Bacteriological evaluation and advanced SYBR-green multiplex real-time PCR assay for detection of minced meat adulteration

Background

Minced meat is a valuable source of nutrients, but it is vulnerable to contamination by microorganisms commonly present in the environment. In addition, there is a risk of adulteration with cheaper meat sources, which can be harmful to consumers.

Aim

It is crucial to identify meat adulteration with distinct microbiological analysis for legal, economic, religious, and public health purposes.

Methods

A total of 100 minced meat samples were collected from several markets in Sharkia Governorate, Egypt. These samples were then subjected to bacteriological testing and an advanced multiplex PCR method. This method enables the detection of bovine, equine, porcine, and dog species in meat samples with just one step.

Results

The adulterated samples had a higher total bacterial count and pH values compared to pure bovine meat. These differences in bacterial count and pH values were statistically significant, with p-values of 0.843 (log10) and 0.233, respectively. The frequency of Escherichia coli occurrence was 13%, and the O111 serotype was predominant in the adulterated samples. Listeria monocytogenes and Staphylococcus aureus were isolated with prevalence rates of 3% and 29%, respectively. Besides, the SYBR-green multiplex real-time PCR assay used in this study detected adulteration with dog, equine, and porcine meats in the examined samples at rates of 9%, 5%, and 4%, respectively.

Conclusion

This method provides a sensitive and specific approach to detect issues related to well-being and safety.

Real-life impact of respiratory panel PCR assay on antibiotic prescription in geriatric acute care in the pre-COVID-19 era

OBJECTIVES

In this era of bacterial resistance, avoiding inappropriate use of antibiotic treatments is of major importance. Respiratory tract infections are frequent among older patients, and differentiating viral from bacterial infections is a challenge. The aim of our study was to evaluate the impact of recently available respiratory PCR testing on antimicrobial prescription in geriatric acute care.

METHODS

We performed a retrospective study, including all hospitalized geriatric patients who had had multiplex respiratory PCR testing prescribed from 1st October 2018 to 30th September 2019. The PCR test comprised a respiratory viral panel (RVP) and a respiratory bacterial panel (RBP). PCR testing could be prescribed at any time during hospitalization by geriatricians. Our primary endpoint was antibiotic prescription after viral multiplex PCR testing results.

RESULTS

All in all, 193 patients were included, 88 (45.6%) of whom had positive RVP, while none had positive RBP. Patients with positive RVP had significantly fewer antibiotic prescriptions following test results than patients with negative RVP (odds ratio (OR) 0.41, 95% confidence interval (CI) 0.22-0.77; p = 0.004). Among positive-RVP patients, factors associated with antibiotic continuation were presence of radiological infiltrate (OR 12.02, 95%CI 3.07-30.29), and detected Respiratory Syncytial Virus (OR 7.54, 95%CI 1.74-32.65). That said, discontinuation of antibiotic treatment seems safe.

CONCLUSION

In this population, the impact of viral detection by respiratory multiplex PCR on antibiotic therapy was low. It could be optimized by means of clearly formulated local guidelines, qualified staff and specific training by infectious disease specialists. Cost-effectiveness studies are necessary.

Development and intralaboratory validation of three Arcidae species using a multiplex polymerase chain reaction assay combined with capillary electrophoresis

Recently, various commercial ark shell products were being sold, and in the case of processed foods, the loss of morphological traits makes species identification visually challenging, which can lead to seafood fraud. Therefore, a multiplex polymerase chain reaction (PCR) assay was developed to simultaneously identify three ark shells. The specific PCR amplicon sizes of the generated species-specific primer pairs were observed to be 99 bp for Anadara kagoshimensis, 148 bp for Anadara broughtonii, and 207 bp for Tegillarca granosa. Specificity was confirmed for 17 fish and shellfish, and only the target was amplified without cross-reactivity. The detection limit for the multiplex PCR assay was 1 pg. Furthermore, 31 commercial products were evaluated to assess the developed assay's applicability. Therefore, the analytical approach used in this study can rapidly and accurately identify ark shells in commercial food, and may be used as an authentication tool in the seafood industry.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01269-2.

