bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case-Control Study of Enteropathogens Associated with Childhood Diarrhea in Dhaka, Bangladesh
Authors: Albert M. John , Faruque A. S. G. , Faruque S. M. , Sack R. B. , Mahalanabis D. 
Published: December 2019

ABSTRACT

The International Centre for Diarrhoeal Disease Research, Bangladesh, is a major center for research into diarrheal diseases. The center treats more than 100,000 patients a year. To obtain useful information representative of all patients, a surveillance system in which a 4% systematic sample of all patients is studied in detail, including etiological agents of diarrhea, was installed in October 1979. The first paper on etiology for the surveillance patients was published in 1982, which identified a potential enteric pathogen in 66% of patients. In subsequent years, several new agents of diarrhea have been identified. To assess the importance of a broader spectrum of diarrheal agents including the ones identified relatively recently, we studied 814 children with diarrhea. The children were up to 5 years of age and were part of the surveillance system. They were matched with an equal number of community controls without diarrhea. The study was conducted from February 1993 to June 1994. A potential enteric pathogen was isolated from 74.8% of diarrheal children and 43.9% of control children (
P
= 0.0001). Even though the first study was not a case-control study, it identified rotavirus,
Campylobacter jejuni
, enterotoxigenic
Escherichia coli
,
Shigella
spp., and
Vibrio cholerae
O1 as major pathogens. The present study identified these pathogens as being significantly associated with diarrhea. In addition, the study also identified six additional agents, including enteropathogenic
E. coli
,
Aeromonas
spp.,
V. cholerae
O139, enterotoxigenic
Bacteroides fragilis
,
Clostridium difficile
, and
Cryptosporidium parvum
, as being significantly associated with diarrhea.
Plesiomonas shigelloides
,
Salmonella
spp., diffusely adherent
E. coli
, enteroaggregative
E. coli
,
Entamoeba histolytica
, and
Giardia lamblia
were not significantly associated with diarrhea. Enteroinvasive
E. coli
, enterohemorrhagic
E. coli
, and
Cyclospora cayetanensis
were not detected in any of the children. The major burden of diseases due to most pathogens occurred in the first year of life. As in the previous study, seasonal patterns were seen for diarrhea associated with rotavirus,
V. cholerae
, and enterotoxigenic
E. coli
, and infections with multiple pathogens were common. With a few exceptions, these findings are in agreement with those from other developing countries. This knowledge of a broader spectrum of etiological agents of diarrhea in the surveillance patients will help us plan studies into various aspects of diarrheal diseases in this population.
Invasive and Noninvasive Group A Streptococcal Isolates with DifferentspeAAlleles in The Netherlands: Genetic Relatedness and Production of Pyrogenic Exotoxins A and B
Authors: Mascini Ellen M. , Jansze Margriet , Schouls Leo M. , Fluit Ad C. , Verhoef Jan , van Dijk Hans 
Published: December 2019

ABSTRACTStreptococcal pyrogenic exotoxin A (SPE-A) and SPE-B have been implicated in the pathogenesis of severe group A streptococcal (GAS) disease. We studied 31 invasive GAS strains including 18 isolates from patients with toxic shock syndrome and 22 noninvasive strains isolated in The Netherlands between 1994 and 1998. These strains were associated with the different allelic variants of the gene encoding SPE-A. We selected endemic strains withspeA-positive M and T serotypes:speA2-associated M1T1 and M22-60T12 strains,speA3-associated M3T3 strains, andspeA4-associated M6T6 strains. SincespeA1-positive isolates were not frequently encountered, we includedspeA1strains of different serotypes. The GAS strains were compared genotypically by pulsed-field gel electrophoresis and phenotypically by the in vitro production of SPE-A and SPE-B. All strains within one M and T type appeared to be of clonal origin. Most strains produced SPE-A and SPE-B, but only a minority of thespeA4-positive isolates did so. Among our isolates,speA1- andspeA3-positive strains produced significantly more SPE-A thanspeA2- andspeA4-carrying strains, while SPE-B production was most pronounced amongspeA1- andspeA2-containing strains. There was a marked degree of variability in the amounts of exotoxins produced in vitro by strains that shared the same genetic profile. We conclude that the differences in the in vitro production of SPE-A and SPE-B between our selected strains with identical M and T types were not related to either genetic heterogeneity or the clinical course of GAS disease in the patient from whom they were isolated.
Escherichia coli
O157:H7 and O157:H
−
Strains That Do Not Produce Shiga Toxin: Phenotypic and Genetic Characterization of Isolates Associated with Diarrhea and Hemolytic-Uremic Syndrome
Authors: Schmidt H. , Scheef J. , Huppertz H. I. , Frosch M. , Karch H. 
Published: December 2019

