bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology of Astrovirus Infection in Young Children Hospitalized with Acute Gastroenteritis in Melbourne, Australia, over a Period of Four Consecutive Years, 1995 to 1998
Authors: Mustafa Huseyin , Palombo Enzo A. , Bishop Ruth F. 
Published: December 2019

ABSTRACT
The incidence of astrovirus infection in children less than 5 years of age hospitalized with acute gastroenteritis in Melbourne, Australia, from 1995 to 1998 was determined. Astrovirus was detected in 40 of 449 specimens tested by Northern hybridization, and astrovirus infection was confirmed by reverse transcription-PCR with or without culture in CaCO-2 cells. This represented 3.0% (40 of 1,327) of all children tested for enteric pathogens, including viral, bacterial, and parasitic pathogens, over the survey period. The incidences of astrovirus infection in each year were 4.4% (1995), 2.2% (1996), 3.9% (1997), and 1.4% (1998). In 1995 and 1997, the incidences of astrovirus infection were greater than the incidence of infection with all individual bacterial pathogens and were either greater than or equal to the incidence of adenovirus infection. Astrovirus exhibited an unusual biennial winter peak of incidence that correlated with a greater incidence of serotype 1 virus and an increased rate of hospitalization of children aged 6 to 12 months. Uncommon (serotype 2 and 4) and rare (serotype 8) serotypes were detected during the survey period. Genetic analysis of ORF2 (which encodes the astrovirus capsid precursor) of Melbourne isolates showed nucleotide sequence variation from year to year. This was not accompanied by significant amino acid substitutions. However, geographical variation was apparent by comparison of Melbourne astrovirus isolates with prototype strains identified in the United Kingdom.
Novel Diagnostic Algorithm for Identification of Mycobacteria Using Genus-Specific Amplification of the 16S-23S rRNA Gene Spacer and Restriction Endonucleases
Authors: Roth Andreas , Reischl Udo , Streubel Anna , Naumann Ludmila , Kroppenstedt Reiner M. , Habicht Marion , Fischer Marga , Mauch Harald 
Published: December 2019

ABSTRACT

A novel genus-specific PCR for mycobacteria with simple identification to the species level by restriction fragment length polymorphism (RFLP) was established using the 16S-23S ribosomal RNA gene (rDNA) spacer as a target. Panspecificity of primers was demonstrated on the genus level by testing 811 bacterial strains (122 species in 37 genera from 286 reference strains and 525 clinical isolates). All mycobacterial isolates (678 strains among 48 defined species and 5 indeterminate taxons) were amplified by the new primers. Among nonmycobacterial isolates, only
Gordonia terrae
was amplified. The RFLP scheme devised involves estimation of variable PCR product sizes together with
Hae
III and
Cfo
I restriction analysis. It yielded 58
Hae
III patterns, of which 49 (84%) were unique on the species level. Hence,
Hae
III digestion together with
Cfo
I results was sufficient for correct identification of 39 of 54 mycobacterial taxons and one of three or four of seven RFLP genotypes found in
Mycobacterium intracellulare
and
Mycobacterium kansasii
, respectively. Following a clearly laid out diagnostic algorithm, the remaining unidentified organisms fell into five clusters of closely related species (i.e., the
Mycobacterium avium
complex or
Mycobacterium chelonae-Mycobacterium abscessus
) that were successfully separated using additional enzymes (
Taq
I,
Msp
I,
Dde
I, or
Ava
II). Thus, next to slowly growing mycobacteria, all rapidly growing species studied, including
M. abscessus
,
M. chelonae
,
Mycobacterium farcinogenes
,
Mycobacterium fortuitum
,
Mycobacterium peregrinum
, and
Mycobacterium senegalense
(with a very high 16S rDNA sequence similarity) were correctly identified. A high intraspecies sequence stability and the good discriminative power of patterns indicate that this method is very suitable for rapid and cost-effective identification of a wide variety of mycobacterial species without the need for sequencing. Phylogenetically, spacer sequence data stand in good agreement with 16S rDNA sequencing results, as was shown by including strains with unsettled taxonomy. Since this approach recognized significant subspecific genotypes while identification of a broad spectrum of mycobacteria rested on identification of one specific RFLP pattern within a species, this method can be used by both reference (or research) and routine laboratories.
Efficacy of Antimicrobial Treatments and Vaccination Regimens for Control of Porcine Reproductive and Respiratory Syndrome Virus and
Streptococcus suis
Coinfection of Nursery Pigs
Authors: Halbur P. , Thanawongnuwech R. , Brown G. , Kinyon J. , Roth J. , Thacker E. , Thacker B. 
Published: December 2019

