bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Analysis of Methicillin-Resistant
Staphylococcus aureus
as a Causative Agent of Bronchopulmonary Infection: Relation to Colonization in the Upper Respiratory Tract
Authors: Watanabe Hiroshi , Masaki Hironori , Asoh Norichika , Watanabe Kiwao , Oishi Kazunori , Kobayashi Shinobu , Sato Akiyoshi , Nagatake Tsuyoshi 
Published: December 2019

ABSTRACT

Using five diagnostic markers, we compared the types of 72 strains of methicillin-resistant
Staphylococcus aureus
(MRSA) isolated simultaneously from the nasal cavity, pharynx, and sputum from 24 patients. Almost identical MRSA types had colonized the nasal cavity and sputum from the same patient for 21 (88%) of the patients. We speculate that most MRSA organisms isolated in sputum are derived from the nasal cavity, while a few are derived from the pharynx.
Diagnostic Value of Immunoglobulin G (IgG) and IgM Anti-Hepatitis E Virus (HEV) Tests Based on HEV RNA in an Area Where Hepatitis E Is Not Endemic
Authors: Lin Chen-Chun , Wu Jaw-Ching , Chang Ting-Tsung , Chang Wen-Yu , Yu Ming-Lung , Tam Albert W. , Wang Shen-Chin , Huang Yi-Hsiang , Chang Full-Young , Lee Shou-Dong 
Published: December 2019

ABSTRACT
Acute hepatitis E (AHE) has rarely been reported in industrialized countries, but the rate of seroprevalence of hepatitis E virus (HEV) antibodies (anti-HEV) is inappropriately high. The sensitivity and specificity of the assay used to test for immunoglobulin G (IgG) and IgM anti-HEV have not been well established in areas where hepatitis E is not endemic (hereafter referred to as “nonendemic areas”). We collected serum samples from 13 AHE patients, 271 healthy subjects, and 160 other liver disease patients in Taiwan to test for HEV RNA by reverse transcription (RT)-PCR and for IgG and IgM anti-HEV by enzyme-linked immunosorbent assays. The sensitivities of IgG and IgM anti-HEV (relative to RT-PCR) were 86.7 and 53.3%, respectively. The specificities of IgG and IgM anti-HEV assays for diagnosing AHE were 92.1 and 98.6%, respectively. The rate of seroprevalence of IgG anti-HEV was 11% among healthy subjects in this nonendemic area, and it increased with age. In summary, IgG anti-HEV is a good diagnostic test for screening for AHE in nonendemic areas. The high rate of prevalence of anti-HEV in healthy subjects indicates that subclinical infection may exist.
Genetic Diversity of Protease and Reverse Transcriptase Sequences in Non-Subtype-B Human Immunodeficiency Virus Type 1 Strains: Evidence of Many Minor Drug Resistance Mutations in Treatment-Naive Patients
Authors: Vergne Laurence , Peeters Martine , Mpoudi-Ngole Eitel , Bourgeois Anke , Liegeois Florian , Toure-Kane Coumba , Mboup Souleymane , Mulanga-Kabeya Claire , Saman Eric , Jourdan Jacques , Reynes Jacques , Delaporte Eric 
Published: December 2019

