bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection and analysis of diverse herpesviral species by consensus primer PCR
Authors: VanDevanter D R , Warrener P , Bennett L , Schultz E R , Coulter S , Garber R L , Rose T M
Published: January 2020

A consensus primer PCR method which amplifies a region of herpesviral DNA-directed DNA polymerase (EC 2.7.7.7) and which uses degenerate primers in a nested format was developed. Primers were designed to target sequences coding for highly conserved amino acid motifs covering a region of approximately 800 bp. The assay was applied to 22 species of herpesviruses (8 human and 14 animal viruses), with PCR products obtained for 21 of 22 viruses. In the process, 14 previously unreported amino acid-coding sequences from herpesviral DNA polymerases were obtained, including regions of human herpesviruses 7 and 8. The 50 to 60 amino acid-coding sequences recovered in the present study were determined to be unique to each viral species studied, with very little sequence variation between strains of a single species when studied. Template dilution studies in the presence of human carrier DNA demonstrated that six human herpesviruses (herpesviruses 1, 2, 3, 4, 5, and 6B) could be detected at levels at or below 100 genome equivalents per 100 ng of carrier DNA. These data suggest that consensus primer PCR targeted to herpesviral DNA polymerase may prove to be useful in the detection and identification of known herpesviruses in clinical samples and the initial characterization of new herpesviral genomes.
DNA fingerprinting of Candida rugosa via repetitive sequence-based PCR
Authors: Redkar R J , Dubé M P , McCleskey F K , Rinaldi M G , Del Vecchio V G
Published: January 2020

A repetitive sequence-based PCR (rep-PCR) technique was developed to characterize the genotypic relatedness among Candida rugosa isolates. Two repetitive sequences, viz., Care-2 and Com29 from Candida albicans, were used to design primers Ca-21, Ca-22, and Com-21, respectively. When used alone or in combination, these primers generated discriminatory fingerprints by amplifying the adjacent variable regions of the genome. Twenty-three isolates from burn patients, eight from other human sources, and four C. rugosa isolates pathogenic in animals were placed into nine fingerprinting groups. Different primers placed these isolates into identical groups, indicating that rep-PCR is a specific and reproducible technique for molecular characterization of C. rugosa. Moreover, these primers unequivocally discriminated among other important Candida species such as C. albicans, C. glabrata, C. tropicalis, C. krusei, C. parapsilosis, C. kefyr, and C. lusitaniae. These data confirm the conservation of repetitive sequences in Candida species. Because of its ease and sensitivity, rep-PCR offers a relatively rapid and discriminatory method for molecular typing of C. rugosa in outbreaks.
Quantification of systemic and local immune responses to individual rotavirus proteins during rotavirus infection in mice
Authors: Ishida S , Feng N , Tang B , Gilbert J M , Greenberg H B
Published: January 2020

The purpose of the present study was to develop a quantitative assay that could be used to measure the local and systemic immune responses to specific rotavirus proteins following rotavirus infection of adult mice. To measure these responses, we used an immunocytochemical staining assay of Spodoptera frugiperda (Sf-9) cells which were infected with recombinant baculovirus expressing selected rotavirus proteins. The specificity of the assay was documented by using a series of monoclonal antibodies to individual rotavirus proteins. We observed that the assay had high levels of sensitivity and specificity for a series of VP7- and VP4-specific neutralizing monoclonal antibodies which recognized conformation-dependent epitopes on their target proteins. We also studied immunoglobulin G (IgG) immune responses in serum and IgA immune responses in the stools of mice infected with wild-type murine rotavirus strain EHPw. In both sera and stools, the most immunogenic proteins were VP6 and VP4. VP2 was less immunogenic than VP6 or VP4, and the immune responses to VP7, NSP2, and NSP4 were very low in serum and undetectable in stools.
Serodiagnosis of Lyme borreliosis by Borrelia burgdorferi sensu stricto, B. garinii, and B. afzelii western blots (immunoblots)
Authors: Norman G L , Antig J M , Bigaignon G , Hogrefe W R
Published: January 2020

The performance of Western blots (immunoblots) prepared with eight strains of Borrelia burgdorferi representing B. burgdorferi sensu stricto, B. garinii, and B. afzelii genospecies was tested with a panel of sera with various clinical presentations collected from eight geographic regions. European sera were generally more reactive to blots prepared with B. garinii or B. afzelii strain antigens, in particular B. garinii 20047 and B. afzelii VS461. North American sera were more reactive with B. burgdorferi sensu stricto strains. Our observation of significant differences in the levels of reactivity of some sera on Western blots of certain strains is potentially important for the development and implementation of generic interpretive criteria. Preferential reactivity of sera from patients with nerve and/or palsy symptoms to B. garinii strains and with cutaneous disease to B. afzelii strains was observed. On the basis of our results, we have concluded that strain 20047 is the best strain to use for the development of a generic Lyme borreliosis Western blot for Europe.
Comparison of efficacy and cost-effectiveness of BIOMIC VIDEO and Vitek antimicrobial susceptibility test systems for use in the clinical microbiology laboratory
Authors: Berke I , Tierno P M
Published: January 2020

