Detection Rate Of Polymerase Chain Reaction Research Articles

Mycoplasma pneumoniae Macrolide Resistance and MLVA Typing in Children in Beijing, China, in 2016: Is It Relevant*

ObjectiveThe aim of this study is to investigate the macrolide resistance rate and molecular type with multiple-locus variable-number tandem-repeat analysis (MLVA) of Mycoplasma pneumoniae of Beijing in 2016 in pediatric patients. MethodsReal-time quantitative polymerase chain reaction (PCR) was used to identify M. pneumoniae, and MLVA was performed. The domain V of the 23S rRNA was sequenced to detect macrolide-resistant point mutations. We also investigated the activities of antibiotics against M. pneumoniae isolates in vitro. ResultsThe PCR detection rate of M. pneumoniae in children in Beijing was 40%, and the macrolide resistance rate was 66%. The A2063G mutation in the 23S rRNA V region is the dominant mutation (137/146, 93.84%), whereas the A2064G mutation is rare (9/146, 6.16%). Seventy-three samples were typed successfully by MLVA typing, including 86.3% (63/73) were MLVA type 4-5-7-2, and 13.7% (10/73) were MLVA type 3-5-6-2. No other types were found. No strains were resistant to levofloxacin or tetracycline. ConclusionIn 2016, a specific decrease in the macrolide resistance rate occurred in Beijing. The detection rate and macrolide resistance rate of outpatients are lower than those of inpatients. The A2063G mutants M. pneumoniae have high levels of resistance to erythromycin and azithromycin. The primary MLVA type is 4-5-7-2, followed by 3-5-6-2. No other MLVA types were detected. No strains resistant to tetracycline or levofloxacin were found in vitro.

Detection of human papillomavirus E6 oncoprotein from urine and vaginal self-collected sample via a novel duplex nanoparticle-assisted polymerase chain reaction assay

To test a new duplex nanoparticle-assisted polymerase chain reaction (PCR) on human papillomavirus (HPV) E6 oncoprotein detection of HPV16/18 positive samples from vaginal and urine self-sampling specimen. Six specimens from cervical biopsy ranging from CIN1 to CIN3, which have been testified by conventional PCR, were used for nanoPCR HPV E6 oncoprotein specificity test. Seven serially diluted templates by ten-fold (3.78?106?3.78?100 copies/μL) chosen from testified CIN3 biopsy were selected for the sensitivity test. Twenty self-sampling vaginal and urine samples each from 20 women in our hospital were tested by nanoPCR and conventional PCR. NanoPCR showed high specificity when detecting HPV16/18 infected CIN2 and CIN3 samples from cervical biopsy and ten-fold higher sensitivity than conventional PCR when detecting HPV16/18 infected CIN3 samples from cervical biopsy. DNA gel electrophoresis showed brighter bands on positive HPV E6 oncoprotein specimen from self-collected vaginal and urine samples compared to conventional PCR and higher clinical detection rate than those by conventional PCR on vaginal and urine self-sampling specimens. Duplex nanoPCR can be used as a better method for HPV E6 oncoprotein detection in the high-risk HPV infection group for its novelty of high specificity in low concentration target detection, as was showed in the specimen comes from vaginal and urine self-sampling, thus promoting self-sampling for better cervical cancer screening.

Detection and molecular identification of Leucocytozoon and Plasmodium species from village chickens in different areas of Myanmar

