bluuebunny/crossref_metadata_2025 huggingface dataset:
Diagnosis of Chlamydia trachomatis infections in asymptomatic men and women by PCR assay
Authors: Toye B , Peeling R W , Jessamine P , Claman P , Gemmill I
Published: January 2020

A PCR assay was evaluated for its ability to detect genital chlamydial infection in asymptomatic men and women. Urethral swab specimens were collected from 472 men for culture and PCR assay, and first-void urine (FVU) specimens were collected from 379 of these men for enzyme immunoassay (EIA) and PCR assay. Cervical swab specimens were collected from 242 women for culture, EIA, and PCR assay. Patients were considered infected if they were culture positive or positive by PCR with both plasmid- and major outer membrane protein-based primers. By using this extended "gold standard," the prevalence of infection in this population was 7.6% for men and 7.9% for women. For men, the sensitivities of urethral swab specimen culture and PCR and FVU specimen EIA and PCR were 61, 72, 55, and 91%, respectively. All assays had specificities of > or = 99.8%. The positive and negative predictive values for PCR testing of FVU specimens were 100 and 99.4%, respectively, compared with values of 96.3 and 97.8%, respectively, for PCR of urethral swab specimens. The sensitivities of cervical swab specimen culture and PCR testing were 42 and 90%, respectively, with corresponding specificities of 100 and 99.3%. All cervical swabs were negative by EIA. Molecular techniques such as PCR assays are valuable tools for the detection of symptomatic genital chlamydial infection. In particular, PCR assays of FVU specimens from men offer a highly sensitive, noninvasive screening tool that will likely improve patient compliance for diagnostic testing.
Flow cytometric immunofluorescence assay for detection of antibodies to human immunodeficiency virus type 1 using insoluble precursor forms of recombinant polyproteins as carriers and antigens
Authors: Hu Y W , Birch P , Balaskas E , Zeibdawi A , Scalia V , Thériault-Valin S A , Gill P , Aye M T
Published: January 2020

A new serological assay, the recombinant flow cytometric immunofluorescence assay (r-FIFA), was developed for the early detection of human immunodeficiency virus type 1 (HIV-1) antibodies by using recombinant insoluble forms of HIV-1 Gag-p45, Gag-gp41 chimeric protein, gp160, Po197 polyprotein as antigens and autologous carriers through flow cytometry. These recombinant proteins were expressed in insect cells by a baculovirus expression system. Eight anti-HIV-1 seroconversion panels, a low-titer anti-HIV-1 panel from Boston Biomedica Inc. (BBI), and three HIV-1 seroconversion specimens from the Provincial Health Laboratory of Ontario, Toronto, Ontario, Canada (PHL), were tested and analyzed by r-FIFA. In sensitivity comparisons between r-FIFA and tests licensed by the U.S. Food and Drug Administration, which were used to test all of the HIV-1 panels from BBI, detection of HIV-1 antibody by r-FIFA was on average greater than 20 days earlier than that by enzyme immunoassay. The sensitivity of r-FIFA has permitted the detection of HIV-1-specific immunoglobulin G (IgG), IgM, and IgA antibodies during seroconversion. A kinetic analysis of HIV-1 antibody production of r-FIFA has shown that either IgG or IgM, or both, can be detected, depending on the phase and type of the immune response in the HIV-1-infected individual. Both primary and secondary immune responses were observed during this period. The r-FIFA results suggest that implementation of r-FIFA may significantly reduce the "window" period from the time of infection to the time of seroconversion, with earlier detection of antibodies after initial infection. This would also make it possible for us to understand the immune response and the precise mechanisms of immunopathogenesis in the early period of HIV-1 infection.
Evaluation of immunochromatographic assay systems for rapid detection of hepatitis B surface antigen and antibody, Dainascreen HBsAg and Dainascreen Ausab
Authors: Sato K , Ichiyama S , Iinuma Y , Nada T , Shimokata K , Nakashima N
Published: January 2020

We evaluated two immunochromatographic assays (ICAs), Dainascreen HBsAg for detecting human hepatitis hepatitis B surface antigen (HBsAg) and Dainascreen Ausab for detecting human hepatitis B surface antibody (anti-HBs) in human serum. The ICA systems are composed of a comb-shaped device that contains nitrocellulose strips on which complexes of HBsAg and anti-HBs can be visualized. The results can be read within 15 min of incubation. The limit of detection for HBsAg was 3.1 ng/ml and that for anti-HBs was 42 mIU/ml. Results of HBsAg detection agreed completely with those of conventional enzyme immunoassays (EIAs) and showed a 100% sensitivity (158 of 158 samples) and a 100% specificity (304 of 304 samples). The Dainascreen Ausab detected 184 of the 199 EIA-positive samples (sensitivity, 92.5%) and yielded 6 positive results among the 281 EIA-negative samples (specificity, 97.9%). The ICA systems are rapid and sensitive methods for detecting HBsAg and anti-HBs. They are low-cost systems that need no complex instrumentation for analysis and can be recommended for routine use in clinical microbiology laboratories.
DNA fingerprinting of Vibrio cholerae strains with a novel insertion sequence element: a tool to identify epidemic strains
Authors: Bik E M , Gouw R D , Mooi F R
Published: January 2020