Antimicrobial susceptibility testing expense may be a significant portion of a clinical microbiology laboratory's budget. This study compares the BIOMIC VIDEO system (Giles Scientific, Inc., New York, N.Y.) with the Vitek system (bioMérieux Vitek, Inc., Hazelwood, Mo.), an established automated method of antimicrobial susceptibility testing with the ability to generate MIC data. The BIOMIC system is relatively inexpensive and automates the reading of the classical disk agar diffusion test to provide both qualitative (susceptibility interpretation) and quantitative (MIC) data. The overall MIC correlation between the two systems for the 2,913 drug-organism combinations tested was 92.6%. The overall agreement for susceptibility interpretation was 97.4%. The BIOMIC system offers a 57.4% savings per test over the Vitek system. The BIOMIC system utilizes an older technology which is more efficient and yet yields results comparable to those of established automated MIC methods. The savings achievable in laboratories and hospitals nationwide may contribute significantly to the containment of national health care expenditures.
Age and prevalence of Porphyromonas gingivalis in children
Authors: McClellan D L , Griffen A L , Leys E J
Published: January 2020

The acquisition of Porphyromonas gingivalis was examined in a cross-sectional study of 198 subjects from 0 to 18 years of age using a PCR-based assay. P. gingivalis was detected in the oral cavities of 37% of subjects and at similar frequencies among subjects of all ages. These data indicate that P. gingivalis may be acquired in the first days of life.
Detection of Haemophilus influenzae and Streptococcus pneumoniae DNA in blood culture by a single PCR assay
Authors: Hassan-King M , Baldeh I , Adegbola R , Omosigho C , Usen S O , Oparaugo A , Greenwood B M
Published: January 2020

A multiplex PCR assay was developed to screen blood cultures from children in The Gambia with suspected pneumonia for the simultaneous detection of Haemophilus influenzae type b and Streptococcus pneumoniae isolates. Analysis of 295 blood cultures showed that PCR detected the organisms in all samples positive by culture in two samples infected with H. influenzae type b and four samples infected with S. pneumoniae that were culture negative, indicating that this method is sensitive for detecting these organisms in blood cultures.
Evaluation of commercial vancomycin agar screen plates for detection of vancomycin-resistant enterococci
Authors: Van Horn K G , Gedris C A , Rodney K M , Mitchell J B
Published: January 2020

Brain heart infusion-6-micrograms/ml vancomycin agar plates obtained from five commercial sources (B-D Microbiology Systems, Carr-Scarborough Microbiologicals, MicroBio Products, PML Microbiologicals, and REMEL) were evaluated with 714 enterococci for detection of vancomycin resistance. All 465 (100%) vancomycin-resistant enterococci (MIC > or = 32 micrograms/ml) were detected by each manufacturer's agar screen plate, and each manufacturer's agar screen plate detected at least 99% of the 177 vancomycin-susceptible enterococci (MIC < or = 4 micrograms/ml). Detection of the 72 vancomycin-intermediate enterococci (MIC = 6 to 16 micrograms/ml) ranged from 94% for B-D Microbiology Systems to 99% for PML Microbiologicals.
Neutralizing antibodies to Escherichia coli Vero cytotoxin 1 and antibodies to O157 lipopolysaccharide in healthy farm family members and urban residents
Authors: Reymond D , Johnson R P , Karmali M A , Petric M , Winkler M , Johnson S , Rahn K , Renwick S , Wilson J , Clarke R C , Spika J
Published: January 2020

An enzyme-linked immunosorbent assay (ELISA) to detect antibodies to Escherichia coli O157 lipopolysaccharide (LPS) was developed with sera from 63 children with confirmed recent E. coli O157 infection and from 256 age-stratified urban controls. The median ELISA values for control and case sera were 0.05 (interquartile range, 0 to 0.20; mean +/- standard deviation [SD], 0.15 +/- 0.22) and 1.41 (interquartile range, 1.11 to 1.59; mean +/- SD, 1.41 +/- 0.53), respectively (P < 0.001). With a breakpoint of 0.59 (mean ELISA value of the control sera + 2 SDs), the assay had a sensitivity, specificity, and positive and negative predictive values of 95, 94, 80, and 98%, respectively, for recent E. coli O157 infection. The O157 LPS assay and Vero cytotoxin (VT) 1-neutralizing-antibody (NAb) assay were used to compare the relative frequencies of O157 LPS antibodies and VT1-NAbs in an age-stratified urban population from Toronto, Ontario, Canada, and in 216 healthy family members from dairy farm in southern Ontario. The frequency of O157 LPS antibodies was about threefold higher in dairy farm residents (12.5%) than in urban residents (4.7%) (P < 0.01). Similarly, the frequency of VT1-NAbs was about sixfold higher in dairy farm residents (42.0%) than in urban residents (7.7%) (P < 0.001). These findings are consistent with a greater level of exposure of dairy farm residents to VT-producing E. coli (VTEC) strains. The high rate of seropositivity to VT1 in farm residents probably reflects the booster effect of repeated VTEC exposures and argues against a sustained generalized immunosuppressive effect of VT1. Seroepidemiological studies may help in assessing the level of exposure of different populations to VTEC strains.
Isolation of methicillin-resistant coagulase-negative staphylococci from chickens
Authors: Kawano J , Shimizu A , Saitoh Y , Yagi M , Saito T , Okamoto R
Published: January 2020

