bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenetic analysis of pathogen-related oral spirochetes
Authors: Choi B K , Wyss C , Göbel U B
Published: January 2020

Recently, Riviere et al. reported as yet uncultivable invasive oral spirochetes that cross-reacted with monoclonal antibodies (MAbs) specific for Treponema pallidum (G. R. Riviere, K. S. Elliot, D. F. Adams, L. G. Simonson, L. B. Forgas, A. M. Nilius, and S. A. Lukehart, J. Periodontol. 63:131-136, 1992; G. R. Riviere, M. A. Wagoner, S. A. Baker-Zander, K. S. Weisz, D. F. Adams, L. Simonson, and S. A. Lukehart, N. Engl. J. Med. 325:539-543, 1991; G. R. Riviere, K. S. Weisz, D. F. Adams, and D. D. Thomas, Infect. Immun. 59:3377-3380, 1991; G. R. Riviere, K. S. Weisz, L. G. Simonson, and S. A. Lukehart, Infect. Immun. 59:2653-2657, 1991). In an attempt to phylogenetically analyze these pathogen-related oral spirochetes, we used immunomagnetic separation, combined with comparative sequence analysis of 16S rRNA genes amplified in vitro by the PCR. The bacteria were immunomagnetically enriched from subgingival plaque samples of patients with rapidly progressive periodontitis by using MAb H9-2 specific for the 37-kDa endoflagellum sheath protein of T. pallidum. After PCR amplification with universal eubacterial primers 16S rRNA gene fragments were cloned into Escherichia coli. A total of 20 randomly selected recombinants were analyzed by sequencing about 200 to 300 bases of the 500-bp inserts. All the spirochetal 16S rRNA sequences clustered to previously described, as yet uncultivable cluster 7 treponemes of group I (B. K. Choi, B. J. Paster, F. E. Dewhirst, and U. B. Göbel, Infect. Immun. 62:1889-1895, 1994). With a sequence similarity of 96.4% the most closely related cultivable treponeme was Treponema vincentii, which also belongs to the group I treponemes. Subsequent immunological analysis of cultured treponemes with MAb H9-2 revealed that only T. vincentii strains showed specific immunofluorescence or a characteristic 37-kDa band in immunoblots. We therefore conclude that pathogen-related oral spirochetes constitute a heterogeneous population of treponemes comprising T. vincentii and T. vincentii-related organisms that have common epitopes cross-reacting with MAb H9-2.
Variation in metabolic enzyme activity of persistent Haemophilus influenzae in respiratory tracts of patients with cystic fibrosis
Authors: Möller L V , Grasselier H , Dankert J , van Alphen L
Published: January 2020

Haemophilus influenzae organisms were isolated from sputum specimens prospectively collected from 40 patients with cystic fibrosis during 2 years to study variations in the metabolic enzyme activities of persistent H. influenzae strains as determined by biotyping. In total, 97 distinct H. influenzae strains without variations in their major outer membrane protein (MOMP) patterns and 73 MOMP variants derived from 30 of these distinct strains were obtained. Twelve distinct strains and 42 MOMP variant strains were isolated at multiple time points during the study period, indicating the persistence of these strains. Among the 54 persistent H. influenzae strains, 22 (41%) strains with stable MOMP compositions showed random variations in biotypes. In 39 of 103 (38%) H. influenzae strains, biotype changes coincided with MOMP variations. Biotype variations were the result of both the loss and the acquisition of enzyme activities. The results of the study indicate that changes in metabolic enzyme activity occur randomly during the persistence of H. influenzae organisms in cystic fibrosis patients, irrespective of MOMP variations.
Substances interfering with direct detection of Mycobacterium tuberculosis in clinical specimens by PCR: effects of bovine serum albumin
Authors: Forbes B A , Hicks K E
Published: January 2020

Interfering substances have been reported to inhibit PCR assays for the direct detection of Mycobacterium tuberculosis in clinical specimens. Using an internal control, we determined that 52% of respiratory specimens interfered with our PCR assay. On the basis of these findings, we tried to circumvent the problem by simply diluting prepared sediments. With sediment from a routinely processed sputum known to be inhibitory to PCR, one aliquot was prepared in a routine manner for PCR. Remaining sediment was diluted in phosphate-buffered saline, Middlebrook 7H10 broth, or BACTEC 12B broth; an internal control was added to all reaction mixtures and controls. Internal control was detected only in the sample diluted with BACTEC 12B medium. Components of the BACTEC 12B medium including PANTA reagent (polymyxin B, amphotericin B, nalidixic acid, trimethoprim, and azlocillin), reconstituting fluid, 0.2% glycerol, 0.05% Tween 80, and 0.05% bovine serum albumin (BSA) were tested in a similar manner. Only 0.05% BSA resulted in amplification of the internal control DNA. Varying concentrations of BSA were added to 11 aliquots of a respiratory sediment known to be inhibitory to the PCR. Internal control was detected in all reaction mixtures containing 0.00038 to 0.1% BSA. To determine the ability of BSA to override inhibition, respiratory specimens were run in triplicate: undiluted, diluted 1:2 with BACTEC 12B medium, or diluted with 0.026% BSA. For 21 of 22 inhibitory specimens, BSA was able to override the presence of interfering substances. These data suggest that the presence of BSA in a PCR assay is critical for the direct detection of M. tuberculosis in respiratory specimens.
Antibody against an Anaplasma marginale MSP5 epitope common to tick and erythrocyte stages identifies persistently infected cattle
Authors: Knowles D , Torioni de Echaide S , Palmer G , McGuire T , Stiller D , McElwain T
Published: January 2020

