Multiplex Method Research Articles

Development of a 1-step multiplex PCR assay for the detection of S. Enteritidis, S. Pullorum, S. Typhimurium, and S. Infantis associated with poultry production

Salmonellosis in poultry is detrimental to the advancement of the breeding industry and poses hazards to human health. Approximately 2,600 Salmonella varieties exist, among which S. Enteritidis, S. Pullorum, S. Typhimurium, and S. Infantis are prevalent serotypes in the poultry industry in recent years. They can also infect humans by contaminating poultry eggs and meat. Therefore, identifying these serotypes is crucial for successful preventive and control interventions. The White-Kauffmann-Le Minor scheme is time-consuming and requires expensive reagents. Whole-genome sequencing (WGS) and other molecular biology techniques require skilled technical staff. In comparison, the polymerase chain reaction (PCR) is more accurate, rapid, and inexpensive, thus proving suitable for widespread application in the poultry industry. Here, we selected 4 specific primers: lygD, mdh, ipaJ, and SIN_02055, which correspond to detecting S. Enteritidis, S. Typhimurium, S. Pullorum, and S. Infantis, respectively. They were integrated into a 1-step multiplex PCR method. We optimized the PCR method by utilizing specificity test results to determine the optimal annealing temperature (57°C). The PCR method exhibited excellent sensitivity for genomic DNA and bacterial cultures. We used the developed method to determine 157 clinical Salmonella isolates from various stages of the poultry production chain. The results aligned with serotype data generated via WGS analysis, demonstrating the method's excellent accuracy. In conclusion, this study developed a 1-step multiplex PCR method that simultaneously identifies S. Enteritidis, S. Typhimurium, S. Pullorum, and S. Infantis, allowing routine mass detection in the grass-root poultry industry.

Rapid multiplex immunohistochemistry for characterizing tumor-immune microenvironment

Intratumoral immune profiles are related to prognosis and therapeutic efficacy, and could result in personalized treatments based on biomarkers. To develop a multiplex, quantitative, and rapid tissue evaluation method based on the clinically established standard immunohistochemistry (IHC), a 6-marker rapid multiplex IHC was developed based on our previously reported 14-marker multiplex IHC by reducing the number of labels and accelerating the staining procedure. First, fewer labels were required to identify the same immunological features linked to prognosis in 14-marker multiplex IHC analyses. The six selected markers showed a significant correlation with the 14 markers in the immune classification. Next, a rapid staining protocol was developed by optimizing the reaction temperature, chromogen, and washing time, allowing the completion of 6-marker analysis in 5 h and 49 min, as opposed to the several days required for conventional multiplex IHC. Validation of benign tonsil and head and neck cancer tissues revealed a significant correlation between rapid and conventional 6-makrer multiplex IHC in terms of staining intensities, densities of T cells, macrophages, lymphoid/myeloid immune cell ratios, and spatial profiles of intratumoral immune infiltrates. This method may enable quantitative assessment of the tumor-immune microenvironment on a clinically feasible time scale, which promotes the development of tissue biomarker-guided therapeutic strategies.

DNA testing for investigative purposes: search for the perpetrator’s DNA profile and kinship analysis = Badania DNA dla celów dochodzeniowo-śledczych – poszukiwania profilu DNA sprawcy i analiza pokrewieństwa

Almost 40 years have passed since Alec Jeffreys’ seminal publications on the use of repetitive DNA marker analysis for human identification. The analysis of STR markers using multiplex PCR methods that followed this discovery has become a standard test for human identification. These methods also have investigative value. They are useful in the search for an unknown perpetrator through mass DNA testing as well as through forensic DNA databases. Another breakthrough is the analysis of long-range relationships. The ability to establish long-range relationships has enabled investigators to find the perpetrator of a crime, even in the absence of investigative hypotheses, by analysing the genealogical links recorded in our genomes. Modern DNA analysis not only provides strong evidence to be presented in court, but can also provide useful investigative leads when the identity of the perpetrator is unknown to the authorities.

