bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of “CandidatusHelicobacter suis” in Gastric Samples of Pigs by PCR: Comparison with Other Invasive Diagnostic Techniques
Authors: De Groote D. , Ducatelle R. , van Doorn L. J. , Tilmant K. , Verschuuren A. , Haesebrouck F. 
Published: December 2019

ABSTRACTRecently, a new 16S ribosomal DNA-based PCR assay was developed for the specific detection of “CandidatusHelicobacter suis” (former “Gastrospirillum suis”) in porcine gastric samples. In the present study, this PCR assay was compared to three other invasive diagnostic methods (rapid urease test, immunohistochemistry, histologic analysis by Giemsa staining). Antral stomach samples from 200 slaughterhouse pigs from Belgium and The Netherlands were examined. Bacterial presence was determined in 77% (154 of 200) of the samples by PCR in combination with Southern blot hybridization, 56% (111 of 200) of the samples by immunohistochemistry, 61% (122 of 200) of the samples by urease testing (20 h postinoculation [p.i.]), 36% (71 of 200) of the samples by urease testing (3 h p.i.), and 33% (65 of 200) of the samples by Giemsa staining. The intrinsic specificity of the PCR assay was assessed by Southern blot analysis with an “CandidatusH. suis”-specific probe and sequencing of PCR products. Interassay sensitivity and specificity values were assessed for each test by pairwise comparisons between tests. Agreement between tests was evaluated by calculating Cohen's kappa coefficient. From that analysis, the PCR assay was considered the most reliable benchmark. Microscopic detection of immunohistochemically labeled or Giemsa-stained “CandidatusH. suis” cells in stomach sections proved to be highly specific (100%) but relatively insensitive (72 and 42%, respectively) compared to the PCR assay. A longer incubation time of the urease test improved its sensitivity considerably (74 versus 55%) but was accompanied by a loss of specificity (72 versus 93%). In conclusion, we found the “CandidatusH. suis”-specific PCR assay to be a sensitive and reliable diagnostic method for the detection of “CandidatusH. suis” in the stomachs of pigs and could prove to be a valuable tool for further epidemiological studies both for “CandidatusH. suis”- and for “Helicobacter heilmannii” type 1-related research.
Comparison of Classic and Molecular Approaches for the Identification of Untypeable Enteroviruses
Authors: Oberste M. Steven , Maher Kaija , Flemister Mary R. , Marchetti George , Kilpatrick David R. , Pallansch Mark A. 
Published: December 2019

ABSTRACTMembers of the familyPicornaviridaeare the most common viruses infecting humans, and species in several genera also infect a wide variety of other mammals. Picornaviruses have traditionally been classified by antigenic type, based on a serum neutralization assay. However, this method is time-consuming and labor-intensive, is sensitive to virus aggregation and antigenic variation, and requires a large number of antisera to identify all serotypes, even when antiserum pools are used. We developed generic reverse transcription (RT)-PCR primers that will amplify all human enterovirus serotypes, as well as many rhinoviruses and other picornaviruses, and used RT-PCR amplification of the VP1 gene and amplicon sequencing to identify enteroviruses that were refractory to typing by neutralization with pooled antisera. Enterovirus serotypes determined by sequencing were confirmed by neutralization with monospecific antisera. Of 55 isolates tested, 49 were of known enterovirus serotypes, two were rhinoviruses, and four were clearly picornaviruses but did not match any known picornavirus sequence. All four untyped picornaviruses were closely related to one another in sequence, suggesting that they are of the same serotype. RT-PCR, coupled with amplicon sequencing, is a simple and rapid method for the typing and classification of picornaviruses and may lead to the identification of many new picornavirus serotypes.
Plasmodium falciparum
Histidine-Rich Protein 2-Based Immunocapture Diagnostic Assay for Malaria: Cross-Reactivity with Rheumatoid Factors
Authors: Iqbal J. , Sher A. , Rab A. 
Published: December 2019

