bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative evaluation of NASBA HIV-1 RNA QT, AMPLICOR-HIV monitor, and QUANTIPLEX HIV RNA assay, three methods for quantification of human immunodeficiency virus type 1 RNA in plasma
Authors: Revets H , Marissens D , de Wit S , Lacor P , Clumeck N , Lauwers S , Zissis G
Published: January 2020

Three commercial assays for quantifying plasma human immunodeficiency virus type 1 (HIV-1) RNA were evaluated. The assays differed in their sample volumes, the means of preparing samples, and methods of amplification and detection. Plasma samples were obtained from 36 HIV-1-infected patients representing all stages of HIV-1 infection and were analyzed as coded specimens. Measurement of HIV-1 RNA baseline levels revealed no significant difference in sensitivity between the three assays. The assays were also applied to the quantitation of HIV-1 RNA levels in the plasma of patients who were changing their antiretroviral therapy. The changes measured in HIV-1 RNA levels in plasma in response to therapy were comparable by the three assays. No close correlation was found between the amount of HIV-1 RNA and the CD4 T-cell count; HIV-1 RNA assays were more sensitive than p24 antigen assays as an indicator of plasma viremia. Overall, the study demonstrates that all three quantitative assays for HIV-1 RNA can be used to measure the HIV-1 RNA copy number representing the HIV-1 viremia status in patients with HIV-1 infection. Since this copy number is likely to be useful in monitoring the effectiveness of antiviral therapy, these quantitative assays for HIV-1 RNA are ready to be built into clinical trials.
Nontoxigenic Vibrio cholerae 01 serotype Inaba biotype El Tor associated with a cluster of cases of cholera in southern India
Authors: Saha P K , Koley H , Mukhopadhyay A K , Bhattacharya S K , Nair G B , Ramakrishnan B S , Krishnan S , Takeda T , Takeda Y
Published: January 2020

Thirteen strains of Vibrio cholerae 01 belonging to the Inaba serotype El Tor biotype isolated from patients during an outbreak of cholera in the town of Warangal in southern India were found to be nontoxigenic (NT), since they did not produce cholera toxin or hybridize with DNA probes specific for cholera toxin, Zot, or Ace. The unheated and heated culture supernatants of the NT V. cholerae 01 evoked a rapid cell-rounding effect when introduced on confluent layers of CHO and HeLa cells which could not be inhibited by antiserum against known toxins. Culture supernatants of two representative NT V. cholerae 01 strains caused an increase in short-circuit current in rabbit ileal tissue mounted on an Ussing chamber, and the pattern of increase in short-circuit current was consistent with the presence of a quickly acting toxin like stable toxin. None of the strains of NT V. cholerae 01 hybridized with a DNA probe specific for the heat-stable enterotoxin of V. cholerae non-01, nor did the factor produced by NT V. cholerae 01 resemble the recently described heat-stable enterotoxin produced by enteroaggregative Escherichia coli as determine by a PCR assay. To our knowledge, this is the first report of NT V. cholerae 01 being associated with a cluster of cases of cholera, and it appears that a clone of NT V. cholerae 01 has the potential to cause localized outbreaks of cholera.
Role of stool screening tests in diagnosis of inflammatory bacterial enteritis and in selection of specimens likely to yield invasive enteric pathogens
Authors: Silletti R P , Lee G , Ailey E
Published: January 2020

The Leuko-Test yielded a negative predictive value of 98.4% when it was used to screen 325 patients for inflammatory bacterial enteritis and a negative predictive value of 99.4% when it was used to screen 416 stool specimens for those from which enteric pathogens would likely be recovered when cultured. Neither microscopy for fecal leukocytes nor an assay for fecal occult blood, alone or in combination, allowed for the reliable detection of invasive bacterial enteritis or the reliable selection of specimens for culture. When positive in the Leuko-Test, specimens collected from patients after the third day of hospitalization did not yield enteric pathogens when the specimens were cultured, and specimens collected from inpatients within the first 3 days of hospitalization or from outpatients did not contain Clostridium difficile toxin A. As a screening test, the Leuko-Test has the ability to generate rapidly a result which can support the presumptive diagnosis of inflammatory bacterial enteritis or which can be used to determine the suitability of stool specimens for bacteriologic culture.
Validation of use of whole-cell repetitive extragenic palindromic sequence-based PCR (REP-PCR) for typing strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex and application of the method to the investigation of a hospital outbreak
Authors: Snelling A M , Gerner-Smidt P , Hawkey P M , Heritage J , Parnell P , Porter C , Bodenham A R , Inglis T
Published: January 2020