Methicillin-resistant coagulase-negative staphylococci were isolated from the nares and skin of 1- to 8-week-old healthy chickens in three flocks from a farm. Isolation of methicillin-resistant coagulase-negative staphylococci was positive for 72 (25.7%) of the 280 chickens tested, with the frequency varying from 2.2 to 100% according to flock. A total of 45 appropriate isolates were selected and subjected to identification. Of the 45 methicillin-resistant coagulase-negative staphylococcal isolates selected, 37 were identified as Staphylococcus sciuri, 5 were identified as Staphylococcus epidermidis, and 3 were identified as Staphylococcus saprophyticus. The distribution of the species was different among the flocks. Comparative analysis of the SmaI-digested chromosomal DNA by pulsed-field gel electrophoresis revealed that the isolates could have originated from a single clone of each of S. sciuri and S. saprophyticus and three clones of S. epidermidis. By two methods based on the PCR technique, the mecA gene was detected in all five representative isolates of each methicillin-resistant coagulase-negative staphylococcal clone. The nucleotide sequence of a PCR fragment obtained from an isolate of S. sciuri was completely identical to the corresponding region of mecA genes reported in human methicillin-resistant Staphylococcus aureus isolates and Staphylococcus epidermidis isolates. The representative methicillin-resistant coagulase-negative staphylococcal isolates were resistant to many beta-lactam antibiotics, and some isolates were also resistant to macrolide and aminoglycoside antibiotics. This is the first evidence of the existence of methicillin-resistant coagulase-negative staphylococci from animals possessing the mecA gene.
Detection by PCR of the nim genes encoding 5-nitroimidazole resistance in Bacteroides spp
Authors: Trinh S , Reysset G
Published: January 2020

A PCR method was developed for detection of the nim genes encoding 5-nitrolmidazole resistance in Bacteroides spp. Two PCR primers specific for nim genes were designed. They allowed amplification of a 458-bp fragment from all characterized plasmid- and chromosome-borne metronidazole resistance genes. The specificity of the method was tested with DNA from metronidazole-sensitive Bacteroides spp. strains and from other strains of unrelated species. Each DNA preparation was analyzed with and without an internal positive control to verify that the absence of PCR amplification product was not due to inhibition of the Taq polymerase inhibitors. By this technique, two newly discovered metronidazole-resistant clinical strains of Bacteroides fragilis were shown to harbor resistance genes undetectable by Southern blotting. In spite of the sequence divergence of the nim genes, the PCR method is thus suitable for epidemiological investigations. The amplification method also revealed that nim-related resistance genes were not present in either Streptomyces strain S6670, a natural producer of 2-nitroimidazole, or in Enterococcus faecalis strains, which have been suggested to possess metronidazole-inactivating enzyme.
Synergistic role of gaseous ammonia in etiology of Pasteurella multocida-induced atrophic rhinitis in swine
Authors: Hamilton T D , Roe J M , Webster A J
Published: January 2020

One-week-old Large White piglets were weaned and allocated to 14 experimental groups, each composed of five animals. Each group was housed in a separate Rochester exposure chamber and exposed continuously to gaseous ammonia at either 0, 5, 10, 15, 25, 35, or 50 ppm (two groups per exposure level). One week after ammonia exposure commenced, the pigs from one group at each exposure level were inoculated intranasally with 9 x 10(7) CFU of Pasteurella multocida type D. After a further 4 weeks of exposure, all the pigs were euthanized and the extent of turbinate degeneration was assessed by using a morphometric index (J.T. Done, D. H. Upcott, D. C. Frewin, and C. N. Hebert, Vet. Rec. 114:33-35, 1984) and a subjective scoring system (Ministry of Agriculture, Fisheries and Food, Atrophic Rhinitis: a System of Snout Grading, 1978). Exposure to ammonia at a concentration of 5 ppm or greater resulted in a significant increase in the severity of turbinate atrophy induced by P. multocida compared with that occurring in pigs kept in 0 ppm of ammonia. This effect was maximal at 10 ppm but decreased progressively at concentrations above 25 ppm. Regression analysis revealed a significant relationship between the severity of turbinate degeneration and the number of P. multocida organisms isolated from the nasal epithelium at the end of the experiment (R2 = 0.86). These findings suggest that exposure to ammonia facilitates the growth and/or survival of P. multocida within the upper respiratory tract of the pig, thereby contributing to the severity of the clinical disease atrophic rhinitis. Furthermore, exposure of pigs to ammonia at 10 ppm or greater, in the absence of either P. multocida or Bordetella bronchiseptica, induced a mild but statistically significant degree of turbinate atrophy. The findings of this study demonstrate that exposure to ammonia, at concentrations within the range encountered commonly in commercial piggeries, contributes to the severity of clinical lesions associated with atrophic rhinitis.
Sequence variation in the 18S rRNA gene, a target for PCR-based malaria diagnosis, in Plasmodium ovale from southern Vietnam
Authors: Kawamoto F , Miyake H , Kaneko O , Kimura M , Nguyen T D , Nguyen T D , Liu Q , Zhou M , Le D D , Kawai S , Isomura S , Wataya Y
Published: January 2020

Field surveys of malaria were performed in southern Vietnam by using an acridine orange staining method for rapid diagnosis and a PCR-based, microtiter plate hybridization method for accurate diagnosis. A total of three patients of Plasmodium ovale infection were detected, but PCR-amplified DNA of the P. ovale isolates from two of the patients did not hybridize with the P. ovale-specific probe. Analysis of the target sequence in the 18S rRNA gene indicated that in the DNA of isolates from both patients three nucleotides in the probe region from the typical P. ovale sequence were different, with deletions of two nucleotides and the substitution of one nucleotide. These results may suggest that in addition to molecular biological methods, careful microscopic examination of stained thin blood films is still required in studies of the prevalence of different malaria species.
Epidemiological differentiation of pathogenic strains of Salmonella enteritidis by ribotyping
Authors: Landeras E , González-Hevia M A , Alzugaray R , Mendoza M C
Published: January 2020

