bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Prevalence of GB Virus C in Brazil and Molecular Evidence for Intrafamilial Transmission
Authors: Pinho João R. R. , Zanotto Paolo M. De A. , Ferreira João L. P. , Sumita Laura M. , Carrilho Flair J. , da Silva Luiz C. , Capacci M. Lourdes , Silva Adávio O. , Guz Betty , Gonçales Fernando L. , Gonçales Neiva S. L. , Buck Gregory A. , Meyers Gregory A. , Bernardini A. Plínio 
Published: December 2019

ABSTRACT
The prevalence of GB virus C (GBV-C) in candidate Brazilian blood donors with normal and elevated alanine aminotransferase levels was found to be 5.2% (5 of 95) and 6.5% (5 of 76), respectively. Among Brazilian patients, GBV-C was found in 9.5% (13 of 137) of cases of hepatitis not caused by hepatitis A virus (HAV), HBV, HCV, HDV, or HEV (non-A-E hepatitis) and in 18.2% (8 of 44) of individuals infected with HCV. Molecular characterization of GBV-C by partial sequencing of the NS3 region showed clustering between members of a single family, implying intrafamilial transmission. In conclusion, these results together suggest that contagion mechanisms which facilitate intrafamilial transmission of GBV-C may partially explain the high prevalence of viremic carriers worldwide.
Incidence of Upper Respiratory Tract
Mycoplasma pneumoniae
Infections among Outpatients in Rhône-Alpes, France, during Five Successive Winter Periods
Authors: Layani-Milon Marie-Paule , Gras Isabelle , Valette Martine , Luciani Jacques , Stagnara Jean , Aymard Michèle , Lina Bruno 
Published: December 2019

ABSTRACT

In this prospective study, nasal swab samples from patients with acute respiratory infections were evaluated for the presence of
Mycoplasma pneumoniae
. This PCR-plus-hybridization-based detection was associated with the detection of other viral agents. During the five winter surveillance periods, 3,897 samples were collected by 75 medical practitioners participating in the Groupe Régional d’Observation de la Grippe surveillance network in Rhône-Alpes (France).
M. pneumoniae
was detected in 283 samples (7.3%); its rate of detection ranged from 10.1 to 2.0% over the five periods, and it was the second most frequently isolated pathogen during the survey, after influenza A. Three high-prevalence winters were observed, yielding an early winter peak of
M. pneumoniae
infection which was observed in all age groups. No statistically significant difference was detected between rates of infections in the different age groups, but
M. pneumoniae
infection was significantly related to lower respiratory tract infection during periods of high prevalence. This study defined the frequency of
M. pneumoniae
detection from nasal swab specimens in patients with acute respiratory infections, confirming its high prevalence and the presence of large outbreaks due to this pathogen.
Epidemiological Study of Paratuberculosis in Wild Rabbits in Scotland
Authors: Greig Alastair , Stevenson Karen , Henderson Dennis , Perez Valentin , Hughes Valerie , Pavlik Ivo , Hines Murray E. , McKendrick Iain , Sharp J. Michael 
Published: December 2019

ABSTRACT
A survey of 22 farms confirmed the presence of paratuberculosis in wild rabbits in Scotland. Regional differences were apparent in the prevalence of the disease in rabbits, with a significantly higher incidence occurring in the Tayside region. Statistical analysis showed a significant relationship between a previous history or current problem of paratuberculosis in cattle and the presence of paratuberculosis in rabbits on the farms. Molecular genetic typing techniques could not discriminate between selected rabbit and cattle isolates from the same or different farms, suggesting that the same strain may infect and cause disease in both species and that interspecies transmission may occur. The possibility of interspecies transmission and the involvement of wildlife in the epidemiology of paratuberculosis have important implications for the control of the disease.
The Calgary Biofilm Device: New Technology for Rapid Determination of Antibiotic Susceptibilities of Bacterial Biofilms
Authors: Ceri H. , Olson M. E. , Stremick C. , Read R. R. , Morck D. , Buret A. 
Published: December 2019

