bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence and serovar distribution of asymptomatic cervical Chlamydia trachomatis infections as determined by highly sensitive PCR
Authors: Lan J , Melgers I , Meijer C J , Walboomers J M , Roosendaal R , Burger C , Bleker O P , van den Brule A J
Published: January 2020

The prevalence rates and serovar distributions of Chlamydia trachomatis cervical infections were investigated in two different groups of women. Group I consisted of 393 asymptomatic young women (aged 17 to 30 years) who were invited to participate in a C. trachomatis screening program. Group II consisted of 734 randomly selected patients (aged 17 to 68 years) attending an inner-city gynecological outpatient clinic. C. trachomatis was detected in cervical scrapes by PCR specific for endogenous plasmid. These plasmid PCR-positive samples were subsequently subjected to genotyping by C. trachomatis-specific omp1 PCR-based restriction fragment length polymorphism analysis (J. Lan, J. M. M. Walboomers, R. Roosendaal, G. J. van Doornum, D. M. MacLaren, C. J. L. M. Meijer, and A. J. C. van den Brule, J. Clin. Microbiol. 31:1060-1065, 1993). The overall prevalence rates of C. trachomatis found in patients younger than 30 years were 9.2 and 11.8% in groups I and II, respectively. A clear age dependency was seen in group II, with the highest prevalence rate (20%) found in patients younger than 20 years, while the rate declined significantly after 30 years of age (5.9%). In women younger than 30 years, the genotyping results showed that serovars E, I, and D (in decreasing order) were frequent in group I, while serovars F, E, and G (in decreasing order) were predominantly found in group II. The study shows that C. trachomatis infections are highly prevalent in asymptomatic young women. The different serovar distributions found most likely reflect the different compositions of the study groups, but additional analysis of the case histories of individual patients suggests that certain serovars might be associated with symptomatic (i.e., serovar G) or asymptomatic (i.e., serovars D and I) infections.
Enhanced recovery of Haemophilus ducreyi from clinical specimens by incubation at 33 versus 35 degrees C
Authors: Schmid G P , Faur Y C , Valu J A , Sikandar S A , McLaughlin M M
Published: January 2020

Isolation rates of Haemophilus ducreyi from cases of chancroid are low. Experts recommend that isolation media be incubated at 33 to 35 degrees C, but the possible effect of this temperature range on the recovery of H. ducreyi has not been evaluated. We inoculated two sets of agar plates with material from genital ulcers and incubated one set at 33 degrees C and one at 35 degrees C; incubation at 33 degrees C identified 21% more cases than did incubation at 35 degrees C (109 versus 85 cases, respectively, of the 116 cases from which an isolation was made; P < 0.01).
Isolation of coronaviruses antigenically indistinguishable from bovine coronavirus from wild ruminants with diarrhea
Authors: Tsunemitsu H , el-Kanawati Z R , Smith D R , Reed H H , Saif L J
Published: January 2020

Diarrheal feces from three sambar deer and one waterbuck in a wild animal habitat and one white-tailed deer on a wildlife farm in Ohio contained coronavirus particles which were agglutinated by antiserum to bovine coronavirus (BCV) in immune electron microscopy. Three coronavirus strains were isolated in human rectal tumor cells from the feces of the sambar and white-tailed deer and the waterbuck, respectively. Hemagglutination, receptor-destroying enzyme activity, indirect immunofluorescence, hemagglutination inhibition, virus neutralization, and Western blot (immunoblot) tests showed close biological and antigenic relationships among the isolates and with selected BCV strains. Gnotobiotic and colostrum-deprived calves inoculated with each of these isolates developed diarrhea and shed coronavirus in their feces and from their nasal passages. In a serological survey of coronavirus infections among wild deer, 8.7 and 6.6% of sera from mule deer in Wyoming and from white-tailed deer in Ohio, respectively, were seropositive against both of the isolates and selected BCV isolates by indirect immunofluorescence tests. These results confirm the existence of coronaviruses in wild ruminants and suggest that these species may harbor coronavirus strains transmissible to cattle.
IS1533-based PCR assay for identification of Leptospira interrogans sensu lato serovars
Authors: Zuerner R L , Alt D , Bolin C A
Published: January 2020

A PCR-based assay was developed for typing L. interrogans sensu lato serovars. The assay is designed to exploit the presence of many copies of the leptospiral insertion sequence IS1533 and IS1533-like sequences present in the genomes of most leptospiral serovars. The PCR primers were designed to amplify DNA of unknown sequence between closely placed IS1533 or IS1533-like sequences. Amplification reactions primed with IS1533-based primers generated products of different sizes. When few copies of IS1533 were present in the genome, amplification of a few products was still detected. These results suggest that IS1533 elements may be found close together. Analysis of DNA amplified from different serovars showed the presence of differently sized products, thus enabling the serovars to be identified. Genetic variation among isolates within the same serovar was also demonstrated with the IS1533-based primers. Amplification reactions using DNA extracted from the urine of infected animals generated specific products which were similar to the products generated from purified bacterial DNA. These results demonstrate that this assay is selective enough to be used for typing leptospiral serovars from clinical material and thus allows leptospiral typing without isolation of the bacteria in pure culture.
Comparison of commercial diagnostic tests for identification of serogroup antigens of Neisseria meningitidis
Authors: van der Ende A , Schuurman I G , Hopman C T , Fijen C A , Dankert J
Published: January 2020