Acinetobacter spp. are being reported with increasing frequency as causes of nosocomial infection. In order to identify reservoirs of infection as quickly as possible, a rapid typing method that can differentiate epidemic strains from environmental and nonepidemic strains is needed. In 1993, a cluster of Acinetobacter baumannii isolates from five patients in the adult intensive therapy unit of our tertiary-care teaching hospital led us to develop and optimize a rapid repetitive extragenic palindromic sequence-based PCR (REP-PCR) typing protocol for members of the Acinetobacter calcoaceticus-A. baumannii complex that uses boiled colonies and consensus primers aimed at repetitive extragenic palindromic sequences. Four of the five patient isolates gave the same REP-PCR typing pattern as isolates of A. baumannii obtained from the temperature probe of a Bennett humidifier; the fifth isolate had a unique profile. Disinfection of the probe with 70% ethanol, as recommended by the manufacturer, proved ineffective, as A. baumannii with the same REP-PCR pattern was isolated from it 10 days after cleaning, necessitating a change in our decontamination procedure. Results obtained with REP-PCR were subsequently confirmed by ribotyping. To evaluate the discriminatory power (D) of REP-PCR for typing members of the A. calcoaceticus-A. baumannii complex, compared with that of ribotyping, we have applied both methods to a collection of 85 strains that included representatives of six DNA groups within the complex. Ribotyping using EcoRI digests yielded 53 patterns (D = 0.98), whereas 68 different REP-PCR patterns were observed (D = 0.99). By computer-assisted analysis of gel images, 74 patterns were observed with REP-PCR (D = 1.0). Overall, REP-PCR typing proved to be slightly more discriminatory than ribotyping. Our results indicate that REP-PCR typing used boiled colonies is a simple, rapid, and effective means of typing members of the A. calcoaceticus-A. baumannii complex.
Antagonistic effect of oral bacteria towards Treponema denticola
Authors: Grenier D
Published: January 2020

This study was designed to isolate oral bacteria exhibiting antagonism towards Treponema denticola and to characterize the inhibitory activity. Eleven bacterial isolates obtained from subgingival sites and identified as either Staphylococcus aureus or Streptococcus mutans were found to inhibit the growth of T. denticola. When the activity spectra of these isolates were analyzed, two additional periodontopathogens (Porphyromonas gingivalis and Prevotella intermedia) were found to be affected, whereas most gram-positive bacteria were not. Strains of S. aureus produce a bacteriocin-like inhibitory substance (heat stable and protease sensitive), whereas the inhibitory effect of S. mutans appears to be related to the production of lactic acid. The negative interactions reported in this paper may govern population shifts observed in subgingival sites.
Nosocomial CDC group IV c-2 bacteremia: epidemiological investigation by randomly amplified polymorphic DNA analysis
Authors: Moissenet D , Tabone M D , Girardet J P , Leverger G , Garbarg-Chenon A , Vu-Thien H
Published: January 2020

The CDC group IV c-2 bacterium is a gram-negative bacillus rarely isolated from clinical specimens. This organism caused catheter-related bacteremia in five immunocompromised children hospitalized in two distinct wards of our institution between November 1993 and October 1994. Three patients recovered on empiric antibacterial chemotherapy combining ceftazidime and amikacin, and a fourth patient required imipenem instead of ceftazidime. The fifth patient recovered without treatment. Catheter removal was never necessary. The randomly amplified polymorphic DNA technique with three different primers was applied to nine isolates recovered by culturing blood from the five children and showed that all of the patients harbored isolates of the same genotype. The source of the outbreak could not be determined.
Restriction fragment length polymorphism of the tdh and trh genes in clinical Vibrio parahaemolyticus strains
Authors: Suthienkul O , Iida T , Park K S , Ishibashi M , Supavej S , Yamamoto K , Honda T
Published: January 2020

The restriction fragment length polymorphism of the genes encoding thermostable direct hemolysin (tdh) and thermostable direct hemolysin-related hemolysin (trh) was analyzed for 137 strains of Vibrio parahaemolyticus isolated from specimens from diarrheal patients in Thailand. The HindIII restriction fragment patterns of tdh and trh were grouped into five and four types, respectively. A strong association between the restriction fragment patterns of tdh and trh was observed with V. parahaemolyticus strains.
Identification of group B rotaviruses with short genome electropherotypes from adult cows with diarrhea
Authors: Parwani A V , Lucchelli A , Saif L J
Published: January 2020

Two field strains (BB-RVLV and KD) of group B rotaviruses from adult dairy cows with diarrhea displayed short genome electropherotypes. Gnotobiotic calves inoculated with fecal filtrates of each group B rotavirus developed diarrhea, and only group B rotaviruses or antigens were detected in the feces by immunoelectron microscopy and in intestinal epithelial cells by immunofluorescent staining, respectively. The feces or intestinal contents of the cows and inoculated calves were negative for group A and C rotaviruses by enzyme-linked immunosorbent assay, immunoelectron microscopy, or cell culture immunofluorescence assays. Comparison of the genome electropherotypes of the calf-passaged BB-RVLV and KD strains with the original samples and reference bovine group A, B, and C rotaviruses revealed conservative of their short-genome electropherotypes and double-stranded RNA migration patterns characteristics of group B rotaviruses. To our knowledge, our previous study (L.J. Saif, K.V. Brock, D.R. Redman, and E.M. Kohler, Vet. Rec. 128:447-449, 1991) and this report are the first description of bovine group B rotaviruses (in a mixed infection with bovine coronavirus or singly in fecal contents) in adult cows with diarrhea and this is the first report of short-genome electropherotypes among group B rotaviruses.
Detection of parvovirus B19 DNA in bone marrow cells by chemiluminescence in situ hybridization
Authors: Musiani M , Roda A , Zerbini M , Gentilomi G , Pasini P , Gallinella G , Venturoli S
Published: January 2020