The usefulness of two-way ribotyping, performed with SphI and PstI, as a genetic marker for a series of pathogenic Salmonella enteritidis strains is reported. Eighteen combined ribotypes were differentiated, a discrimination index of 0.77 was reached, a genetic relationship dendrogram was traced, and the results were applied in an epidemiological study.
Isolation of Campylobacter concisus from feces of children with and without diarrhea
Authors: Van Etterijck R , Breynaert J , Revets H , Devreker T , Vandenplas Y , Vandamme P , Lauwers S
Published: January 2020

A prospective study compared fecal isolation rates of Campylobacter concisus for children with diarrhea and without diarrhea by a filter technique in which media were incubated for 4 days in a microaerobic atmosphere. No statistically significant difference in isolation rates was found (13.2% in patients with diarrhea and 9% in controls). Moreover, 35 of 37 children attending the same day care center harbored different C. concisus strains, as was demonstrated by arbitrary primer PCR DNA fingerprinting. These data suggest a lack of a pathogenic role for C. concisus in enteritis.
Detection of human herpesvirus 6 and human herpesvirus 7 in the submandibular gland, parotid gland, and lip salivary gland by PCR
Authors: Sada E , Yasukawa M , Ito C , Takeda A , Shiosaka T , Tanioka H , Fujita S
Published: January 2020

In order to define the major sites of persistence of human herpesvirus 6 (HHV-6) and HHV-7, PCR with DNAs from more than 100 specimens of 3 different salivary glands was performed. HHV-6 DNA was detected in 52 (88.1%) of 59 submandibular gland, 17 (63.0%) of 27 parotid gland, and 9 (52.9%) of 17 lip salivary gland specimens. On the other hand, HHV-7 DNA was detected in 59 (100%) of 59 submandibular gland, 23 (85.2%) of 27 parotid gland, and 10 (58.8%) of 17 lip salivary gland specimens. These findings demonstrate that salivary glands are a site of persistent infection of both HHV-6 and HHV-7 and that among the three types of salivary gland examined, the submandibular gland is the primary one in which these herpesviruses, especially HHV-7, persist.
Multiplex PCR provides a low-cost alternative to DNA probe methods for rapid identification of Mycobacterium avium and Mycobacterium intracellulare
Authors: Cousins D , Francis B , Dawson D
Published: January 2020

A multiplex PCR designed to differentiate Mycobacterium tuberculosis complex organisms from M. avium and M. intracellulare was used to test 105 isolates identified by DNA probe methods as M. avium, M. intracellulare, or M. avium complex type X. The multiple PCR correctly identified 33 of 34 isolates identified by commercial probe methods as M. avium and all 51 isolates identified as M. intracellulare. The 20 isolates identified as M. avium complex type X by probe were identified as Mycobacterium spp. by the multiplex method. These results confirm that the multiplex PCR, which is simple to perform and cheaper than commercial probe methods, is suitable for routine identification of M. avium and M. intracellulare.
Clinical evaluation of difco ESP culture system II for growth and detection of mycobacteria
Authors: Woods G L , Fish G , Plaunt M , Murphy T
Published: January 2020

The reliability of the ESP Culture System II (ESP II; Difco Laboratories, Detroit, Mich.), a continuously monitoring mycobacterial culture system, was evaluated by comparing its performance with the BACTEC TB 460 (BACTEC TB) and Middlebrook 7H11/7H11 selective agar systems. A total of 2,283 specimens of all types (70.7% were respiratory specimens) were cultured; 149 (6.5%) yielded mycobacteria. The most common species recovered were Mycobacterium avium complex (MAC, 73 isolates) and Mycobacterium tuberculosis complex (MTBC, 53 isolates). The recovery rates by individual system were 87, 81, and 65% for ESP II, BACTEC TB, and Middlebrook agar, respectively, for all mycobacteria; the recovery rates were 89, 92, and 89%, respectively, for MTBC. For liquid plus solid medium system combinations, recovery rates for all mycobacteria and for MTBC, respectively, were 91 and 94% for ESP II plus Middlebrook agar and 85 and 96% for BACTEC TB plus Middlebrook agar. The difference between the recovery rates of all mycobacteria by ESP II and by BACTEC TB was not significant, whereas for the individual species, the only significant difference was recovery of more isolates of MAC by ESP II. For those isolates recovered in the individual systems, mean times to detection of all mycobacteria, MTBC, and MAC, respectively, were 13.1, 15.5, and 10.9 days for ESP II; 14.4, 16.6, and 12.1 days for BACTEC TB; and 17.8, 18.3, and 18.8 days for Middlebrook agar. ESP II is a reliable, nonradiometric, less labor-intensive alternative to BACTEC TB for growth and detection of mycobacteria, but as with other liquid culture methods, ESP II should be used in combination with a solid medium, not as a stand-alone system.
Comparison of plasma virus loads among individuals infected with hepatitis C virus (HCV) genotypes 1, 2, and 3 by quantiplex HCV RNA assay versions 1 and 2, Roche Monitor assay, and an in-house limiting dilution method
Authors: Hawkins A , Davidson F , Simmonds P
Published: January 2020