In the study that is described the sensitivities and specificities of three commercial tests and the standard Reference Laboratory test, used since 1961, to identify Neisseria meningitidis serogroups were compared. The tests marketed by Difco, Murex/Wellcome, and Sanofi/Pasteur showed overall sensitivities of 92, 95, and 100%, respectively, and specificities of 67, 88, and 82%, respectively. When limited to the common serogroups A, B, and C, the three tests yielded sensitivities of 93, 97, and 100%, respectively, and specificities of 98, 100, and 98%, respectively. However, determination of the uncommon serogroups X, W-135, Y, Z, and 29E with these tests is either unreliable or not possible.
Detection of respiratory syncytial virus by reverse transcription-PCR and hybridization with a DNA enzyme immunoassay
Authors: Freymuth F , Eugene G , Vabret A , Petitjean J , Gennetay E , Brouard J , Duhamel J F , Guillois B
Published: January 2020

Nasal aspirates from 238 infants hospitalized with acute respiratory infections during the winter of 1994 and 1995 were tested for respiratory syncytial virus (RSV) by immunofluorescence assay (IFA) and the viral isolation technique (VIT) and by two PCR and hybridization methods: reverse transcription PCR 1 (RT-PCR1), which amplifies the RNAs of all RSV strains, and RT-PCR-2, which allows subgroup classification of RSV. RT-PCR-1 and RT-PCR-2 detected viral sequences in 56.7% (135 of 238) and 48.3% (115 of 238) of the samples, respectively, while only 80 (33.6%) samples were found to be positive by IFA and VIT. Of the PCR-positive specimens, 57 were missed by these routine techniques in RT-PCR-1 and 45 were missed in RT-PCR-2. Although the RSV-PCR-1 and RSV-PCR-2 techniques amplified two different sequences of the RSV genome, they gave similar results for 218 (91.6%) nasal aspirates. Compared with conventional methods, the sensitivity, specificity, and agreement were 97.5, 63.9, and 75.2%, respectively, for RT-PCR-1 and 89.7, 71.9, and 77.7%, respectively, for RT-PCR-2, and for these two RT-PCR assays, the positive predictive value (PPV) and the index of agreement (kappa) were comparable and moderate, respectively: PPV was 57.8% and kappa was 0.52 in RT-PCR-1, and PPV was 60.9% and kappa was 0.54 in RT-PCR-2. However, there was a perfect correlation between the two RT-PCRs, with a PPV of 100% and an excellent index of agreement (kappa = 0.88). Therefore, most RT-PCR results were really true positive, and VIT and IFA, which missed some of them, appeared to be less sensitive.
Comparison of BacT/Alert with Signal blood culture system
Authors: Rohner P , Pepey B , Auckenthaler R
Published: January 2020

The BacT/Alert (Organon Teknika Corp., Durham, N.C.) is an automated blood culture system. It is based on the detection of CO2 by means of a colorimetric sensor internally attached to the bottom of culture bottles. The aerobic and anaerobic media of this system were compared with one bottle of the Signal system (Oxoid Ltd., Hampshire, United Kingdom). At bedside, 20 ml of blood was drawn from each adult patient. The two BacT/Alert bottles were inoculated with 5 ml of blood each; the Signal bottle was inoculated with 10 ml. A total of 5,284 sets (2,483 patients; 2.1 cultures per patient) consisting of three bottles each were evaluated, of which 781 sets (14.8%) revealed microorganisms (n = 892); 642 of these were considered to be pathogenic. Significantly more (P < 0.0001) pathogens were isolated from the two BacT/Alert bottles together (n = 584) than from the single Signal bottle (n = 515). Escherichia coli (P = 0.007), gram-negative bacteria other than members of the family Enterobacteriaceae or Pseudomonas spp. (P = 0.006), and yeasts (P = 0.02) were isolated more often from both or either BacT/Alert bottle. Comparing the systems in terms of 388 different organisms per septic episode, the difference between BacT/Alert and Signal was significant for the total number of septicemia cases (P = 0.003). More contaminants grew in the BacT/Alert system (173 versus 116; P = 0.0001). False-positive indications were more frequent in the BacT/Alert system, 198 (3.7%) aerobic bottles and 57 (1.1%) anaerobic bottles, than in the Signal bottles, 24 (0.5%) bottles. Pathogens could be detected significantly earlier (P < 0.0001) in the BacT/Alert system than in the Signal system. The BacT/Alert instrument with two bottles allowed earlier detection as well as the isolation of more microorganisms than the manual, one-bottle Signal system.
Detection of Mycobacterium tuberculosis directly from spiked human sputum by Q-beta replicase-amplified assay
Authors: Shah J S , Liu J , Buxton D , Stone B , Nietupski R , Olive D M , King W , Klinger J D
Published: January 2020

We report on a rapid, sensitive, Q-Beta replicase-amplified nucleic acid hybridization assay for the detection of Mycobacterium tuberculosis directly from spiked human sputum. Specimens were processed by either an N-acetyl-L-cysteine-NaOH or a 2% NaOH digestion-decontamination method and then washed to neutralize the pH of the cell pellet. The washed sputum pellets were heated at 100 degrees C to inactivate the M. tuberculosis organisms. The heat-inactivated samples were mechanically lysed at 5,000 rpm for 6 min in the GENE-TRAK Sample Processing Instrument in the presence of zirconium oxide beads and a buffer containing guanidine thiocyanate. The released nucleic acid was subjected to the GENE-TRAK Q-Beta replicase-amplified, dual-capture assay. The assay sensitivity was 10(3) purified rRNA targets or 1 CFU of M. tuberculosis spiked into M. tuberculosis-negative human sputum. There was a low level of noise because of the limitations of performing a signal amplification assay in an open system. High levels of other mycobacterial rRNA (approximately 10(7) organisms), including rRNAs of Mycobacterium avium and Mycobacterium gordonae, did not interfere with the sensitivity of the assay.
Detection of Yersinia pestis fraction 1 antigen with a fiber optic biosensor
Authors: Cao L K , Anderson G P , Ligler F S , Ezzell J
Published: January 2020

