Polymerase Chain Reaction Reaction Research Articles

A Thermocycler Using a Chip Resistor Heater and a Glass Microchip for a Portable and Rapid Microchip-Based PCR Device.

This study proposes a rapid and inexpensive thermocycler that enables rapid heating of samples using a thin glass chip and a cheap chip resistor to overcome the on-site diagnostic limitations of polymerase chain reaction (PCR). Microchip PCR devices have emerged to miniaturize conventional PCR systems and reduce operation time and cost. In general, PCR microchips require a thin-film heater fabricated through a semiconductor process, which is a complicated process, resulting in high costs. Therefore, this investigation substituted a general chip resistor for a thin-film heater. The proposed thermocycler consists of a compact glass microchip of 12.5 mm × 12.5 mm × 2 mm that could hold a 2 μL PCR sample and a surface-mounted chip resistor of 6432 size (6.4 mm × 3.2 mm). Improving heat transfer from the chip resistor heater to the PCR reaction chamber in the microchip was accomplished via the design and fabrication of a three-dimensional chip structure using selective laser-induced etching, a rapid prototyping technique that allowed to be embedded. The fabricated PCR microchip was combined with a thermistor temperature sensor, a blower fan, and a microcontroller. The assembled thermocycler could heat the sample at a maximum rate of 28.8 °C/s per second. When compared with a commercially available PCR apparatus running the same PCR protocol, the total PCR operating time with a DNA sample was reduced by about 20%.

Molecular Analysis of HBV in Histologically Confirmed Hepatocellular Carcinoma in a Tertiary Hospital in Ghana.

Hepatocellular carcinoma (HCC) is a leading cause of death in Africa. Viral hepatitis B is a leading cause of hepatocellular cancer in Ghana and most African countries except Egypt where hepatitis C virus is more prevalent. This study aims at reviewing the histopathological patterns of HCC and its association with hepatitis B virus in our environment. Demographics and histological diagnosis were retrieved from the surgical daybook and archival FFPE tissue samples with histopathologically confirmed HCC were used for this study. Sections (10μm) were taken from the tissues and digested to obtain DNA lysates. The DNA lysates were used in polymerase chain reaction (PCR) to determine the prevalence of HBV in the biopsies. Of the 24 confirmed cases of HCC seen in the 5-year period, there were 17 males and 7 females with M:F ratio of 2.4:1. The mean age of our patients was 39.92 ± 1.98 years with age range 13-85 years. 50% of the cases were moderately differentiated while 25% each were well and poorly differentiated. Out of the 24 archival HCC biopsies screened, HBV DNA PCR amplification was achieved in 11 (45.83%) after the restriction fragment length polymorphism PCR reaction. Out of the 24 archival HCC biopsies screened, HBV DNA PCR amplification was achieved in 11 (45.83%) after the restriction fragment length polymorphism PCR reaction. Eight of the 11 cases were found in the male and 3 in females. Of the 11 (45.83%) samples that were positive for HBV DNA, 3 were above 40 years and 8 were 40 years and younger. The overall prevalence of HBV DNA in our study was 45.83% and a greater proportion seen in ≤ 40 years. This suggests that most of our patients are infected with HBV early in life in our environment.

A double signal amplification strategy for sensitive detection of Hg2+ based on exonuclease III and PCR

A double signal amplification method was developed for sensitive detection of Hg2+ based on exonuclease III (Exo III) and Polymerase Chain Reaction (PCR). In the presence of Hg2+, the ineffective primers could bind with helper DNA to form dsDNA by T-Hg(II)-T mismatch for the first signal amplification. Then, the ineffective primers were digested by Exo III to effective primers which initiate PCR reaction for the second signal amplification. This conversion from ineffective to effective primers for triggering PCR reaction has not been reported for the detection of Hg2+. Through the double signal amplification strategy, the sensitivity of this proposed method was significantly improved with the limit of detection 1.46 nM. With the specific T-Hg(II)-T recognition, the selectivity of this new method was satisfactory. And the recoveries were between 92.3 % and 109.0 %. These results suggested that the proposed method was reliable to detect Hg2+ in water samples.