The accuracy of different methods for the quantitation of hepatitis C virus in plasma was measured with samples from individuals infected with different genotypes and by using RNA transcripts of predetermined concentrations. Highly reproducible results were observed upon repeat testing of samples by both the original version of the Chiron branched-DNA (bDNA) assay (Quantiplex RNA assay; bDNA-1) and the currently available version (Quantiplex HCV RNA 2.0 assay; bDNA-2). A greater variability was observed in the Roche Monitor assay (correlation coefficient of 0.537, compared with 0.942 and 0.964 for the bDNA-1 and bDNA-2 assays, respectively). Significant differences in the efficiency of detection of genotypes 1, 2, and 3 were observed for the bDNA-1 and Roche Monitor assays, whereas the bDNA-2 assay and nested PCR at limiting dilution were able to quantify genotypes with equal sensitivity. By quantifying RNA transcripts of different genotypes, the sensitivities of the Roche Monitor assay for sequences of the type 2 and type 3 transcripts were estimated to be 11 and 8% of those achieved for genotype 1. When correction factors based upon these results and those from quantitation of circulating viral RNA sequences in samples from blood donors were used, the genotype-specific differences in virus load in samples from blood donors were no longer observed, consistent with previous studies with corrected values from the bDNA-1 assay. These results suggest that many of the previous studies evaluating the effect of genotype and virus load on the response to interferon using methods such as the Roche Monitor assay and other competitive PCR methods require reinterpretation. Differences in efficiency of quantitation should be taken into account in future investigations of the relationship between genotype and virus load.
Detection of Cryptosporidium parvum DNA in formed human feces by a sensitive PCR-based assay including uracil-N-glycosylase inactivation
Authors: Gobet P , Buisson J C , Vagner O , Naciri M , Grappin M , Comparot S , Harly G , Aubert D , Varga I , Camerlynck P , Bonnin A
Published: January 2020

We developed a PCR-based method that can be used to identify Cryptosporidium parvum in human feces. Fecal oocysts were concentrated by centrifugation on a sodium chloride gradient and filtration on a nitrocellulose filter prior to DNA extraction and PCR amplification of a 452-bp C. parvum-specific DNA sequence with a protocol including dUTP and uracil-N-glycosylase. All samples obtained from naturally infected humans (n = 10), calves (n = 4), and goats (n = 2) were positive. A 100% detection rate was achieved with both formed and solid stools (n = 10) seeded with 1,000 C. parvum oocysts per g. Procedures based on stool concentration by a modified Ritchie method and subsequent oocyst identification by immunofluorescent labeling or acid-fast staining require concentrations of 50,000 to 500,000 oocysts per g to achieve a 100% detection rate with formed stools. The described PCR-based assay thus has a 50- to 500-fold increase in sensitivity compared to those of the methods commonly used to analyze formed feces.
Multiplex PCR for diagnosis of AIDS-related central nervous system lymphoma and toxoplasmosis
Authors: Roberts T C , Storch G A
Published: January 2020

A nested multiplex PCR assay was designed for the simultaneous detection of Epstein-Barr virus and Toxoplasma gondii DNA from the cerebrospinal fluid of AIDS patients. T. gondii DNA was detected in 8 of 8 patients with Toxoplasma encephalitis and in 0 of 6 patients without toxoplasmosis, and Epstein-Barr virus DNA was found in 9 of 14 patients with central nervous system lymphoma and in 2 of 38 patients without disease.
Rapid and effective method for preparation of fecal specimens for PCR assays
Authors: Lou Q , Chong S K , Fitzgerald J F , Siders J A , Allen S D , Lee C H
Published: January 2020

We have developed a novel method for the preparation of fecal specimens for PCR assays. Approximately 100 mg of solid stool or 200 microliters of liquid fecal sample was thoroughly suspended in 1 ml of water. Fecal debris was removed by low-speed centrifugation (2,800 x g for 2 min). The supernatant was then boiled for 10 min in a water bath and further clarified by high-speed centrifugation (12,000 x g for 5 min). Fifty microliters of the clarified supernatant was then purified by Sepharose CL-6B spin column chromatography, and a portion of the purified supernatant was used for PCR. By this method, stools containing enterotoxigenic Escherichia coli H10407 were amplified by colonization factor antigen I fimbrial gene PCR, with a sensitivity of 100 organisms per reaction. The method was also effective for processing stool specimens for Clostridium difficile toxin A and B gene PCRs. This method is rapid, effective, and simple to perform and will improve the applications of PCR to stool specimens for diagnostic purposes.
Evaluation of PCR for diagnosis of visceral leishmaniasis
Authors: Osman O F , Oskam L , Zijlstra E E , Kroon N C , Schoone G J , Khalil E T , El-Hassan A M , Kager P A
Published: January 2020

An evaluation of Leishmania PCR was performed with bone marrow, lymph node, and blood samples from 492 patients, 60 positive controls, and 90 negative controls. Results were compared with microscopy results for Giemsa-stained smears. PCR and microscopy of lymph node and bone marrow aspirates from patients with microscopically confirmed visceral leishmaniasis (VL) were equally sensitive. However, in patients clinically suspected of having VL and in whom parasites could not be demonstrated by microscopy, PCR was positive for 12 of 23 (52.2%) lymph node aspirates and 8 of 12 (66.7%) bone marrow aspirates, thus confirming the clinical diagnosis of VL. With PCR on filter paper, Leishmania DNA was detected in the blood of 33 of 47 (70%) patients with confirmed VL and in 2 of 11 (19%) patients suspected of having VL. Positive PCR results were more frequently found for blood samples on filter paper than for samples stored in EDTA. In conclusion, PCR is a more sensitive method than microscopy for the detection of Leishmania in lymph node and bone marrow aspirates, being especially useful for the confirmation of cases of suspected VL. Blood from a finger prick may be used for the initial PCR screening of people suspected of having VL. If the PCR of blood is negative, one should perform PCR with lymph node and/or bone marrow material, because PCR with these materials is more often positive.
Determination of the etiology of presumptive feline leprosy by 16S rRNA gene analysis
Authors: Hughes M S , Ball N W , Beck L A , de Lisle G W , Skuce R A , Neill S D
Published: January 2020