A fiber optic biosensor was used to detect the fraction 1 (F1) antigen from Yersinia pestis, the etiologic agent of plague. The instrument employs an argon ion laser (514 nm) to launch light into a long-clad fiber and measures the fluorescence produced by an immunofluorescent complex formed in the evanescent wave region. This sensing area is a short section (12.5 cm) at the end of the optical fiber from which the cladding has been removed and in which the silica core has been tapered. Capture antibodies, which bind to F1 antigen, were immobilized on the core surface to form the basis of the sandwich fluoroimmunoassay. The ability to detect bound F1 antigen was provided by adding tetramethylrhodamine-labeled anti-plaque antibody to form fluorescent complexes. The evanescent wave has a limited penetration depth (< 1 lambda), which restricts detection of the fluorescent complexes bound to the fiber's surface. The direct correlation between the F1 antigen concentration and the signal provided an effective method for sample quantitation. This method achieved a high level of accuracy for determining F1 antigen concentrations from 50 to 400 ng/ml in phosphate-buffered saline, serum, plasma, and whole blood, with a 5-ng/ml limit of detection. Subsequent blind studies, which included serum samples from patients, yielded results in good agreement with measurements by enzyme-linked immunosorbent assay. A major advantage of the fiber optic biosensor is that results can be generated within minutes while isolating the user from hazardous samples. These factors favor development of this biosensor into a facile and rapid diagnostic device.
Specific, sensitive, and rapid assay for human immunodeficiency virus type 1 pol mutations associated with resistance to zidovudine and didanosine
Authors: Frenkel L M , Wagner L E , Atwood S M , Cummins T J , Dewhurst S
Published: January 2020

The effectiveness of antiretroviral therapy may be limited by the development of human immunodeficiency virus type 1 (HIV-1) resistance. Monitoring for resistance will perhaps allow changes in therapy prior to deterioration in the patient's clinical or immunologic status. Our objective was to develop a rapid, specific, and sensitive genotypic assay for HIV-1 resistance to zidovudine (ZDV) and didanosine (ddI) which is simple to perform. In our assay the DNA of HIV-1 pol was amplified by PCR using two sets of nested oligonucleotide primers. Mutations of reverse transcriptase (RT) encoding amino acids (aa) 74 and 41, 70, and 215 which have been associated with HIV-1 resistance to ddI and ZDV, respectively, were detected with a ligase detection reaction (LDR) and indicated colorimetrically. The RT genotypes of 35 patient specimens (140 codons) blindly assessed for these mutations were in agreement by PCR-LDR and by dideoxynucleotide sequencing. To evaluate the limits of the assay, other specimens with mutations close to the ligation site were evaluated by PCR-LDR. The assay was sensitive and specific for all specimens except when mutations occurred within 2 bases on either side of the ligation site. In summary, this PCR-LDR assay specifically, sensitively, and rapidly detected pol mutations (RT aa 74, 41, 70, and 215) associated with HIV-1 resistance to ddI and ZDV.
Evidence for absence in northern Europe of especially virulent clonal types of Actinobacillus actinomycetemcomitans
Authors: Haubek D , Poulsen K , Asikainen S , Kilian M
Published: January 2020

Genetic analysis of an Actinobacillus actinomycetemcomitans population consisting of 88 clinically well characterized Finnish isolates performed by multilocus enzyme electrophoresis confirmed that the five serotypes divide into two phylogenetic lineages, one comprising serotypes b and c and one comprising serotypes a, d, and e. There was no association between any subpopulation and the periodontal health status of the subject from whom the isolates originated, suggesting that the role of A. actinomycetemcomitans in periodontitis is largely opportunistic in the population examined. Southern blot analyses of genomic DNA digested with each of the restriction endonucleases MspI, RsaI, and TaqI revealed extremely limited genetic polymorphism of the structural leukotoxin gene, ltxA, and its associated promoter. All isolates hybridized to a 530-bp DNA fragment derived from the promoter region of the leukotoxin gene operon of a minimally leukotoxic A. actinomycetemcomitans strain. Deletion of the 530-bp sequence has been associated with significantly increased toxin production detected among isolates from patients with juvenile periodontitis in North America but was detected neither among the 88 isolates in the present collection analyzed nor among more than 60 strains in another population of northern European A. actinomycetemcomitans isolates analyzed previously.
Evaluation of ligase chain reaction for use with urine for identification of Neisseria gonorrhoeae in females attending a sexually transmitted disease clinic
Authors: Smith K R , Ching S , Lee H , Ohhashi Y , Hu H Y , Fisher H C , Hook E W
Published: January 2020

