bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic and Genomic Variation among
Staphylococcus epidermidis
Strains Infecting Joint Prostheses
Authors: Galdbart Jacques-Olivier , Morvan Anne , Desplaces Nicole , el Solh Nevine 
Published: December 2019

ABSTRACT

We studied the
Sma
I and
Sst
II macrorestriction patterns of 54
Staphylococcus epidermidis
strains isolated from 14 patients infected following the implantation of joint prostheses. Multiple strains from pus and infected tissue specimens of each patient were selected on the basis of different colony morphologies and drug resistance patterns. The same criteria were used to select 23
S. epidermidis
strains from hand swabs of eight healthy individuals. For 10 of the 14 patients, all the intrapatient strains appeared to be closely or possibly related, whereas related strains were detected in the skin flora of only one of the eight healthy individuals. This observation suggests that, in most cases, the patients were infected by a single
S. epidermidis
clone which subsequently underwent rearrangements that yielded derivatives with divergent phenotypes and, occasionally, divergent macrorestriction patterns. The four patients whose specimens contained unrelated
S. epidermidis
strains were probably infected with several polyclonal strains.
Molecular Characterization of a New Ribotype of
Vibrio cholerae
O139 Bengal Associated with an Outbreak of Cholera in Bangladesh
Authors: Faruque Shah M. , Siddique A. K. , Saha Manujendra N. , Asadulghani  , Rahman M. Mostafizur , Zaman K. , Albert M. John , Sack David A. , Sack R. Bradley 
Published: December 2019

ABSTRACT

Vibrio cholerae
O139 Bengal initially appeared in the southern coastal region of Bangladesh and spread northward, causing explosive epidemics during 1992 and 1993. The resurgence of
V. cholerae
O139 during 1995 after its transient displacement by a new clone of El Tor vibrios demonstrated rapid changes in the epidemiology of cholera in Bangladesh. A recent outbreak of cholera in two north-central districts of Bangladesh caused by
V. cholerae
O139 led us to analyze strains collected from the outbreak and compare them with
V. cholerae
O139 strains isolated from other regions of Bangladesh and neighboring India to investigate their origins. Analysis of restriction fragment length polymorphisms in genes for conserved rRNA (ribotype) revealed that the recently isolated
V. cholerae
O139 strains belonged to a new ribotype which was distinct from previously described ribotypes of toxigenic
V. cholerae
O139. All strains carried the genes for toxin-coregulated pili (
tcpA
and
tcpI
) and accessory colonization factor (
acfB
), the regulatory gene
toxR
, and multiple copies of the lysogenic phage genome encoding cholera toxin (CTXΦ) and belonged to a previously described
ctxA
genotype. Comparative analysis of the
rfb
gene cluster by PCR revealed the absence of a large region of the O1-specific
rfb
operon downstream of the
rfaD
gene and the presence of an O139-specific genomic region in all O139 strains. Southern hybridization analysis of the O139-specific genomic region also produced identical restriction patterns in strains belonging to the new ribotype and those of previously described ribotypes. These results suggested that the new ribotype of Bengal vibrios possibly originated from an existing strain of
V. cholerae
O139 by genetic changes in the rRNA operons. In contrast to previously isolated O139 strains which mostly had resistance to trimethoprim, sulfamethoxazole, and streptomycin encoded by a transposon (SXT element), 68.6% of the toxigenic strains analyzed in the present study, including all strains belonging to the new ribotype, were susceptible to these antibiotics. Molecular analysis of the SXT element revealed possible deletion of a 3.6-kb region of the SXT element in strains which were susceptible to the antibiotics. Thus,
V. cholerae
O139 strains in Bangladesh are also undergoing considerable reassortments in genetic elements encoding antimicrobial resistance.
Evaluation of the INNO-LIA HTLV I/II Assay for Confirmation of Human T-Cell Leukemia Virus-Reactive Sera in Blood Bank Donations
Authors: Sabino Ester C. , Zrein Maan , Taborda Carlos P. , Otani Marcia M. , Ribeiro-Dos-Santos Gabriela , Sáez-Alquézar Amadeo 
Published: December 2019