[First report of invasive Pomacea snails in Shandong Province]

OBJECTIVE

To characterize the species of invasive Pomacea snails that were discovered for the first time in Shandong Province.

METHODS

Pomacea snails samples were collected in the field of Jining City, Shandong Province on October 2021 for morphological identification. Pomacea snails were randomly sampled and genomic DNA was extracted from foot muscle tissues of Pomacea snails for multiplex PCR amplification. The PCR amplification product was sequenced. Then, the sequence was aligned and a phylogenetic tree was created using the software MegAlign 7.1.0. In addition, Angiostongylus cantonensis infection was detected in Pomacea snails with the lung microscopy.

RESULTS

A total of 104 living Pomacea snails were collected, and all were characterized as Pomacea spp. based on morphological features. Of 12 randomly selected adult Pomacea snails, multiplex PCR assay and sequencing identified eleven snails as P. canaliculata and one as P. maculata. No A. cantonensis infection was detected in 104 Pomacea snails.

CONCLUSIONS

This is the first report of invasive Pomacea snails in Shandong Province, where P. canaliculata and P. maculata are found.

A Multicenter Study of Viral Aetiology of Community-Acquired Pneumonia in Hospitalized Children in Chinese Mainland

Community-acquired pneumonia (CAP) is one of the leading causes of morbidity and mortality in children worldwide. In this study, we aimed to describe the aetiology of viral infection of pediatric CAP in Chinese mainland. During November 2014 to June 2016, the prospective study was conducted in 13 hospitals. The hospitalized children under 18 years old who met the criteria for CAP were enrolled. The throat swabs or nasopharyngeal aspirates (NPAs) were collected which were then screened 18 respiratory viruses using multiplex PCR assay. Viral pathogens were present in 56.6% (1539/2721) of the enrolled cases, with the detection rate of single virus in 39.8% of the cases and multiple viruses in 16.8% of the cases. The most frequently detected virus was respiratory syncytial virus (RSV) (15.2%, 414/2721). The highest detection rate of virus was in < 6-month-age group (70.7%, 292/413). RSV, human metapneumovirus (HMPV), human parainfluenza viruses (HPIVs) and influenza B virus (Flu B) showed the similar prevalence patterns both in north and south China, but HPIVs, Flu A, human bocavirus (HBoV), human adenovirus (HAdV) and human coronaviruses (HCoVs) showed the distinct circulating patterns in north and south China. Human enterovirus/human rhinovirus (HEV/HRV) (27.6%, 27/98), HBoV (18.4%, 18/98), RSV (16.3%, 16/98) and HMPV (14.3%, 14/98) were the most commonly detected viruses in severe pneumonia cases with single virus infection. In conclusion, viral pathogens are frequently detected in pediatric CAP cases and may therefore play a vital role in the aetiology of CAP. RSV was the most important virus in hospitalized children with CAP in Chinese mainland.

Developmental validation study of a 32-plex STR direct amplification system for forensic reference samples

The STRtyper-32G PCR Amplification Kit is a 6-dye multiplex system that combines the 30 autosomal STR loci with an Indel site (Y_Indel) and the sex-determinant locus Amelogenin. In addition to more loci, Master Mix has been optimized to amplify DNA on different substrates. The autosomal STR loci contained in this novel system meet the compatibility of requirements for databasing. In this study, the developmental validation study of the STRtyper-32G Kit followed the guidelines of SWGDAM (Scientific Working Group on DNA Analysis Methods), including PCR-based studies, species specificity, inhibitors, sensitivity, precision, repeatability, stutter, DNA mixtures, concordance studies, and population genetics studies. The validation results indicate that the new multiplex system is a robust tool for forensic database applications.

A multiplex PCR assay for six Aedini species, including Aedes albopictus

Background

Mosquitoes, as vectors of various human pathogens, are significant drivers of serious human illness. In particular, those species in the Aedini tribe, which typically transmit dengue virus, Chikungunya fever virus, and Zika virus, are increasing their range because of climate change and international commerce. In order to evaluate the risk of disease transmission, accurate mosquito species identification and monitoring are needed. The goal of this work was to develop a rapid and simple molecular diagnostic method for six morphologically similar Aedini species (Aedes flavopictus, Aedes albopictus, Ochlerotatus koreicus, Ochlerotatus japonicus, Ochlerotatus togoi and Ochlerotatus hatorii) in Korea.