The high sensitivity of nucleic acid amplification tests such as ligase chain reaction (LCR) has the potential to simplify specimen collection for the microbiologic diagnosis of gonorrhea. We screened first-void urine specimens from 283 women attending a Birmingham, Ala., sexually transmitted disease (STD) clinic by using LCR and compared the results to those of cervical and urethral cultures for gonorrhea diagnosis. Fifty-three (18.7%) women had positive cervical cultures for gonorrhea, and 41 of the 53 (77%) also had positive urethral cultures. One additional patient had only a positive urethral culture (the cervical gonorrhea culture was negative). LCR testing of urine specimens for gonorrhea yielded positive results for 51 of 54 (94.4%) women with positive cervical or urethral cultures. Of 229 women with both urethral and cervical cultures negative for gonorrhea, 2 (0.8%) had positive urine LCR results as well. To resolve the discrepancies between urine LCR and culture results, LCR tests of simultaneously collected urethral and cervical swab specimens and LCR tests of the same urine specimens using different nucleotide primers were conducted. After evaluation of five discrepant results, the sensitivity, specificity, positive predictive value, and negative predictive value of LCR for the detection of gonorrhea in urine specimens were 94.6%, 100%, 100%, and 98.7%, respectively. We conclude that urine LCR testing for Neisseria gonorrhoeae is a practical alternative to culture for the detection of gonorrhea in women. Urine testing for STD diagnosis has the potential to simplify and expand the opportunities for STD screening and surveillance of women.
Mixed infection of different Borrelia species among Apodemus speciosus mice in Hokkaido, Japan
Authors: Nakao M , Miyamoto K
Published: January 2020

The wood mouse (Apodemus speciosus) serves as a wildlife reservoir for Lyme disease spirochetes in Hokkaido, Japan. To isolate Borrelia species, we captured 34 wood mice in an area where Borrelia species are endemic during October 1993. The earlobes (right and left), heart, spleen, and urinary bladder from each mouse were used as culture sources. As a result of culture 73 isolates from 21 mice were classified by rRNA gene restriction fragment length polymorphism analysis. Ribotype groups III (Borrelia afzelii) and IV (unknown species) were detected among those isolates. Thirty-one (77.5%) of 40 earlobe isolates were classified as group IV. In contrast, 6 (40.0%) of 15 heart isolates, 5 (50.0%) of 10 spleen isolates, and 7 (87.5%) of 8 urinary bladder isolates were B. afzelii. Seven mice showed mixed infection with B. afzelii and group IV. The data indicate that different Borrelia species can coexist in a reservoir host that is suitable for them.
A new sensitive sandwich enzyme-linked immunosorbent assay to detect galactofuran in patients with invasive aspergillosis
Authors: Stynen D , Goris A , Sarfati J , Latgé J P
Published: January 2020

A double-direct sandwich enzyme-linked immunosorbent assay that uses a rat anti-galactomannan monoclonal antibody as the acceptor and detector antibody was designed. This immunoassay, which detects less than 1 ng of galactomannan per ml, was assessed in a retrospective study with samples from patients with invasive aspergillosis. Serum is more appropriate than urine for use in the search for circulating galactomannan. Antigenemia does not have a transient character. Galactomannan can be detected at least 39 days before the death of the patients.
Molecular epidemiology of Xanthomonas maltophilia colonization and infection in the hospital environment
Authors: Laing F P , Ramotar K , Read R R , Alfieri N , Kureishi A , Henderson E A , Louie T J
Published: January 2020

Between April 1992 and December 1993, 80 Xanthomonas maltophilia isolates were collected from 63 patients in three acute-care hospitals in Calgary, Alberta, Canada. On the basis of Centers for Disease Control and Prevention definitions, 48 patients had nosocomial and 15 had community-acquired X. maltophilia. Thirty-eight of the patients were colonized and 25 were infected. Sixty-four percent of patients who acquired X. maltophilia in the intensive care unit (ICU) became infected, whereas 32% of patients in a non-ICU setting became infected. ICU patients tended to be hospitalized for a shorter period of time than non-ICU patients before the onset of X. maltophilia infection. Regardless of being colonized or infected, all patients had debilitating conditions, with respiratory disease being the most common underlying illness (35%). Forty-two patients (88%) with hospital-acquired X. maltophilia received prior antibiotic therapy which included gentamicin, tobramycin, ceftazidime, piperacillin, and imipenem. Agar dilution MICs showed that patient isolates were resistant to these antimicrobial agents that patients had received. Pulsed-field gel electrophoresis of SpeI-digested genomic DNA revealed that six epidemiologically linked patient isolates from the ICU of one acute-care hospital had identical DNA profiles. In contrast, isolates from patients from the other two hospitals had unique genotype profiles (n = 57) regardless of the presence or absence of an epidemiologic association. In these patients there was genetic evidence against the acquisition of a resident hospital clone. These results indicate that pulsed-field gel electrophoresis can resolve genotypically distinct strains of X. maltophilia and, consequently, is a useful tool for evaluating nosocomial infections caused by X. maltophilia.
Borrelia burgdorferi in an urban environment: white-tailed deer with infected ticks and antibodies
Authors: Magnarelli L A , Denicola A , Stafford K C , Anderson J F
Published: January 2020

Ticks and blood samples were collected from white-tailed deer (Odocoileus virginianus) in forests located in an insular, urban area of Bridgeport, Conn., and in rural south central Connecticut during 1992 and 1993. Immature and adult Ixodes scapularis ticks were tested for Borrelia burgdorferi, the etiologic agent of Lyme borreliosis, by indirect fluorescent-antibody staining methods. Deer sera were analyzed for antibodies to this bacterium by an enzyme-linked immunosorbent assay. Infected ticks parasitized deer in Bridgeport from May through December; the prevalence of infection varied from 1.1% of 93 larvae to 28.1% of 114 adult females. The percentages of infected males (10.5% of 380 ticks) and females (13.7% of 328 ticks) were relatively lower in south central Connecticut. In antibody tests, the prevalence of seropositive specimens collected in Bridgeport (61% of 146 serum specimens) was more than twofold greater than that of specimens obtained in south central Connecticut (26.7% of 116 serum specimens). Foci for Lyme borreliosis can occur in forested, urban settings as well as in rural areas if there are ticks, rodents, birds, and large mammals present. Human exposure to ticks in such sites should be considered as a possible source of B. burgdorferi infection.
Detection of hepatitis C virus RNA by a combined reverse transcription PCR assay: comparison with nested amplification and antibody testing
Authors: Young K K , Archer J J , Yokosuka O , Omata M , Resnick R M
Published: January 2020