ABSTRACT

Determination of the MIC, based on the activities of antibiotics against planktonic bacteria, is the standard assay for antibiotic susceptibility testing. Adherent bacterial populations (biofilms) present with an innate lack of antibiotic susceptibility not seen in the same bacteria grown as planktonic populations. The Calgary Biofilm Device (CBD) is described as a new technology for the rapid and reproducible assay of biofilm susceptibilities to antibiotics. The CBD produces 96 equivalent biofilms for the assay of antibiotic susceptibilities by the standard 96-well technology. Biofilm formation was followed by quantitative microbiology and scanning electron microscopy. Susceptibility to a standard group of antibiotics was determined for National Committee for Clinical Laboratory Standards (NCCLS) reference strains:
Escherichia coli
ATCC 25922,
Pseudomonas aeruginosa
ATCC 27853, and
Staphylococcus aureus
ATCC 29213. Growth curves demonstrated that biofilms of a predetermined size could be formed on the CBD at specific time points and, furthermore, that no significant difference (
P
> 0.1) was seen between biofilms formed on each of the 96 pegs. The antibiotic susceptibilities for planktonic populations obtained by the NCCLS method or from the CBD were similar. Minimal biofilm eradication concentrations, derived by using the CBD, demonstrated that for biofilms of the same organisms, 100 to 1,000 times the concentration of a certain antibiotic were often required for the antibiotic to be effective, while other antibiotics were found to be effective at the MICs. The CBD offers a new technology for the rational selection of antibiotics effective against microbial biofilms and for the screening of new effective antibiotic compounds.
Design and Evaluation of a Human Immunodeficiency Virus Type 1 RNA Assay Using Nucleic Acid Sequence-Based Amplification Technology Able To Quantify Both Group M and O Viruses by Using the Long Terminal Repeat as Target
Authors: de Baar Michel P. , van der Schoot Audrey M. , Goudsmit Jaap , Jacobs Femke , Ehren Ron , van der Horn Karin H. M. , Oudshoorn Peter , de Wolf Frank , de Ronde Anthony 
Published: December 2019

ABSTRACT

Currently available human immunodeficiency virus type 1 (HIV-1) RNA quantification assays can detect most viruses of the group M subtypes, but a substantial number are missed or not quantified reliably. Viruses of HIV-1 group O cannot be detected by any commercially available assay. We developed and evaluated a quantitative assay based on nucleic acid sequence-based amplification (NASBA) technology, with primers and probes located in the conserved long terminal repeat (LTR) region of the HIV-1 genome. In 68 of 72 serum samples from individuals infected with HIV-1 subtypes A to H of group M, viruses could be detected and quantified. In serum samples from two patients infected with HIV-1 group O viruses, these viruses as well could be detected and quantified. In contrast, the currently used
gag
-based assay underestimated the presence of subtype A viruses and could not detect subtype G and group O viruses. The discrepancy between the results of the two assays may be explained by the number of mismatches found within and among the probe and primer regions of the subtype isolates. These data indicate that LTR-based assays, including the NASBA format chosen here, are better suited to monitoring HIV-1 therapy than are
gag
-based assays in an era in which multiple HIV-1 subtypes and groups are spreading worldwide.
Susceptibility Testing of Anaerobic Bacteria: Evaluation of the Redesigned (Version 96) bioMérieux ATB ANA Device
Authors: Dubreuil L. , Houcke I. , Singer E. 
Published: December 2019

ABSTRACT

We compared the susceptibility results for 200 clinical anaerobes with nine antibiotics obtained by using a new ATB ANA (bioMérieux) device against those obtained by the National Committee for Clinical Laboratory Standards (NCCLS) standard agar dilution method. For better evaluation of the device, we added some resistant
Bacteroides fragilis
group strains from our own collection: 3, 6, and 12 strains that were resistant to imipenem, ticarcillin plus clavulanic acid, and co-amoxiclav, respectively, and 2 other strains with decreased susceptibility to metronidazole. For some strains that did not grow on ATB S medium, tests were performed by using West-Wilkins medium supplemented with 1.5% agar. The new ATB ANA device made clinical categorization of the investigated strains possible, according to French (Committee of the Antibiogram of the French Society of Microbiology) or U.S. (NCCLS) breakpoints, with the following respective results: category agreement, 94.3 and 94.9%; minor errors, 4.8 and 3.8%; major errors, 0.4 and 0.8%; and very major errors 4.6 and 4.2%. The ATB ANA device was able to detect low-level metronidazole-resistant
B. fragilis
strains according to the French breakpoints but not the NCCLS ones. For
B. fragilis
and β-lactamase-positive
Prevotella
strains, the clustering effect of amoxicillin MICs around the French breakpoints led to more frequent minor errors. ATB ANA is a very convenient method to determine the antibiotic susceptibilities of anaerobes. Results obtained by ATB ANA correlated well with those obtained by the reference method.
Nasopharyngeal Carriage of Penicillin-Resistant
Streptococcus pneumoniae
among Children with Acute Respiratory Tract Infections in Thailand: a Molecular Epidemiological Survey
Authors: Dejsirilert Surang , Overweg Karin , Sluijter Marcel , Saengsuk Leelawadee , Gratten Mike , Ezaki Takayuki , Hermans Peter W. M. 
Published: December 2019

