Rapid detection of bacterial atypical pneumonia agents by multiplex PCR

Approximately one third of community acquired pneumonia cases are caused by atypical pneumonia agents, Mycoplasma pneumoniae, Legionella pneumophila, and Chlamydophila pneumoniae (formerly Chlamydia pneumoniae). The laboratory diagnosis of these organisms is difficult and time-consuming by conventional microbiological techniques. Polymerase chain reaction (PCR) is one of the important tools which can circumvent this problem. A multiplex PCR assay was developed to achieve the diagnosis of these three organisms in a single tube. Primers used in PCR were selected in a way that they amplified different length DNA fragments from different agents but they all worked at the same amplification conditions. Therefore the organisms could be diagnosed according to the length of amplified products by agarose gel electrophoresis without using any hybridization probes. After development of the multiplex PCR method, totally 309 clinical samples which were sent to our laboratory for single-agent PCR, were also evaluated by this technique. The results showed that the multiplex PCR assay is a sensitive, useful, cheap, and rapid diagnostic tool for the management of pneumonia patients.

Evaluation of 120 mycobacterial strains isolated from clinical specimens to the species level by polymerase chain reaction-restriction enzyme analysis

In this study, a total of 120 mycobacterial strains isolated from clinical specimens in Hacettepe University Hospital Clinical Pathology Laboratories were evaluated by polymerase chain reaction-restriction enzyme analysis (PRA), which analyses the common mycobacterial heat shock protein gene (hsp65). 95 of 120 strains (79.1%) were identified as Mycobacterium tuberculosis and 25 (20.8%) were identified as non-tuberculous mycobacteria (NTM). M. gordonae I and IV were the most common NTM species (3.3% each) followed by M. chelonae (2.5%). Other NTM species isolated were M. gordonae III, M. avium, M. peregrinum (1.6%), M. fortuitum, M. flavescens, M. malmoense and M. mucogenicum (0.8%). Four isolates had PRA patterns that did not match any patterns previously described. The patients who had NTM had underlying diseases; the most frequent clinical diagnosis among these was chronic obstructive pulmonary disease (COPD) and chronic renal failure. AIDS and pulmonary carcinoma were the other underlying diseases detected.

Epidemiology of chronic Pseudomonas aeruginosa infections in cystic fibrosis

Chronic lung infection with Pseudomonas aeruginosa is primarily responsible for pulmonary deterioration of cystic fibrosis patients. The purpose of this study was to type the P. aeruginosa isolates collected sequentially from cystic fibrosis patients, chronically colonized with P. aeruginosa, by random amplified polymorphic DNA fingerprinting-PCR (RAPD-PCR). Sequential P. aeruginosa isolates (n: 130) that had been collected from 20 CF patients over at least 9 years were investigated. The isolates were analyzed by RAPD-PCR using two arbitrary primers. Antimicrobial susceptibility testing of all isolates was performed by the disc diffusion method. RAPD-PCR typing demonstrated that strains dissimilar in colony morphotype and of different antibiotic susceptibility patterns could be of the same genotype. Some CF patients were colonized with a rather constant P. aeruginosa flora, with strains of different phenotypes but of one genotype. However, some patients may be colonized with more than one genotype. The results also demonstrated that there might be a risk of cross-colonization between CF patients followed-up at the same center.

Examination of mycosis fungoides for the presence of Epstein-Barr virus and human herpesvirus-6 by polymerase chain reaction

BACKGROUND

The aetiology of cutaneous T-cell lymphoma (CTCL) remains unknown despite numerous investigations. In recent years, retroviruses and human herpesviruses have been implicated to play a causal part in CTCL.

OBJECTIVE

The aim of this study was to elucidate the possible aetiopathogenetic role of human herpesviruses (HHV) in mycosis fungoides (MF).

METHODS

Polymerase chain reaction was used to study formalin-fixed, paraffin-embedded lesional skin biopsies from 92 subjects with MF to evidence possible presence of Epstein-Barr virus (EBV) and HHV-6.

RESULTS

Biopsy specimens from nine subjects (9.8%) evidenced EBV DNA, whereas all except one of the subjects (1.1%) lacked HHV-6 DNA.