A protein epitope of major surface protein 5 (MSP5), defined by monoclonal antibody (MAb) ANAF16C1, is conserved among Anaplasma species (E. S. Visser, T. C. McGuire, G. H. Palmer, W. C. Davis, V. Shkap, E. Pipano, and D. P. Knowles, Jr., Infect. Immun. 60:5139-5144, 1992) and is expressed in the salivary glands of infected ticks. A competitive inhibition ELISA (cELISA) for the detection of bovine anti-MSP5 antibodies was developed by using purified recombinant MSP5 fusion protein and MAb ANAF16C1. The specificity of the recombinant-MSP5 cELISA within North America was established by using 261 serum samples from cattle in the regions of Hawaii and Northern Ontario where anaplasmosis is not endemic and from cattle proven by splenectomy or subinoculation of whole blood into susceptible splenectomized recipients to be uninfected. The maximum percent inhibition by these sera was 18%. Sera known to be positive were obtained from 35 cattle either experimentally inoculated with infected erythrocytes or exposed to infected Dermacentor andersoni ticks. Thirty-four of the 35 serum samples inhibited MAb ANAF16C1 binding by > or = 25%. During acute infection, the MSP5 cELISA detected antibodies prior to or concomitantly with the appearance of rickettsiae in erythrocytes. Antibodies were detectable in sera from persistently infected cattle inoculated as long as 6 years previously.
Identification of Mycobacterium avium complex in sarcoidosis
Authors: el-Zaatari F A , Naser S A , Markesich D C , Kalter D C , Engstand L , Graham D Y
Published: January 2020

Cell wall-defective bacteria which later reverted to acid-fast bacilli have been isolated from sarcoid tissue. These have not been conclusively shown to be mycobacteria. Specific PCR assays were applied to identify mycobacterial nucleic acids in these cultured isolates and in fresh specimens obtained from patients with sarcoidosis. Positive amplification and hybridization were observed with Mycobacterium avium complex- and/or Mycobacterium paratuberculosis-specific probes in five of the six cultured isolates and two fresh skin biopsy samples and one cerebrospinal fluid specimen. There was no amplification or hybridization with Mycobacterium tuberculosis or M. avium subsp. silvaticum probes, respectively. Patients' sera were also tested for antibody reactivities by immunoblotting with M. paratuberculosis recombinant clones expressing the 36,000-molecular-weight antigen (36K antigen) (p36) and the 65K heat shock protein (PTB65K). All seven sarcoidosis, four of six tuberculosis, and all six leprosy patient serum specimens showed strong reactivity with p36 antigen. In contrast, 13 of 38 controls showed only weak reactivity with p36 (P = 0.002 for controls versus sarcoidosis samples). Similarly, PTB65K reacted with high intensity with sera from 5 of 5 sarcoidosis, 5 of 6 tuberculosis, and 5 of 6 leprosy patients, compared with its low-intensity reaction with 5 of 22 controls (P = 0.001 for controls versus sarcoidosis samples). This study demonstrates the isolation and/or identification of M. paratuberculosis or a closely related M. avium complex strain from sarcoid skin lesions and cerebrospinal fluid. Furthermore, the reactivity of antibodies in sarcoid patient sera against p36 and PTB65K antigens was comparable to the reactivity of sera obtained from patients with known mycobacterial disease. Collectively, these data provide further support for the theory of the mycobacterial etiology of sarcoidosis.
Rapid detection of point mutations of the Neisseria gonorrhoeae gyrA gene associated with decreased susceptibilities to quinolones
Authors: Deguchi T , Yasuda M , Nakano M , Ozeki S , Ezaki T , Maeda S , Saito I , Kawada Y
Published: January 2020

Mutations in the gyrA gene resulting in amino acid changes at Ser-91 and Asp-95 are significantly associated with decreased susceptibilities to quinolones in Neisseria gonorrhoeae. To detect these mutations, we developed a rapid and simple assay based on amplification of the region of the gyrA gene containing the mutation sites by PCR and digestion of the PCR product with a restriction enzyme. A naturally occurring HinfI restriction site was present in the region containing the Ser-91 codon, and an artificial HinfI restriction site was created in the region containing the Asp-95 codon by the method of primer-specified restriction site modification. The mutations generating alterations at Ser-91 and Asp-95 were detected as restriction fragment length polymorphisms of the PCR products digested with HinfI. Fifty-five clinical strains of N. gonorrhoeae were examined for mutations in the gyrA gene by this method. Mutations at Ser-91 and/or Asp-95 were detected in all the 31 strains in which the mutations had been confirmed by DNA sequencing. Our method allows simultaneous testing of a large number of strains and provides results within 8 h. This rapid and simple assay could be a useful screening device for genetic alterations associated with decreased susceptibilities to quinolones in N. gonorrhoeae and could facilitate epidemiological studies on clinical isolates of N. gonorrhoeae with decreased susceptibilities to quinolones.
In vivo detection of porcine reproductive and respiratory syndrome virus RNA by in situ hybridization at different times postinfection
Authors: Sur J H , Cooper V L , Galeota J A , Hesse R A , Doster A R , Osorio F A
Published: January 2020

