Measurement of Microbial DNA Polymerase Activity Enables Detection and Growth Monitoring of Microbes from Clinical Blood Cultures

Surveillance of bloodstream infections (BSI) is a high priority within the hospital setting. Broth-based blood cultures are the current gold standard for detecting BSI, however they can require lengthy incubation periods prior to detection of positive samples. We set out to demonstrate the feasibility of using enzymatic template generation and amplification (ETGA)-mediated measurement of DNA polymerase activity to detect microbes from clinical blood cultures. In addition to routine-collected hospital blood cultures, one parallel aerobic blood culture was collected and immediately refrigerated until being transported for ETGA analysis. After refrigeration holding and transport, parallel-collected cultures were placed into a BACTEC incubator and ETGA time-course analysis was performed. Of the 308 clinical blood cultures received, 22 were BACTEC positive, and thus were initially selected for ETGA time course analysis. The ETGA assay detected microbial growth in all 22 parallel-positive blood cultures in less time than a BACTEC incubator and also yielded genomic DNA for qPCR-based organism identification. In summary, feasibility of detecting microbes from clinical blood culture samples using the ETGA blood culture assay was demonstrated. Additional studies are being considered towards development of clinically beneficial versions of this methodology.     

Evaluation of Radiometric System for Detecting Bacteremia

An automated radiometric system (BACTEC, Johnston Laboratories) for detection of bacteremia was evaluated in parallel with a standard blood culture system in use in our laboratory. Of 1,445 blood cultures from 484 patients with possible bacteremia, 106 sets of cultures (excluding 39 presumed contaminated), representing 56 patients, were positive by both methods. The conventional system yielded 85 positive cultures from 48 patients, whereas the BACTEC system yielded 84 positive cultures from 43 patients. The BACTEC system failed to detect 22 cultures that were positive in the conventional system, and the conventional system failed to detect 21 cultures that were positive in the BACTEC system. The detection efficiency was generally equivalent in the two systems except for the lower detection rates of anaerobes and Enterobacter aerogenes by the BACTEC system and the lower detection rates of Torulopsis glabrata and, possibly, Pseudomonas sp. (group IVD) in the conventional system. The BACTEC system had a slight advantage over the conventional system in the time interval to detection of positivity. Approximately 20% of the positive cultures detected by the BACTEC system were detected on the first day of incubation compared with 7% by the conventional system. The recovery rates and detection times of anaerobes were less efficient by the BACTEC system than by the conventional system. It does not appear that the radiometric method has much advantage over available conventional methods.     

Enhancement of mycobacterial growth in middlebrook 7H12 medium by polyoxyethylene stearate

Studies were carried out to enhance mycobacterial growth in 7H12 (BACTEC 12A) radiometric medium. Out of 10 different additives investigated, addition of 100 mcg polyoxy-ethylene stearate (POES)/ml enhanced growth of many mycobacteria, especially ofMycobacterium tuberculosis andM. bovis (TB), with no adverse effects.Evaluation of the growth-enhancing effect of POES in 7H12 medium during primary isolation of 117 mycobacterial cultures from clinical specimens indicated significant time saving due to the rapid growth of mycobacteria, especially of TB. The growth index (GI) in 7H12 medium increased much more rapidly in the POES-containing medium, with smears for acid-fast bacilli available sooner owing to higher biomass. This enhanced growth also allowed earlier differentiation of TB from other mycobacteria by the BACTEC NAP test and earlier initiation of indirect drug susceptibility tests, with results available approximately 2–3 days sooner.     

The role of speciation in positive Lowenstein-Jensen culture isolates from a high tuberculosis burden country

Objective

To determine the need for routine speciation of positive Lowenstein-Jensen mycobacterial cultures in HIV-infected patients suspected of having pulmonary tuberculosis at Mulago Hospital in Kampala, Uganda.

