bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Genetic Grouping of Factor H-Binding Protein (Genome-Derived Neisserial Antigen 1870), a Promising Group B Meningococcal Vaccine Candidate
Authors: Beernink Peter T. , Leipus Arunas , Granoff Dan M. 
Published: July 2006

ABSTRACT

The most important antigen component of a promising multicomponent group B meningococcal recombinant protein vaccine is based on genome-derived neisserial antigen 1870, which recently was renamed factor H-binding protein (FHBP) to reflect one of its critical functions as a complement regulatory protein.
Neisseria meningitidis
strains can be subdivided into three FHBP variant groups based on divergence of FHBP amino acid sequences. Within each variant group, amino acid sequences are >90% conserved. To develop an FHBP-based group B vaccine, it is important to know the distribution of FHBP variant 1, 2, and 3 strains in different geographic regions, since antibodies against FHBP are bactericidal against strains within the homologous group but show minimal activity against strains from other groups. We have devised a high-throughput, quantitative PCR-based method that allows rapid and precise assignment of FHBP genes into each of the three major variant lineages. Among 48 group B isolates from patients hospitalized in California in 2003 to 2004, 83%, 13%, and 4%, respectively, had variant 1, 2, and 3 genes. Thus, a vaccine based on the variant 1 protein has the potential to prevent the majority of cases of group B disease. The quantitative PCR-based method will be useful for determining and monitoring the prevalence of meningococcal isolates with genes encoding different FHBP variant proteins. The technique also is suitable for monitoring variation of genes encoding other protein antigens targeted for vaccination.
Comparison of Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Antimicrobial Susceptibility Typing for Characterization of
Salmonella enterica
Serotype Newport Isolates
Authors: Harbottle H. , White D. G. , McDermott P. F. , Walker R. D. , Zhao S. 
Published: July 2006

ABSTRACT

In the United States, multidrug-resistant phenotypes of
Salmonella enterica
serotype Newport (commonly referred to as MDR-AmpC) have emerged in animals and humans and have become a major public health problem. Although pulsed-field gel electrophoresis (PFGE) is the current “gold standard” typing method for
Salmonella
, multilocus sequence typing (MLST) may be more relevant to investigations exploring evolutionary and population biology relationships. In this study, 81
Salmonella enterica
serotype Newport isolates from humans, food animals, and retail foods were examined for antimicrobial susceptibility and characterized using PFGE and MLST of seven genes,
aroC
,
dnaN
,
hemD
,
hisD
,
purE
,
sucA
, and
thrA
. Forty-nine percent of the isolates were resistant to nine or more of the tested antimicrobials.
Salmonella
isolates displayed resistance most often to sulfamethoxazole (57%), streptomycin (56%), tetracycline (56%), ampicillin (52%), and ceftiofur (49%) and, to a lesser extent, to kanamycin (19%), trimethoprim-sulfamethoxazole (17%), and gentamicin (11%). A total of 43 PFGE patterns were generated using XbaI, indicating a genetically diverse population. The largest PFGE cluster contained isolates from clinically ill swine, cattle, and humans. MLST resulted in 12 sequence types (STs), with one type encompassing 62% of the strains. Ten new sequence types and one novel allele type were identified. Furthermore, MLST typing showed that strains closely related by PFGE clustered in major STs, whereas more distantly related strains were separated into two clusters by PFGE. The results of this study demonstrated that the MLST scheme employed here clustered
S. enterica
serovar Newport isolates in distinct molecular populations, and strain discrimination was enhanced by combining PFGE, antimicrobial susceptibility, and MLST results.
Classifying
spa
Types in Complexes Improves Interpretation of Typing Results for Methicillin-Resistant
Staphylococcus aureus
Authors: Ruppitsch Werner , Indra Alexander , Stöger Anna , Mayer Barbara , Stadlbauer Silke , Wewalka Günther , Allerberger Franz 
Published: July 2006