Establishment and Validation of a Multiplex PCR Detection System for the Identification of Six Common Edible Meat Components.

To establish a rapid, accurate, and sensitive multiplex PCR detection method for the simultaneous identification of the six common edible meats (beef, lamp, chicken, pork, goose, duck), and to evaluate its application value in meat adulteration identification. Based on complete mitochondrial genomic sequences of six species in the GenBank database, DNA sequences (cattle：16S rRNA; sheep：COX-1; chickens：Cytb; pig：COX-1; goose：NADH2; duck：16S rRNA) with intra-species conservation and inter-species specificity were screened, and species-specific primers were designed to construct a multiplex PCR detection system that can simultaneously detect the meat of six common species. The species specificity, sensitivity and reproducibility of the system were studied, and the simulated mixture sample detection was performed. This study successfully constructed a multiplex PCR detection system that can detect the meats of six common species simultaneously. The system was not effective in DNA amplification of non-target species. When the DNA template sizes were 0.062 5-2 ng/μL, the amplified products of all six species could be detected. The duck component was still detected when the mixing ratio of duck and beef was as low as 0.5%. This study constructs and establishes a multiplex PCR detection system with strong specificity, high sensitivity, and good reproducibility. It can accurately identify the components of animal origin in common edible meats and provide a simple and practical method for identifying adulteration of common edible meats and meat products in China.

Measuring Systems with Power Supply to the Transmitting Part from the Receiving Part

Abstract: In the article, the author presents the results of an analysis of the metrological parameters of optoelectronic measuring systems with power supply to the transmitting parts from the receiving parts through separate and combined channels for transmitting information and energy. It is shown that circuits with separate channels for transmitting information and energy do not deteriorate the metrological characteristics of the information-measuring measuring system and do not impose any restrictions on the structure of its transmitting part associated with its energy consumption. For circuits with combined channels, with phase or spectral channel multiplexing methods, due to the mutual influence of optical radiation transmitting energy and information on each other, a deterioration in the signal-to-noise ratio of the information-measuring part of the sensor occurs due to the effects of continuum generation and stimulated Raman scattering only in in case where the optical radiation power is significant. If the compaction of the channels is temporary, the mutual influence of the channels can be neglected.

Consensus Subspace Graph Regularization based on prior information for multiplex network clustering

Multiplex network clustering can identify the common cluster structure shared by all layers, which is of great significance for downstream research such as personalized recommendations of social relationships and the mining of social media communication behaviors. Traditional multiplex network clustering methods rely only on the topological structure and are suitable for networks with clear structures. However, real-world networks often suffer from sparse connectivity and noisy edges. In addition, the current methods based on prior information only use the obtained consensus prior information as a preprocessing method for multiplex networks, and do not fully utilize and integrate the prior information in the clustering process, resulting in a low accuracy. To solve the problem of insufficient utilization of prior information, we propose a Consensus Subspace Graph Regularization (CSGR) approach for multiplex network clustering, which integrates topological information with the consensus prior information of a network. We first construct the consensus prior matrix of a network by a non-overlapping greedy search method, which represents a subset of the network that consists of nodes with high edge density. Then we construct a graph regularization term, which encodes the consensus prior information, to optimize the generation of a joint low-dimensional representation within the consensus subspace for the entire multiplex network. Finally, we employ the consensus prior matrix to denoise each network layer, thereby yielding a precise low-dimensional representation of each layer for consensus subspace fusion. In addition, comprehensive experiments have demonstrated that CSGR improves the clustering accuracy of real-world networks by an average of 1.56%.

