Small Colony Variants of Escherichia coli.
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Bacteriological Techniques↗
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Synthetic fiber battings as plugging materials in microbiology.
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Bacteriological Techniques↗
KINETICS OF DRY RUPTURE OF BACTERIAL SPORES IN THE PRESENCE OF SALT.
Sacks, L. E. (U.S. Department of Agriculture, Albany, Calif.), Peter B. Percell, Richard S. Thomas, and Glen F. Bailey. Kinetics of dry rupture of bacterial spores in the presence of salt. J. Bacteriol. 87:952-960. 1964.-The kinetics of breaking spores in the dry state by use of an excess of sodium chloride and a steel ball in a shaking device were investigated. Under most conditions, disruption is a first-order process. The disruption-rate constant varies directly with the weight of the ball and inversely with the weight of the capsule contents (spores plus salt). Different spore batches differ somewhat in susceptibility to dry rupture. The dry-rupture process is highly reproducible and it is relatively simple to obtain preparations in which exactly 50%, or 90%, of the spores are broken. The procedure is uniquely suited to the disruption of small (5 to 20 mg) samples, but 150 mg of spores have been handled with conventional equipment. Apparently, the chief function of the salt is to separate the spores from one another with a relatively hard, energy-nonabsorbing matrix, preventing aggregation and consequent cushioning of the ball's impact. However, under certain conditions (small ball, high salt, large crystals) appreciable breakage results from collisions of spores with the salt crystals. The minimal salt-spore ratio for efficient breakage depends on the spore batch, but is usually greater than 3:1. Fine glass beads or inorganic salts other than sodium chloride will also serve as the matrix. Electron micrographs of the spores in various stages of disruption are shown, as are electron micrographs of the spore coats of Bacillus macerans, B. megaterium, B. cereus, B. coagulans, and Clostridium bifermentans. Prolonged agitation disintegrates spore coats. The spore coats of B. macerans exhibit a characteristic ribbed structure, previously detected only by carbon replicas of intact spores. Possible application to other biological materials is considered.
Bacillus↗
Two-center collaborative evaluation of performance of the BD phoenix automated microbiology system for identification and antimicrobial susceptibility testing of gram-negative bacteria.
The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, MD) was assessed for identification (ID) and antimicrobial susceptibility testing (AST) of the majority of clinically encountered bacterial isolates in a European collaborative two-center trial. A total of 494 bacterial isolates including various species of the Enterobacteriaceae and 110 nonfermentative gram-negative bacteria were investigated: of these, 385 were single patient isolates, and 109 were challenge strains tested at one center. The performance of the Phoenix extended-spectrum beta-lactamase (ESBL) test was also evaluated for 203 strains of Escherichia coli, Klebsiella pneumoniae, and Klebsiella oxytoca included in the study. Forty-two antimicrobial drugs were tested, including members of the following drug classes: aminoglycosides, beta-lactam antibiotics, beta-lactam/beta-lactamase inhibitors, carbapenems, cephems, monobactams, folate antagonists, quinolones, and others. Phoenix system ID results were compared to those of the laboratories' routine ID systems (API 20E and API CHE, ATB ID32E, ID32GN, and VITEK 2 [bioMérieux, Marcy l'Etoile, France]); Phoenix AST results were compared to those of frozen standard broth microdilution (SBM) panels according to NCCLS (now CLSI) guidelines (NCCLS document M100-S9, approved standard M7-A4). Discrepant results were repeated in duplicate. Concordant IDs of 98.4 and 99.1% were observed for the Enterobacteriaceae and the nonfermentative group, respectively. For AST results, the overall essential agreement was 94.2%; the category agreement was 97.3%; and the very major error rate, major error rate, and minor error rate were 1.6, 0.6, and 1.9%, respectively. In terms of ESBL detection, Phoenix results were 98.5% concordant with those of the reference system, with 98.0% sensitivity and 98.7% specificity. In conclusion, the Phoenix ID results showed high agreement with results of the systems to which they were being compared: the AST performance was highly equivalent to that of the SBM reference method, and the system proved to be very accurate for the detection of ESBL producers.
Automation↗
Comparison of API 20E and invA PCR for identification of Salmonella enterica isolates from swine production units.
API 20E and invA PCR were evaluated for the identification of Salmonella enterica isolates from swine farms. API 20E had the highest agreement with other tests at the 99.9% likelihood level. Both tests had 100% sensitivity and 96% specificity compared to 16S rRNA sequencing. Compared to serotyping, both tests had 96% sensitivity; specificity was 86% for API 20E and 79% for invA PCR.
