagated
Chlamydia trachomatis
L2 434, diluted according to swab and urine protocols for APTIMA Combo 2 (AC2), ProbeTec ET (PT), and Amplicor (AMP) assays. AC2 was 1,000-fold more sensitive than PT and 10-fold more sensitive than AMP on mock swab specimens. For urine, AC2 analytical sensitivity was 100-fold greater than those of the other assays. Spiking an aliquot of each clinical-trial sample from 298 women demonstrated inhibition rates in first-void urine (FVU), cervical swabs (CS), and vaginal swabs (VS) of 12.1%, 12.8%, and 10.4% for AMP; 27.2%, 2%, and 2%, for PT; and 0.3%, 1.7%, and 1.3% for AC2. Inhibition of our
C. trachomatis
spike and the PT or AMP amplification controls from the manufacturers showed less than 50% correlation. Using an infected-patient reference standard (a specimen positive in at least two tests or a single test positive in two of three samples) in AC2, the VS identified 68/69 (98.6%) infected women compared to CS (89.9%) or FVU (81.2%). Significantly fewer women were identified by PT (65.2%, 63.8%, and 66.7%) or AMP (65.2%, 59.4%, and 56.5%) with the three specimens. By individual specimen type, AC2 confirmed virtually all PT- and AMP-positive specimens, but rates of AC2 confirmation by AMP or PT ranged from 62.9 to 80.3%. The AC2 test identified significantly more women infected with
C. trachomatis
(
P
= 0.001). Vaginal swabs appear to be the specimen of choice for screening.
Application of Pulsed-Field Gel Electrophoresis To Identify Potential Outbreaks of Campylobacteriosis in New Zealand
Authors: Gilpin Brent , Cornelius Angela , Robson Beth , Boxall Naomi , Ferguson Alan , Nicol Carolyn , Henderson Tom 
Published: February 2006

ABSTRACT

Since 2002, New Zealand's incidence of campylobacteriosis has exceeded 300 cases per 100,000 people per annum. To evaluate genetic variation in human isolates, 183
Campylobacter
isolates were collected from a single clinical laboratory in Christchurch: 77 during an 8-week period in spring, and the rest 3 months later over a second 8-week period in autumn. Isolates were identified to the species level and subtyped using Penner serotyping (
Campylobacter jejuni
only) and pulsed-field gel electrophoresis (PFGE) using both SmaI and KpnI. Approximately two-thirds of the isolates could be grouped into clusters of between 2 and 26 isolates with indistinguishable SmaI and KpnI patterns. Less than 10% of the isolates were of the same type between the two sampling periods. The epidemiological relevance of the PFGE clusters was supported by temporal clustering, some spatial clustering, and some statistically significant demographic similarities among cases in a cluster. Conversely, patient cases yielding isolates which did not cluster with isolates from other cases were more likely to report recent overseas travel and less likely to live within larger urban centers. To identify whether these clusters actually represent common-source outbreaks, however, would require the detailed, rapid, and reiterative epidemiological investigation of cases within a PFGE cluster. The combined and timely application of subtyping and epidemiological investigation would appear to be a promising strategy for understanding campylobacteriosis in New Zealand.
Partial Nucleotide Sequencing of themecAGenes ofStaphylococcus aureusIsolates from Cats and Dogs
Authors: Malik Seidu , Peng Haihong , Barton Mary D. 
Published: February 2006

ABSTRACTMethicillin-resistant staphylococci (MRS) pose a challenge to clinicians and health administrators in human medicine, but MRS infections in cats and dogs are not perceived as a problem in veterinary medicine. Ten methicillin-resistant staphylococcal isolates obtained from healthy and diseased cats and dogs were subjected to partial DNA sequencing of themecAgene. Sequence analysis shows that MRS isolates from both healthy and diseased cats and dogs can harbor themecAgene. ThemecAgenes of animal isolates were identical to that found in human MRS strains, and therefore the possibility of zoonotic transfer must be considered.
Comparison of Serum Hepatitis C Virus (HCV) RNA and Core Antigen Levels in Patients Coinfected with Human Immunodeficiency Virus and HCV and Treated with Interferon plus Ribavirin
Authors: Pivert A. , Payan C. , Morand P. , Fafi-Kremer S. , Deshayes J. , Carrat F. , Pol S. , Cacoub P. , Perronne C. , Lunel F. 
Published: February 2006