ABSTRACTWe have evaluated a new serological confirmatory test (INNO-LIA HTLV I/II Ab [INNO-LIA]) for human T-cell leukemia virus (HTLV) using a large collection of samples from Brazilian blood donors (São Paulo region) and compared the results with those obtained by Western blotting (WB) tests (WB2.3 and WB2.4). Blood donations were initially screened by enzyme-linked immunosorbent assays (ELISAs) based on viral lysates, and repeatedly reactive samples were further tested by WB2.3. When available, samples were also tested by PCR, two additional ELISAs based on recombinant antigens (recombinant ELISAs), a new-generation WB assay (WB2.4), and the INNO-LIA. Of the 18,169 samples tested, 292 (1.61%) were repeatedly reactive in the ELISAs (viral lysate based) and were further tested by WB2.3; 97 were positive (19 that were typed as HTLV type I [HTLV-I], 12 that were typed as HTLV type II [HTLV-II], and 66 that were nontypeable), 17 were negative, and 178 had indeterminate results. Of the samples with indeterminate results, 172 were tested by INNO-LIA, which could resolve 153 samples as negative. Regarding the positive samples, WB2.3 and INNO-LIA produced concordant results for all HTLV-I-positive samples, whereas for HTLV-II they agreed for 10 of 12 samples; the 2 samples with discordant results were considered to be positive for HTLV-II by WB with WB2.3 but negative for HTLV-II by INNO-LIA and the two recombinant ELISAs. Furthermore, of the 66 nontypeable samples, 60 underwent testing by INNO-LIA; 54 turned out to be negative by the latter test as well as by recombinant ELISAs. In conclusion, the new serological confirmatory assay for HTLV (INNO-LIA HTLV I/II Ab) resolved the results for the majority of the indeterminate and positive-untypeable samples frequently observed by WB assays.
Prevalence of
Borrelia burgdorferi
in
Ixodes ricinus
Ticks in Urban Recreational Areas of Helsinki
Authors: Junttila Juha , Peltomaa Miikka , Soini Hanna , Marjamäki Merja , Viljanen Matti K. 
Published: December 2019

ABSTRACT

Lyme borreliosis, an infection caused by the tick-borne spirochete
Borrelia burgdorferi
, is a major health problem for populations in areas of endemicity in the Northern Hemisphere. In the present study we assessed the density of ticks and the prevalence of
B. burgdorferi
sensu lato among ticks in popular urban recreational areas of Helsinki, Finland. Altogether 1,688
Ixodes ricinus
ticks were collected from five areas located within 5 km of the downtown section of Helsinki, and 726 of them (303 nymphs, 189 females, and 234 males) were randomly chosen for laboratory analysis. The midguts of the ticks were divided into three pieces, one for dark-field microscopy, one for cultivation in BSK-II medium, and one for PCR analysis. Ticks were found in all the study areas; their densities varied from 1 to 36 per 100 m along which a cloth was dragged. The rate of tick infection with
B. burgdorferi
sensu lato varied from 19 to 55%, with the average being 32%.
Borellia afzelii
was the most predominant genospecies in all the areas, and no
B. burgdorferi
sensu stricto isolates were detected. Only two ticks were concurrently infected with both
B. afzelii
and
Borrelia garinii
. Dark-field microscopy gave more positive results for
B. burgdorferi
than did cultivation or PCR analysis. However, the agreement between all three methods was fairly good. We conclude that Lyme borreliosis can be contracted even in urban environments not populated with large mammals like deer or elk. The disease should be taken into account in the differential diagnosis of certain symptoms of patients from these areas, and the use of measures to improve the awareness of the general population and health care officials of the risk of contracting the disease is warranted.
Evaluation of Human Seroreactivity to
Bartonella
Species in Sweden
Authors: Holmberg M. , McGill S. , Ehrenborg C. , Wesslén L. , Hjelm E. , Darelid J. , Blad L. , Engstrand L. , Regnery R. , Friman G. 
Published: December 2019

ABSTRACT

Among the species that compose the expanding genus
Bartonella
, thus far only
B. henselae
and
B. quintana
have reportedly been isolated from humans in Europe. To evaluate the prevalence of
Bartonella
infection in Sweden, we conducted a retrospective serological examination of 126 human serum samples. These samples were analyzed for antibodies to
B. henselae
,
B. quintana
, and
B. elizabethae
. Serum samples from 100 blood donors, who spanned the ages of 20 to 60 and had no apparent clinical signs of illness, were also studied as a control group. An immunoglobulin G indirect fluorescence antibody assay revealed 4 and 8.3%
Bartonella
positivity rates for the blood donor and patient group, respectively, when a cutoff titer of ≥64 was chosen. Among the blood donors, four were seropositive to
B. elizabethae
; one of these also had concordant positive titer to
B. henselae
. In the patient group, 14 serum samples were positive against
Bartonella
spp. These serum specimens represented nine patients. In three of these seropositive patients, paired serum samples displayed a fourfold increase in antibody titer to at least one of the three antigens. These three patients are discussed. In this report we also present a case study of a 60-year-old Swedish male with fatal myocarditis. Postmortem serological analysis revealed a high titer against
B. elizabethae
. PCR and nucleotide sequencing of the myocardial tissue from this patient, and of liver tissue from one of the other three patients, showed sequences similar to
B. quintana
. The age, geographical origin, animal contacts, and serological response pattern to the different
Bartonella
antigens differed among the four patients. This study substantiates the presence of
Bartonella
spp. in Sweden, documents the seroreactivity to three
Bartonella
antigens in Swedish patients, and reports the first two cases of
B. quintana
-like infections in Sweden.
Comparison of E-Test and Broth Microdilution Methods for Antifungal Drug Susceptibility Testing of Molds
Authors: Szekely Adrien , Johnson Elizabeth M. , Warnock David W. 
Published: December 2019