Methods

Sputum and bronchoalveolar lavage Lowenstein-Jensen mycobacterial culture isolates from consecutive, HIV-infected patients admitted to Mulago Hospital with 2 weeks or more of cough were subjected to IS6110 PCR and rpoB genetic analysis to determine the presence of Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM).

Results

Eighty (100%) mycobacterial cultures from 65 patients were confirmed to be members of MTBC. Subsequent analysis of the cultures from 54 patients by PCR and sequence analyses to identify co-infection with NTM confirmed the presence of MTBC as well as the presence of Micrococcus luteus (n = 4), Janibacter spp. (n = 1) and six cultures had organisms that could not be identified.

Conclusions

Presumptive diagnosis of tuberculosis on the basis of a positive Lowenstein-Jensen culture is sufficient in HIV-infected Ugandans suspected of having tuberculosis. Routine molecular confirmation of positive Lowenstein-Jensen cultures is unnecessary in this low resource setting.     

Automatized PCR evaluation of Mycobacterium tuberculosis complex in respiratory and nonrespiratory specimens

In this study, Mycobacterium tuberculosis complex isolates recovered from respiratory and nonrespiratory specimens with culture were evaluated using an automatized PCR method. Specimens with suspected tuberculous disease were decontaminated and concentrated using the standard N-acetyl-L-cysteine NaOH method and were inoculated onto glycerol-supplemented L?wenstein-Jensen media and BACTEC B12 vials. Forty-one specimens with typical colonies on solid media and 127 specimens identified as M. tuberculosis complex in a BACTEC system were selected as the study group. As the control group, 46 specimens without growth on either culture media were selected. The PCR results were positive in 33 (80.5%) and 87 (68.5%) samples that were culture-positive on solid and liquid media, respectively. All (100%) culture-negative specimens within the control group were also negative in the COBAS AMPLICOR Mycobacterium tuberculosis (MTB) PCR method. In conclusion, although it is a fast method for identifying M. tuberculosis complex isolates from clinical specimens, the COBAS AMPLICOR MTB PCR method is found to be less sensitive than culture techniques, we propose therefore that it should only be used in combination with culture results in the clinical diagnosis of tuberculosis.     

Comparison of the BACTEC System with Blind Subculture for the Detection of Bacteremia

One thousand blood specimens were cultured in BACTEC vials containing modified Columbia broth in aerobic, anaerobic, and hypertonic formulations. Radiometric readings and subcultures were performed on aerobic and hypertonic vials at 24 h and 7 days, and on anaerobic vials at 48 h and 7 days. Significant numbers of false-positive BACTEC readings were obtained. Although all positive cultures were eventually detected by the BACTEC, approximately 20% of blood specimens yielding positive subcultures at 24 h did not give positive BACTEC readings until 48 h.     

Rapid detection and monitoring therapeutic efficacy of Mycobacterium tuberculosis complex using a novel real-time assay

We combined real-time RT-PCR and real-time PCR (R/P) assays using a hydrolysis probe to detect Mycobacterium tuberculosis complex (MTBC)-specific 16S rRNA and its rRNA gene (rDNA). The assay was applied to 28 nonrespiratory and 207 respiratory specimens from 218 patients. Total nucleic acids (including RNA and DNA) were extracted from samples, and results were considered positive if the repeat RT-PCR threshold cycle was < or =35 and the ratio of real-time RT-PCR and real-time PCR load was > or =1.51. The results were compared with those from existing methods, including smear, culture, and real-time PCR. Following resolution of the discrepant results between R/P assay and culture, the overall sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV) of all samples (including nonrespiratory and respiratory specimens) were 98.2%, 97.2%, 91.7%, and 99.4%, respectively, for R/P assay, and 83.9%, 89.9%, 72.3%, and 94.7%, respectively, for real-time PCR. Furthermore, the R/P assay of four patient samples showed a higher ratio before treatment than after several days of treatment. We conclude that the R/P assay is a rapid and accurate method for direct detection of MTBC, which can distinguish viable and nonviable MTBC, and thus may guide patient therapy and public health decisions.     