PCR-amplified 16S rRNA gene sequences were obtained directly from tissue specimens from eight cats with presumptive feline leprosy. Acid-fast bacilli were observed in sections from all eight specimens, but culture for mycobacteria was successful for one specimen only. Analysis of the V2 variable region of each 16S rRNA PCR product identified a sequence with 100% nucleotide identity to the sequences of Mycobacterium lepraemurium, Mycobacterium avium, and Mycobacterium paratuberculosis in four of the specimens from cats with feline leprosy. Separate M. paratuberculosis- and M. avium-specific PCR amplifications of the four specimens were negative, thus substantiating the identification of M. lepraemurium in these specimens from cats with feline leprosy. Further sequence analysis of the V3 variable region of one of the four specimens provided conclusive evidence of the presence of M. lepraemurium. This is the first report of the definitive identification of M. lepraemurium in cats with feline leprosy by molecular biology-based analyses. M. avium, which is rarely reported in cats, and Mycobacterium chitae, a reported nonpathogenic, rapidly growing mycobacterial species found in the environment, were identified in the specimen from which acid-fast bacilli were cultured. Two of the specimens from cats were infected with a potentially novel species of mycobacteria which had a 16S rRNA gene sequence sharing the closest nucleotide sequence identity with that of Mycobacterium malmoense. Molecular biology-based analyses provided for the accurate and rapid diagnosis of mycobacterial infections in cats and circumvented the problems of culture and misdiagnosis of feline leprosy associated with traditional methods.
Use of different molecular typing techniques for bacteriological follow-up in a clinical trial with AIDS patients with Mycobacterium avium bacteremia
Authors: Picardeau M , Varnerot A , Lecompte T , Brel F , May T , Vincent V
Published: January 2020

One hundred ninety-six Mycobacterium avium isolates from blood samples recovered from 93 AIDS patients for several months were typed by serotyping, by IS1245 restriction fragment length polymorphism (RFLP) analysis and in some cases RFLP analysis with plasmids pVT2 and pLR7 as probes, and by pulsed-field gel electrophoresis (PFGE). PCR typing of single colonies was also used to detect polyclonal infections. Strains belonged mainly to serotypes 1, 4, and 8. pVT2- and pLR7-related plasmids were detected in strains from 49% of the patients. The IS1245 RFLP and PFGE analyses showed a 96.8% diversity of the M. avium strains from the 93 patients. The vast majority (95.2%) of infections were monoclonal, indicating that recent infection is unlikely, even at an advanced stage of AIDS. For one patient, sequential isolates gave divergent patterns of sensitivity and resistance to clarithromycin, but all were identified as the initial clone. RFLP analysis and PCR typing of single colonies allowed for the detection of three polyclonal infections during the bacteriological follow-up. Among strains from patients whose samples were positive by culture after treatment for 2 to 15 months, 97.4% were the same as the initial strain. In conclusion, relapses and failures were mostly due to the initial strain. These relapses and failures resulted either from the selection of resistant mutants or the reappearance of sensitive strains, suggesting the persistence of nonsterilized tissue reservoirs.
Are clinical laboratories in California accurately reporting vancomycin-resistant enterococci?
Authors: Rosenberg J , Tenover F C , Wong J , Jarvis W , Vugia D J
Published: January 2020

In order to determine whether hospital-based clinical laboratories conducting active surveillance for vancomycin-resistant enterococci in three San Francisco Bay area counties (San Francisco, Alameda, and Contra Costa counties) were accurately reporting vancomycin resistance, five vancomycin-resistant enterococcal strains and one vancomycin-susceptible beta-lactamase-producing enterococcus were sent to 31 of 32 (97%) laboratories conducting surveillance. Each strain was tested by the laboratory's routine antimicrobial susceptibility testing method. An Enterococcus faecium strain with high-level resistance to vancomycin (MIC, 512 microg/ml) was correctly reported as resistant by 100% of laboratories; an E. faecium strain with moderate-level resistance (MIC, 64 microg/ml) was correctly reported as resistant by 91% of laboratories; two Enterococcus faecalis strains with low-level resistance (MICs, 32 microg/ml) were correctly reported as resistant by 97 and 56% of laboratories, respectively. An Enterococcus gallinarum strain with intrinsic low-level resistance (MIC, 8 microg/ml) was correctly reported as intermediate by 50% of laboratories. A beta-lactamase-producing E. faecalis isolate was correctly identified as susceptible to vancomycin by 100% of laboratories and as resistant to penicillin and ampicillin by 68 and 44% of laboratories, respectively; all 23 (74%) laboratories that tested for beta-lactamase recognized that it was a beta-lactamase producer. This survey indicated that for clinically significant enterococcal isolates, laboratories in the San Francisco Bay area have problems in detecting low- to moderate-level but not high-level vancomycin resistance. Increasing accuracy of detection and prompt reporting of these isolates and investigation of cases are the next steps in the battle for control of the spread of vancomycin resistance.
Microsatellite in the beta-tubulin gene of Toxoplasma gondii as a new genetic marker for use in direct screening of amniotic fluids
Authors: Costa J M , Dardé M L , Assouline B , Vidaud M , Bretagne S
Published: January 2020

