bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salmonella entericaSerotype Dublin Infection: an Emerging Infectious Disease for the Northeastern United States
Authors: McDonough Patrick L. , Fogelman David , Shin Sang J. , Brunner Michael A. , Lein Donald H. 
Published: December 2019

ABSTRACTSalmonella entericasubspeciesentericaserotype Dublin (S. entericaDublin) emerged for the first time in New York, Pennsylvania, and Ohio in 1988. Since that time this host-adapted serotype has spread throughout the veal- and dairy beef-raising operations in the region; very few dairy farms have experienced clinicalS. entericaDublin infections. This study details the epidemiology of the outbreaks in cattle. During the period 1988 through 1995, nine New York and four Pennsylvania counties have been affected; 13 different locations were involved in New York, and 10 were involved in Pennsylvania. The morbidity and mortality and seasonal distribution of outbreaks, which totaled 35, is described. The antimicrobial susceptibility pattern of isolates revealed that many of the strains were resistant to a number of commonly used drugs. Clinical case details and pathology information are provided, with a caution to clinicians and microbiologists presented with suspect animals, i.e., most cases occurred in older calves, which is atypical for salmonellosis for this region (calves were 8 or more weeks old) and presented as pneumonia and septicemia rather than the primarily diarrheal syndrome that is more typically recognized for the region. The epidemiology of cases is analyzed through cluster analysis of bacterial isolates and their fatty acid methyl ester profiles; at least six clones appeared in the region during the study period. Results of the epidemiology analysis are used to support a hypothesis regarding the source ofS. entericaDublin for the region and its manner of dissemination.
Helicobacter pylori
Infection in Indigenous Families of Central America: Serostatus and Oral and Fingernail Carriage
Authors: Dowsett S. A. , Archila L. , Segreto V. A. , Gonzalez C. R. , Silva A. , Vastola K. A. , Bartizek R. D. , Kowolik M. J. 
Published: December 2019

ABSTRACT

Helicobacter pylori
infection remains one of the most common in humans, but the route of transmission of the bacterium is still uncertain. This study was designed to elucidate possible sources of infection in an isolated, rural population in Guatemala. A total of 242 subjects in family units participated in the study. A medical history, including a history of dyspepsia, was taken by a physician and immunoglobulin G antibodies to
H. pylori
were detected with the QuickVue (Quidel, San Diego, Calif.) onsite serology test. Overall, 58% of subjects were seropositive, with a positive relationship between mother and child (
P
= 0.02) and a positive correlation between the serostatuses of siblings (intraclass correlation coefficient = 0.63). There was no association between serostatus and gastric symptoms. Oral
H. pylori
was detected from periodontal pockets of various depths and the dorsum of the tongue by nested PCR. Eighty-seven percent of subjects had at least one oral site positive for
H. pylori
, with the majority of subjects having multiple positive sites. There was no association between periodontal pocket depth and the detection of
H. pylori
. Nested PCR was also used to detect
H. pylori
from beneath the nail of the index finger of each subject’s dominant hand. Overall, 58% of subjects had a positive fingernail result, with a significant positive relationship between fingernail and tongue positivity (
P
= 0.002). In conclusion, the results of this study suggest that oral carriage of
H. pylori
may play a role in the transmission of infection and that the hand may be instrumental in transmission.
Development and Clinical Evaluation of a Highly Sensitive PCR-Reverse Hybridization Line Probe Assay for Detection and Identification of Anogenital Human Papillomavirus
Authors: Kleter Bernhard , van Doorn Leen-Jan , Schrauwen Lianne , Molijn Anco , Sastrowijoto Suprapto , ter Schegget Jan , Lindeman Jan , ter Harmsel Bram , Burger Matthé , Quint Wim 
Published: December 2019