Many of the current reverse transcription (RT)-PCR assays for the detection of hepatitis C virus (HCV) RNA are multistep processes which use multiple enzymes and buffers. The assays are also often suboptimal, requiring nested amplification to achieve the desired levels of sensitivity. As a result, these assays are cumbersome and prone to false-positive results. The susceptibility to contamination is further aggravated by the lack of carryover controls. We have previously reported the development of a combined RT-PCR assay for HCV RNA detection which is sensitive and simple to perform. We have since successfully integrated dUTP-uracil-N-glycosylase carryover prevention into the combined assay. Restriction of as much as 0.5 microliter of deoxyuridine-containing amplification products has been achieved. The performance of the improved combined assay was compared directly with conventional nested RT-PCR and antibody detection. The combined assay was found to have sensitivity similar to that of nested RT-PCR in detecting HCV RNA from HCV antibody-positive specimens. In an analysis of hepatitis B virus antibody-positive specimens, nested amplification had false-positive rates ranging from 8 to 31%, while no false-positive results were seen with the combined assay. In comparison with serological methods, the combined assay had specificity and sensitivity of 100 and 95%, respectively.
Recombinant 46-kilodalton surface antigen (P46) of Mycoplasma hyopneumoniae expressed in Escherichia coli can be used for early specific diagnosis of mycoplasmal pneumonia of swine by enzyme-linked immunosorbent assay
Authors: Futo S , Seto Y , Okada M , Sato S , Suzuki T , Kawai K , Imada Y , Mori Y
Published: January 2020

The 46-kDa surface antigen (P46) is the early and species-specific immunogenic protein of Mycoplasma hyopneumoniae. Three TGA codons encoding tryptophan in the P46 gene were replaced with TGG by an in vitro mutagenesis technique. The mutated P46 gene was expressed in Escherichia coli by using the chelating peptide tag system. The purified recombinant P46 was successfully used in an enzyme-linked immunosorbent assay for detection of antibodies against M. hyopneumoniae in swine serum. It did not cross-react with sera from swine infected with Mycoplasma flocculate, Mycoplasma hyorhinis, or Mycoplasma hyosynoviae. With this method, mycoplasmal pneumonia of swine was detectable within 2 weeks after infection.
Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR
Authors: Herrewegh A A , de Groot R J , Cepica A , Egberink H F , Horzinek M C , Rottier P J
Published: January 2020

A nested reverse transcriptase PCR (RT-nPCR) was developed for the detection of feline coronavirus (FCoV) RNA in the feces, tissues, and body fluids of infected cats. The RT-nPCR was targeted to the highly conserved 3'-untranslated region of the viral genome and will detect most, if not all, feline coronaviruses in the field. With the RT-nPCR, FCoV RNA was detected in plasma samples from experimentally infected cats as early as 2 days postinoculation. FCoV RNA was also detected in serum, plasma, or ascitic fluid samples from 14 of 18 cats (78%) with naturally occurring feline infectious peritonitis (FIP). The use of RT-PCR for FIP diagnosis is limited because of the occurrence of apparently healthy FCoV carriers. These asymptomatic cats shed the virus in the feces and, in a number of cases, also had detectable virus in the plasma. Because of the nature of FCoV infections, our RT-PCR assay with plasma or serum cannot be used to establish a definite diagnosis of FIP. However, this assay does provide a new means to identify asymptomatic FCoV carriers. As such, RT-nPCR will be of use to screen cats before their introduction into FCoV-free catteries. Moreover, this assay provides an important tool to study the epidemiology of FCoV.
Nested PCR approach for detection and typing of epidermodysplasia verruciformis-associated human papillomavirus types in cutaneous cancers from renal transplant recipients
Authors: Berkhout R J , Tieben L M , Smits H L , Bavinck J N , Vermeer B J , ter Schegget J
Published: January 2020

The epidermodysplasia verruciformis (EV)-associated human papillomaviruses (HPVs) constitute a group of HPV genotypes isolated mostly from the cutaneous lesions of patients with the genetic disorder of EV. Broad-spectrum detection of EV HPVs in cutaneous lesions of non-EV patients was previously difficult because no EV HPV consensus PCR was available. We describe a nested PCR that enables the detection of all known EV HPV types at relatively low-copy-number levels. The deduced sequences of a 92-amino-acid stretch of the L1 open reading frames of all types are shown for convenient typing. The technique proved very valuable in viral studies of skin cancers from renal transplant recipients. A high prevalence (81%) of EV HPV types was found in skin cancer biopsies. A wide spectrum of EV HPV types that differed from HPV-5 and -8 was found to be involved. The technique also proved useful in detecting potentially novel EV HPV types in skin cancers. The relationship of these new types to known HPV types is demonstrated by phylogenetic tree analysis.
Improved detection of Malassezia species in lipid-supplemented Peds Plus blood culture bottles
Authors: Nelson S C , Yau Y C , Richardson S E , Matlow A G
Published: January 2020

