1
|
Fusco G, Cardillo L, Valvini O, Pucciarelli A, Picazio G, Cerrone A, Napoletano M, Pellicanò R, Ottaiano M, de Martinis C, De Falco F, Cutarelli A, Sannino E, Borriello G, Tittarelli M, Roperto S, De Carlo E. Detection and quantification of Brucella abortus DNA in water buffaloes ( bubalus bubalis) using droplet digital polymerase chain reaction. Vet Q 2024; 44:1-8. [PMID: 39148364 PMCID: PMC11328813 DOI: 10.1080/01652176.2024.2390944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 07/08/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024] Open
Abstract
Brucellosis represents a major public health concern worldwide. Human transmission is mainly due to the consumption of unpasteurized milk and dairy products of infected animals. The gold standard for the diagnosis of Brucella spp in ruminants is the bacterial isolation, but it is time-consuming. Polymerase Chain Reaction (PCR) is a quicker and more sensitive technique than bacterial culture. Droplet digital PCR (ddPCR) is a novel molecular assay showing high sensitivity in samples with low amount of DNA and lower susceptibility to amplification inhibitors. Present study aimed to develop a ddPCR protocol for the detection of Brucella abortus in buffalo tissue samples. The protocol was validated using proficiency test samples for Brucella spp by real time qPCR. Furthermore, 599 tissue samples were examined. Among reference materials, qPCR and ddPCR demonstrated same performance and were able to detect up to 225 CFU/mL. Among field samples, ddPCR showed higher sensitivity (100%), specificity and accuracy of 93.4% and 94.15%, respectively. ddPCR could be considered a promising technique to detect B. abortus in veterinary specimens, frequently characterized by low amount of bacteria, high diversity in matrices and species and poor storage conditions.
Collapse
Affiliation(s)
- Giovanna Fusco
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Lorena Cardillo
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Ornella Valvini
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Alessia Pucciarelli
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Gerardo Picazio
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Anna Cerrone
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Michele Napoletano
- Caserta Section, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Caserta, Italy
| | - Roberta Pellicanò
- Regional Observatory of Epidemiology and Biostatistic, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Maria Ottaiano
- Regional Observatory of Epidemiology and Biostatistic, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Claudio de Martinis
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Francesca De Falco
- Department of Veterinary Medicine and Animal Productions, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Anna Cutarelli
- Department of Food Inspection, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Emanuela Sannino
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Giorgia Borriello
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Manuela Tittarelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Campo Boario, Italy
| | - Sante Roperto
- Department of Veterinary Medicine and Animal Productions, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Esterina De Carlo
- National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Salerno, Italy
| |
Collapse
|
2
|
Dass M, Ghai M. Development of a multiplex PCR assay and quantification of microbial markers by ddPCR for identification of saliva and vaginal fluid. Forensic Sci Int 2024; 362:112147. [PMID: 39067179 DOI: 10.1016/j.forsciint.2024.112147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/11/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024]
Abstract
The identification of biological fluids at crime scenes contributes to crime scene reconstruction and provides investigative leads. Traditional methods for body fluid identification are limited in terms of sensitivity and are mostly presumptive. Emerging methods based on mRNA and DNA methylation require high quality template source. An exploitable characteristic of body fluids is their distinct microbial profiles allowing for the discrimination of body fluids based on microbiome content. Microbial DNA is highly abundant within the body, robust and stable and can persist in the environment long after human DNA has degraded. 16S rRNA sequencing is the gold standard for microbial analysis; however, NGS is costly, and requires intricate workflows and interpretation. Also, species level resolution is not always achievable. Based on the current challenges, the first objective of this study was to develop a multiplex conventional PCR assay to identify vaginal fluid and saliva by targeting species-specific 16S rRNA microbial markers. The second objective was to employ droplet digital PCR (ddPCR) as a novel approach to quantify bacterial species alone and in a mixture of body fluids. Lactobacillus crispatus and Streptococcus salivarius were selected because of high abundance within vaginal fluid and saliva respectively. While Fusobacterium nucleatum and Gardnerella vaginalis, though present in healthy humans, are also frequently found in oral and vaginal infections, respectively. The multiplex PCR assay detected L. crispatus and G. vaginalis in vaginal fluid while F. nucleatum and S. salivarius was detected in saliva. Multiplex PCR detected F. nucleatum, S. salivarius and L. crispatus in mixed body fluid samples while, G. vaginalis was undetected in mixtures containing vaginal fluid. For samples exposed at room temperature for 65 days, L. crispatus and G. vaginalis were detected in vaginal swabs while only S. salivarius was detected in saliva swabs. The limit of detection was 0.06 copies/µl for F. nucleatum (2.5 ×10-9 ng/µl) and S. salivarius (2.5 ×10-6 ng/µl). L. crispatus and G. vaginalis had detection limits of 0.16 copies/µl (2.5 ×10-4 ng/µl) and 0.48 copies/µl (2.5 ×10-7 ng/µl). All 4 bacterial species were detected in mixtures and aged samples by ddPCR. No significant differences were observed in quantity of bacterial markers in saliva and vaginal fluid. The present research reports for the first time the combination of the above four bacterial markers for the detection of saliva and vaginal fluid and highlights the sensitivity of ddPCR for bacterial quantification in pure and mixed body fluids.