Methods

A total of 109 samples were assayed in this study. The internal transcribed spacer 2 (ITS2) regions from all six species were amplified, sequenced and analyzed using Mega 6. Following the identification of regions that were consistently different in terms of sequence between all six species, multiplex primers were designed to amplify these regions to generate species-specific fragments distinguishable by their size.

Results

Uniquely sized fragments were generated in Ae. flavopictus (495 bp), Ae. albopictus (438 bp), Oc. koreicus (361 bp), Oc. togoi (283 bp), Oc. hatorii (220 bp) and Oc. japonicus (160 bp). Pairwise distance analysis showed that the difference was 35.0 ± 1.5% between Aedes spp. and Ochlerotatus spp., 17.4 ± 0.2% between Ae. albopictus and Ae. flavopictus and 11.1 ± 0.3% between Oc. koreicus and Oc. japonicus.

Conclusions

In this study, a multiplex PCR assay for six species of the Aedini tribe was developed. This assay is more accurate than morphological identification and will be useful for monitoring and controlling these vector mosquitoes.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04871-7.

Multiplex PCR assay for the identification of eight Anopheles species belonging to the Hyrcanus, Barbirostris and Lindesayi groups

BACKGROUND

Genus Anopheles mosquitoes are the primary vectors of human malaria, which is a serious threat to public health worldwide. To reduce the spread of malaria and identify the malaria infection rates in mosquitoes, accurate species identification is needed. Malaria re-emerged in 1993 in the Republic of Korea (ROK), with numbers peaking in 2004 before decreasing to current levels. Eight Anopheles species (Anopheles sinensis, Anopheles pullus, Anopheles belenrae, Anopheles lesteri, Anopheles kleini, Anopheles sineroides, Anopheles koreicus, Anopheles lindesayi) are distributed throughout Korea. Members of the Anopheles Hyrcanus group currently cannot be identified morphologically. The other species of Anopheles can be identified morphologically, except when specimens are damaged in traps. The purpose of this study was to develop a rapid and accurate method for simultaneous molecular identification of the eight Anopheles species present in the ROK.

METHODS

Anopheles spp. used in this study were collected near/in the demilitarized zone in ROK, where most malaria cases are reported. DNA from 165 of the Anopheles specimens was used to develop a multiplex PCR assay. The internal transcribed spacer 2 (ITS2) region of each species was sequenced and analysed for molecular identification.

RESULTS

DNA from a total of 165 Anopheles specimens was identified to species using a multiplex diagnostic system. These included: 20 An. sinensis, 21 An. koreicus, 17 An. lindesayi, 25 An. kleini, 11 An. lesteri, 22 An. sineroides, 23 An. belenrae, and 26 An. pullus. Each species was clearly distinguished by electrophoresis as follows: 1,112 bp for An. sinensis; 925 bp for An. koreicus; 650 bp for An. lindesayi; 527 bp for An. kleini; 436 bp for An. lesteri; 315 bp for An. sineroides; 260 bp for An. belenrae; and, 157 bp for An. pullus.

CONCLUSION

A multiplex PCR assay was developed to identify Anopheles spp. distributed in ROK. This method can be used to accurately identify Anopheles species that are difficult to identify morphologically to determine species distributions and malaria infection rates.