ABSTRACT
Most human immunodeficiency virus (HIV) drug susceptibility studies have involved subtype B strains. Little information on the impact of viral diversity on natural susceptibility to antiretroviral drugs has been reported. However, the prevalence of non-subtype-B (non-B) HIV type 1 (HIV-1) strains continues to increase in industrialized countries, and antiretroviral treatments have recently become available in certain developing countries where non-B subtypes predominate. We sequenced the protease and reverse transcriptase (RT) genes of 142 HIV-1 isolates from antiretroviral-naive patients: 4 belonged to group O and 138 belonged to group M (9 subtype A, 13 subtype B, 2 subtype C, 5 subtype D, 2 subtype F1, 9 subtype F2, 4 subtype G, 5 subtype J, 2 subtype K, 3 subtype CRF01-AE, 67 subtype CRF02-AG, and 17 unclassified isolates). No major mutations associated with resistance to nucleoside reverse transcriptase inhibitors (NRTIs) or protease inhibitors were detected. Major mutations linked to resistance to non-NRTI agents were detected in all group O isolates (A98G and Y181C) and in one subtype J virus (V108I). In contrast, many accessory mutations were found, especially in the protease gene. Only 5.6% of the 142 strains, all belonging to subtype B or D, had no mutations in the protease gene. Sixty percent had one mutation, 22.5% had two mutations, 9.8% had three mutations, and 2.1% (all group O strains) had four mutations. In order of decreasing frequency, the following mutations were identified in the protease gene: M36I (86.6%), L10I/V (26%), L63P (12.6%), K20M/R (11.2%), V77I (5.6%), A71V (2.8%), L33F (0.7%), and M46I (0.7%). R211K, an accessory mutation associated with NRTI resistance, was also observed in 43.6% of the samples. Phenotypic and clinical studies are now required to determine whether multidrug-resistant viruses emerge more rapidly during antiretroviral therapy when minor resistance-conferring mutations are present before treatment initiation.
Development of a Highly Sensitive and Specific Enzyme-Linked Immunosorbent Assay Based on Recombinant Matrix Protein for Detection of Avian Pneumovirus Antibodies
Authors: Gulati Baldev R. , Cameron Kjerstin T. , Seal Bruce S. , Goyal Sagar M. , Halvorson David A. , Njenga M. Kariuki 
Published: December 2019

ABSTRACT

The matrix (M) protein of avian pneumovirus (APV) was evaluated for its antigenicity and reliability in an enzyme-linked immunosorbent assay (ELISA) for diagnosis of APV infection, a newly emergent disease of turkeys in United States. Sera from APV-infected turkeys consistently contained antibodies to a 30-kDa protein (M protein). An ELISA based on recombinant M protein generated in
Escherichia coli
was compared with the routine APV ELISA that utilizes inactivated virus as antigen. Of 34 experimentally infected turkeys, 33 (97.1%) were positive by M protein ELISA whereas only 18 (52.9%) were positive by routine APV ELISA 28 days after infection. None of the serum samples from 41 uninfected experimental turkeys were positive by M protein ELISA. Of 184 field sera from turkey flocks suspected of having APV infection, 133 (72.3%) were positive by M protein ELISA whereas only 99 (53.8%) were positive by routine APV ELISA. Twelve serum samples, which were negative by M protein ELISA but positive by routine APV ELISA, were not reactive with either recombinant M protein or denatured purified APV proteins by Western analysis. This indicates that the samples had given false-positive results by routine APV ELISA. The M protein ELISA was over six times more sensitive than virus isolation (11.5%) in detecting infections from samples obtained from birds showing clinical signs of APV infection. Taken together, these results show that ELISA based on recombinant M protein is a highly sensitive and specific test for detecting antibodies to APV.
Quality of Human Immunodeficiency Virus Viral Load Testing in Australia
Authors: Best Susan J. , Gust Anthony P. , Johnson Elizabeth I. M. , McGavin Catherine H. , Dax Elizabeth M. 
Published: December 2019

