bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability in the Distribution of Genes Encoding Virulence Factors and Putative Extracellular Proteins of Streptococcus pyogenes in India, a Region with High Streptococcal Disease Burden, and Implication for Development of a Regional Multisubunit Vaccine
Authors: Sagar Vivek , Bergmann René , Nerlich Andreas , McMillan David J. , Nitsche Schmitz D. Patric , Chhatwal Gursharan S. 
Published: September 2012

ABSTRACTStreptococcus pyogenescauses a wide variety of human diseases and is a significant cause of morbidity and mortality. Attempts to develop a vaccine were hampered by the genetic diversity ofS. pyogenesacross different regions of the world. This study sought to identify streptococcal antigens suitable for a region-specific vaccine in India. We used a two-step approach, first performing epidemiological analysis to identify the conserved antigens among Indian isolates. The second step consisted of validating the identified antigens by serological analysis. The 201 streptococcal clinical isolates from India used in this study represented 69 differentemmtypes, withemm12 being the most prevalent. Virulence profiling of the North and South IndianS. pyogenesisolates with a custom-designed streptococcal virulence microarray identified seven conserved putative vaccine candidates. Collagen-like surface protein (SCI), putative secreted 5′-nucleotidase (PSNT), and C5a peptidase were found in 100% of the isolates, while R28, a putative surface antigen (PSA), and a hypothetical protein (HYP) were found in 90% of the isolates. A fibronectin binding protein, SfbI, was present in only 78% of the isolates. In order to validate the identified potential vaccine candidates, 185 serum samples obtained from patients with different clinical manifestations were tested for antibodies. Irrespective of clinical manifestations, serum samples showed high antibody titers to all proteins except for SCI and R28. Thus, the data indicate that PSNT, C5a peptidase, PSA, HYP, and SfbI are promising candidates for a region-specific streptococcal vaccine for the different parts of India.
Western Blotting Is an Efficient Tool for Differential Diagnosis of Paracoccidioidomycosis and Pulmonary Tuberculosis
Authors: Bertoni Thâmara Aline , Perenha-Viana Maysa Cláudia Zolin , Patussi Eliana Valéria , Cardoso Rosilene Fressatti , Svidzinski Terezinha Inez Estivalet 
Published: September 2012

ABSTRACTSputum and sera from 134 patients screened for tuberculosis (TB) were analyzed to investigate TB and paracoccidioidomycosis (PCM). Of these patients, 11 (8.2%) were confirmed to have TB, but six (4.5%) were positive only for PCM. All patients with PCM presented anti-43-kDa-component antibodies in Western blotting (WB) assays, while in the TB-positive patients these antibodies did not appear. This preliminary study suggests WB as a potential tool for differential laboratory diagnosis between TB and PCM.
Misdiagnosis of Late-Onset Lyme Arthritis by Inappropriate Use of Borrelia burgdorferi Immunoblot Testing with Synovial Fluid
Authors: Barclay Sam S. , Melia Michael T. , Auwaerter Paul G. 
Published: September 2012

ABSTRACTThe primary objective of this study was to determine whether patients with putative late-onset Lyme arthritis based upon synovial fluidBorrelia burgdorferiIgM and IgG immunoblot testing offered by commercial laboratories satisfied conventional criteria for the diagnosis of Lyme arthritis. Secondary objectives included assessing the prior duration and responsiveness of associated antibiotic therapy. We conducted a retrospective analysis of 11 patients referred to an academic medical center infectious disease clinic during the years 2007 to 2009 with a diagnosis of Lyme disease based upon previously obtained synovial fluidB. burgdorferiimmunoblot testing. Ten of the 11 (91%) patients with a diagnosis of late-onset Lyme arthritis based upon interpretation of synovial fluidB. burgdorferiimmunoblot testing were seronegative and did not satisfy published criteria for the diagnosis of late-onset Lyme arthritis. None of the 10 patients had a clinical response to previously received antibiotics despite an average course of 72 days. Diagnosis of Lyme arthritis should not be based on synovial fluidB. burgdorferiimmunoblot testing. This unvalidated test does not appear useful for the diagnosis of Lyme disease, and this study reinforces the longstanding recommendation to useB. burgdorferiimmunoblot testing only on serum samples and not other body fluids. Erroneous interpretations of “positive” synovial fluid immunoblots may lead to inappropriate antibiotic courses and delays in diagnosis of other joint diseases.
Measles Virus IgG Avidity Assay for Use in Classification of Measles Vaccine Failure in Measles Elimination Settings
Authors: Mercader Sara , Garcia Philip , Bellini William J. 
Published: September 2012