A novel Vibrio cholerae insertion sequence element, designated IS1004, was characterized and used for DNA fingerprinting of Vibrio spp. IS1004 comprises 628 bp and contains an open reading frame whose product shows a large degree of sequence identity with the IS200-encoded transposase. IS1004 was present in one to eight copies in most of the V. cholerae strains analyzed. The IS1004-generated fingerprints of epidemic V. cholerae strains with serotype O1 were closely related, although it was possible to distinguish between the two biotypes, classical and El Tor. Non-O1 serotype strains generally showed heterogeneous patterns unrelated to those of the epidemic O1 strains. Several strains were observed with identical or related fingerprint patterns but expressed different serotypes. Conversely, strains with different fingerprint patterns but identical serotypes were also found. These observations indicate that the gene clusters coding for distinct O antigens may be transferred horizontally between V. cholerae strains. Two examples of non-O1 strains with a fingerprint resembling that of epidemic O1 strains were found; they were the O139 Bengal strain and an O37 strain. The O139 Bengal strain is closely related to the El Tor biotype. The O37 strain was responsible for a large cholera outbreak in Sudan in 1968 and was classified as a noncholera vibrio. Our study, however, shows that the O37 Sudan strain is genetically closely related to classical O1 strains. Similar to O139 Bengal, O37 Sudan lacked most of the O1 antigen cluster but did contain flanking genes. Thus, O37 Sudan represents a second example of an epidemic V. cholerae strain carrying non-O1 antigens. This study underlines the importance of genotypic methods for the differentiation of V. cholerae strains and for recognition of strains with epidemic potential.
Typing of Staphylococcus aureus by PCR for DNA sequences flanked by transposon Tn916 target region and ribosomal binding site
Authors: Cuny C , Witte W
Published: January 2020

The continuous intra- and interhospital spread of multiresistant Staphylococcus aureus demands a rapid molecular typing system. This study describes the fingerprinting of S. aureus by PCR amplification of DNA sequences flanked by the target site for transposon Tn916 and the ribosomal binding site and neighboring nucleotides (target 916-Shine-Dalgarno PCR [tar 916-shida PCR]). Both starting points for PCR are known to be randomly distributed on the S. aureus chromosome. By use of SmaI-macrorestriction patterns as the reference method it was shown that this PCR genotyping discriminates among strains of the major clonal groups of the species S. aureus (strains with phage patterns 29, +, 94, 96, and 95 as well as group II and group III patterns) and identifies the six epidemic methicillin-resistant S. aureus strains prevalent in German hospitals. All of the investigated strains including methicillin-sensitive. S. aureus were typeable. Tar 916-shida patterns are stable during the dissemination of epidemic methicillin-resistant S. aureus among different hospitals.
Comparison of outbreak and nonoutbreak Acinetobacter baumannii strains by genotypic and phenotypic methods
Authors: Dijkshoorn L , Aucken H , Gerner-Smidt P , Janssen P , Kaufmann M E , Garaizar J , Ursing J , Pitt T L
Published: January 2020

Thirty-one Acinetobacter baumannii strains, comprising 14 strains from 14 outbreaks in different northwestern European cities and 17 sporadic strains, were compared by investigating various properties of the strains including biotype, antibiogram, cell envelope protein electrophoretic profile, ribotype pattern, and the band pattern generated by a novel genomic fingerprinting method, named AFLP, which is based on the selective amplification of restriction fragments. Results showed that 12 strains from unrelated outbreaks were linked together in two clusters according to their similarities by these typing methods, whereas sporadic strains were more heterogeneous. Outbreak strains appeared to be markedly more resistant to antibiotics than nonoutbreak strains. The uniformity of typing characters in two sets of outbreak strains suggests that strains in each cluster have a common clonal origin.
Prevalence of fluorescent monoclonal antibody-nonreactive Neisseria gonorrhoeae in five North American sexually transmitted disease clinics
Authors: Smith K R , Fisher H C , Hook E W
Published: January 2020

We compared a direct fluorescent monoclonal antibody (DFA) test with alternative enzymatic and fermentation tests for identifying presumptive gonococcal isolates in a systematic sample from patients attending five sexually transmitted disease clinics in five cities. Fourteen (2.5%) of 556 isolates from three clinics were nonreactive with DFA confirmatory reagent and reactive by both the Quad-Ferm (BioMerieux Vitek Inc.) and the Rapid NH (Innovative Diagnostic Systems, Inc.) tests. The prevalence of DFA-nonreactive Neisseria gonorrhoeae isolates varies geographically and is independent of local methods for the identification of possible gonococci.
Extended incubation of culture plates improves recovery of Bordetella spp
Authors: Katzko G , Hofmeister M , Church D
Published: January 2020

Extended incubation of culture plates was studied to see if the recovery of Bordetella spp. from nasopharyngeal swabs could be improved. Forty-eight Bordetella isolates were recovered from 103 children (overall positive-culture rate, 46.6%) who met the clinical case definition of pertussis. Seven of 44 (16%) B. pertussis isolates and 2 of 4 (50%) B. parapertussis isolates were recovered only after extended incubation of nasopharyngeal cultures up to 12 days.
Highly toxic clone of Actinobacillus actinomycetemcomitans in geographically widespread cases of juvenile periodontitis in adolescents of African origin
Authors: Haubek D , Poulsen K , Westergaard J , Dahlèn G , Kilian M
Published: January 2020

The bacterium Actinobacillus actinomycetemcomitans has been implicated in the pathogenesis of juvenile periodontitis as the etiologic agent on the basis of several lines of circumstantial evidence. A matter of extensive debate is whether A. actinomycetemcomitans is an exogenous contagious pathogen or an opportunistic pathogen that resides in the normal oral microflora. Here we show evidence of a single clone of A. actinomycetemcomitans isolated from multiple patients with juvenile periodontitis in members of families of African origin living in geographically widespread areas. The clone is characterized by a 530-bp deletion in the leukotoxin gene operon, resulting in a significantly increased production of leukotoxin.
Rare association of human herpesvirus 6 DNA with human papillomavirus DNA in cervical smears of women with normal and abnormal cytologies
Authors: Romano N , Romano F M , Viviano E , Vitale F , Villafrate M R , Perna A M , Bonura F , Guttadauro R
Published: January 2020