ABSTRACT

A total of 382 isolates of methicillin-resistant
Staphylococcus aureus
originating from three Austrian regions and one adjacent Italian region (Vienna, Lower Austria, North Tyrol, and South Tyrol) were typed by DNA sequence analysis of the variable repeat region of the protein A gene (
spa
typing). The strain collection consisted of arbitrarily chosen isolates originating from clinical specimens taken in the years 2003 to 2005 at 17 hospitals. The most common
spa
types found were t001 (28.8% of all isolates), t190 (27.0%), t008 (14.1%), and t041 (11.3%). The 42 remaining
spa
types accounted for ≤2.4% each. The dominating
spa
types varied between the different regions. As short sequence DNA repeat units are unstable entities, the 46
spa
types were classified into seven
spa
complexes with respect to short sequence repeat unit composition and organization. Such classification into complexes can provide additional information for the hospital epidemiologist, empowering one to differentiate the introduction of a new strain from mere variation of endemic
spa
types.
Real-Time PCR Assays for Hepatitis C Virus (HCV) RNA Quantitation Are Adequate for Clinical Management of Patients with Chronic HCV Infection
Authors: Halfon Philippe , Bourlière Marc , Pénaranda Guillaume , Khiri Hacène , Ouzan Denis 
Published: July 2006

ABSTRACT

Because of the use of viral kinetics during polyethylene glycol (PEG)-interferon-ribavirin therapy and the development of specific new anti-hepatitis C virus (anti-HCV) drugs, assessment of the efficacy of anti-HCV drugs needs to be based not on end-point PCR assays but on real-time PCR. The aim of this study was to determine if the two available commercial real-time PCR assays, the Abbott RealTime HCV assay and the Roche Cobas TaqMan HCV assay, can become the standard for HCV RNA quantification. We investigated the prognostic relevance of HCV RNA viral loads at baseline, week 4, and week 12 to a rapid and early virological response to antiviral therapy by using the two assays. Of 59 naïve patients chronically infected by HCV (41 infected with genotype 1) who were treated with ribavirin plus PEG-interferon alfa-2b for 48 weeks, 24 patients (41%) showed a sustained virological response (SVR). With the two assays, viral loads were highly correlated, irrespective of genotype (
R
2
= 0.94 for all cases). No difference in diagnostic value was found between the Abbott and Roche assays at week 4, with respective negative predictive values (NPVs) of 84% and 78% and positive predictive values (PPVs) of 62% and 56% (not significant), and at week 12, the respective NPVs were 91% and 90% and PPVs were 44% and 46% (not significant). At week 12, 83% (20/24) and 96% (23/24) of patients with SVR tested negative for HCV RNA by the Abbott and Roche assays, respectively (the difference is not significant). In conclusion, the high sensitivities and large dynamic ranges of the Abbott and Roche assays show that a single real-time quantitative PCR assay is fully adequate for clinical and therapeutic management of HCV.
High Prevalence of Multiple Human Herpesviruses in Saliva from Human Immunodeficiency Virus-Infected Persons in the Era of Highly Active Antiretroviral Therapy
Authors: Miller Craig S. , Berger Joseph R. , Mootoor Yunanan , Avdiushko Sergei A. , Zhu Hua , Kryscio Richard J. 
Published: July 2006