Screening for Group A Streptococcal Disease via Solid-State Nanopore Detection of PCR Amplicons.

Single-molecule detection methods are becoming increasingly important for diagnostic applications. Practical early detection of disease requires sensitivity down to the level of single copies of the targeted biomarkers. Of the candidate technologies that can address this need, solid-state nanopores show great promise as digital sensors for single-molecule detection. Here, we present work detailing the use of solid-state nanopores as downstream sensors for a polymerase chain reaction (PCR)-based assay targeting group A streptococcus (strep A), which can be readily extended to detect any pathogen that can be identified with a short nucleic acid sequence. We demonstrate that with some simple modifications to the standard PCR reaction mixture, nanopores can be used to reliably identify strep A in clinical samples. We also discuss methodological best practices for both adapting PCR-based assays to solid-state nanopore readout and analytical approaches by which to decide on sample status.

Rapid Extraction of Plant Nucleic Acids by Microneedle Patch for In-Field Detection of Plant Pathogens.

Plant diseases pose a significant threat to global food security. Molecular diagnosis currently plays a crucial role in mitigating the negative impacts of plant diseases by accurately identifying the disease-causing pathogens and revealing their genotypes. However, current molecular assays are constrained to the laboratory because of the cumbersome protocols involved in plant nucleic acid extraction. To streamline this, we have developed a polymeric microneedle (MN) patch-based nucleic acid extraction method, which can be applied to various plant tissues and easily performed in field settings without using bulky laboratory equipment. The MN patch instantly isolates both host and pathogen's DNA and RNA from plant leaves by two simple steps: press and rinse with a buffer solution or nuclease-free water. The MN-extracted DNA and RNA are purification-free and directly applicable to downstream molecular assays such as polymerase chain reaction (PCR), reverse transcription-polymerase chain reaction (RT-PCR), loop-mediated isothermal amplification (LAMP), and reverse transcription loop-mediated isothermal amplification (RT-LAMP). Here, we describe the fabrication procedures of the MN patch and demonstrate the application of the MN method by extracting Phytophthora infestans DNA and tomato spotted wilt virus (TSWV) RNA from infected tomato leaves. After MN extraction, we directly utilize the MN-extracted nucleic acid samples to run PCR, RT-PCR, LAMP, or RT-LAMP reactions to amplify various biomarker genes, such as the ribulose-bisphosphate carboxylase (rbcL) gene of host tomato DNA, internal transcribed spacer (ITS) region of P. infestans DNA, and nucleocapsid (N) gene of TSWV RNA. Furthermore, this simple and rapid nucleic acid method can be integrated with portable nucleic acid amplification platforms such as smartphone-based microscopy devices to achieve "sample-to-answer" detection of plant pathogens directly in the field.

Miniaturized and IoT Enabled Continuous-Flow-Based Microfluidic PCR Device for DNA Amplification.

Herein, a continuous-flow driven microfluidic device has been designed and fabricated using the CO2 laser ablation method for polymerase chain reaction (PCR). The device consists of a polymethyl methacrylate (PMMA) microfluidic channel with 30 serpentine thermal cycles, an arduino board, two custom-made cartridge heaters, and thermocouple sensors. The portable thermal management system, with aluminium blocks placed on a wooden substrate, working on the PID controller principle, is low-cost, battery-powered, automated, integrated, and IoT-enabled. The device with dimensions 80×72×36 mm3 (L × W × H) has a temperature accuracy of ±0.2 °C. The IoT module enables accessing and storage of real-time temperature values directly onto the smartphone through ThingSpeak analytics. It was developed to achieve desirable accurate temperature at two thermal zones, denaturation and annealing (95 °C and 60 °C) on the microfluidic thermal management platform. A PCR mixture of [Formula: see text] was infused into the serpentine-based microchannel using a syringe pump. Amplification of DNA template with 594-base pair (bp) fragment of the rat GAPDH gene was successfully performed on the miniaturized thermal management system. The total time required for a complete PCR reaction was 32 min at an optimum flow rate of [Formula: see text]/min. The amplified sample of the target DNA obtained from the PCR microchannel was then separated by agarose gel electrophoresis and was further analyzed using a gel-doc system. Finally, the obtained results were compared to the conventional PCR instrument showing excellent performance.