The growth of Malassezia species in BACTEC Peds Plus blood culture bottles was optimized by using various lipid supplements. Palmitic acid (3%, wt/vol) was superior and overcame the inhibitory effect of blood in mock clinical specimens. Palmitic acid (3%) supplementation of Peds Plus bottles may improve recovery of Malassezia species in the BACTEC NR 660.
Typing of human astroviruses from clinical isolates by enzyme immunoassay and nucleotide sequencing
Authors: Noel J S , Lee T W , Kurtz J B , Glass R I , Monroe S S
Published: January 2020

A typing enzyme immunoassay (TYPE-EIA) was used to determine the antigenic types of 64 astrovirus-positive specimens from nine collections from seven countries. Six of the seven known astrovirus types were detected in the collections, with HAstV-1 predominating in all collections for one from the United Kingdom. Selected specimens were analyzed further by reverse transcriptase PCR and nucleotide sequencing of 348 bp within the capsid protein precursor region of the genome. The phylogenetic groupings (genotypes) determined from the sequences were entirely consistent with the antigenic groupings (serotypes) of isolates obtained by using the TYPE-EIA. The genetic variation within genotypes was small compared with the variation between genotypes, allowing unambiguous categorization of all specimens. Although some strains from widely separated geographic areas had identical sequences, in general, within a region most strains of the same type were identical. The TYPE-EIA may help further our understanding of the epidemiology of astrovirus and the possible role of serotype-specific immunity, while further knowledge of sequences could facilitate the development of simpler molecular methods of typing astrovirus strains.
Diagnosis of intestinal microsporidiosis by examination of stool and duodenal aspirate with Weber's modified trichrome and Uvitex 2B strains
Authors: DeGirolami P C , Ezratty C R , Desai G , McCullough A , Asmuth D , Wanke C , Federman M
Published: January 2020

Severe, chronic diarrhea is a frequent complication of human immunodeficiency virus disease, and intestinal microsporidiosis is being recognized with increasing frequency in patients with AIDS. Noninvasive, cost-effective techniques are needed to optimize its diagnosis. Weber's modified trichrome stain (MTS) and the fluorochrome Uvitex 2B stain were used to detect microsporidial spores in smears of stool and duodenal aspirate (DA) samples received from human immunodeficiency virus-infected patients for examination for ova and parasites. Of 305 samples (292 stool and 13 DA samples) from 140 patients examined by MTS, 83 samples from 26 (18.6%) of the patients were positive for microsporidia (23 patients diagnosed initially and 3 diagnosed upon review). A subset of the samples studied by MTS consisting of 108 smears of stool and DA specimens from 60 patients was examined by Uvitex 2B. All 44 samples positive by MTS were also positive by Uvitex 2B. In addition, seven specimens and three patients were initially detected as positive by Uvitex 2B only (all three patients were positive also by MTS upon review). Confirmation of the diagnosis was obtained for 24 of 26 smear-positive patients by duodenal biopsy and/or stool transmission electron microscopy. Of 114 patients with stained smears negative for microsporidia, 23 had duodenal biopsies which showed no microsporidia. For the 43 patients who underwent duodenal biopsy, the sensitivity of both the MTS and the Uvitex 2B methods compared with biopsy results was 100%. Of six patients with negative duodenal biopsies and positive stained smears, four had microsporidia demonstrated by stool transmission electron microscopy. The examination of stool and DA smears stained by Uvitex 2B and/or MTS is a sensitive, noninvasive test for diagnosis of intestinal microsporidiosis which can be successfully implemented in a clinical laboratory. Strict adherence to precise diagnostic criteria is necessary to avoid incorrect results. The simultaneous use of both staining methods enhances performance and may provide greater accuracy, especially for patients with light infections.
Evaluation of a new identification system, Crystal Enteric/Non-Fermenter, for gram-negative bacilli
Authors: Wauters G , Boel A , Voorn G P , Verhaegen J , Meunier F , Janssens M , Verbist L
Published: January 2020

A total of 505 fermentative and 201 nonfermentative gram-negative bacilli, identified by conventional methods, were tested by the Crystal Enteric/Non-Fermenter ID kit and by the API 20E or API 20NE identification system. The overall correct results for fermenters were 92.9% by the Crystal kit and 89.1% by the API 20E system. The false identifications (genus and species incorrect) accounted for 3.1 and 7.1% for the Crystal and API systems, respectively. For nonfermenters, figures for correct identifications by the two systems were comparable (Crystal, 75.9%; API 20NE, 75.3%) while the API 20NE system gave twice as many incorrect results (13.8%) as Crystal (6.3%); however, Crystal failed to precisely identify several species included in a "miscellaneous" group. The Crystal Enteric/Non-Fermenter system is an easy-to-use kit which compares favorably with other commercial systems.
In vitro culture and serologic and molecular identification of Septata intestinalis isolated from urine of a patient with AIDS
Authors: Visvesvara G S , da Silva A J , Croppo G P , Pieniazek N J , Leitch G J , Ferguson D , de Moura H , Wallace S , Slemenda S B , Tyrrell I
Published: January 2020