ABSTRACT

Human papillomavirus (HPV) can be detected by amplification of viral DNA. A novel PCR primer set generating a short PCR fragment (SPF PCR) was used for amplification of a fragment of only 65 bp from the L1 region and permitted ultrasensitive detection of a broad spectrum of HPV genotypes. The intra- and intertypic sequence variations of the 22-bp interprimer region of this amplimer were studied. Among 238 HPV sequences from GenBank and clinical specimens, HPV genotypes were correctly identified based on the 22-bp sequence in 232 cases (97.2%). Genotype-specific probes for HPV genotypes 6, 11, 16, 18, 31, 33 to 35, 39, 40, 42 to 45, 51 to 54, 56, 58, 59, 66, 68, 70, and 74 were selected, and a reverse hybridization line probe assay (LiPA) (the INNO-LiPA HPV prototype research assay) was developed. This LiPA permits the use of amplimers generated by the SPF as well as the MY 09/11 primers. The assay was evaluated with a total of 1,354 clinical specimens, comprising cervical scrapes (classifications ranging from normal cytology to severe dyskaryosis) and formalin-fixed, paraffin-embedded cervical carcinoma samples. LiPA results were highly concordant with sequence analysis of the SPF amplimer, genotype-specific PCR, and sequence analysis of amplimers generated by MY 09/11 primers. The sensitivity of the SPF primers was higher than that of the GP5
+
/6
+
primers over a broad range of HPV types, especially when multiple HPV genotypes were present. In conclusion, the SPF LiPA method allows extremely sensitive detection of HPV DNA as well as reliable identification of HPV genotypes in both cervical smears and paraffin-embedded materials.
Detection of Dengue Virus RNA in Patients after Primary or Secondary Dengue Infection by Using the TaqMan Automated Amplification System
Authors: Laue Thomas , Emmerich Petra , Schmitz Herbert 
Published: December 2019

ABSTRACT

In consecutive serum samples from 25 tourists with acute dengue fever, virus-specific RNA was detected by using fully automated TaqMan reverse transcriptase PCR. For this amplification technique new primers and special fluorochrome-labeled probes had to be synthesized. During amplification the increasing amount of viral DNA could simultaneously be measured in the tightly sealed tubes. Dengue virus RNA was found in almost all patients (17 of 18), if the samples had been taken soon after the onset of symptoms and before anti-dengue virus antibody had been produced. RNA was detectable in only one of five persons who had anti-dengue virus immunoglobulin M (IgM) antibodies but not yet IgG antibodies. In 30 late samples with both IgG and IgM antibodies viral RNA was no longer demonstrable. In two early samples from two frequent travelers obtained 1 and 2 days after the onset of symptoms significant IgG antibody titers were present but there were no anti-dengue virus IgM antibodies. In these samples a viral load of >5 × 10
6
dengue virus RNA copies (dengue types 1 and 2) was detectable. These findings of a high viral load in the presence of anti-dengue virus IgG antibody are suggestive of a secondary dengue virus infection. In the 20 tourists (17 plus 1 plus 2) in whom viral RNA was found, the dengue virus serotype could be related to the area where the infection had taken place. Most of our patients came from southeast Asia and most frequently had dengue virus type 1 infections (8 of 20).
Development of Calibrated Viral Load Standards for Group M Subtypes of Human Immunodeficiency Virus Type 1 and Performance of an Improved AMPLICOR HIV-1 MONITOR Test with Isolates of Diverse Subtypes
Authors: Michael Nelson L. , Herman Steven A. , Kwok Shirley , Dreyer Kimberly , Wang June , Christopherson Cindy , Spadoro Joanne P. , Young Karen K. Y. , Polonis Victoria , McCutchan Francine E. , Carr Jean , Mascola John R. , Jagodzinski Linda L. , Robb Merlin L. 
Published: December 2019

ABSTRACT
Accurate determination of plasma human immunodeficiency virus type 1 (HIV-1) RNA levels is critical for the effective management of HIV-1 disease. The AMPLICOR HIV-1 MONITOR Test, a reverse transcription-PCR-based test for quantification of HIV-1 RNA in plasma, was developed when little sequence information on HIV-1 isolates from outside North America was available. It has since become apparent that many non-subtype B isolates, particularly subtypes A and E, are detected inefficiently by the test. We describe here the AMPLICOR HIV-1 MONITOR Test, version 1.5, an upgraded test developed to minimize subtype-related variation. We also developed a panel of HIV-1 standards containing 30 HIV-1 isolates of subtypes A through G. The virus particle concentration of each cultured viral stock was standardized by electron microscopic virus particle counting. We used this panel to determine the performance of the original AMPLICOR HIV-1 MONITOR Test and version 1.5 of the test with HIV-1 subtypes A through G. The original test underestimated the concentration of HIV-1 subtype A, E, F, and G RNA by 10-fold or more, whereas version of the 1.5 test yielded equivalent quantification of HIV-1 RNA regardless of the subtype. In light of the increasing intermixing of HIV-1 subtypes worldwide, standardization of PCR-based tests against well-characterized viral isolates representing the full range of HIV-1 diversity will be essential for the continued utility of these important clinical management tools.
Identification of Two Novel
Mycobacterium avium
Allelic Variants in Pig and Human Isolates from Brazil by PCR-Restriction Enzyme Analysis
Authors: Leão Sylvia Cardoso , Briones Marcelo R. S. , Sircili Marcelo Palma , Balian Simone Carvalho , Mores Nelson , Ferreira-Neto José Soares 
Published: December 2019