ABSTRACT

Trak-C (Ortho-Clinical Diagnostics) is an enzyme-linked immunosorbent assay-based method capable of quantifying hepatitis C virus (HCV) core antigen (CA) in serum and could be an alternative to molecular detection and quantification of HCV RNA. We have evaluated the Trak-C assay in comparison with an HCV RNA quantitative assay (Versant HCV v3.0; Bayer Diagnostics) in the follow-up of 348 treated, human immunodeficiency virus (HIV)/HCV-coinfected patients included in the ANRS HC02 RIBAVIC trial. ANRS HC02 RIBAVIC is a therapeutic, multicenter, randomized protocol comparing the efficacy of alpha interferon 2b (IFN-α2b) (3 million units three times a week)-ribavirin (800 mg/day) to that of pegylated IFN-α2b (1.5 μg/kg of body weight/week)-ribavirin (800 mg/day) during 48 weeks of treatment of HIV/HCV-coinfected patients naïve to HCV treatment. Patients were assessed for virological analysis at day 0 and weeks 4, 12, 24, 48, and 72. Correlation of HCV RNA and HCV CA at the initiation of treatment was excellent (
r
= 0.92). HCV RNA and CA kinetics were similar during follow-up of HCV treatment from day 0 to week 72 whatever the group of response and genotype. The positive and negative predictive values of response to the treatment at week 4 were 59 and 94%, respectively, for HCV RNA load reduction of >2 log and 54 and 94%, respectively, for HCV CA below the threshold value (4.18 log
10
pg/ml · 10
4
). Trak-C, a new assay able to quantify CA in HIV/HCV-coinfected patients, correlates well with quantitative HCV RNA assays and is cheaper and easier to perform than molecular technology. HCV CA could be a valuable alternative test for therapeutic follow-up of coinfected patients treated with IFN plus ribavirin in developing countries.
Real-Time PCR Quantification of Genital Shedding of Herpes Simplex Virus (HSV) and Human Immunodeficiency Virus (HIV) in Women Coinfected with HSV and HIV
Authors: Legoff Jérôme , Bouhlal Hicham , Grésenguet Gérard , Weiss Helen , Khonde Nzambi , Hocini Hakim , Désiré Nathalie , Si-Mohamed Ali , de Dieu Longo Jean , Chemin Cécile , Frost Eric , Pépin Jacques , Malkin Jean-Elie , Mayaud Philippe , Bélec Laurent 
Published: February 2006

ABSTRACT

The accuracy and usefulness of laboratory-developed real-time PCR procedures using a Light Cycler instrument (Roche Diagnostics) for detecting and quantifying human immunodeficiency virus type 1 (HIV-1) RNA and DNA as well as herpes simplex virus type 1 (HSV-1)/HSV-2 DNA in cervicovaginal secretions from women coinfected with HIV and HSV were evaluated. For HIV-1, the use of the NEC152 and NEC131 primer set and the NEC-LTR probe in the long terminal repeat gene allowed us to detect accurately the majority of HIV-1 subtypes of group M circulating in sub-Saharan Africa, including subtypes A, B, C, D, and G as well as circulating recombinant forms 02 and 11. The detection threshold of real-time PCR for HIV in cervicovaginal lavage samples was 5 copies per assay for both RNA and DNA; the intra- and interassay coefficients of variation of

C
T

values were 1.30% and 0.69% (HIV-1 RNA) and 1.84% and 0.67% (HIV-1 DNA), respectively. Real-time PCR for HSV using primers and probe targeting the HSV DNA polymerase gene allowed both detection and quantification of HSV DNA and also differentiation between HSV-1 and HSV-2 genotypes. The detection threshold of real-time PCR for HSV was 5 copies per assay; the intra- and interassay coefficients of variation of

C
T

values were 0.96% and 1.49%, respectively. Both manual and automated silica-based procedures were appropriate for combined extraction of HIV and HSV genomes from female genital secretions. Taken together, these findings indicate that real-time PCR may be used as a unique nucleic acid amplification procedure to detect and quantify HIV and HSV genomes in cervicovaginal secretions and thus to assess at reduced costs the genital shedding of both viruses in women included in intervention studies.
Sequencing ofhsp65Distinguishes among Subsets of theMycobacterium aviumComplex
Authors: Turenne Christine Y. , Semret Makeda , Cousins Debby V. , Collins Desmond M. , Behr Marcel A. 
Published: February 2006

ABSTRACTTheMycobacterium aviumcomplex consists of epidemiologically distinct subsets. The classification of these subsets is complicated by a number of factors, including the ambiguous results obtained with phenotypic and genetic assays and the recent appreciation that human and avian strains appear to be distinct. In previous work, sequencing based on a 441-bp portion of thehsp65gene has proven to efficiently classify isolates within theMycobacteriumgenus but provides low resolution for distinguishing among members of theM. aviumcomplex. Therefore, in this study, we have targeted the more variable 3′ region of thehsp65gene to determine whether it can effectively discriminateM. aviumcomplex isolates at the levels of species and subspecies. Primers designed for this target consistently generated amplicons for all organisms classified asM. aviumcomplex. Sequences obtained indicate thatM. intracellulareis genetically divergent fromM. aviumorganisms, and distinct sequevars were obtained forM. aviumsubsets, includingM. aviumsubsp.avium(bird type),M. aviumsubsp.hominissuis, andM. aviumsubsp.paratuberculosis. In addition, sequence differences served to distinguish bovine from ovine strains ofM. aviumsubsp.paratuberculosis. A unique profile forM. aviumsubsp.silvaticumwas not obtained. These results indicate that sequencing the 3′ region of thehsp65gene can simply and unambiguously distinguish species and subspecies of theM. aviumcomplex.