bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitive Assays for Isolation and Detection of Simian Foamy Retroviruses
Authors: Khan Arifa S. , Sears Johnna F. , Muller Jacqueline , Galvin Teresa A. , Shahabuddin Muhammad 
Published: December 2019

ABSTRACT

Simian foamy viruses (SFVs) are highly prevalent in a variety of nonhuman primate species ranging from prosimians to apes. SFVs possess a broad host range, and human infections can occur by cross-species transfer (W. Heneine et al., Nat. Med. 4:403–407, 1998). Retrovirus screening of potential sources of infection, such as laboratory research animals and simian-derived biological products, could minimize human exposure to SFVs by reducing the risk of potential retrovirus infection in humans. We describe a variety of sensitive assays for SFV isolation and detection which were developed with a prototype strain of SFV serotype 2. The
Mus dunni
cell line (M. R. Lander and S. K. Chattopadhyay, J. Virol. 52:695–698, 1984) was found to be highly sensitive for SFV production on the basis of various general and specific retrovirus detection assays such as reverse transcriptase assay, transmission electron microscopy, immunofluorescence assay, and Western blotting. A highly sensitive PCR assay was developed on the basis of the sequences in primary SFV isolates obtained from pig-tailed macaques (
Macaca nemestrina
) and rhesus macaques (
Macaca mulatta
). Analysis of naturally occurring SFV infection in macaques indicated that analysis by a combination of assays, including both highly sensitive, specific assays and less sensitive, broadly reactive assays, is important for evaluation of retrovirus infection.
Rapid Slide Latex Agglutination Test for Detection of Methicillin Resistance in
Staphylococcus aureus
Authors: van Griethuysen Arjanne , Pouw Miranda , van Leeuwen Nan , Heck Max , Willemse Piet , Buiting Anton , Kluytmans Jan 
Published: December 2019

ABSTRACT

The MRSA screen test (Denka Seiken Co., Ltd.), a commercially available, rapid (20-min) slide latex agglutination test for the determination of methicillin resistance by detection of PBP 2a in
Staphylococcus aureus
, was compared with the oxacillin agar screen test and PCR detection of the
mecA
gene. A total of 563
S. aureus
isolates were tested. Two hundred ninety-six of the isolates were methicillin-susceptible isolates from cultures of blood from consecutive patients. Also, 267 methicillin-resistant isolates that comprised 248 different phage types were tested. Methicillin resistance was defined as the presence of the
mecA
gene. Of the 267
mecA
gene-positive isolates, 263 were positive by the MRSA screen test (sensitivity, 98.5%), and all the
mecA
-gene negative strains were negative by the MRSA screen test (specificity, 100%). The oxacillin agar screen test detected methicillin resistance in 250 of the
mecA
gene-positive isolates (sensitivity, 93.6%). The sensitivity of the MRSA screen test was statistically significantly higher than the sensitivity of the oxacillin agar screen test (
P
< 0.05). The MRSA screen test is a highly sensitive and specific test for the detection of methicillin resistance. Also, it offers results within half an hour and is easy to perform, which makes this test a valuable tool in the ongoing battle against methicillin-resistant
S. aureus
.
Evidence of Clonal Dissemination of Multidrug-Resistant
Streptococcus pneumoniae
in Hong Kong
Authors: Ip Margaret , Lyon Donald J. , Yung Raymond W. H. , Chan Colin , Cheng Augustine F. B. 
Published: December 2019

ABSTRACT

The relationship between the phenotypic and genotypic characteristics of 105 penicillin-intermediate or -resistant
Streptococcus pneumoniae
isolates saved during 1994 to 1997 at the Prince of Wales Hospital and Pamela Youde Nethersole Eastern Hospital, Hong Kong, was studied. The
pbp
genes for penicillin-binding proteins 1a, 2b, and 2x for each isolate were amplified by PCR, and the products were digested with restriction enzymes
Hin
fI and
Alu
I. A combination of the pulsed-field gel electrophoresis (PFGE) profiles,
pbp
fingerprints, and phenotypic characteristics of capsular types and antibiograms enabled these isolates to be divided into four major groups. Seventy-four percent (78 of 105) of the strains, belonging to serotypes 23F, 19F, and 14, showed indistinguishable
pbp
fingerprint patterns (group A1, 1-1-1, 1-1-1), with PFGE patterns belonging to group A and its subtypes, suggesting that these strains were closely related. Eighty-three percent (65 of 78) of these isolates were also resistant to tetracycline, erythromycin, chloramphenicol, and trimethoprim. The type 23F isolates were indistinguishable from representative strains of the Spanish 23F clone by these molecular methods, indicating that these strains may be variants of the Spanish 23F clone. Serotype 6B accounted for 19% (20 of 105) of the isolates with reduced penicillin susceptibility and was made up of variants belonging to four different
pbp
fingerprint groups with the PFGE pattern group B, the predominant group being indistinguishable from that of the Spanish 6B clone. Other PFGE and fingerprint groups were mainly obtained from penicillin-susceptible strains of various serotypes. The results suggest that the rapid emergence of drug-resistant
S. pneumoniae
in Hong Kong has been due to the rapid dissemination of several successful clones.
Value of a Single-Tube Widal Test in Diagnosis of Typhoid Fever in Vietnam
Authors: Parry Christopher M. , Hoa Nguyen Thi Tuyet , Diep To Song , Wain John , Chinh Nguyen Tran , Vinh Ha , Hien Tran Tinh , White Nicholas J. , Farrar Jeremy J. 
Published: December 2019