We studied the distribution of porcine reproductive and respiratory syndrome virus (PRRSV) RNA in tissues by in situ hybridization at different times postinfection (p.i.). The probe used for in situ hybridization was prepared by reverse transcription of PRRSV RNA, followed by PCR amplification of the cDNA. The sequence amplified corresponded to 433 bp from PRRSV open reading frame 7, which is contained in the nucleocapsid protein gene and which is highly conserved in both European and American strains (H. Mardassi, L. Wilson, S. Mounir, and S. Dea, J. Clin. Microbiol. 32:2197-2203, 1994). An immunohistochemical technique was used to detect PRRSV antigen in tissue from virus-infected animals by using a monoclonal antibody specific for the PRRSV nucleocapsid protein (E.A. Nelson, J. Christopher-Hennings, T. Drew, G. Wensvoort, J.E. Collins, and D.A. Benfield, J. Clin. Microbiol. 31:3184-3189, 1993). The detection of PRRSV RNA was conducted in tissues of 6-week-old pigs that had been infected with one of three different field PRRSV isolates and collected at times ranging from 4 to 42 days p.i. Hybridization signals specific for PRRSV RNA were detected in lung, lymphoid tissues, alveolar macrophages (obtained by lavage at the time of necropsy), Peyer's patches, and kidney. The PRRSV-positive cells in these tissues appeared to be predominantly macrophages. In lung tissue we also obtained evidence suggesting the involvement of type II pneumocytes in the replication of PRRSV. During the acute period of infection there was a close correlation between the detection of RNA and the detection of nucleocapsid protein in individual cells. At later times p.i. (28 and 42 days p.i.), instead, more cells containing only PRRSV RNA than those containing PRRSV RNA and also expressing PRRSV nucleocapsid protein were detected. These results suggest that PRRSV RNA might persist in the tissues of infected animals for a longer time than PRRSV antigen expression.
Accelerated infectivity of tick-transmitted Lyme disease spirochetes to vector ticks
Authors: Shih C M , Liu L P
Published: January 2020

We determined whether the span of infectivity of Lyme disease spirochetes (Borrelia burgdorferi) to vector ticks varies with the mode of infection in laboratory mice. Noninfected larval deer ticks were permitted to feed on two strains of spirochete-infected mice that had been naturally (via tick bite) and parenterally (via needle injection) infected with B. burgdorferi 2, 4, or 8 weeks earlier, and engorged ticks were dissected and examined for spirochetes by direct immunofluorescence microscopy. After initial infection, spirochetal infectivity to ticks was less efficient in needle-infected mice than in mice infected via tick bites. Tick-transmitted spirochetes develop more rapidly from the skin of infected mice and do not induce a strong antispirochete antibody response during the early stage of infection.
Screening protocol for Torulopsis (Candida) glabrata
Authors: Land G , Burke J , Shelby C , Rhodes J , Collett J , Bennett I , Johnson J
Published: January 2020

A screening test has been developed for the presumptive identification of Torulopsis (Candida) glabrata from other common clinical isolates of yeast-like fungi. An interlaboratory comparison of a protocol consisting of morphology on cornmeal Tween 80 agar and trehalose fermentation at 42 degrees C was successful in differentiating T. glabrata from other taxa that are frequent or possible clinical isolates. The screening results for 517 clinical yeast isolates, 241 of which were T. glabrata, were compared with their final identification via commercial systems (API20C Yeast Identification System [bioMERIEUX, Hazelwood, Mo.] and Rapid Yeast Identification Panel [Dade Microscan, Sacramento, Calif.]). The trehalose screening test has a sensitivity and a specificity of 97.8 and 95.8%, respectively, and a positive predictive value of 97.4% and a negative predictive value of 96.5%. Overall, the trehalose screen had an efficiency rating of 93.9% for ruling in or out T. glabrata. Since T. glabrata represents a substantial part of the workload in a clinical laboratory, a significant reduction in direct and indirect costs should be realized.
Serologic diagnosis of canine and equine borreliosis: use of recombinant antigens in enzyme-linked immunosorbent assays
Authors: Magnarelli L A , Flavell R A , Padula S J , Anderson J F , Fikrig E
Published: January 2020

Serum samples from dogs and equids suspected of having canine or equine borreliosis, respectively, were analyzed in polyvalent enzyme-linked immunosorbent assays (ELISAs) with whole-cell or recombinant antigens of Borrelia burgdorferi sensu stricto. Purified preparations of recombinant antigens included outer surface protein A (OspA), OspB, OspC, OspE, OspF, and p41-G (a fragment of flagellin). Of the 36 dog sera that reacted positively to whole-cell antigen, 32 (88.9%) contained antibodies to one or more recombinant antigens. Reactivities to OspF (88.9% positive) and p41-G (75% positive) were most prevalent. In analyses of 30 equid sera positive in an ELISA with whole cells, 24 (80%) contained antibodies to one or more recombinant antigens. Seropositivities in ELISAs with p41-G (50% positive) and OspF (46.7% positive) were more than twofold greater than in ELISAs with OspA, OspB, or OspC (10 to 20% positive). In parallel tests of eight canine and three equine sera, there was good agreement in results of Western blot (immunoblot) analyses and ELISAs. Although dog and equid sera with antibodies to whole-cell B. burgdorferi frequently reacted positively to one or more recombinant antigens, the inclusion of OspF and p41-G antigens in ELISAs was most useful in the serologic diagnosis of canine and equine borreliosis.
Isolation of catalase-negative Listeria monocytogenes strains from listeriosis patients and their rapid identification by anti-p60 antibodies and/or PCR
Authors: Bubert A , Riebe J , Schnitzler N , Schönberg A , Goebel W , Schubert P
Published: January 2020