ABSTRACT

The prevalence of penicillin-resistant
Streptococcus pneumoniae
in Thailand has dramatically increased over the last decade. During a national survey, which was conducted from 1992 to 1994, 37.2% of the pneumococci isolated from the nasopharynges of children with acute respiratory tract infections were penicillin resistant (MIC, ≥0.1 μg/ml). In order to investigate the prevalence and clonal relatedness of nasopharyngeal carriage of penicillin-resistant
S. pneumoniae
in Thailand, a molecular epidemiological survey was undertaken. To this end, 53 penicillin-resistant pneumococcal isolates from children who suffered from acute respiratory tract infections and who originated from five distinct regions of the country were characterized in detail. DNA fingerprint analysis demonstrated 13 clusters, i.e., genotypes shared by two or more strains, and 14 unique genotypes. The cluster size varied from 2 (nine clusters) to 11 strains (one cluster). Six of the 13 restriction fragment end labeling clusters consisted of two or more distinct serotypes, indicating frequent horizontal transfer of capsular genes. Geographical distribution of the genotypes among the five regions of Thailand demonstrated that only four genetic clusters were restricted to single areas of the country, whereas the other nine clusters represented isolates collected in two or more districts. These observations demonstrate that the majority of the genetic clusters are spread throughout the country. The most predominant genetic cluster, representing 21% of the isolates, was identical to the Spanish pandemic clone 23F. In addition, the second largest cluster matched the Spanish-French international clone 9V. These data indicate that the genetic clones 23F and 9V, which are widely spread throughout the world, are the most predominant multidrug-resistant pneumococcal clones in Thailand. Therefore, we conclude that these pandemic clones are primarily responsible for the increase in the prevalence of pneumococcal penicillin resistance in Thailand.
Phylogenetic Analysis of Ara
+
and Ara
−
Burkholderia pseudomallei
Isolates and Development of a Multiplex PCR Procedure for Rapid Discrimination between the Two Biotypes
Authors: Dharakul Tararaj , Tassaneetrithep Boonratn , Trakulsomboon Suwanna , Songsivilai Sirirurg 
Published: December 2019

ABSTRACT

A
Burkholderia pseudomallei
-like organism has recently been identified among some soil isolates of
B. pseudomallei
in an area with endemic melioidosis. This organism is almost identical to
B. pseudomallei
in terms of morphological and biochemical profiles, except that it differs in ability to assimilate
l
-arabinose. These Ara
+
isolates are also less virulent than the Ara
−
isolates in animal models. In addition, clinical isolates of
B. pseudomallei
available to date are almost exclusively Ara
−
. These features suggested that these two organisms may belong to distinctive species. In this study, the 16S rRNA-encoding genes from five clinical (four Ara
−
and one Ara
+
) and nine soil isolates (five Ara
−
and four Ara
+
) of
B. pseudomallei
were sequenced. The nucleotide sequences and phylogenetic analysis indicated that the 16S rRNA-encoding gene of the Ara
+
biotype was similar to but distinctively different from that of the Ara
−
soil isolates, which were identical to the classical clinical isolates of
B. pseudomallei
. The nucleotide sequence differences in the 16S rRNA-encoding gene appeared to be specific for the Ara
+
or Ara
−
biotypes. The differences were, however, not sufficient for classification into a new species within the genus
Burkholderia
. A simple and rapid multiplex PCR procedure was developed to discriminate between Ara
−
and Ara
+
B. pseudomallei
isolates. This new method could also be incorporated into our previously reported nested PCR system for detecting
B. pseudomallei
in clinical specimens.
Occurrence ofLeishmania infantumParasitemia in Asymptomatic Blood Donors Living in an Area of Endemicity in Southern France
Authors: le Fichoux Yves , Quaranta Jean-François , Aufeuvre Jean-Pierre , Lelievre Alain , Marty Pierre , Suffia Isabelle , Rousseau Deborah , Kubar Joanna 
Published: December 2019