A chemiluminescence in situ hybridization method was developed for the search of B19 parvovirus DNA in bone marrow cells, employing digoxigenin-labeled B19 DNA probes, immunoenzymatically detected with a highly sensitive 1,2-dioxetane phosphate as chemiluminescent substrate. The light emitted from the in situ-hybridized probe was analyzed and measured by a high-performance luminograph connected to an optical microscope and to a personal computer for the quantification of the photon fluxes from the single cells and for image analysis. The chemiluminescence in situ hybridization was applied to bone marrow cell smears of patients with aplastic crisis or hypoplastic anemia, who had been previously tested by in situ hybridization with colorimetric detection, dot blot hybridization, and nested PCR. The chemiluminescent assay provided an objective estimation of the data, proved specific, and showed an increased sensitivity in detecting B19 DNA compared with in situ hybridization with colorimetric detection.
Quantitative detection of human immunodeficiency virus (HIV) antigen by the Enzymun-Test: comparison with alternative assays and nucleic acid sequence-based amplification of HIV type 1 RNA
Authors: Weber B , Melchior W , Preiser W , Hess G , Wahl M , Braner J , Doerr H W
Published: January 2020

A new modular automated enzyme immunoassay (EIA) (Enzymun-Test HIV Ag: Boehringer Mannheim) for quantitative human immunodeficiency virus (HIV) antigen detection was evaluated by testing a panel of 1,506 serum samples, including seroconversions, dilution series, follow-up samples from patients under antiretroviral therapy, single serum specimens from HIV-seropositive individuals in different stages of infection, potentially cross-reactive samples, and sera from HIV-negative hospitalized patients. The Abbott HIV type 1 (HIV-1) antigen monoclonal antibody assay served as the reference assay, and nucleic acid sequence-based amplification (Organon Teknika) for quantitative amplification of HIV-1 RNA was used for follow-up of patients under antiretroviral chemotherapy. The Boehringer Mannheim and Abbott EIAs showed concordant results for the early detection of HIV antigen in all the seroconversion panels. The follow-up samples from 29 HIV-infected individuals under antiretroviral therapy gave divergent results between both antigen tests. For the detection of HIV antigen in single serum samples from HIV-infected patients in different stages of HIV infection, a higher number of positive samples was detected with the Abbott HIV-1 antigen monoclonal antibody assay in samples from patients in stages II and III of HIV infection. The Enzymun-Test detected three or more positive samples than did the Abbott assay among the samples of patients with AIDS. The concordance on a sample-to-sample basis between the Boehringer Mannheim and Abbott EIAs was 98.6%. The sensitivity of the Enzymun-Test in comparison to the reference assay was 97.2%; the specificity was 98.8%. Although no close correlation could be found between the amount of viral RNA in serum detected by nucleic acid sequence-based amplification and the concentration of HIV antigen, a high HIV-1 RNA copy number was mostly associated with high levels of HIV antigen. In conclusion, the Enzymun-Test permits accurate HIV antigen detection and offers, in contrast to previous assays, the possibility of completely automated detection.
Case of fatal systemic infection with an Aureobacterium sp.: identification of isolate by 16S rRNA gene analysis
Authors: Saweljew P , Kunkel J , Feddersen A , Baumert M , Baehr J , Ludwig W , Bhakdi S , Husmann M
Published: January 2020

The case of a 75-year-old man who succumbed to a disseminated infection most likely caused by a species of the genus Aureobacterium is reported. Identification of the isolate was achieved by comparative 16S rRNA gene analysis. Aureobacteria are commonly found in the environment. However, only recently have they been recognized as a cause of infections including septicemia and soft tissue infections. To our knowledge, this is the first documentation of a fatal infection caused by an Aureobacterium sp.
Complicated soft tissue infection with prepatellar bursitis caused by Paecilomyces lilacinus in an immunocompetent host: case report and review
Authors: Westenfeld F , Alston W K , Winn W C
Published: January 2020

Documented Paecilomyces lilacinus infections are quite rare. Most reports involve immunocompromised patients or implanted objects. We report the first case of complicated soft tissue infection caused by P. lilacinus in an immunocompetent host. The spectrum of infections involving this fungus is reviewed.
Molecular typing of nosocomial strains of Legionella pneumophila by arbitrarily primed PCR
Authors: Grattard F , Berthelot P , Reyrolle M , Ros A , Etienne J , Pozzetto B
Published: January 2020

Arbitrarily primed PCR with two different primers was compared with ribotyping and monoclonal antibody analysis for typing Legionella strains. Applied to 11 epidemiologically unrelated strains, arbitrarily primed PCR resulted in an index of discrimination of 100% with both primers. It was found able to identify an epidemic clone of Legionella pneumophila serogroup 1 that was isolated from both patients and a hot water circuit of the same hospital.
Identification of IS1356, a new insertion sequence, and its association with IS402 in epidemic strains of Burkholderia cepacia infecting cystic fibrosis patients
Authors: Tyler S D , Rozee K R , Johnson W M
Published: January 2020