ABSTRACT

Human immunodeficiency virus (HIV) infection is associated with an increased risk for human herpesviruses (HHVs) and their related diseases. Methods for limiting the transmission of HHVs require a better understanding of the prevalence and infectiousness of oral HHVs in HIV-infected patients. We performed quantitative PCR to investigate the prevalence, quantity, risk, and correlates of salivary HHVs from 58 HIV-seropositive individuals in a case control study. HHVs were significantly more prevalent in the salivas of HIV-seropositive persons than in those of the controls (odds ratios [ORs], 4.2 to 26.2;
P
≤ 0.008). In HIV-infected patients, Epstein-Barr virus (EBV), human herpesvirus 8 (HHV-8), cytomegalovirus (CMV), and herpes simplex virus type 1 (HSV-1) were detected in 90%, 57%, 31% and 16% of samples, respectively, compared with 48%, 24%, 2%, and 2%, respectively, of samples from controls. Multiple HHVs were observed in 71% of HIV-seropositive persons and only 16% of controls (OR, 13.0; 95% confidence interval, 5.29 to 32.56). HIV-positive patients had significantly higher EBV loads than HIV-negative persons (
P
< 0.0001). HIV-infected patients with CD4 counts above 200 cells/μl had increased probability for having HHV-8 in saliva (
P
= 0.009) compared with patients whose counts were less than 200. In contrast, HSV-1, EBV, and CMV were detected more often when CD4 counts were low. High salivary HHV loads were detected for those (
n
= 7) with oral lesions. These findings suggest that saliva is a potential risk factor for the acquisition of multiple HHVs, and several host factors may function to accelerate HHV reactivation or replication in patients with HIV infection.
Lamivudine Resistance of Hepatitis B Virus Masked by Coemergence of Mutations in Probe Region of the COBAS AMPLICOR Assay
Authors: Lindh Magnus , Hannoun Charles , Malmström Sebastian , Lindberg Johan , Norkrans Gunnar 
Published: July 2006

ABSTRACT
The COBAS AMPLICOR hepatitis B virus assay targets a conserved region of the genome and is widely used to monitor treatment of hepatitis B in order to identify emerging resistance. However, the assay failed to recognize increasing viremia levels when YMDD mutations were paralleled by mutations in the segment targeted by the COBAS AMPLICOR probe.
Candida guilliermondii
Fungemia in Patients with Hematologic Malignancies
Authors: Girmenia Corrado , Pizzarelli Giampaolo , Cristini Francesco , Barchiesi Francesco , Spreghini Elisabetta , Scalise Giorgio , Martino Pietro 
Published: July 2006

ABSTRACT

The microbiological, clinical, and epidemiological features of most non-
Candida albicans Candida
species are well known, but much less is known about species such as
Candida guilliermondii
, an uncommon pathogen causing a variety of deep-seated infections in immunocompromised hosts. To characterize
C. guilliermondii
fungemia in patients with hematological malignancies and its susceptibility to antifungal drugs, all cases of
C. guilliermondii
fungemia diagnosed in our department between 1983 and 2005 were retrospectively analyzed and the literature was reviewed.
C. guilliermondii
caused 29/243 (11.7%) candidemia episodes diagnosed during the study period. Central venous catheters were the documented sources of candidemia in 19/29 episodes (65.5%), and invasive tissue infections were documented in 2 (6.9%). In the remaining eight, the catheter was not removed and the source of the fungemia remained obscure. Seven episodes ended in death, but only one could be attributed to invasive
C. guilliermondii
infection. Molecular typing data reveal no evidence of common infection sources. Isolates displayed high rates of in vitro susceptibility to amphotericin B (100%), voriconazole (95%), and fluconazole (90%) and lower rates of in vitro susceptibility to flucytosine (86%), itraconazole (76%), and caspofungin (33%). Our literature review confirms that
C. guilliermondii
is a significantly more frequent cause of candidemia among cancer patients compared with the general hospital population. It accounted for <1% of the total number of
Candida
bloodstream isolates reported in the articles we reviewed, with higher rates in Europe (1.4%) and Asia (1.8%) compared with North America (0.3%).
Cluster of Cases of Human
Rickettsia felis
Infection from Southern Europe (Spain) Diagnosed by PCR
Authors: Oteo José A. , Portillo Aránzazu , Santibáñez Sonia , Blanco José R. , Pérez-Martínez Laura , Ibarra Valvanera 
Published: July 2006