Animal Husbandry↗
Identification of alpha-hemolytic streptococci by pyrosequencing the 16S rRNA gene and by use of VITEK 2.
Alpha-hemolytic streptococci are very difficult to identify by phenotypic methods. In this study, a pyrosequencing method for the identification of streptococcal species based on two variable regions of the 16S rRNA gene is described. Almost all studied streptococcal species (n = 51) represented by their type strains could be differentiated except for some closely related species of the Streptococcus bovis or S. salivarius group. The pyrosequencing results of alpha-hemolytic streptococci isolated from blood (n = 99) or from the normal pharyngeal microbiota (n = 25) were compared to the results obtained by the VITEK 2 with GP card (bioMérieux, Marcy l'Etoile, France). As expected, the results of the two methods did not completely agree, but 93 (75.0%) of the isolates assigned to the same streptococcal group by both methods and 57 (46.0%) reached consistent results at the species level. However, 10 strains remained unidentified by VITEK 2, and 4 isolates could not be assigned to any streptococcal group by pyrosequencing. Identification of members of the S. mitis and S. sanguinis groups proved difficult for both methods. Furthermore, the pyrosequencing analysis revealed great sequence variation, since only 43 (32.3%) of the 133 isolates analyzed by pyrosequencing had sequences identical to a type strain. The variation was greatest in the pharyngeal isolates, slightly lower in the blood culture isolates, and nonexistent in invasive pneumococcal isolates (n = 17) that all had the S. pneumoniae type strain sequence. The resolution of the results obtained by the two methods is impeded by the lack of a proper gold standard.
Bacterial Typing Techniques↗
Rapid identification of material colonization with group B streptococci by use of fluorescent antibody.
To identify women colonized with group B streptococci during parturition, we used pooled type-specific fluorescent antibody to examine vaginal swabs enriched by preincubation in selective broth medium. In preliminary experiments, group B streptococcus strain III-Bell was reliably detectable with fluorescent antibody at concentrations of greater than 10(5) colony-forming units per ml, achieved after 6 h of incubation of small inocula (18 to 26 colony-forming units). Of the vaginal swabs from 924 parturient women examined prospectively by both fluorescent antibody and selective bacteriology techniques, group B streptococci were isolated in 154. The sensitivity of the fluorescent antibody technique increased with increasing incubation time and ranged from 49% (3 to 6 h) to 81% (7 to 12 h) to 83% (13 to 18 h) to 93% (greater than 18 h). Colonized mothers identified within 6 h by the fluorescent antibody technique had higher rates of vertical transmission to their newborn infants (61%) than colonized mothers whose fluorescent antibody examinations were negative within this time interval (32%; P = 0.027). However, because of the timing of their admissions, none of the colonized mothers of the four infants who developed early-onset group B streptococcal sepsis were identified with fluorescent antibody until after delivery. Although its sensitivity approaches selective culture methods after 6 h of incubation, fluorescent antibody examination of vaginal swabs does not appear to offer a practical approach to identifying colonized parturient women for intrapartum antibiotic prophylaxis of group B streptococcal infection.
Female↗
Evaluation of autoscan-4 for identification of members of the family Enterobacteriaceae.
A study was performed to compare the Autoscan-4 (MicroScan, Inc., Mahwah, N.J.) with conventional biochemical methods for identifying clinical isolates of the family Enterobacteriaceae. The Autoscan-4 yielded correct identification of 95.4% of the isolates at the species level and 98.4% at the genus level. Only one misidentification was observed. The identification of both common and less-common isolates of Enterobacteriaceae makes this system highly efficient.
Bacterial Typing Techniques↗
Application of gas-liquid chromatographic analysis of cellular fatty acids for species identification and typing of coagulase-negative staphylococci.
Gas-liquid chromatography (GLC) of bacterial cellular fatty acids was used to analyze 264 isolates of coagulase-negative staphylococci, of which 178 were Staphylococcus epidermidis. The presence and amounts of individual fatty acids were determined to generate fatty acid profiles for each of the seven coagulase-negative species tested. The fatty acid profiles were then analyzed by computerized correlation and cluster analysis to calculate mean correlation values between isolates belonging to the same or different species, as well as to establish cluster analysis dendrograms. These data ultimately allowed the clustering of individual samples into species-specific clusters. Species identification by the GLC clustering was highly consistent with species identification by biochemical assays; the results were similar in 92.4% of the cases. The GLC profile correlation analysis was further used to analyze multiple blood isolates from 60 patients in order to determine the usefulness of this methodology in establishing identity, as well as differences, between consecutive patient isolates. The correlation between those multiple S. epidermidis isolates determined to be identical by standard techniques (such as the antibiogram, biotype, and plasmid profile) was significantly (P less than 0.001) higher than that between random isolates of the same species. The correlation coefficient was greater than 97 for 40 (97.6%) of the 41 patients with multiple identical blood isolates, compared with less than 95 in all 19 (100.0%) patients with multiple nonidentical isolates. The successful use of the computerized GLC analysis in this study demonstrated its appropriate application for species identification and typing of coagulase-negative staphylococci.