Burkholderia cepacia is now recognized as an important opportunistic pathogen in cystic fibrosis (CF) and other compromised patients. Epidemicity among CF patients has been attributed to at least one particularly infectious strain (strain ET12), and both genetic evidence and anecdotal evidence suggest that this strain, currently endemic in Ontario, and those causing an epidemic in the United Kingdom, are indeed the same. Our study was conducted to determine whether there was any association between the presence of various insertion sequence (IS) elements, the cable pilin subunit gene (cblA), electrophoretic type (ET), and ribotype (RT) in a collection of 97 clinical and 2 environmental isolates of B. cepacia. No apparent linkage was found for IS elements IS401, IS402, IS406, IS407, and IS408 with ET or RT. The cblA target, said to be a marker for high infectivity, was detected in 100% (38 of 38) of strains of B. cepacia ET12 and in a single strain of ET13 that differed in a single enzyme allele. A new IS, IS1356, identified during the investigation, was present in 71.7% of all isolates, and 50.7% of these isolates harbored IS1356 as a hybrid IS element inserted into IS402. IS1356 is 1,353 bp in length, and when it is inserted into IS402 it results in a 10-bp duplication at the site of insertion. IS1356 contains one major open reading frame of 1,260 bp coding for a putative transposase which has significant homology to ISRm3 in Rhizobium meliloti (59%) and to an undesignated IS element in Corynebacterium diphtheriae (49%). The IS402-IS1356 element was found exclusively in the epidemic strains from Ontario and the United Kingdom, being detected in 94.7% (36 of 38 isolates) of B. cepacia ET12 isolates. Of the two ET12 isolates found to be devoid of the IS402-IS1356 element, both contained IS1356 unassociated with IS402, one was temporally unrelated to the epidemic, and the other was from a CF patient in a geographic area remote from Ontario and the United Kingdom. It is evident that the IS402-IS1356 hybrid element, the cblA pilin subunit gene, and the allelic suite represented by multilocus enzyme electrophoretic type ET12 may provide useful markers for the epidemic, highly transmissible transatlantic strain isolated in Ontario and the United Kingdom.
Molecular characterization of Mycobacterium paratuberculosis isolates from sheep, goats, and cattle by hybridization with a DNA probe to insertion element IS900
Authors: Bauerfeind R , Benazzi S , Weiss R , Schliesser T , Willems H , Baljer G
Published: January 2020

Mycobactin J-dependent mycobacterial isolates from sheep, goat, and cattle herds with Johne's disease in Morocco, South Africa, the United States, and Germany were tested for the repetitive insertion sequence IS900 of Mycobacterium paratuberculosis by PCR. The IS900 PCR target sequence was detected in 90 of 93 fecal culture isolates tested (96.8%). Restriction fragment length polymorphisms (RFLPs) and in vitro growth characteristics were studied in 46 of the IS900-positive isolates and in two bovine vaccine strains of M. paratuberculosis. Five different RFLP types were identified in PvuII digests of genomic DNA by Southern hybridization with a DNA probe specific for IS900. All isolates of M. paratuberculosis could be classified into two major clusters by their growth rates as well as the relatedness of their PvuII-RFLP hybridization patterns. All of the sheep isolates were classified into cluster I (extremely slow growth), while all cattle and goat isolates were members of cluster II (moderately slow growth). Different PvuII-RFLP patterns were detected in different sheep flocks from Morocco and South Africa. Our results demonstrate that genetically and phenotypically different strains of M. paratuberculosis were present in ruminant populations. The strains from sheep in Morocco and South Africa tested in the study appeared to belong to a unique group of M. paratuberculosis strains that might have adapted to this host species. The presence of several genetically distinct strains in different sheep flocks suggested that analysis of IS900-specific RFLP patterns may provide a useful tool for the epidemiologic investigation of ovine paratuberculosis outbreaks.
Epidemic typhoid in Chile: analysis by molecular and conventional methods of Salmonella typhi strain diversity in epidemic (1977 and 1981) and nonepidemic (1990) years
Authors: Fica A E , Prat-Miranda S , Fernandez-Ricci A , D'Ottone K , Cabello F C
Published: January 2020

From 1977 to 1986, Chile experienced an important typhoid fever epidemic, despite statistics that indicated apparently improving levels of sanitation of drinking water and sewage disposal. The lack of antibiotic resistance among the Salmonella typhi strains isolated during this period, the mild clinical presentation of the disease, and the initially low level of efficacy of the S. typhi Ty21a vaccine in the population exposed to the epidemic suggested that this epidemic might have resulted from the dissemination of S. typhi strains with unique characteristics. To investigate this hypothesis, we used conventional methods (bacteriophage typing and biotyping) and molecular methods (restriction fragment length polymorphism analysis, ribotyping, IS200 typing, and PCR amplification of the fliC-d gene) to study a population of 149 S. typhi isolates during 1977, 1981, and 1990, the years that included periods with low (when the disease was endemic) and high (when the disease was epidemic) morbidities. Our results indicate that these S. typhi isolates in Chile represent a number of highly diverse variants of the clone of S. typhi with a worldwide distribution described by Selander et al. (R. K. Selander, P. Beltran, N.H. Smith, R. Helmuth, F.A. Rubin, D.J. Kopecko, K. Ferris, B.D. Tall, A. Cravioto, and J.M. Musser, Infect. Immun. 58:2262-2275, 1990). For example, we detected 26 PstI and 10 ClaI ribotypes among 47 and 16 S. typhi strains belonging to this clone, respectively. These results suggest that the Chilean epidemic was probably produced by multiple sources of infection because of deficient sanitary conditions. These findings illustrate the usefulness of molecular methods for characterizing the potential causes of the typhoid epidemics and the possible routes of transmission of S. typhi strains in typhoid epidemics.
Evaluation of CHROMagar Orientation for differentiation and presumptive identification of gram-negative bacilli and Enterococcus species
Authors: Merlino J , Siarakas S , Robertson G J , Funnell G R , Gottlieb T , Bradbury R
Published: January 2020