Two catalase-negative Listeria monocytogenes serovar 1/2b strains were isolated from listeriosis patients in 1995 in Germany. The infections appeared in individuals from different cities at different seasons and were caused by L. monocytogenes strains of different clonal types. In particular, the catalase reaction of one strain isolated from blood was consistently negative, whereas this reaction was only reversibly blocked when the strain was freshly isolated from ascitic fluid. After subculturing, the catalase-positive reaction was restored. Initially, identification of these isolates was difficult to achieve not only because of the lack of a catalase reaction, which generally distinguishes L. monocytogenes from other morphologically similar pathogenic gram-positive bacteria, but also because other routinely used biochemical tests such as CAMP and the commercial API test gave unclear results. However, rapid and unequivocal identification of these strains was possible by analyzing secretions of the p60 protein in culture supernatants by enzyme-linked immunosorbent assay or Western blot (immunoblot) analysis with our recently developed Listeria- and L. monocytogenes-specific anti-p60 antibodies. Additionally, the identifications were confirmed by Listeria- and L. monocytogenes-specific PCR analyses with primers derived from the iap, hly, and prfA genes. Immunoanalyses also allowed for the differentiation of these two strains, whereas no differentiation was possible by PCR when the internal, variable repetitive iap gene portion was analyzed. However, size variations of the PCR products comprising these gene portions which were obtained from a number of L. monocytogenes strains belonging to the same serotypes indicated that this type of PCR is not only useful for specific identifications but may be used in parallel as an additional marker for epidemiological studies. In conclusion, the data suggest that catalase production should not be taken as a strict criterion for the identification of listeriae. Furthermore, at least the infection caused by the stably catalase-negative strain supports the notion that catalase does not seem to be necessary for the intracellular growth of L. monocytogenes.
Serodiagnosis of Helicobacter pylori infection: comparison and correlation between enzyme-linked immunosorbent assay and rapid serological test results
Authors: Chen T S , Chang F Y , Lee S D
Published: January 2020

CLOser is a new, one-step, qualitative anti-Helicobacter pylori immunoglobulin G test having the advantage of convenience and simplicity. We aimed to evaluate its diagnostic accuracy and to compare it with a quantitative enzyme-linked immunosorbent assay (ELISA) (HEL-pTEST II) in a study of 86 adult dyspeptic patients by using the results from histology and urease testing of gastric biopsies as a "gold standard." Forty-six patients were H. pylori positive. The sensitivities, specificities, and positive and negative predictive values were 95.7, 72.5, 80.0, and 93.5%, respectively, for CLOser and 93.5, 92.5, 93.5, and 92.5%, respectively, for HEL-pTEST II. The grade of the colored test bands in CLOser was correlated with antibody titers in HEL-pTEST II (r = 0.71; p < 0.001). The mean antibody titers were 13, 74, 186, and 328 U/ml for the negative, faint, thin, and thick bands, respectively, of CLOser. We concluded that the CLOser rapid serological test yielded sensitivity similar to that of the conventional ELISA. Although CLOser is not suitable for epidemiologic screening for H. pylori infection on account of lower specificity, it is particularly convenient and very easy to perform. Therefore, it may eventually become widely used in the office-based care of patients and lead to more cost-effective patient management decisions.
Comparative evaluation of two commercial amplification assays for direct detection of Mycobacterium tuberculosis complex in respiratory specimens
Authors: Piersimoni C , Callegaro A , Nista D , Bornigia S , De Conti F , Santini G , De Sio G
Published: January 2020

Two commercial assays detecting the presence of Mycobacterium tuberculosis complex in clinical specimens by rRNA target amplification (Gen-Probe Amplified M. tuberculosis Direct Test [AMTD]) and PCR (Amplicor) were evaluated. The tests were applied to 327 digested, decontaminated respiratory specimens collected from 236 patients. Results were compared with those of acid-fast staining and culture. The combination of culture and clinical diagnosis was considered the "gold standard." A total of 60 specimens were collected from 27 patients with a diagnosis of pulmonary tuberculosis. Thirteen of these specimens were from patients receiving standard antituberculosis therapy and therefore were not included in the comparison. Of the remaining 47 specimens, 33 were smear positive, 40 were culture positive, 45 were AMTD positive, and 39 were Amplicor positive. After resolution of discrepant results, the overall sensitivities, specificities, and positive and negative predictive values were 77, 100, 100, and 95 for staining; 87, 100, 100, and 97.4 for culture; 95.9, 98.9, 94, and 99.2 for AMTD; and 85.4, 99.6, 97.9, and 97.1 for Amplicor, respectively. Agreement between AMTD and Amplicor assay results was 96.8%. It is concluded that although both nucleic acid amplification methods are rapid and specific for the detection of M. tuberculosis complex in respiratory specimens, AMTD appeared to be more sensitive than Amplicor.
Comparison of identifications of human and animal source gram-negative bacteria by API 20E and crystal E/NF systems
Authors: Peele D , Bradfield J , Pryor W , Vore S
Published: January 2020

