bluuebunny/crossref_metadata_2025 huggingface dataset:
Amplification of rRNA for assessment of treatment response of pulmonary tuberculosis patients during antimicrobial therapy
Authors: Moore D F , Curry J I , Knott C A , Jonas V
Published: January 2020

The time course of persistence of Mycobacterium tuberculosis as measured by detection of rRNA, acid-fast bacillus (AFB) smear, and culture was determined for pulmonary tuberculosis patients during antimicrobial therapy. Twenty-three patients who were initially AFB smear positive and who subsequently completed a course of antimicrobial therapy were selected for the study. Sequential specimens were tested by AFB smear, culture, and rRNA amplification (Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test [MTD]). The initial diagnostic specimens of all patients were positive by culture; those of 22 patients (96%) also were positive by MTD. Overall, MTD results remained positive longer than both smear and culture results. The median times to the last positive test result were 9 days for AFB smear, 26 days for culture, and 30 days for MTD. The last positive test result was the AFB smear result in 4% of cases, the culture result in 22%, and the MTD result in 52%. Fifty-six percent of patients had a period of shedding of noncultivable M. tuberculosis which was detected by MTD after culture results had converted to negative. This noncultivable period lasted 7 to 245 days. All three tests became reproducibly negative before the end of therapy and remained negative during follow-up for up to 1 year. These results indicate that during successful antimicrobial therapy, M. tuberculosis is eliminated in sputum samples as measured by amplification of rRNA, as well as by AFB smear and culture. No long-term rRNA carrier state was detected. While the time course of clearance of M. tuberculosis measured by rRNA overall was longer than with the two traditional tests, the rRNA test results allow sensitive and precise measurement of the clearance of noncultivable M. tuberculosis from respiratory specimens. This attribute may allow rRNA testing to be useful in clarifying patient response to antimicrobial therapy.
Annual incidence, serotype distribution, and genetic diversity of human astrovirus isolates from hospitalized children in Melbourne, Australia
Authors: Palombo E A , Bishop R F
Published: January 2020

The incidence of astrovirus infection in children under 5 years of age hospitalized for acute gastroenteritis in Melbourne, Australia, during 1995 was determined. Astrovirus was detected in 16 fecal specimens by Northern (RNA) dot blot analysis of RNA isolated from feces with an astrovirus-specific cDNA probe. The incidence of astrovirus infection was determined as 4.2% (16 of 378 total samples) compared with rates of 63.2, 3.7, and 4.2% for rotavirus, adenovirus, and all bacterial pathogens, respectively. Astrovirus was detected during the winter season and mainly in infants between 6 and 12 months of age. Serotyping of samples was carried out by reverse transcriptase PCR and direct sequencing of a 348-bp region of the capsid protein gene. Type 1 strains predominated (11 of 13 typeable samples), although type 4 isolates were also detected. Astrovirus was retrospectively identified in 13 fecal samples collected from hospitalized infants between 1980 and 1985 and shown to contain small viruses by electron microscopy. Type 1 isolates were again the most common, although a type 5 strain was also found. Comparative sequence analysis indicated that type 1 astroviruses exhibited up to 7% sequence divergence over a 15-year period; however, all mutations were silent. The incidence of astrovirus reported here indicates that the virus is a significant cause of severe diarrhea in young children. The genetic analysis also provides important molecular epidemiological information relevant to the development of preventative therapies.
Probable new species of Desulfovibrio isolated from a pyogenic liver abscess
Authors: Tee W , Dyall-Smith M , Woods W , Eisen D
Published: January 2020

A fastidious, slowly growing, spiral gram-negative bacterium was isolated from the liver abscess of an 82-year-old man with a 3-week history of febrile illness. The organism was an obligate anaerobe that grew at 37 and 42 degrees C but not at 25 degrees C. Its vibrioid or spiral morphology on Gram staining, rapid progressive motility, electron micrograph features, and biochemical tests were all consistent with the organism belonging to the genus Desulfovibrio. 16S rRNA gene sequencing of this organism demonstrated a 97% similarity to Desulfovibrio desulfuricans with 45 nucleotide differences, suggesting that it is a new species of Desulfovibrio.
Detection of Cryptosporidium parvum DNA in human feces by nested PCR
Authors: Balatbat A B , Jordan G W , Tang Y J , Silva J
Published: January 2020

Cryptosporidium parvum is a coccidian protozoan that causes diarrhea in humans, often chronic and severe in patients with AIDS. Conventionally, diagnosis is made by concentration of stools followed by acid-fast staining (AF) or immunofluorescent staining. The threshold of detection in human stool specimens by these methods may require the presence of 50,000 (immunofluorescent staining) to 500,000 (AF) oocysts per g of stool. In this study, a nested PCR assay was developed to detect C. parvum DNA directly from stool specimens. After extraction of DNA from formalinized stool, a 400-bp fragment of C. parvum DNA was amplified with two 26-mer outer primers. The amplicon from this reaction was amplified with a second primer pair. With these nested primers, a 194-bp DNA fragment was amplified and confirmed as C. parvum DNA by internal probing with an enzyme-linked chemiluminescence system. This PCR-based test allowed the detection of 500 oocysts per g of stool or 100 ng of C. parvum DNA. Studies indicate that the primers utilized are specific for the DNA of C. parvum. DNA sequences were also detected in stool specimens from 4 of 28 patients previously reported negative by AF. In summary, a rapid, sensitive, and specific assay for the detection of C. parvum directly from stool specimens has been developed. This test has the potential for detecting asymptomatic infection, monitoring the response to therapy, and detecting the organism in environmental sources.
Differential diagnoses of influenza A virus, influenza B virus, and respiratory syncytial virus infections by direct immunofluorescence using mixtures of monoclonal antibodies of different isotypes
Authors: Murphy P , Roberts Z M , Waner J L
Published: January 2020