ABSTRACT

This study determined the proficiencies of laboratories measuring human immunodeficiency virus type 1 (HIV-1) viral loads and the accuracies of two assays used for HIV-1 viral load measurement in Australia and investigated the variability of the new versions of these assays. Quality assessment program panels containing (i) dilutions of HIV-1 subtype B, (ii) replicates of identical samples of HIV-1 subtype B, and (iii) samples of subtype E and B were tested by laboratories. Total variability (within and between laboratories) was tested with quality control samples. The coefficients of variation (CVs) for the Roche AMPLICOR HIV-1 MONITOR version (v) 1.0 and Chiron Quantiplex bDNA 2.0 assays ranged from 53 to 87% and 22 to 31%, respectively. The widespread occurrence of invalid runs with the AMPLICOR HIV-1 MONITOR 1.0 assay was identified. The CVs of the new versions of the assays were 82 to 86% for the AMPLICOR HIV-1 MONITOR v 1.5 assay and 16 to 23% for the Quantiplex bDNA 3.0 assay. For virus dilution samples, all but 5 of 19 laboratories obtained results within 2 standard deviations of the mean. The Quantiplex bDNA 2.0 assay reported values lower than those reported by the AMPLICOR HIV-1 MONITOR version 1.0 assay for samples containing HIV-1 subtype B, whereas the reverse was true for subtype E. Identification and resolution of the problem of invalid runs markedly improved the quality of HIV-1 viral load testing. The variability observed between laboratories and between assays, even the most recent versions, dictates that monitoring of viral load in an individual should always be by the same laboratory and by the same assay. Results for an individual which differ by less than 0.5 log
10
HIV-1 RNA copy number/ml should not be considered clinically significant.
Human T-Cell Lymphotropic Virus Type 1 Gag Indeterminate Western Blot Patterns in Central Africa: Relationship toPlasmodium falciparumInfection
Authors: Mahieux Renaud , Horal Peter , Mauclère Philippe , Mercereau-Puijalon Odile , Guillotte Micheline , Meertens Laurent , Murphy Edward , Gessain Antoine 
Published: December 2019

ABSTRACTTo gain insight on the significance of human T-cell lymphotropic virus type 1 (HTLV-1) indeterminate serological reactivities, we studied villagers of South Cameroon, focusing on a frequent and specific HTLV-1 Gag indeterminate profile (HGIP) pattern (gagp19, p26, p28, and p30 without p24 or Env gp21 and gp46). Among the 102 sera studied, 29 from all age groups had a stable HGIP pattern over a period of 4 years. There was no epidemiological evidence for sexual or vertical transmission of HGIP. Seventy-five percent of HGIP sera reacted positively on MT2 HTLV-1-infected cells by immunofluorescence assay. However, we could not isolate any HTLV-1 virus or detect the presence of p19 Gag protein in cultures of peripheral blood mononuclear cells obtained from individuals with strong HGIP reactivity. PCR experiments conducted with primers for HTLV-1 and HTLV-2 (HTLV-1/2 primers) encompassing different regions of the virus did not yield HTLV-1/2 proviral sequences from individuals with HGIP. Using 11 peptides corresponding to HTLV-1 or HTLV-2 immunodominant B epitopes in an enzyme-linked immunosorbent assay, one epitope corresponding to the Gag p19 carboxyl terminus was identified in 75% of HGIP sera, while it was recognized by only 41% of confirmed HTLV-1-positive sera. A positive correlation between HTLV-1 optical density values and titers of antibody toPlasmodium falciparumwas also demonstrated. Finally, passage of sera through aP. falciparum-infected erythrocyte-coupled column was shown to specifically abrogate HGIP reactivity but not the HTLV-1 pattern, suggesting the existence of cross-reactivity between HTLV-1 Gag proteins and malaria-derived antigens. These data suggest that in Central Africa, this frequent and specific Western blot is not caused by HTLV-1 infection but could instead be associated withP. falciparuminfection.
Evaluation of PCR-Based Methods for Discrimination of
Francisella
Species and Subspecies and Development of a Specific PCR That Distinguishes the Two Major Subspecies of
Francisella tularensis
Authors: Johansson Anders , Ibrahim Ashraf , Göransson Ingela , Eriksson Ulla , Gurycova D. , Clarridge Jill E. , Sjöstedt Anders 
Published: December 2019