ABSTRACT

Seventy-six, crossbred, porcine reproductive and respiratory syndrome virus (PRRSV)-free pigs were weaned at 12 days of age and randomly assigned to seven groups of 10 to 11 pigs each. Pigs in group 1 served as unchallenged controls. Pigs in groups 2 to 7 were challenged intranasally with 2 ml of high-virulence PRRSV isolate VR-2385 (10
4.47
50% tissue culture infective doses per 2 ml) on day 0 of the study (30 days of age). Seven days after PRRSV challenge, pigs in groups 2 to 7 were challenged intranasally with 2 ml of
Streptococcus suis
serotype 2 (10
8.30
CFU/2 ml). Group 2 pigs served as untreated positive controls. Antimicrobial treatments included daily intramuscular injection with 66,000 IU of procaine penicillin G per kg of body weight on days 8 to 10 (group 3), drinking water medication with 23.1 mg of tiamulin per kg during days 8 to 10 (group 4), and daily intramuscular injection of 5.0 mg of ceftiofur hydrochloride per kg on days 8 to 10 (group 5). Vaccination regimens included two intramuscular doses of an autogenous killed
S. suis
vaccine (group 6) prior to
S. suis
challenge or a single 2-ml intramuscular dose of an attenuated live PRRSV vaccine (group 7) 2 weeks prior to PRRSV challenge. Mortality was 0, 63, 45, 54, 9, 40, and 81% in groups 1 to 7, respectively. Ceftiofur treatment was the only regimen that significantly (
P
< 0.05) reduced mortality associated with PRRSV and
S. suis
coinfection. The other treatments and vaccinations were less effective. We conclude that ceftiofur administered by injection for three consecutive days following
S. suis
challenge was the most effective regimen for minimizing disease associated with PRRSV and
S. suis
coinfection.
Molecular Characterization of
Cryptosporidium
Isolates Obtained from Human Immunodeficiency Virus-Infected Individuals Living in Switzerland, Kenya, and the United States
Authors: Morgan Una , Weber Rainer , Xiao Lihua , Sulaiman Irshad , Thompson R. C. Andrew , Ndiritu Wangeci , Lal Altaf , Moore Anne , Deplazes Peter 
Published: December 2019

ABSTRACT

A total of 22
Cryptosporidium
isolates from human immunodeficiency virus-infected patients from Kenya, Switzerland, and the United States were examined at three genetic loci: the 18S ribosomal DNA, HSP-70, and acetyl coenzyme A synthetase genes. Four distinct
Cryptosporidium
genotypes were identified: (i) the
Cryptosporidium parvum
“human” genotype, (ii) the
C. parvum
“cattle” genotype, (iii)
Cryptosporidium felis
, and (iv)
Cryptosporidium meleagridis
. This is the first report of
C. meleagridis
in a human host. These results and those of others indicate that immunocompromised individuals are susceptible to a wide range of
Cryptosporidium
species and genotypes. Future studies are required to understand the full public health significance of
Cryptosporidium
genotypes and species in immunocompromised hosts.
Novel Screening Method for Urine Cultures Using a Filter Paper Dilution System
Authors: Kunin Calvin M. , Buesching William J. 
Published: December 2019