Village chicken production, a traditional, small-scale, and extensive backyard poultry industry, has been profitable for local farmers in Myanmar. However, there is scanty information available concerning the infection of these chickens with avian pathogens, including haemoprotozoan parasites. In the present study, we provide the first report of microscopic detection and molecular identification of Leucocytozoon and Plasmodium parasites from seven different areas of Myanmar. Leucocytozoon gametocytes were detected in 17.6% (81/461) of the blood smears from village chickens. The nested polymerase chain reaction (PCR) for targeting Leucocytozoon mitochondrial cytochrome b (cyt b) genes had a 17.6% positive rate. Although the positive rate of nested PCR targeting Plasmodium/Haemoproteus cyt b was 34.3%, the PCR protocol was observed to possibly amplify DNA of a certain species of Leucocytozoon. There were no obvious clinical signs in the infected birds. Statistical analysis of the microscopic detection and PCR detection rates using the age and sex of birds as internal factors revealed that the statistical significances differed according to the study area. The sequencing of 32 PCR products obtained from each study area revealed infection by Leucocytozoon caulleryi in three birds, Leucocytozoon sabrazesi in two birds, Leucocytozoon schoutedeni in two birds, Leucocytozoon sp. in eighteen birds, and Plasmodium juxtanucleare in seven birds; however, Haemoproteus infection was not detected. While L. sabrazesi was detected in chickens from the central region of Myanmar, the other haemosporidians were detected in those from different areas. In the haplotype analysis, we detected 17 haemosporidian cyt b haplotypes, including two for L. caulleryi, one for L. sabrazesi, two for L. schoutedeni, nine for Leucocytozoon sp., and three for P. juxtanucleare. Phylogenetic analysis of the cyt b haplotypes revealed a considerably close genetic relationship among chicken haemosporidians detected in Myanmar, Thailand, and Malaysia. These results indicate that well-recognized widespread species of chicken Leucocytozoon and Plasmodium are distributed nationwide in Myanmar, providing new insights into the ecosystem and control strategies of haemosporidian parasites in domesticated chickens in Myanmar.

The diagnostic value of serological tests and real-time polymerase chain reaction in children with acute Mycoplasma pneumoniae infection

BackgroundThis study set out to evaluate the clinical significance and diagnostic effectiveness of serological tests and real-time polymerase chain reactions (RT-PCR) in children of different age groups and disease durations infected with Mycoplasma pneumoniae (MP).MethodsPediatric patients with lower respiratory tract infection (LRTI) confirmed by polymerase chain reaction (PCR) were enrolled and subjected to bronchoalveolar lavage fluid PCR (BALF-PCR) for MP infection. The diagnostic values of the serum immunoglobulin M (IgM) test, paired sera immunoglobulin G (IgG) test, RT PCR applied to nasopharyngeal aspirates (NPA-PCR), and combined IgM and NPA-PCR test were evaluated.ResultsWhen BALF PCR was used as the gold standard, the MP positivity rate of combined IgM and NPA PCR was 78.85%in children aged 3–5 years. The positivity rates of IgM, NPA PCR, and combined IgM and NPA PCR in children older than 5 years were 71.21%, 72.72%, and 84.85%, respectively. The detection rate of combined IgM and NPA PCR was consistent with BALF PCR (Kappa =0.727). The MP positivity rates of combined IgM and NPA PCR at 1–2 weeks was as high as 91.11%, and was consistent with the BALF PCR (Kappa =0.756). Moreover, the positivity rates of IgM or NPA PCR at 2-3 weeks were 63.16%, and were consistent with each other (Kappa =0.771).ConclusionsCombined IgM and NPA PCR is the optimal test to confirm MP infection among children aged 3–5 years in cases with a disease duration of less than2 weeks, and either NPA PCR or IgM is recommended for children older than 5 years with a disease duration of 2–3 weeks.KeywordsMycoplasma pneumoniae pneumonia (MPP); diagnosis; children; age; disease duration

Detection of bacterial DNA in infected body fluids using 16S rRNA gene sequencing: Evaluation as a rapid diagnostic tool