This study compared the abilities of API 20E and BBL Crystal E/NF identification systems to correctly identify human and animal source gram-negative bacilli of known identifications, as provided by the American Type Culture Collection, Rockville, Md., and the Research Diagnostic and Investigative Laboratory, Columbia, Mo. Also addressed in the comparison are the cost, the relative ease of performing and interpreting the tests, and the potential problems surrounding each system. The two systems were comparable in terms of their respective costs and abilities to identify the bacteria tested. The cost per test was calculated as $4.69 for API 20E and $4.62 for Crystal E/NF. Of the animal source bacteria tested, Crystal E/NF identified 68% to the correct genus and species and 90% to the correct genus or group. The remaining 10% of the animal source bacteria were unidentified by Crystal. Human source bacteria tested by BBL Crystal E/NF gave very similar results: 47% correctly identified to genus and species, 90% correctly identified to genus or group, 7% unidentified, and 3% incorrectly identified. API 20E results were as follows for animal source bacteria: 53% correctly identified to genus and species, 76% correctly identified to genus or group, and 24% unidentified; the results for human source bacteria were as follows: 40% correctly identified to genus and species, 83% correctly identified to genus or group, and 17% unidentified. API 20E has a slightly more labor-intensive protocol for setting up the test than BBL Crystal E/NF but produced fewer questionable results.
Characterization of a spotted fever group Rickettsia from Ixodes ricinus ticks in Sweden
Authors: Nilsson K , Jaenson T G , Uhnoo I , Lindquist O , Pettersson B , Uhlén M , Friman G , Påhlson C
Published: January 2020

A spotted fever group rickettsia isolated from the common tick, Ixodes ricinus, was genetically characterized by PCR and genomic sequencing. This study was performed with nymphal and adult ticks collected in southern and central Sweden. I. ricinus is the only North European tick species of medical importance which is regularly collected from humans. No species of the genus Rickettsia has previously been found in Scandinavian ticks, nor has any case of domestic rickettsial infection in humans or animals been reported. According to the nucleotide sequencing, the present Rickettsia sp. belongs to the spotted fever group of rickettsiae. Ticks are the most common arthropod reservoirs and vectors of the rickettsiae of this group. Among 748 ticks investigated, 13 (1.7%) were positive for a Rickettsia sp. Borrelia burgdorferi was detected in 52 (7%) of the ticks, a prevalence similar to or somewhat lower than that previously been recorded in other Swedish studies. There was no evidence of ehrlichial or chlamydial DNA in these ticks. The Rickettsia sp. was further characterized by 16S ribosomal DNA (rDNA) sequencing and restriction fragment length polymorphism (RFLP). The 16S rDNA sequencing resulted in a sequence identical to that described for Rickettsia helvetica, but the pattern obtained with RFLP of the citrate synthetase gene diverged from previously known patterns. The rickettsial agent of one tick which was positive by PCR was confirmed by transmission electron microscopy. The morphology of this rickettsia was similar to that of the spotted fever and typhus group rickettsiae. This represents the first documented isolate of a Rickettsia sp. from Swedish ticks.
Specificity of a sandwich enzyme-linked immunosorbent assay for detecting Aspergillus galactomannan
Authors: Swanink C M , Meis J F , Rijs A J , Donnelly J P , Verweij P E
Published: January 2020

The specificity of a sandwich enzyme-linked immunosorbent assay (ELISA) for detecting Aspergillus galactomannan was tested with exoantigens of 29 fungi cultured from clinical specimens. Cross-reactivity was observed with Penicillium chrysogenum, Penicillium digitatum, and Paecilomyces variotii. Furthermore, 40 serum samples obtained from bacteremic patients with hematologic malignancies were retrospectively tested by sandwich ELISA. False-positive reactions with the serum were reproducible but did not correspond with the results of culture of specific microorganisms. Moreover, the microorganisms cultured from the blood showed no reactivity by the sandwich ELISA.
Correlation of conversion of Salmonella enterica serovar enteritidis phage type 1, 4, or 6 to phage type 7 with loss of lipopolysaccharide
Authors: Baggesen D L , Wegener H C , Madsen M
Published: January 2020

Studies of pairs of Salmonella enterica serovar Enteritidis isolates from different poultry flocks showed that phage type (PT) 7 may be derived from PT 1, 4, and 6. The conversion appeared to be associated with loss of lipopolysaccharide. It is concluded that PT 7 may be of little value as an epidemiological marker of S. enterica serovar Enteritidis.
Identification of capsular antigens in Serratia marcescens
Authors: Aucken H M , Wilkinson S G , Pitt T L
Published: January 2020

Previous studies with 31 strains of Serratia marcescens, including 28 reference O-serotype strains, have indicated that 19 of them have an acidic polysaccharide which copurifies with lipopolysaccharide during phenol-water extraction. Polysaccharide in crude extracts from 18 of the 19 strains was precipitated with Cetavlon (hexadecyltrimethyl ammonium bromide), and capsules were demonstrated around these 18 strains by Indian ink exclusion zones. Capsule-antibody binding by the Quellung reaction suggested that the acidic polysaccharide formed the capsule around the bacterial cells. Anticapsular (anti-K) antibody was detected in reference O antisera which had been prepared against boiled whole cells. Cross-titration and absorption studies revealed 14 different K antigens among these strains.
Molecular characterization of a 35-kilodalton protein of Borrelia burgdorferi, an antigen of diagnostic importance in early Lyme disease
Authors: Gilmore R D , Kappel K J , Johnson B J
Published: January 2020