ABSTRACT

Previous studies have demonstrated that the four subspecies of the human pathogen
Francisella tularensis
, despite showing marked variations in their virulence for mammals and originating from different regions in the Northern Hemisphere, display a very close phylogenetic relationship. This property has hampered the development of generally applicable typing methods. To overcome this problem, we evaluated the use of PCR for discrimination of the subspecies using various forms of long arbitrary primers or primers specific for repetitive extragenic palindromic sequences (REP) or enterobacterial repetitive intragenic consensus (ERIC) sequences. Patterns generated by use of REP, ERIC, or long arbitrary primers allowed differentiation at the species level and of the four subspecies of
F. tularensis
. With each of these three methods, similar or identical clustering of strains was found, and groups of strains of different geographical origins or differing in virulence showed distinct patterns. The discriminatory indices of the methods varied from 0.57 to 0.65; thus, the patterns were not sufficiently discriminatory to distinguish individual strains. The sequence of a fragment generated by amplification with an arbitrary primer was determined, and a region showing interstrain heterogeneity was identified. Specific primers were designed, and a PCR was developed that distinguished strains of
F. tularensis
subsp.
holarctica
from strains of other
F. tularensis
subspecies, including strains of the highly virulent
F. tularensis
subsp.
tularensis
. Notably, one European isolate showed the genetic pattern typical of the highly virulent
F. tularensis
subsp.
tularensis
, generally believed to exist only in North America. It is proposed that a combination of the specific PCR together with one method generating subspecies-specific patterns is suitable as a rapid and relatively simple strategy for discrimination of
Francisella
species and subspecies.
Emergence of
Vibrio cholerae
O1 Biotype El Tor Serotype Inaba from the Prevailing O1 Ogawa Serotype Strains in India
Authors: Garg Pallavi , Nandy Ranjan K. , Chaudhury Papiya , Chowdhury Nandini Roy , De Keya , Ramamurthy T. , Yamasaki Shinji , Bhattacharya S. K. , Takeda Yoshifumi , Nair G. Balakrish 
Published: December 2019

ABSTRACT

The toxigenic Inaba serotype of
Vibrio cholerae
O1 biotype El Tor reappeared in India in 1998 and 1999, almost 10 years after its last dominance in Calcutta in 1989. Extensive molecular characterization by ribotyping, restriction fragment length polymorphism, and pulsed-field gel electrophoresis indicated that recent Inaba strains are remarkably different from the earlier Inaba strains but are very similar to the prevailing
V. cholerae
O1 Ogawa El Tor biotype strains. The antibiograms of the Inaba strains were also similar to those of the recent
V. cholerae
Ogawa strains. These
V. cholerae
O1 Inaba strains appear to have evolved from the currently prevailing Ogawa strains and are likely to dominate in the coming years.
Evaluation of a Commercial DNA Enzyme Immunoassay for Detection of Enterovirus Reverse Transcription-PCR Products Amplified from Cerebrospinal Fluid Specimens
Authors: Young Pampee P. , Buller Richard S. , Storch Gregory A. 
Published: December 2019

ABSTRACT
We evaluated the DiaSorin DNA enzyme immunoassay (DEIA) kit for detection of enteroviral reverse transcription-PCR (RT-PCR) products amplified from cerebrospinal fluid. By use of an optical density of 0.05 as the absorbance cutoff, 35% of 198 specimens were PCR positive, whereas 16% were culture positive. DEIA was rapid and sensitive and can help implement enterovirus RT-PCR in clinical laboratories.
Detection of Hepatitis G Virus (HGV) RNA and Antibodies to the HGV Envelope Protein E2 in a Cohort of Hemodialysis Patients
Authors: Pérez-Gracia T. , Galán F. , Girón-González J. A. , Lozano A. , Benavides B. , Fernández E. , Rodríguez-Iglesias M. 
Published: December 2019

ABSTRACT
An analysis of the evolution of hepatitis G virus (HGV) infection markers was performed for a cohort of 58 hemodialyzed patients. During follow-up (4.88 ± 0.42 years), a group of these patients cleared their antibodies against the envelope protein E2 with (4 of 29 cases; 13.8%) or without (9 of 29 cases; 31%) the reappearance of viremia. This finding implies a temporally limited protection in patients previously infected with HGV.
Value of Examining Three Acid-Fast Bacillus Sputum Smears for Removal of Patients Suspected of Having Tuberculosis from the “Airborne Precautions” Category
Authors: Craft David W. , Jones Melissa C. , Blanchet Cherie N. , Hopfer Roy L. 
Published: December 2019