Differences between isotypes of monoclonal antibodies were employed to detect influenza A and B viruses and respiratory syncytial virus by direct immunofluorescence using fluorescein isothiocyanate or Texas Red conjugates. Examination of 56 specimens for influenza A and B viruses and 112 specimens for influenza A virus and respiratory syncytial virus showed the mixed-isotype test to be comparable to the conventional procedure.
Search for the presence of six Mycoplasma species in peripheral blood mononuclear cells of subjects seropositive and seronegative for human immunodeficiency virus
Authors: Kovacic R , Launay V , Tuppin P , Lafeuillade A , Feuillie V , Montagnier L , Grau O
Published: January 2020

The prevalence of Mycoplasma fermentans, Mycoplasma pirum, Mycoplasma genitalium, Mycoplasma pneumoniae, Mycoplasma hominis, and Mycoplasma penetrans was investigated by using specific PCR assays with peripheral blood mononuclear cells from subjects infected or not infected with the human immunodeficiency virus (HIV). Only M. fermentans was detected in 5.8% of 154 HIV-seropositive and 11.1% of 90 HIV-seronegative subjects.
Development of novel assays for botulinum type A and B neurotoxins based on their endopeptidase activities
Authors: Hallis B , James B A , Shone C C
Published: January 2020

A novel assay method based on the endopeptidase activities of the botulinum neurotoxins has been developed and applied to the detection of botulinum type A and B toxins. An assay system developed for the detection of botulinum type B neurotoxin (BoNT/B) is based on the cleavage of a synthetic peptide substrate representing amino acid residues 60 to 94 of the intracellular target protein for the toxin, VAMP (vesicle-associated membrane protein, or synaptobrevin). In this assay system, immobilized VAMP (60-94) peptide substrate is cleaved by BoNT/B at the Gln-76-Phe-77 bond, leaving the C-terminal cleavage fragment on the solid phase. This fragment is then detected by the addition of an antibody-enzyme reagent which specifically recognizes the newly exposed N terminus of the cleavage product. The developed assay was specific to BoNT/B, showing no cross-reactivity with other clostridial neurotoxins, and had a sensitivity for BoNT/B of 0.6 to 4.5 ng/ml, which could be increased to 0.1 to 0.2 ng/ml by using an assay amplification system based on catalyzed reporter deposition. Trypsin treatment of BoNT/B samples, which converts the single-chain toxin to the active di-chain form, was found to increase the sensitivity of the endopeptidase assay from 5- to 10-fold. An endopeptidase assay for BoNT/A, based on the cleavage of a peptide substrate derived from the protein SNAP-25 (synaptosome-associated protein), was also developed and characterized.
Improved plaque assays for Rickettsia prowazekii in Vero 76 cells
Authors: Policastro P F , Peacock M G , Hackstadt T
Published: January 2020

Typhus group rickettsiae, including Rickettsia prowazekii and R. typhi, produce visible plaques on primary chick embryo fibroblasts and low-passage mouse embryo fibroblasts but do not form reproducible plaques on continuous cell culture lines. We tested medium overlay modifications for plaque formation of typhus group rickettsiae on the continuous fibroblast cell line Vero76. A procedure involving primary overlay with medium at pH 6.8, which was followed 2 to 3 days later with secondary overlay at neutral pH containing 1 microgram of emetine per ml and 20 micrograms of NaF per ml, resulted in visible plaques at 7 to 10 days postinfection. A single-step procedure involving overlay with medium containing 50 ng of dextran sulfate per ml also resulted in plaque formation within 8 days postinfection. These assays represent reproducible and inexpensive methods for evaluating the infectious titers of typhus group rickettsiae, cloning single plaque isolates, and testing the susceptibilities of rickettsiae to antibiotics.
Evidence of presence of poliovirus genomic sequences in cerebrospinal fluid from patients with postpolio syndrome
Authors: Leparc-Goffart I , Julien J , Fuchs F , Janatova I , Aymard M , Kopecka H
Published: January 2020

The postpolio syndrome (PPS) is characterized by new neuromuscular symptoms occurring 30 to 40 years after the acute episode of poliomyelitis paralysis. The presence of the poliovirus RNA genome in the cerebrospinal fluid from 10 patients with PPS and from 23 control patients was sought by using reverse transcription and a PCR specific for polioviruses and/or other enteroviruses. Poliovirus-specific genomic sequences in the 5' untranslated region and in the capsid region (VP1) were detected by reverse transcription PCR in 5 of 10 patients with PPS but in none of the control patients. Sequencing confirmed the presence of mutated poliovirus sequences. This finding suggests persistent viral infection in the central nervous system related to the presence of poliovirus genomes.
Differentiation of spotted fever group rickettsiae by sequencing and analysis of restriction fragment length polymorphism of PCR-amplified DNA of the gene encoding the protein rOmpA
Authors: Roux V , Fournier P E , Raoult D
Published: January 2020