A new chromogenic plate medium, CHROMagar Orientation, was evaluated for use in the differentiation and presumptive identification of gram-negative bacilli and Enterococcus species by a multipoint inoculation (replicator) technique. In this study, 1,404 gram-negative bacilli and 74 enterococcal isolates were tested on CHROMagar Orientation. Six control American Type Culture Collection strains were also included with the testing to ensure quality control of the media. Of the Escherichia coli isolates (n = 588) tested, 99.3% produced a pink-to-red color. Only in four isolates that were O-nitrophenyl-beta-D-galactopyranoside (ONPG) negative did this result differ. Proteus mirabilis and P. vulgaris were well differentiated on this medium. P. mirabilis (n = 184) produced a clear colony with diffusible brown pigment around the periphery. By contrast, 15 of 16 P. vulgaris isolates produced bluish-green colonies with a slight brown background. All Aeromonas hydrophila isolates (n = 26) tested produced clear to pink colonies at 35 to 37 degrees C. This colony color changed to blue after 2 to 3 h of incubation at room temperature. A. hydrophila exhibited stronger color and better growth at 30 degrees C. Serratia marcescens (n = 29) demonstrated an aqua blue color that deepened to a darker blue when exposed to room temperature. All enterococcal isolates (n = 74) resulted in a blue color and gave pinpoint colonies on purity subcultures at 35 to 37 degrees C after 18 h of incubation. Similarity in color resulted in failure to discriminate accurately between Klebsiella, Enterobacter, and Citrobacter species. However, these species could be readily differentiated from other members of the family Enterobacteriaceae. Pseudomonas aeruginosa (n = 151) was easily differentiated from members of the Enterobacteriaceae but was less easily distinguishable from other gram-negative nonmembers of the Enterobacteriaceae. The medium was found to facilitate easy visual detection of mixed bacterial isolates in culture. When used in a replicator system, it easily detected mixed growths of organisms which may have otherwise led to false antibiotic susceptibility results. These mixed growths were not obvious on the routine susceptibility testing medium (Isosensitest).
Microwave-accelerated direct immunofluorescent staining for respiratory syncytial virus and influenza A virus
Authors: Hite S A , Huang Y T
Published: January 2020

A microwave-accelerated direct immunofluorescence staining method which requires only 20 min from specimen receipt to interpretation is as effective as conventional methods for detecting respiratory syncytial virus and influenza A virus antigens in clinical specimens. The time required compares favorably with that for the less sensitive Abbott Test Pack RSV.
Restriction endonuclease analysis of Penicillium marneffei
Authors: Vanittanakom N , Cooper C R , Chariyalertsak S , Youngchim S , Nelson K E , Sirisanthana T
Published: January 2020

Forty-six isolates of Penicillium marneffei were differentiated into two DNA types on the basis of their restriction fragment length polymorphisms. Of the 22 human isolates of P. marneffei, 16 (72.7%) were type I and 6 (27.3%) were type II. Of the 23 bamboo rat isolates, 20 from Rhizomys sumatrensis were type I and 3 from Cannomys badius were type II. The soil isolate was type II. These data represent the first molecular epidemiological study of this important emerging fungal pathogen.
A novel genital human papillomavirus (HPV), HPV type 74, found in immunosuppressed patients
Authors: Longuet M , Cassonnet P , Orth G
Published: January 2020

The genome of a novel human papillomavirus (HPV) type, HPV74, was cloned from an iatrogenically immunosuppressed woman with persisting low-grade vaginal intraepithelial neoplasia. HPV74 was found to be phylogenetically related to the low-risk HPV types 6, 11, 44, and 55. HPV74 or a variant of this type was found in specimens from three additional immunosuppressed women but not in about 3,000 anogenital specimens from immunocompetent patients.
Rapid diagnosis of human parainfluenza virus type 1 infection by quantitative reverse transcription-PCR-enzyme hybridization assay
Authors: Fan J , Henrickson K J
Published: January 2020

The detection and quantitation of human parainfluenza virus type 1 (HPIV-1) RNA in nasal wash specimens from 49 children with lower respiratory infections were performed by a reverse transcription-PCR-enzyme hybridization assay (RT-PCR-EHA). The HPIV-1 RT-PCR-EHA was then used to test 40 samples from asymptomatic children. Primers and probes were designed from regions within the HPIV-1 hemagglutinin-neuraminidase gene which are highly conserved among all known genotypes. HPIV-1 was detected in all nine children who were culture positive. Other common respiratory viruses (HPIV-2, -3, and -4, mumps virus, respiratory syncytial virus, and influenza virus) were not detected by the HPIV-1 assay. Forty symptomatic children were negative by culture, and four of these were positive by RT-PCR-EHA. All of the samples from asymptomatic children were negative by culture and RT-PCR-EHA. RT-PCR-EHA was 100% sensitive (95% confidence interval, 0.66 to 1.00) and 95% specific (95% confidence interval, 0.88 to 0.99) compared with culture. The four false-positive results (relative to the results of culture) were in children with lower respiratory infections compatible with HPIV-1 infection and suggest that RT-PCR-EHA may be more sensitive than culture. Our data indicate that HPIV-1 may be underdiagnosed by routine culturing methods. RT-PCR-EHA has been demonstrated to be an easy, rapid, sensitive, and specific test for diagnosing HPIV-1 infection and provides a methodology for the rapid detection of closely related respiratory viruses.
Detection and characterization of antigens in urine of patients with acute, congenital, and chronic Chagas' disease
Authors: Corral R S , Altcheh J , Alexandre S R , Grinstein S , Freilij H , Katzin A M
Published: January 2020