Development and validation of a forensic six-dye multiplex assay with 29 STR loci

This paper describes the development and validation of a novel 31-locus, six-dye STR multiplex system, which is designed to meet the needs of the rapidly growing Chinese forensic database. This new assay combines 20 extended-CODIS core loci (D3S1358, D5S818, TPOX, CSF1PO, TH01, vWA, D7S820, D21S11, D8S1179, D18S51, D16S539, D13S317, FGA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045), nine highly polymorphic loci in Chinese Han population (D3S3045, D6S1043, D6S477, D8S1132, D10S1435, D15S659, D19S253, Penta D, and Penta E), and two gender determining markers, amelogenin and Y-Indel, which could amplify DNA from extracts, as well as direct amplification from substrates. To demonstrate the suitability for forensic applications, this system was validated by precision and accuracy evaluation, concordance tests, case sample tests, sensitivity, species specificity, stability, stutter calculation, and DNA mixtures, according to the guidelines described by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and regulations published by the China Ministry of Public Security. The validation results indicate the robustness and reliability of this new system, and it could be a potentially helpful tool for human identification and paternity testing in the Chinese population, as well as facilitating global forensic DNA data sharing.

Developmental validation of VeriFiler™ Plus PCR Amplification Kit: A 6-dye multiplex assay designed for casework samples

The VeriFiler™ Plus PCR Amplification Kit is a 6-dye multiplex assay that simultaneously amplifies a set of 23 autosomal markers (D3S1358, vWA, D16S539, CSF1PO, D6S1043, D8S1179, D21S11, D18S51, D5S818, D2S441, D19S433, FGA, D10S1248, D22S1045, D1S1656, D13S317, D7S820, Penta E, Penta D, TH01, D12S391, D2S1338, and TPOX), a quality indicator system, and two sex-identification markers. Combined, the markers satisfy the requirements of the Chinese National autosomal DNA database as well as expanded CODIS (Combined DNA Index System). The VeriFiler Plus kit was developed with an improved Master Mix which incorporates the brighter TED™ dye, and accommodates a higher sample loading volume thus allowing for increased sensitivity and enabling maximum information recovery from challenging casework samples including touch, degraded, and inhibited samples. Here, we report the results of the developmental validation study which followed the SWGDAM (Scientific Working Group on DNA Analysis Methods) guidelines and includes data for PCR-based studies, sensitivity, species specificity, stability, precision, reproducibility and repeatability, concordance, stutter, DNA mixtures, and performance on mock casework samples. The results validate the multiplex design as well as demonstrate the kit's robustness, reliability, and suitability as an assay for human identification with casework DNA samples.

End Point Multiplex PCR for Diagnosis of Haemoprotozoan Diseases in Cattle

BACKGROUND

Theileriosis, trypanosomosis and babesiosis are the three major haemoprotozoan diseases causing huge economic losses worldwide. Difficulty in diagnosis of these diseases lies with the detection of carrier state with low parasitemia and concurrent infection.

PURPOSE

The present study was conducted to standardize and evaluate multiplex PCR assay for specific, fast and simultaneous detection of Theileria annulata, Trypanosoma evansi and Babesia bovis in bovines.

METHODS

Positive parasitic DNA was obtained from microscopically positive samples. Simplex PCR assay was developed targeting repetitive nucleotide sequences for Trypanosoma evansi and gene coding enzyme carbamoyl phosphate synthetase II for Babesia bovis. For theileriosis conditions already standardized targeting cytochrome b gene was used. Gradient PCR assay was used to determine common amplification conditions and develop multiplex PCR assay. Limit of detection was determined using tenfold serial dilution of parasitic DNA. Blood samples collected from 117 bovines suspected for haemoparasite infection was tested by simplex and multiplex PCR assay.

RESULTS

Simplex PCR assay was able to detect Theileria annulata, Trypanosoma evansi and Babesia bovis at dilution 10^-9, 10^-8 and 10^-8 which corresponds to copy number 1, 10 and 10, respectively, whereas of multiplex PCR assay was found to be 10^-7 dilution corresponding to 100 copy number. PCR products bands obtained in multiplex PCR assay at 257, 312 and 446 bp were easily distinguishable. Results of simplex PCR assay for detection of individual parasites revealed 48 (41.02%), 27 (23.07%) and 5 (4.27%) samples positive for T. annulata, T. evansi and B. bovis, respectively. Sixty-three (53.8%) samples were found positive by multiplex PCR assay with 15 samples (23.8%) showing mixed infection.