CONTEXT: Rapid detection of pathogens in infected body fluids will help in establishing an aetiological diagnosis, thereby facilitating specific therapy. Molecular methods have an advantage over conventional bacteriological techniques in particularly identifying slow-growing, fastidious or non-cultivable organisms. AIM: The aim of this study is to evaluate the use of 16S rRNA polymerase chain reaction (PCR) for detecting bacterial pathogens in body fluids and compare with conventional culture methods. SETTINGS AND DESIGN: This study was done at the Clinical Laboratory of the Department of Microbiology. This was a cross-sectional study design. MATERIALS AND METHODS: A total of 100 consecutive samples which included synovial fluid, cerebrospinal fluid, ascitic fluid and pleural fluid received in the laboratory during the study period were subjected to PCR for 16S rRNA using specific primers and conventional culture by standard protocol. Samples which were positive for 16S rRNA were sequenced to identify the organism. Results of sequenced products were compared in terms of number of organisms, with culture isolates. RESULTS: The detection rate of 16S rRNA PCR was at 13% as compared to culture at 3% (P = 0.0009). The diagnostic sensitivity and specificity of the PCR were 100% and 89.7%, respectively. The concordance of PCR and culture for both identical positive and negative samples was 90%. CONCLUSIONS: The 16S rRNA PCR proved to be rapid method for detection of bacterial pathogens in body fluids. It may be a valuable tool in the diagnostic armamentarium for differentiating bacterial infection from others and starting empiric treatment.

Identification of the Plasmodium species in clinical samples from children residing in five epidemiological strata of malaria in Cameroon

BackgroundMalaria in Cameroon was previously known to be caused solely by Plasmodium falciparum but today, evidence points to other Plasmodium species including P. vivax, P. ovale and P. malariae. The purpose of this study was to identify the Plasmodium species in clinical samples from children residing in five epidemiological strata of malaria in Cameroon, so as to advise control policies.MethodsOne thousand six hundred nine febrile children (≤15 years) were recruited from five epidemiological strata of malaria including the Sudano-sahelian (SS) strata, the High inland plateau (HIP) strata, the South Cameroonian Equatorial forest (SCEF) strata, the High western plateau (HWP) strata and the Coastal (C) strata. Malaria parasites were detected by Giemsa microscopy (GM) while a multiplex polymerase chain reaction (PCR) was used to identify the Plasmodium species. Statistical analysis performed included the Pearson chi-square test, and statistical significance was set at p < 0.05.ResultsThe PCR-adjusted prevalence of malaria was 17.6%. The detection rate of PCR was higher than GM (p = 0.05). However, GM demonstrated a high sensitivity (85.5%) and specificity (100%) and, overall, a perfectly correlated agreement with PCR (97.5%). The prevalence of malaria was significantly higher in children between 60 and 119 months (p < 0.001) and in Limbe (in the Coastal strata) (p < 0.001). Contrariwise, the prevalence of malaria was not associated with gender (p = 0.239). P. falciparum was identified in all (100%) the cases of malaria; P. ovale, P. vivax, P. malariae and P. knowlesi were all absent. No case of mixed infection was identified.ConclusionsP. falciparum was the only species causing clinical malaria in the target population, which is contrary to studies that have reported P. vivax, P. malariae and P. ovale as causing clinical malaria in Cameroon.

Application of RLEP Real-Time PCR for Detection of M. leprae DNA in Paraffin-Embedded Skin Biopsy Specimens for Diagnosis of Paucibacillary Leprosy

The TaqMan real-time polymerase chain reaction (PCR) assay was evaluated systematically with respect to the standard curve, linear range, and used for detecting Mycobacterium leprae DNA in paraffin-embedded skin biopsy specimens from 60 confirmed leprosy patients and three healthy individuals and 29 other dermatoses and bacterial DNA from 21 different species. The test was further evaluated with 51 paucibacillary (PB) patients. The results showed that the test had good sensitivity (8 fg) and good specificity with no cross-reactivity with 21 other bacterial species and the control specimens, except one with Xanthomatosis. The real-time PCR detection rate for the 51 PB specimens was 74.5% (38 of 51). We conclude that the real-time PCR test is a useful adjunct test for diagnosing early stage or PB leprosy cases.