We investigated by nested PCR the possible association of human herpesvirus 6 (HHV-6) and human papillomavirus (HPV) genomes in the cervixes of 109 women with normal and abnormal cytological smears. HPV DNA was detected in 8.33% of 24 women with normal cytologies and in 41.1% of 85 women with abnormal cytologies; the proportion of HPV DNA was directly related to the severity of the lesions. HHV-6 DNA was found in only one patient, who had a cytological pattern of koilocytosis. The HHV-6 genome was classified by restriction enzyme analysis as variant B. The study indicates that detection of the HHV-6 genome in the cervixes of women with a wide spectrum of gynecological complaints is a rare event and rules out the possible association between HHV-6 and HPV genomes in cervical cancer lesions.
Rapid diagnosis of respiratory syncytial virus infections in immunocompromised adults
Authors: Englund J A , Piedra P A , Jewell A , Patel K , Baxter B B , Whimbey E
Published: January 2020

Although rapid antigen detection methods for the documentation of respiratory syncytial virus (RSV) infections are widely used with pediatric patients, these tests have not been prospectively evaluated in immunocompromised (IC) adults. For bone marrow transplant recipients and adult patients undergoing chemotherapy for leukemia who had recent onset of respiratory symptoms, respiratory samples (combined nasal wash [NW]-throat swab [TS], endotracheal tube [ET] aspirate, or bronchoalveolar lavage [BAL] samples) were collected for simultaneous culture and rapid antigen detection with the Directigen test kit (Becton Dickinson, Cockeysville, Md.). NW specimens from hospitalized pediatric patients with suspected RSV infection were also evaluated. Viral quantitation was performed on aliquots of the original specimens. A total of 539 samples from 372 adult patients were evaluated. RSV was isolated from 56 specimens (40 NW-TS, 7 ET aspirate, and 9 BAL specimens). By using culture as the "gold standard," rapid antigen detection had a sensitivity of 15% for adult NW-TS specimens, 71.4% for ET aspirate specimens, and 88.9% for BAL specimens; the specificity was > or = 97% for all specimen types. Significantly greater viral quantities were present in pediatric NW specimens than in adult NW specimens. In adults, more virus was present in BAL and ET aspirate specimens than in NW-TS specimens. Rapid detection of antigen respiratory samples obtained from the lower respiratory tracts of IC adults is sensitive and specific, but detection in upper respiratory tract samples is insensitive. The lower sensitivity of antigen detection in NW-TS specimens may be due to decreased viral load. A BAL specimen is more sensitive than an NW-TS specimen for the rapid diagnosis of RSV disease in IC adults.
Evaluation of Pyloriset Dry, a new rapid agglutination test for Helicobacter pylori antibody detection
Authors: Lozniewski A , De Korwin J D , Conroy M C , Plenat F , Weber M
Published: January 2020

We evaluated the performance of a new latex agglutination test, Pyloriset Dry (Orion Diagnostica, Espoo, Finland), in the simultaneous detection of immunoglobulin G (IgG), IgA, and IgM antibodies to Helicobacter pylori and compared it with that of the Pyloristat test (BioWhittaker, Fontenay-sous-Bois, France), an enzyme-linked immunosorbent assay detecting IgG to H. pylori, for 96 untreated dyspeptic patients who had undergone gastroduodenal endoscopy. Infection was diagnosed in 56 cases by positive culture and/or positive Giemsa stain and rapid urease test (antral biopsies) and was associated with chronic gastritis in 52 patients. Forty noninfected patients did not have chronic gastritis. The sensitivity of Pyloriset Dry was 91.1%. The sensitivity of Pyloristat was 91.1 or 82.1%, depending on whether equivocal results were considered positive or negative, respectively. Both tests had a specificity of 87.5%. Their performances were not statistically different. Thus, Pyloriset Dry is an alternative to serological tests for adults, particularly when a small number of serum samples has to be tested.
Comparison of amplicor and 32-kilodalton PCR for detection of Mycobacterium tuberculosis from sputum specimens
Authors: Soini H , Agha S A , El-Fiky A , Viljanen M K
Published: January 2020

The commercial PCR test Amplicor was compared with the 32-kDa PCR for detection of Mycobacterium tuberculosis from 76 sputum specimens from Egyptian patients. Both tests performed with rather equal efficacy (resolved sensitivity of 88.9% for both tests; specificity of 98.0% for Amplicor and 93.9% for 32-kDa PCR). PCR was found to be useful in detection of auramine fluorescent stain-positive, culture-negative specimens.
Infrequent detection of lipoarabinomannan antibodies in human immunodeficiency virus-associated mycobacterial disease. Swiss HIV Cohort Study
Authors: Boggian K , Fierz W , Vernazza P L
Published: January 2020

A commercially available test for the serologic diagnosis of tuberculosis was evaluated for its applicability in human immunodeficiency virus (HIV)-positive patients. Antibodies to lipoarabinomannan were detectable in sera from only 9 of 85 HIV-positive patients with a confirmed diagnosis of tuberculosis. Given the low degree of sensitivity of the assay with sera from HIV-infected patients, the study does not support the use of this serologic assay for the diagnosis of tuberculosis in HIV-infected patients.
Strain variation among and antifungal susceptibilities of isolates of Candida krusei
Authors: Berrouane Y F , Hollis R J , Pfaller M A
Published: January 2020