Collapse
Affiliation(s)
- Mishka Dass
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal - Westville Campus, Private Bag X 54001, Durban, KwaZulu Natal, South Africa.
| | - Meenu Ghai
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal - Westville Campus, Private Bag X 54001, Durban, KwaZulu Natal, South Africa.
| |
Collapse
|
3
|
Li Y, Huang K, Yin J, Tan Z, Zhou M, Dai J, Yi B. Clinical evaluation of a multiplex droplet digital PCR for pathogen detection in critically ill COVID-19 patients with bloodstream infections. Infection 2024; 52:1027-1039. [PMID: 38127118 PMCID: PMC11143000 DOI: 10.1007/s15010-023-02157-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Nosocomial bloodstream infections (nBSI) have emerged as a clinical concern for physicians treating COVID-19 patients. In this study, we aimed to evaluate the effectiveness of a multiplex ddPCR in detecting bacterial pathogens in the blood of COVID-19 critically ill patients. METHODS This prospective diagnostic study included RT-PCR-confirmed COVID-19 patients admitted to our hospital from December 2022 to February 2023. A multiplex ddPCR assay was used to detect common bacterial pathogens and AMR genes in blood samples of the patients, along with antimicrobial susceptibility testing (AST). The diagnostic performance of the ddPCR assay was evaluated by comparing the results with those obtained through blood culture and clinical diagnosis. Additionally, the ability of ddPCR in detecting bacterial resistance was compared with the AST results. RESULTS Of the 200 blood samples collected from 184 patients, 45 (22.5%) were positive using blood culture, while 113 (56.5%) were positive for bacterial targets using the ddPCR assay. The ddPCR assay outperformed blood culture in pathogen detection rate, mixed infection detection rate, and fungal detection rate. Acinetobacter baumannii and Klebsiella pneumoniae were the most commonly detected pathogens in COVID-19 critically ill patients, followed by Enterococcus and Streptococcus. Compared to blood culture, ddPCR achieved a sensitivity of 75.5%, specificity of 51.0%, PPV of 30.9%, and NPV of 87.8%, respectively. However, there were significant differences in sensitivity among different bacterial species, where Gram-negative bacteria have the highest sensitivity of 90.3%. When evaluated on the ground of clinical diagnosis, the sensitivity, specificity, PPV and NPV of ddPCR were 78.1%, 90.5%, 94.7%, and 65.5%, respectively. In addition, the ddPCR assay detected 23 cases of blaKPC, which shown a better consistent with clinical test results than other detected AMR genes. Compared to blaKPC, there were few other AMR genes detected, indicating that the application of other AMR gene detection in the COVID-19 critically ill patients was limited. CONCLUSION The multiplex ddPCR assay had a significantly higher pathogen detection positivity than the blood culture, which could be an effective diagnostic tool for BSIs in COVID-19 patients and to improve patient outcomes and reduce the burden of sepsis on the healthcare system, though there is room for optimization of the panels used.- Adjusting the targets to include E. faecalis and E. faecium as well as Candida albicans and Candida glabrata could improve the ddPCR' s effectiveness. However, further research is needed to explore the potential of ddPCR in predicting bacterial resistance through AMR gene detection.