ABSTRACT

We have developed a novel method for urine culture for office practice based on the use of filter paper as a solid-phase dilution device. Filtration dilutes and spreads the inoculum onto a solid culture surface. Experiments were conducted to determine the optimum inoculum size, microbial permeability through filter papers, and ability to exclude vaginal epithelial cells. The filter paper dilution system was compared to the standard streak method to detect bacteriuria in specimens submitted to the diagnostic laboratory. The sensitivity and specificity of the filter paper dilution system for detection of high-count (≥10
4
CFU/ml) gram-negative bacteriuria in 487 urine specimens were 98.2 and 97.4%, respectively. The sensitivity and specificity for gram-positive bacteriuria in 404 urine specimens were 91.2 and 99.2%, respectively. Low-count gram-negative bacteriuria (<10
4
CFU/ml) was detected by the filter paper dilution system in five of nine specimens (55.6%). In addition, the filter paper dilution system was able to detect gram-negative bacteria in 12 of 41 (29.3%) mixed cultures.
Lactobacillus
and
Gardnerella
organisms in urine specimens were excluded by the filter paper dilution system. Only three of eight
Candida
sp. isolates were detected at counts of ≥10
4
CFU/ml. The system has good storage properties and can be inoculated at the point of source without the need for refrigeration or preservatives. It should be a useful screening method for office practice, where members of the family
Enterobacteriaceae
and staphylococci cause most infections. Standard culture methods are preferred for hospital diagnostic microbiology laboratories, where there is a need to detect yeasts and fastidious microorganisms and to isolate individual colonies from mixed cultures.
Otitis Externa Associated with
Malassezia sympodialis
in Two Cats
Authors: Crespo M. J. , Abarca M. L. , Cabañes F. J. 
Published: December 2019

ABSTRACT

The lipid-dependent species
Malassezia sympodialis
was isolated from two cats with otitis externa. To our knowledge, this is the first report of the isolation of lipid-dependent species of the genus
Malassezia
associated with skin disease in domestic animals.
Outbreak of Infections Caused by
Pseudomonas aeruginosa
Producing VIM-1 Carbapenemase in Greece
Authors: Tsakris Athanassios , Pournaras Spyros , Woodford Neil , Palepou Marie-France I. , Babini Gioia S. , Douboyas John , Livermore David M. 
Published: December 2019

ABSTRACT

Resistance to imipenem and meropenem was observed in 211 (16.5%) isolates of
Pseudomonas aeruginosa
recovered in a Greek university hospital during 1996 to 1998. In six isolates selected from throughout this period, high-level resistance to both carbapenems (MICs ≥ 128 μg/ml) was associated with production of the class B β-lactamase VIM-1.
bla
VIM
-bearing isolates belonged to serotype O:12 and were indistinguishable by pulsed-field gel electrophoresis.
Serological and Virological Characterization of Clinically Diagnosed Cases of Measles in Suburban Khartoum
Authors: Mubarak H. Sittana El , Van De Bildt Marco W. G. , Mustafa Omer A. , Vos Helma W. , Mukhtar Maowia M. , Groen Jan , Hassan Ahmed M. El , Niesters Hubert G. M. , Ibrahim Salah A. , Zijlstra Edward E. , Wild T. Fabian , Osterhaus Albert D. M. E. , De Swart Rik L. 
Published: December 2019

ABSTRACT
Measles continues to be a major childhood disease in terms of global morbidity and mortality. In the main areas of its endemicity the only available means of diagnosis are based on clinical criteria: the presence of a maculopapular rash and fever accompanied by cough, coryza, and/or conjunctivitis. We have studied 38 clinically diagnosed cases of measles in Khartoum, Sudan, by means of serology, reverse transcriptase PCR (RT-PCR) on throat swabs and virus isolation from lymphocytes. On the basis of serology, 28 patients were diagnosed as having an acute measles virus (MV) infection, while in 10 cases the clinical symptoms proved to have other causes. It was shown that in cases with low serum immunoglobulin M (IgM) levels, an additional measurement of IgG or virus-neutralizing antibodies was necessary to discriminate between patients with an acute MV infection sampled during an early stage of the disease and patients who had experienced an MV infection in the more distant past. The serological laboratory diagnosis was validated by an MV-specific RT-PCR: for all confirmed measles cases tested a fragment of the correct size which hybridized with a third MV-specific primer could be amplified, while all serologically negative cases were also RT-PCR negative. MV could be isolated from 17 out of 23 of the serologically confirmed cases, demonstrating that virus isolation is less reliable as a diagnostic tool than serology or RT-PCR. This study stresses the urgent need for a rapid diagnostic field test for measles.
Emergence of Drug Resistance Mutations in Human Immunodeficiency Virus Type 2-Infected Subjects Undergoing Antiretroviral Therapy
Authors: Rodés Berta , Holguín Africa , Soriano Vincent , Dourana Manuela , Mansinho Kamal , Antunes Francisco , González-Lahoz Juan 
Published: December 2019