CONCLUSIONS

Although these findings do not support a primary aetiological role for EBV and HHV-6 in classical CTCL, the possibility remains that both viruses, particularly EBV, may act as potential cofactors in the development of CTCL.

Induction of mycobacteremia by intravesical bacillus Calmette-Guerin instillation in an experimental animal model and detection with polymerase chain reaction

PURPOSE

The aim of this study was to detect mycobacteremia by polymerase chain reaction (PCR), induced by the instillation of bacillus Calmette-Guerin (BCG) to guinea pig bladder. We also investigated the peak time and the effect of the dose of BCG in injured and non-injured bladder. The sensitivities of routine culture and PCR were also compared.

MATERIALS AND METHODS

Five different doses (0, 0.069, 0.69, 6.9 and 69 mg.) of BCG were instilled into 5 injured and 5 non-injured bladders. Blood samples were collected at 0, 5, 15, 30 and 60 minutes following instillation for routine culture and PCR for each dose. A total of 50 female guinea pigs were used.

RESULTS

Three of 5 samples (60%) obtained 30 minutes after the instillation of 69 mg. BCG into injured bladders were PCR positive. Furthermore, 4 of 5 samples (80%) were PCR positive when samples were obtained at the 60th minute following instillation. All the other samples were negative for PCR and routine culture. All the routine tuberculosis culture results were negative, including those which were PCR positive.

CONCLUSIONS

Mycobacteremia was detected only in injured bladders and with high doses of BCG. PCR is a highly sensitive and rapid diagnostic method for detection of mycobacteremia.

In vitro activities of antibiotics alone and in combination against Brucella melitensis at neutral and acidic pHs

Brucellae survive acidic pHs in phagolysosomes. Azithromycin, streptomycin, and quinolones were active against Brucella melitensis at pH 7.0 but not at pH 5.0; rifampin and doxycycline retained activity at pH 5.0. Regardless of pH, azithromycin-rifampin and ofloxacin-rifampin showed less synergy than established streptomycin-doxycycline and rifampin-doxycycline combinations.

Detection of Listeria monocytogenes in milk by the polymerase chain reaction

A on the polymerase chain reaction (PCR) method based was developed for detection of Listeria monocytogenes in milk samples after enrichment culture. It consists of culturing samples in Listeria enrichment broth, followed by DNA extraction and detection of the organism using PCR. Dilutions of L. monocytogenes in milk were subjected to PCR amplification after enrichment culture. When determining the sensitivity of the method, it was found to be possible to detect 37 CFU (colony forming unit gl/ml) of the bacterium in milk. The method was assessed as a sensitive, specific, times-saving and practical way of detecting L. monocytogenes in milk samples.

Comparison of three different primer pairs for the detection of Mycobacterium tuberculosis by polymerase chain reaction in paraffin-embedded tissues

SETTING

More than five different primer pairs have been used for the detection of Mycobacterium tuberculosis deoxyribonucleic acid (DNA) with the polymerase chain reaction (PCR).

OBJECTIVE

The sensitivity and specificity of PCR were evaluated using three different primer pairs in the detection of M. tuberculosis in paraffin-embedded tissues.

DESIGN

Thirty-eight tissue specimens from 23 patients were studied. Eighteen samples were obtained from 10 tuberculosis patients, and 20 samples obtained from 13 patients with other diseases were used as negative controls. DNA extracted from paraffin-embedded tissues was used directly for PCR amplification using primers IS1 and IS2 to amplify a 123 base pair (bp) region of IS6110, sjMT3 and sjMTr2 to amplify a 281 bp region of protein antigen b, and INS1 and INS2 to amplify a 245 bp region of IS986. Each amplification was performed double-blinded and repeated three times including positive and negative control samples.

RESULTS

IS1 and IS2 gave a positive result in each of the double samples obtained from eight tuberculosis patients and in the single samples obtained in the two others, sjMT3 and sjMTr2 detected 13 of the 18 tuberculosis samples, and INS1 and INS2 detected only three of the 18.

CONCLUSION

These results highlight the importance of selecting appropriate primers to obtain high sensitivity in detecting M. tuberculosis in paraffin-embedded tissues by PCR.