ABSTRACT

We have isolated one sorbitol-nonfermenting (SNF)
Escherichia coli
O157:H7 isolate and five sorbitol-fermenting (SF)
E. coli
O157:H
−
isolates that do not contain Shiga toxin (Stx) genes (
stx
). Isolates originated from patients with diarrhea (
n
= 4) and hemolytic-uremic syndrome (HUS) (
n
= 2). All isolates harbored a chromosomal
eae
gene encoding gamma-intimin as well as the plasmid genes E-
hly
and
etp
. The
E. coli
O157:H7 isolate was
katP
and
espP
positive. Respective sera obtained from the patient with HUS contained antibodies to the O157 lipopolysaccharide antigen. The
stx
-negative
E. coli
O157:H7 isolate is genetically related to
stx
-positive SNF
E. coli
O157:H7. All
stx
-negative SF
E. coli
O157:H
−
isolates belong to the same genetic cluster and are closely related to
stx
-positive SF
E. coli
O157:H
−
isolates. Our data indicate that
stx
-negative
E. coli
O157:H7/H
−
variants may occur at a low frequency and cannot be recognized by diagnostic methods that target Stx.
Amplification of Reiterated Sequences of Herpes Simplex Virus Type 1 (HSV-1) Genome To Discriminate between Clinical HSV-1 Isolates
Authors: Maertzdorf J. , Remeijer L. , Van Der Lelij A. , Buitenwerf J. , Niesters H. G. M. , Osterhaus A. D. M. E. , Verjans G. M. G. M. 
Published: December 2019

ABSTRACT
Herpes simplex virus type 1 (HSV-1)-related disease ranges from a localized, self-limiting illness to fatal disease in immunocompromised individuals. The corneal disease herpetic keratitis may develop after reactivation of a latent virus or reinfection with an exogenous herpesvirus. Molecular analysis of the virus involved may allow distinction between these two options. The HSV-1 genome contains several hypervariable regions that vary in numbers of reiterating regions (reiterations I to VIII [ReI to ReVIII]) between individual strains. Twenty-four HSV-1 clones, derived by subcloning of HSV-1 (strain F) twice in limiting dilutions, were tested in a PCR-based assay to analyze the stabilities of ReI, ReIII, ReIV, and ReVII. ReI and ReIII proved to vary in size upon subcloning, whereas ReIV and ReVII were stable. Subsequently, 37 unrelated isolates and 10 sequential isolates from five patients, all with HSV-1-induced keratitis, were genotyped for ReIV and ReVII. Of the 37 unrelated samples, 34 (92%) could be discriminated, while the genotypes of the viruses in sequential samples were identical for each individual. Conclusively, the data show that the approach presented allows the rapid and accurate discrimination of HSV-1 strains in studies that address the transmission and pathogenesis of HSV-1 infections.
Detection of Decreased Fluoroquinolone Susceptibility in Salmonellas and Validation of Nalidixic Acid Screening Test
Authors: Hakanen Antti , Kotilainen Pirkko , Jalava Jari , Siitonen Anja , Huovinen Pentti 
Published: December 2019