Candida krusei is an emerging pathogen that is well known for its propensity to develop resistance to fluconazole and other azoles. Despite the potential clinical significance of C. krusei, little is known of its epidemiology and genetic diversity as defined by the newer DNA-based typing methods. We investigated the genotypic diversity and antifungal susceptibility of 67 clinical isolates from 44 patients and 5 health care workers from six different medical centers. Strain delineation was performed by restriction endonuclease analysis of genomic DNA (REAG) with the restriction enzyme HinfI followed by conventional electrophoresis. The susceptibility of the isolates to the antifungal agents amphotericin B, flucytosine, fluconazole, and itraconazole was determined by methods recommended by the National Committee for Clinical Laboratory Standards. The MICs at which 90% of the isolates were inhibited ranged from 1.0 microgram/ml for itraconazole to 64 micrograms/ml for fluconazole. In general, isolates from a given patient, or epidemiologically related isolates from a single institution, were identical by molecular typing methods. Epidemiologically unrelated isolates were distinctly different by the REAG typing method employed. These data document the genetic diversity and antifungal susceptibility of clinical isolates of C. krusei.
Reevaluation of interpretive criteria for Haemophilus influenzae by using meropenem (10-microgram), imipenem (10-microgram), and ampicillin (2- and 10-microgram) disks
Authors: Zerva L , Biedenbach D J , Jones R N
Published: January 2020

A collection of 300 Haemophilus influenzae clinical strains was used to assess in vitro susceptibility to carbapenems (meropenem, imipenem) by MIC and disk diffusion methods and to compare disk diffusion test results with two potencies of ampicillin disks (2 and 10 micrograms). The isolates included ampicillin-susceptible or- intermediate (167 strains), beta-lactamase-positive (117 strains), and beta-lactamase-negative ampicillin-resistant (BLNAR; 16 strains) organisms. Disk diffusion testing was performed with 10-micrograms meropenem disks from two manufacturers. Meropenem was highly active against H. influenzae strains (MIC50, 0.06 microgram/ml; MIC90, 0.25 microgram/ml; MIC50 and MIC90, MICs at which 50 and 90%, respectively, of strains are inhibited) and was 8- to 16-fold more potent than imipenem (MIC50, 1 microgram/ml; MIC90, 2 micrograms/ml). Five non-imipenem-susceptible strains were identified (MIC, 8 micrograms/ml), but the disk diffusion test indicated susceptibility (zone diameters, 18 to 21 mm). MIC values of meropenem, doxycycline, ceftazidime, and ceftriaxone for BLNAR strains were two- to fourfold greater than those for other strains. The performance of both meropenem disks was comparable and considered acceptable. A single susceptible interpretive zone diameter of > or = 17 mm (MIC, < = or 4 micrograms/ml) was proposed for meropenem. Testing with the 2-micrograms ampicillin disk was preferred because of an excellent correlation between MIC values and zone diameters (r = 0.94) and superior interpretive accuracy with the susceptible criteria at > or = 17 mm (MIC, < or = 1 microgram/ml) and the resistant criteria at < or = 13 mm (MIC, > or = 4 micrograms/ml). Among the BLNAR strains tested, 81.3% were miscategorized as susceptible or intermediate when the 10-micrograms ampicillin disk was used, while the 2-micrograms disk produced only minor interpretive errors (12.5%). Use of these criteria for testing H. influenzae against meropenem and ampicillin should maximize reference test and standardized disk diffusion test performance with the Haemophilus Test Medium. The imipenem disk diffusion test appears compromised and should be used with caution for detecting strains for which imipenem MICs are elevated.
Bacteremia due to Gordona sputi in an immunocompromised patient
Authors: Riegel P , Ruimy R , de Briel D , Eichler F , Bergerat J P , Christen R , Monteil H
Published: January 2020

We report a case of bacteremia due to a strain identified as Gordona sputi in a patient with metastatic melanoma. The origin of infection remains unknown, but extensive cutaneous lesions due to interleukin-2 treatment may have been the portal of entry. The isolate was related to G. sputi on the basis of its biochemical and genomic properties but exhibited some differences from the type strain.
Use of multiple PCR primer sets for optimal detection of human papillomavirus
Authors: Karlsen F , Kalantari M , Jenkins A , Pettersen E , Kristensen G , Holm R , Johansson B , Hagmar B
Published: January 2020

Using multiple PCR primer sets, we tried to optimize the detection of human papillomavirus (HPV) in DNA samples isolated from 361 frozen biopsy specimens from patients with invasive cervical carcinomas. The HPVs detected were placed into three distinct groups, including group I/Inex at Telelab (Skien, Norway) and group Ineg and group II at the Norwegian Radium Hospital (Oslo, Norway). The consensus primer sets were Oli-1b-oli-2i, My09-My11, Gp5-Gp6, and Gp(5+)-Gp6+ from the HPV L1 gene and CpI-CpIIG from the E1 gene. Using these consensus primers together with the type-specific primers from E6-E7, we found that 355 patients (98%) were HPV positive. Type-specific primers for HPV types 11, 16, 18, 31, 33, and 35 detected more HPV-infected patients than the most sensitive consensus primer set, while the three consensus primer sets My, Gp/Gp+, and Cp together detected more HPV-positive patients than the type-specific primers. Testing of sensitivity of the PCR with SiHa cells serially diluted in lymphocytes (HPV-negative cells) indicated a detection limit of 6,300 HPV type 16 DNA copies with consensus primers (My, Gp+, and Cp) and 126 original HPV type 16 DNA copies with type-specific primers. Comparison of the amplification results for consensus L1 primers and type-specific E6-E7 primers indicated the presence of L1 deletions in 23 of 56 samples. The conclusion is that in PCR detection systems, multiple consensus primers and type-specific primers should be used in order to detect all patients harboring HPV.
Candida albicans serotype analysis by flow cytometry
Authors: Mercure S , Sénéchal S , Auger P , Lemay G , Montplaisir S
Published: January 2020