Activity of amoxicillin/clavulanate in patients with tuberculosis

Some beta-lactam antibiotics are active in vitro against Mycobacterium tuberculosis. There are anecdotal reports of successful treatment of tuberculosis caused by multiple-drug-resistant strains of M. tuberculosis with regimens that included amoxicillin/clavulanate. Reduction of M. tuberculosis in the sputum of patients with pulmonary tuberculosis during administration of amoxicillin/clavulanate was measured by a quantitative culture method to determine the activity in vivo. Patients were randomized to receive isoniazid, ofloxacin, or amoxicillin/clavulanate for 7 days. Isoniazid was the most effective agent, reducing M. tuberculosis after 2 days at a mean rate (+/- standard deviation) of 0.60 +/- 0.30 log10 cfu/mL per day, compared with 0.32 +/- 0.05 and 0.34 +/- 0.03 for ofloxacin and amoxicillin/clavulanate, respectively. The early bactericidal activity of amoxicillin/clavulanate was comparable to that reported for antituberculous agents other than isoniazid. Further studies of beta-lactam antibiotics with in vitro activity against M. tuberculosis are warranted to define their role in treatment of tuberculosis.

Typing of urinary JC virus DNA offers a novel means of tracing human migrations

Although polyomavirus JC (JCV) is the proven pathogen of progressive multifocal leukoencephalopathy, the fatal demyelinating disease, this virus is ubiquitous as a usually harmless symbiote among human beings. JCV propagates in the adult kidney and excretes its progeny in urine, from which JCV DNA can readily be recovered. The main mode of transmission of JCV is from parents to children through long cohabitation. In this study, we collected a substantial number of urine samples from native inhabitants of 34 countries in Europe, Africa, and Asia. A 610-bp segment of JCV DNA was amplified from each urine sample, and its DNA sequence was determined. A worldwide phylogenetic tree subsequently constructed revealed the presence of nine subtypes including minor ones. Five subtypes (EU, Af2, B1, SC, and CY) occupied rather large territories that overlapped with each other at their boundaries. The entire Europe, northern Africa, and western Asia were the domain of EU, whereas the domain of Af2 included nearly all of Africa and southwestern Asia all the way to the northeastern edge of India. Partially overlapping domains in Asia were occupied by subtypes B1, SC, and CY. Of particular interest was the recovery of JCV subtypes in a pocket or pockets that were separated by great geographic distances from the main domains of those subtypes. Certain of these pockets can readily be explained by recent migrations of human populations carrying these subtypes. Overall, it appears that JCV genotyping promises to reveal previously unknown human migration routes: ancient as well as recent.

Gyrase mutations in laboratory-selected, fluoroquinolone-resistant mutants of Mycobacterium tuberculosis H37Ra

To characterize mechanisms of resistance to fluoroquinolones by Mycobacterium tuberculosis, mutants of strain H37Ra were selected in vitro with ofloxacin. Their quinolone resistance-determining regions for gyrA and gyrB were amplified and sequenced to identify mutations in gyrase A or B. Three types of mutants were obtained: (i) one mutant (TKp1) had no mutations in gyrA or gyrB; (ii) mutants that had single missense mutations in gyrA, and (iii) mutants that had two missense mutations resulting in either two altered gyrase A residues or an altered residue in both gyrases A and B. The TKp1 mutant had slightly reduced levels of uptake of [14C]norfloxacin, which was associated with two- to fourfold increases in the MICs of ofloxacin, ciprofloxacin, and sparfloxacin. Gyrase mutations caused a much greater increase in the MICs of fluoroquinolones. For mutants with single gyrA mutations, the increases in the MICs were 4- to 16-fold, and for mutants with double gyrase mutations, the MICs were increased 32-fold or more compared with those for the parent. A gyrA mutation in TKp1 secondary mutants was associated with 32- to 128-fold increases in the MICs of ofloxacin and ciprofloxacin compared with the MICs for H37Ra and an eight-fold increase in the MIC of sparfloxacin. Sparfloxacin was the most active fluoroquinolone tested. No sparfloxacin-resistant single-step mutants were selected at concentrations of > 2.5 micrograms/ml, and high-level resistance (i.e., MIC, > and = 5 micrograms/ml) was associated with two gyrase mutations. Mutations in gyrB and possibly altered levels of intracellular accumulation of drug are two additional mechanisms that may be used by M. tuberculosis in the development of fluoroquinolone resistance. Because sparfloxacin is more active in vitro and selection of resistance appears to be less likely to occur, it may have important advantage over ofloxacin or ciprofloxacin for the treatment of tuberculosis.