CONCLUSION

Multiplex PCR assay was found to be highly specific and can be used for easy, early, sensitive, specific and simultaneous diagnosis of haemoprotozoan diseases in epidemiological survey as a robust tool.

Development and application of multiplex PCR assay for the simultaneous detection of Babesia vogeli, Ehrlichia canis and Hepatozoon canis in dogs

A multiplex PCR assay was standardized and evaluated to simultaneously detect the DNA of Babesia vogeli, Ehrlichia canis and Hepatozoon canis in dogs of selected districts of Punjab state, India. Amplicons of 602 bp, 380 bp and 306 bp corresponding to B. vogeli (18S rRNA gene), E. canis (VirB9 gene), and H. canis (18S rRNA gene) were obtained, without any non-specific amplification. The results of multiplex PCR assay were further compared with the corresponding singleplex PCR assay. The diagnostic sensitivity and specificity of multiplex PCR assay with respect to singleplex PCR assay in the detection of B. vogeli, E. canis and H. canis varied from 50% to 100% and 92.08% to 98.79%, respectively revealing "moderate" to "very good" agreement by kappa value statistics. Blood samples from 322 dogs collected from selected districts of Punjab state, India, when screened by microscopy revealed the prevalence of B. vogeli, E. canis and H. canis as 0.31%, 0.93% and 1.86%, respectively whereas with multiplex PCR assay the values were 0.93%, 10.24% and 4.65%, respectively, with concurrent infection of E. canis & H. canis (1.86%) and B. vogeli & E. canis (0.31%). The diagnostic sensitivity and specificity of multiplex PCR assay with respect to microscopy in the detection of B. vogeli, E. canis and H. canis varied from 69.15% to 100% and 85.11% to 92.33%, respectively revealing "fair" agreement by kappa value statistics and the data was statistically significant. The analytical sensitivity of multiplex PCR assay in the detection of B. vogeli, E. canis and H. canis was 100 pg, 10 pg and 0.1 pg, respectively, whereas the values for the singleplex counterpart were 0.1 pg, 0.01 pg and 0.01 pg. Furthermore, various risk factors viz. age, breed, sex, season and districts were non-significantly associated with the prevalence of these haemoparasites except for E. canis that revealed a significant association with districts by multiplex PCR assay. Therefore the multiplex PCR assay developed may be useful in identification of the aetiological agents of these diseases during their early phase, which may in turn be useful in development of better health care and appropriate treatment of suspected dogs, particularly in endemic regions.

Rapid identification of bloodstream bacterial and fungal pathogens and their antibiotic resistance determinants from positively flagged blood cultures using the BioFire FilmArray blood culture identification panel

BACKGROUND/PURPOSE

Rapid and accurate identification of pathogens and their antibiotic resistance directly from flagged blood cultures can aid clinicians in optimizing early antibiotic treatment and improve the clinical outcomes, especially in settings associated with high rates of bloodstream infection caused by vancomycin-resistant Enterococci (VRE) and carbapenem-resistant Enterobacteriaceae (CRE). We compared the results of the BioFire FilmArray Blood Culture Identification (BCID) panel with those of conventional methods for identifying the pathogens and their antibiotic susceptibility status.

METHODS

In total, 100 randomly selected positive blood cultures (BACTEC Plus Aerobic/F bottles or BACTEC Anaerobic Lytic/10 bottles) were analyzed. The pathogen detection efficiency of FilmArray BCID panel was compared with that of conventional method using MALDI-TOF MS system (Bruker MALDI Biotyper) and susceptibility testing by the Vitek 2 system. The sequencing analysis of antibiotic resistance genes was performed for discrepant results obtained from MALDI Biotyper and Vitek 2.

RESULTS

Among the 100 positively flagged blood cultures, 94% of FilmArray BCID panel results were consistent with the MALDI Biotyper results. All five VRE isolates positive for vanA/vanB genes, 10 of 12 Staphylococcus species positive for mecA gene, and only one Klebsiella pneumoniae isolate positive for K. pneumoniae carbapenemase gene (bla_KPC) detected in the FilmArray BCID panel were also concordant with results by the results by conventional susceptibility testing/molecular confirmation.