ABSTRACT

We examined the potential risk of tuberculosis transmission if we modified our policy for release of patients from the “airborne precautions” category from three negative acid-fast bacillus (AFB) smears to two, or even one. Over a 4-year period, respiratory cultures from 42 patients grew
Mycobacterium tuberculosis
. Of these, 36 patients (81%) had a positive AFB smear result on the first submitted specimen. One additional patient (2%) had a first smear-positive finding on the second submitted specimen, and no patients had a first smear-positive result on the third submitted specimen. Respiratory cultures from five patients (12%) grew
M. tuberculosis
without ever having a positive AFB smear result. These data indicate that in our institution, reducing the number of negative smears required before removal of patients from the airborne precautions category would pose little, if any, increase in the risk of spreading tuberculosis.
White Grain Mycetoma Caused by a
Cylindrocarpon
sp. in India
Authors: Hemashettar B. M. , Siddaramappa B. , Padhye A. A. , Sigler L. , Chandler F. W. 
Published: December 2019

ABSTRACT

We describe a case of white grain eumycetoma of the foot of an Indian male caused by a slow-growing, poorly sporulating fungus that does not match any known agent of this infection. Histologic examination of a biopsy tissue specimen showed oval, lobular, white granules composed of hyaline, septate hyphae, and thick-walled chlamydospores. Culture of granules from a draining sinus yielded compact, very-slow-growing, poorly sporulating colonies producing a strong reddish brown pigment that diffused into the medium. The fungus was identified as a
Cylindrocarpon
sp. based on the development of rare cylindrical conidia borne from solitary phialides lacking collarettes, in addition to chlamydospores formed singly or in short chains.
Use of Whole Blood Specimens for Routine Clinical Quantitation of Hepatitis C Virus RNA Does Not Increase Assay Sensitivity
Authors: Cook Linda , Ross Angela M. , Knight Glenn B. , Agnello Vincent 
Published: December 2019

ABSTRACT
The measurement of hepatitis C virus (HCV) RNA levels in the blood has, in the last few years, become a critical component in the therapy of patients with HCV infections. Initially, extraction methods for serum and plasma were used, but a newer method that uses Catrimox-14 as the extraction agent for whole blood has been reported. Because the whole blood extraction method may yield higher virus levels if significant levels of virus are present in the white blood cells (WBC), the method was evaluated for use in our clinical diagnostic laboratory despite its higher reagent costs and more time-consuming methodology. RNA was simultaneously extracted from 39 clinical samples by four different methods: Catrimox-14–Trizol extraction from whole blood, Trizol extraction from whole blood, Trizol extraction from serum, and a commercial serum extraction method, the EZNA total RNA kit. In addition, in an effort to quantitate the amount of HCV RNA virus in the WBC, Trizol extraction from isolated WBC was also performed. Quantitative results for samples from which RNA was extracted by all four methods were essentially the same; the Catrimox-14–Trizol method did not yield increased virus levels. Insignificant levels of virus were found in the WBC. The results did not demonstrate a clinical usefulness for the Catrimox-14–Trizol method.
Molecular Epidemiology of Penicillin-Nonsusceptible
Streptococcus pneumoniae
among Children in Greece
Authors: Bogaert Debby , Syrogiannopoulos George A. , Grivea Ioanna N. , de Groot Ronald , Beratis Nicholas G. , Hermans Peter W. M. 
Published: December 2019