A multiplex one-step fluorescence quantitative differential diagnosis method for severe hand, foot and mouth disease caused by coxsackievirus A16

Hand foot and mouth disease (HFMD) is a common childhood infectious disease which is caused by human enterovirus. The objective of this study was to develop a rapid, sensitive, and accurate method for detecting severe HFMD caused by coxsackievirus A16 (CV-A16). A closed-tube sensitive multiplex one-step reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was applied to detect CV-A16 in the early stage of severe HFMD. This assay targeted the CV-A16 structure protein VP1 to distinguish CV-A16 from other coxsackieviruses The 5’UTR region of enteric viruses was used for detecting the enterovirus and ribonuclease P (RNaseP) was adopted as the internal reference gene. The multiplex MGB probe assay system was used to detect PCR amplicons with different fluorescence reporters in the same system. The limit of detection (LOD) of the RT-qPCR assay for the CV-A16 VP1 gene was 125.893 copies/μl, for the 5′ UTR was 50.1187 copies/μl and for the RNaseP gene was 158.49 copies/μl. Furthermore, specificity analysis showed that the multiplex RT-PCR had no cross-reactivity with the influenza virus, herpangina virus and SARS-COV-2. In correlation analysis, the sensitivity of the multiplex RT-qPCR assay for CV-A16 detection was 100 % (288/288) and the specificity of the multiplex RT-qPCR assay was 99.94 % (3395/3397). The overall agreement between the multiplex RT-qPCR and the results of clinical diagnosis was 99.95 % (3683/3685) and kappa value was 0.996 (p<0.001). The entire procedure, from specimen processing to result reporting, could be completed within 1.5 hours. The one-step multiplex RT-qPCR assay for detecting CV-A16 developed in this study is a good laboratory diagnostic tool for rapid and reliable distinguished detection of CV-A16, especially for severe HFMD patients at an early stage in the disease with low virus load of CV-A16.

Multiplex Imaging for Cell Phenotyping of Early Human Atherosclerosis.

Previous studies using animal models and cultured cells suggest that vascular smooth muscle cells (SMCs) and inflammatory cytokines are important players in atherogenesis. Validating these findings in human disease is critical to designing therapeutics that target these components. Multiplex imaging is a powerful tool for characterizing cell phenotypes and microenvironments using biobanked human tissue sections. However, this technology has not been applied to human atherosclerotic lesions and needs to first be customized and validated. For validation, we created an 8-plex imaging panel to distinguish foam cells from SMC and leukocyte origins on tissue sections of early human atherosclerotic lesions (n=9). The spatial distribution and characteristics of these foam cells were further analyzed to test the association between SMC phenotypes and inflammation. Consistent with previous reports using human lesions, multiplex imaging showed that foam cells of SMC origin outnumbered those of leukocyte origin and were enriched in the deep intima, where the lipids accumulate in early atherogenesis. This new technology also found that apoptosis or the expression of pro-inflammatory cytokines were not more associated with foam cells than with nonfoam cells in early human lesions. More CD68+ SMCs were present among SMCs that highly expressed interleukin-1β. Highly inflamed SMCs showed a trend of increased apoptosis, whereas leukocytes expressing similar levels of cytokines were enriched in regions of extracellular matrix remodeling. The multiplex imaging method can be applied to biobanked human tissue sections to enable proof-of-concept studies and validate theories based on animal models and cultured cells.

Molecular survey of certain protozoan agents that cause diarrhea in children in Sudan.