ABSTRACT
The reverse transcriptase (RT) and protease genes from 12 human immunodeficiency virus type 2 (HIV-2)-infected individuals who had been exposed to antiretroviral drugs for longer than 6 months were examined for the presence of mutations which could be involved in drug resistance. Four individuals carried virus genotypes with amino acid substitutions potentially associated with resistance to nucleoside analogues: two at codon 70 (K→R) and two at codon 184 (M→V). Moreover, the latter two patients harbored a codon Q151M mutation which is associated to multidrug resistance in HIV-1, and one of these subjects carried some of the typically linked mutations at codons 65 and 69. With regard to the protease inhibitors, substitutions associated with resistance to protease inhibitors at codon 46 were observed in all individuals. Moreover, minor resistance mutations, as well as new ones of unknown meaning, were often seen in the protease gene. In conclusion, amino acid changes in the HIV-2 RT and protease genes which could be associated with drug resistance seem to occur at positions identical to those for HIV-1.
Antipneumococcal Activity of Telithromycin by Agar Dilution, Microdilution, E Test, and Disk Diffusion Methodologies
Authors: Davies Todd A. , Kelly Linda M. , Jacobs Michael R. , Appelbaum Peter C. 
Published: December 2019

ABSTRACT

Agar dilution and microdilution (both in air) and E test and disk diffusion (both in air and CO
2
) were used to test the activity of telithromycin against 110 erythromycin-susceptible and 106 erythromycin-resistant pneumococci. The MICs at which 50 and 90% of strains are inhibited (MIC
50
s and MIC
90
s, respectively) for erythromycin-susceptible strains varied between 0.008 and 0.016 μg/ml and 0.016 and 0.03 μg/ml when the samples were incubated in air. By comparison, telithromycin MIC
50
s and MIC
90
s for erythromycin-resistant strains were in air 0.03 to 0.125 and 0.125 to 0.5 μg/ml, respectively. When agar dilution was used as the reference method, essential agreement was found for 112 of 216 strains (51.9%) for microdilution, 168 of 216 (77.8%) for E test in air, and 132 of 216 (61.1%) for E test in CO
2
. With the exception of four strains tested by E test in CO
2
, all organisms were susceptible to a proposed telithromycin susceptibility breakpoint of ≤1 μg/ml. By disk diffusion with 15-μg telithromycin disks, all strains but one had zones of inhibition ≥19 mm in diameter when incubated in CO
2
, while all strains had zone diameters of ≥22 mm when incubated in air. Zone diameters in air were generally 4 to 5 mm larger than in CO
2
. By all methods, MICs and zones of all erythromycin-resistant strains occurred in clusters separated from those seen with erythromycin-susceptible strains. The results for macrolide-resistant strains with
erm
and
mef
resistance determinants were similar. The results show that (i) telithromycin is very active against erythromycin-susceptible and -resistant strains irrespective of macrolide resistance mechanism; (ii) susceptibility to telithromycin can be reliably tested by the agar, microdilution, E test, and disk diffusion methods; and (iii) incubation in CO
2
led to smaller zones by disk diffusion and higher MICs by E test, but at a susceptible MIC breakpoint of ≤1 μg/ml and a susceptible zone diameter cutoff of ≥19 mm in CO
2
, 215 of 216 strains were found to be susceptible to telithromycin.
Fractionation of Membrane Components from Tachyzoite Forms ofToxoplasma gondii: Differential Recognition by Immunoglobulin M (IgM) and IgG Present in Sera from Patients with Acute or Chronic Toxoplasmosis
Authors: Giraldo Mónica , Cannizzaro Hélia , Ferguson Michael A. J. , Almeida Igor C. , Gazzinelli Ricardo T. 
Published: December 2019