ABSTRACT

Recently introduced rapid nonmicroscopic immunocapture assays for the diagnosis of malaria infection are being evaluated for their sensitivity and specificity in various epidemiological settings. A
Plasmodium falciparum
histidine-rich protein 2 (PfHRP-2)-based assay (ICT) and a
Plasmodium
-specific lactate dehydrogenase test (OptiMAL) were evaluated for their specificities in different groups of patients who tested negative for malaria infection by microscopy. The patients were selected from different disease groups: rheumatoid arthritis, hepatitis C, toxoplasmosis, schistosomiasis, and hydatid disease. One hundred thirty-three of the 225 patients were positive for rheumatoid factor. Thirty-five of the 133 (26%) rheumatoid factor-positive patients gave a false-positive reaction with the ICT assay, but only 4 of these gave false-positive reactions with the OptiMAL test. Thirty-three of the 35 false-positive specimens became negative when repeat tested with the ICT assay after absorbing out the rheumatoid factor activity. Our study shows that the PfHRP-2-based ICT assay gave a false-positive reaction in 26% of the patients who had rheumatoid factors, but were negative for malaria by microscopy.
Comparison of Two Commercial Methods for Measurement of Cytomegalovirus Load in Blood Samples after Renal Transplantation
Authors: Tong C. Y. William , Cuevas Luis E. , Williams Helen , Bakran Ali 
Published: December 2019

ABSTRACT

A cohort of 77 renal transplant recipients was prospectively studied for comparison of two commercially available cytomegalovirus (CMV) load assays, i.e., the COBAS AMPLICOR CMV Monitor test (Amplicor), using plasma samples, and the Murex Hybrid Capture System (HCS), using whole blood. The manufacturer of the HCS assay changed the version of the test from 1.0 (HCS-1) to 2.0 (HCS-2) after the first 37 patients had been tested. Despite the differences in principle and type of specimen used, the Amplicor and HCS assays gave comparable results. The regression line correlating the HCS-1 assay to the Amplicor assay was similar to that correlating the HCS-2 assay to the Amplicor assay. The HCS results could be converted to Amplicor-equivalent units by using linear-regression equations [log
10
HCS-1 result = 0.49 (log
10
Amplicor result) + 2.58, and log
10
HCS-2 result = 0.61 (log
10
Amplicor result) + 2.18]. The HCS-2 assay appeared to have the lowest detection limit, followed by the Amplicor assay and then the HCS-1 assay. When a sliding scale of cutoff values in Amplicor-equivalent units (>1,000, >2,500, >6,000, >16,000, >40,000, and >100,000 copies/ml) was applied to diagnose CMV disease, similar patterns of sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were observed with the Amplicor and HCS assays. A cutoff value of >40,000 copies/ml has a low sensitivity (Amplicor, 29.4%; HCS, 41.2%) but is specific (Amplicor, 96.7%; HCS, 93.3%) and can be used for the differential diagnosis of CMV disease (PPV, 71.4% [Amplicor] or 63.6% [HCS]; NPV, 82.9% [Amplicor] or 84.8% [HCS]). A lower cutoff value of >1,000 copies/ml improves the sensitivity (Amplicor, 76.5%; HCS, 82.4%) and has a high NPV (Amplicor, 91.8%; HCS, 94.2%) but, due to the low PPV (Amplicor, 46.2%; HCS, 56%), is useful only for exclusion of CMV disease.
Etiology of Sexually Transmitted Infections among Street-Based Female Sex Workers in Dhaka, Bangladesh
Authors: Rahman Motiur , Alam Ashraful , Nessa Khairun , Hossain Anowar , Nahar Shamsun , Datta Dilip , Alam Khan Shahnewaz , Amin Mian Ruhul , Albert M. John 
Published: December 2019

ABSTRACT

An etiological study of sexually transmitted infections (STIs) was conducted among female sex workers (FSWs) in Dhaka, Bangladesh. Endocervical swab and blood samples from 269 street-based FSWs were examined for
Neisseria gonorrhoeae
,
Chlamydia trachomatis
, and
Trichomonas vaginalis
as well as for antibodies to
Treponema pallidum
and herpes simplex virus 2 (HSV-2). Sociodemographic data and data regarding behavior were also collected. A total of 226 of the 269 FSWs (84%) were positive for the STI pathogens studied. Among the 269 FSWs, 35.5% were positive for
N. gonorrhoeae
, 25% were positive for
C. trachomatis
, 45.5% were positive for
T. vaginalis
, 32.6% were seropositive for
T. pallidum
, 62.5% were seropositive for HSV-2, and 51% had infections with two or more pathogens.
Molecular Characterization of
Brucella
Strains Isolated from Marine Mammals
Authors: Bricker Betsy J. , Ewalt Darla R. , MacMillan Alastair P. , Foster Geoff , Brew Simon 
Published: December 2019