ABSTRACT

The diagnostic value of an acute-phase single-tube Widal test for suspected typhoid fever was evaluated with 2,000 Vietnamese patients admitted to an infectious disease referral hospital between 1993 and 1998. Test patients had suspected typhoid fever and a blood culture positive for
Salmonella typhi
(
n
= 1,400) or
Salmonella paratyphi
A (
n
= 45). Control patients had a febrile illness for which another cause was confirmed (malaria [
n
= 103], dengue [
n
= 76], or bacteremia due to another microorganism [
n
= 156] or tetanus (
n
= 265). An O-agglutinin titer of ≥100 was found in 18% of the febrile controls and 7% of the tetanus patients. Corresponding values for H agglutinins were 8 and 1%, respectively. The O-agglutinin titer was ≥100 in 83% of the blood culture-positive typhoid fever cases, and the H-agglutinin titer was ≥100 in 67%. The disease prevalence in investigated patients in this hospital was 30.8% (95% confidence interval, 26.8 to 35.1%); at this prevalence, an elevated level of H agglutinins gave better positive predictive values for typhoid fever than did O agglutinins. With a cutoff titer of ≥200 for O agglutinin or ≥100 for H agglutinin, the Widal test would diagnose correctly 74% of the blood culture-positive cases of typhoid fever. However, 14% of the positive results would be false-positive, and 10% of the negative results would be false-negative. The Widal test can be helpful in the laboratory diagnosis of typhoid fever in Vietnam if interpreted with care.
Molecular Characterization and Antibiotic Susceptibilities of Ocular Isolates of
Staphylococcus epidermidis
Authors: Sechi Leonardo A. , Pinna Antonio , Pusceddu Cinzia , Fadda Giovanni , Carta Francesco , Zanetti Stefania 
Published: December 2019

ABSTRACT

Nineteen isolates of
Staphylococcus epidermidis
from patients with ocular infections were analyzed. Patients were selected in retrospect, by choosing cases in which
S. epidermidis
was the sole isolate. Twelve different patterns were obtained after hybridization with a probe with high-level homology to insertion sequences found in
S. epidermidis
. Susceptibilities to penicillin, methicillin, gentamicin, tetracycline, erythromycin, ciprofloxacin, vancomycin, and teicoplanin were determined. Six strains were resistant to three or more antibiotics.
Replacement for 30-Milliliter Flat-Bottomed, Glass-Stoppered, Round Bottles Used in VDRL Antigen Preparation
Authors: Pope Victoria , Castro Arnold 
Published: December 2019

ABSTRACT
When the flat-bottomed, glass-stoppered, round bottle traditionally used to make VDRL antigen was discontinued, an appropriate substitute was needed. Although many laboratories have switched to one of the other nontreponemal tests for syphilis serology screening, the VDRL test remains the only approved procedure for testing spinal fluids of patients with possible neurosyphilis. We tested 25-ml glass-stoppered, convex-bottomed Erlenmeyer flasks to determine if these could be used as appropriate substitutes. We tested 52 reactive sera and 54 nonreactive sera by using one reference antigen prepared in the traditional flat-bottomed bottles and five antigens prepared in the Erlenmeyer flasks. Results with all serum samples were comparable. We also tested two lots of a commercial antigen plus an additional lot of reference antigen. Again there was no difference in the reactivity of the antigens. Therefore, we conclude that 25-ml glass-stoppered Erlenmeyer flasks can be used as an appropriate substitute for glass-stoppered, flat-bottomed, round glass bottles in the making of VDRL antigen.
Molecular Epidemiology of Ceftazidime-Resistant Gram-Negative Bacilli on Inanimate Surfaces and Their Role in Cross-Transmission during Nonoutbreak Periods
Authors: D’Agata Erika M. C. , Venkataraman Lata , DeGirolami Paola , Samore Matthew 
Published: December 2019