Monoclonal antibodies raised against purified Trypanosoma cruzi urinary antigens were used in an enzyme-linked immunosorbent assay (ELISA) capture test for parasite antigens present in urine specimens of Argentinean and Brazilian patients with Chagas' disease. At diagnosis, antigenuria was demonstrated by ELISA in all acutely and congenitally infected infants studied. Moreover, T. cruzi urinary antigens were detected in samples from three of five patients with acute infections and four of five patients with congenital infections following chemotherapy. At least one ELISA-positive urine specimen from each individual was recorded in a longitudinal survey of 12 chronic chagasic patients. The same parasitic antigens (90 to 80 kDa, pI 5.7 to 6.0; 70 to 65 kDa, pI 4.9 to 4.5; 50 to 45 kDa, pI 5.3 to 5.1; and 40 to 35 kDa, pI 4.8 to 4.5) were identified by immunoprecipitation and two-dimensional polyacrylamide gel electrophoresis analysis of urine samples from patients with different forms of chagasic infection. The 90- to 80-kDa urinary protein resembles a trypomastigote-shed antigen. Determination of antigenuria proved valuable for early diagnosis of Chagas' disease and also for diagnosis of chronic cases with conflicting serology.
Vancomycin-resistant Aureobacterium species cellulitis and bacteremia in a patient with acute myelogenous leukemia
Authors: Nolte F S , Arnold K E , Sweat H , Winton E F , Funke G
Published: January 2020

A 39-year-old male with acute myelogenous leukemia and concomitant porphyria cutanea tarda was admitted to the hospital for consolidation chemotherapy of his leukemia. During his hospitalization, he developed cellulitis of the left hand and persistent bacteremia with a yellow-pigmented, nonfermenting coryneform bacterium that was identified as Aureobacterium sp. The portal of entry for the Aureobacterium infection was probably through the skin lesions due to porphyria cutanea tarda. The infection developed while the patient was receiving vancomycin prophylaxis, and the vancomycin MIC for the isolate was 32 micrograms/ml.
Proposed MIC quality control guidelines for National Committee for Clinical Laboratory Standards susceptibility tests using seven veterinary antimicrobial agents: ceftiofur, enrofloxacin, florfenicol, penicillin G-novobiocin, pirlimycin, premafloxacin, and spectinomycin
Authors: Marshall S A , Jones R N , Wanger A , Washington J A , Doern G V , Leber A L , Haugen T H
Published: January 2020

The present multicenter study proposes broth microdilution quality control (QC) ranges for the antimicrobial agents ceftiofur, enrofloxacin, florfenicol, penicillin G-novobiocin, pirlimycin, premafloxacin, and spectinomycin, which are used in veterinary practice. Six separate laboratories tested replicates of National Committee for Clinical Laboratory Standards (NCCLS)-recommended QC organisms (Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 29213, and Enterococcus faecalis ATCC 29212) on medium lots both common and unique to all laboratories. The proposed ranges were within 3 or 4 log2 dilution steps of the modal MICs for all organism-antimicrobial agent pairs, depending on their MIC distributions. With > or = 94.7% of all MIC results being within the proposed QC ranges, all combinations tested comply with NCCLS guidelines and all have been accepted by the NCCLS subcommittee developing susceptibility testing procedures for veterinary laboratories.
Subtyping Listeria monocytogenes isolates genetically related to the Swiss epidemic clone
Authors: Boerlin P , Bannerman E , Jemmi T , Bille J
Published: January 2020

Macrorestriction analysis by pulsed-field gel electrophoresis was used to assess the diversity of strains within the epidemic-associated electrophoretic type 1 (ET1) clone of Listeria monocytogenes. For this purpose, a total of 144 isolates from Switzerland shown by multilocus enzyme electrophoresis to belong to the ET1 were examined. These isolates were subtyped by macrorestriction analysis using the enzymes ApaI and SmaI and field inversion gel electrophoresis. Among these 144 isolates, 45 were isolated in human listeriosis cases of the postepidemic period of 1988 to 1993 and 44 were isolated in animal listeriosis cases of the same period. Forty-seven isolates were from the epidemic period of 1983 to 1987, and eight additional isolates were from cattle from two different farms. Twenty-nine different subtypes could be identified among the 144 isolates tested. Five major subtypes were found more frequently than the others during the postepidemic period, both in humans and in animals. Two of these subtypes had been previously implicated in outbreaks of listeriosis, thus suggesting that particular pulsed-field gel electrophoresis subtypes may be frequently associated with disease in humans and animals. Two of these frequent subtypes were also suspected to be related to small clusters of listeriosis cases during the postepidemic period. The results obtained by typing epidemiologically related isolates from different animals within the same farms and from different body sites of a given patient confirmed the potential of macrorestriction analysis for epidemiological studies restricted to short periods of time and to small number of isolates. The analysis of 47 isolates related to the Swiss listeriosis epidemic period of 1983 to 1987 and the use of Southern blotting and hybridization experiments show that the interpretation of relatedness between isolates presenting slightly different macrorestriction patterns may be more complex than commonly accepted. In such cases, careful interpretation of the potential molecular mechanisms leading to the differences observed between patterns is necessary.
A 16S rRNA-based PCR assay for detection and identification of granulocytic Ehrlichia species in dogs, horses, and cattle
Authors: Engvall E O , Pettersson B , Persson M , Artursson K , Johansson K E
Published: January 2020