Candida albicans strains can be assigned to either of two major serogroups, A or B. Antigenic surface determinants present only in serotype A strains allow such a distinction, which has epidemiologic relevance. Reports have established that the relative distributions of the two serotypes can vary depending on the geographic origin of the isolates. A prevalence of susceptibility to an antifungal agent, flucytosine, was also observed with isolates of serotype A. More recently, it was suggested that the occurrence of serotype B isolates in various clinical forms of candidiasis is increasing. However, this latest finding remains controversial since serotyping results vary widely from one laboratory to another because of the lack of standardized methodologies. Difficulty in interpretation of results, which may lead to erroneous serotype identification, is the major setback associated with current methods. For this study, we thus devised a procedure that relies on flow cytometry and that may eliminate ambiguities in serotype determination. The validation of results was achieved with two types of serotype A-specific antisera, Iatron Factor 6 antiserum and an anti-C. albicans antiserum adsorbed on serotype B yeast cells. Agreement between results obtained with these two reagents was 100% with a wide array of Candida strains. These results confirmed the potential of the flow cytometric procedure as a reliable and reproducible method to establish the serotypes of C. albicans strains. Furthermore, some applications of this procedure to the epidemiological study of this human pathogen are presented.
Microwell hybridization assay for detection of PCR products from Mycobacterium tuberculosis complex and the recombinant Mycobacterium smegmatis strain 1008 used as an internal control
Authors: Kox L F , Noordhoek G T , Kunakorn M , Mulder S , Sterrenburg M , Kolk A H
Published: January 2020

A microwell hybridization assay was developed for the detection of the PCR products from both Mycobacterium tuberculosis complex bacteria and the recombinant Mycobacterium smegmatis strain 1008 that is used as an internal control to monitor inhibition in the PCR based on the M. tuberculosis complex-specific insertion sequence IS6110. The test is based on specific detection with digoxigenin-labeled oligonucleotide probes of biotinylated PCR products which are captured in a microtiter plate coated with streptavidin. The captured PCR products are hybridized separately with two probes, one specific for the PCR product from IS6110 from M. tuberculosis complex and the other specific for the PCR fragment from the modified IS6110 fragment from the recombinant M. smegmatis 1008. The microwell hybridization assay discriminates perfectly between the two types of amplicon. The amount of PCR product that can be detected by this assay is 10 times less than that which can be detected by agarose gel electrophoresis. The test can be performed in 2 h. It is much faster and less laborious than Southern blot hybridization. Furthermore, the interpretation of results is objective. The assay was used with 172 clinical samples in a routine microbiology laboratory, and the results were in complete agreement with those of agarose gel electrophoresis and Southern blot hybridization.
Fluconazole disk diffusion procedure for determining susceptibility of Candida species
Authors: Barry A L , Brown S D
Published: January 2020

A simple disk diffusion test was defined for quick determination of the susceptibility of Candida species to fluconazole. The standard macrotube dilution reference method, the fluconazole E test, and a 25-microgram fluconazole disk test were all performed with each of 250 Candida species selected to provide a broad range of fluconazole MICs. All three methods were in excellent agreement. On RPMI 1640-glucose agar, isolates with inhibition zone diameters of > or = 19 mm were all susceptible (MIC, < or = 8.0 micrograms/ml) by the E test and 94% were susceptible by the macrotube method. Strains with smaller zones were either resistant, intermediate (dose-dependent susceptibility), or susceptible by the reference methods. The disk test did not adequately separate fully resistant strains from those with dose-dependent susceptibility: additional quantitative tests are needed for the few strains that are not unequivocally susceptible by the disk method.
Detection of hepatitis C virus by PCR in second-generation enzyme immunoassay-seropositive blood donors by using matched pairs of fresh frozen plasma and pilot tube sera
Authors: Krajden M , Zhao J , Bourke C , Scalia V , Gill P , Lau W
Published: January 2020

Between April 1993 and March 1995, 429 of 334,454 (0.13%) blood donations at the Toronto Centre of the Canadian Red Cross were reactive for hepatitis C virus (HCV) by second-generation enzyme immunoassay (EIA-2). Of the 429 EIA-2-positive donations, 189 (44%), 138 (32%), and 102 (24%) were positive, indeterminate, and negative by Second-Generation Recombinant Immunoblot Assay (RIBA-2). To assess HCV viremia and minimize the risk that specimen handling affected PCR-based detection, the qualitative AMPLICOR HCV test was performed on both pilot tube sera (PTS) and the corresponding fresh frozen plasma (FFP) from 294 EIA-2-reactive donations. AMPLICOR PCR results for PTS and FFP were 100% concordant and were confirmed by nested HCV PCR for 27 of 294 donations. The AMPLICOR HCV test was positive for 127 of 140 (91%) of RIBA-2-positive donations (81, 91, and 96% of donations with two, three, and four reactive bands, respectively), 5 of 88 (5.7%) indeterminate donations, and 0 of 66 (0%) RIBA-2-negative donations. The Third-Generation Recombinant Immunoblot Assay (RIBA-3) was performed on RIBA-2-negative, -indeterminate, and -positive, PCR-negative donations. RIBA-3 demonstrated enhanced specificity and resolved 18 of 88 (20%) of RIBA-2-indeterminate samples as HCV antibody positive. The study demonstrates that PTS are as suitable as FFP for PCR-based detection of HCV and can be used to determine if EIA-2-reactive blood donors are viremic at the time of donation.
Serological cross-reactions between Bartonella quintana, Bartonella henselae, and Coxiella burnetii
Authors: La Scola B , Raoult D
Published: January 2020