Diarrhea is a significant health problem in the Third World. Identification of the pathogen that causes diarrhea is vital for measures to prevent and control this disease. There are also very few reports of diarrhea in Sudan. Our study aimed to determine the Prevalence of specific protozoan pathogens ( Entamoeba histolytica, Cryptosporidium parvum., and Giardia spp) in children in Khartoum, Sudan. We conducted a cross-sectional survey among children under five years of age who were hospitalized with acute diarrhea between April and December 2014. Diarrheal stool samples were collected and E. histolytica, C. parvum, and Giardia spp were examined using multiplex real-time PCR. Four hundred and thirty-seven children with acute diarrheawere included in this study; the higher Prevalence of diarrhea was in the age less than ≤ 2 years old (403,92.2%). The male-to-female ratio in this study was 1:1.7. infection with intestinal parasite was found in 155 (35.5%) cases, and co-infection was detected in 16 (10.3%) cases. Giardia spp(18.8%) and C. parvum (15.8 %) were the most frequently identified parasites, followed by E. histolytica (0.9). The parasite infection rate was highest and lowest in the under 2-year-old group (92.3%) and the 2-4-year-old group (7.3%). The infection rate was higher in boys (67.1%) than in girls (32.9%). The incidence of protozoan infection was higher in the rainy season (August to December) (92.2%), corresponding with that in the dry Season (April to June). (7.8%). Our present study demonstrated the high prevalence of Giardia spp and C. parvum in children with diarrhea in the Khartoum region and the usefulness of the multiplex real-time method in disclosing pathogenic protozoal agents. Our result highlighted the necessity of developing intervention measurement and control strategies to deal with childhood parasitic diarrhea in this region.

Research on high-power and high-efficiency emission of crosswell electromagnetic logging

Crosswell electromagnetic (EM) logging has useful applications in oil, gas, and water monitoring as well as carbon sequestration estimation. Difficulties in the efficient propagation of EM waves through a steel casing inhibit crosswell EM logging at distances greater than 300 m. This study investigates whether high-power transmission and high-efficiency transmitting antennas can resolve the challenges of long-distance crosswell EM logging through steel casings. Theoretical analysis indicates that the emission moment should be at least 12,000 A·m2. By calculating the equivalent relative permeability and selecting the appropriate coil materials and magnetic cores, the maximum emission magnetic moment can create a high-power transmission. Based on series and parallel resonant circuits and the alternating current/direct current cable core multiplexing power supply method, the effective transmission bandwidth is broadened and the transmission efficiency increases by three times. The emission unit is fabricated and tested using single, double, and fiberglass casing. We observe that the crosswell EM technology performs better for nonmetal casing wells than that for metal casing wells. The amplitude and phase curves between two fiberglass casing wells in the range of 425 m are quite smooth. However, the receiving signals in the double-layer steel casing decrease to only a few tenths of the value in the fiberglass casing wells, highlighting the difficulty of long-distance EM wave transmission when using steel casings. Thus, studies on EM transmission through four or more layers of steel casings should be conducted in the future.

High-density polarization multiplexed holograms using azo-carbazole films for diverse applications

In this study, we have demonstrated diverse applications of high-density polarization multiplexed holograms in an azo-carbazole polymer film. We investigate three distinct multiplexing methods, namely i) hybrid polarization-angular multiplexing for high-density data storage, ii) hybrid spatial-polarization multiplexing for a dynamic display, and iii) hybrid polarization-depth multiplexing for depth selective 3D display. Up to 24 images were successfully recorded and then retrieved individually from a single hologram without any cross-talk, using the first multiplexing scheme. Similarly, by employing the second multiplexing scheme, six new images were composed (reconstructed) from a hologram recorded with elemental patterns. Finally, images that can be selectively reconstructed at different depths have been demonstrated using the third multiplexing scheme. In this paper, up to three data recordings at one position in the thin azo-carbazole polymer film are demonstrated for the first time to the best of our knowledge. Our findings underscore the suitability of azo-carbazole copolymer-based composite films for various applications, spanning data storage and display technologies.

Multiplex microarray PCR Unyvero BCU system to accelerate relevant antimicrobial treatment in polymicrobial bloodstream infection.