Use of growth indices from radiometric culture for quantification of sheep strains of Mycobacterium avium subsp. paratuberculosis

A simple method for using growth indices from radiometric BACTEC cultures was evaluated for the enumeration of Australian sheep strains of Mycobacterium avium subsp. paratuberculosis. The numbers of viable organisms in inocula were determined by end-point titration in BACTEC cultures. Growth indices were measured by using a BACTEC 460 machine. There was a linear relationship between the number of days taken for the cumulative growth index to reach 1,000 (dCGI1000) and log(10) inoculum size. The use of dCGI1000 was shown to be as effective as the use of growth index data from the entire growth cycle for the estimation of inoculum size. For particular isolates characterized by end-point titration, the dCGI1000 of a single BACTEC vial provided estimates of viable numbers within narrow prediction limits. Predictive relationships were also established for the enumeration of M. avium subsp. paratuberculosis from field samples by using the dCGI1000 of a single BACTEC vial, with prediction limits of +/-1 to 2 log units. Organisms from feces or contaminated soil grew more slowly than those from cultures or tissues, and separate equations were developed for enumeration from these sources.     

Synthesis and antituberculosis activity of new 3-alkylsulfanyl-1,2,4-triazole derivatives

The increasing clinical importance of drug-resistant mycobacterial pathogens has lent additional urgency to microbiological research and new antimycobacterial compound development. For this purpose, new alkylsulfanyltriazoles were synthesized and evaluated for antituberculosis activity. The reaction of thienyl-2-acetic acid with thiocarbohydrazide gave the mercaptotriazoles (II). The 4-amino-5-(2-thienylmethyl)-3-[1-(2-thienyl)-3-aryl) propion-3-yl] sulfanyl-4H-1,2,4-triazole (III) derivatives were synthesized by reacting the mercaptotriazoles with chalcones (I). Antituberculosis activities of the synthesized compounds were determined by broth microdilution assay, the Microplate Alamar Blue Assay, in BACTEC 12B medium and results were screened in-vitro, using BACTEC 460 Radiometric System against Mycobacterium tuberculosis H37Rv (ATCC 27294) at 6.25 microg/ml and the tested compounds showed considerable inhibition ranging from 58-84%.     

Evaluation of the BD MGIT TBc Identification Test (TBc ID), a rapid chromatographic immunoassay for the detection of Mycobacterium tuberculosis complex from liquid culture

The BACTEC MGIT 960 system is increasingly used to culture Mycobacterium tuberculosis. We evaluated the performance of the new immunochromatographic assay BD MGIT TBc Identification Test (TBc ID) for the rapid identification of M. tuberculosis complex in clinical samples when performed directly from BACTEC MGIT 960 culture positive for acid-fast bacilli (AFB).Of 92 cultures evaluated, the sensitivity and specificity of the TBc ID test was 98.5% and 100%, respectively compared to sequencing of the 16S rRNA gene. One culture that was TBc ID test negative but that was identified as M. tuberculosis by 16S rRNA sequencing was confirmed to have a mutation in the mpt64 gene.The TBc ID test is an easy and sensitive method for the identification of M. tuberculosis complex in liquid culture medium, does not require a high level of skills, neither any additional specific equipment and gives results in 15 min, which provide a good alternative for the rapid identification of M. tuberculosis complex in liquid medium.     