The clinical manifestations of Q fever and bartonelloses can be confused, especially in cases of infectious endocarditis. Differential diagnosis of the diseases is important because the treatments required for Q fever and bartonelloses are different. Laboratory confirmation of a suspected case of either Q fever or bartonelloses is most commonly made by antibody estimation with an indirect immunofluorescence assay. With an indirect immunofluorescence assay, 258 serum samples from patients with Q fever were tested against Bartonella henselae and Bartonella quintana antigens, and 77 serum samples from patients with infection by Bartonella sp. were tested against Coxiella burnetii antigen. Cross-reactivity was observed: more than 50% of the chronic Q fever patients tested had antibodies which reacted against B. henselae antigen to a significant level. This cross-reaction was confirmed by a cross-adsorption study and protein immunoblotting. However, because the levels of specific antibody titers in cases of Bartonella endocarditis are typically extremely high, low-level cross-reaction between C. burnetii antibodies and B. henselae antigen in cases of Q fever endocarditis should not lead to misdiagnosis, provided serology testing for both agents is performed.
Evaluation of a novel PCR-based diagnostic assay for detection of Mycobacterium tuberculosis in sputum samples
Authors: Maher M , Glennon M , Martinazzo G , Turchetti E , Marcolini S , Smith T , Dawson M T
Published: January 2020

We report on a PCR-based assay we have developed for the detection of Mycobacterium tuberculosis in sputum samples. One hundred sputum specimens, which included 34 culture-positive and 66 culture-negative specimens, were evaluated with this system. Of the 34 culture-positive specimens, 31 were PCR positive, and 60 of the culture-negative specimens were PCR negative. An internal standard has been included in the assay system to monitor PCR inhibition and to confirm the reliability of the PCR assay.
Rapid differentiation of bovine and human tubercle bacilli based on a characteristic mutation in the bovine pyrazinamidase gene
Authors: Scorpio A , Collins D , Whipple D , Cave D , Bates J , Zhang Y
Published: January 2020

Bovine tuberculosis (TB) caused by Mycobacterium bovis is an important veterinary disease that can also afflict humans. Although M. bovis shares an almost identical genome with M. tuberculosis, subtle differences in host specificity and several biochemical parameters can be used to distinguish the two closely related species. The current method for distinguishing M. bovis from M. tuberculosis relies on tedious testing of biochemical parameters, including natural resistance to pyrazinamide and defective pyrazinamidase (PZase) activity of M. bovis strains. In this study, we report the development of a rapid PCR-single-strand conformation polymorphism (SSCP) assay to differentiate M. bovis from M. tuberculosis strains, based on the detection of a single characteristic point mutation in the PZase gene (pncA) of M. bovis. Eighty-seven of 89 M. bovis strains could be distinguished from M. tuberculosis strains. Surprisingly, two animal isolates which were initially identified as M. bovis were shown to be M. africanum because they had a wild-type pncA sequence with positive PZase. These two M. africanum strains contain multiple (three and six) copies of insertion sequence IS6110, a feature they have in common with M. tuberculosis. The implication of this finding for the taxonomy of M. tuberculosis complex is discussed in relation to host preference and epidemiology. The development of a rapid PCR-SSCP test for distinguishing M. bovis from M. tuberculosis will be useful for monitoring the spread of bovine TB to humans in areas where bovine TB is endemic and for directing the treatment of human TB caused by M. bovis.
Human papillomavirus type 16 sequence variants: identification by E6 and L1 lineage-specific hybridization
Authors: Wheeler C M , Yamada T , Hildesheim A , Jenison S A
Published: January 2020

A catalog of human papillomavirus (HPV) type 16 (HPV-16) E6 and L1 signature nucleotides was used to develop PCR-based oligonucleotide probe systems capable of distinguishing HPV-16 class and subclass variants. Twenty-three E6-specific oligonucleotide probes targeting 13 variant nucleotide positions and 12 L1-specific oligonucleotide probes targeting 6 variant nucleotide positions were used to characterize HPV-16-containing cervicovaginal lavage specimens. Nucleotide positions that could be distinguished included E6 nucleotides 109, 131, 132, 143, 145, 178, 183, 286, 289, 335, 350, 403, and 532 and L1 nucleotides 6695, 6721, 6803, 6854, 6862, and 6994. Combined hybridization patterns were assigned on the basis of the predicted HPV-16 class, subclass, or minor class variants described previously (T. Yamada, C. M. Wheeler, A. L. Halpern, A.-C. M. Stewart, A. Hildesheim, and S.A. Jenison, J. Virol. 69:7743-7753, 1995). The major HPV-16 variant lineages detected included European prototype-like (E-P), Asian (As), Asian-American (AA), and African (Af1 and Af2) lineages. In addition, E-G131, an E-class variant, and AA-G183, an AA-class variant, were also identified. For each clinical specimen, DNA hybridization results were compared to nucleotide sequence determinations. Targeted L1 and E6 marker nucleotides covaried within all HPV-16 variant isolates examined. These hybridization-based methods result in minimal misclassification error, are amenable to targeting additional lineage-specific nucleotide positions, and should facilitate the large-scale, low-cost analysis of HPV-16 variants in epidemiologic investigations. Specifically, these methods will facilitate epidemiologic studies of HPV-16 transmission and natural history, as well as studies of associations between HPV variants, host immune responses, and cervical neoplasia.
Cholera from raw seaweed transported from the Philippines to California
Authors: Vugia D J , Shefer A M , Douglas J , Greene K D , Bryant R G , Werner S B
Published: January 2020