Currently, the genotypic identification of the spotted fever group (SFG) rickettsiae is based on restriction fragment length polymorphism analysis of PCR-amplified genes coding for the enzyme citrate synthase and the surface proteins rOmpA and rOmpB. A set of useful restriction endonucleases was found following comparison of Rickettsia rickettsii and R. prowazekii sequences. However, by using three PCR amplifications and four enzyme digestions with this set, it was impossible to differentiate between all of the known serotypes of the SFG rickettsiae. We amplified by PCR and sequenced using an automated laser fluorescent DNA sequencer a fragment of the gene encoding the protein rOmpA from 21 serotypes of the SFG rickettsiae. A 632-bp amplification product was obtained for most of the strains, although no product could be obtained by using R. akari, R. australis, R. helvetica, and R. bellii DNAs. We found a characteristic sequence for all strains studied except the two isolates of R. massiliae, isolates GS and Mtul. Using the software package BISANCE, we determined the restriction map of this fragment and identified five potentially useful endonucleases, RsaI, AluI, PstI, XbaI, and AvaII. We confirmed the computer analysis-derived profiles by PCR-restriction fragment length polymorphism analysis. The combination of the profiles obtained after digestion of the PCR product by RsaI and PstI allowed for the differentiation of 16 strains. The use of AluI and XbaI allowed for the characterization of R. parkeri and strain HA-91, respectively. R. africae and strain S were differentiated by AvaII digestion. Thus, using a single PCR amplification, we were able to differentiate all of the SFG rickettsiae whose ompA gene was amplified by PCR.
Use of in-house studies of molecular epidemiology and full species identification for controlling spread of vancomycin-resistant Enterococcus faecalis isolates
Authors: Bodnar U R , Noskin G A , Suriano T , Cooper I , Reisberg B E , Peterson L R
Published: January 2020

Infection with multidrug-resistant (MDR) organisms is a major clinical challenge, and few, if any, therapeutic options remain available. Increasingly, infection control measures have taken on greater importance in preventing the nosocomial transmission of MDR organisms. During December 1994 and January 1995, we identified a cluster of vancomycin-resistant Enterococcus faecalis isolates involving 16 patients situated in different areas of our university-affiliated teaching hospital. Initial review of laboratory requisition forms for the patients' locations revealed no common association, suggesting that the occurrence was not due to horizontal spread. However, using genomic DNA extraction, restriction enzyme analysis, and gel electrophoresis, we found that 12 patients were infected with isolates originating from a single clone, 2 other patients were infected with isolates from a different clone, and the remaining 2 patients were infected with unique strains. Because the typing data suggested nosocomial spread, chart review was undertaken to determine a possible common exposure source. With three exceptions, clonal isolates were linked to patient movement between surgical floors, intensive care units, and a rehabilitation unit. A detailed review of patient records revealing the association would not have been performed without realization of clonality. Thus, the data demonstrate the utility of genomic typing for epidemiological purposes. In turn, targeted infection control measures that halted the spread of the potentially lethal MDR pathogen were instituted.
Immunoblot assay using excreted-secreted antigens of Trypanosoma cruzi in serodiagnosis of congenital, acute, and chronic Chagas' disease
Authors: Umezawa E S , Nascimento M S , Kesper N , Coura J R , Borges-Pereira J , Junqueira A C , Camargo M E
Published: January 2020

Immunoblotting with trypomastigote excreted-secreted antigens (TESA blot) of Trypanosoma cruzi was evaluated as a method for diagnosis of chronic and acute phases as well as congenital (in newborn children) Chagas' disease. Serum samples from acute-phase and congenital infections were considered to be positive when they reacted with ladder-like bands of 130- to 200-kDa antigens, recognized by immunoglobulin M (IgM) and IgG antibodies, while IgG from chronic-phase sera recognized a broad band antigen of 150 to 160 kDa. Nonchagasic sera were not reactive to these antigens. The study was carried out on 512 patients, 111 of whom were nonchagasic but included cases of leishmaniasis or other pathologies, and 401 chagasic patients. The latter group comprised 361 chronic cases, 36 acute cases, and 4 congenital cases in newborn children. Among the chronic cases, 256 were from areas in which T. cruzi is endemic but which differed widely in the pathogenic expression of T. cruzi infection and in parasitemia levels. These patients at the same time showed a broad range of low, medium, and high reactivity to conventional enzyme-linked immunosorbent assays and indirect immunofluorescence serotests for Chagas' disease. For these reasons they may better represent the universe of chagasic patients than would a sample of highly reactive sera obtained from chagasic patients in a single area endemic for T. cruzi. All acute and congenital cases showed positivity in the IgM and IgG TESA blots, while chronic cases were 100% positive for IgG antibodies. In nonchagasic sera, including 30 cases of visceral and muco-cutaneous leishmaniasis, the specificity index was 1.000, and no cross-reactions were observed. The TESA blot thus seems to be useful as a sensitive and specific diagnostic assay in cases of suspected acute or congenital T. cruzi infection and as a general confirmatory test for conventional Chagas' disease serology.
Techniques for investigation of an apparent outbreak of infections with Candida glabrata
Authors: Arif S , Barkham T , Power E G , Howell S A
Published: January 2020