ABSTRACT

A total of 145 penicillin-nonsusceptible
Streptococcus pneumoniae
strains were isolated from young carriers in Greece and analyzed by antibiotic susceptibility testing, serotyping, restriction fragment end labeling (RFEL), and penicillin-binding protein (PBP) genotyping. The serotypes 23A and 23F (54%), 19A and 19F (25%), 9V (5%), 15A, 15B, and 15C (4%), 6A and 6B (4%), and 21 (4%) were most prevalent in this collection. Fifty-three distinct RFEL types were identified. Sixteen different RFEL clusters, harboring 2 to 32 strains each, accounted for 82% of all strains. Eight of these genetic clusters representing 60% of the strains were previously identified in other countries. A predominant lineage of 66 strains (46%) harboring five RFEL types and the serotypes 19F and 23F was closely related to the pandemic clone Spain
23F
-1 (genetic relatedness of ≥85%). Another lineage, representing 11 strains, showed close genetic relatedness to the pandemic clone France
9V
-3. Another lineage of 8 serotype 21 strains was Greece specific since the RFEL types were not observed in an international collection of 193 genotypes from 16 different countries. Characterization of the PBP genes
pbp1a
,
pbp2b
, and
pbp2x
revealed 20 distinct PBP genotypes of which PBP type 1-1-1, initially observed in the pandemic clones 23F and 9V, was predominantly present in 11 RFEL types in this Greek collection of penicillin-nonsusceptible strains (55%). Sixteen PBP types covering 52 strains (36%) were Greece specific. This study underlines the strong contribution of penicillin-resistant international clones to the prevalence and spread of penicillin-nonsusceptible pneumococci among young children in Greece.
Clonal Groups of Penicillin-Nonsusceptible
Streptococcus pneumoniae
in Baltimore, Maryland: a Population-Based, Molecular Epidemiologic Study
Authors: McEllistrem M. Catherine , Pass Margaret , Elliott John A. , Whitney Cynthia G. , Harrison Lee H. 
Published: December 2019

ABSTRACT

Few data are available on the molecular subtypes of all penicillin-nonsusceptible
Streptococcus pneumoniae
(PNSP) from a defined population base. Pulsed-field gel electrophoresis (PFGE), serotyping, and antibiotic susceptibility testing were performed for all available invasive PNSP isolates for which the penicillin (MIC) was ≥0.1 μg/ml from Baltimore, Md., during 1995–1996 (
n
= 143). The dendrogram analysis of PFGE patterns included 32 distinct clonal groups. Six major clonal groups included two-thirds of the PNSP strains. Major clonal groups 2, 3, 4, and 6 strains were genetically related to four previously described international clones and were all multidrug resistant. Major clonal group 3 was genetically related to the Tennessee
23F
-4 clone and contained all four strains for which the penicillin MIC was 8 μg/ml. Most of the clonal group 1 and 5 strains had intermediate susceptibility to penicillin and were rarely multidrug resistant. The latter clonal groups represent two previously undescribed penicillin-intermediate pneumococcal clones. Clonal group homogeneity was greater for serotype 9V, 19A, and 23F strains than for serotype 6A, 6B, 14, and 19F strains. The classification of PNSP strains into clonal groups is essential for future population-based epidemiologic studies of PNSP.
Restriction Endonuclease Analysis Discriminates
Bordetella bronchiseptica
Isolates
Authors: Sacco Randy E. , Register Karen B. , Nordholm Gwen E. 
Published: December 2019

ABSTRACT

One hundred ninety-five
Bordetella bronchiseptica
isolates from 12 different host species worldwide were characterized by restriction enzyme analysis (REA). These isolates had previously been categorized into 19
Pvu
II ribotypes. Twenty restriction endonucleases were evaluated for use in REA. Digestion of chromosomal DNA with
Hin
fI, followed by submarine electrophoresis in agarose gels and staining with ethidium bromide, produced DNA fragments in the 4.0- to 10-kb range, which readily discriminated
B. bronchiseptica
isolates, resulting in 48 fingerprint patterns. Moreover,
Alu
I digestion of chromosomal DNA produced 39 distinct fingerprint profiles with DNA fragments ranging from 6.0 to 20.0 kb. While REA frequently provided more discriminatory power than ribotyping, there were examples where the use of ribotyping was more discriminatory than REA. Passage of selected isolates up to passage 25 did not change the REA profile. Moreover, the Bvg phase did not alter the fingerprint profile of chromosomal DNA from
B. bronchiseptica
strains digested with
Hin
fI or
Alu
I. Based on the results presented herein, the combination of REA and ribotyping should provide valuable information in understanding the molecular epidemiology of
B. bronchiseptica
infections.