ABSTRACT

We compared the E test with a broth microdilution method, performed according to National Committee for Clinical Laboratory Standards document M27-A guidelines, for determining the in vitro susceptibilities of 90 isolates of pathogenic molds (10
Absidia corymbifera
, 10
Aspergillus flavus
, 10
Aspergillus fumigatus
, 10
Aspergillus niger
, 10
Aspergillus terreus
, 10
Exophiala dermatitidis
, 10
Fusarium solani
, 10
Scedosporium apiospermum
, 5
Scedosporium prolificans
, and 5
Scopulariopsis brevicaulis
). Overall, there was 71% agreement between the results of the two methods for amphotericin B (E-test MICs within ±2 log
2
dilutions of broth microdilution MICs) and 88% agreement with the results for itraconazole. The overall levels of agreement (within ±2 log
2
dilutions) were ≥80% for 5 of the 10 species tested against amphotericin B and 8 of the 10 species tested against itraconazole. The best agreement between the results was seen with
A. fumigatus
and
A. terreus
(100% of results for both agents within ±2 log
2
dilutions). The poorest agreement was seen with
S. apiospermum
,
S. prolificans
, and
S. brevicaulis
tested against amphotericin B (20% of results within ±2 log
2
dilutions). In every instance, this low level of agreement was due to isolates for which the broth microdilution MICs were low but for which the E-test MICs were much higher. The E test appears to be a suitable alternative procedure for testing the susceptibility of
Aspergillus
spp. and some other molds to amphotericin B or itraconazole.
Characterization of Group C Rotaviruses Associated with Diarrhea Outbreaks in Feeder Pigs
Authors: Kim Yunjeong , Chang Kyeong-Ok , Straw Barbara , Saif Linda J. 
Published: December 2019

ABSTRACT
Feces and serum specimens were collected from three farms in Michigan on which ∼50-lb (8- to 9-week-old) pigs experienced diarrhea just after placement into all-in-all-out finishing barns. The clinical signs (profuse watery diarrhea lasting about 2 weeks and no vomiting) were similar on all farms, and the morbidity rate was high (ranging from 60 to 80%) but without mortality. Eleven diarrheic fecal samples from the farms were tested for group A and C rotaviruses by immune electron microscopy (IEM) and various assays. IEM indicated that the fecal samples reacted only with antiserum against group C rotaviruses, and polyacrylamide gel electrophoresis indicated that the samples had characteristic genomic electropherotypes for group C rotavirus. Group C rotavirus was detected by cell culture immunofluorescence (CCIF) tests in nine fecal samples, but no group A rotavirus was detected by enzyme-linked immunosorbent assay or CCIF. By reverse transcription (RT)-PCR, all 11 fecal samples were positive for group C rotaviruses, with only 2 samples positive for group A rotaviruses. However, a second amplification of RT-PCR products using nested primers detected group A rotaviruses in all samples. Analysis of nucleotide and deduced amino acid sequences of the RT-PCR product (partial-length VP7) of the group C rotavirus showed 87.2 to 91% nucleotide identity and 92.6 to 95.9% amino acid identity among two strong samples from the different farms and the Cowden strain of porcine group C rotavirus. All nine convalescent-phase serum samples tested had neutralizing antibodies to the Cowden strain, and the majority of them had neutralizing antibody against group A rotaviruses (OSU or/and Gottfried strains) by fluorescent focus neutralization tests. Although group C rotaviruses have been reported as a cause of sporadic diarrhea in suckling or weanling pigs, to our knowledge, this is the first report of epidemic diarrhea outbreaks associated with group C rotavirus in older pigs.
A Highly Sensitive Assay for Detection and Quantitation of Human Cytomegalovirus DNA in Serum and Plasma by PCR and Electrochemiluminescence
Authors: Boom René , Sol Cees , Weel Jan , Gerrits Yvette , de Boer Monique , Wertheim-van Dillen Pauline 
Published: December 2019