A cluster of Candida glabrata isolates recovered from seven patients in an intensive care unit over a 10-week period were compared with a collection of isolates from six epidemiologically distinct outpatients and a reference strain by several DNA typing methods. Restriction enzyme analysis with HinII distinguished 13 strains from the 14 sources and was the method of choice. Pulsed-field gel electrophoresis and random amplification of polymorphic DNA both detected nine types from the 14 sources; however, the results of these two methods did not always correlate. These methods demonstrated that five of the seven patients had distinguishable strains and that cross-infection was unlikely.
Rubella reimmunization: comparative analysis of the immunoglobulin G response to rubella virus vaccine in previously seronegative and seropositive individuals
Authors: Mitchell L A , Ho M K , Rogers J E , Tingle A J , Marusyk R G , Weber J M , Duclos P , Tepper M L , Lacroix M , Zrein M
Published: January 2020

Rubella virus (RV)-specific immunoglobulin G (IgG) antibodies were studied in military recruits undergoing unselected immunization with live attenuated measles, mumps, and rubella virus (MMR) vaccine. Three different whole-RV enzyme immunoassays (EIAs) and an epitope-specific EIA with a synthetic peptide (BCH-178c) representing a heutralization domain on the RV E1 envelope protein were used. Before vaccination, 84.2, 87.7, and 84.5% of the subjects tested (n = 399) were found to be seropositive (> 10 IU/ml or assay equivalent) by the three whole-RV EIAs, respectively, while only 82.5% were seropositive by the BCH-178c EIA. Although prevaccination seropositivity rates were similar for the whole-RV EIAs (sensitivity, 94 to 100%), many sera considered seropositive by the whole-RV EIAs had E1 peptide EIA antibody levels of < 10 IU/ml (sensitivity, 77.4 to 80.7%). One month after vaccination, 97.8, 97.2, and 93.5% of the subjects who were followed (n = 356) were seropositive by the three whole-RV EIAs, respectively, while 89% had BCH-178c peptide-specific IgG titers of > 10 IU/ml. After vaccination, depending on the assay used, up to 20.6% of initially seropositive individuals exhibited a greater than fourfold increase in RV-specific IgG, while up to 47.3% showed a greater than twofold increase. Increased antibody titers after vaccination (seroboosting) were most frequently associated with low levels of BCH-178c peptide-specific IgG before vaccination. RV protein-specific IgG was also studied by immunoblot assays in a subset (n = 56) of individuals receiving the MMR vaccine. Of these, 89.4 and 91.1% exhibited RV protein (E1, E2, and C protein)-specific IgG before and after vaccination, respectively. Seroboosting (two- to fourfold increase in EIA titers of individuals seropositive by the whole-RV EIA before vaccination) was usually accompanied by a shift in the IgG immunoblot pattern from a single (E1) to multiple (E1-E1, E1-C, or E1-E2-C) specificities, suggesting exposure of new epitopes as a result of viral replication.
Genotyping of Mycobacterium tuberculosis with additional markers enhances accuracy in epidemiological studies
Authors: Warren R , Richardson M , Sampson S , Hauman J H , Beyers N , Donald P R , van Helden P D
Published: January 2020

Two highly polymorphic Mycobacterium tuberculosis genomic domains, characterized by hybridization to the oligonucleotide (GTG)5, were identified as potential DNA fingerprinting probes. These domains were cloned [pMTB484(1) and pMTB484(2K4), respectively] and shown to be useful for genotype analysis by Southern blotting. These probes were used to genotype geographically linked strains of M. tuberculosis previously shown to have identical IS6110 fingerprints. Subsequent DNA fingerprints generated with MTB484(1) and MTB484(2K4) showed a high degree of polymorphism, allowing subclassification of IS6110-defined clusters into composites of smaller clusters and unique strains. Correlation of the molecular data with patient interviews and clinical records confirmed the sensitivity of these probes, as contacts were established only within subclusters. These findings demonstrate the requirement for multiple probes to accurately classify M. tuberculosis strains, even those with high copy numbers of IS6110. The enhanced accuracy of strain typing should, in turn, further our understanding of the epidemiology of tuberculosis.
Molecular typing of Yersinia pseudotuberculosis by using an IS200-like element
Authors: Odaert M , Berche P , Simonet M
Published: January 2020

The IS200-like insertion sequence (IS) is a 708-bp element recently found in Yersinia pestis. Its nucleotide sequence is 85% identical to that of IS200 recovered in most Salmonella enterica isolates. It is also present in multiple copies in Y. pseudotuberculosis. In contrast, this IS is found in some (biotype 1B strains) but not other Y. enterocolitica strains and is absent in the nonpathogenic yersiniae: Y. frederiksenii, Y. kristensenii, Y. intermedia, Y. bercovieri, and Y. mollaretii. The number and locations of the ISs in the Y. pseudotuberculosis genome vary among strains, resulting in a high degree of polymorphism, but IS fingerprints are stable after multiple subcultures of clinical isolates. The discriminative power of IS typing is better than that of ribotyping and almost as good as that of the time-consuming method of pulsotyping. Overall, IS200-like is a useful molecular marker in determining the epidemiology of Y. pseudotuberculosis infections.
Modified India ink preparation for Cryptococcus neoformans in cerebrospinal fluid specimens
Authors: Zerpa R , Huicho L , Guillén A
Published: January 2020

A novel modified India ink technique for the diagnosis of Cryptococcus neoformans in cerebrospinal fluid specimens is described. It employs 2% chromium mercury and India ink. This technique allows a clear identification of some external and internal structures of the organism. Three layers from the outer capsule that have previously been discerned only by electron microscopy are distinguished.
The mtp40 gene is not present in all strains of Mycobacterium tuberculosis
Authors: Weil A , Plikaytis B B , Butler W R , Woodley C L , Shinnick T M
Published: January 2020