CONCLUSIONS

The FilmArray BCID panel results not only demonstrated good correlation with conventional blood culture identification and susceptibility results but also provided results rapidly, especially for the early detection of MRSA, VRE and bla_KPC-mediated CRE.

Development of a multiplex PCR assay for the simultaneous and rapid detection of six pathogenic bacteria in poultry

Escherichia coli, Pasteurella multocida, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella spp. and Staphylococcus aureus are six bacterial pathogens of avian. However, these pathogens may cause many similar pathological changes, resulting in clinical isolates that are difficult to quickly and simultaneously detect and identify. Here, a multiplex polymerase chain reaction (m-PCR) assay is reported to rapidly identify targets genes (phoA, KMT1, ureR, toxA, invA, and nuc) of these six pathogens in clinical samples. Six pairs of specific primers were designed. The optimal reaction conditions, specificity, and sensitivity of the m-PCR assay were investigated. The results showed that betaine remarkably improved amplification of the target genes. Specific test results showed that all six pathogens were detected by the proposed m-PCR protocol without cross-amplification with viruses or parasites. Sensitivity test results showed that the m-PCR system could amplify the six target genes from bacterial genomes or cultures with template amounts of 500 pg or 2.8-8.6 × 10³ colony forming units, respectively. Furthermore, the six bacterial pathogens isolated from the infected tissue samples were successfully identified. The proposed m-PCR assay is a useful tool to monitor and diagnose bacterial infection in birds with high specificity, sensitivity and throughput.

Usefulness of the FilmArray meningitis/encephalitis (M/E) panel for the diagnosis of infectious meningitis and encephalitis in Taiwan

BACKGROUND/PURPOSE

Early recognition of causative pathogens is critical for the appropriate management of central nervous system infection and improved outcomes. The BioFire^® FilmArray^® Meningitis/Encephalitis Panel (BioFire^® ME Panel, BioFire Diagnostics) is the first U.S. Food and Drug Administration (FDA)-approved multiplex PCR assay that allows the rapid detection of 14 pathogens, including bacteria (n = 6), viruses (n = 7), and fungi (n = 1), from cerebrospinal fluid (CSF). The performance of the panel is expected to be dependent on the epidemiology of M/E in different geographical regions.

METHODS

In this preliminary study, we used the BioFire^® ME Panel in 42 subjects who presented to the emergency department with symptoms of M/E in our hospital. The results were compared to conventional culture, antigen detection, PCR, and various laboratory findings.

RESULTS

The panel detected six positive samples, of which five were viral and one bacterial. We observed an overall agreement rate of 88% between the BioFire^® ME Panel results and the conventional methods. There were no false-positive findings, but five discordant results were observed for enterovirus, herpes simplex virus type 1, Escherichia coli, and Cryptococcus species.

CONCLUSIONS

The BioFire^® ME Panel performed equivalently to the traditional PCR methods for virus detection, and better than bacterial cultures. This revolutionary system represents a paradigm shift in the diagnosis of M/E and may aid in the rapid identification of community-acquired M/E. However, the usefulness of this tool is limited in regions with a high prevalence of infectious M/E caused by microorganisms not included in the panel.

[Application of multiplex PCR assay to study early multiple herpesviruses infection during HSCT]

目的

采用多重PCR方法分析造血干细胞移植（HSCT）患者多种疱疹病毒的感染状况，并探讨HSCT患者多种疱疹病毒感染与临床特征的相关性及其对移植并发症和预后的影响。

方法

以苏州大学附属第一医院血液科2017年2月至2017年8月行HSCT的90例患者为研究对象，收集预处理至移植后90 d内不同时间点的外周血标本共734份，Lab-Aid824核酸提取Mini试剂抽提DNA，应用多重PCR方法同时扩增8种人类疱疹病毒，分析多种疱疹病毒感染发生率及其与临床特征的相关性及对移植后并发症和预后的影响。