Collapse
Affiliation(s)
- Yanbing Li
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Kangkang Huang
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Jun Yin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Zheren Tan
- Intensive Care Unit, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Manli Zhou
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Jiaoyang Dai
- Department of Laboratory Medicine, Xiangya Medical School, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Bin Yi
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| |
Collapse
|
4
|
Khan S, Rathod P, Gupta VK, Khedekar PB, Chikhale RV. Evolution and Impact of Nucleic Acid Amplification Test (NAAT) for Diagnosis of Coronavirus Disease. Anal Chem 2024; 96:8124-8146. [PMID: 38687959 PMCID: PMC11112543 DOI: 10.1021/acs.analchem.3c05225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Sumbul
Fatma Khan
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Priyanka Rathod
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Vivek K. Gupta
- Department
of Biochemistry, National JALMA Institute
for Leprosy & Other Mycobacterial Diseases (ICMR), Agra -282004, India
| | - Pramod B. Khedekar
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Rupesh V. Chikhale
- UCL
School of Pharmacy, Department of Pharmaceutical and Biological Chemistry, University College London, London WC1N 1AX, United Kingdom
| |
Collapse
|
5
|
Pacini A, Paredes F, Heckel S, Ibarra G, Petreli MV, Perez M, Agnella Y, Piskulic L, Allasia MB, Caprile L, Colaneri A, Sesma J. Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR. Front Public Health 2024; 11:1340420. [PMID: 38298257 PMCID: PMC10829044 DOI: 10.3389/fpubh.2023.1340420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
Introduction The declaration of the end of the Public Health Emergency for COVID-19 on May 11th, 2023, has shifted the global focus led by WHO and CDC towards monitoring the evolution of SARS-CoV-2. Augmenting these international endeavors with local initiatives becomes crucial to not only track the emergence of new variants but also to understand their spread. We present a cost-effective digital PCR-based pooled sample testing methodology tailored for early variant surveillance. Methods Using 1200 retrospective SARS-CoV-2 positive samples, either negative or positive for Delta or Omicron, we assessed the sensitivity and specificity of our detection strategy employing commercial TaqMan variant probes in a 1:9 ratio of variant-positive to variant-negative samples. Results The study achieved 100% sensitivity and 99% specificity in 10-sample pools, with an Area Under the Curve (AUC) exceeding 0.998 in ROC curves, using distinct commercial TaqMan variant probes. Discussion The employment of two separate TaqMan probes for both Delta and Omicron establishes dual validation routes, emphasizing the method's robustness. Although we used known samples to model realistic emergence scenarios of the Delta and Omicron variants, our main objective is to demonstrate the versatility of this strategy to identify future variant appearances. The utilization of two divergent variants and distinct probes for each confirms the method's independence from specific variants and probes. This flexibility ensures it can be tailored to recognize any subsequent variant emergence, given the availability of its sequence and a specific probe. Consequently, our approach stands as a robust tool for tracking and managing any new variant outbreak, reinforcing our global readiness against possible future SARS-CoV-2 waves.
Collapse
Affiliation(s)
- Antonella Pacini
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
| | - Franco Paredes
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sofia Heckel
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guadalupe Ibarra
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maria Victoria Petreli
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Marilina Perez
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
| | - Yanina Agnella
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Veterinarias, Universidad Nacional de Rosario, Casilda, Argentina
| | - Laura Piskulic
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maria Belen Allasia
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luis Caprile
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
| | - Alejandro Colaneri
- Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Juliana Sesma
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| |
Collapse
|
6
|
Heinzelmann D, Lindner B, Renner B, Fischer S, Schulz P, Schmidt M. Droplet digital PCR: A comprehensive tool for genetic analysis and prediction of bispecific antibody assembly during cell line development. N Biotechnol 2023; 78:42-51. [PMID: 37797917 DOI: 10.1016/j.nbt.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/15/2023] [Accepted: 10/01/2023] [Indexed: 10/07/2023]
Abstract
Molecular biological methods have emerged as inevitable tools to accompany the process of cell line development for the generation of stable and highly productive manufacturing cell lines in the biopharmaceutical industry. PCR-based methods are especially useful for screening and characterization of cell lines due to their low cost, scalability, precision and propensity for multidimensional read-outs. In this study, the diverse applications of droplet digital PCR (ddPCR) as a molecular biological tool for cell line development are demonstrated. Specifically, it is shown that ddPCR can be used to enable precise, sensitive and reproducible absolute quantification of genomically integrated transgene copies during cell line development and cell bank characterization. Additionally, an amplitude multiplexing approach is applied to simultaneously run multiple assays on different genetic targets in a single reaction and advance clonal screening by measuring gene expression profiles to predict the assembly and homogeneity of difficult-to-express (DTE) proteins. The implementation of ddPCR-based assays during cell line development allows for early screening at a transcriptional level, particularly for complex, multidomain proteins, where balanced polypeptide chain ratios are of primary importance. Moreover, it is demonstrated that ddPCR-based genomic characterization improves the robustness, efficiency and comparability of absolute transgene copy number quantification, an essential genetic parameter that must be demonstrated to regulatory authorities during clinical trial and market authorization application submissions to support genetic stability and consistency of the selected cell substrate.