A multiple PCR-based assay that targets IS6110 and the mtp40 gene was evaluated for the rapid differentiation of Mycobacterium bovis and M. tuberculosis, two of the causative agents of tuberculosis. The IS6110 target is present in both species, whereas the mtp40 gene was thought to be specific for M.tuberculosis (P. Del Portillo, L.A. Murillo, and M.E. Patarroyo, J. Clin. Microbiol. 29:2163-2168, 1991). However, the mtp-40 gene is not present in all M. tuberculosis strains and, hence, is not useful for differentiating M.tuberculosis and M.bovis.
Diagnosis of Helicobacter pylori infection in a colony of rhesus monkeys (Macaca mulatta)
Authors: Handt L K , Fox J G , Yan L L , Shen Z , Pouch W J , Ngai D , Motzel S L , Nolan T E , Klein H J
Published: January 2020

Twenty-three young adult rhesus monkeys from China were evaluated for the presence of Helicobacter pylori. Gastric body and antral biopsy samples were tested for H. pylori by PCR analysis, culture, rapid urease testing, and histologic evaluation. Serologic testing to detect H. pylori immunoglobulin G (IgG) antibodies was performed by using a commercially available human-based enzyme-linked immunosorbent assay (ELISA) test and an ELISA test which utilized homologous H. pylori antigens and an anti-rhesus IgG conjugate. PCR analysis with H. pylori-specific 26-kDa protein primers detected H. pylori in 21 of the 23 rhesus monkeys (91%). Culture testing identified the organism in 12 of the 23 animals (52%). Rapid urease tests were positive for all animals. H. pylori was diagnosed by histological examination in 11 of 23 monkeys (48%). Of the 21 monkeys positive for H. pylori by PCR, only 3 (14%) had positive results by the commercial ELISA test, yielding a sensitivity of 14%, a specificity of 100%, and an accuracy of 22%. However, 19 of the 21 PCR-positive animals (90%) had positive results by the ELISA test with homologous rhesus H. pylori antigen and anti-monkey conjugate, with predicted index values greater than or equal to 0.7 considered positive and values between 0.5 and 0.7 considered equivocal. This test had a sensitivity of 90%, a specificity of 100%, and an accuracy of 91%. Therefore, the ELISA test with rhesus monkey origin components was more accurate for detecting infected animals than the human-based ELISA.
Detection of Antibodies to Pasteurella multocida by capture enzyme immunoassay using a monoclonal antibody against P37 antigen
Authors: Peterson R R , Deeb B J , DiGiacomo R F
Published: January 2020

As infection with Pasteurella multocida is common in rabbits, an enzyme immunoassay (EIA) was developed for its detection. A murine immunoglobulin G monoclonal antibody was used to capture a 37-kDa polypeptide of P. multocida serotype A:12 in an EIA to detect antibodies to P. multocida. The 37-kDa antigen was selected since it was previously shown to be a major immunogen during P. multocida infection in rabbits. The sensitivity of the P37 EIA, determined with sera from 56 rabbits infected with P. multocida, was 98%. Specificity, evaluated with sera from 62 rabbits from colonies free of P. multocida, was 92%. Titration curves of sera from rabbits immunized with P. multocida serotype A:3 or A:12 coincided, indicating that the P37 EIA was equally efficient in detecting antibodies to the two major serotypes of the organism. Comparison of the P37 EIA with the current serodiagnostic test, a bacterial lysate EIA, revealed relatively good correlation (r = 0.68). However, specificity was greatly improved, as 34% of uninfected rabbits were falsely positive by the lysate EIA whereas only 3% of uninfected rabbits were falsely positive by the P37 EIA. The coefficient of variation for same-day tests was 10%, and that for interday tests was 15%, indicating good reproducibility. The greater sensitivity and specificity of the P37 EIA should significantly enhance diagnostic capability to identify rabbits infected with P. multocida.
Borrelia burgdorferi enzyme-linked immunosorbent assay for discrimination of OspA vaccination from spirochete infection
Authors: Zhang Y Q , Mathiesen D , Kolbert C P , Anderson J , Schoen R T , Fikrig E , Persing D H
Published: January 2020

Recombinant Lyme disease vaccines based on purified preparations of outer surface protein A (OspA) have been shown to be effective in preventing transmission of Borrelia burgdorferi in experimental animal models and are now being tested in humans. Since the most widely used screening tests for Lyme disease are based on a whole-cell sonicate of B. burgdorferi, serologic false positivity in vaccinated persons could result from reactivity to OspA within the antigen preparation. In order to avoid serologic false positivity in vaccinated subjects, we developed an immunoassay based on a low-passage-number, naturally occurring variant of B. burgdorferi which lacks the plasmid encoding OspA and OspB. The use of an antigen preparation derived from this organism provided sensitive and specific detection of B. burgdorferi seropositivity in experimental animals and in human Lyme disease cases. The OspA-B-negative enzyme-linked immunosorbent assay (ELISA) also appeared to be capable of discriminating the vaccinated state from vaccine failure and natural infection in experimental animals. Sera from human subjects participating in a vaccine trial gave false-positive results with an ELISA based on an OspA-containing strain, but no such reactivity was observed when the OspA-negative ELISA was used. We conclude that low-passage-number OspA-B-negative isolates in immunoassays may become useful for the immunologic discrimination of the vaccinated state, natural infection, and vaccine failure.
Comparison of ligase chain reaction and culture for detection of Neisseria gonorrhoeae in genital and extragenital specimens
Authors: Stary A , Ching S F , Teodorowicz L , Lee H
Published: January 2020