ABSTRACT

Mycobacterium avium
complex (MAC) is composed of environmental mycobacteria found widely in soil, water, and aerosols that can cause disease in animals and humans, especially disseminated infections in AIDS patients. MAC consists of two closely related species,
M. avium
and
M. intracellulare
, and may also include other, less-defined groups. The precise differentiation of MAC species is a fundamental step in epidemiological studies and for the evaluation of possible reservoirs for MAC infection in humans and animals. In this study, which included 111 pig and 26 clinical MAC isolates, two novel allelic
M. avium
PCR-restriction enzyme analysis (PRA) variants were identified, differing from the
M. avium
PRA prototype in the
Hae
III digestion pattern. Mutations in
Hae
III sites were confirmed by DNA sequencing. Identification of these isolates as
M. avium
was confirmed by PCR with DT1-DT6 and IS
1245
primers, nucleic acid hybridization with the AccuProbe system, 16S ribosomal DNA sequencing, and biochemical tests. The characterization of
M. avium
PRA variants can be useful in the elucidation of factors involved in mycobacterial virulence and routes of infection and also has diagnostic significance, since they can be misidentified as
M. simiae
II and
M. kansasii
I if the PRA method is used in the clinical laboratory for identification of mycobacteria.
Identification of Human Rotavirus Strains with the P[14] Genotype by PCR
Authors: Arista Serenella , Vizzi Esmeralda , Alaimo Cristina , Palermo Daniela , Cascio Antonio 
Published: December 2019

ABSTRACT

A seminested PCR typing assay has been extended to identify rotavirus strains with the P[14] genotype. The specificity of the method was confirmed by Southern hybridization and by restriction analysis with the enzyme
Alu
I. One out of four human rotavirus (HRV) strains with unusual subgroup-electropherotype linkage but none out of 50 HRV strains with usual linkage was typed as P[14].
Monitoring of Transmission of Tuberculosis between Wild Boars and Cattle: Genotypical Analysis of Strains by Molecular Epidemiology Techniques
Authors: Serraino Andrea , Marchetti Giulia , Sanguinetti Valeria , Rossi Maria Cristina , Zanoni Renato Giulio , Catozzi Lidia , Bandera Alessandra , Dini Walter , Mignone Walter , Franzetti Fabio , Gori Andrea 
Published: December 2019

ABSTRACT

An epidemiological survey for the monitoring of bovine tuberculosis transmission was carried out in western Liguria, a region in northern Italy. Fifteen
Mycobacterium bovis
strains were isolated from 63 wild boar samples (62 from mandibular lymph nodes and 1 from a liver specimen). Sixteen mediastinal lymph nodes of 16 head of cattle were collected, and 15
Mycobacterium bovis
strains were subsequently cultured. All
M. bovis
strains isolated from cattle and wild boars were genotyped by spoligotyping and by restriction fragment length polymorphism (RFLP) analysis with the IS
6110
and IS
1081
probes. All
M. bovis
strains showed the typical spoligotype characterized by the absence of the 39 to 43 spacers in comparison with the number in
M. tuberculosis
. A total of nine different clusters were identified by spoligotyping. The largest cluster included 9 strains isolated from wild boars and 11 strains isolated from cattle, thus confirming the possibility of transmission between the two animal species. Fingerprinting by RFLP analysis with the IS
6110
probe showed an identical single-band pattern for 29 of 30 strains analyzed, and only 1 strain presented a five-band pattern. The use of IS
1081
as a second probe was useful for differentiation of
M. bovis
from
M. bovis
BCG but not for differentiation among
M. bovis
strains, which presented the same undifferentiated genomic profile. In relation to the epidemiological investigation, we hypothesized that the feeding in pastures contaminated by cattle discharges could represent the most probable route of transmission of
M. bovis
between the two animal species. In conclusion, our results confirmed the higher discriminatory power of spoligotyping in relation to that of RFLP analysis for the differentiation of
M. bovis
genomic profiles. Our data showed the presence of a common
M. bovis
genotype in both cattle and wild boars, confirming the possible interspecies transmission of
M. bovis.
Molecular Characterization of the Genera
Proteus
,
Morganella
, and
Providencia
by Ribotyping
Authors: Pignato S. , Giammanco G. M. , Grimont F. , Grimont P. A. D. , Giammanco G. 
Published: December 2019