Identification of TCT, a novel knockdown resistance allele mutation and analysis of resistance detection methods in the voltage-gated Na+ channel of Culex pipiens pallens from Shandong Province, China

The present study aimed to investigate deltamethrin resistance in Culex pipiens pallens (C. pipiens pallens) mosquitoes and its correlation with knockdown resistance (kdr) mutations. In addition, mosquito‑resistance testing methods were analyzed. Using specific primers in polymerase chain reaction (PCR) and allele-specific (AS)-PCR, kdr gene sequences isolated from wild C. pipiens pallens mosquitoes were sequenced. Linear regression analysis was used to determine the correlation between the mutations and deltamethrin resistance. A kdr allelic gene was cloned and sequenced. Analysis of the DNA sequences revealed the presence of two point mutations at the L1014 residue in the IIS6 transmembrane segment of the voltage‑gated sodium channel (VGSC): L1014F, TTA→TTT, replacing a leucine (L) with a phenylalanine (F); L1014S, TTA→TCA, replacing leucine (L) with serine (S). Two alternative kdr-like mutations, L1014F and L1014S, were identified to be positively correlated with the deltamethrin-resistant phenotype. In addition a novel mutation, TCT, was identified in the VGSC of C. pipiens pallens. PCR and AS-PCR yielded consistent results with respect to mosquito resistance. However, the detection rate of PCR was higher than that of AS-PCR. Further studies are required to determine the specific resistance mechanism. PCR and AS-PCR demonstrated suitability for mosquito resistance field tests, however, the former method may be superior to the latter.

Comparison of Feces versus Rectal Swabs for the Molecular Detection of Lawsonia Intracellularis in Foals with Equine Proliferative Enteropathy

The purpose of the current study was to compare the molecular detection rate of Lawsonia intracellularis between feces and rectal swabs collected from 42 foals with suspected equine proliferative enteropathy (EPE). Fecal samples and rectal swabs were processed for DNA purification by using an automated extraction system. The purified DNA was then analyzed by real-time polymerase chain reaction (PCR) for the presence of the aspartate ammonia lyase (aspA) gene of L. intracellularis. Absolute quantitation was calculated by using a standard curve for L. intracellularis and expressed as copy numbers of the aspA gene of L. intracellularis per microliter of purified DNA. The combined PCR detection rate for L. intracellularis was 90%, with 38 foals testing PCR positive in feces (33 samples), rectal swabs (32), or both (27). Six foals tested PCR positive only in feces, whereas 5 tested positive only in rectal swabs. Feces yielded a significantly higher aspA gene copy number of L. intracellularis than rectal swabs. Feces and rectal swabs tested PCR negative from 4 foals. In conclusion, the results showed that feces yielded similar numbers of PCR-positive results, with a higher L. intracellularis aspA gene load than rectal swabs. By analyzing dual samples, the PCR detection rate for L. intracellularis increased from 76% and 79% for rectal swabs and feces, respectively, to 90%. Rectal swabs should be considered as an alternative sample type for EPE-suspected patients with decreased or no fecal output.

Detection ofAnaplasma phagocytophilumandBorrelia burgdorferiSensu Lato in Dogs in the Czech Republic

The aim of this study is to present molecular, serologic, and clinical findings for dogs that were naturally infected with Anaplasma phagocytophilum or Borrelia burgdorferi sensu lato (s. l.) in the Czech Republic. This data can provide information relevant to human infection. In total, blood samples from 296 dogs and 118 engorged ticks were examined. Samples were tested for A. phagocytophilum using polymerase chain reaction (PCR) amplification, nested PCR, and direct sequencing of the 16S rDNA, and for B. burgdorferi s. l. using PCR amplification of the 16S rDNA and restriction fragment length polymorphism analysis of the 5S-23S rDNA intergenic spacer. In addition, blood samples were screened for antibodies to these bacteria. Ten (3.4%) dogs were PCR-positive for A. phagocytophilum. Morulae of A. phagocytophilum in granulocytes were found in two of these dogs. Nine of the PCR-positive dogs had clinical signs related to anaplasmosis. Statistically significant differences in the PCR detection rates were found between breeds and between symptomatic and asymptomatic dogs. Infection with Borrelia garinii was detected by PCR in a dog with meningoencephalitis. DNA of A. phagocytophilum and B. burgdorferi s. l. (B. garinii or Borrelia afzelii) was detected in 8.5% and 6.8% of ticks, respectively. Immunoglobulin (Ig) G seropositivity to A. phagocytophilum was 26%. Significant differences were found with respect to breed and gender. IgM and IgG antibodies to B. burgdorferi s. l. were detected in 2.4% and 10.3% of dogs, respectively. Our findings suggest that the exposure to B. burgdorferi s. l. exists in dogs in the Czech Republic, and exposure to A. phagocytophilum is common.