In March 1994, a California woman without any recent travel developed acute, profuse, watery diarrhea. Her astute physician diagnosed cholera after ordering the appropriate stool culture, and the patient improved on an oral antibiotic. Epidemiologic investigation implicated seaweed from the Philippines that was transported by a friend to California and subsequently eaten raw as the vehicle of infection.
Evaluation of eight enzyme immunoassays for detection of immunoglobulin G against Helicobacter pylori
Authors: Meijer B C , Thijs J C , Kleibeuker J H , van Zwet A A , Berrelkamp R J
Published: January 2020

Eight commercial enzyme-linked immunosorbent assays (ELISAs) were used to test sera taken from 102 patients in whom Helicobacter pylori infection status had been determined by means of biopsy culture, PCR, histology, and urease production and by 13C urea breath test. By those means, 61 patients had been found to be infected. Assays were compared by receiver operating characteristic analysis. Sensitivities ranged from 86 to 98%; specificities ranged from 83 to 98%. In a group consisting of the assays by Bio-Whittaker, Meddens Biotech, Orion (Pyloriset EIA G, new version), and Enteric Products, Inc. (HM Cap), differences in performance were not statistically significant. Sensitivities in this group ranged from 93 to 98%; specificities ranged from 95 to 98%. Assays from this group may be useful in addition to biopsy-based methods in diagnosing H. pylori infection.
Comparison of EDTA and acid-citrate-dextrose collection tubes for detection of cytomegalovirus antigenemia and infectivity in leukocytes before and after storage
Authors: Landry M L , Cohen S , Huber K
Published: January 2020

Duplicate blood samples collected in EDTA and acid-citrate-dextrose (ACD) were compared by cytomegalovirus (CMV) pp65 antigenemia and CMV infectivity on the day of sample collection and after 1 and 2 days of storage at 4 degrees C. No significant difference was detected between EDTA and ACD. However, CMV antigenemia was more sensitive than culture at all time points tested.
Use of pulsed-field gel electrophoresis to investigate an outbreak of Serratia marcescens
Authors: Shi Z Y , Liu P Y , Lau Y J , Lin Y H , HU B S
Published: January 2020

Pulsed-field gel electrophoresis (PFGE) typing was applied to the epidemiological investigation of 20 Serratia marcescens isolates collected from urine specimens of 17 patients and three urinals over a 2-month period. Twenty-five epidemiologically unrelated strains were also tested to determine the discriminatory power of PFGE. The PFGE fingerprints of each isolate were consistent in three different tests. The 20 outbreak isolates had an identical PFGE fingerprint pattern, while the epidemiologically unrelated strains demonstrated unique PFGE fingerprint patterns. The source of the outbreak was inadequately disinfected urinals. We conclude that PFGE served as a highly discriminatory and reproducible method for the epidemiological investigation of the outbreak of S. marcescens infection addressed by this study.
Identification of Abiotrophia adiacens and Abiotrophia defectiva by 16S rRNA gene PCR and restriction fragment length polymorphism analysis
Authors: Ohara-Nemoto Y , Tajika S , Sasaki M , Kaneko M
Published: January 2020

Abiotrophia adiacens and Abiotrophia defectiva, previously referred to as nutritionally variant streptococci, Streptococcus adjacens and Streptococcus defectivus, respectively, are causes of infective endocarditis. We describe a method of identifying these two species and also of distinguishing them from 15 other major etiological pathogens of infective endocarditis by means of 16S rRNA gene PCR amplification followed by restriction fragment length polymorphism analysis (PCR-RFLP). The 16S rRNA genes were successfully amplified with a set of universal primers from all 17 species of bacteria examined, including viridans group streptococci. The RFLP patterns of A. adiacens and A. defectiva obtained by HaeIII or MspI digestion were readily distinguished from each other and from those of other bacteria. When PCR analysis was performed with the supernatant of a suspension of a boiled colony, the 16S rRNA genes of 80 of 82 isolates (97%) of A. adiacens and all isolates (11 of 11) of A. defectiva were amplified. The HaeIII RFLP patterns of the isolates were the same as those of the corresponding type strains, although 28% of A. adiacens isolates revealed intraspecies polymorphism. The detection limit of this method was 0.1 pg of genomic DNA, as assessed by using the digoxigenin-labeling DNA detection system. Thus, the PCR-RFLP analysis that we developed is applicable for the routine detection of Abiotrophia from clinical specimens.
Molecular epidemiology of Mycobacterium tuberculosis strains isolated during a 3-year period (1993 to 1995) in Seville, Spain
Authors: Safi H , Aznar J , Palomares J C
Published: January 2020

The genetic polymorphism of Mycobacterium tuberculosis strains isolated in Seville, Spain, was studied by using computer-assisted analysis of the IS6110 fingerprint in order to determine the current situation and to evaluate the human-to-human transmission of this pathogen. One hundred seventy-six isolates from 175 patients among the 205 patients diagnosed with tuberculosis (TB) during a 3-year period (1993 to 1995) were cultured and analyzed. One hundred nine patients (62%) were infected with genetically different isolates, and 67 isolates (38%) were grouped into 19 clusters. These results demonstrate that the level of clustering of strains in Seville is intermediate between those in developed and developing countries. Epidemiological relatedness was shown for isolates from only 10 of these clusters. Active and high transmission rates exist in children and in human immunodeficiency virus (HIV)-infected adults, while in non-HIV-infected adults this transmission rate is moderate. Although transmission from children to adults is uncommon, the probability of transmission from HIV-infected patients to young adults not infected with HIV may be higher. On the basis of these observations, we predict a constant rise in the rate of TB transmission among HIV-infected patients and probably in young adult patients not infected with HIV if measures for the effective prevention of TB among the HIV-infected population are not implemented.
Detection of enterotoxigenic Bacteroides fragilis by PCR
Authors: Pantosti A , Malpeli M , Wilks M , Menozzi M G , D'Ambrosio F
Published: January 2020