A PCR-based assay was developed for detecting DNA of granulocytic ehrlichiae in blood samples from dogs, horses, and cattle, Primers were designed from 16S rRNA sequence information to specifically amplify DNA from a newly identified Swedish Ehrlichia species. The 16S rRNA nucleotide sequence of this Swedish species differs in only two and three positions from the sequences of Ehrlichia phagocytophila and Ehrlichia equi, respectively, which were also amplified by this PCR system. For evaluation, PCR results were compared with microscopic examination of stained blood smears for the detection of granulocytes containing ehrlichiae (morulae). Thirty-four of 36 microscopically positive samples were also positive by PCR, and 6 microscopically negative samples were negative by PCR as well. Six samples, in which morulae-like structures had been seen, were negative by PCR, also at a lower annealing temperature and when a reamplification of the first PCR products was performed. The identities of the PCR products from some canine and equine isolates were verified by direct DNA sequencing and were found to be identical with the Ehrlichia sequence found in these animal species that had been obtained earlier. The sequences of a segment of approximately 600 nucleotides from two bovine isolates were identical to that of E. phagocytophila, whereas the sequence of another bovine isolate differed in two positions from that of E. phagocytophila and in three positions from the sequences of the canine and equine isolates. Serum samples were analyzed by indirect fluorescent-antibody testing. Seventy-three percent of the animals which were positive by microscopy and PCR also had positive antibody titers. However, it was not possible to rely on a single serological result for diagnosis of present infection. It was, therefore, concluded that PCR was the most reliable method, useful in the clinical laboratory for specific and early diagnosis of granulocytic ehrlichiosis in animals.
Diagnosis of disseminated candidiasis by measurement of urine D-arabinitol/L-arabinitol ratio
Authors: Lehtonen L , Anttila V J , Ruutu T , Salonen J , Nikoskelainen J , Eerola E , Ruutu P
Published: January 2020

Relative amounts of D-arabinitol (fungal origin) and L-arabinitol (part of normal human metabolism) in urine were determined by gas chromatography and mass spectrometry from 61 hospitalized patients with hematological malignancies. Seventeen neutropenic patients with acute leukemia (with 53 samples) had disseminated yeast infections and received empiric antifungal therapy before confirmation of the diagnosis. Control groups consisted of 22 hematologic patients (76 samples) with either mucosal (n = 10) or urinary (n = 12) Candida colonization and 22 neutropenic patients (34 samples) with no clinical or laboratory signs of invasive yeast infection. Reference values were also obtained from 50 healthy adults (50 samples). The mean urine D-arabinitol/L-arabinitol ratio +/- standard deviation (range) was 16.91 +/- 41.79 (1.41 to 254.75) in patients with disseminated infection, 2.73 +/- 2.48 (1.11 to 19.00) in colonized hematologic patients, 2.12 +/- 0.84 (1.16 to 5.84) in neutropenic controls, and 1.95 +/- 0.34 (0.97 to 3.44) in healthy adults (P < 0.001 between patients with disseminated infection and all control groups). The sensitivity and specificity of the assay for detecting disseminated yeast infection were, respectively, 88 and 91% per patient (upper limit of normal, 4.00). Seventy-one percent of patients already expressed elevated values at the onset of empiric antifungal therapy. The diagnosis of disseminated infection was confirmed on average 21.7 days after the first elevation of the D-arabinitol/L-arabinitol ratio. The method contributes to diagnosis of disseminated yeast infection and helps in monitoring patients at risk, to support the initiation of antifungal therapy at an early stage of the disease.
Identification and molecular characterization of serological group C streptococci isolated from diseased pigs and monkeys in Indonesia
Authors: Soedarmanto I , Pasaribu F H , Wibawan I W , Lämmler C
Published: January 2020

The present study was designed to comparatively investigate 34 beta-hemolytic streptococci isolated from infected pigs and monkeys from various islands in Indonesia. According to the serological and biochemical data, all 34 isolates were Lancefield's serological group C streptococci and could be identified as Streptococcus equi subsp. zooepidemicus. Of the 34 group C streptococci investigated, 28 grew on solid media in large, mucoid colonies, in fluid media at a uniform turbidity, and in soft agar in diffuse colonies. A decapsulation test with a hyaluronidase-producing Staphylococcus aureus strain revealed the hyaluronic acid nature of the capsular material. The remaining six streptococci grew on solid media in small, nonmucoid colonies, in fluid media as sediment with clear supernatant, and in soft agar in compact colonies. Determination of surface hydrophobicity by salt aggregation revealed a hydrophilic surface for the encapsulated bacteria and a hydrophobic surface for the unencapsulated group C streptococci. To further analyze the epidemiological relationships, all 34 mucoid and nonmucoid isolates from pigs and monkeys were subjected to protein and DNA fingerprinting. The latter was performed by pulsed-field gel electrophoresis. The protein profiles of all 34 isolates and the DNA profiles of 32 isolates appeared to be identical, with the DNA profiles of 2 isolates being closely related, indicating that a single virulent clone is responsible for this disease outbreak in Indonesia.
Comparison of mycobacteria growth indicator tube with BACTEC 460 for detection and recovery of mycobacteria from clinical specimens
Authors: Badak F Z , Kiska D L , Setterquist S , Hartley C , O'Connell M A , Hopfer R L
Published: January 2020