In addition to the urogenital tract, Neisseria gonorrhoeae infects extragenital sites such as the pharynx and anorectal canal. Culture and a ligase chain reaction (LCR)-based assay were compared for their performance for the diagnosis of N. gonorrhoeae infection with specimens from various urogenital and extragenital sites of 200 men and 125 women. The sensitivity and specificity of the LCR assay with male urethral swabs were both 100%, compared to values of 95.9 and 100%, respectively, for culture of urethral swabs or 98.0 and 100%, respectively, for LCR with first-void urine (FVU). For women, LCR with FVU showed the highest sensitivity (94.7%), and culture of urethral samples showed the lowest sensitivity (63.2%) (P < 0.05). In a selected subgroup of 47 men and 22 women at increased risk, the rates of pharyngeal infection were 15 and 18%, respectively, and those of anorectal infection were 13 and 45%, respectively. The sensitivity of LCR was greater than that of culture for both pharyngeal and anorectal specimens. Thus, the overall performance of LCR testing with swabs or FVU was better than that of culture for the diagnosis of genital or extragenital gonorrhea.
Use of a PCR method based on IS6110 polymorphism for typing Mycobacterium tuberculosis strains from BACTEC cultures
Authors: Otal I , Samper S , Asensio M P , Vitoria M A , Rubio M C , Gómez-Lus R , Martín C
Published: January 2020

Two PCR typing methods, based on polymorphism of the insertion sequence IS6110, were compared with Mycobacterium tuberculosis strains by using a single primer complementary to the inverted repeats of IS6110. Total M. tuberculosis DNA either was amplified directly (IS6110-PCR) or was amplified following digestion and ligation (IS6110-inverse-PCR). Both PCR techniques showed a similar degree of discrimination. Because of its simplicity, IS6110-PCR was chosen to confirm that a single M. tuberculosis strain was responsible for an outbreak of tuberculosis in a secondary school. IS6110-PCR was used to study the degree of differentiation in 85 clinical M. tuberculosis isolates from BACTEC 12B broth cultures. Results were consistent with those of the standardized IS6110 restriction fragment length polymorphism (RFLP) analysis method, showing identical PCR types for identical RFLPs, although the degree of discrimination was greater by RFLP analysis. The study concludes that due to its simplicity, IS6110-PCR is a good screening method when quick differentiation between M. tuberculosis strains is needed because BACTEC cultures may be used directly.
A fatal case of Mycoplasma hominis meningoencephalitis in a full-term newborn
Authors: Alonso-Vega C , Wauters N , Vermeylen D , Muller M F , Serruys E
Published: January 2020

We report the case of a 20-day-old full-term baby, born to a mother who had had an uncomplicated pregnancy and delivery, who died 13 days after the onset of meningitis. Mycoplasma hominis was the sole agent repeatedly recovered from cerebrospinal fluid and from postmortem brain tissue.
Detection of herpes simplex virus in clinical specimens by cytospin-enhanced direct immunofluorescence
Authors: Landry M L , Ferguson D , Wlochowski J
Published: January 2020

For 275 samples tested for herpes simplex virus (HSV), cytospin-enhanced direct immunofluorescence using Chemicon HSV monoclonal antibodies identified 80 (95%) and culture identified 77 (92%) of 84 confirmed positive specimens. Cytospin-prepared slides contained a greater number of total cells than standard cell spots, resulting in fewer inadequate cell smears and a higher HSV detection rate.
Shieh medium supplemented with tobramycin for selective isolation of Flavobacterium columnare (Flexibacter columnaris) from diseased fish
Authors: Decostere A , Haesebrouck F , Devriese L A
Published: January 2020

Tobramycin was found to be less inhibitory to Flavobacterium columnare (formerly Flexibacter columnaris) than to other fish-associated bacteria. The selective capacity of Shieh medium, an isolation medium described for this species, was markedly enhanced by adding tobramycin at a concentration of 1 microgram/ml.
Helcococcus kunzii as sole isolate from an infected sebaceous cyst
Authors: Peel M M , Davis J M , Griffin K J , Freedman D L
Published: January 2020

Helcococcus kunzii was isolated in pure culture from pus drained from an infected sebaceous cyst associated with marked cellulitis. The cyst was excised one month later after the inflammation had subsided with flucloxacillin treatment. This is the first report of the isolation of H. kunzii as the sole pathogen from an infected site.
Detection of adeno-associated virus type 2 sequences in the human genital tract
Authors: Friedman-Einat M , Grossman Z , Mileguir F , Smetana Z , Ashkenazi M , Barkai G , Varsano N , Glick E , Mendelson E
Published: January 2020