To evaluate the performance of a rapid multiplex microarray-based method (Unyvero BCU system, BCU) to identify microorganisms and detect antimicrobial resistance directly from positive blood culture (BC) bottles with polymicrobial growth, and to assess relevance of information provided for timely guidance of polymicrobial bloodstream infection treatment. Accuracy, time-to-actionable results and potential impact of BCU on antimicrobial treatment were compared with those of standard of care during a prospective study for the sample analysis (November 2017-November 2018) and a retrospective study for the clinical data analysis and the time-to-result analysis. The study was complemented with an experimental study, based on spiked blood cultures to assess the ability of the method to detect antimicrobial resistance genes. Sixty-five clinical polymicrobial BC samples (163 total microorganisms) and 30 simulated polymicrobial BC samples (60 strains) were included. BCU reported 84.6% samples as polymicrobial, correctly identified all the bacteria of the mix for 72.3% samples (47/65) and detected bacteria that were missed by the conventional culture for 13.8% samples. All identifications and antimicrobial resistances were accurately detected for 61.5% (40/65) samples. Limitations concerned the detection of anaerobes, enterococci and enterobacterial susceptibility to third generation cephalosporins. BCU results would have guided antimicrobial treatment for 50.8% of the cases (33/65) in a timely and relevant manner, had no impact for 27.7% (18/65) and been misleading for 18.5% (12/65). Despite some limitations, the Unyvero BCU system is a rapid and reliable method for polymicrobial BC sample analysis.

Comparison of ERIC carbapenem-resistant Enterobacteriaceae test, BD Phoenix CPO detect panel, and NG-test CARBA 5 for the detection of main carbapenemase types of carbapenem-resistant Enterobacterales

BackgroundThis study aimed to assess the performance of three commercial panels, the ERIC Carbapenem-Resistant Enterobacteriaceae Test (ERIC CRE test), the NG-Test CARBA 5 (NG CARBA 5), and the BD Phoenix CPO Detect Panel (CPO panel), for the detection of main types of carbapenemases among carbapenem-resistant Enterobacterales (CRE). MethodsWe collected 502 isolates of carbapenem-resistant Enterobacterales (CRE) demonstrating intermediate or resistant profiles to at least one carbapenem antibiotic (ertapenem, imipenem, meropenem, or doripenem). Carbapenemase genes and their specific types were identified through multiplex PCR and sequencing methods. Subsequently, the ERIC CRE test, CPO panel, and NG CARBA 5 assay were conducted on these isolates, and the results were compared with those obtained from multiplex PCR. ResultsThe results indicated that the ERIC CRE test exhibited an overall sensitivity and specificity of 98.1% and 93.6%, respectively, which were comparable to 99.1% and 90.6% for the NG CARBA 5. However, the CPO panel demonstrated a sensitivity of only 56.2% in identifying Ambler classes, exhibiting the poorest sensitivity for class A. Moreover, while the ERIC CRE test outperformed the NG CARBA 5 in identifying multi-gene isolates with multiple carbapenemase-encoding genes, the CPO panel failed to accurately classify these isolates. ConclusionsOur findings support the utilization of the ERIC CRE test as one of the methods for detecting carbapenemases in clinical laboratories. Nonetheless, further optimization is imperative for the CPO panel to enhance its accuracy in determining carbapenemase classification and address limitations in detecting multi-gene isolates.

Phenotypic and Genotypic Antibiotic Resistance Patterns of Clinical Shigella Isolates from Tehran, Iran

