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A novel method for processing respiratory specimens to improve culture and acid-fast staining of mycobacteria is introduced. This new method utilizedN,N-dimethyl-N-(n-octadecyl)-N-(3-carboxypropyl)ammonium inner salt (Chemical Abstract Service no. 78195-27-4), also known as C18-carboxypropylbetaine (CB-18). In a blinded, five-center study, CB-18-based processing was compared to the standard method combining NALC and NaOH (NALC/NaOH). A total of 573 respiratory specimens were tested. Individual specimens were split approximately equally; the host institutions processed half of each specimen by the NALC/NaOH method, while the other half was processed with CB-18 at Quest Diagnostics—Baltimore. A total of 106 specimens were culture positive for acid-fast bacilli (AFB). Replacement of the primary decontamination agent with CB-18 caused changes in all diagnostic parameters. Aggregate culture sensitivity improved by approximately 43% (P < 0.01), and smear sensitivity improved by approximately 58% (P < 0.01). The sensitivity of smear relative to that of M. tuberculosis isolates exceeded 93% (P < 0.01) when specimens were processed with CB-18. The average times to a positive result were reduced by 7.3 days in liquid culture (P < 0.01) and 5.3 days on solid media (P < 0.05); however, the CB-18 method had a 20.8% contamination rate in liquid culture versus a rate of approximately 7.5% with NALC/NaOH processing. There were also unusual reductions in liquid culture sensitivity and smear specificity among CB-18-processed specimens. The characteristics of the latter parameters suggested that refinement of the CB-18 processing method should allow further improvements in culture sensitivity. This study showed that the CB-18 method has the potential to improve both smear and culture detection for these important human pathogens.

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The C18-carboxypropylbetaine (CB-18) procedure for processing respiratory specimens for the detection of mycobacteria was shown to provide significant increases in sensitivity by smear and culture. However, the procedure also produced increased contamination, a loss in liquid culture sensitivity, and a reduction in smear specificity. Because of these observations, the toxicity of CB-18 and the nature of the contamination were characterized. Preincubation in 1 mM CB-18 impacted viability in a time-dependent fashion, but the magnitude of the loss was species and isolate dependent.Mycobacterium tuberculosis isolates were the most susceptible, losing 20 to 30% of the CFU within 30 min and 30 to 60% after 3 h, whereas Mycobacterium avium andMycobacterium fortuitum isolates were unaffected by CB-18. In liquid culture, when the concentration of CB-18 exceeded 5 μg/ml, there was an impact on growth characteristics for the most susceptibleM. tuberculosis isolate. In contrast, M. fortuitum isolates were able to grow in 100 μg of CB-18 per ml. In liquid culture, the deleterious effects of CB-18 were enhanced in the presence of antibiotics, whereas growth on solid media was not similarly affected. Supplementation of the resuspension buffer with 0.15% lecithin alleviated toxicity. Initial attempts to modify the CB-18 procedure to control contamination incorporated acids or alkalis; however, losses in culture sensitivity occurred. Studies to identify these contaminants led to the development of a sediment resuspension buffer that contained lytic enzymes to combat contamination and lecithin to alleviate toxicity. This formulation included lysozyme, zymolyase, and Cytophaga and Trichodermaextracts and was seen to reduce contamination to acceptable levels (<5%).

A novel method for site-directed mutagenesis of DNA sequences based on the use of the PCR is described. The method uses two oligonucleotide primers that contain the desired sequence change and overlap at their $' ends. In addition, the thymine residues in the overlap region have been substituted with deoxyuracil. Amplification of the template plasmid by PCR results in incorporation of the primers and the desired mutation into the PCR product. Excision of the deoxyuracil residues in the PCR products by uracil DNA glycosylase (UDG) destablizes base-pairing at the ends of DNA molecules and thus generates 3' protruding ends in the opposite strand. Due to overlapping nature of the primers, the resulting 3' protruding ends are complementary and can anneal rapidly after treatment with UDG. When the entire plasmid is amplified, a linear mutant PCR product is generated that circularizes after treatment with UDG. Circularized molecules can then be transformed into competent cells without ligation, generating transformants with the mutant genotype. Alternatively, the gene of interest is amplified in two segments using overlapping mutant primers and cloned in the desired orientation into pAMP1 by UDG cloning. Application of this method to site-specific mutagenesis of the IncZ (~ gene and the human c-raf on-cogene was demonstrated. The accuracy of the mutations was confirmed by nucleotide sequence analysis as well as phenotypic assays. The method is rapid, highly efficient (~99%), and applicable to genes cloned in any vector as well as to genomic DNA or RNA. The versatility of the method allows single base mutagenesis as well as insertions and deletions. UDG mutagenesis should prove to be a general, rapid, and high-fidelity method for site-directed mutagenesis.