LoopTag FRET Probe System for Multiplex qPCR Detection of Borrelia Species.

Background: Laboratory diagnosis of Lyme borreliosis refers to some methods with known limitations. Molecular diagnostics using specific nucleic acid probes may overcome some of these limitations. Methods: We describe the novel reporter fluorescence real-time polymerase chain reaction (PCR) probe system LoopTag for detection of Borrelia species. Advantages of the LoopTag system include having cheap conventional fluorescence dyes, easy primer design, no restrictions for PCR product lengths, robustness, high sequence specificity, applicability for multiplex real-time PCRs, melting curve analysis (single nucleotide polymorphism analysis) over a large temperature range, high sensitivity, and easy adaptation of conventional PCRs. Results: Using the LoopTag probe system we were able to detect all nine tested European species belonging to the Borrelia burgdorferi (sensu lato) complex and differentiated them from relapsing fever Borrelia species. As few as 10 copies of Borrelia in one PCR reaction were detectable. Conclusion: We established a novel multiplex probe real-time PCR system, designated LoopTag, that is simple, robust, and incorporates melting curve analysis for the detection and in the differentiation of European species belonging to the Borrelia burgdorferi s.l. complex.

A proof-of-principle study on implementing polymerase chain displacement reaction (PCDR) to improve forensic low-template DNA analysis

Polymerase chain reaction (PCR) plays an important role in forensic DNA analysis. However, the amplification of low-template DNA (LTDNA) samples usually encounters unsatisfactory results for the limited efficiency of PCR, which would interfere with the subsequent profile interpretation. Polymerase chain displacement reaction (PCDR) is a highly-efficient technique characterized by combining PCR and strand displacement reaction into a single PCDR cycle. This study explored the feasibility of PCDR for improving forensic LTDNA analysis. STR markers commonly used in forensic genetics were subjected to PCDR amplification and capillary electrophoresis detection. The results of singleplex reactions indicated that PCDR surpassed original PCR in efficiency for STR amplification. The average peak height of alleles in PCDR profiles was linearly correlated to the number of outer primers adopted for initiating the strand displacement process. Further, we assessed the multiplexing potential of PCDR by incorporating 17 STRs included in the expanded CODIS core loci and Amelogenin gene into a multiplex PCDR system. For pristine DNA templates ranged from 200 pg to 12.5 pg, the multiplex PCDR system consistently exhibited higher allele peak height as well as less allele dropout compared to the multiplex PCR references. Meanwhile, a significant reduction of stutter ratio was extensively observed in PCDR profiles. We also tested mock casework samples to verify the practical ability of multiplex PCDR for LTDNA detection. With DNA input varying from 48.1 pg to 6.6 pg, the multiplex PCDR system consistently obtained more allelic information than multiplex PCR methods. Our data collectively suggested that it is feasible to apply PCDR in forensic LTDNA analysis.

High Expression of TWIST-1 in the Chronic Myeloid Leukemia Patients with T315I Mutation

Background: Among the known ABL mutations in chronic myeloid leukemia (CML), T315I is of particular importance. The T315I mutation may develop resistant cells that increase disease progression. TWIST-1 expression is impaired in patients with increased drug resistance. Objectives: The current study aimed to measure the expression of TWIST-1 gene in CML patients to investigate its association with T315I mutation. Methods: Peripheral blood samples were taken from 40 CML patients. The expression of TWIST-1 and BCR-ABL1 genes was quantified by real-time polymerase chain reaction (PCR). The gene expression was evaluated by REST software. cDNA was used for amplification refractory mutation system (ARMS)-PCR reaction. Results: Of the 40 patients (age range: 19 - 72 years) participating in the study, 23 (57.7%) were female, and 17 (42.5%) were male. The expression of TWIST-1 gene was 43 ± 184.09-fold. The T315I mutation was detected in 3 (7.5%) patients. Conclusions: According to our results, the TWIST-1 gene expression in patients with T315I mutation was significantly higher than patients without that mutation.