Collapse
Affiliation(s)
- Daniel Heinzelmann
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach, Germany.
| | - Benjamin Lindner
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach, Germany
| | - Benjamin Renner
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach, Germany
| | - Simon Fischer
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach, Germany
| | - Patrick Schulz
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach, Germany
| | - Moritz Schmidt
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach, Germany
| |
Collapse
|
7
|
Lamb CH, Kang B, Myhrvold C. Multiplexed CRISPR-based Methods for Pathogen Nucleic Acid Detection. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023; 27:100471. [PMID: 37398931 PMCID: PMC10310064 DOI: 10.1016/j.cobme.2023.100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Bacterial and viral pathogens are devastating to human health and well-being. In many regions, dozens of pathogen species and variants co-circulate. Thus, it is important to detect many different species and variants of pathogens in a given sample through multiplexed detection methods. CRISPR-based nucleic acid detection has shown to be a promising step towards an easy-to-use sensitive, specific, and high-throughput method to detect nucleic acids from DNA and RNA viruses and bacteria. Here, we review the current state of multiplexed nucleic acid detection methods with a focus on CRISPR-based methods. We also look toward the future of multiplexed point-of-care diagnostics.
Collapse
Affiliation(s)
- Caitlin H Lamb
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brian Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| |
Collapse
|
8
|
Yang J, Xu H, Ke Z, Kan N, Zheng E, Qiu Y, Huang M. Absolute quantification of viable Vibrio cholerae in seawater samples using multiplex droplet digital PCR combined with propidium monoazide. Front Microbiol 2023; 14:1149981. [PMID: 37362935 PMCID: PMC10288211 DOI: 10.3389/fmicb.2023.1149981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Toxigenic Vibrio cholerae serogroup O1 and O139 are the pathogens responsible for the global cholera epidemic. V. cholerae can settle in the water and spread via the fecal-oral route. Rapid and accurate monitoring of live V. cholerae in environmental water has become an important strategy to prevent and control cholera transmission. Conventional plate counting is widely used to detect viable bacteria but requires time and effort. Methods This study aims to develop a new assay that combines triplex droplet digital PCR (ddPCR) with propidium monoazide (PMA) treatment for quantitatively detecting live V. cholerae O1/O139 and cholera enterotoxin. Specific primers and probes were designed according to the conserved regions of gene rfb O1, rfb O139, and ctxA. The amplification procedures and PMA treatment conditions were optimized. The specificity, sensitivity, and ability of PMA-ddPCR to detect viable bacteria-derived DNA were evaluated in simulated seawater samples. Results and Discussion The results revealed that the optimal primer concentrations of rfb O1, rfb O139, and ctxA were 1 μM, while the concentrations of the three probes were 0.25, 0.25, and 0.4 μM, respectively. The best annealing temperature was 58°C to obtain the most accurate results. The optimal strategy for distinguishing dead and live bacteria from PMA treatment was incubation at the concentration of 20 μM for 15 min, followed by exposure to a 650-W halogen lamp for 20 min. In pure culture solutions, the limit of detection (LODs) of V. cholerae O1 and O139, and ctxA were 127.91, 120.23 CFU/mL, and 1.5 copies/reaction in PMA-triplex ddPCR, respectively, while the LODs of the three targets were 150.66, 147.57 CFU/mL, and 2 copies/reaction in seawater samples. The PMA-ddPCR sensitivity was about 10 times higher than that of PMA-qPCR. When detecting spiked seawater samples with live bacterial concentrations of 1.53 × 102 and 1.53 × 105 CFU/mL, the assay presented a higher sensitivity (100%, 16/16) than qPCR (50.00%, 8/16) and a perfect specificity (100%, 9/9). These results indicate that the developed PMA-triplex ddPCR is superior to the qPCR regarding sensitivity and specificity and can be used to rapidly detect viable toxigenic V. cholerae O1 and O139 in suspicious seawater samples.