ABSTRACTWe described the molecular epidemiology of expanded-spectrum cephalosporin-resistant gram-negative bacilli (RGN) recovered from inanimate surfaces. RGN were isolated from 9% of environmental cultures. Numerous species, each with multiple unique strains, were recovered. Epidemiological links between environmental, personnel, and patient strains suggested the exogenous acquisition of RGN from the hospital environment.
Detection of
Chlamydia trachomatis
Endocervical Infections by Ligase Chain Reaction versus ACCESS
Chlamydia
Antigen Assay
Authors: Waites K. B. , Smith K. R. , Crum M. A. , Hockett R. D. , Wells A. H. , Hook E. W. 
Published: December 2019

ABSTRACT
Ligase chain reaction (LCR) was compared with ACCESS immunoassay for detection of chlamydial infections in females. Despite efforts to improve ACCESS performance by evaluation of specimens that were in the test performance “grey zone,” LCR remained more sensitive and was less expensive to perform. ACCESS had a sensitivity of 83.9%, a specificity of 99.7%, a positive predictive value of 96.3%, and a negative predictive value of 98.5%.
Characterization ofStaphylococcus aureusCoagulase Type VII Isolates from Staphylococcal Food Poisoning Outbreaks (1980–1995) in Tokyo, Japan, by Pulsed-Field Gel Electrophoresis
Authors: Shimizu Akira , Fujita Manabu , Igarashi Hideo , Takagi Michihiro , Nagase Naoko , Sasaki Asako , Kawano Junichi 
Published: December 2019

ABSTRACTStaphylococcus aureuscoagulase type VII strains have been the strains most frequently isolated from staphylococcal food poisoning outbreaks in Tokyo, Japan. We applied pulsed-field gel electrophoresis (PFGE) of chromosomal DNA digested withSmaI to characterize 129 coagulase type VII strains. These were isolated from 129 cases occurring in outbreaks in 35 districts during a 16-year period (1980–1995). The 129 outbreak strains were classified into three types, designated A (n= 115), B (n= 10), and C (n= 4). Types A and C were further divided into 33 (A1 to A33) and 4 (C1 to C4) subtypes, respectively. Strains of the same subtypes were isolated from food poisoning cases in the same districts at time intervals of 1 or 2 to 5 years. PFGE typing appears to be a useful method for subdividing strains ofS. aureuscoagulase type VII. A combination of coagulase typing and PFGE typing would provide more detailed information than the former method alone in epidemiologic investigations of staphylococcal food poisoning.
Prevalence of O1/K1- and O2/K3-Reactive
Actinobacillus suis
in Healthy and Diseased Swine
Authors: Slavić ĐurĐa , Toffner Tania L. , Monteiro Mario A. , Perry Malcolm B. , MacInnes Janet I. 
Published: December 2019

ABSTRACT

A cell surface antigen-typing system was devised for the swine pathogen
Actinobacillus suis
and used to examine the prevalence of different lipopolysaccharide (O) types in healthy and diseased pigs. The strains examined in this study were isolated from a variety of locations in Canada and from Kansas. Lipopolysaccharide preparations of 151 isolates of
A. suis
were characterized by immunoblotting using polyclonal antisera generated to strains SO4 (O1/K1), H89-1173 (O2/K3), and VSB 3714, a rough strain. Approximately 54% (62 of 114) of
A. suis
isolates from diseased pigs, all (11 of 11) isolates from healthy pigs, and all (4 of 4) reference strains reacted with O1/K1 antiserum. More than 80% (18 of 22) of
A. suis
strains used for bacterin production and approximately 41% (47 of 114) of isolates from diseased pigs bound O2/K3 antiserum. One isolate appeared to be rough, and five were untypeable. O1/K1- and O2/K3-reactive strains were equally prevalent in Kansas, whereas O2/K3-reactive strains were more common in Québec and western Canada and O1/K1 strains were most common in Ontario. The fact that virtually all of the strains submitted for bacterin production were O2/K3-reactive strains is consistent with the notion that these strains may be more virulent than O1/K1 strains; alternatively, this may reflect geographic or other biases. In addition, we observed cross-reactivity between
A. suis
cell surface antigens and swine antisera to several other important pathogens. This finding may explain why previous attempts to develop a simple serodiagnostic test for
A. suis
have been unsuccessful.
Evaluation of Phenotypic and Genotypic Methods for SubtypingCampylobacter jejuniIsolates from Humans, Poultry, and Cattle
Authors: Nielsen Eva Møller , Engberg Jørgen , Fussing Vivian , Petersen Lise , Brogren Carl-Henrik , On Stephen L. W. 
Published: December 2019