Quantitative culture of Mycobacterium tuberculosis from clinical sputum specimens and dilution endpoint of its detection by the Amplicor PCR assay

The minimum number of Mycobacterium tuberculosis CFU detectable in clinical sputum specimens by the Amplicor PCR test was estimated by performing the test on duplicate samples of quantitatively cultured serial dilutions of sputum. Positive PCR test results were obtained for all samples that contained 42 CFU of M. tuberculosis. The detection limits of the PCR assay for decontaminated (N-acetyl-L-cysteine [NALC]-NaOH) and nondecontaminated (NALC only) specimens were equivalent, even though the number of CFU cultured from decontaminated samples was only 11 to 20% of the number cultured from nondecontaminated samples. Thus, the 42 CFU that could be detected in nondecontaminated specimens by the Amplicor PCR test correspond to the approximately 8 CFU (0.20 x 42) that could be recovered in culture after decontamination with NALC-NaOH.

Detection of Mycobacterium tuberculosis in sputum samples by polymerase chain reaction using a simplified procedure

A repetitive sequence of Mycobacterium tuberculosis DNA was amplified by polymerase chain reaction (PCR), from sputum samples, for the diagnosis of pulmonary tuberculosis. The method of heating the sample in a boiling water bath to break down the bacterial cell wall and to release the DNA was compared with that of enzymatic lysis of bacteria and then phenol-chloroform extraction of DNA. Heating the sample was the better method with a sensitivity of approximately 10 microorganisms. A total of 78 sputum specimens prepared by heating were examined by PCR, and the results were compared with the results of acid-fast stained smears, cultures, and clinical data. M. tuberculosis was detected by PCR in all smear- and culture-positive and smear-negative, culture-positive cases. Additionally, PCR was capable of detecting four of nine cases which were smear and culture negative but clinically suspected of tuberculosis. DNA amplification by PCR is a sensitive and specific method for the diagnosis of tuberculosis, and with this simplified DNA isolation procedure it can be used in routine clinical practice.

[In vitro sensitivity of Actinobacillus actinomycetemcomitans to various antibiotics]

In this study, 7 strains of Actinobacillus actinomycetemcomitans (A.a.) were isolated from Localized juvenile periodontitis (LJP) patients and antibiotic susceptibility test by disc diffusion method was utilized. The purpose of this study is to find out the most useful antibiotic against A.a. which is the most important microbial agent in LJP. All seven strains of A.a. were found susceptible to tetracycline, doxycycline, erythromycin, ciprofloxacin and cefuroxime. Two strains were found intermediate susceptible to cephradine. One strain was found resistant to penicillin and another one was found resistant to ampicillin.

[In vitro activity of various antibiotic agents against gram-negative nosocomial bacteremia pathogens]

Empiric therapy is essential in Gram-negative nosocomial bacteremia. Therapy is initiated according to the most frequently isolated organisms and their susceptibility profiles. In order to determine the appropriate antibiotics for this purpose, a study was conducted in 176 blood isolates in Hacettepe University Hospitals. Antibiotic susceptibilities were determined by microbroth dilution tests. The results showed amikacin, ofloxacin and ciprofloxacin to be the most effective antibiotics in-vitro. It is suggested that these agents should be employed in empirical therapy until the causative agent is defined.

[The in vitro activity of ciprofloxacin against clinically-isolated strains of Pseudomonas aeruginosa and comparison with some other antibiotics]

In this study the susceptibility to ciprofloxacin of 100 Pseudomonas aeruginosa strains isolated from various clinical specimens was investigated by disk diffusion test and macrodilution method, and was compared with other various antibiotics. Both of the methods showed that 98 of the strains were susceptible to ciprofloxacin. MIC50 of ciprofloxacin was found to be 0.12, and MIC90 0.50 mcgr/ml for these strains. Pseudomonas aeruginosa strains were found to be highly susceptible to ciprofloxacin in in-vitro conditions.