Bacterial Typing Techniques↗
Identification of coagulase-negative staphylococci by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and rRNA restriction patterns.
A total of 1,417 staphylococcal and micrococcal strains were collected from the beards and scalps of 10 subjects over a period of 8 months. Sixteen strains identified as Staphylococcus epidermidis with an API system had distinctive yellow colonies on nutrient agar plates and sodium dodecyl sulfate-polyacrylamide gel electrophoresis whole-cell polypeptide profiles similar to those of Staphylococcus capitis; this identification was confirmed by analysis of rRNA gene restriction patterns.
Bacterial Proteins↗
Gas-permeable lifecell tissue culture flasks give improved growth of Helicobacter pylori in a liquid medium.
Experiments were conducted to investigate the microaerobic culture of Helicobacter pylori in a liquid medium by using gas-permeable Lifecell tissue culture flasks. Growth in Lifecell tissue culture flasks was 1.2 to 1.6 log units greater than that in glass control bottles. These results were comparable to those reported by the use of gyrated media.
Bacteriological Techniques↗
Reevaluation of the API 20E identification system versus conventional biochemicals for identification of members of the family Enterobacteriaceae: a new look at an old product.
The API 20E bacterial identification system has been used for 19 years, often as the standard with which other identification systems are compared. Because the accuracy of this system compared with conventional biochemical tests has not been determined in many years, we evaluated the API 20E linear strip by using 291 typical and atypical strains of the family Enterobacteriaceae taken from a culture collection. At 24 h, the API 20E correctly identified by genus and species 229 of 291 (78.7%) of the strains, using Salmonella and Shigella serotyping where indicated. At 48 h, 95.2% were correctly identified by using additional biochemical tests as recommended by the manufacturer. The API 20E misidentified eight (2.7%) strains; these strains were not limited to any particular genus. When 81 of these Enterobacteriaceae strains were arranged into a weighted assortment correlating to the frequency with which they might be found in a clinical laboratory, the API 20E correctly identified 71 (87.7%) at 24 h and 78 (96.3%) at 48 h. This evaluation concluded that the accuracy of the identification of Enterobacteriaceae strains at 24 h (78.7%) may be significantly lower than that of earlier evaluations. However, there is no significant difference in the ability of the API 20E to correctly identify "challenge" type organisms (229 of 291) versus routine hospital isolates (71 of 81) (P greater than 0.05), but the system is not as accurate as the conventional biochemical method of identification.
Bacterial Typing Techniques↗
Development of DNA probes for early diagnosis and epidemiological study of cryptococcosis in AIDS patients.
We report the isolation of middle-repetitive DNA sequences from Cryptococcus neoformans that are species and variety specific. These probes were used for assessing strain relatedness among cryptococcal isolates from patients with and without AIDS who were from Zaire and the United States. Five distinct hybridization patterns were observed for the 60 isolates examined, regardless of the restriction enzyme used for digestion. The most common pattern among the isolates from the patients without AIDS was also the most common among the isolates from the patients with AIDS who were from the United States and was the only pattern observed for all isolates tested from patients with AIDS who were from Zaire. On the basis of the high specificity and sensitivity of the signals observed by hybridization, we suggest that these sequences provide a means for both biotyping and early diagnosis of C. neoformans.
Acquired Immunodeficiency Syndrome↗
Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool.
In order to develop a technique for distinguishing between isolates of Mycobacterium tuberculosis, we cloned two hypervariable DNA fragments from NdeII-digested genomic DNA. The cloned DNA fragments of 3.8 and 4.7 kb were found to contain the same repetitive element, which was different from previously characterized repetitive elements. It is present in at least 30 copies per genome and is distributed among mycobacterial species other than those of the tuberculosis complex, including M. kansaii, M. gastri, and M. szulgai. When used as a probe on restriction enzyme-digested DNA, it can distinguish between strains from unrelated cases of tuberculosis while demonstrating identical banding patterns for isolates from epidemiologically related cases.