Background: The emergence of multidrug-resistant (MDR) Shigella is a health concern in both developed and developing countries. The indiscriminate use of antibiotics without considering resistance patterns has led to the emergence of resistant strains. Objectives: This study aimed to investigate the phenotypic and genotypic patterns of antibiotic resistance and virulence gene distribution in Shigella isolates from patients in Tehran, Iran. Methods: In this cross-sectional study, 60 Shigella isolates were collected from patients referred to Milad Hospital and Pasargad Laboratory in Tehran. The isolates were gathered over four months, from February 2023 to June 2023. After biochemical and genetic confirmation of the isolates, the disk diffusion method was employed to determine antibiotic resistance patterns. The distribution of beta-lactamase genes (blaCTX-M1, blaCTX-M2, blaCTX-M8, blaSHV, blaTEM, and blaOXA) and virulence genes (ial, virF, invE, sigA, and pic) was investigated in Shigella isolates using the multiplex PCR method. SPSS statistical software version 22 was used for data analysis. Results: Thirty-six percent of isolates were found to be MDR. The highest rate of resistance was against tetracycline (90%) and ampicillin (80%). The lowest resistance rate was against azithromycin (1.9%) and amikacin (7.1%). The blaCTX-M1 and blaCTX-M8 genes were more prevalent, detected in 38.3% and 50% of the isolates, respectively. However, the blaSHV and blaCTX-M2 genes were not detected in any of the isolates. Additionally, 32% of the MDR isolates harbored both the blaCTX-M1 and blaCTX-M8 genes simultaneously. The distribution of virulence genes ial, virF, invE, sigA, and pic in the studied isolates was 28.3%, 85%, 68.3%, 81.7%, and 15%, respectively. Conclusions: The present study emphasizes the increasing trend of MDR Shigella isolates. Therefore, serious measures are needed to prevent the spread of resistant genes. Furthermore, the detection of virulence factors could help in controlling shigellosis, which is a significant global health issue.

Molecular Characterization of Hepatitis B Virus among HIV Positive and HIV Negative Pregnant Antenatal Women in Federal Capital Territory Abuja Hospital

A significant contributor to chronic hepatitis, cirrhosis and hepatocellular carcinoma is the Hepatitis B Virus (HBV). Hepatitis B Virus (HBV) is a major cause of Chronic Hepatitis, cirrhosis and Hepatocellular Cancer (HCC). The incidence of HBV-related HCC cases is projected to increase for at least two decades due to the high prevalence of chronic HBV infection throughout the world. The overall aim of this study is to determine the sero-prevalence and molecular characterization of hepatitis B virus among HIV positive and HIV negative antenatal women attending Federal Capital Territory Abuja hospitals. A total number of 302 samples were collected from 302 participants between the ages of 18-55 years. The samples were screened for HIV, HBV, HBV serology markers, using rapid test kits, HBV Viral load and HBV genotyping was carried out using multiplex PCR method and data was analyzed using appropriate tools. Nine tested positive for HIV, 34 tested positive for HBV and 2 tested positive for both HIV and HBV, corresponding to 2.9 % (95% CI; 1.2 – 3.8) prevalence for HIV, 11.3% (95% CI; 8.7 – 13.6) for Hepatitis B and 0.7% for HIV/HBV co-infection. Age 25-35 years old had the highest prevalence of HBV 22(7.3%) followed by those of less than 25 years old 8(2.8%) and 1(0.7%) each for age range 36-45 years, 2(0.7%) and 46-55 years. HBeAb and HBcAb were expressed highest among subject within the age range of 25 – 35 year 14 (41.2%) and 22 (64.7 %,) participants respectively, followed by the age range of less than 25 years 5 (14.7%) and 8 (36.4%), for HBeAb and HBcAb respectively. There was no Hepatitis B envelop antigen (HBeAg) nor Hepatitis B surface antibody (HBsAb) among the study group. Of the 34 samples, 20 (62%) had undetectable viral load, while 14 (38%) had detectable viral load. Genotype E was three times more prevalent among those of 25 years old and above than those less than 25 years old detected (75% and 25%). However, genotype B/E mixed was more expressed (60% of cases) among those less than 25 years old, than those greater than 25 years of age (40%). There was no significant difference in the prevalence of genotype E and B/E serotype between HBV+/HIV-patients and their HBV+/HIV+ counterpart (P=0.08 and P=0.15, respectively). HBV Genotype E single infection viral load was significantly (P=0.01) more expressed among those 25 years of age and above than less than 25 years old (4,354,703 ± 346865 IU/ml versus 55.6 ±28.1 IU/ml). Mixed infection genotype B/E was significantly (P=0.04) more expressed among those less than 25 years of age than those 25 years old and above (730.9 ± 238 IU/ml versus IU/ml versus 91.1 ± 48 IU/ml). There was no significant difference between the mean of HBV Viral load HBV+/HIV- patients and their HBV+/HIV+ counterpart (T-test =0.009; P=0.92). In conclusion FCT is 11.3% prevalence rate of HBV and genotypes E and B/E are in circulation among pregnant women among the pregnant women attending antenatal clinic in FCT hospital in Abuja.