Polymerase chain reaction detection of Pneumocystis jiroveci: evaluation of 9 assays

Various polymerase chain reaction (PCR) amplification strategies have been described for detecting Pneumocystis jiroveci in clinical specimens. Different combinations of primer/target and platforms have been reported to yield varying PCR detection rates. PCR was evaluated on clinical specimens using internal transcribed spacer regions of the rRNA nested, dihydropteroate synthase single and nested, dihydrofolate reductase nested, major surface glycoprotein heminested, mitochondrial large subunit rRNA (mtLSUrRNA) single and nested, 18S rRNA 1-tube nested, and real-time 5S rRNA PCR. The most sensitive PCR was subsequently compared with routine diagnostic immunofluorescence (IF) microscopy. Discrepant PCR and IF results were resolved after review of clinical and histology/cytology records. Major discrepancies were observed among the methods investigated. mtLSUrRNA nested PCR was the most sensitive, produced less false-negative results, and displayed the highest degree of concordance with histology. Direct comparison of mtLSUrRNA nested PCR versus IF yielded low sensitivity and specificity, which were improved for PCR and lowered for IF on review of clinical and laboratory records.

Use of a PCR assay for the specific and sensitive detection of Trypanosoma Spp. in naturally infected dairy cattle in peri-urban Kampala, Uganda.

The objective of this study was to compare the sensitivity and specificity of the polymerase chain reaction (PCR) with the hematocrit centrifugation technique (HCT) and the mini-anion-exchange centrifugation technique (m-AECT) for diagnosis of trypanosome infections in livestock. In a cross-sectional study, 486 cattle from 50 randomly selected farms in Mukono County, Uganda were investigated in June 1994. The direct parasitological techniques were performed in the field, resulting in 45 (9.3%) animals positive by HCT and 78 (16%) positive by m-AECT. The total prevalence (combined evidence of HCT and m-AECT) was 18.9%, with 78.2% Trypanosoma brucei only, 10.9% T. vivax and 10.9% mixed (T. bruceil T. vivax) infections. Trypanosomes of the subgenus Nannomonas were not detected. DNA was prepared by lysis from 181 randomly selected blood samples and amplified by PCR using species-specific oligonucleotide primers. Overall, the PCR gave positive results in 63 (34.8%) blood samples, with 76.2% positive only for T. brucei, 20.6% positive only for T. vivax and 3.2% positive for mixed (T. bruceil T. vivax) infections. The preliminary results from this study demonstrate that the detection rate of PCR is about two times higher than that of the direct parasitological techniques, suggesting a higher sensitivity. The higher proportion of T. vivax infections detected by PCR as compared to HCT/m-AECT is likely to be due to false parasitological classifications which might occur under field conditions.