ABSTRACT

The first cluster of cases of human
Rickettsia felis
infection in Spain diagnosed by PCR is reported.
Assignment of
Staphylococcus
Isolates to Groups by
spa
Typing, SmaI Macrorestriction Analysis, and Multilocus Sequence Typing
Authors: Strommenger B. , Kettlitz C. , Weniger T. , Harmsen D. , Friedrich A. W. , Witte W. 
Published: July 2006

ABSTRACT

The implementation of the new clustering algorithm
B
ased
U
pon
R
epeat
P
attern (BURP) into the Ridom StaphType software tool enables clustering based on
spa
typing data for
Staphylococcus aureus
. We compared clustering results obtained by
spa
typing/BURP to those obtained by currently well-established methods, i.e., SmaI macrorestriction analysis and multilocus sequence typing/eBURST. A total of 99 clinical
S. aureus
strains, including MRSA and representing major clonal lineages associated with important kinds of infections which have been prevalent in Germany and Central Europe during the last 10 years, were used for comparison. SmaI macrorestriction analysis revealed the highest discriminatory power, and clustering results for all three methods resulted in concordance values ranging from 96.8% between the two sequence-based methods to 93.4% between
spa
typing/BURP and SmaI macrorestriction/cluster analysis. The results of this study indicate that
spa
typing, together with BURP clustering, is a useful tool in
S. aureus
epidemiology, especially because of ease of use and the advantages of unambiguous sequence analysis as well as reproducibility and exchange of typing data.
Evaluation of the Genotype MTBDR Assay for Rapid Detection of Rifampin and Isoniazid Resistance in
Mycobacterium tuberculosis
Isolates
Authors: Cavusoglu Cengiz , Turhan Ajda , Akinci Pinar , Soyler Ilknur 
Published: July 2006

ABSTRACT

A novel PCR-based reverse hybridization method Genotype MTBDR assay (Hain Lifescience GmbH, Nehren, Germany) was evaluated for rapid detection of rifampin (RIF) and isoniazid (INH) resistance in Turkish
Mycobacterium tuberculosis
isolates. The Genotype MTBDR assay is designed to detect mutations within the 81-bp hotspot region of
rpoB
and mutations at
katG
codon 315. A total of 41 RIF-resistant
M. tuberculosis
isolates with
rpoB
mutations that were previously tested by the INNO-LiPA Rif.TB kit and also characterized by DNA sequencing were included in the study. Thirty-seven of these isolates were also resistant to INH. RIF resistance was correctly identified in 39 of 41 isolates (95.1%) with the Genotype MTBDR assay probes specific for these mutations. One isolate with a Gln-490-His mutation and another one with a CGG insertion between codons 514 and 515 were identified as RIF sensitive by the Genotype MTBDR assay. While the INNO-LiPA Rif.TB kit was able to determine the CGG insertion between codons 514 and 515, the Gln-490-His mutation outside the 81-bp hotspot region was not detected by the INNO-LiPA Rif.TB kit. These isolates had MICs of ≥32 μg/ml for RIF. The Genotype MTBDR assay also correctly identified 27 of 37 INH-resistant isolates (73%) with mutations in
katG
codon 315. In conclusion, the Genotype MTBDR assay may be useful for the rapid diagnosis of the most common mutations found in multidrug-resistant
M. tuberculosis
strains. However, the test results should always be confirmed with phenotypic methods.
Evaluation of the TB-Biochip Oligonucleotide Microarray System for Rapid Detection of Rifampin Resistance in
Mycobacterium tuberculosis
Authors: Caoili Janice C. , Mayorova Angelina , Sikes David , Hickman Laura , Plikaytis Bonnie B. , Shinnick Thomas M. 
Published: July 2006