ABSTRACTIn regions where endemic measles virus has been eliminated, diagnostic assays are needed to assist in correctly classifying measles cases irrespective of vaccination status. A measles IgG avidity assay was configured using a commercially available measles-specific IgG enzyme immunoassay by modifying the protocol to include three 5-min washes with diethylamine (60 mM; pH 10.25) following serum incubation; serum was serially diluted, and the results were expressed as the end titer avidity index. Receiver operating characteristic analysis was used for evaluation and validation and to establish low (≤30%) and high (≥70%) end titer avidity thresholds. Analysis of 319 serum specimens expected to contain either high- or low-avidity antibodies according to clinical and epidemiological data indicated that the assay is highly accurate, with an area under the curve of 0.998 (95% confidence interval [CI], 0.978 to 1.000), sensitivity of 91.9% (95% CI, 83.2% to 97.0%), and specificity of 98.4% (95% CI, 91.6% to 100%). The assay is rapid (<2 h) and precise (standard deviation [SD], 4% to 7%). In 18 samples from an elimination setting outbreak, the assay identified 2 acute measles cases with low-avidity results; both were IgM-positive samples. Additionally, 11 patients (15 samples) with modified measles who were found to have high-avidity IgG results were classified as secondary vaccine failures; one sample with an intermediate-avidity result was not interpretable. In elimination settings, measles IgG avidity assays can complement existing diagnostic tools in confirming unvaccinated acute cases and, in conjunction with adequate clinical and epidemiologic investigation, aid in the classification of vaccine failure cases.
Two Outer Membrane Lipoproteins from Histophilus somni Are Immunogenic in Rabbits and Sheep and Induce Protection against Bacterial Challenge in Mice
Authors: Guzmán-Brambila Carolina , Rojas-Mayorquín Argelia E. , Flores-Samaniego Beatriz , Ortuño-Sahagún Daniel 
Published: September 2012

ABSTRACTHistophilus somniis an economically important pathogen of cattle and other ruminants and is considered one of the key components of the bovine respiratory disease (BRD) complex, the leading cause of economic loss in the livestock industry. BRD is a multifactorial syndrome, in which a triad of agents, including bacteria, viruses, and predisposing factors or “stressors,” combines to induce disease. Although vaccines againstH. somnihave been used for many decades, traditional bacterins have failed to demonstrate effective protection in vaccinated animals. Hence, the BRD complex continues to produce strong adverse effects on the health and well-being of stock and feeder cattle. The generation of recombinant proteins may facilitate the development of more effective vaccines againstH. somni, which could confer better protection against BRD. In the present study, primers were designed to amplify, clone, express, and purify two recombinant lipoproteins fromH. somni, p31 (Plp4) and p40 (LppB), which are structural proteins of the outer bacterial membrane. The results presented here demonstrate, to our knowledge for the first time, that when formulated, an experimental vaccine enriched with these two recombinant lipoproteins generates high antibody titers in rabbits and sheep and exerts a protective effect in mice against septicemia induced byH. somnibacterial challenge.
Clonal Analysis of Neisseria meningitidis Serogroup B Strains in South Africa, 2002 to 2006: Emergence of New Clone ST-4240/6688
Authors: Moodley Chivonne , du Plessis Mignon , Ndlangisa Kedibone , de Gouveia Linda , Klugman Keith P. , von Gottberg Anne ,   for GERMS-SA (Group for Enteric, Respiratory and Meningeal Disease Surveillance in South Africa)
Published: September 2012