The Modified Recombinant Proinsulin: A Simple and Efficient Way to Produce Insulin Glargine in E. coli

Background: Recombinant insulin glargine, a long-acting analog of insulin, is expressed as proinsulin in the host cell and, after purification and refolding steps, is processed to mature insulin by using trypsin and carboxypeptidase B. Because of several internal residues of arginine and lysine in the proinsulin B and C chains, several unwanted products are formed after treatment with these enzymes. To overcome this problem, we introduced three thrombin recognition sites into the proinsulin encoding sequence. Materials and methods: After the design, the modified proinsulin encoding sequence containing the 5′ His-Tag tail and three thrombin recognition sites located between the His-Tag and B chain, B and C chains, and C and A chains, respectively, was synthesized by overlap extension Polymerase Chain Reaction (PCR) using seven specific primers in multiple sequential PCR reactions. The final amplified fragment was cloned in the pGEM-5zf vector by the EcoRV enzyme. After sequencing, the modified proinsulin encoding sequence was subcloned into the pET-26b(+) vector using NdeI and XhoI enzymes. Finally, the modified proinsulin was expressed in E. coli BL-21(DE3) by induction with Isopropyl β-d-1-thiogalactopyranoside (IPTG). Results: The accuracy of the synthesized modified proinsulin sequence was confirmed by DNA sequencing. The modified proinsulin cloning was evaluated by PCR with specific primers and digestion with specific restriction enzymes. In this study, the modified proinsulin protein was expressed up to 40%. The modified proinsulin protein expression was assessed using sodium dodecyl Sulfate–Polyacrylamide Gel Electrophoresis (SDS-PAGE) and western blotting. Conclusions: This modified proinsulin can be used to easily and efficiently produce insulin glargine without any impurities after processing with thrombin in one step in a nickel chromatographic column.

ПРОТОКОЛ ДЕТЕКЦІЇ ГЕНЕТИЧНИХ МАРКЕРІВ У СЛИНІ, ВИКОРИСТОВУЮЧИ ПОЛІМЕРАЗНУ ЛАНЦЮГОВУ РЕАКЦІЮ БЕЗ ОЧИСТКИ НУКЛЕЇНОВИХ КИСЛОТ: ТЕСТУВАННЯ SARS-COV-2 ТА GAPDH МАРКЕРІВ

Introduction. Polymerase chain reaction (PCR)-based diagnostic tests use purifi ed nucleic acids (NAs) from clinical samples. The NAs purifi cation step adds time, cost, and aff ects the quality of testing. The objective of this study was to develop a protocol for direct use of saliva in tests for genetic markers, without purifi cation of nucleic acids. Methods. PCR, real-time RT-PCR and isothermal amplifi cation tests were used for direct detection of genetic markers, without purifi cation of nucleic acids. Results. We report a protocol for the direct detection of genetic markers in saliva. The protocol is based on a collection of saliva in a solution containing a detergent and ethanol and is compatible with isothermal amplifi cation (LAMP), real-time RT-PCR and RT-PCR. SARS-CoV-2 and GAPDH markers were used as reference markers. We observed that mild detergents allow effi cient detection of external reference and intracellular endogenous markers, while strong detergent, e.g. sodium dodecyl sulfate, inhibited the PCR reaction. Under these conditions, saliva samples can be stored for 24 h at +4°C or –18°C with the preservation of markers. Storage at room temperature led to the deterioration of marker detection. Snap heating of saliva samples at the time of collection, followed by storage at room temperature, provided partial protection. Conclusion. The protocol presented in this report describes the collection and storage of saliva for direct detection of genetic markers and is compatible with PCR and LAMP tests.