ABSTRACT

The TB-Biochip oligonucleotide microarray system is a rapid system to detect mutations associated with rifampin (RIF) resistance in mycobacteria. After optimizing the system with 29 laboratory-generated rifampin-resistant mutants of
Mycobacterium tuberculosis
, we evaluated the performance of this test using 75 clinical isolates of
Mycobacterium tuberculosis
. With this small sample set, the TB-Biochip system displayed a sensitivity of 80% and a specificity of 100% relative to conventional drug susceptibility testing results for RIF resistance. For these samples (∼50% tested positive), the positive predictive value was 100% and the negative predictive value was 85%. Four of the seven observed discrepancies were attributed to rare and new mutations not represented in the microarray, while three of the strains with discrepant results did not carry mutations in the RIF resistance-determining region. The results of this study confirm the utility of the system for rapid detection of RIF resistance and suggest approaches to increasing its sensitivity.
Sepsis Caused byVeillonella parvulaInfection in a 17-Year-Old Patient with X-Linked Agammaglobulinemia (Bruton's Disease)
Authors: Strach Magdalena , Siedlar Maciej , Kowalczyk Danuta , Zembala Marek , Grodzicki Tomasz 
Published: July 2006

ABSTRACTA case of a male, 17-year-old, X-linked agammaglobulinemia patient with bacteremia caused byVeillonella parvula, without a defined primary site of infection, is presented. The report demonstrates thatV. parvulashould not be regarded as a nonpathogenic microorganism, at least not in patients with certain forms of immunodeficiency disease.
Canine Strangles Case Reveals a New Host Susceptible to Infection with
Streptococcus equi
Authors: Ladlow Jane , Scase Timothy , Waller Andrew 
Published: July 2006

ABSTRACT

We report the first documented case of canine strangles due to infection with
Streptococcus equi
in a dog with enlarged lymph nodes. Genetic typing, via sequencing of 12 housekeeping genes and the SeM gene, demonstrated the isolate to be a member of a common equine strain type circulating in the United Kingdom.
Nonrandom Distribution of
Burkholderia pseudomallei
Clones in Relation to Geographical Location and Virulence
Authors: Vesaratchavest Mongkol , Tumapa Sarinna , Day Nicholas P. J. , Wuthiekanun Vanaporn , Chierakul Wirongrong , Holden Matthew T. G. , White Nicholas J. , Currie Bart J. , Spratt Brian G. , Feil Edward J. , Peacock Sharon J. 
Published: July 2006

ABSTRACT

Burkholderia pseudomallei
is a soil-dwelling saprophyte and the causative agent of melioidosis, a life-threatening human infection. Most cases are reported from northeast Thailand and northern Australia. Using multilocus sequence typing (MLST), we have compared (i) soil and invasive isolates from northeast Thailand and (ii) invasive isolates from Thailand and Australia. A total of 266 Thai
B. pseudomallei
isolates were characterized (83 soil and 183 invasive). These corresponded to 123 sequence types (STs), the most abundant being ST70 (
n
= 21), ST167 (
n
= 15), ST54 (
n
= 12), and ST58 (
n
= 11). Two clusters of related STs (clonal complexes) were identified; the larger clonal complex (CC48) did not conform to a simple pattern of radial expansion from an assumed ancestor, while a second (CC70) corresponded to a simple radial expansion from ST70. Despite the large number of STs, overall nucleotide diversity was low. Of the Thai isolates, those isolated from patients with melioidosis were overrepresented in the 10 largest clones (
P
< 0.0001). There was a significant difference in the classification index between environmental and disease isolates (
P
< 0.001), confirming that genotypes were not distributed randomly between the two samples. MLST profiles for 158 isolates from Australia (mainly disease associated) contained a number of STs (96) similar to that seen with the Thai invasive isolates, but no ST was found in both populations. There were also differences in diversity and allele frequency distribution between the two populations. This analysis reveals strong genetic differentiation on the basis of geographical isolation and a significant differentiation on the basis of virulence potential.
Diagnosis of Streptococcal Pharyngitis by Detection of
Streptococcus pyogenes
in Posterior Pharyngeal versus Oral Cavity Specimens
Authors: Fox James W. , Marcon Mario J. , Bonsu Bema K. 
Published: July 2006