Establishment and application of multiplex PCR for rapid detection of three mink diarrhea-associated viruses

In this report, a multiplex PCR method was developed for the detection of three diarrhea-associated viruses in mink, including circovirus (MCV), bocavirus (MBoV), and enteritis virus (MEV). Three compatible sets of primers specific for each virus were designed respectively based on their conserved sequences. After optimization of the crucial factors such as primer concentration and annealing temperature in single and multiple amplification, three specific fragments were simultaneously amplified with the highest sensitivity and specificity in one PCR reaction. The fragments amplified were 259 bp (MCV)，455 bp (MBoV) and 671 bp (MEV). The sensibility of this one-step multiplex PCR is about 10 times lower than that of regular singleplex PCR. There were no cross-reactions with some relevant pathogens like mink coronavirus, canine distemper virus, and aleutian mink disease virus. In our study we analyzed viral DNA in mink fecal samples by multiplex PCR assay from China, which revealed the occurrence of MCV, MBoV, and MEV as 3.1 %, 5.7 %, and 9.8 %, respectively. The testing results of multiplex PCR agreed with the singleplex PCR results with a coincidence rate of 100 %. These results indicated that the method could provide technical support for rapid detection of the three diarrhea-associated viruses, and epidemiological investigation of mink viral diarrhea.

A novel multiplex fluorescent-labeling method for the visualization of mixed-species biofilms in vitro.

In nature, bacteria usually exist as mixed-species biofilms, where they engage in a range of synergistic and antagonistic interactions that increase their resistance to environmental challenges. Biofilms are a major cause of persistent infections, and dispersal from initial foci can cause new infections at distal sites thus warranting further investigation. Studies of development and spatial interactions in mixed-species biofilms can be challenging due to difficulties in identifying the different bacterial species in situ. Here, we apply CellTrace dyes to studies of biofilm bacteria and present a novel application for multiplex labeling, allowing identification of different bacteria in mixed-species, in vitro biofilm models. Oral bacteria labeled with CellTrace dyes (far red, yellow, violet, and CFSE [green]) were used to create single- and mixed-species biofilms, which were analyzed with confocal spinning disk microscopy (CSDM). Biofilm supernatants were studied with flow cytometry (FC). Both Gram-positive and Gram-negative bacteria were well labeled and CSDM revealed biofilms with clear morphology and stable staining for up to 4 days. Analysis of CellTrace labeled cells in supernatants using FC showed differences in the biofilm dispersal between bacterial species. Multiplexing with different colored dyes allowed visualization of spatial relationships between bacteria in mixed-species biofilms and relative coverage by the different species was revealed through segmentation of the CSDM images. This novel application, thus, offers a powerful tool for studying structure and composition of mixed-species biofilms in vitro.IMPORTANCEAlthough most chronic infections are caused by mixed-species biofilms, much of our knowledge still comes from planktonic cultures of single bacterial species. Studies of formation and development of mixed-species biofilms are, therefore, required. This work describes a method applicable to labeling of bacteria for in vitro studies of biofilm structure and dispersal. Critically, labeled bacteria can be multiplexed for identification of different species in mixed-species biofilms using confocal spinning disk microscopy, facilitating investigation of biofilm development and spatial interactions under different environmental conditions. The study is an important step in increasing the tools available for such complex and challenging studies.