Antibodies against a 35-kDa antigen of Borrelia burgdorferi are detectable in the serum of about half of patients with early Lyme disease. The gene encoding this antigen was isolated from a genomic library of B. burgdorferi B31 (low passage), and full-length expression of the recombinant gene product was achieved in Escherichia coli. Antiserum raised against the recombinant protein was reactive with a B. burgdorferi protein of the same molecular size as the diagnostic 35-kDa antigen cited in an earlier study of criteria for the sero-diagnosis of early Lyme disease. Also, the recombinant protein was reactive with serum from patients with early Lyme disease who were seropositive for the 35-kDa antigen. DNA sequence analysis of the gene indicated an open reading frame of 909 bp encoding a protein with a calculated molecular mass of 34.3 kDa. This gene did not possess the usual initiation codon ATG but rather probably used a TTG codon. The deduced amino acid sequence of the N terminus exhibited a motif similar to that for signal peptides of lipoproteins. Southern blotting revealed a chromosomal location for this gene; and it was specific for B. burgdorferi, B. afzellii, and B. garinii but not for B. hermsii, B. coriaciae, or B. turicatae.
LEPTO dipstick, a dipstick assay for detection of Leptospira-specific immunoglobulin M antibodies in human sera
Authors: Gussenhoven G C , van der Hoorn M A , Goris M G , Terpstra W J , Hartskeerl R A , Mol B W , van Ingen C W , Smits H L
Published: January 2020

We studied a dipstick assay for the detection of Leptospira-specific immunoglobulin M (IgM) antibodies in human serum samples. A high degree of concordance was observed between the results of the dipstick assay and an IgM enzyme-linked immunosorbent assay (ELISA). Application of the dipstick assay for the detection of acute leptospirosis enabled the accurate identification, early in the disease, of a high proportion of the cases of leptospirosis. Analysis of a second serum sample is recommended, in order to determine seroconversion or increased staining intensity. All serum samples from the patients who were confirmed to be positive for leptospirosis by either a positive microscopic agglutination test or a positive culture but were found to be negative by the dipstick assay were also judged to be negative by the IgM ELISA or revealed borderline titers by the IgM ELISA. Some cross-reactivity was observed for sera from patients with diseases other than leptospirosis, and this should be taken into account in the interpretation of test results. The dipstick assay is easy to perform, can be performed quickly, and requires no electricity or special equipment, and the assay components, a dipstick and a staining reagent, can be stored for a prolonged period without a loss of reactivity, even at elevated temperatures.
Comparative evaluation of use of cna, fnbA, fnbB, and hlb for genomic fingerprinting in the epidemiological typing of Staphylococcus aureus
Authors: Smeltzer M S , Gillaspy A F , Pratt F L , Thames M D
Published: January 2020

We used a genomic fingerprinting protocol to characterize 59 Staphylococcus aureus strains and a single S. intermedius isolate, all of which were previously typed by 13 different methods (F. C. Tenover et al., J. Clin. Microbiol. 32:407-415, 1994). These 60 strains were divided into three groups of 20 strains each, with each group including internal controls. Two of the three groups (groups SB and SC) included 29 strains from four relatively well-defined outbreaks. The epidemiological relationships of the strains in the third group (group SA) were unclear. Fingerprints were established by Southern blotting with HaeIII-digested genomic DNA and a probe mixture consisting of DNA fragments corresponding to the S. aureus collagen adhesin (cna), fibronectin-binding protein (fnbA and fnbB), and beta-toxin (hlb) genes. An unambiguous fingerprint was obtained for all S. aureus isolates. No hybridization signal was observed with S. intermedius. Twenty-seven of the 29 related strains in the SB and SC groups were correctly identified as belonging to one of the four epidemiologically related groups. Our protocol was less successful with respect to the exclusion of unrelated strains. Specifically, only 6 of 11 unrelated strains in the SB and SC groups had a fingerprint that was distinct by comparison to the fingerprints of the outbreak strains. Nevertheless, our protocol was relatively accurate by comparison to the accuracies of the other methods and was one of only six methods that accurately identified all of the repetitive strains included as internal controls.
Detection of Pneumocystis carinii DNA in air samples: likely environmental risk to susceptible persons
Authors: Bartlett M S , Vermund S H , Jacobs R , Durant P J , Shaw M M , Smith J W , Tang X , Lu J J , Li B , Jin S , Lee C H
Published: January 2020

The means by which humans acquire Pneumocystis carinii is not well understood. Whether it can be acquired from specific environmental sources or transmitted from person to person has not been determined. This study was designed to detect nucleic acids of P. carinii in air samples from various locations, including P. carinii-infected patients' homes and hospital rooms, non-P. carinii-infected patients' hospital rooms, empty hospital rooms, offices at Indiana University, and other homes in different locations. DNA was extracted from cellulose-ester filters through which air samples had been filtered, and the P. carinii DNA was amplified by PCR with primers specific for the internal transcribed spacer regions of rRNA. P. carinii DNA was found in 17 of 30 air samples (57%) from the rooms of P. carinii-infected patients. It was also found in 6 of the 21 other hospital rooms sampled (29%) but was not found in any of the offices, storage areas, or control homes. Environmental sampling suggests that the airborne presence of P. carinii genetic material and infectious organisms is plausible. The organism was also detected in locations where P. carinii patients were not immediately proximate, such as the hospital rooms of non-P. carinii-infected patients.
Fatal Penicillium citrinum pneumonia with pericarditis in a patient with acute leukemia
Authors: Mok T , Koehler A P , Yu M Y , Ellis D H , Johnson P J , Wickham N W
Published: January 2020