ABSTRACT
Carbohydrate antigen detection, nucleic acid probe detection, and bacterial culture are commonly used to confirm group A streptococcus (GAS) pharyngitis. Compared to standard throat swab specimens, the sensitivities of these tests with mouth specimens are poor. When testing for GAS pharyngitis, the throat remains the optimum site for sampling.
Voriconazole Susceptibilities of Dermatophyte Isolates Obtained from a Worldwide Tinea Capitis Clinical Trial
Authors: Ghannoum M. , Isham N. , Sheehan D. 
Published: July 2006

ABSTRACT
In this study, the voriconazole susceptibilities of dermatophyte isolates obtained from a worldwide tinea capitis trial were compared to their susceptibilities to fluconazole and griseofulvin. The MIC ranges of voriconazole, fluconazole, and griseofulvin, were 0.002 to 0.06 μg/ml, 0.25 to 32 μg/ml, and 0.125 to 2.0 μg/ml, respectively.
Effect of Storage Temperature on Survival of
Chlamydia trachomatis
after Lyophilization
Authors: Eley Adrian , Geary Ian , Bahador Abbas , Hakimi Hamid 
Published: July 2006

ABSTRACT

Lyophilized preparations of
Chlamydia trachomatis
were made to investigate how well they would survive storage at four relevant incubation temperatures for 1 week and 1 month. Good viability was maintained by storage at either 4°C or 20°C for 1 week. If the ambient temperature is not too high, short-term transportation of
C. trachomatis
is achievable through lyophilization.
Molecular Characterization of Nontypeable Group B Streptococcus
Authors: Ramaswamy Srinivas V. , Ferrieri Patricia , Flores Aurea E. , Paoletti Lawrence C. 
Published: July 2006

ABSTRACT

Traditionally, the capsular polysaccharide (CPS) antigen has been used to distinguish between the nine known serotypes of group B streptococcus (GBS) by classical antibody-antigen reactions. In this study, we used PCR for all CPSs and selected protein antigens, multilocus sequencing typing (MLST), and pulsed-field gel electrophoresis (PFGE) to molecularly characterize 92 clinical isolates identified as nontypeable (NT) by CPS-specific antibody-antigen reactivity. The PCR and MLST were performed on blinded, randomly numbered isolates. All isolates contained the
cfb
gene coding for CAMP factor. While most (56.5%) contained a single CPS-specific gene, 40 isolates contained either two or three CPS-specific genes. Type V CPS-specific gene was present in 66% of the isolates, and all serotypes except types IV, VII, and VIII were represented. Most (44.5%) of the isolates contained a single protein antigen gene (
bca
,
bac
,
rib
,
alp1
, or
alp3
), and the remaining isolates had multiple protein antigen genes. Of the 61 isolates that had the V CPS-specific gene, 48 (78.6%) had the
alp3
gene. PFGE analysis classified the isolates into 21 profile groups, while MLST analysis divided the isolates into 16 sequence types. Forty-two (69%) of 61 isolates with the V CPS-specific gene were in PFGE profile group 4; 41 of these 42 were sequence type 1 by MLST. These data shed new light on the antigenic complexity of NT GBS isolates, information that can be valuable in the formulation of an effective GBS vaccine.
Clearance ofCellulosimicrobium cellulansBacteremia in a Child without Central Venous Catheter Removal
Authors: Rowlinson Marie-Claire , Bruckner David A. , Hinnebusch Claudia , Nielsen Karin , Deville Jaime G. 
Published: July 2006

ABSTRACTCellulosimicrobium cellulans(formerly known asOerskovia xanthineolytica) rarely causes human infection. Infections have been reported in immunocompromised hosts or in patients with foreign bodies, such as catheters, where treatment has generally involved removal of the foreign body. We report on a case in which the organism was isolated in multiple blood cultures from a 13-year-old male. After initial therapy failed, treatment with vancomycin and rifampin resulted in infection clearance without removal of the central venous catheter.