ABSTRACTVisceral leishmaniosis (VL) due toLeishmania infantum(L. chagasi) is a lethal disease if untreated, but asymptomaticL. infantuminfections have been reported previously. A better understanding of parasite transmission, dissemination, and survival in the human host is needed. The purpose of this study was to assess whetherL. infantumcirculated in peripheral blood of subjects with no history of VL. Sera from 565 blood donors were screened by Western blotting to detectLeishmania-specific antibodies and identify individuals with probable past exposure toLeishmania. Seropositivity was found in 76 donors whose buffy coats were examined by PCR and direct culture. The parasite minicircle kinetoplast DNA was amplified from blood samples of nine donors. Promastigotes were detected by culture in blood samples from nine donors. Only two donors were PCR and culture positive. These results indicate thatL. infantumcirculates intermittently and at low density in the blood of healthy seropositive individuals, who thus appear to be asymptomatic carriers. Implications for the safety of blood transfusion are discussed.
One-Step Reverse Transcriptase PCR Method for Detection of
Borrelia burgdorferi
mRNA in Mouse Lyme Arthritis Tissue Samples
Authors: Limbach F. X. , Jaulhac B. , Piémont Y. , Kuntz J. L. , Monteil H. , Sibilia J. 
Published: December 2019

ABSTRACT

A one-step reverse transcriptase PCR (RT-PCR) method for detection of
Borrelia burgdorferi
mRNA in infected C3H mice is described. This simple procedure, less prone to nucleic acid cross-contamination than the standard method, was found to be 10-fold more sensitive than a classical two-step RT-PCR assay. By using one-step RT-PCR, flagellin mRNAs were detected in synovial and heart tissues from all seven infected mice tested.
Increased Frequency of Detection of
Ureaplasma urealyticum
and
Mycoplasma genitalium
in AIDS Patients without Urethral Symptoms
Authors: Martinelli F. , Garrafa E. , Turano A. , Caruso A. 
Published: December 2019

ABSTRACT

The roles of
Mycoplasma genitalium
and
Ureaplasma urealyticum
in nongonococcal urethritis are not yet well established. The aim of this study was to determine the presence of these microorganisms in the urethral tracts of 187 human immunodeficiency virus type 1 (HIV-1)-infected male patients with no clinical signs of urethritis. The results indicate that the prevalence of
M. genitalium
and
U. urealyticum
was higher in AIDS patients than in asymptomatic, HIV-1-infected patients and in healthy individuals. The high rate of mycoplasmas and ureaplasmas detected in AIDS patients, in the absence of urethritis, argues against major roles in causing disease at the urethral mucosal level for these microorganisms.
Bacteremia Caused by a Novel Isolate Resembling
Leptotrichia
Species in a Neutropenic Patient
Authors: Patel Jean Baldus , Clarridge Jill , Schuster Mindy S. , Waddington Michael , Osborne Janet , Nachamkin Irving 
Published: December 2019

ABSTRACT

We report a case of
Leptotrichia
species bacteremia in a patient undergoing treatment for acute myelogenous leukemia. Like previously reported
Leptotrichia
species, this is a gram-variable, pleomorphic rod that is catalase negative and utilizes glucose and sucrose. However, it is more fastidious than previously reported isolates of
Leptotrichia
and may represent a novel species.
Improved Methods for Immunoassay of Mycothiol
Authors: Unson Mia D. , Newton Gerald L. , Arnold Karen F. , Davis Charles E. , Fahey Robert C. 
Published: December 2019

ABSTRACT

Improved enzyme-linked immunosorbent assay (ELISA) methods have been developed for the determination of femtomole amounts of mycothiol (MSH), the main low-molecular-weight thiol in mycobacteria. The immunoassays utilize an affinity-purified rabbit polyclonal antibody that is highly specific for the pseudodisaccharide moiety of MSH. MSH was first biotinylated by the thiol-specific reagent 3-(
N
-maleimidopropionyl)biocytin. The MSH-biotin adduct was then captured with immobilized avidin and detected with anti-MSH antibody (biotin-capture ELISA) or was captured with immobilized anti-MSH antibody and detected with alkaline phosphatase-labelled avidin (MSH-capture ELISA). The MSH-capture ELISA was the most sensitive method, measuring as little as 0.3 fmol of MSH. Methods for biotinylating MSH directly from
Mycobacterium
spp. are described. The MSH-capture ELISA was tested for the detection of
M. avium
seeded in human urine or cerebrospinal fluid samples and for screening mutant
M. smegmatis
strains to detect MSH production.
Differentiation of
Burkholderia
Species by PCR-Restriction Fragment Length Polymorphism Analysis of the 16S rRNA Gene and Application to Cystic Fibrosis Isolates
Authors: Segonds Christine , Heulin Thierry , Marty Nicole , Chabanon Gerard 
Published: December 2019