ABSTRACT

The so-called
Proteus-Providencia
group is constituted at present by three genera and 10 species. Several of the recognized species are common opportunistic pathogens for humans and animals. Different methods based on the study of phenotypic characters have been used in the past with variable levels of efficiency for typing some species for epidemiological purposes. We have determined the rRNA gene restriction patterns (ribotypes) for the type strains of the 10 different species of the genera
Proteus
,
Morganella
, and
Providencia
. Visual inspection of
Eco
RV- and
Hin
cII-digested DNA from the type strains showed remarkably different patterns for both enzymes, but
Eco
RV provided better differentiation. Both endonucleases were retained to study a large number of wild and collection strains belonging to the different species. Clinical isolates of
Proteus mirabilis
,
Proteus penneri
,
Morganella morganii
, and
Providencia heimbachae
showed patterns identical or very similar to those of the respective type strains, so that groups of related patterns (ribogroups) were found to correspond to the diverse species. On the contrary, distinct ribogroups were detected within
Providencia alcalifaciens
(two ribogroups with both enzymes),
Providencia rettgeri
(four ribogroups with
Eco
RV and five with
Hin
cII),
Providencia stuartii
(two ribogroups with
Eco
RV),
Providencia rustigianii
(two ribogroups with
Hin
cII), and
Proteus vulgaris
(two ribogroups with both enzymes). The pattern shown by the ancient
P. vulgaris
type strain NCTC 4175 differed considerably from both
P. vulgaris
ribogroups as well as from the newly proposed type strain ATCC 29905 and from any other strain in this study, thus confirming its atypical nature. Minor differences were frequently observed among patterns of strains belonging to the same ribogroup. These differences were assumed to define ribotypes within each ribogroup. No correlation was observed between ribogroups or ribotypes and biogroups of
P. vulgaris
,
P. alcalifaciens
,
P. stuartii
, and
P. rettgeri
. Since, not only different species showed different rRNA gene restriction patterns, but also different ribogroups and ribotypes have been found in the majority of the species, ribotyping would be a sensitive method for molecular characterization of clinical isolates belonging to the genera
Proteus
,
Morganella
, and
Providencia
.
Immunomagnetic Isolation of
Streptococcus suis
Serotypes 2 and 1/2 from Swine Tonsils
Authors: Gottschalk Marcelo , Lacouture Sonia , Odierno Liliana 
Published: December 2019

ABSTRACT

Isolation of specific serotypes of
Streptococcus suis
from the tonsils, nasal cavities, and genital tract is difficult, since low-pathogenic serotypes and untypeable strains also inhabit these sites. An immunomagnetic separation (IMS) technique for the selective isolation of
S. suis
serotypes 2 and 1/2 was standardized. Superparamagnetic polystyrene beads (immunomagnetic beads or IMB) were coated with either a purified monoclonal antibody (MAb) directed to a capsular sialic acid-containing epitope or purified rabbit immunoglobulin G (polyclonal antibody [PAb]), both specific for
S. suis
serotypes 2 and 1/2. The amount of antibodies required for optimum coating of the beads, the number of IMB required for optimum bacterial recovery, and the nonspecific carryover were considerably higher with the MAb-IMS technique than with the PAb-IMS technique. The sensitivity of the IMS technique was 10
1
CFU/0.1 g of tonsil. The presence of serotype 1/2 bacteria did not considerably affect the recovery rate of a serotype 2 strain and vice versa. To validate the technique, PAb-coated beads were used to study 192 tonsils from animals from
S. suis
serotype 2- or 1/2-infected herds. Results showed that significantly more positive tonsils were detected by the IMS technique than by the standard procedure. This method represents an innovative and highly sensitive approach for the isolation of
S. suis
serotypes 2 and 1/2 from carrier animals.
Quantitation of Hepatitis B Virus Genomic DNA by Real-Time Detection PCR
Authors: Abe Aki , Inoue Kazuaki , Tanaka Takeshi , Kato Junko , Kajiyama Naoki , Kawaguchi Ryuji , Tanaka Satoshi , Yoshiba Makoto , Kohara Michinori 
Published: December 2019