Thermal study of polymerase chain reaction with capillary tubes

Polymerase Chain Reaction (PCR) amplifies specific deoxyribonucleic acid (DNA) targets whereby the reaction vessels are placed in high thermal inertia media and subjected to multiple cycles of discrete temperatures to effect denaturation, annealing and extension events. Precise temperature control and efficient heat transfer are crucial factors in achieving amplification reproducibility and reliability as well as in reducing the time required for PCR. Understanding the temperature distribution and transfer characteristics during PCR will facilitate system optimization to enhance the efficiency of DNA amplification. We describe a numerical thermal study investigating temperature profiles achieved using the classical method of manual transfer of PCR reaction vessels through a series of temperature-controlled media compared with that of a more recently reported method that displaces reaction vessels spatially by tilting through different temperature zones. It was found that while the classical method allows the reagent to achieve uniform temperature distribution, natural convection effects would necessitate translation speeds in excess of 150 mm/min in order to limit the reagent temperature drop to within 10 °C. With the tilt method, uniform temperature distributions as well as temperature settling times within 5 s could be attained. The simulation results demonstrated here indicate that the tilt method can be developed further to augment extreme PCR requiring less than 2s for each cycle.

English

The Zygosaccharomyces is notorious for its remarkable spoilage characteristics. In the present study, the visual and rapid identification of the genus Zygosaccharomyces was performed by a loop-mediated isothermal amplification (LAMP) assay using specific primers in Mini Dry Bath within 30 min at 65°C followed by a lateral flow dipstick (LFD) detection. The sensitivity evaluation revealed LAMP-LFD assay with 1.0×101 copies/μL of Zygosaccharomyces DNA as its detection limit, which was the same as the methods of real-time quantitative PCR (qPCR) and conventional polymerase chain reaction (PCR). However, qPCR or PCR methods not only need to be performed in a specialist analytical laboratory with expensive equipment but also with risk of aerosol pollution. The LAMP-LFD assay had no cross-reactivity against 10 other yeast species and its specificity was 100%. A total of 25 Qiangli loquat Dew samples (17 bottles bulged and eight normal-appearing) were detected within 40 min with 100 and 92.0% accurately and specifically, when compared with the qPCR assay and the microbiology culture method, respectively. Therefore, the simple, fast, sensitive and low-cost LAMP-LFD assay is an effective and useful tool for the on-site identification of the genus Zygosaccharomyces.   Key words: Zygosaccharomyces, on-site detection, loop-mediated isothermal amplification (LAMP), lateral flow dipstick (LFD).

Ultrafast and Real-Time Nanoplasmonic On-Chip Polymerase Chain Reaction for Rapid and Quantitative Molecular Diagnostics.

Advent and fast spread of pandemic diseases draw worldwide attention to rapid, prompt, and accurate molecular diagnostics with technical development of ultrafast polymerase chain reaction (PCR). Microfluidic on-chip PCR platforms provide highly efficient and small-volume bioassay for point-of-care diagnostic applications. Here we report ultrafast, real-time, and on-chip nanoplasmonic PCR for rapid and quantitative molecular diagnostics at point-of-care level. The plasmofluidic PCR chip comprises glass nanopillar arrays with Au nanoislands and gas-permeable microfluidic channels, which contain reaction microchamber arrays, a precharged vacuum cell, and a vapor barrier. The on-chip configuration allows both spontaneous sample loading and microbubble-free PCR reaction during which the plasmonic nanopillar arrays result in ultrafast photothermal cycling. After rapid sample loading less than 3 min, two-step PCR results for 40 cycles show rapid amplification in 264 s for lambda-DNA, and 306 s for plasmids expressing SARS-CoV-2 envelope protein. In addition, the in situ cyclic real-time quantification of amplicons clearly demonstrates the amplification efficiencies of more than 91%. This PCR platform can provide rapid point-of-care molecular diagnostics in helping slow the fast-spreading pandemic.

Evaluation and application of an efficient plant DNA extraction protocol for laboratory and field testing.