ABSTRACT

Burkholderia cepacia
, which is an important pathogen in cystic fibrosis (CF) owing to the potential severity of the infections and the high transmissibility of some clones, has been recently shown to be a complex of five genomic groups, i.e., genomovars I, II (
B. multivorans
), III, and IV and
B. vietnamiensis. B. gladioli
is also involved, though rarely, in CF. Since standard laboratory procedures fail to provide an accurate identification of these organisms, we assessed the ability of restriction fragment length polymorphism (RFLP) analysis of amplified 16S ribosomal DNA (rDNA), with the combination of the patterns obtained with six endonucleases, to differentiate
Burkholderia
species. This method was applied to 16 type and reference strains of the genus
Burkholderia
and to 51 presumed
B. cepacia
clinical isolates, each representative of one clone previously determined by PCR ribotyping. The 12
Burkholderia
type strains tested were differentiated, including
B. cepacia
,
B. multivorans
,
B. vietnamiensis
, and
B. gladioli
, but neither the genomovar I and III reference strains nor the genomovar IV reference strain and
B. pyrrocinia
T
were distinguishable. CF clinical isolates were mainly distributed in RFLP group 2 (which includes
B. multivorans
T
) and RFLP group 1 (which includes
B. cepacia
genomovar I and III reference strains, as well as nosocomial clinical isolates). Two of the five highly transmissible clones in French CF centers belonged to RFLP group 2, and three belonged to RFLP group 1. The remaining isolates either clustered with other
Burkholderia
species (
B. cepacia
genomovar IV or
B. pyrrocinia
,
B. vietnamiensis
, and
B. gladioli
) or harbored unique combinations of patterns. Thus, if further validated by hybridization studies, PCR-RFLP of 16S rDNA could be an interesting identification tool and contribute to a better evaluation of the respective clinical risks associated with each
Burkholderia
species or genomovar in patients with CF.
Molecular Subtyping of
Clostridium perfringens
by Pulsed-Field Gel Electrophoresis To Facilitate Food-Borne-Disease Outbreak Investigations
Authors: Maslanka Susan E. , Kerr Jared G. , Williams Glen , Barbaree James M. , Carson Loretta A. , Miller J. Michael , Swaminathan Bala 
Published: December 2019

ABSTRACT

Clostridium perfringens
is a common cause of food-borne illness. The illness is characterized by profuse diarrhea and acute abdominal pain. Since the illness is usually self-limiting, many cases are undiagnosed and/or not reported. Investigations are often pursued after an outbreak involving large numbers of people in institutions, at restaurants, or at catered meals. Serotyping has been used in the past to assist epidemiologic investigations of
C. perfringens
outbreaks. However, serotyping reagents are not widely available, and many isolates are often untypeable with existing reagents. We developed a pulsed-field gel electrophoresis (PFGE) method for molecular subtyping of
C. perfringens
isolates to aid in epidemiologic investigations of food-borne outbreaks. Six restriction endonucleases (
Sma
I,
Apa
I,
Fsp
I,
Mlu
I,
Ksp
I, and
Xba
I) were evaluated with a select panel of
C. perfringens
strains.
Sma
I was chosen for further studies because it produced 11 to 13 well-distributed bands of 40 to ∼1,100 kb which provided good discrimination between isolates. Seventeen distinct patterns were obtained with 62 isolates from seven outbreak investigations or control strains. In general, multiple isolates from a single individual had indistinguishable PFGE patterns. Epidemiologically unrelated isolates (outbreak or control strains) had unique patterns; isolates from different individuals within an outbreak had similar, if not identical, patterns. PFGE identifies clonal relationships of isolates which will assist epidemiologic investigations of food-borne-disease outbreaks caused by
C. perfringens.