To examine the correlation between Toxoplasma gondii genotype and congenital human toxoplasmosis, the polymorphism of the microsatellite consisting of a dinucleotide (TG) repeat in the intron of the beta-tubulin gene was investigated by PCR. Thirty-four reference strains were studied, including 7 strains virulent in mice and 27 strains avirulent in mice. The seven virulent strains had a (TG)8 microsatellite, and the avirulent strains had a (TG)7 microsatellite. This confirms the dichotomy already observed for virulent and avirulent strains. Additionally, 37 samples of amniotic fluid from infected fetuses were tested. All of them had the (TG)7 microsatellite marker. This result confirms that most of the human cases of congenital toxoplasmosis are due to strains avirulent in mice. Nevertheless, their virulence in human fetuses was obvious, as numerous abnormalities were observed on ultrasonic examination. The new genetic marker is the first one directly used for typing T. gondii isolates without any bias due to cultivation of the parasite. This microsatellite marker is not sufficient to type the strains which are avirulent in mice; however, seeking more polymorphic microsatellites should be worthwhile to obtain new genetic markers for direct screening of biological samples.
Rapid identification of causative species in patients with Old World leishmaniasis
Authors: Minodier P , Piarroux R , Gambarelli F , Joblet C , Dumon H
Published: January 2020

Conventional methods for the identification of species of Leishmania parasite causing infections have limitations. By using a DNA-based alternative, the present study tries to develop a new tool for this purpose. Thirty-three patients living in Marseilles (in the south of France) were suffering from visceral or cutaneous leishmaniasis. DNA of the parasite in clinical samples (bone marrow, peripheral blood, or skin) from these patients were amplified by PCR and were directly sequenced. The sequences observed were compared to these of 30 strains of the genus causing Old World leishmaniasis collected in Europe, Africa, or Asia. In the analysis of the sequences of the strains, two different sequence patterns for Leishmania infantum, one sequence for Leishmania donovani, one sequence for Leishmania major, two sequences for Leishmania tropica, and one sequence for Leishmania aethiopica were obtained. Four sequences were observed among the strains from the patients: one was similar to the sequence for the L. major strains, two were identical to the sequences for the L. infantum strains, and the last sequence was not observed within the strains but had a high degree of homology with the sequences of the L. infantum and L. donovani strains. The L. infantum strains from all immunocompetent patients had the same sequence. The L. infantum strains from immunodeficient patients suffering from visceral leishmaniasis had three different sequences. This fact might signify that some variants of L. infantum acquire pathogenicity exclusively in immunocompromised patients. To dispense with the sequencing step, a restriction assay with HaeIII was used. Some restriction patterns might support genetic exchanges in members of the genus Leishmania.
Detection and rapid differentiation of human enteroviruses following genomic amplification
Authors: Kuan M M
Published: January 2020

By employing a nested PCR (n-PCR) with specific primers derived from the 5' nontranslated and consensus region of the human enterovirus genome, we detected enterovirus RNA from 32 different serotypes of prototypic strains. A specific 297-bp fragment was amplified by this method from all of these strains. Not only was the method highly sensitive, detecting enterovirus RNA extracted from 0.01 50% tissue culture infective dose/50 microl (which is more sensitive than our current routine method of enterovirus diagnosis, based on the virus isolation and serotypic neutralization), but it was also relatively rapid. By using this technology, we also detected enterovirus RNA in uncultured specimens (including throat swabs and stools) from patients with respiratory illness and acute flaccid paralysis syndrome. This method enabled us to rapidly and directly distinguish enterovirus-infected specimens from nonenterovirus specimens in laboratory diagnosis. Furthermore, restriction fragment length polymorphism was assessed as an alternative means of differentiating various serotypes of prototypical enteroviruses. Fourteen of 16 human enterovirus-infected specimens exhibited restriction patterns identical to those of the corresponding prototypes.
Development of a novel antigen detection test for histoplasmosis
Authors: Gomez B L , Figueroa J I , Hamilton A J , Ortiz B L , Robledo M A , Restrepo A , Hay R J
Published: January 2020

Histoplasmosis is an important systemic fungal infection, particularly among immunocompromised individuals living or travelling in areas of endemicity, who, without antifungal therapy, may develop a progressive disseminated fatal infection. For such patients, the detection of antibody responses by immunodiffusion or complement fixation test is of limited use. In contrast, the detection of Histoplasma capsulatum circulating antigens may provide a more practical approach to the rapid diagnosis of the disease. Accordingly, an inhibition enzyme-linked immunosorbent assay (ELISA) for the detection of a 69- to 70-kDa H. capsulatum-specific determinant and incorporating a species-specific murine monoclonal antibody was developed. With sera from patients with different forms of the disease (n = 35), the overall sensitivity of the test was found to be 71.4%, while the specificity was found to be 98% with normal human sera from areas of endemicity (n = 44) and 85.4% with sera from patients with other chronic fungal or bacterial infections (n = 48). This novel, highly specific ELISA provides a significant addition to the existing diagnostic tests for the detection of histoplasmosis.
A practical approach to genetic screening for influenza virus variants
Authors: Zou S
Published: January 2020