We compared the Mycobacteria Growth Indicator Tube (MGIT) system with the BACTEC 460 (B460) and Lowenstein Jensen (LJ) systems for the recovery of mycobacteria (acid-fast bacteria [AFB]) from 1,441 clinical specimens. Excluding 13 isolates of Mycobacterium gordonae, 178 significant AFB isolates were recovered from 113 patients. Isolates (119) of the Mycobacterium avium complex (MAC) accounted for 67% of all isolates, while isolates (30) of the Mycobacterium tuberculosis complex (MTB) accounted for 17% of isolates. The MGIT system recovered 98 (82%) MAC and 27 (90%) MTB isolates, while the B460 system recovered 101 (85%) MAC and 28 (93%) MTB isolates and the LJ system recovered 91 (76%) MAC and 25 (83%) MTB isolates. Overall, the MGIT system recovered 152 isolates of AFB (85.4% sensitivity), and the B460 and LJ systems recovered 151 (84.8% sensitivity) and 137 (76.9% sensitivity) AFB isolates, respectively. The recoveries of AFB with combinations of media were as follows: MGIT + LJ, 93.2%; B460 + LJ, 92.1%; and MGIT + B460, 96.6%. Although the sensitivity of MGIT was equivalent to that of B460, MGIT required a longer incubation (median, 11 days) than did B460 (median, 8 days) to become positive (P < 0.05).
Second-generation line probe assay for hepatitis C virus genotyping
Authors: Stuyver L , Wyseur A , van Arnhem W , Hernandez F , Maertens G
Published: January 2020

Because of the enormous variability of hepatitis C virus (HCV), the development of reliable genotyping assays is a formidable challenge. The optimal genotyping region appears to be the 5' untranslated region (UR) because of high conservation within, but considerable variability between, genotypes. In this study, 21 probes dispersed over seven variable 5' UR areas were applied to a line probe assay (LiPA) and used to analyze 506 HCV-infected sera from different geographical regions representing a multitude of subtypes. At least 31 different reactivity patterns emerged, with 404 (80%) of 506 distributed over 11 prototype patterns, in general corresponding to subtypes 1a, 1b, 2a/2c, 2b, 3a, 5a, and 6a and several type 4 subtypes. Subtyping specificity ranged from 97% in Hong Kong to 90% in Europe but was only 11% in West Africa, while typing specificity was always 100% when samples from Vietnam were excluded. In a second evaluation, the subtype prediction by LiPA of 448 GenBank 5' UR HCV sequences was scored. Of the 58 theoretically predicted patterns, 321 sequences (72%) were covered by the 11 prototype patterns. We concluded that (i) the selected probes detected the corresponding signature motifs in the seven variable regions with 100% reliability; (ii) these motifs allowed correct type interpretation of samples collected worldwide, with the exclusion of Vietnam, Thailand, or Vietnamese patients residing in European hospitals; and (iii) subtyping specificities vary according to geographical region, with 11 prototype subtyping patterns identifying the majority of samples from Europe and the Americas. These results indicate that the LiPA is a reliable assay applicable to routine typing and subtyping of HCV specimens.
Epidemiologic evidence for Lancefield group C beta-hemolytic streptococci as a cause of exudative pharyngitis in college students
Authors: Turner J C , Hayden F G , Lobo M C , Ramirez C E , Murren D
Published: January 2020

The isolation rates of strains of group C beta-hemolytic streptococci from throat swab cultures of patients with exudative pharyngitis, the common cold, and healthy controls were compared. By using a cohort study design in a college health service, patients with exudative pharyngitis were retrospectively identified by description of tonsillar exudate on chart review. Patients with rhinoviral infection were prospectively identified during a common cold study. Healthy controls were prospectively recruited from patients presenting with noninfectious conditions. Isolation of Lancefield group A and C beta-hemolytic streptococci from throat cultures was used as an outcome measurement. A total of 265 students (62% female; average age 20.2 years) with exudative pharyngitis were identified. A total of 75 students (60% female; average age, 21.7 years) from a common cold study with rhinoviral infection were identified. A total of 162 students (53% female; average age, 22.6 years) were recruited as healthy controls. Group A beta-hemolytic streptococci were isolated from 5% of patients with pharyngitis but none of those with rhinovirus (P = 0.045) and none of the controls (P = 0.007). Group C Streptococcus dysglactiae subsp. equisimilis was isolated from 11% of patients with pharyngitis but none of those with rhinovirus (P = 0.006) and 2% of controls (P = 0.001). Lancefield group C Streptococcus anginosus was isolated from 8% of patients with pharyngitis but 3% of those with rhinovirus (P = 0.18) and 1% of controls (P = 0.006). Heavier growth of colonies on the primary culture plate was observed for patients from whom S. equisimilis and group A beta-hemolytic streptococci were isolated. Lancefield group C beta-hemolytic streptococci appear to be associated with exudative pharyngitis in college students.
Persistence of Borrelia burgdorferi in experimentally infected dogs after antibiotic treatment
Authors: Straubinger R K , Summers B A , Chang Y F , Appel M J
Published: January 2020

In specific-pathogen-free dogs experimentally infected with Borrelia burgdorferi by tick exposure, treatment with high doses of amoxicillin or doxycycline for 30 days diminished but failed to eliminate persistent infection. Although joint disease was prevented or cured in five of five amoxicillin- and five of six doxycycline-treated dogs, skin punch biopsies and multiple tissues from necropsy samples remained PCR positive and B. burgdorferi was isolated from one amoxicillin- and two doxycycline-treated dogs following antibiotic treatment. In contrast, B. burgdorferi was isolated from six of six untreated infected control dogs and joint lesions were found in four of these six dogs. Serum antibody levels to B. burgdorferi in all dogs declined after antibiotic treatment. Negative antibody levels were reached in four of six doxycycline- and four of six amoxicillin-treated dogs. However, in dogs that were kept in isolation for 6 months after antibiotic treatment was discontinued, antibody levels began to rise again, presumably in response to proliferation of the surviving pool of spirochetes. Antibody levels in untreated infected control dogs remained high.