ABSTRACTSix methods for subtyping ofCampylobacter jejuniwere compared and evaluated with a collection of 90 isolates from poultry, cattle, and sporadic human clinical cases as well as from a waterborne outbreak. The applied methods were Penner heat-stable serotyping; automated ribotyping (RiboPrinting); random amplified polymorphic DNA typing (RAPD); pulsed-field gel electrophoresis (PFGE); restriction fragment length polymorphisms of the flagellin gene,flaA(fla-RFLP); and denaturing gradient gel electrophoresis offlaA(fla-DGGE). The methods were evaluated and compared on the basis of their abilities to identify isolates from one outbreak and discriminate between unrelated isolates and the agreement between methods in identifying clonal lines. All methods identified the outbreak strain. For a collection of 80 supposedly unrelated isolates, RAPD and PFGE were the most discriminatory methods, followed byfla-RFLP and RiboPrinting.fla-DGGE and serotyping were the least discriminative. All isolates included in this study were found to be typeable by each of the methods. Thirteen groups of potentially related isolates could be identified using a criterion that at least four of the methods agreed on clustering of isolates. None of the subtypes could be related to only one source; rather, these groups represented isolates from different sources. Furthermore, in two cases isolates from cattle and human patients were found to be identical according to all six methods.
Detection and Quantitation of Human Immunodeficiency Virus Type 1 in the Female Genital Tract
Authors: Baron Penny , Bremer James , Wasserman Steven S. , Nowicki Marek , Driscoll Barbara , Polsky Bruce , Kovacs Andrea , Reichelderfer Patricia S. 
Published: December 2019

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) was detected in the genital tracts of 59% of 225 women by RNA PCR and in 7% of the women by culture. In a comparison of two sampling methods, endocervical swabs were more sensitive than cervicovaginal lavage for HIV-1 RNA detection by PCR but not by culture and their sensitivity was independent of the concentration of HIV-1 RNA.
Performance of Five Agar Media for Recovery of Fungi from Isolator Blood Cultures
Authors: Procop G. W. , Cockerill F. R. , Vetter E. A. , Harmsen W. S. , Hughes J. G. , Roberts G. D. 
Published: December 2019

ABSTRACT

We studied the recovery of 1,270 fungal isolates from 176,144 Isolator blood cultures (0.72% positive) on bacterial and fungal media, under routine and differing incubation conditions. Except with
Histoplasma capsulatum
, chocolate agar incubated for only 3 days proved to be an excellent medium for the recovery of fungi from the Isolator system.
Evaluation of Different Preservation and Storage Methods forMalasseziaspp
Authors: Crespo M. J. , Abarca M. L. , Cabañes F. J. 
Published: December 2019

ABSTRACTFreezing at −80°C, lyophilization, preservation in distilled water, and storage in different culture media were performed in order to find a suitable method that allowed a prolonged storage ofMalasseziaspp. Freezing at −80°C was the only method successful at maintaining all species.
VP4 and VP7 Genotyping by Reverse Transcription-PCR of Human Rotavirus in Mexican Children with Acute Diarrhea
Authors: Rodríguez Castillo Araceli , Villa Andrés Velasco , Ramírez González JoséErnesto , Mayén Pimentel Elvira , Melo Munguía Martín , Díaz de Jesús Benita , Olivera Díaz Hiram , García Lozano Herlinda 
Published: December 2019

ABSTRACT
Dual typing (VP4 and VP7) of rotavirus obtained from 257 Mexican children during three epidemiological seasons was performed by reverse transcription-PCR. The P1G1 genotype was the most prevalent (40%), followed by P1G3 (19%) and P2G2 (16%). Thirty-one specimens (12%) presented mixed infections, while some genotypes were not found. This is the first dual typing of isolates from diarrhea cases in Mexico.
Granulomatous Amebic Encephalitis in a Patient with AIDS: Isolation of
Acanthamoeba
sp. Group II from Brain Tissue and Successful Treatment with Sulfadiazine and Fluconazole
Authors: Seijo Martinez M. , Gonzalez-Mediero G. , Santiago P. , Rodriguez de Lope A. , Diz J. , Conde C. , Visvesvara G. S. 
Published: December 2019