ABSTRACT

We evaluated 1,010
Salmonella
isolates classified as fluoroquinolone susceptible according to the National Committee for Clinical Laboratory Standards guidelines for susceptibility to nalidixic acid and three fluoroquinolones. These isolates were divided into two distinct subpopulations, with the great majority (
n
= 960) being fully ciprofloxacin susceptible and a minority (
n
= 50) exhibiting reduced ciprofloxacin susceptibility (MICs ranging between 0.125 and 0.5 μg/ml). The less ciprofloxacin-susceptible isolates were uniformly resistant to nalidixic acid, while only 12 (1.3%) of the fully susceptible isolates were nalidixic acid resistant. A similar association was observed between resistance to nalidixic acid and decreased susceptibility to ofloxacin or norfloxacin. A mutation of the
gyrA
gene could be demonstrated in all isolates for which the ciprofloxacin MICs were ≥0.125 μg/ml and in 94% of the nalidixic acid-resistant isolates but in none of the nalidixic acid-susceptible isolates analyzed. Identification of nalidixic acid resistance by the disk diffusion method provided a sensitivity of 100% and a specificity of 87.3% as tools to screen for isolates for which the MICs of ciprofloxacin were ≥0.125 μg/ml. We regard it as important that microbiology laboratories endeavor to recognize these less susceptible
Salmonella
strains, in order to reveal their clinical importance and to survey their epidemic spread.
Genotypic and Phenotypic Relationships between Clinical and Environmental Isolates of
Stenotrophomonas maltophilia
Authors: Berg Gabriele , Roskot Nicolle , Smalla Kornelia 
Published: December 2019

ABSTRACT

While the gram-negative bacterium
Stenotrophomonas maltophilia
is used in biotechnology (e.g., for biological control of plant pathogens and for bioremediation), the number of
S. maltophilia
diseases in humans has dramatically increased in recent years. A total of 40
S. maltophilia
isolates from clinical and environmental sources (plant associated and water) was investigated to determine the intraspecies diversity of the group and to determine whether or not the strains could be grouped based on the source of isolation. The isolates were investigated by phenotypic profiling (enzymatic and metabolic activity and antibiotic resistance patterns) and by molecular methods such as temperature-gradient gel electrophoresis of the 16S rRNA gene fragment, PCR fingerprinting with BOX primers, and pulsed-field gel electrophoresis (PFGE) after digestion with
Dra
I. Results of the various methods revealed high intraspecies diversity. PFGE was the most discriminatory method for typing
S. maltophilia
when compared to the other molecular methods. The environmental strains of
S. maltophilia
were highly resistant to antibiotics, and the resistance profile pattern of the strains was not dependent on their source of isolation. Computer-assisted cluster analysis of the phenotypic and genotypic features did not reveal any clustering patterns for either clinical or environmental isolates.
Comparison of the OptiMAL Test with PCR for Diagnosis of Malaria in Immigrants
Authors: Iqbal Jamshaid , Sher Ali , Hira Parsotam R. , Al-Owaish Rashed 
Published: December 2019