结果

至随访终点，中位随访时间为192（35~308）d。移植前疱疹病毒感染发生率为35.6%（32/90），其中1种疱疹病毒感染发生率为12.2%（11/90），多种病毒感染的发生率为23.3%（21/90）。移植后疱疹病毒感染发生率为77.8%（70/90），其中1种疱疹病毒感染发生率为20.0%（18/90），多种疱疹病毒感染的发生率为57.8%（52/90）。在多种疱疹病毒感染的患者中，2种病毒感染30例（57.7%），3种疱疹病毒感染18例（34.6%），不同时间点样本检测的4种疱疹病毒感染4例（7.7%）。移植后多种疱疹病毒感染中，HHV-6和HHV-7感染存在相关性（OR=13.880，Q=0.026），EBV和HHV-7感染也存在相关性（OR=0.093，Q=0.044）。25例患者移植后出现疱疹病毒感染相关临床表现，主要为出血性膀胱炎、间质性肺炎、肠炎、病毒性脑炎和不明原因发热。移植前HHV-1感染与年龄、HHV-2感染与发病时间、CMV感染与原发病为淋巴瘤具有一定的相关性。移植后EBV感染与HLA不全相合、供受者ABO血型不一致及Ⅱ~Ⅳ度急性GVHD呈正相关；多种疱疹病毒感染与HLA不全相合、非血缘供者及Ⅱ~Ⅳ度急性GVHD呈正相关。

结论

HSCT前后存在多种疱疹病毒感染，HLA不全相合、非血缘供者和Ⅱ~Ⅳ度急性GVHD与移植后多种疱疹病毒感染存在一定的相关性。

Multiplex PCR for the rapid detection of insulin-like growth factor in the Pacific oyster, Crassostrea gigas: a useful indicator for growth assessment

Insulin-like growth factor (IGF) expression plays a critical role in the endocrine regulation of proliferation, differentiation, and growth in shellfish as well as in fish. The Pacific oyster, Crassostrea gigas, is a significant aquaculture species that comprises a large percentage of the Korean shellfish industry; moreover, its growth is economically important in aquaculture. However, when measuring the growth rate in shellfish, the soft tissue weight is difficult to determine because of the shell weight. In the present study, we describe an indirect method of measuring the growth rate using multiplex polymerase chain reaction (PCR) and analyzing levels of molluscan insulin-related peptide (MIP), the acid labile subunit of the IGF-binding protein complex (IGFBP ALS), and insulin-related peptide receptor (CIR) in Pacific oysters. The predicted sizes of amplicons were 776, 537, 380, and 198 bp, and the detection limit of the annealing temperatures was confirmed to be 65 °C. The annual expression of MIP and IGFBP ALS in tissues reached high levels in the winter following the condition index (CI). MIP and IGFBP ALS in male gonads and CIR in female gonads were related to the CI. This newly improved multiplex PCR provides an indirect measure of the growth rate; thus, it can be used to rapidly assess the growth rate. In addition, this method can supplement traditional growth data from oyster farms.

Developmental validation of GlobalFiler™ PCR amplification kit: a 6-dye multiplex assay designed for amplification of casework samples

The GlobalFiler™ PCR Amplification Kit is a single multiplex assay that amplifies a set of 24 markers, which encompass the European Standard Set and CODIS (Combined DNA Index System) recommended composite set of loci. In addition to more loci and a 6-dye chemistry format, the Master Mix has been formulated to allow higher sample loading volume for trace DNA samples. The GlobalFiler™ Kit has been optimized to deliver high performance on casework samples, while also delivering fast thermal cycling, with an amplification time of approximately 80 min. Here, we report the results of the developmental validation study which followed the SWGDAM (Scientific Working Group on DNA Analysis Methods) guidelines and includes data for PCR-based studies, sensitivity, species specificity, stability, precision, reproducibility and repeatability, concordance, stutter, DNA mixtures, and performance on mock casework samples. The results validate the multiplex design as well as demonstrate the kit's robustness, reliability, and suitability as an assay for human identification with casework DNA samples.