ABSTRACT

Recently, gram-negative bacteria isolated from a variety of marine mammals have been identified as
Brucella
species by conventional phenotypic analysis. This study found the 16S rRNA gene from one representative isolate was identical to the homologous sequences of
Brucella abortus
,
B. melitensis
,
B. canis
, and
B. suis
. IS
711
-based DNA fingerprinting of 23 isolates from marine mammals showed all the isolates differed from the classical
Brucella
species. In general, fingerprint patterns grouped by host species. The data suggest that the marine mammal isolates are distinct types of
Brucella
and not one of the classical species or biovars invading new host species. In keeping with historical precedent, the designation of several new
Brucella
species may be appropriate.
Detection of
Giardia lamblia
and
Cryptosporidium parvum
Antigens in Human Fecal Specimens Using the ColorPAC Combination Rapid Solid-Phase Qualitative Immunochromatographic Assay
Authors: Garcia Lynne S. , Shimizu Robyn Y. 
Published: December 2019

ABSTRACT

The ColorPAC
Giardia/Cryptosporidium
(Becton Dickinson) is a solid-phase qualitative immunochromatographic assay that detects and distinguishes between
Giardia lamblia
and
Cryptosporidium parvum
in human stool. Agreement between the Alexon-Trend ProSpecT
Giardia
Rapid EIA and the ColorPAC assay was 166 of 172 (96.5%). Agreement between the Alexon-Trend ProSpecT
Cryptosporidium
Rapid EIA and the ColorPAC assay was 169 of 171 (98.8%). No cross-reactions were seen with other parasites or human cells.
Experimental Inoculation with Human Granulocytic Ehrlichia Agent Derived from High- and Low-Passage Cell Culture in Horses
Authors: Pusterla Nicola , Madigan John E. , Asanovich Kristin M. , Chae Joon-Seok , Derock Elfriede , Leutenegger Christian M. , Pusterla Jeannine Berger , Lutz Hans , Dumler J. Stephen 
Published: December 2019

ABSTRACTWe report the successful infection throughout intravenous inoculation with low and high passage of in vitro-grown human granulocytic ehrlichiosis (HGE) agent in horses. Differences in disease severity but not in incubation time, hematological changes, PCR detection, ehrlichial load, seroconversion time, and titer range were noted between horses infected with a low and a high passage of in vitro-grown HGE agent.
Potential Errors in Recognition of
Erysipelothrix rhusiopathiae
Authors: Dunbar Sherry A. , Clarridge Jill E. 
Published: December 2019

ABSTRACT

Here we describe four isolations of
Erysipelothrix rhusiopathiae
associated with polyarthralgia and renal failure, septic arthritis, classic erysipeloid, and peritonitis. Although the biochemical identification was straightforward in each case, recognition presented a challenge to the clinical microbiologist, since in three cases
E. rhusiopathiae
was not initially considered due to unusual clinical presentations, in two cases the significance might not have been appreciated because growth was in broth only, and in one case the infection was thought to be polymicrobic. Because the Gram stain can be confusing, abbreviated identification schemes that do not include testing for H
2
S production could allow
E. rhusiopathiae
isolates to be misidentified as
Lactobacillus
spp. or
Enterococcus
spp. in atypical infections.
Evaluation of the Wider System, a New Computer-Assisted Image-Processing Device for Bacterial Identification and Susceptibility Testing
Authors: Cantón Rafael , Pérez-Vázquez María , Oliver Antonio , Sánchez Del Saz Begoña , Gutiérrez M. Olga , Martínez-Ferrer Manuel , Baquero Fernando 
Published: December 2019