ABSTRACTTachyzoite forms ofToxoplasma gondiiwere subjected to a sequential organic solvent extraction, which allows fractionation of membrane components according to their degrees of hydrophobicity, yielding three fractions named F1 (most hydrophobic) to F3 (least hydrophobic). Fractions F2 (80.85% specificity and 86.95% sensitivity) and F3 (89.36% specificity and 93.61% sensitivity) gave the best results, being preferentially recognized by immunoglobulin M (IgM) and IgG in sera from patients with acute and chronic toxoplasmosis, respectively. Improved scores of specificity (100%) and sensitivity (100%) were achieved when a secondary antibody against human IgG1 instead of total IgG was employed to measure the reactivity of IgG antibodies with the F3 fraction. To purify tachyzoite antigens recognized by human IgM or IgG antibodies, the F2 or F3 fraction was loaded onto an octyl-Sepharose column and eluted with a propan-1-ol gradient. The main antigen(s) recognized by IgM or IgG eluted in a single peak from the octyl-Sepharose resin loaded with either F2 (30 to 50% propan-1-ol) or F3 (15 to 35% propan-1-ol), respectively. These semipurified fractions gave improved scores when used to detectT. gondii-specific IgM (95.7% specificity and 81.8% sensitivity) or IgG (100% specificity and 93.75% sensitivity) in an enzyme-linked immunosorbent assay. Further biochemical and immunological analyses of antigens partially purified from F2 and F3 indicate that glycoinositolphospholipids are preferentially recognized by IgM, whereas proteins of approximately 30 to 40 kDa are recognized by IgG, elicited duringT. gondiiinfection in humans.
Evaluation of Diagnostic Value and Epidemiological Implications of PCR for
Pneumocystis carinii
in Different Immunosuppressed and Immunocompetent Patient Groups
Authors: Sing Andreas , Trebesius Karlheinz , Roggenkamp Andreas , Rüssmann Holger , Tybus Karin , Pfaff Friederike , Bogner Johannes R. , Emminger Christoph , Heesemann Jürgen 
Published: December 2019

ABSTRACT

To evaluate the value of single and nested PCRs for diagnosis of
Pneumocystis carinii
pneumonia (PCP) in a variety of respiratorily distressed patient groups, 574 respiratory samples from 334 patients (89 human immunodeficiency virus [HIV]-positive patients, 61 transplant recipients, 66 malignancy patients, 34 otherwise immunosuppressed patients, and 84 immunocompetent patients) were prospectively examined by microscopy and single and nested PCRs. The resulting data were correlated with clinical evidence of PCP. Microscopy and single PCR of bronchoalveolar lavage (BAL) specimens from HIV patients were 100% sensitive and specific in detecting PCP, whereas nested PCR, although being 100% sensitive, reached a specificity of only 97.5%. In the three non-HIV immunosuppressed patient groups, both single and nested PCR invariably produced lower positive predictive values than microscopy. Among immunocompetent patients, the positive predictive values of both PCRs were 0%. Therefore, the diagnostic values of the PCR methods tested do not seem to offer any additional advantage compared to that of conventional microscopy for these patient groups. However, nested PCR identified a significant percentage of clinically silent
P. carinii
colonizations in about 17 to 20% of immunocompetent and immunosuppressed non-HIV patients.
Identification of
Campylobacter jejuni
,
C. coli
,
C. lari
,
C. upsaliensis
,
Arcobacter butzleri
, and
A. butzleri
-Like Species Based on the
glyA
Gene
Authors: Al Rashid Shahnaz Tahihra , Dakuna Irene , Louie Helena , Ng David , Vandamme Peter , Johnson Wendy , Chan Voon Loong 
Published: December 2019