This report describes a quick genetic approach to the screening of influenza virus variants. Multiplex reverse transcription (MRT) and multiplex PCR (MPCR) were used to amplify and differentiate the hemagglutinin (HA) genes of different types and subtypes of influenza viruses. Heteroduplex mobility assay (HMA) was then used to differentiate strains within the same type and subtype. Three primers complementary to the consensus 3' termini of viral genomic RNA segments of human influenza virus types A, B, and C were used in a single MRT reaction to prime the synthesis of cDNA of all the viral genome segments. The cDNA was then amplified in an MPCR containing primers for the HA genes of the H1 and H3 subtypes of type A, the HA gene of type B, and the counterpart of type C virus. Amplicons of the different types and subtypes differ in size, thus allowing typing and subtyping. The regions amplified cover most of the HA1 portion of the HA genes and therefore amplicons of variants identified by the described HMA can be sequenced directly. In the HMA, the amplicon of an individual strain was mixed with that of a reference strain and heteroduplexes derived from mismatches migrated more slowly than homoduplexes of the same size in electrophoresis, with the mobility shift pattern indicating the divergence of amplicons. The whole process from viral RNA extraction to HMA can be completed within 2 days and thus provides a quick screening before further analysis by hemagglutination inhibition testing and sequencing. In addition, all segments of the viral genome can be amplified from a single MRT reaction, which can yield valuable sources of products for future genetic analyses. This method should facilitate genetic screening and characterization of influenza virus variants.
Rapid diagnosis of Brucella bacteremia by using the BACTEC 9240 system
Authors: Bannatyne R M , Jackson M C , Memish Z
Published: January 2020

Almost 93% of 97 separate patient isolates of Brucella bloodstream infections were recovered within 5 days of incubation by using the BACTEC 9240 continuous-monitoring blood culturing system.
Immunomagnetic separation and PCR for detection of Mycobacterium ulcerans
Authors: Roberts B , Hirst R
Published: January 2020

We have developed a technique based on the use of monodisperse magnetic beads to isolate Mycobacterium ulcerans from heterogenous mixtures, prior to PCR amplification. Using this method, we were able to detect M. ulcerans in water samples taken from Phillip Island, Australia, the site of several outbreaks of M. ulcerans disease in recent times.
Quantification of cytomegalovirus DNA in peripheral blood leukocytes by a branched-DNA signal amplification assay
Authors: Chernoff D N , Miner R C , Hoo B S , Shen L P , Kelso R J , Jekic-McMullen D , Lalezari J P , Chou S , Drew W L , Kolberg J A
Published: January 2020

Quantification of cytomegalovirus (CMV) DNA in blood may aid in the identification of patients at highest risk for developing CMV disease, the evaluation of new therapeutics, and the prompt recognition of drug-resistant CMV strains. A branched-DNA (bDNA) assay was developed for the reliable quantification of CMV DNA in peripheral blood leukocytes. The bDNA assay allowed for the highly specific and reproducible quantification of CMV DNA in clinical specimens. Furthermore, the bDNA assay was at least as sensitive as culture techniques and displayed a nearly 3 log10 dynamic range in quantification. Changes in CMV DNA levels measured by the bDNA assay in a human immunodeficiency virus-positive patient undergoing therapy were consistent with CMV culture, antigen, and genotype results and correlated with disease progression and resistance markers. The bDNA assay for the quantification of CMV DNA may provide a useful tool that can be used to aid physicians in monitoring disease progression, evaluating therapeutic regimens, and recognizing viral resistance and drug failure.
Rapid detection of Pneumocystis carinii in bronchoalveolar lavage specimens from human immunodeficiency virus-infected patients: use of a simple DNA extraction procedure and nested PCR
Authors: Rabodonirina M , Raffenot D , Cotte L , Boibieux A , Mayençon M , Bayle G , Persat F , Rabatel F , Trepo C , Peyramond D , Piens M A
Published: January 2020

We report on the development of a rapid nested PCR protocol for the detection of Pneumocystis carinii DNA in bronchoalveolar lavage (BAL) specimens in which the protocol included the use of a commercially available DNA extraction kit (GeneReleaser). GeneReleaser enabled us to obtain amplification-ready DNA within 20 min without requiring the purification of the DNA. The nested PCR was performed with the primers pAZ102-E, pAZ102-H, and pAZ102-L2 (A. E. Wakefield, F. J. Pixley, S. Banerji, K. Sinclair, R. F. Miller, E. R. Moxon, and J. M. Hopkin, Lancet 336:451-453, 1990.). Results were obtained in about 4 h with the adoption of denaturation, annealing, and extension steps shortened to 20 seconds. The sensitivity of the nested PCR was tested with a P. carinii cyst suspension and was found to be less than one cyst (one to eight nuclei). The detection limit was the same with the use of GeneReleaser or proteinase K-phenol chloroform for DNA extraction. The nested PCR assay was prospectively compared with staining with Giemsa and methenamine silver stains for the detection of P. carinii in 127 BAL samples from 105 human immunodeficiency virus-infected patients investigated for acute respiratory illness. Twenty-five BAL specimens (20%) were positive by staining and the nested PCR and 25 (20%) were negative by staining and positive by the nested PCR. These 25 BAL specimens with conflicting results were obtained from 23 patients, 82% of whom were receiving prophylactic therapy against P. carinii pneumonia (PCP). Only two patients were diagnosed with possible PCP. The final diagnosis was not PCP for 20 patients who were considered to be colonized or to have a low level of infection. This colonization is not of clinical importance but is of epidemiological importance. Our rapid, simple, and sensitive amplification protocol may be performed in clinical laboratories for the routine diagnosis of PCP with BAL specimens.