ABSTRACT

From August 1999 through July 2002, hyperinvasive
Neisseria meningitidis
serogroup B (MenB) clonal complexes (CCs), namely, ST-32/ET-5 (CC32) and ST-41/44/lineage 3 (CC41/44), were predominant in the Western Cape Province of South Africa. This study analyzed MenB invasive isolates from a national laboratory-based surveillance system that were collected from January 2002 through December 2006. Isolates were characterized by pulsed-field gel electrophoresis (PFGE) (
n
= 302), and multilocus sequence typing (MLST) and PorA and FetA typing were performed on randomly selected isolates (34/302, 11%). In total, 2,400 cases were reported, with the highest numbers from Gauteng Province (1,307/2,400, 54%) and Western Cape Province (393/2,400, 16%); 67% (1,617/2,400) had viable isolates and 19% (307/1,617) were identified as serogroup B. MenB incidence remained stable over time (
P
= 0.77) (average incidence, 0.13/100,000 population [range, 0.10 to 0.16/100,000 population]). PFGE (302/307, 98%) divided isolates (206/302, 68%) into 13 clusters and 96 outliers. The largest cluster, B1, accounted for 25% of isolates (76/302) over the study period; its prevalence decreased from 43% (20/47) in 2002 to 13% (8/62) in 2006 (
P
< 0.001), and it was common in the Western Cape (58/76, 76%). Clusters B2 and B3 accounted for 10% (31/302) and 6% (19/302), respectively, and showed no significant change over time and were predominant in Gauteng. Randomly selected isolates from clusters B1, B2, and B3 belonged to CC32, CC41/44, and the new CC4240/6688, respectively. Overall, 15 PorA and 12 FetA types were identified. MenB isolates were mostly diverse with no single dominant clone; however, CC32 and CC41/44 accounted for 35% and the new CC4240/6688 was the third most prevalent clone.
Molecular Typing of Treponema pallidum: a 5-Year Surveillance in Shanghai, China
Authors: Dai Ting , Li Kang , Lu Haikong , Gu Xin , Wang Qianqiu , Zhou Pingyu 
Published: September 2012

ABSTRACT

Previously, a small study showed that 14f was the predominant subtype of
Treponema pallidum
in Shanghai, China. The result was quite different from the genotype distribution in other areas of China. This study aimed to identify the strain types of
Treponema pallidum
in samples collected over a 5-year period in Shanghai. From 2007 to 2011, genital swabs were collected from patients with syphilis from the Shanghai Skin Disease Hospital. Positive specimens were typed by the enhanced typing method by adding a
tp0548
gene to the existing
arp
and
tpr
genotype system. In total, 304 of the 372 enrolled patients yielded fully typeable DNA. Ten
arp
types (4, 6, 8, 9, 11, 12, 13, 14, 15, and 19), 3
tpr
types (a, d, and o), and 5
tp0548
types (a, c, f, g, and i) were identified. In total, 12 subtypes were identified with a combination of the
arp
and
tpr
genes. Subtype 14d was found in 270 samples (88.8%). When the combination included the
tp0548
gene, the 12 CDC subtypes identified were divided into 14 strain types. The predominant type was 14d/f (88.8%), followed by 15d/f (3.6%), 13d/f (1.3%), and 19d/c (1.3%). Two of the 44 14d/f-infected patients and both of the 19d/c-infected patients who underwent a lumbar puncture were diagnosed with neurosyphilis. This study showed that the predominant type in Shanghai was 14d/f. While this is in keeping with data from other areas in China, it is different from an earlier report showing that 14f is the most common genotype in Shanghai. Further studies are needed to better understand the association between strain types and neurosyphilis.
Longitudinal Analysis of the Evolution and Dissemination of Neisseria gonorrhoeae Strains (Saskatchewan, Canada, 2005 to 2008) Reveals Three Major Circulating Strains and Convergent Evolution of Ciprofloxacin and Azithromycin Resistance
Authors: Vidovic Sinisa , Thakur Sidharath D. , Horsman Greg B. , Levett Paul N. , Anvari Vahid , Dillon Jo-Anne R. 
Published: September 2012

ABSTRACTA longitudinal study combining multilocus sequence typing with molecular evolutionary analysis determined the distribution, population structure, and evolution of antibiotic resistance inNeisseria gonorrhoeaeisolates in Saskatchewan that were collected between 2005 and 2008. Of 195 gonococcal isolates examined, 29 sequence types (STs) were identified with 3 major circulating strains (ST-1 through ST-3) comprising 52% of all gonococcal isolates studied. The prevalences, persistence, distribution patterns, and clonalities of these isolates strongly suggest that gonorrhea endemicity within this broad geographic region was driven by these 3 circulating strains. ST-1 exhibited a significantly (P= 0.001) higher prevalence throughout the study than did the others, accounting for ∼25% of the tested isolates each year. The spatial distributions of the gonococcal strains indicated that ST-1 in 2007 entered a linear component of the sexual network, reaching the remote north and resulting in the further spread and maintenance of infection. Ciprofloxacin and azithromycin resistances were observed in distantly related gonococcal lineages, clearly indicating the convergent acquisition of these antibiotic-resistant phenotypes. In addition, all ciprofloxacin- and azithromycin-resistant lineages were found at the edges of the minimum spanning tree, far from the major lineages, suggesting that these antibiotic phenotypes were most likely introduced into the province. In contrast, resistance to penicillin was found mostly in the endemic gonococcal lineages, suggesting that penicillin resistance was probably acquired in Saskatchewan as a result of spontaneous mutations in already-established lineages. Tetracycline resistance was present in all STs except one, indicating its ubiquitous nature in the gonococcal population studied.
Molecular Epidemiology of Outbreak-Associated and Wild-Waterfowl-Derived Newcastle Disease Virus Strains in Finland, Including a Novel Class I Genotype
Authors: Lindh Erika , Ek-Kommonen Christine , Väänänen Veli-Matti , Alasaari Jukka , Vaheri Antti , Vapalahti Olli , Huovilainen Anita 
Published: September 2012