Direct detection of Mycobacterium tuberculosis complex in pulmonary and extrapulmonary samples by BDProbeTec ET system

BDProbeTec ET (Becton Dickinson, Sparks, Md, USA) is a fully automated walkaway system based on strand displacement amplification (SDA) technology that provides a method for the direct detection of Mycobacterium tuberculosis complex (MTBC) target sequence. The purpose of this study was to evaluate the ability of BDProbeTec ET system to detect MTBC directly from clinical specimens and compare the results with staining and culture. From February 2002 through December 2003 a total of 1521 [pulmonary (n=1329) and extrapulmonary (n=192)] specimens from 1518 patients were examined by BDProbeTec ET system for the detection of MTBC and the results were compared to those obtained by microscopy and liquid culture (BACTEC 9000 MB, Becton Dickinson). MTBC was cultivated from 65 specimens (60 pulmonary and 5 extrapulmonary) of which 43 (66.2%) (42 pulmonary and 1 extrapulmonary) were smear positive and 22 (33.8%) (18 pulmonary and 4 extrapulmonary) were smear negative. BDProbeTec ET detected MTBC in 58 (55 pulmonary and 3 extrapulmonary) of the 65 culture-positive specimens. Although the BDProbeTec ET system gave five false-negative results among the 18 smear-negative culture-positive pulmonary specimens, our results demonstrate that the BDProbeTec ET system is a reliable tool in smear-positive samples and given its technical characteristics it can be used for the rapid detection of MTBC in either pulmonary or extrapulmonary samples.     

Development of a m-PCR assay for simultaneous identification of Campylobacter jejuni and C. coli

Multiplex PCR assay (m-PCR) with three sets of primers was developed for simultaneous identification of Campylobacter jejuni and C. coli. Poultry faecal samples were enriched in Preston broth for 24 h and streaking on selective media was performed before and after enrichment. m-PCR was applied on bacterial cultures harvested from media plates. The data showed a selective effect of Preston broth which favoured the growth of C. coli. Identification of the species by the hippurate hydrolysis test and by the m-PCR was performed on 294 isolates of Campylobacter. The efficiency of the identification by the biochemical test is only 34% in comparison to 100% efficiency with the PCR. The use of our m-PCR in combination with the culture method allowed reliable detection and identification of C. jejuni and C. coli within 3-4 d.     

Direct and simultaneous identification of Mycobacterium tuberculosis complex (MTBC) and Mycobacterium tuberculosis (MTB) by rapid multiplex nested PCR-ICT assay

The Mycobacterium tuberculosis (MTB) shows different virulence and host infection range from other members of the M. tuberculosis complex (MTBC). Differential identification of MTB from MTBC is thus important in certain occasions. The currently commercially available molecular assays which use either IS6110 or 16S rDNA fragment as identification targets are mainly designed for identifying MTBC but not for MTB. Comparative genomic DNA analysis has provided valuable information on regions of difference (RD) present in MTB but not in other members of the MTBC. RD9 region is further suggested to be a potential target for differential identification of MTB from MTBC. In this study, using IS6110 and Rv3618 (belong to RD9) as the specific identification targets for MTBC and MTB, respectively, we developed and tested a multiplex nested PCR-ICT (immuno-chromatography test) assay for simultaneously and directly detecting not only MTBC but also MTB from 1500 clinical sputum specimens. The results were compared with traditional culture and biochemical identification results together with patients' clinical assessments. This assay showed a 95.5% sensitivity, 97.9% specificity, 2.1% false positive rate and 4.5% false negative rate towards detection of MTBC, and a 93.0% sensitivity, 99.8% specificity, 0.2% false positive rate and 7.0% false negative rate for detection of MTB. This detection system shows great potential in clinical application.     

Use of Growth Indices from Radiometric Culture for Quantification of Sheep Strains of Mycobacterium avium subsp. paratuberculosis

A simple method for using growth indices from radiometric BACTEC cultures was evaluated for the enumeration of Australian sheep strains of Mycobacterium avium subsp. paratuberculosis. The numbers of viable organisms in inocula were determined by end-point titration in BACTEC cultures. Growth indices were measured by using a BACTEC 460 machine. There was a linear relationship between the number of days taken for the cumulative growth index to reach 1,000 (dCGI1000) and log₁₀ inoculum size. The use of dCGI1000 was shown to be as effective as the use of growth index data from the entire growth cycle for the estimation of inoculum size. For particular isolates characterized by end-point titration, the dCGI1000 of a single BACTEC vial provided estimates of viable numbers within narrow prediction limits. Predictive relationships were also established for the enumeration of M. avium subsp. paratuberculosis from field samples by using the dCGI1000 of a single BACTEC vial, with prediction limits of ±1 to 2 log units. Organisms from feces or contaminated soil grew more slowly than those from cultures or tissues, and separate equations were developed for enumeration from these sources.     