Development of Strain-Specific Primers for Identification of Bifidobacterium bifidum BGN4

Bifidobacterium bifidum BGN4 (BGN4) has many proven beneficial effects, including antiallergy and anticancer properties. It has been commercialized and used in several probiotic products, and thus strain-specific identification of this strain is very valuable for further strain-dependent physiological study. For this purpose, we developed novel multiplex polymerase chain reaction (PCR) primer sets for strain-specific detection of BGN4 in commercial products and fecal samples of animal models. The primer set was tested on seven strains of B. bifidum and 75 strains of the other Bifidobacterium species. The BGN4-specific regions were derived using megaBLAST against genome sequences of various B. bifidum databases and four sets of primers were designed. As a result, only BGN4 produced four PCR products simultaneously whereas the other strains did not. The PCR detection limit using BGN4-specific primer sets was 2.8 × 10¹ CFU/ml of BGN4. Those primer sets also detected and identified BGN4 in the probiotic products containing BNG4 and fecal samples from a BGN4-fed animal model with high specificity. Our results indicate that the PCR assay from this study is an efficient tool for the simple, rapid, and reliable identification of BGN4, for which probiotic strains are known.

A simple and sensitive two-tube multiplex PCR assay for simultaneous detection of ten meat species

A sensitive and reliable technique for meat species identification is required to prevent food adulteration, particularly in meat production. This work developed an optimized multiplex PCR assay for simultaneous identification of five commonly consumed and five commonly banned meat species in meat products. We designed primers that specifically amplified mitochondrial ATPase subunit 8 gene regions of different lengths of bovine, ovine, swine, chicken, turkey, cat, dog, mouse and human DNAs. The developed multiplex PCR assay proved to be specific, sensitive down to 30pg DNA per reaction, reproducible and economical. It could be used with a variety of raw meats and processed food samples and is easily applicable in a routine laboratory analysis without specific sophisticated equipment.

Development of a multiplex PCR assay for rapid virulence factor profiling of extraintestinal pathogenic Escherichia coli isolated from cattle

Virulence factor (VF) profiling is important for the control of extraintestinal pathogenic Escherichia coli (ExPEC) infection because VF prevalence is highly variable. We analyzed the VF profile of ExPEC isolated from cattle in Yamagata prefecture, Japan, 2000-2015 and developed a rapid VF profiling method using a multiplex PCR assay.

Evaluation of a multiplex OnSpot Primer-Extension PCR assay in the diagnosis of sepsis

For evaluation of the Anagnostics Pathogens DNA xA (PxA) assay in the diagnosis of sepsis 58 blood specimens were tested in comparison with the LightCycler SeptiFast assay and blood culture as gold standard. The PxA assay had a lower sensitivity (0.63 vs. 0.8), but higher specificity (0.83 vs. 0.67) than SeptiFast.

Design of an improved multiplex PCR method for diagnosis of enterohaemoraghic E.coli and enteropathogic E.coli pathotypes

AIM

We aimed to develop a multiplex PCR assay for specific detection of EPEC and EHEC pathotypes based on specific marker genes.

BACKGROUND

About 2.5 million infant's morbidity in developing countries occurs by E.coli pathotypes because of diarrhea and intestinal diseases. The traditional phenotypic methods are time consuming and sometimes detection and differentiation of the pathotypes are not done easily. Multiplex PCR technology is used as a sensitive, specific and rapid molecular method for detection of various pathogens.

PATIENTS AND METHODS

PCR reactions were performed with primers which targeted the virulence genes selected for each category (stx 1 , stx 2 genes for EHEC and bfpA for EPEC). For preparation of a positive control, the PCR products were cloned in pTZ57R/T plasmid. The same PCR reactions were done but in presence of genomes of various negative control bacteria for evaluation of test specificity.

RESULTS

As expected, gel agarose electrophoresis of PCR products of the stx 1 , stx 2 and bfpA, showed 329bp, 586bp and459bp bands respectively. Result of amplification using negative control genomes as template was negative.

CONCLUSION

The multiplex PCR assay followed by capillary electrophoresis presented in the present paper provides a simple, reliable, and rapid procedure that in a single reaction identifies the four main pathotypes of E. coli. This assay will replace the previous molecular genetics methods used in our laboratory and work as an important supplement to the more time consuming phenotypic assays.