Microsporidian spores were identified, on the basis of Weber's staining, in urine, stool, nasal, and saliva samples of an AIDS patient with diarrhea, hematuria, dysuria, and dementia. Urine and stool samples contained numerous spores, whereas few spores were seen in the nasal and saliva samples. Spores were concentrated from urine samples and inoculated into monkey kidney cell (E6) monolayers. After 6 to 8 weeks of culture, infected E6 cells filled with spores as well as spores free in the culture supernatants were seen daily. Transmission electron microscopy revealed that all stages of the parasite (CDC:V297) developed within septated, honeycomb-shaped parasitophorous vacuoles. Indirect immunofluorescence and immunoblotting studies using rabbit anti-Encephalitozoon cuniculi, anti-Encephalitozoon hellem, and anti-CDC:V297 sera revealed that CDC:V297 reacted intensely with the homologous serum but minimally with the heterologous sera. DNA isolated from CDC:V297, when PCR amplified with E. hellem and E. cuniculi primers, did not produce the diagnostic bands of approximately 547 and approximately 549 bp characteristic of E. hellem and E. cuniculi, respectively. On the basis of these studies, we concluded that CDC:V297 fits the description of Septata intestinalis (A. Cali, D. P. Kotler, and J. M. Orenstein, J. Eukaryot, Microbiol. 40:101-112, 1993).
Effect of ambient temperature on competence of deer ticks as hosts for Lyme disease spirochetes
Authors: Shih C M , Telford S R , Spielman A
Published: January 2020

We determined whether the temperature of extrinsic incubation affects the competence of vector ticks as hosts for Lyme disease spirochetes (Borrelia burgdorferi). Larval Ixodes dammini ticks that had engorged on spirochete-infected C3H mice were incubated continuously at various temperatures, and the gut contents of the resulting nymphs were examined for spirochetes by direct immunofluorescence microscopy. Spirochetes were present in virtually all nymphs kept at 27 degrees C or less for 6 months, in only 10% of those kept at 33 degrees C, and in none kept at 37 degrees C. Spirochetes became undetectable within 8 weeks when nymphs were warmed from 27 to 33 degrees C beginning at the time of molting. Nymphs became virtually noninfective for mice after incubation at temperatures higher than 27 degrees C for 2 weeks or longer. We conclude that ambient temperatures in excess of 27 degrees C are not permissive for transmission of the agent of Lyme disease.
Controlled evaluation of BacT/Alert standard aerobic and FAN aerobic blood culture bottles for detection of bacteremia and fungemia
Authors: Weinstein M P , Mirrett S , Reimer L G , Wilson M L , Smith-Elekes S , Chuard C R , Joho K L , Reller L B
Published: January 2020

A new medium, FAN, designed to enhance the recovery of microorganisms, has been developed for the BacT/Alert blood culture system (Organon Teknika Corp., Durham, N.C.). We compared the yield and speed of detection of microorganisms in 6,847 adequately filled paired aerobic standard and FAN bottles at four university hospitals. Of 499 clinically significant microorganisms isolated from one or both bottles, significantly more Staphylococcus aureus isolates (P < 0.001), coagulase-negative staphylococci (P < 0.001), yeasts (P < 0.01), and all microorganisms combined (P < 0.001) were recovered from the FAN bottles. Overall, the speeds of detection of positive cultures did not differ between the two medium formulations; mean times to detection in the standard and FAN bottles were 16.1 and 16.0 h, respectively. When a subset of patients on antimicrobial therapy was evaluated, significantly enhanced yield from the FAN bottle was evident for staphylococci. Overall, the FAN bottle outperformed the standard aerobic BacT/Alert bottle.
Analysis of Salmonella enteritidis isolates by arbitrarily primed PCR
Authors: Fadl A A , Nguyen A V , Khan M I
Published: January 2020

An arbitrarily primed PCR (AP-PCR) was developed to analyze the genomic DNAs of Salmonella enteritidis isolates from human outbreaks and from avian sources. The AP-PCR generated seven distinct randomly amplified DNA patterns among the S. enteritidis isolates studied. Differences in the DNA patterns among isolates of S. enteritidis phage types 13a and 8 as well as among S. enteritidis phage type 14b were observed. The AP-PCR analysis can be used to determine the differences among isolates within the same phage types and may be useful for tracing back the source of S. enteritidis outbreaks in humans more precisely.
Molecular analysis of Salmonella enteritidis by pulsed-field gel electrophoresis and ribotyping
Authors: Thong K L , Ngeow Y F , Altwegg M , Navaratnam P , Pang T
Published: January 2020

A total of 61 isolates of Salmonella enteritidis were analyzed by the techniques of pulsed-field gel electrophoresis (PFGE) and ribotyping. Twenty-three of the isolates were from Zurich, Switzerland, and 38 isolates were from the University Hospital, Kuala Lumpur, Malaysia. Five of the Malaysian isolates were hospital-related outbreak strains and were shown to be indistinguishable by PFGE analysis following digestion with three different restriction endonucleases, XbaI (5'-TCTAGA-3'), SpeI (5'-ACTAGT-3'), and AvrII (5'-CCTAGG-3'). The PFGE pattern of an isolate from a suspected carrier staff nurse was found to be identical to those of the hospital outbreak isolates. These isolates were also indistinguishable by ribotyping with SmaI and SphI. The same single PFGE pattern was also detected in 29 of 32 sporadic isolates of S. enteritidis. Four closely related ribotypes were detected among these 29 isolates. Similarly, outbreak-related strains from Switzerland showed close genetic identity by PFGE and ribotyping. Strains obtained from poultry showed more variations in their PFGE patterns and ribotypes, although the patterns were still closely related. In addition, SphI ribotypes A and D among the Swiss strains correlated with phage types 4 and 8, respectively. No correlation of phage types with PFGE pattern was noted. Both PFGE and ribotyping indicate that the S. enteritidis strains circulating in Malaysia and Switzerland are very similar and may be clonally related. Comparison of the PFGE patterns with the ribotypes for 23 Swiss and 16 Malaysian isolates showed that there was a 69% concordance in the grouping of isolates. We conclude that the close genetic similarity observed between epidemiologically unrelated and outbreak-related isolates of S. enteritidis suggests that both PFGE and ribotyping are of limited value in the epidemiological analysis of these particular isolates, possibly because of the highly clonal nature of pathogenic strains of S. enteritidis.
Long PCR-ribotyping of nontypeable Haemophilus influenzae
Authors: Smith-Vaughan H C , Sriprakash K S , Mathews J D , Kemp D J
Published: January 2020