Adeno-associated virus (AAV) is a defective parvovirus with unknown pathogenicity. It requires helper functions for its normal replication in human tissue and therefore is not readily isolated from clinical specimens. We have used the PCR method to examine the following clinical samples for the presence of AAV sequences: (i) 15 nasopharyngeal aspirates from symptomatic patients, (ii) 7 swab or fluid specimens from vesicles of patients suspected of having varicella-zoster virus infections, (iii) 21 human papilloma virus-positive genital biopsy specimens, (iv) 61 genital swab specimens from women suspected of having herpes simplex virus (HSV) infection examined either directly or following propagation in tissue culture, (v) 62 samples of first-trimester aborted material, including 38 samples from spontaneous abortions and 24 samples from induced abortions, (vi) 11 samples of chorionic villi taken from women undergoing genetic prenatal diagnosis, and (vii) three lots of cultured human embryonic cells. AAV sequences were detected only in samples taken from the genital tracts of women suspected of having HSV infection and not in any of the other types of samples. Samples from 11 patients were positive for AAV: for 4 patients the original swab sample was positive, for 4 patients the cultured swab sample was positive, and for 3 patients both the original swab samples and the cultures were positive. Five of the 11 patients were infected with HSV. Our study demonstrates the presence of AAV in the female genital tract. However, in contrast to a previous report (E. Tobiasch, M. Rabreau, K. Geletneky, S. Larue-Charlus, F. Severin, N. Becker, and J. R. Schlehofer, J. Med. Virol. 44:215-222, 1994), we did not find solid evidence of its replication in maternal or embryonal tissues from the first trimester of pregnancy. The questions of a potential pathogenic etiology of AAV and the interaction with HSV remain open.
Routine use of PCR-restriction fragment length polymorphism analysis for identification of mycobacteria growing in liquid media
Authors: Taylor T B , Patterson C , Hale Y , Safranek W W
Published: January 2020

A PCR-restriction fragment length polymorphism (PCR-RFLP) procedure capable of rapidly identifying 28 species of clinically encountered mycobacteria was evaluated for use in the routine identification of acid-fast isolates growing in BACTEC 12B and 13A liquid media. PCR-RFLP identified 100 of 103 acid-fast isolates recovered from 610 patient specimens submitted for culture during the study. The three isolates unidentifiable by PCR-RFLP produced restriction patterns not included in the PCR-RFLP algorithm and could therefore not be assigned to a species. These isolates were characterized by their morphologic and biochemical characteristics. Two of the isolates were identified as M. terrae complex and M. gordonae. The third isolate could not be definitively identified and could only be characterized as a Mycobacterium sp. most closely resembling M. chelonae. PCR-RFLP identifications agreed with the conventional identifications for 96 of the 100 isolates identified by PCR-RFLP. Subsequent identification of the four discordant isolates by gas chromatography analysis supported the PCR-RFLP identification of each isolate. Amplification products were also obtained from isolates of Streptococcus albus and Rhodococcus equi recovered from patient specimens; however, the restriction patterns of these nonmycobacterial species did not resemble the patterns of any mycobacterial species included in the PCR-RFLP algorithm. PCR-RFLP seems to be a reliable procedure for the routine identification of mycobacteria and has the potential for providing identifications of mycobacterial isolates which are more accurate than conventional identification techniques based on morphologic and biochemical characteristics.
Multicenter evaluation of the MicroScan Rapid Gram-Negative Identification Type 3 Panel
Authors: Bascomb S , Abbott S L , Bobolis J D , Bruckner D A , Connell S J , Cullen S K , Daugherty M , Glenn D , Janda J M , Lentsch S J , Lindquist D , Mayhew P B , Nothaft D M , Skinner J R , Williams G B , Wong J , Zimmer B L
Published: January 2020

The accuracy and performance of the revised MicroScan Rapid Gram-Negative Identification Type 3 Panel (Dade MicroScan Inc., West Sacramento, Calif.) were examined in a multicenter evaluation. The revised panel database includes data for 119 taxa covering a total of 150 species, with data for 12 new species added. Testing was performed in three phases: the efficacy, challenge, and reproducibility testing phases. A total of 405 fresh and stock gram-negative isolates comprising 54 species were tested in the efficacy phase; 96.8% of these species were identified correctly in comparison to the identification obtained either with the API 20E system (bioMérieux Vitek, Hazelwood, Mo.) or by the conventional tube method. The number of correctly identified isolates in the challenge phase, including new species added to the database, was 221 of 247, or 89.5%, in comparison to the number correctly identified by the conventional tube method. A total of 465 isolates were examined for intra- and interlaboratory identification reproducibility and gave an agreement of 464 of 465, or 99.8%. The overall reproducibility of each individual identification test or substrate was 14,373 of 14,384, or 99.9%. The new Rapid Gram-Negative Identification Type 3 Panel gave accurate and highly reproducible results in this multiple-laboratory evaluation.
PCR detection, identification to species level, and fingerprinting of Campylobacter jejuni and Campylobacter coli direct from diarrheic samples
Authors: Linton D , Lawson A J , Owen R J , Stanley J
Published: January 2020

Three sets of primers were designed for PCR detection and differentiation of Campylobacter jejuni and Campylobacter coli. The first PCR assay was designed to coidentify C. jejuni and C. coli based on their 16S rRNA gene sequences. The second PCR assay, based on the hippuricase gene sequence, identified all tested reference strains of C. jejuni and also strains of that species which lack detectable hippuricase activity. The third PCR assay, based on the sequence of a cloned (putative) aspartokinase gene and the downstream open reading frame, identified all tested reference strains of C. coli. The assays will find immediate application in the rapid identification to species level of isolates. The assays combine with a protocol for purification of total DNA from fecal samples to allow reproducible PCR identification of campylobacters directly from stools. Of 20 clinical samples from which campylobacters had been cultured, we detected C. jejuni in 17, C. coli in 2, and coinfection of C. jejuni and Campylobacter hyointestinalis in 1. These results were concordant with culture and phenotypic identification to species level. Strain typing by PCR-restriction fragment length polymorphism of the flagellin (flaA) gene detected identical flaA types in fecal DNA and the corresponding campylobacter isolate. Twenty-five Campylobacter-negative stool samples gave no reaction with the PCR assays. These PCR assays can rapidly define the occurrence, species incidence, and flaA genotypes of enteropathogenic campylobacters.
Typing of Staphylococcus aureus and Staphylococcus epidermidis strains by PCR analysis of inter-IS256 spacer length polymorphisms
Authors: Deplano A , Vaneechoutte M , Verschraegen G , Struelens M J
Published: January 2020