ABSTRACT

The OptiMAL test (Flow Inc., Portland, Oreg.), which detects a malaria parasite lactate dehydrogenase (pLDH) antigen, has not been evaluated for its sensitivity in the diagnosis of malaria infection in various epidemiological settings. Using microscopy and a PCR as reference standards, we performed a comparison of these assays with the OptiMAL test for the detection of
Plasmodium falciparum
and
Plasmodium vivax
infection in 550 immigrants who had come from areas where malaria is endemic to reside in Kuwait, where malaria is not endemic. As determined by microscopy, 125 (23%) patients had malaria, and of these, 84 (67%) were infected with
P. vivax
and 36 were infected with
P. falciparum
; in 5 cases the parasite species could not be determined due to a paucity of the parasites. The PCR detected malaria infection in 145 (26%) patients; 102 (70%) of the patients had
P. vivax
infection and 43 had
P. falciparum
infection. Of the five cases undetermined by microscopy, the PCR detected
P. falciparum
infection in two cases,
P. vivax
infection in two cases, and mixed (
P. falciparum
plus
P. vivax
) infection in one case. Correspondingly, the OptiMAL test detected malaria infection in 95 patients (17%); of these, 70 (74%) had
P. vivax
infection and 25 were infected with
P. falciparum
. In this study, 61 (49%) of the 125 malaria cases, as confirmed by microscopy, had a degree of parasitemia of <100 parasites per μl, and 23 (18%) of the cases had a degree of <50 parasites per μl. Our results show that the sensitivity of the OptiMAL test is high (97%) at a high level of parasitemia (>100 parasites/μl) but drops to 59% when the level is <100 parasites/μl and to 39% when it is <50 parasites/μl. In addition, the OptiMAL test failed to identify four patients whose blood smears contained
P. falciparum
gametocytes only. We conclude that the sensitivity and specificity of the OptiMAL test are comparable to those of microscopy in detecting malaria infection at a parasitemia level of >100 parasites/μl; however, the test failed to identify more than half of the patients with a parasitemia level of <50 parasites/μl. Thus, the OptiMAL test should be used with great caution, and it should not replace conventional microscopy in the diagnosis of malaria infection.
Ability of the Digene Hybrid Capture II Test To Identify
Chlamydia trachomatis
and
Neisseria gonorrhoeae
in Cervical Specimens
Authors: Schachter Julius , Hook Edward W. , McCormack William M. , Quinn Thomas C. , Chernesky Max , Chong Sylvia , Girdner Jennifer I. , Dixon Paula B. , DeMeo Lynette , Williams Eva , Cullen Allison , Lorincz Attila 
Published: December 2019

ABSTRACT

The Digene Hybrid Capture II (HCII CT/GC) test is a combination test designed to detect
Chlamydia trachomatis
and
Neisseria gonorrhoeae
in a single specimen. It is a nucleic acid hybridization test which uses signal amplification to increase sensitivity. We compared its performance to that of culture on cervical specimens from 1,370 women. Direct fluorescent-antibody assay was used to resolve discrepant results for
C. trachomatis
. Samples were collected with a proprietary cervical brush or with endocervical swabs. The HCII CT/GC test proved to be sensitive and specific in detecting these organisms. Compared to
N. gonorrhoeae
culture, it had a sensitivity of 93% (87/94) and a specificity of 98.5% (1,244/1,263). Compared to
C. trachomatis
culture, the sensitivity was 97.7% (129/132) and specificity was 98.2% (1,216/1,238). Testing of some specimens with discrepant results by PCR suggested that the test would actually prove to be even more specific if it were compared to a nucleic acid amplification test (NAAT). The sensitivity of
C. trachomatis
culture was somewhat less, at 88.6% (117/132). The endocervical brush appeared to be better than Dacron swabs for collecting specimens. The HCII CT/GC test offers an attractive format that allows simultaneous detection of
C. trachomatis
and
N. gonorrhoeae
with a single specimen. An initial positive result is followed by repeat tests with probes to identify chlamydiae or gonococci. This test is more sensitive than
C. trachomatis
culture and is at least as sensitive as culture for gonococci. It deserves further evaluation and comparison with NAATs and may well offer an attractive alternative for diagnosis and screening of these infections.
Detection of Human Herpesvirus 6 by Reverse Transcription-PCR
Authors: Norton Renee A. , Caserta Mary T. , Hall Caroline Breese , Schnabel Kenneth , Hocknell Peter , Dewhurst Stephen 
Published: December 2019