Nucleic acids in plant tissue lysates can be captured quickly by a cellulose filter paper and prepared for amplification after a quick purification. In this study, a published filter paper strip method was modified by sticking the filter paper on a polyvinyl chloride resin (PVC) sheet. This modified method is named EZ-D, for EASY DNA extraction. Compared with the original cetyl trimethylammonium bromide (CTAB) method, DNA extracted by EZ-D is more efficient in polymerase chain reaction (PCR) amplification due to the more stable performance of the EZ-D stick. The EZ-D method is also faster, easier, and cheaper. PCR analyses showed that DNA extracted from several types of plant tissues by EZ-D was appropriate for specific identification of biological samples. A regular PCR reaction can detect the EZ-D-extracted DNA template at concentration as low as 0.1 ng/μL. Evaluation of the EZ-D showed that DNA extracts could be successfully amplified by PCR reaction for DNA fragments up to 3000 bp in length and up to 80% in GC content. EZ-D was successfully used for DNA extraction from a variety of plant species and plant tissues. Moreover, when EZ-D was combined with the loop-mediated isothermal amplification (LAMP) method, DNA identification of biological samples could be achieved without the need for specialized equipment. As an optimized DNA purification method, EZ-D shows great advantages in application and can be used widely in laboratories where equipment is limited and rapid results are required.

Fluorescent-dependent comparative Ct method for qPCR gene expression analysis in IVF clinical pre-implantation embryonic testing.

The use of quantitative PCR (qPCR) and other polymerase chain reaction (PCR)-based methods in the field of human in vitro fertilization blastocoel fluid analysis can potentially be utilized for assisting clinicians in embryo selection based on specific gene expression patterns. Since typical Comparative cycle threshold (Ct) analysis utilizes one threshold for runs per gene target and requires an inherent control group, this method is inadequate for analysis of small stochastic systems, such as embryonic-derived fluid. We mathematically demonstrate analytical modifications upon the Comparative Ct qPCR workflow to incorporate a variable fluorescence threshold (utilizing only the parameters defined in the Comparative Ct method), and subsequently demonstrate the typical workflow in which this modified method can successfully quantifiably analyze embryonic blastocoel fluid qPCR analysis.

Ammonium sulfate improves sensitivity and avoids false negatives of polymerase chain reaction (PCR) for scale drop disease virus (SDDV) detection

Accuracy is crucial for polymerase chain reaction (PCR) diagnostic laboratories. We noticed inconsistent PCR results or false negatives that sometimes occurred when changing commercial brand of Taq DNA polymerase enzyme. Here, we tested 6 primer sets specific for 3 important aquaculture viruses (scale drop disease virus (SDDV), tilapia lake virus (TiLV), and white spot syndrome virus (WSSV)) using 7 brands of Taq DNA polymerase enzymes (RBC Bioscience, Invitrogen, PCRBiosystems, Bio-Helix, biotechrabbit, GeneAll, and New England BioLabs) with their original reaction buffers. False negative detection and variation in sensitivity of 10–1000 times were observed. Interestingly, only enzymes from RBC Bioscience and Invitrogen could amplify SDDV 252 bp products, while 5 other brands failed to do so. The use of reaction buffer from RBC Bioscience with Taq polymerase enzymes from other brands resulted in improvement of detection sensitivity and avoided false negatives. Comparison of ingredients of the 7 reaction buffers indicated that bovine serum albumin (BSA) and ammonium sulfate were present in the RBC Bioscience buffer but absent or not specified in 6 other brands. Subsequently, we found that adding ammonium sulfate to the original buffers of the 4 selected brands improved detection efficiency for most test reactions, while adding BSA alone or BSA plus ammonium sulfate showed no or little improvement. When tested with serial dilutions of DNA extracted from 2 SDDV-infected fish, adding ammonium sulfate into the original buffer of biotechrabbit brand could improve detection sensitivity 100 times, equal to the result of RBC Bioscience kit. We thus recommend that PCR reaction buffer with ammonium sulfate (10 mM) added might improve detection sensitivity and avoid false negative results in PCR detection assays.