We report here a case of fatal Penicillium citrinum infection. The patient, who suffered from acute myeloid leukemia, developed signs and symptoms typical of fungal pneumonia and pericardial tamponade after undergoing standard induction chemotherapy. Despite attaining complete remission of her leukemia, the patient succumbed 8 weeks after presentation. At autopsy, multiple nodular cavitary pulmonary lesions with invasion by fungal hyphae were found. Pericardial and lung tissue obtained at autopsy grew P. citrinum, a fungus ubiquitous in the environment but seldom reported as a pathogen. The microbiological findings were consistent with the histopathological features and confirmed this as a case of true P. citrinum infection causing fatal pulmonary and pericardial complications in an immunocompromised host.
Diagnostic accuracy of a rapid whole-blood test for detection of Helicobacter pylori
Authors: Enroth H , Rigo R , Hultén K , Engstrand L
Published: January 2020

In this study, we evaluated a rapid whole-blood test, BM-test Helicobacter pylori, for detection of H. pylori infection in 144 and 48 patients with other gastrointestinal symptoms and with gastric cancer, respectively. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the test correlated well with the standards used for the calculation, i.e., serology by enzyme-linked immunosorbent assay or culture and histology.
Heterogeneity of BmpA (P39) among European isolates of Borrelia burgdorferi sensu lato and influence of interspecies variability on serodiagnosis
Authors: Roessler D , Hauser U , Wilske B
Published: January 2020

The molecular and antigenic variabilities of BmpA (P39) among European isolates of Borrelia burgdorferi were analyzed. The bmpA sequences of 12 isolates representing all three species of B. burgdorferi sensu lato pathogenic for humans were amplified by PCR, cloned, and sequenced. The BmpA protein of Borrelia garinii is heterogeneous, with an amino acid sequence identity ranging from 91 to 97%, whereas the BmpA proteins of Borrelia afzelii and B. burgdorferi sensu stricto strains appear to be highly conserved (>98.5% intraspecies identity). The interspecies identities ranged from 86 to 92%. Cluster analysis of BmpA reflected the subdivision of B. burgdorferi sensu lato isolates into the three species as well as a considerable heterogeneity among B. garinii strains. The BmpA protein of each species of B. burgdorferi sensu lato was recombinantly expressed in Escherichia coli, purified, and used to generate monoclonal antibodies. Seven BmpA-specific antibodies were identified; six of them recognized conserved epitopes of all three species, whereas one was specific for BmpA of B. afzelii and B. garinii. A monoclonal antibody (H1141) recommended by the Centers for Disease Control and Prevention for use in the standardization of immunoblots showed strong reactivity with BmpA of B. burgdorferi sensu stricto but no or only weak reactivity with BmpA of B. garinii and B. afzelii, respectively. Sera from 86 European patients with Lyme borreliosis in different stages and 73 controls were tested in immunoglobulin G (IgG) and IgM immunoblots with the recombinant BmpA proteins of the three species, revealing specificities of 98.6 to 100%. IgM antibodies against recombinant BmpA were only rarely detected (1.1 to 8.1%). With the BmpA proteins of B. afzelii and B. garinii, sensitivities for the IgG test (sera from stages I to III) were 36.0 and 34.9%, respectively, in contrast to 13.9% with BmpA of B. burgdorferi sensu stricto. Therefore, we recommend that recombinant BmpA of B. afzelii or B. garinii should be used solely, or in addition to B. burgdorferi sensu stricto BmpA, in serodiagnostic tests for Lyme borreliosis in Europe.
Genotype-specific RNA probes for direct identification of wild polioviruses by blot hybridization
Authors: De L , Yang C F , Da Silva E , Boshell J , Cáceres P , Gómez J R , Pallansch M , Kew O
Published: January 2020

We have developed RNA probes for the direct identification of wild poliovirus isolates by blot hybridization. The probes are complementary to sequences of the first 30 to 32 codons of VP1, which evolve more extensively (approximately 1.5-fold) than the rest of VP1. To illustrate our general approach, we describe the design of probes specific to each of four major genotypes recently endemic (1981 to 1991) to the Americas: Andean type 1, Brazil type 1, Brazil type 3, and Central America-Mexico type 3. A wild isolate of each genotype was selected according to molecular and epidemiologic criteria to be representative of the principal lineages in circulation. Variable VP1 sequences of the representative isolates were amplified by the reverse transcriptase PCR and were inserted into a plasmid vector containing a T7 promoter. The in vitro transcripts, labeled with digoxigenin, served as probes. These formed stable hybrids only with RNAs of isolates of the corresponding genotypes. Hybrids were detected by a sensitive chemiluminescence assay, capable under normal diagnostic conditions of detecting specific wild poliovirus sequences in samples containing up to a 100-fold excess of Sabin vaccine strain-related sequences of the same serotype.
Use of multiplex PCR for simultaneous detection of four bacterial species in middle ear effusions
Authors: Hendolin P H , Markkanen A , Ylikoski J , Wahlfors J J
Published: January 2020

A multiplex PCR procedure was developed for the simultaneous detection of Alloiococcus otitidis, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae in middle ear effusions (MEEs) from patients with chronic otitis media with effusion. The bacterial 16S rRNA gene was chosen as the target, and the procedure used one common lower primer and four species-specific upper primers. The reaction was optimized by changing the primer concentrations to yield equal amounts of amplification products. The specificity of the reaction was verified with various bacterial species found in the nasopharynx. The performance of the procedure was examined with 25 MEE specimens, and the results were compared to those obtained by conventional culture methods. A detection level of 10 bacterial cells/reaction for each of the study organisms was achieved. By conventional culture methods, 8 (32%) of the specimens showed growth of one of the study organisms. In contrast, 21 (84%) of the specimens tested positive by the multiplex PCR. None of the culture-positive specimens were PCR negative, whereas three (12%) of the PCR-positive specimens tested positive for two of the four study organisms. Thus, the multiplex PCR method improves the detection rate significantly compared to that of the conventional culture method.
Effects of specimen collection, processing, and storage conditions on stability of human immunodeficiency virus type 1 RNA levels in plasma
Authors: Ginocchio C C , Wang X P , Kaplan M H , Mulligan G , Witt D , Romano J W , Cronin M , Carroll R
Published: January 2020