Bacterial Typing Techniques↗
Identification of mycobacteria from animals by restriction enzyme analysis and direct DNA cycle sequencing of polymerase chain reaction-amplified 16S rRNA gene sequences.
Two methods, based on analysis of the polymerase chain reaction-amplified 16S rRNA gene by restriction enzyme analysis (REA) or direct cycle sequencing, were developed for rapid identification of mycobacteria isolated from animals and were compared to traditional phenotypic typing. BACTEC 7H12 cultures of the specimens were examined for "cording," and specific polymerase chain reaction amplification was performed to identify the presence of tubercle complex mycobacteria. Combined results of separate REAs with HhaI, MspI, MboI, and ThaI differentiated 12 of 15 mycobacterial species tested. HhaI, MspI, and ThaI restriction enzyme profiles differentiated Actinobacillus species from mycobacterial species. Mycobacterium bovis could not be differentiated from M. bovis BCG or Mycobacterium tuberculosis. Similarly, Mycobacterium avium and Mycobacterium paratuberculosis could not be distinguished from each other by REA but were differentiated by cycle sequencing. Compared with traditional typing, both methods allowed rapid and more accurate identification of acid-fast organisms recovered from 21 specimens of bovine and badger origin. Two groups of isolates were not typed definitively by either molecular method. One group of four isolates may constitute a new species phylogenetically very closely related to Mycobacterium simiae. The remaining unidentified isolates (three badger and one bovine) had identical restriction enzyme profiles and shared 100% nucleotide identify over the sequenced signature region. This nucleotide sequence most closely resembled the data base sequence of Mycobacterium senegalense.
Animals↗
Differentiation of Salmonella phase 1 flagellar antigen types by restriction of the amplified fliC gene.
The large antigenic diversity (over 2,300 serotypes) expressed by Salmonella strains can probably be observed at the genetic level. The phase 1 flagellin gene fliC was amplified, and the amplified fragment was cleaved with a mixture of both endonucleases TaqI and ScaI. The restriction patterns observed allowed differentiation of flagellar types b, i, d, j, l,v, and z10. Flagellar group g (g,m, g,p, or g,m,s) could be differentiated from the other flagellar types. Flagellar types r and e,h could not be separated, although they could be distinguished from the other flagellar types studied. Practical applications of flagellar gene restriction are the distinction between serotype Gallinarum-Pullorum, which carries a cryptic gene for flagellar type g,m, and nonmotile Vi-negative variants of serotype Typhi, and the tentative assignation of nonmotile variants of Salmonella serotypes to a flagellar type.
Antigens, Bacterial↗
Molecular strain typing of Mycobacterium tuberculosis to confirm cross-contamination in the mycobacteriology laboratory and modification of procedures to minimize occurrence of false-positive cultures.
Molecular strain typing by restriction fragment length polymorphism analysis was used to demonstrate that two clusters of Mycobacterium tuberculosis cultures involving six patients resulted from cross-contamination in the mycobacteriology laboratory. Contaminated cultures were processed by the decontamination procedure and were read on the BACTEC instrument following acid-fast bacillus smear-positive specimens from patients with active tuberculosis. Investigation of these episodes suggested opportunities for modification of laboratory procedures to minimize cross-contamination and confirmed the adverse medical and public health consequences of false-positive cultures. Strain-typing results were used in decisions regarding patient care, including the curtailment of unnecessary treatment in one patient. Molecular strain typing appears to be a valuable means of identifying false-positive cultures of M. tuberculosis in selected settings.
Bacterial Typing Techniques↗
Routine application of high-performance liquid chromatography for identification of mycobacteria.
Mycolic acid analysis by high-performance liquid chromatography (HPLC) was introduced in our laboratory as the routine technique for identifying all clinical isolates of mycobacteria referred to us. HPLC identified 96.1% of the 1,103 strains analyzed, whereas the biochemical procedures and/or the commercial DNA probes identified 98.3% of strains, for an overall agreement of 94.4%. Compared with the probes, there was 100% specificity and 98.9% sensitivity for Mycobacterium tuberculosis identification. HPLC allowed early detection and identification of the rare mycobacterial species M. haemophilum, M. malmoense, M. shimoidei, and M. fallax as well as uncharacteristic strains of M. simiae. After 18 months of routine use, HPLC proved to be reliable, easy to perform, rapid, and less costly than other identification methods.
Bacterial Typing Techniques↗