PCR-ribotyping, a new typing method based on long PCR, has been developed for nontypeable Haemophilus influenzae (NTHi). Ribosomal operons of NTHi were amplified by long PCR and were found to be highly polymorphic for internal HaeIII sites. The technique was applied to 49 isolates previously subjected to conventional ribotyping, and the two methods showed a high level of concordance for serial isolates from individual subjects. PCR-ribotyping provides a powerful new typing tool for strain characterization in epidemiological investigations of NTHi.
Molecular subtyping scheme for Salmonella panama
Authors: Stanley J , Baquar N , Burnens A
Published: January 2020

We describe a genotyping scheme for Salmonella panama. Defined probes specific for the 16S rRNA gene and the DNA insertion element IS200 were generated by PCR from S. panama and were used to probe genomic Southern blots made with enzymes selected to cut within and outside the probed sequences. Plasmid profiles were determined. The typeability and discriminatory power of the individual methods were compared. Ribotyping with 16S rRNA gene probe alone was slightly more discriminatory than phage typing, but unlike the latter, ribotyping was able to type all strains. IS200 profiling was the single most discriminatory method for S. panama, having an index of discrimination (D) of 0.8 and 100% typeability. Plasmid profiling, which had moderate discriminatory power but only 50% typeability, was valuable as an adjunct technique. The use of all three methods together or simply the combination of IS200 profiling with the two most discriminatory enzymes and plasmid profiling yielded a molecular typing scheme whose discriminatory power (D = 0.97) approached the maximum theoretical value. This should prove both useful and robust for epidemiological investigations of S. panama.
Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens
Authors: Spatafora J W , Mitchell T G , Vilgalys R
Published: January 2020

Because of their ability to display yeast-like growth forms in various environmental conditions, dematiaceous (melanized) hyphomycetes of the form-genera Exophiala, Rhinocladiella, and Wangiella have been informally termed "black yeasts." Cladistic analysis of 1,050 bp of the genes coding for small-subunit rRNA (SSU rDNA) supported a close relationship among species of these black yeasts with other dematiaceous hyphomycetes in the form-genera Fonsecaea, Phialophora, and Ramichloridium. The conventional categories of these fungi based on asexual states are not supported by phylogenetic analysis of SSU rDNA sequences. Isolates exhibiting annellidic modes of blastic conidiogenesis (e.g., Exophiala spp.) were not monophyletic and were placed as sister taxa to isolates that produce phialides or sympodulae. The results indicated very close relationships between isolates of Wangiella dermatitidis and Exophiala mansonii and between Rhinocladiella aquaspersa and Exophiala jeanselmei. This clade of dematiaceous hyphomycetes was a sister group to a clade comprising members of two orders of cleistothecial ascomycetes, Eurotiales and Onygenales. The etiological agents of chromoblastomycosis were found to be a closely related group (clade), while the agents of phaeohyphomycosis displayed a broader distribution on the SSU rDNA tree.
Evaluation of new agglutination test for identification of oxacillin-susceptible and oxacillin-resistant Staphylococcus aureus
Authors: Tveten Y
Published: January 2020

A new agglutination test (Monostaph +; Bionor, Skien, Norway) has been developed. This new agglutination test has been compared with two other agglutination tests for the identification of 128 isolates of Staphylococcus aureus and 82 coagulase-negative staphylococci. The sensitivities of both Monostaph + and Pastorex Staph-Plus were excellent (98.7 and 97.4%, respectively) in detection of oxacillin-resistant Staphylococcus aureus. The specificity was 96.4% (two Staphylococcus epidermidis isolates and one Staphylococcus hominis isolate were false positive).
Detection of the turkey pathogens Mycoplasma meleagridis and M. iowae by amplification of genes coding for rRNA
Authors: Boyle J S , Good R T , Morrow C J
Published: January 2020

PCR-based diagnostic tests using oligonucleotides specific to 16S rRNA were designed for the specific detection of the turkey pathogens Mycoplasma meleagridis and M. iowae. This method of detection was shown to be rapid, species specific, and unaffected by strain variation or the presence of other organisms. Detection of M. meleagridis in clinical samples by PCR was achieved and later confirmed by culture and growth inhibition. Definitive identification by culture and growth inhibition required up to 3 weeks, whereas positive results from PCR testing were obtained within a day and negative samples were confirmed within 4 days.
Stability of free and complexed human immunodeficiency virus type 1 antigen at 4 degrees C and at room temperature
Authors: Griffith B P , Garner R B , Chacko T M
Published: January 2020

Free and immune-complex-dissociated (ICD) human immunodeficiency virus type 1 (HIV-1) antigenemias in serum specimens stored at room temperature (RT) and 4 degrees C for 1 to 35 days were evaluated. At all time points examined, there was no significant loss in detectable levels of ICD HIV-1 antigen at either RT or 4 degrees C. Free HIV-1 antigen was not stable in serum samples stored at RT for more than 2 days but was stable in samples stored at 4 degrees C for up to 4 days. Loss of free antigen occurred more rapidly in samples with high antigen content at baseline. Use of the ICD antigen assay allowed accurate quantitation of antigen in samples stored at RT or 4 degrees C for as long as 1 month.