ABSTRACT
We describe a diagnostic PCR assay (D-PCR) and a quantitative PCR assay (Q-PCR) for the detection of human cytomegalovirus (CMV) in plasma and serum. In the D-PCR, DNA was purified from plasma or serum together with internal control (IC) DNA, which monitored both DNA extraction efficiency and PCR efficiency. DNA was subjected to PCR with a single primer pair, and the amount of PCR products was determined by electrochemiluminescence (ECL) in the QPCR System 5000 (Perkin-Elmer) after hybridization with Tris (2,2′-bipyridine) ruthenium (II) chelate-labeled probes. The lower limit of sensitivity of the D-PCR was reached at about 25 CMV particles/ml. Even with extremely low DNA inputs (four molecules of IC DNA/200 μl of plasma), very high yields (near 100%) were reached. DNA extracted from specimens that were CMV positive by the D-PCR was subsequently used in the Q-PCR, which was similar to the D-PCR. The viral load was calculated directly from the ratio of CMV and IC signals obtained by ECL. The Q-PCR assay is quantitative in the range of 100 to 150,000 copies of CMV/ml, independent of the anticoagulant. Interassay variation, intra-assay variation, and interspecimen variation were about 25%, suggesting that the Q-PCR will reliably detect fourfold differences in viral load. Comparison of paired serum and plasma specimens from CMV-infected individuals showed that serum CMV loads were frequently more than 10-fold lower than plasma CMV loads.
New Enzyme Immunoassays for Sensitive Detection of Circulating
Candida albicans
Mannan and Antimannan Antibodies: Useful Combined Test for Diagnosis of Systemic Candidiasis
Authors: Sendid Boualem , Tabouret Marc , Poirot Jean Louis , Mathieu Daniel , Fruit Jeanine , Poulain Daniel 
Published: December 2019

ABSTRACT

Two standardized enzyme immunoassays for the serological diagnosis of candidiasis were developed. The first one detects antimannan antibodies, while the second one detects mannan with a sensitivity of 0.1 ng/ml. These tests were applied to 162 serum samples retrospectively selected from 43 patients with mycologically and clinically proven candidiasis caused by
Candida albicans
. Forty-three serum samples were positive for mannan, and 63 had significant antibody levels. Strikingly, only five serum samples were simultaneously positive by both tests. When the results were analyzed per patient, 36 (84%) presented at least one serum positive by one test. For 30 of them, positivity by one test was always associated with negative results by the other test for any of the tested sera. For six patients whose sera were positive for either an antigen or an antibody response, a balance between positivity by each test was evidenced by kinetic analysis of sera drawn during the time course of the infection. Controls consisted of 98 serum samples from healthy individuals, 93 serum samples from patients hospitalized in intensive care units, and 39 serum samples from patients with deep mycoses. The sensitivities and specificities were 40 and 98% and 53 and 94% for mannanemia or antibody detection, respectively. These values reached 80 and 93%, respectively, when the results of both tests were combined. These observations, which clearly demonstrate a disparity between circulation of a given mannan catabolite and antimannan antibody response, suggest that use of both enzyme immunoassays may be useful for the routine diagnosis of candidiasis.
Rapid PCR Test for Discriminating between
Candida albicans
and
Candida dubliniensis
Isolates Using Primers Derived from the pH-Regulated
PHR1
and
PHR2
Genes of
C. albicans
Authors: Kurzai Oliver , Heinz Werner J. , Sullivan Derek J. , Coleman David C. , Frosch Matthias , Mühlschlegel Fritz A. 
Published: December 2019

ABSTRACT

The development of a satisfactory means to reliably distinguish between the two closely related species
Candida albicans
and
Candida dubliniensis
in the clinical mycology laboratory has proved difficult because these two species are phenotypically so similar. In this study, we have detected homologues of the pH-regulated
C. albicans PHR1
and
PHR2
genes in
C. dubliniensis
. Restriction fragment length polymorphism analysis suggests that there are significant sequence differences between the genes of the two species. In order to exploit this apparent difference, oligonucleotide primers based on the coding sequence of the
C. albicans PHR1
structural gene were designed and used in PCR experiments. Use of these primers with
C. albicans
template DNA from 17 strains yielded a predicted 1.6-kb product, while
C. dubliniensis
template DNA from 19 strains yielded no product. We therefore propose that PCR using these primers is a rapid and reliable means of distinguishing the two germ tube- and chlamydospore-producing species
C. albicans
and
C. dubliniensis
.
Evaluation of MRSA-Screen, a Simple Anti-PBP 2a Slide Latex Agglutination Kit, for Rapid Detection of Methicillin Resistance in
Staphylococcus aureus
Authors: Cavassini Matthias , Wenger Aline , Jaton Katia , Blanc Dominique S. , Bille Jacques 
Published: December 2019