ABSTRACT
The role of human herpesvirus 6 (HHV-6) in disease beyond primary infection remains unclear. We have developed and validated a new reverse transcription-PCR (RT-PCR) assay for HHV-6 that can determine the presence of HHV-6 in clinical specimens and differentiate between latent and replicating virus. Peripheral blood mononuclear cells from 109 children were evaluated for HHV-6 by RT-PCR, DNA PCR, and viral culture. Of these samples, 106 were suitable for analysis. A total of 20 samples were positive for HHV-6 by culture and DNA PCR, of which 19 were positive by RT-PCR (sensitivity, 95%). All 28 samples from children that were negative by viral culture, but positive by DNA PCR, were negative for viral transcripts by our RT-PCR assay. One positive RT-PCR result was observed in 56 samples that were negative by tissue culture and DNA PCR. This indicates a low rate of false-positive results (1.2%) and a specificity of 98.8%. This RT-PCR assay can reliably differentiate between latent and actively replicating HHV-6 and should allow insight into the pathogenesis of this ubiquitous virus.
Phenotypic and Genotypic Heterogeneity among Cultivable Pathogen-Related Oral Spirochetes and
Treponema vincentii
Authors: Riviere G. R. , Smith K. S. , Willis S. G. , Riviere K. H. 
Published: December 2019

ABSTRACT

Recent findings challenge the assumption that pathogen-related oral spirochetes (PROS) are related to
Treponema pallidum. Treponema vincentii
, grown in OMIZ-Pat media, cross-reacted with monoclonal antibody H9-2 against
T. pallidum
, and cultivable PROS had 16S rRNA gene sequences similar to those of
T. vincentii
(C.-B. Choi, C. Wyss, and U. B. Göbel. J. Clin. Microbiol. 34:1922–1925, 1996). Aims of the present study were to determine whether antigen phenotypes of oral treponemas were influenced by growth conditions and to evaluate the genetic relatedness of cultivable PROS to
T. pallidum
and
T. vincentii
. Results show that three
T. pallidum
monoclonal antibodies (H9-1, H9-2, and F5) cross-reacted with whole cells from four
Treponema
species grown in modified OMIZ-Pat medium, but not with treponemas grown in NOS medium. Only H9-2 reacted in immunoblots with reduced proteins from cultivable PROS and
T. vincentii
. Three of five PROS isolates were amplified by
T. vincentii
-specific PCR, and one was amplified by
Treponema medium
-specific PCR. None were amplified by
T. pallidum
-specific PCR. Three of five PROS isolates had 16S ribosomal DNA restriction fragment length polymorphism patterns identical to that of
T. vincentii
, and the patterns of two isolates resembled that of
T. medium
. Arbitrarily primed-PCR profiles from whole genomic DNA were distinct among five PROS isolates and two
T. vincentii
strains. Thus, PROS isolates represent a heterogeneous group of treponemas that share some 16S rRNA gene sequences with
T. vincentii
and
T. medium
, but not with
T. pallidum
. It is proposed that the PROS nomenclature be dropped.
Field Evaluation of the Determine Rapid Human Immunodeficiency Virus Diagnostic Test in Honduras and the Dominican Republic
Authors: Palmer Carol J. , Dubon Jose M. , Koenig Ellen , Perez Eddy , Ager Arba , Jayaweera Dushyantha , Cuadrado Raul R. , Rivera Ada , Rubido Alex , Palmer Dennis A. 
Published: December 2019