Detection of Mycobacterium avium subsp. paratuberculosis in ovine tissues and blood by the polymerase chain reaction

A direct polymerase chain reaction (PCR) test was applied to DNA extracted from blood, liver, ileocecal lymph node and ileum from twelve ewes in poor condition with histologically confirmed paratuberculosis and ten clinically normal sheep which had no evidence of paratuberculosis. The assay was compared with four serological tests: complement fixation test (CFT), gel diffusion test (AGID) and two enzyme-linked immunosorbent assays (ELISA). The PCR detection rate of Mycobacterium avium subsp. paratuberculosis, when results of single tests were interpreted in duplicate, was 72% for ileocecal lymph node, 90% for liver, and 100% for ileum in sheep with confirmed paratuberculosis. A single PCR test detected the target DNA in 66% of 0.5 ml blood samples. Sensitivities of serological tests compared with histological diagnosis were: 33% for CFT, 66% for AGID, 75% for the Central Animal Health Laboratory (CAHL) ELISA, and 83% for the ‘modified’ Commonwealth Serum Laboratories (CSL) ELISA. The PCR assay gave no positive reaction in samples collected from 10 sheep considered to be free of paratuberculosis. Similarly, all four serological tests were also 100% specific. The results raise some hope for the development of a PCR-based test using liver biopsy specimens, or possibly blood, in the diagnosis of paratuberculosis in sheep.

Optimal primer selection for clonality assessment by polymerase chain reaction analysis III. Intermediate and high-grade B-cell neoplasms

Previous studies have reported that low-grade B-cell lymphoproliferative disorders have variable B-cell monoclonality detection rates by polymerase chain reaction (PCR) analysis. For instance, monoclonal B-cell populations from chronic lymphocytic leukemia/small lymphocytic leukemia and mantle cell lymphoma are most often readily amplified with a single primer pair, whereas follicular lymphomas and plasma cell neoplasms require alternative strategies to approach these higher diagnostic sensitivity standards. Because most published reports have not focused on the variation in PCR B-cell monoclonality detection among subtypes of intermediate and high-grade B-cell neoplasms, additional information is necessary to determine primer selection strategies and identify problematic tumor subtypes within this group. The current investigation, the third part in a series, was aimed at documenting the efficiency of B-cell monoclonality detection by PCR in 71 aggressive B-cell neoplasms of various types using a comprehensive approach. A predetermined panel of primer sets was used in an algorithmic fashion. Specifically, all samples were analyzed with the standard VH-FRIII/JH assay previously shown to have the highest efficiency of monoclonality detection within low-grade B-cell lymphoproliferative disorders. Negative samples were further evaluated with primer sets in the following order until a positive result was observed, or all primer sets were used: (1) bcl-2/JH, (2) VH-FRI family specific/JH, and (3) VH-FRI consensus/JR. Forty-three (61%) of the 71 B-cell neoplasms evaluated with VH-FRIII/JH showed monoclonal B-cell populations. Sequential use of the three reserve primer sets in samples negative with this initial primer pair resulted in an overall improvement in PCR detection from 61% to 82% (58 of 71 specimens) ( P < .001). The VH-FRI family specific assay identified B-cell monoclonality in 11 (73%) of these 15 specimens and was the most productive reserve primer set. Individual categories exhibited the following initial (I) and final (F) PCR detection rates: acute lymphoblastic leukemia/ lymphoblastic lymphoma, 11 specimens (I = 91% to F = 91%); small noncleaved cell lymphoma, 14 specimens (I = 79% to F = 86% [ P > .25]); diffuse large cell lymphoma, 33 specimens (I = 52% to F = 85% [ P < .005]) and large cell, immunoblastic lymphoma, 13 specimens (I = 38% to F = 62% [ P < .01]). The authors have shown that comprehensive PCR analysis is capable of detecting B-cell monoclonality in a significant proportion of samples from each subtype of intermediate and high-grade B-cell neoplasm. The VH-FRIII/JH assay was an adequate initial primer set, but required augmentation with the reserve PCR assays to attenuate the false negative rate and improve diagnostic sensitivity. The B-cell clonality PCR assay is optimally used as a screening tool and when used in this fashion, the more laborious and time-consuming restriction fragment-Southern blot hybridization (RF-SBH) method for IgH gene rearrangement detection may be limited to a relatively small proportion of PCR-negative aggressive B-cell neoplasms.