ABSTRACT

A patient with AIDS, treated with highly active antiretroviral therapy and trimethoprim-sulfamethoxazole, presented with confusion, a hemifield defect, and a mass lesion in the right occipital lobe. A brain biopsy confirmed granulomatous amebic encephalitis (GAE) due to
Acanthamoeba castellanii
. The patient was treated with fluconazole and sulfadiazine, and the lesion was surgically excised. This is the first case of AIDS-associated GAE responding favorably to therapy. The existence of a solitary brain lesion, absence of other sites of infection, and intense cellular response in spite of a very low CD4 count conditioned the favorable outcome. We review and discuss the diagnostic microbiologic options for the laboratory diagnosis of infections due to free-living amebae.
Recognition of Two Novel Phenons of the Genus
Acinetobacter
among Non-Glucose-Acidifying Isolates from Human Specimens
Authors: Nemec Alexandr , Dijkshoorn Lenie , Ježek Petr 
Published: December 2019

ABSTRACT

Genomic species diversity among 147
Acinetobacter
clinical isolates not belonging to the
A. calcoaceticus- A. baumannii
(ACB) complex was investigated by phenotypic and genotypic identification methods. The isolates were obtained between 1991 and 1999 from numerous diagnostic laboratories in the Czech Republic and were studied by numerical probabilistic identification using two biochemical frequency matrices and amplified rDNA restriction analysis (ARDRA). Their final identification was derived from the combined phenotypic and ARDRA results. In total, 102 isolates were unambiguously (
n
= 89) or presumptively (
n
= 13) identified as
A. lwoffii
(
n
= 63), genomic species 13BJ/14TU (
n
= 9),
A. johnsonii
(
n
= 7),
A. haemolyticus
(
n
= 6),
A. junii
(
n
= 5), and other genomic species (
n
< 5 isolates each). Forty-five isolates could not be identified as belonging to any described species. Among the unidentified isolates two large groups of non-glucose-acidifying, nonhemolytic, and non-gelatinase-producing isolates were distinguished. These groups, designated phenon 1 (
n
= 17) and phenon 2 (
n
= 15), had distinctive phenotypic features and novel ARDRA profiles, which suggests that they represent hitherto undescribed
Acinetobacter
species. Phenon 2 included mainly clinically insignificant isolates from outpatients, while phenon 1 comprised clinically relevant isolates mostly from the blood of hospitalized patients, and its precise taxonomic definition may therefore be of medical importance. Overall, the development of practical methods for identification required for the elucidation of the biological significance of the (genomic) species within the genus
Acinetobacter
remains a challenging task.
Outbreak of
Bacillus cereus
Infections in a Neonatal Intensive Care Unit Traced to Balloons Used in Manual Ventilation
Authors: Van Der Zwet Wil C. , Parlevliet Gerard A. , Savelkoul Paul H. , Stoof Jeroen , Kaiser Annie M. , Van Furth A. Marceline , Vandenbroucke-Grauls Christina M. 
Published: December 2019

ABSTRACT

In 1998, an outbreak of systemic infections caused by
Bacillus cereus
occurred in the Neonatal Intensive Care Unit of the University Hospital Vrije Universiteit, Amsterdam, The Netherlands. Three neonates developed sepsis with positive blood cultures. One neonate died, and the other two neonates recovered. An environmental survey, a prospective surveillance study of neonates, and a case control study were performed, in combination with molecular typing, in order to identify potential sources and transmission routes of infection. Genotypic fingerprinting by amplified-fragment length polymorphism (AFLP) showed that the three infections were caused by a single clonal type of
B. cereus
. The same strain was found in trachea aspirate specimens of 35 other neonates. The case control study showed mechanical ventilation with a Sensormedics ventilation machine to be a risk factor for colonization and/or infection (odds ratio, 9.8; 95% confidence interval, 1.1 to 88.2). Prospective surveillance showed that colonization with
B. cereus
occurred exclusively in the respiratory tract of mechanically ventilated neonates. The epidemic strain of
B. cereus
was found on the hands of nursing staff and in balloons used for manual ventilation. Sterilization of these balloons ended the outbreak. We conclude that
B. cereus
can cause outbreaks of severe opportunistic infection in neonates. Typing by AFLP proved very useful in the identification of the outbreak and in the analysis of strains recovered from the environment to trace the cause of the epidemic.