ABSTRACT

The Wider system is a newly developed computer-assisted image-processing device for both bacterial identification and antimicrobial susceptibility testing. It has been adapted to be able to read and interpret commercial MicroScan panels. Two hundred forty-four fresh consecutive clinical isolates (138 isolates of the family
Enterobacteriaceae
, 25 nonfermentative gram-negative rods [NFGNRs], and 81 gram-positive cocci) were tested. In addition, 100 enterobacterial strains with known β-lactam resistance mechanisms (22 strains with chromosomal AmpC β-lactamase, 8 strains with chromosomal class A β-lactamase, 21 broad-spectrum and IRT β-lactamase-producing strains, 41 extended-spectrum β-lactamase-producing strains, and 8 permeability mutants) were tested. API galleries and National Committee for Clinical Laboratory Standards (NCCLS) microdilution methods were used as reference methods. The Wider system correctly identified 97.5% of the clinical isolates at the species level. Overall essential agreement (±1 log
2
dilution for 3,719 organism-antimicrobial drug combinations) was 95.6% (isolates of the family
Enterobacteriaceae
, 96.6%; NFGNRs, 88.0%; gram-positive cocci, 95.6%). The lowest essential agreement was observed with
Enterobacteriaceae
versus imipenem (84.0%), NFGNR versus piperacillin (88.0%) and cefepime (88.0%), and gram-positive isolates versus penicillin (80.4%). The category error rate (NCCLS criteria) was 4.2% (2.0% very major errors, 0.6% major errors, and 1.5% minor errors). Essential agreement and interpretive error rates for eight β-lactam antibiotics against isolates of the family
Enterobacteriaceae
with known β-lactam resistance mechanisms were 94.8 and 5.4%, respectively. Interestingly, the very major error rate was only 0.8%. Minor errors (3.6%) were mainly observed with amoxicillin-clavulanate and cefepime against extended-spectrum β-lactamase-producing isolates. The Wider system is a new reliable tool which applies the image-processing technology to the reading of commercial trays for both bacterial identification and susceptibility testing.
Intraspecies Diversity of
Cryptococcus laurentii
as Revealed by Sequences of Internal Transcribed Spacer Regions and 28S rRNA Gene and Taxonomic Position of
C. laurentii
Clinical Isolates
Authors: Sugita Takashi , Takashima Masako , Ikeda Reiko , Nakase Takashi , Shinoda Takako 
Published: December 2019

ABSTRACT

The intraspecies diversity of an opportunistic yeast pathogen,
Cryptococcus laurentii
, was revealed by analysis of the sequences of the internal transcribed spacer regions and the 28S rRNA gene. Ten strains of
C. laurentii
were grouped into two major phylogenetic groups and were further divided into at least seven species. Four of the strains isolated from patients did not represent a single species but showed heterogeneity. These results suggest that
C. laurentii
is a genetically heterogeneous species, and this must be taken into consideration when identifying
C. laurentii
clinical isolates.
A Simple PCR Method for Rapid Genotype Analysis of
Mycobacterium ulcerans
Authors: Stinear Timothy , Davies John K. , Jenkin Grant A. , Portaels Françoise , Ross Bruce C. , OppEdIsano Frances , Purcell Maria , Hayman John A. , Johnson Paul D. R. 
Published: December 2019

ABSTRACT

Two high-copy-number insertion sequences, IS
2404
and IS
2606
, were recently identified in
Mycobacterium ulcerans
and were shown by Southern hybridization to possess restriction fragment length polymorphism between strains from different geographic origins. We have designed a simple genotyping method that captures these differences by PCR amplification of the region between adjacent copies of IS
2404
and IS
2606
. We have called this system 2426 PCR. The method is rapid, reproducible, sensitive, and specific for
M. ulcerans
, and it has confirmed previous studies suggesting a clonal population structure of
M. ulcerans
within a geographic region.
M. ulcerans
isolates from Australia, Papua New Guinea, Malaysia, Surinam, Mexico, Japan, China, and several countries in Africa were easily differentiated based on an array of 4 to 14 PCR products ranging in size from 200 to 900 bp. Numerical analysis of the banding patterns suggested a close evolutionary link between
M. ulcerans
isolates from Africa and southeast Asia. The application of 2426 PCR to total DNA, extracted directly from
M. ulcerans
-infected tissue specimens without culture, demonstrated the sensitivity and specificity of this method and confirmed for the first time that both animal and human isolates from areas of endemicity in southeast Australia have the same genotype.
Diversity in a Variable-Number Tandem Repeat from
Yersinia pestis
Authors: Adair D. M. , Worsham P. L. , Hill K. K. , Klevytska A. M. , Jackson P. J. , Friedlander A. M. , Keim P. 
Published: December 2019

ABSTRACT

We have identified a tetranucleotide repeat sequence, (CAAA)
N
, in the genome of
Yersinia pestis
, the causative agent of plague. This variable-number tandem repeat (VNTR) region has nine alleles and great diversity (calculated as 1 minus the sum of the squared allele frequencies) (diversity value, 0.82) within a set of 35 diverse
Y. pestis
strains. In contrast, the nucleotide sequence of the
lcrV
(low-calcium-response) gene differed only slightly among these strains, having a haplotype diversity value of 0.17. Replicated cultures, phenotypic variants of particular strains, and extensively cultured replicates within strains did not differ in VNTR allele type. Thus, while a high mutation rate must contribute to the great diversity of this locus, alleles appear stable under routine laboratory culture conditions. The classic three plague biovars did not have single identifying alleles, although there were allelic biases within biovar categories. The antiqua biovar was the most diverse, with four alleles observed in 5 strains, while the orientalis and mediaevalis biovars exhibited five alleles in 21 strains and three alleles in 8 strains, respectively. The CAAA VNTR is located immediately adjacent to the transcriptional promoters for flanking open reading frames and may affect their activity. This VNTR marker may provide a high-resolution tool for epidemiological analyses of plague.
Development of a Serological Test for
Haemophilus ducreyi
for Seroprevalence Studies
Authors: Elkins Christopher , Yi Kyungcheol , Olsen Bonnie , Thomas Christopher , Thomas Kevin , Morse Stephen 
Published: December 2019