ABSTRACT
Newcastle disease (ND) is a highly contagious, severe disease of poultry caused by pathogenic strains of Newcastle disease virus (NDV; or avian paramyxovirus-1). NDV is endemic in wild birds worldwide and one of the economically most important poultry pathogens. Most of the published strains are outbreak-associated strains, while the apathogenic NDV strains that occur in wild birds, posing a constant threat to poultry with their capability to convert into more virulent forms, have remained less studied. We screened for NDV RNA in cloacal and oropharyngeal samples from wild waterfowl in Finland during the years 2006 to 2010: 39 of 715 birds were positive (prevalence, 5.5%). The partial or full-length F genes of 37 strains were sequenced for phylogenetic purposes. We also characterized viruses derived from three NDV outbreaks in Finland and discuss the relationships between these outbreak-associated and the wild-bird-associated strains. We found that all waterfowl NDV isolates were lentogenic strains of class I or class II genotype I. We also isolated a genetically distinct class I strain (teal/Finland/13111/2008) grouping phylogenetically together with only strain HIECK87191, isolated in Northern Ireland in 1987. Together they seem to form a novel class I genotype genetically differing from other known NDVs by at least 12%.
Rapid Detection of Carbapenemase-Producing Pseudomonas spp
Authors: Dortet Laurent , Poirel Laurent , Nordmann Patrice 
Published: September 2012

ABSTRACT

A novel biochemical technique, the Carba NP test, has been evaluated to detect carbapenemase production in
Pseudomonas
spp. This test was specific (100%), sensitive (94.4%), and rapid (<2 h). This cost-effective test, which could be implemented in any microbiology laboratory, offers a reliable technique for identification of carbapenemase-producing
Pseudomonas
spp.
Antimicrobial Treatment and Containment Measures for an Extremely Drug-Resistant Klebsiella pneumoniae ST101 Isolate Carrying pKPN101-IT, a Novel Fully Sequenced
bla
KPC-2
Plasmid
Authors: Frasson Ilaria , Lavezzo Enrico , Franchin Elisa , Toppo Stefano , Barzon Luisa , Cavallaro Antonietta , Richter Sara N. , Palù Giorgio 
Published: September 2012

ABSTRACT

An extremely drug-resistant
Klebsiella pneumoniae
isolate, sequence type ST101, was isolated from a patient in Italy. We describe antibiotic treatment, measures to clear and contain the infection, and a complete sequence analysis of a novel large plasmid, pKPN101-IT, harboring the
bla
KPC-2
gene and arising from the threatening recombination of different worldwide-distributed backbones.
Next-Generation Ion Torrent Sequencing of Drug Resistance Mutations in Mycobacterium tuberculosis Strains
Authors: Daum Luke T. , Rodriguez John D. , Worthy Sue A. , Ismail Nazir A. , Omar Shaheed V. , Dreyer Andries W. , Fourie P. Bernard , Hoosen Anwar A. , Chambers James P. , Fischer Gerald W. 
Published: September 2012