R/B Enteric Differential System for Identification of Enterobacteriaceae

The R/B Enteric Differential System for identifying enteric bacteria has been evaluated with 451 "unknown" cultures from the stock culture collection of the Center for Disease Control. An average of 89.6% of these cultures were correctly identified by the R/B system, when used as recommended by the manufacturer but without the assistance of serology. This percentage ranged, however, from 47% for Klebsiella to 100% for Serratia and Providencia. Of 11 groups or genera of Enterobacteriaceae tested, only three (Enterobacter, Serratia, and Providencia) were identified with 95% or better accuracy. Four groups (Arizona, Citrobacter, Escherichia, and Salmonella) attained 90 to 95% accuracy of identification, and three groups (Edwardsiella, Proteus, and Shigella) scored between 85 and 90% accuracy. We recommend the R/B system as a screening device which is reasonably successful in grouping bacteria but not as a substitute for more exacting conventional procedures.     

Usefulness of the BACTEC MYCO/F lytic system for detection of mycobacteremia in a clinical microbiology laboratory

278 BACTEC MYCO/F lytic system blood cultures for mycobacteria were evaluated between 1997 and 1999. Sixty of them were read as positive by the system, being considered 15 of them as false positives. Twenty-seven yielded mycobacterial growth (13 Mycobacterium avium from 3 patients and 14 Mycobacterium tuberculosis from 8 patients). Other bacteria isolated were coagulase-negative Staphylococcus (13 samples), Corynebacterium sp. (5 samples), Salmonella enteritidis (2 samples) and Klebsiella pneumoniae (1 sample). Five of these isolates were considered as true episodes of bacteremia. The average time for detection of mycobacteria was 12.6 days for M. avium and 26.4 days for M. tuberculosis. BACTEC MYCO/F lytic system is useful for detection of mycobacteremia in clinical microbiology laboratories.     

Detection by polymerase chain reaction of Clostridium perfringens producing epsilon toxin in faeces and in gastrointestinal contents of goats

F.A. UZAL, J.J. PLUMB, L.L. BLACKALL, D. O'BOYLE AND W.R. KELLY. 1996. A polymerase chain reaction (PCR) was used to identify the gene-encoding epsilon toxin production in Clostridium perfringens types B and D in faeces and in gastrointestinal contents of goats. The samples were cultured in thioglycollate broth and centrifuged. The upper layer of the pellet was used as a template for PCR, obviating the need for DNA extraction. This technique specifically differentiated Cl. perfringens types B and D from Cl. perfringens types A and C and from Escherichia coli . When used to identify Cl. perfringens type D in samples artificially spiked with the micro-organism, the PCR detected as few as 1.4 × 10² cfu g⁻¹ of sample. Gastrointestinal contents and faeces were collected from 20 goats at slaughter and processed by PCR. Several positive results were obtained from the first five goats that were slaughtered and sampled a few days after their arrival at the abattoir, but only a few samples gave positive results during the following weeks, after the goats had been fed a concentrated ration containing monensin. A possible role of this drug in control of enterotoxaemia is suggested.     