To define the optimal blood collection parameters for plasma human immunodeficiency virus type 1 (HIV-1) viral load testing, plasma HIV-1 RNA levels were quantitated with the NASBA HIV-1 RNA QT System from blood specimens that were collected, processed, and stored under a variety of conditions that might have affected HIV-1 RNA stability. We determined that when whole blood was processed within 2 h of specimen collection the levels of HIV-1 RNA detected in EDTA-, heparin-, and acid citrate dextrose (ACD)-anticoagulated plasma samples were comparable. The levels of HIV-1 RNA in serum specimens (mean = 4.126 log units) were significantly lower (P < 0.01) than the levels in corresponding plasma samples (mean = 4.501 log units). One cycle of freeze-thaw (-70 degrees C) did not significantly reduce the level of HIV-1 RNA detected in EDTA-, heparin-, or ACD-anticoagulated plasmas. The EDTA-anticoagulated plasmas showed the smallest decrease in HIV-1 RNA copies (0.050 log units). HIV-1 RNA levels decreased over a 6-month time period in serum as well as in EDTA-, ACD-, and heparin-anticoagulated plasmas stored at -70 degrees C. However, the only significant decreases were for serum (mean decrease = 0.317 log units) and heparin-anticoagulated samples (mean decrease = 0.384 log units). A comparison of the levels of HIV-1 RNA in cell-free plasma collected in VACUTAINER EDTA Plasma Preparation Tubes and in standard VACUTAINER EDTA tubes determined that HIV-1 RNA levels were stable for up to 30 h after collection when stored at either room temperature (mean standard deviation [SD] = +/- 0.101 log units) or at 4 degrees C (mean SD = +/- 0.102 log units) as cell-free plasma or as EDTA-anticoagulated whole blood (mean SD = +/- 0.109 log units). These data indicate that EDTA-anticoagulated plasma is the most suitable and stable matrix for HIV-1 RNA quantitation.
Application of immunohistochemistry and in situ hybridization for detection of bovine coronavirus in paraffin-embedded, formalin-fixed intestines
Authors: Zhang Z , Andrews G A , Chard-Bergstrom C , Minocha H C , Kapil S
Published: January 2020

A monoclonal antibody (MAb) (Z3A5) against spike protein subunit of bovine coronavirus (BCV) reacted with the virus in formalin-fixed intestines in an immunoperoxidase test. We found an 88% correlation between immunohistochemistry with Z3A5 and in situ hybridization with a BCV nucleoprotein cDNA probe. MAb Z3A5 reacted with 90 BCV isolates from the United States and was an effective reagent for the diagnosis of BCV.
The aerobic and anaerobic bacteriology of perirectal abscesses
Authors: Brook I , Frazier E H
Published: January 2020

The microbiology of perirectal abscesses in 144 patients was studied. Aerobic or facultative bacteria only were isolated in 13 (9%) instances, anaerobic bacteria only were isolated in 27 (19%) instances, and mixed aerobic and anaerobic flora were isolated in 104 (72%) instances. A total of 325 anaerobic and 131 aerobic or facultative isolates were recovered (2.2 anaerobic isolates and 0.9 aerobic isolates per specimen). The predominant anaerobes were as follows: Bacteroides fragilis group (85 isolates), Peptostreptococcus spp. (72 isolates), Prevotella spp. (71 isolates), Fusobacterium spp. (21 isolates), Porphyromonas spp. (20 isolates), and Clostridium spp. (15 isolates). The predominant aerobic and facultative bacteria were as follows: Staphylococcus aureus (34 isolates), Streptococcus spp. (28 isolates), and Escherichia coli (19 isolates). These data illustrate the polymicrobial aerobic and anaerobic microbiology of perirectal abscesses.
Rapid pulsed-field gel electrophoresis protocol for typing of Escherichia coli O157:H7 and other gram-negative organisms in 1 day
Authors: Gautom R K
Published: January 2020

Genomic DNA patterns generated by pulsed-field gel electrophoresis are highly specific for different strains of an organism and have significant value in epidemiologic investigations of infectious-disease outbreaks. Unfortunately, time-consuming and tedious specimen processing is an inherent problem which limits the use of this powerful technology as a real-time epidemic investigational tool. Here, I describe a rapid method to improve the response time and provide specific bacterial strain identification for the typing of Escherichia coli O157:H7 and other gram-negative organisms in a single day.
Characterization to species level of Mycobacterium avium complex strains from human immunodeficiency virus-positive and -negative patients
Authors: Kyriakopoulos A M , Tassios P T , Matsiota-Bernard P , Marinis E , Tsaousidou S , Legakis N J
Published: January 2020

Forty human clinical Mycobacterium avium-M. intracellulare complex strains isolated in Greece were characterized to the species level by PCR with three sets of primers specific for one or both species. M. avium predominated in both human immunodeficiency virus-positive and -negative patients, but the frequency of M. intracellulare isolation appeared to be higher in the latter.