Resurgence of common respiratory viruses in patients with community-acquired pneumonia (CAP)—A prospective multicenter study

BackgroundCommunity-acquired pneumonia (CAP) is a major global cause of death and hospitalization. Bacteria or community-acquired viruses (CARVs) cause CAP. COVID-19 associated restrictions effectively reduced the circulation of CARVs. ObjectivesThe aim of this study was to analyze the proportion of CARVs in adult patients with CAP from mid-2020 to mid-2023. Specifically, we aimed to compare the rate of influenza virus, SARS-CoV-2, and RSV detections in patients aged 18–59 years and ≥60 years. Study designWe analyze the proportion of 21 community-acquired respiratory viruses (CARVs) and three atypical bacteria (Bordetella pertussis, Legionella pneumophila, and Mycoplasma pneumoniae) in nasopharyngeal swab samples using molecular multiplex methods within the prospective, multicentre, multinational study of the German study Group CAPNETZ. We used stringent inclusion criteria throughout the study. ResultsWe identified CARVs in 364/1,388 (26.2 %) patients. In detail, we detected SARS-CoV-2 in 210/1,388 (15.1 %), rhino-/enterovirus in 64/1,388 (4.6 %), influenza virus in 23/1,388 (1.6 %) and RSV in 17/1,388 (1.2 %) of all patients. We detected RSV and influenza more frequently in patients ≥60 years, especially in 22/23 compared to the previous season. None of the atypical bacteria were detected. ConclusionsBeginning in 2023, we demonstrate a re-emergence of CARVs in CAP patients. Effective vaccines or specific antiviral therapies for more than two thirds of the detected viral infections are currently available. High detection rates of vaccine-preventable viruses in older age groups support targeted vaccination campaigns.

Молекулярные методы аутентификации молочного сырья в сыре: обзор

The modern dairy industry needs authentic raw milk in cheese production to provide high-quality product control and consumer protection. Unfortunately, unreliable cheese producers sometimes replace goat’s or sheep’s milk with cow’s milk. This process is associated with seasonality and the high cost of milk from small ruminants. The article reviews the methods molecular genetics used to detect milk adulteration in cheese making. It highlights the problems and prospects of applying molecular genetics to complex food matrices, such as cheese. Modern PCR methods prove quite efficient in identifying species-specific sequences by using mitochondrial DNA (mtDNA) as markers. Multiplex PCR, quantitative PCR (qPCR), and digital droplet PCR (ddPCR) have their advantages and shortcomings. The multiplex PCR method presupposes a simultaneous amplification of multiple DNA targets in a single tube while the qPCR method provides a quantitative profile. These methods make it possible to maintain high industry standards by ensuring the authenticity of cheeses and cheese products. In addition, molecular methods provide supply chain stability, increase consumer confidence, and advance dairy technology.

A multiplex method for the detection of food microorganisms based on suspension microarrays combined with recombinase-aided amplification

Foodborne diseases caused by foodborne pathogenic microorganisms have long been a severe public health problem. Timely and accurate detection of food-borne microorganisms can minimize their harm and enable the development of efficient control strategies. In this study, we establish a multiplex nucleic acid detection method based on recombinase-aided amplification reaction on a suspension microarray (referred to as SC-RAA) to identify and quantify microorganisms. The experimental results confirmed that this approach has an outstanding sensitivity, with a limit of detection (LOD) of 0.8 fM and a linear range of 0.8 fM–80 pM, spanning five orders of magnitude. Moreover, the prepared method also showed exquisite specificity, which the amplified signal can be detected only when the target nucleic acid is present. The recovery rate of the SC-RAA assay was 82.2%–113.4%, suggesting that the SC-RAA assay is performing well and accurately measuring the concentration of the substance in the sample. In addition, the consistency analysis showed that the results of the SC-RAA detection were also in good agreement with those of traditional qPCR detection (R2 > 0.95). These results highlight the potential of the SC-RAA assay to be applied as a multiplex and sensitive DNA detection platform for identifying and quantifying foodborne pathogenic microorganisms.