Collapse
Affiliation(s)
- Jinsong Yang
- Fujian Center for Disease Control and Prevention, Fuzhou, China
- Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Haibin Xu
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Zili Ke
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Naipeng Kan
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Enhui Zheng
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Yufeng Qiu
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Mengying Huang
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| |
Collapse
|
9
|
Liu J, Song Z, Ta N, Tian G, Yang X, Zhao H, Piao D, Fan Y, Zhang Y, Jiang H. Development and evaluation of a droplet digital PCR assay to detect Brucella in human whole blood. PLoS Negl Trop Dis 2023; 17:e0011367. [PMID: 37267228 DOI: 10.1371/journal.pntd.0011367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/09/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND With the development of domestic animal husbandry, the spread of brucellosis has accelerated, and the scope of the epidemic has expanded. The timely and accurate diagnosis of human brucellosis continues to challenge clinicians in endemic areas. Droplet digital PCR (ddPCR) technology can quickly and accurately determine DNA load in samples, providing laboratory evidence for diagnosis, prognosis and management of brucellosis patients. In this study, a ddPCR method was established to accurately quantify Brucella DNA load in whole blood samples, and its diagnostic, prognostic, and therapeutic value for human brucellosis was evaluated. METHODS Annealing temperature, primers, and probe targeting the Brucella bcsp31 gene were optimised, and the sensitivity, specificity and repeatability of the ddPCR assay were assessed using 94 whole blood samples from 61 confirmed and 33 suspected cases. Results were compared with those of quantitative PCR (qPCR). Nine follow-up brucellosis patients were also analysed by the two methods after 2 and 6 months of treatment. RESULTS Optimal primer and probe concentrations were 800 nmol/L and 400 nmol/L, respectively, and the optimal annealing temperature was 55.3 °C. The ddPCR results showed that the limit of detection was 1.87 copies per reaction, with high repeatability. The positive rates for ddPCR and qPCR were 88.5% and 75.4% among 61 serum agglutination test (SAT) positive patients. In addition, 57.6% (19/33) of suspected sero-negative samples were positive by ddPCR, but only 36.3% (12/33) were positive by qPCR. Analysis of nine post-therapy follow-up brucellosis patients revealed that the Brucella DNA load in the whole blood samples decreased after 2 and 6 months of treatment, and was slightly increased following relapse and continuous exposure. CONCLUSION The ddPCR assay showed good accuracy for whole blood samples, and could be a potential diagnostic and prognostic tool for detecting Brucella.
Collapse
Affiliation(s)
- Jiayin Liu
- National Key Laboratory of Intelligent Tracing and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Wengniute Banner Center for Disease Control and Prevention, Chifeng, Inner Mongolia Autonomous Region, China
| | - Zhichun Song
- Wengniute Banner Center for Disease Control and Prevention, Chifeng, Inner Mongolia Autonomous Region, China
| | - Na Ta
- Inner Mongolia Autonomous Region Comprehensive Center for Disease Control and Prevention, Hohhot, Inner Mongolia Autonomous Region, China
| | - Guozhong Tian
- National Key Laboratory of Intelligent Tracing and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaowen Yang
- National Key Laboratory of Intelligent Tracing and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongyan Zhao
- National Key Laboratory of Intelligent Tracing and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongri Piao
- National Key Laboratory of Intelligent Tracing and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Fan
- National Key Laboratory of Intelligent Tracing and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Zhang
- National Key Laboratory of Intelligent Tracing and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hai Jiang
- National Key Laboratory of Intelligent Tracing and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|