Synthesis and antituberculosis activity of new 3-alkylsulfanyl-1,2,4-triazole derivatives

The increasing clinical importance of drug-resistant mycobacterial pathogens has lent additional urgency to microbiological research and new antimycobacterial compound development. For this purpose, new alkylsulfanyltriazoles were synthesized and evaluated for antituberculosis activity. The reaction of thienyl-2-acetic acid with thiocarbohydrazide gave the mercaptotriazoles (II). The 4-amino-5-(2-thienylmethyl)-3-[1-(2-thienyl)-3-aryl)propion-3-yl]sulfanyl-4H-1,2,4-triazole (III) derivatives were synthesized by reacting the mercaptotriazoles with chalcones (I). Antituberculosis activities of the synthesized compounds were determined by broth microdilution assay, the Microplate Alamar Blue Assay, in BACTEC12B medium and results were screened in-vitro, using BACTEC 460 Radiometric System against Mycobacterium tuberculosis H₃₇Rv (ATCC 27294) at 6.25?μg/ml and the tested compounds showed considerable inhibition ranging from 58–84%.     

Evaluation of the G145R Mutant of the Hepatitis B Virus as a Minor Strain in Mother-to-Child Transmission

The role of the hepatitis B virus (HBV) mutant G145R, with a single change in amino acid 145 of the surface protein, as a minor population remains unknown in mother-to-child transmission. The minor strain as well as the major strain of the G145R mutant were evaluated in three cohorts using a locked nucleic acid probe-based real-time PCR. The breakthrough cohort consisted of children who were born to HBV carrier mothers and became HBV carriers despite immnoprophylaxis (n = 25). The control cohort consisted of HBV carriers who had no history of receiving the hepatitis B vaccine, hepatitis B immunoglobulin or antiviral treatment (n = 126). The pregnant cohort comprised pregnant women with chronic HBV infection (n = 31). In the breakthrough cohort, 6 showed positive PCR results (major, 2; minor, 4). In the control cohort, 13 showed positive PCR results (major, 0; minor, 13). HBeAg-positive patients were prone to have the G145R mutant as a minor population. Deep sequencing was performed in a total of 32 children (PCR positive, n = 13; negative, n = 19). In the breakthrough cohort, the frequency of the G145R mutant ranged from 0.54% to 6.58%. In the control cohort, the frequency of the G145R mutant ranged from 0.42% to 4.1%. Of the 31 pregnant women, 4 showed positive PCR results (major, n = 0; minor, n = 4). All of the pregnant women were positive for HBeAg and showed a high viral load. Three babies born to 3 pregnant women with the G145R mutant were evaluated. After the completion of immunoprophylaxis, 2 infants became negative for HBsAg. The remaining infant became negative for HBsAg after the first dose of HB vaccine. G145R was detected in one-fourth of the children with immunoprophylaxis failure. However, the pre-existence of the G145R mutant as a minor population in pregnant women does not always cause breakthrough infection in infants.     

Growth Characteristics, Bile Sensitivity, and Freeze Damage in Colonial Variants of Lactobacillus acidophilus

Rough (R) and smooth (S) colonial variants were isolated from a heterogeneous culture of Lactobacillus acidophilus RL8K. R and S types were stable upon repeated transfer on agar, but revertant colonies did appear after broth transfers. When propagated in commercial MRS broth, R and S cultures showed similar growth characteristics, and both cell types were insensitive to freezing and frozen storage at −20°C. Alternatively, during growth in scratch MRS broth, R cultures shifted to a reduced rate of growth during the late logarithmic phase. R cells grown under these conditions were susceptible to death by freezing and injury at −20°C. Microscopically, R cells were observed as long gram-positive rods with small nonstainable blebs protruding from the cell wall. In bile sensitivity studies of R and S cells plated on MRS agar plus oxgall, the S culture was resistant to 1% bile, whereas the R culture was sensitive to 0.6% bile. Differences in the bile resistance and freeze damage of R and S cells suggest that colonial and cellular morphologies are important considerations for the selection of Lactobacillus strains as dietary adjuncts and for the development of growth conditions for preparing frozen concentrated cultures from either cell type.