Strains of enterotoxigenic Bacteroides fragilis (ETBF) are associated with diarrhea in young farm animals and, at least in particular settings, in children. Enterotoxin production by ETBF is currently detected by a tissue culture assay with HT-29 cells. We have developed a PCR assay based on the detection of the enterotoxin gene to identify ETBF in culture and in stool samples. Overall, 113 bacterial strains were examined, including 3 B. fragilis reference strains, 75 B. fragilis isolates (comprising 40 ETBF isolates), 20 Bacteroides spp. other than B. fragilis, and 15 strains belonging to other genera. Complete agreement was found between the results of the tissue culture assay and those of the PCR for our strains. PCR was also used to detect ETBF directly in fecal samples. Stools from two healthy volunteers were spiked with known numbers of ETBF and were processed by three different methods. A culture method, which required inoculation of the stools on selective plates and the collection of the whole bacterial growth ("sweeps"), was found to be the most sensitive. PCR performed with the plate sweeps yielded amplification products with a detection limit of 10(5) to 10(4) CFU/g of feces. By this method 18 samples of diarrheic stools (10 positive and 8 negative for ETBF) were examined. The results of the PCR were in accordance with the culture results in all cases. The proposed PCR assay represents a diagnostic tool for the rapid identification of ETBF in culture as well as in fecal samples.
Human isolates of Staphylococcus caprae: association with bone and joint infections
Authors: Shuttleworth R , Behme R J , McNabb A , Colby W D
Published: January 2020

Staphylococcus caprae is a coagulase-negative, DNase-positive member of the genus Staphylococcus usually associated with goats, but since 1991 a few laboratories have reported isolating the organism from human clinical specimens. We report on the isolation of 14 strains from human specimens and note that 10 strains were obtained from patients with bone and joint infections. Nine of the 10 infections started with traumatic fractures, and the other was a case of mastoiditis. Seven of these 10 infections were in patients with orthopedic prostheses, which appears to be a risk factor. Three of the 14 strains were from transplant patients. For three of the patients, S. caprae was the only organism isolated. S. caprae may be misidentified because it is not represented in the current MicroScan or Vitek identification systems which are in use in many laboratories, but the organism can be differentiated by a few biochemical tests. S. caprae produces positive results for DNase, pyrrolidonyl aminopeptidase, and acid production from mannitol and maltose; it produces negative results for ornithine decarboxylase and tube coagulase.
Advantage of combining resin with lytic BACTEC blood culture media
Authors: Rohner P , Pepey B , Auckenthaler R
Published: January 2020

The BACTEC 9240 (Becton Dickinson, Sparks, Md.) automated blood culture system is based on the continuous monitoring of CO2 production by means of a fluorescent sensor attached to the bottom of a culture vial. We compared two media for this system, resin-containing Plus aerobic/F and Lytic anaerobic/F. Sets of Plus aerobic/F and Lytic anaerobic/F vials inoculated with similar volumes (9 +/- 2.5 ml) were evaluated. In the laboratory, the vials were introduced into the system in accordance with the recommendations of the manufacturer and incubated at 35 degrees C for 5 days. A total of 10,914 sets consisting of two bottles each were obtained from 3,674 patients (2.97 cultures per patient). Of these, 1,233 (11%) were culture positive, including 1,074 (10%) yielding at least one pathogen, and 178 (2%) were contaminated. A total of 1,135 isolates were considered clinically relevant in 624 septic episodes; we isolated 894 from Plus aerobic/F and 852 from Lytic anaerobic/F (P = 0.06 [not significant]). More S. aureus isolates (P = 0.05), Pseudomonas spp. (P < 0.0001), other gram-negative bacteria (P = 0.004), and yeasts (P < 0.0001) were isolated from Plus aerobic/F medium, but more streptococci (P < 0.0001), E. coli (P = 0.02) strains and anaerobes (P < 0.0001) were detected with Lytic anaerobic/F medium. Lytic anaerobic/F vials were significantly (P < 0.0001) more often positive at least 6 h before Plus aerobic/F vials (n = 112 versus 52, respectively). Significantly more (P < 0.0001) Plus aerobic/F vials (n = 210; 1.9%) than Lytic anaerobic/F vials (n = 42; 0.4%) were unconfirmed positives. Plus aerobic/F and Lytic anaerobic/F proved to be a valuable pair of blood culture media. Plus aerobic/F performs better for patients under antibiotic treatment, due to the antimicrobial-neutralizing effect of resins. For patients without antibiotic therapy, more microorganisms could be isolated from Lytic anaerobic/F due to cell lysis.
Molecular epidemiology and changing distribution of genotypes of measles virus field strains in Japan
Authors: Katayama Y , Shibahara K , Kohama T , Homma M , Hotta H
Published: January 2020

Based on phylogenetic and restriction fragment length polymorphism analyses of the hemagglutinin and nucleoprotein gene sequences, measles virus strains obtained in western Japan were divided into two types. Type 1 isolates have largely replaced type 2 isolates during the last 10 years in the area surveyed.