ABSTRACT

Currently, the detection and identification of
Campylobacter
and
Arcobacter
species remains arduous, largely due to cross-species phenotypic similarities and a relatively narrow spectrum of biochemical reactivity. We have developed a PCR-hybridization strategy, wherein degenerate primers are used to amplify
glyA
fragments from samples, which are then subjected to species-specific oligodeoxyribonucleotide probe hybridizations, to identify and distinguish between
Campylobacter jejuni
,
C. coli
,
C. lari
,
C. upsaliensis
,
Arcobacter butzleri
, and an
A. butzleri
-like species. Evaluation of this strategy with genomic DNA from different type strains suggests that this approach is both specific and sensitive and thus may be applicable in a diagnostic assay to identify and differentiate these highly related species.
Evaluation of Ciprofloxacin as a Representative of Veterinary Fluoroquinolones in Susceptibility Testing
Authors: Riddle Christa , Lemons Carol L. , Papich Mark G. , Altier Craig 
Published: December 2019

ABSTRACT
Currently in veterinary medicine, ciprofloxacin is often used in susceptibility testing to represent the entire class of fluoroquinolone antimicrobials. Using quality control organisms as well as clinical isolates, we compared the MIC of ciprofloxacin to those of three other fluoroquinolones used in animals and found that ciprofloxacin is not an adequate representative of other members of this class.
Restriction Fragment Length Polymorphism Analysis Using Random Chromosomal Gene Probes for Epidemiological Analysis of
Campylobacter jejuni
Infections
Authors: Fujimoto Shuji , Umene Kenichi , Saito Mitsumasa , Horikawa Kazumi , Blaser Martin J. 
Published: December 2019

ABSTRACT

We have evaluated the ability of a new genotyping method for
Campylobacter jejuni
based on restriction fragment length polymorphisms using random chromosomal gene probes. DNAs from
C. jejuni
strains digested with each of three restriction enzymes,
Hha
I,
Hae
III, and
Hpa
II, were analyzed by Southern hybridization using each of two unrelated cosmid clones, P14 and P15 (respectively containing 30- and 35-kb genomic DNA fragments of
C. jejuni
strain OH4384). The method reported provides a stable and discriminating means for identifying
C. jejuni
strains and should be useful for epidemiological analyses.
Evaluation of a New Commercially Available Immunoglobulin M and Immunoglobulin G Immunochromatographic Test for Diagnosis of Melioidosis Infection
Authors: Cuzzubbo Andrea J. , Chenthamarakshan V. , Vadivelu Jamuna , Puthucheary Savithiri D. , Rowland Denise , Devine Peter L. 
Published: December 2019

ABSTRACT

An immunochromatographic test for the rapid determination of immunoglobulin M (IgM) and IgG antibodies to
Burkholderia pseudomallei
was evaluated by using sera from bacteriologically confirmed melioidosis patients and high-risk and clinically suspected patients, along with disease control groups. The sensitivities were 100 and 93% for the IgG and IgM tests, respectively, while the specificity was 95% for both assays. The test was rapid and simple to perform, with results obtained in 10 min.
Pooling of Urine Specimens for Detection of Asymptomatic
Chlamydia trachomatis
Infections by PCR in a Low-Prevalence Population: Cost-Saving Strategy for Epidemiological Studies and Screening Programs
Authors: Morré Servaas A. , Meijer Chris J. L. M. , Munk Christian , Krüger-Kjaer Susanne , Winther Jeanette F. , Jørgensens Hans O. , van den Brule Adriaan J. C. 
Published: December 2019

ABSTRACT
Pooling, in groups of five, of urine specimens from asymptomatically infected men in a population with 4% prevalence, as determined by case finding, is 100% sensitive and specific and results in a 60.5% reduction in the number of tests needed. Pooling of urine specimens in groups of 10 for the estimation of population-based prevalence is 96.1% sensitive and 100% specific and saves 90% of the test costs.