ABSTRACT

We developed a new enzyme immunoassay (rpEIA) for use in determining the seroprevalence of chancroid. Three highly conserved outer membrane proteins from
Haemophilus ducreyi
strain 35000 were cloned, overexpressed, and purified from
Escherichia coli
for use as antigens in the rpEIA. Serum specimens from patients with and without chancroid were assayed to determine optimum sensitivity and specificity and to establish cutoff values. On the basis of these data, rpEIA was found to be both sensitive and specific when used to test a variety of serum specimens from patients with genital ulcers and urethritis and from healthy blood donors.
Borrelia burgdorferi
B31 Erp Proteins That Are Dominant Immunoblot Antigens of Animals Infected with Isolate B31 Are Recognized by Only a Subset of Human Lyme Disease Patient Sera
Authors: Miller Jennifer C. , El-Hage Nazira , Babb Kelly , Stevenson Brian 
Published: December 2019

ABSTRACT

Sera from animals infected with
Borrelia burgdorferi
isolates yield intense immunoblot signals from the B31 ErpA/I/N and ErpB/J/O proteins, which have apparent molecular masses of 19 and 60 kDa, respectively. Since
B. burgdorferi
proteins with those molecular masses are of immunodiagnostic importance, Lyme disease patient sera were used in studies of B31 lysates and recombinant B31 ErpA/I/N and ErpB/J/O proteins. Immunoblot analyses indicated that only a minority of the patients produced antibodies that recognized the tested B31 Erp proteins. Southern blot analyses of Lyme disease spirochetes cultured from 16 of the patients indicated that all these bacteria contain genes related to the B31
erpA/I/N
and
erpB/J/O
genes, although signal strengths indicated only weak similarities in many cases, suggestive of genetic variability of
erp
genes among these bacteria. These data indicate that Erp proteins are generally not the 19- and 60-kDa antigens observed on serodiagnostic immunoblots.
Desulfovibrio desulfuricans
Bacteremia in a Dog
Authors: Shukla Sanjay K. , Reed Kurt D. 
Published: December 2019

ABSTRACT

Desulfovibrio desulfuricans
was isolated from the blood of a dog presenting with fever, anorexia, and rear limb stiffness. The isolate was identified by 16S rRNA gene amplification and sequencing.
Rapid Identification and Differentiation ofBartonellaSpecies Using a Single-Step PCR Assay
Authors: Jensen Wayne A. , Fall Majilinde Z. , Rooney Jane , Kordick Dorsey L. , Breitschwerdt Edward B. 
Published: December 2019

ABSTRACTFive species ofBartonellahave been reported to infect humans and cause a variety of diseases that can be difficult to diagnose. Four species ofBartonellahave been reported to infect cats and dogs, and two of these species are considered to be zoonotic pathogens. Diagnosis ofBartonellainfections is hampered by the slow, fastidious growth characteristics ofBartonellaspecies. We report on the development of a single-step PCR-based assay for the detection and differentiation of medically relevantBartonellaspecies. PCR-mediated amplification of the 16S-23S rRNA intergenic region resulted in a product of a unique size for eachBartonellaspecies, thereby allowing differentiation without the necessity of restriction fragment length polymorphism analysis or sequencing of the amplified product. The ability of the single-step PCR assay to differentiate betweenBartonellaspecies was determined with characterized isolates and blood samples from animals known to be infected with eitherBartonella henselae,B. clarridgeiae, orB. vinsoniisubsp.berkhoffii. The sensitivity of the single-step PCR assay relative to that of in vitro culture was determined with blood samples fromB. henselae-infected cats.B. henselaetarget DNA was amplified from 100% of samples with greater than 50 CFU/ml and 80% of samples with 10 to 30 CFU/ml. The single-step assay described in the report expedites PCR-based detection and differentiation of medically relevantBartonellaspecies.