ABSTRACT

Rapid detection of human immunodeficiency virus (HIV) infection can result in improved patient care and/or faster implementation of public health preventive measures. A new rapid test, Determine (Abbott, Abbott Park, Ill.), detects HIV type 1 (HIV-1) and HIV-2 antibodies within 15 min by using 50 μl of serum or plasma. No specialized equipment or ancillary supplies are required, and results are read visually. A positive result is noted by the appearance of a red line. An operational control (red line) indicates proper test performance. We evaluated the Determine rapid HIV detection test with a group of well-characterized serum samples (CD4 counts and viral loads were known) and serum samples from HIV-positive individuals at field sites in Honduras and the Dominican Republic. In the field evaluations, the results obtained by the Determine assay were compared to those obtained by local in-country HIV screening procedures. We evaluated serum from 100 HIV-positive patients and 66 HIV-negative patients. All samples gave the expected results. In a companion study, 42 HIV-positive samples from a Miami, Fla., serum bank were tested by the Determine assay. The samples had been characterized in terms of CD4 counts and viral loads. Fifteen patients had CD4 counts <200 cells/mm
3
, while 27 patients had CD4 counts >200 cells/mm
3
. Viral loads ranged from 630 to 873,746 log
10
copies/ml. All samples from the Miami serum bank were positive by the Determine test. Combined results from the multicenter studies indicated that the correct results were obtained by the Determine assay for 100% (142 of 142) of the HIV-positive serum samples and 100% (66 of 66) of the HIV-negative serum samples. The Determine test was simple to perform and the results were easy to interpret. The Determine test provides a valuable new method for the rapid identification of HIV-positive individuals, especially in developing countries with limited laboratory infrastructures.
Similar Signature of the Prion Protein in Natural Sheep Scrapie and Bovine Spongiform Encephalopathy-Linked Diseases
Authors: Baron Thierry G. M. , Madec Jean-Yves , Calavas Didier 
Published: December 2019

ABSTRACT

It has been suggested that specific molecular features could characterize the protease-resistant prion protein (PrP
res
) detected in animal species as well as in humans infected by the infectious agent strain that causes bovine spongiform encephalopathy (BSE). Studies of glycoform patterns in such diseases in French cattle and cheetahs, as well as in mice infected by isolates from both species, revealed this characteristic molecular signature. Similar studies of 42 French isolates of natural scrapie, from 21 different flocks in different regions of France, however, showed levels of the three glycoforms comparable to those found in BSE-linked diseases. Moreover, the apparent molecular size of the unglycosylated form was also indistinguishable among all different sheep isolates, as well as isolates from BSE in cattle. Overall results suggest that scrapie cases with features similar to those of BSE could be found more frequently in sheep than previously described.
Comparison of MB/BacT and BACTEC 460 TB Systems for Recovery of Mycobacteria in a Routine Diagnostic Laboratory
Authors: Roggenkamp Andreas , Hornef Mathias W. , Masch Adelheid , Aigner Bettina , Autenrieth Ingo B. , Heesemann Jürgen 
Published: December 2019

ABSTRACT

MB/BacT, BACTEC 460 TB, and Löwenstein-Jensen (LJ) medium were evaluated in parallel for recovery of mycobacteria from 3,700 continuous clinical specimens in a routine laboratory. Mycobacteria were identified from 123 (3.3%) specimens. The recovery rates for all mycobacteria by the different systems were 91.0, 73.0, and 53.6% for BACTEC 460 TB, MB/BacT, and LJ medium, respectively. The recovery rates for
Mycobacterium tuberculosis
complex were 97.1, 80.2, and 67.6%, respectively. The lack of sensitivity of the MB/BacT system was more pronounced with smear-negative specimens and resulted in a failure to detect three patients with infectious tuberculosis.
Molecular Markers Reveal Exclusively Clonal Reproduction inTrichophyton rubrum
Authors: Gräser Y. , Kühnisch J. , Presber W. 
Published: December 2019

ABSTRACTGenotypic variability among 96Trichophyton rubrumstrains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin.
Isolation of
Rickettsia prowazekii
from Blood by Shell Vial Cell Culture
Authors: Birg Marie-Laure , La Scola Bernard , Roux Véronique , Brouqui Philippe , Raoult Didier 
Published: December 2019

ABSTRACT

A blood sample from a patient who returned from Algeria with a fever inoculated on human embryonic lung fibroblasts by the shell vial cell culture technique led to the recovery of
Rickettsia prowazekii
. The last clinical strain was isolated 30 years ago. Shell vial cell culture is a versatile method that could replace the classic animal and/or embryonated egg inoculation.