ABSTRACT

The MRSA-Screen test (Denka Seiken Co., Ltd., Tokyo, Japan), consisting of a slide latex agglutination kit that detects PBP 2a with a monoclonal antibody, was blindly compared to the oxacillin disk diffusion test, the oxacillin-salt agar screen, and PCR of the
mecA
gene for the detection of methicillin resistance in
Staphylococcus aureus
. A total of 120 methicillin-susceptible
S. aureus
(MSSA) and 80 methicillin-resistant
S. aureus
(MRSA) isolates, defined by the absence or presence of the
mecA
gene, respectively, were tested. The MRSA-Screen test, the oxacillin disk diffusion test, and the oxacillin-salt agar screening test showed sensitivities of 100, 61.3, and 82.5% and specificities of 99.2, 96.7, and 98.3%, respectively. We conclude that the MRSA-Screen is a very accurate, reliable, and fast test (15 min) for differentiation of MRSA from MSSA colonies on agar plates.
Use of Nucleic Acid Probes for Identification of
Mycobacterium tuberculosis
Directly from MB/BacT Bottles
Authors: Badak F. Zuhre , Goksel Servet , Sertoz Ruchan , Nafile Bedii , Ermertcan Safak , Cavusoglu Cengiz , Bilgic Altinay 
Published: December 2019

ABSTRACT

The feasibility of using nucleic acid probes directly from positive MB/BacT broth to identify mycobacteria was determined in this study. A total number of 2,727 specimens were cultured into the MB/BacT (Organon Teknika) automated system and on conventional Loweinstein-Jensen (LJ) slants. The Gen-Probe AccuProbe culture identification tests (DNA probes) were used on samples from bottles which were identified as positive for mycobacteria by MB/BacT. Samples of positive MB/BacT broth (0.1 ml) were used directly in the broth culture method for the DNA probes as published by Gen-Probe. Centrifugation of the contents of the bottle was not done prior to probe testing. The number of mycobacteria detected by MB/BacT and LJ was 253 (221 isolates of
M. tuberculosis
and 32 isolates of mycobacteria other than
M. tuberculosis
[MOTT]). A total of 96.4% (213 of 221) of the bottles growing
M. tuberculosis
produced a positive direct DNA probe result for
M. tuberculosis
complex. One hundred percent (16 of 16) of the bottles growing
M. gordonae
produced a positive direct DNA probe result for
M. gordonae
. A total of 3.6% (8 of 221) of the bottles growing
M. tuberculosis
did not yield a positive direct DNA probe result for
M. tuberculosis
complex. The testing of subcultures made onto solid media from the positive bottles by AccuProbe identified six of these eight
M. tuberculosis
isolates. Two (0.9%)
M. tuberculosis
isolates gave a negative result for the
M. tuberculosis
probe test applied on the MB/BacT broth and its subculture. The rest of the positive MB/BacT bottles growing MOTT (16 of 32) were negative for
M. gordonae
,
M. avium
,
M. intracellulare
, and
M. kansasii
probes. The sensitivity and specificity of AccuProbe for the identification of
M. tuberculosis
and
M. gordonae
directly from MB/BacT broth were 96.4 and 100% for
M. tuberculosis
and 100 and 100% for
M. gordonae
, respectively. The direct testing of positive MB/BacT broth by AccuProbe, without prior centrifugation, allows for the accurate and rapid identification of
M. tuberculosis
and
M. gordonae
.
Disk Diffusion Method for Determining Susceptibilities of
Candida
spp. to MK-0991
Authors: Lozano-Chiu Mario , Nelson Page W. , Paetznick Victor L. , Rex John H. 
Published: December 2019

ABSTRACT

We have developed an agar-based methodology for testing susceptibilities of
Candida
spp. to the new antifungal agent MK-0991, a glucan synthase inhibitor. Results obtained with this method correlated well with the results obtained by the National Committee for Clinical Laboratory Standards M27-A broth microdilution reference method. However, as noted with prior comparisons of broth- and agar-based systems, some isolates yielded inhibition zones which were not consistent with the MICs obtained for them. Understanding the implications of these differences will require testing in an in vivo system.