IS256 elements are present in multiple copies in the staphylococcal genome, either flanking the transposon Tn4001 or independent of it. PCR-based analysis of inter-IS256 spacer polymorphisms was developed for typing of methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis strains. Using SmaI macrorestriction analysis resolved by pulsed-field gel electrophoresis (PFGE) as the reference method for MRSA typing, excellent reproducibility (100%), discriminatory power (97%), and in vivo stability were observed. Good concordance of the results with those of other molecular typing methods was found for two MRSA collections. Inter-IS256 PCR analysis of a U.S. collection of MRSA strains (n = 36), previously characterized by 15 typing methods, showed more limited discrimination. Agreement was 78% with PFGE analysis and 83% with ribotyping (HindIII). Analysis of a second set of Belgian MRSA strains (n = 17), categorized into two widespread epidemic clones by PFGE analysis, showed 65% agreement. For typing of S. epidermidis strains (n = 26), inter-IS256 PCR showed complete typeability (100%) and good discriminatory power (85%). Inter-IS256 PCR analysis is proposed as an efficient molecular typing assay for epidemiological studies of MRSA or S. epidermidis isolates.
Evaluation of a fluorescence-labelled oligonucleotide probe targeting 23S rRNA for in situ detection of Salmonella serovars in paraffin-embedded tissue sections and their rapid identification in bacterial smears
Authors: Nordentoft S , Christensen H , Wegener H C
Published: January 2020

A method for the detection of Salmonella based on fluorescence in situ hybridization (FISH) has been developed and applied for the direct detection of Salmonella in pure cultures and in formalin-fixed, paraffin-embedded tissue sections. On the basis of the 23S rRNA gene sequences representing all of the S. enterica subspecies and S. bongori, an 18-mer oligonucleotide probe was selected. The specificity of the probe was tested by in situ hybridization to bacterial cell smears of pure cultures. Forty-nine of 55 tested Salmonella serovars belonging to subspecies I, II, IIIb, IV, and VI hybridized with the probe. The probe did not hybridize to serovars from subspecies IIIa (S. arizonae) or to S. bongori. No cross-reaction to 64 other strains of the family Enterobacteriaceae or 18 other bacterial strains outside this family was observed. The probe was tested with sections of formalin-fixed, paraffin-embedded tissue from experimentally infected mice or from animals with a history of clinical salmonellosis. In these tissue sections the probe hybridized specifically to Salmonella serovars, allowing for the detection of single bacterial cells. The development of a fluorescence-labelled specific oligonucleotide probe makes the FISH technique a promising tool for the rapid identification of S. enterica in bacterial smears, as well as for the detection of S. enterica in histological tissue sections.
DNA typing suggests pigeon droppings as a source of pathogenic Cryptococcus neoformans serotype D
Authors: Garcia-Hermoso D , Mathoulin-Pélissier S , Couprie B , Ronin O , Dupont B , Dromer F
Published: January 2020

The unusual proportion of serotype D strains of Cryptococcus neoformans infecting patients diagnosed with cryptococcosis in some parts of France prompted the analysis of DNA fingerprints obtained with 26 clinical and 29 environmental isolates from the same area. Our results suggest that pigeon droppings are a potential source of pathogenic strains of C. neoformans serotype D, as previously demonstrated for serotype A.
PCR-enzyme-linked immunosorbent assay and sequencing as an alternative to serology for M-antigen typing of Streptococcus pyogenes
Authors: Saunders N A , Hallas G , Gaworzewska E T , Metherell L , Efstratiou A , Hookey J V , George R C
Published: January 2020

A rapid PCR-enzyme-linked immunosorbent assay for identification of 10 important emm gene types of Streptococcus pyogenes was developed. The emm genotypes of a coded panel of strains of known M serotype were determined, and in 144 of 149 cases (97%) the results were congruous. Strains of types that were not included in the panel of capture probes were emm genotyped by sequencing.
Evaluation of the AMPLICOR CMV test for direct detection of cytomegalovirus in plasma specimens
Authors: Hiyoshi M , Tagawa S , Takubo T , Tanaka K , Nakao T , Higeno Y , Tamura K , Shimaoka M , Fujii A , Higashihata M , Yasui Y , Kim T , Hiraoka A , Tatsumi N
Published: January 2020

We evaluated the AMPLICOR CMV test (PCR) for the direct detection of cytomegalovirus in plasma. Sixty-eight specimens were involved for the comparison between the AMPLICOR test and the antigenemia assay. The sensitivities, specificities, and positive and negative predictive values were 97.1, 100, 100, and 97.1%, respectively, for the AMPLICOR test and 79.4, 100, 100, and 82.9%, respectively, for the antigenemia assay.