PREVALENCE OF SALMONELLA SPECIES, CLOSTRIDIUM PERFRINGENS, AND CLOSTRIDIUM DIFFICILE IN THE FECES OF HEALTHY ELEPHANTS (LOXODONTA SPECIES AND ELEPHAS MAXIMUS) IN EUROPE.

Pathogenic Salmonella spp., Clostridium perfringens, and Clostridium difficile have been reported to infect and cause severe enteritis and enterotoxemia in African (Loxodonta spp.) and Asian elephants (Elephas maximus). However, little information exists on whether healthy elephants carry and possibly shed these gastrointestinal organisms. This study was conducted to investigate the prevalence of all three bacteria in feces from healthy elephants in European zoos. Bacterial identification was performed by selective culture on fecal samples and a polymerase chain reaction (PCR) amplification protocol, on the basis of primers targeting the hilA gene (Salmonella spp.), the cpa gene (C. perfringens), and the tpi gene (C. difficile) from deoxyribonucleic acid extracted from elephant feces. The PCR protocol was validated prior to initiation of the investigation. Fecal samples collected from 50 African and 86 Asian elephants originating from 30 European zoologic institutions were investigated. The PCR validation revealed detection limits ranging from 104 to 106 colony-forming units per gram of feces of each gene. Only C. perfringens (one type A and two type E) was detected in the initial sampling (2.2%, three Asian elephants), whereas no Salmonella spp. or C. difficile was detected. At a follow-up sampling from C. perfringens-positive animals and relatives, 2 mo after the initial sampling, three animals were culture positive for Salmonella enterica spp. enterica. All positive samples were obtained with bacterial culture, whereas no PCR reactions were positive. Despite carrying these pathogens, all culture-positive animals were clinically healthy and did not develop signs of gastrointestinal disease during the study period. The findings indicate that prevalence of Salmonella spp., C. perfringens, and C. difficile in feces from healthy Asian and African elephants in Europe is very low.

A new Trypanosoma cruzi genotyping method enables high resolution evolutionary analyses.

BACKGROUNDTrypanosoma cruzi is an important human pathogen in Latin America with nearly seven million people infected. It has a large degree of genetic diversity, classified into six discrete typing units (DTUs), which probably influences its physiological behavior and clinical manifestations. Several genotyping methods are available, with distinct performance on easiness, cost, resolution and applicability; no method excels in all parameters.OBJECTIVES AND METHODS To devise a molecular method for T. cruzi genotyping, based on polymerase chain reaction (PCR) amplification of a single target with multiple copies in the nuclear genome by large scale sequencing. We have applied this method to 29 T. cruzi isolates, comprising all described DTUs.FINDINGS We were able to classify all samples into sub DTU level with high robustness. Evolutionary relationship between DTUs were ascertained, suggesting that TcIII and TcIV DTUs are non-hybrid, and DTU IV is more similar to the common ancestral.CONCLUSION As the TS-LSS method is based on a single PCR reaction, comprising several copies of the target, it is probably useful for clinical samples, when the amount of DNA is a limiting factor. As large scale sequencing systems become more common, the TS-LSS method can be increasingly applied for T. cruzi genotyping.

Clinical significance of laboratory diagnostics of coxyellosis in children.

The urgency of the problem of coxyellosis in children is determined by the endemic nature of this pathology for a number of regions of Russia. The purpose of the study: to evaluate the results of diagnosis of coxyellosis in children using the methods of complement binding reaction (RSC), enzyme immunoassay (ELISA), and polymerase chain reaction (PCR). Retrospective analysis of the survey on Coxiella in 3 groups of children aged 7 to 17 years: group 1 (n=30) method RSK; group 2 (n=34) - by ELISA; group 3 (n=35) - PCR, were hospitalized in GBUZ «Regional clinical infectious hospital named. A. M. Nicholi» Astrakhan in the period from January 2010 to January 2020. The most informative methods of diagnosis of coxyellosis in children during the first 7 days from the onset of the disease is the PCR reaction (specificity-94%, sensitivity-91%), after the 7th day of the disease ELISA (specificity -91%, sensitivity - 94%).The sensitivity of the RSC method is 70%, the specificity is 87%.