ABSTRACT

Quantitation of hepatitis B virus (HBV) DNA in serum is a useful method for the monitoring of HBV replication. We attempted to develop a quantitative assay system for HBV DNA that is more sensitive, accurate, and reproducible than existing systems. We detected HBV DNA by real-time detection PCR (RTD-PCR) based on Taq Man chemistry. The efficacy of this assay was evaluated by quantitatively measuring sequential levels of synthetic DNA and DNA in clinical serum samples. The detection limit of this system was as few as 10 DNA copies/reaction. A linear standard curve was obtained between 10
1
and 10
8
DNA copies/reaction. The coefficient of variation for both intra- and interexperimental variability indicated remarkable reproducibility. This system detected HBV DNA in 100% of chronic hepatitis B patients tested and never detected HBV DNA in healthy volunteers who were negative for HBV markers. These observations suggest that RTD-PCR is an excellent candidate for a standard HBV quantification method.
International Multicenter Evaluation of the Clinical Utility of a Dipstick Assay for Detection of
Leptospira
-Specific Immunoglobulin M Antibodies in Human Serum Specimens
Authors: Smits Henk L. , Ananyina Yulia V. , Chereshsky Annette , Dancel Louella , Lai-A-Fat Rudy F. M. , Chee Howard D. , Levett Paul N. , Masuzawa Toshiyuki , Yanagihara Yasutake , Muthusethupathi M. A. , Sanders Eduard J. , Sasaki David M. , Domen Harry , Yersin Claude , Aye Tin , Bragg Sandra L. , Gussenhoven George C. , Goris Marga G. A. , Terpstra Wiepko J. , Hartskeerl Rudy A. 
Published: December 2019

ABSTRACT

We performed a multicenter evaluation of a robust and easily performed dipstick assay for the serodiagnosis of human leptospirosis. The assay is aimed at the detection of
Leptospira
-specific immunoglobulin M (IgM) antibodies. The study involved 2,665 serum samples collected from 2,057 patients with suspected leptospirosis in 12 countries on five continents with different levels of endemicity and different surveillance systems. The patients were grouped as laboratory-confirmed leptospirosis case patients and noncase patients based on the results of culturing and the microscopic agglutination test. Paired samples from 27.7% of the subjects were tested. Of the 485 case patients, 87.4% had a positive dipstick result for one or more samples. Of the 1,513 noncase patients, only 7.2% had a positive result. Whereas most (88.4%) of the positive samples from the case patients showed moderate to strong (2+ to 4+) staining in the dipstick assay, most (68.1%) of the positive samples from the noncase patients showed weak (1+) staining. The sensitivity of the dipstick assay increased from 60.1% for acute-phase serum samples to 87.4% for convalescent-phase samples. The specificities for these two groups of samples were 94.1 and 92.7%, respectively. The dipstick assay detected a broad variety of serogroups. The results of the dipstick assay were concordant (observed agreement, 93.2%; kappa value, 0.76) with the results of an enzyme-linked immunosorbent assay for the detection of specific IgM antibodies, a test which is often used in the laboratory diagnosis of current or recent leptospirosis. This study demonstrated that this easily performed dipstick assay is a valuable and useful test for the quick screening for leptospirosis; has a wide applicability in different countries with different degrees of endemicity; can be used at all levels of the health care system, including the field; and will be useful for detecting and monitoring outbreaks of leptospirosis.
Polymorphism of the Human Immunodeficiency Virus Type 1 (HIV-1) Protease Gene and Response of HIV-1-Infected Patients to a Protease Inhibitor
Authors: Bossi Philippe , Mouroux Mireille , Yvon Anne , Bricaire François , Agut Henri , Huraux Jean-Marie , Katlama Christine , Calvez Vincent 
Published: December 2019

ABSTRACT

In order to analyze the impact of protease gene polymorphism on response to regimens containing a protease inhibitor, the entire protease coding domain from 58 human immunodeficiency virus type 1 (HIV-1)-infected patients who were protease inhibitor naive was sequenced before therapy was started. Plasma HIV-1 RNA levels were measured at baseline and at month 3 and month 6 after treatment. All patients were treated with a combination of two reverse transcriptase inhibitors and a protease inhibitor (saquinavir EOF [
n
= 28], ritonavir [
n
= 16], or indinavir [
n
= 14]). Before treatment, 30 different positions whose codons differed from the subtype B consensus sequence were observed. Major mutations associated with protease inhibitor resistance were not observed. No statistical correlation between the number of amino acid differences and the treatment efficacy at month 3 (−2.4 log) or month 6 (−2.7 log) was observed. At baseline, genotypic analysis of the HIV-1 protease gene of patients who have never received a protease inhibitor does not allow prediction of the efficacy of regimens containing a protease inhibitor.