ABSTRACT

A novel protocol for full-length
Mycobacterium tuberculosis
gene analysis of first- and second-line drug resistance was developed using the Ion Torrent Personal Genome Machine (PGM). Five genes—
rpoB
(rifampin),
katG
(isoniazid),
pncA
(pyrazinamide),
gyrA
(ofloxacin/fluoroquinolone), and
rrs
(aminoglycosides)—were amplified and sequenced, and results were compared to those obtained by genotypic Hain line probe assay (LPA) and phenotypic Bactec MGIT 960 analysis using 26 geographically diverse South African clinical isolates collected between July and November 2011. Ion Torrent sequencing exhibited 100% (26/26) concordance to phenotypic resistance obtained by MGIT 960 culture and genotypic
rpoB
and
katG
results by LPA. In several rifampin-resistant isolates, Ion Torrent sequencing revealed uncommon substitutions (H526R and D516G) that did not have a defined mutation by LPA. Importantly, previously uncharacterized mutations in
rpoB
(V194I),
rrs
(G878A), and
pncA
(Q122Stop) genes were observed. Ion Torrent sequencing may facilitate tracking and monitoring geographically diverse multidrug-resistant and extensively drug-resistant strains and could potentially be integrated into selected regional and reference settings throughout Africa, India, and China.
Characterization of Methicillin-Resistant Staphylococcus aureus Strains Recovered from a Phase IV Clinical Trial for Linezolid versus Vancomycin for Treatment of Nosocomial Pneumonia
Authors: Mendes Rodrigo E. , Deshpande Lalitagauri M. , Smyth Davida S. , Shopsin Bo , Farrell David J. , Jones Ronald N. 
Published: September 2012

ABSTRACT

A total of 434 methicillin-resistant
Staphylococcus aureus
(MRSA) baseline isolates were collected from subjects enrolled in a prospective, double-blind randomized trial comparing linezolid versus vancomycin for the treatment of nosocomial pneumonia. Isolates were susceptibility tested by broth microdilution, examined for inducible clindamycin resistance by D-test, and screened for heterogeneous resistance to vancomycin (hVISA) by the Etest macromethod. All strains were subjected to Panton-Valentine leukocidin (PVL) screening, and SCC
mec
, pulsed-field gel electrophoresis (PFGE), and
spa
typing. Selected strains were evaluated by multilocus sequence typing (MLST). Clonal complexes (CCs) were assigned based on the
spa
and/or MLST results. Most strains were CC5 (56.0%), which originated from North America (United States) (CC5-MRSA-SCC
mec
II/IV; 70.0%), Asia (CC5-MRSA-II; 14.0%) and Latin America (CC5-MRSA-I/II; 12.3%). The second- and third-most-prevalent clones were CC8-MRSA-IV (23.3%) and CC239-MRSA-III (11.3%), respectively. Furthermore, the CC5-MRSA-I/II clone predominated in Asia (50.7% within this region) and Latin America (66.7%), followed by CC239-MRSA-III (32.8% and 28.9%, respectively). The European strains were CC8-MRSA-IV (34.5%), CC22-MRSA-IV (18.2%), or CC5-MRSA-I/II/IV (16.4%), while the U.S. MRSA isolates were CC5-MRSA-II/IV (64.4%) or CC8-MRSA-IV (28.8%). Among the U.S. CC8-MRSA-II/IV strains, 73.7% (56/76 [21.2% of all U.S. MRSA strains]) clustered within USA300. One strain from the United States (USA800) was intermediate to vancomycin (MIC, 4 μg/ml). All remaining strains were susceptible to linezolid, daptomycin, vancomycin, and teicoplanin. hVISA strains (14.5%) were predominantly CC5-MRSA-II, from South Korea, and belonged to a single PFGE type. Overall, each region had two predominant clones. The USA300 rate corroborates previous reports describing increased prevalence of USA300 strains causing invasive infections. The prevalence of hVISA was elevated in Asia, and these strains were associated with CC5.
Isolation of Kerstersia gyiorum from a Patient with Cholesteatomatous Chronic Otitis Media
Authors: Almuzara Marisa N. , Barberis Claudia M. , Traglia German M. , Ordoñez Andrea Martinez , Famiglietti Angela M. R. , Ramirez Maria S. , Vay Carlos A. 
Published: September 2012

ABSTRACTWe describe the first case of aKerstersia gyiorumstrain isolated from a patient with cholesteatomatous chronic otitis media. We emphasize the isolation of members of the familyAlcaligenaceaein serious infections and unusual sites and the importance of polyphasic identification addressing the definitive identification.
Novel Primer-Probe Sets for Detection and Identification of Mycobacteria by PCR-Microarray Assay
Authors: Lazzeri Elisa , Santoro Francesco , Oggioni Marco R. , Iannelli Francesco , Pozzi Gianni 
Published: September 2012

ABSTRACT

A PCR-microarray assay was developed in which PCR primers and hybridization probes were designed for the 16S rRNA genes of 16 clinically relevant mycobacteria and for IS
6110
of
Mycobacterium tuberculosis
. The assay, based on a multiplex PCR followed by hybridization with oligonucleotide probes, was tested against 16
Mycobacterium
species and 70 clinical samples.