151
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Wang D, Liu E, Liu H, Jin X, Niu C, Gao Y, Su X. A droplet digital PCR assay for detection and quantification of Verticillium nonalfalfae and V. albo-atrum. Front Cell Infect Microbiol 2023; 12:1110684. [PMID: 36710974 PMCID: PMC9874294 DOI: 10.3389/fcimb.2022.1110684] [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: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Verticillium nonalfalfae and V. albo-atrum are notorious pathogenic fungi that cause a destructive vascular disease called Verticillium wilt worldwide. Thus, timely and quantitative monitoring of fungal progression is highly desirable for early diagnosis and risk assessment. In this study, we developed a droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify V. nonalfalfae and V. albo-atrum. The performance of this assay was validated in comparison with that of a quantitative real-time polymerase chain reaction (qPCR) assay. The standard curve analysis of the ddPCR assay showed good linearity. The ddPCR assay indicated similar detection sensitivity to that of qPCR on pure genomic DNA, while it enhanced the positive rate for low-abundance fungi, especially in alfalfa stems. Receiver operating characteristic analysis revealed that ddPCR provided superior diagnostic performance on field tissues compared to qPCR, and the area under curve values were 0.94 and 0.90 for alfalfa roots and stems, respectively. Additionally, the quantitative results of the two methods were highly concordant (roots: R2 = 0.91; stems: R2 = 0.76); however, the concentrations determined by ddPCR were generally higher than those determined by qPCR. This discrepancy was potentially caused by differing amplification efficiencies for qPCR between cultured and field samples. Furthermore, the ddPCR assays appreciably improved quantitative precision, as reflected by lower coefficients of variation. Overall, the ddPCR method enables sensitive detection and accurate quantification of V. nonalfalfae and V. albo-atrum, providing a valuable tool for evaluating disease progression and enacting effective disease control.
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Affiliation(s)
- Di Wang
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Enliang Liu
- 2Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiyang Liu
- 3Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xi Jin
- 4Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Chunyan Niu
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yunhua Gao
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
| | - Xiaofeng Su
- 5Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
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152
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Sommer KM, Lee Y, Donovan SM, Dilger RN. Purification methods to reduce interference by dextran sodium sulfate with quantification of gene expression in intestinal tissue samples from a piglet model of colitis. J Anim Sci 2023; 101:skad202. [PMID: 37330677 PMCID: PMC10317179 DOI: 10.1093/jas/skad202] [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: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Dextran sodium sulfate (DSS) is commonly used to induce intestinal (i.e., colonic) inflammation in a variety of animal models. However, DSS is known to cause interference when using quantitative-real time polymerase chain reaction (qRT-PCR) methods, thereby invalidating accurate and precise measurement of tissue gene expression. Therefore, the goal of this study was to determine whether different mRNA purification methods would reduce DSS-interference. Colonic tissue samples were collected at postnatal days (PND) 27 or 28 from pigs that had not been administered DSS (Control), and two independent groups of pigs that received 1.25 g of DSS/kg of BW/d (DSS-1 and DSS-2) from PND 14 to 18. Tissue samples collected were subsequently stratified into three purification methods (i.e., 9 total treatment × method combinations), including: 1) no purification, 2) purification with lithium chloride (LiCl), or 3) purification using spin column filtration. All data were analyzed using a one-way ANOVA in the Mixed procedure of SAS. The average RNA concentrations across all treatments were between 1,300 and 1,800 μg/μL for all three in vivo groups. Although there were statistical differences among purification methods, the 260/280 and 260/230 ratios fell between acceptable limits of 2.0 to 2.1 and 2.0 to 2.2, respectively, for all treatment groups. This confirms the RNA quality was adequate and not influenced by purification method in addition to suggesting the absence of phenol, salts, and carbohydrate contamination. For pigs in the Control group that did not receive DSS, qRT-PCR Ct values of four cytokines were achieved, though these values were not altered by purification method. For pigs that had undergone DSS dosing, those tissues subjected to either no purification or purification using LiCl did not generate applicable Ct values. However, when tissues derive from DSS-treated pigs underwent spin column purification, half of the samples from DSS-1 and DSS-2 groups generated appropriate Ct estimates. Therefore, spin column purification appeared to be more effective than LiCl purification, but no method was 100% effective, so caution should be exercised when interpreting gene expression results from studies where animals are exposed to DSS-induced colitis.
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Affiliation(s)
- Kaitlyn M Sommer
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
| | - Youngsoo Lee
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, Illinois, USA
| | - Sharon M Donovan
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, Illinois, USA
| | - Ryan N Dilger
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
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153
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Wu F, Oghuan J, Gitter A, Mena KD, Brown EL. Wide mismatches in the sequences of primers and probes for monkeypox virus diagnostic assays. J Med Virol 2023; 95:e28395. [PMID: 36504122 DOI: 10.1002/jmv.28395] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/25/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Rapid and accurate diagnosis of infections is fundamental to containment of disease. Several monkeypox virus (MPV) real-time diagnostic assays have been recommended by the CDC; however, the specificity of the primers and probes in these assays for the ongoing MPV outbreak has not been investigated. We analyzed the primer and probe sequences present in the CDC recommended MPV generic real-time PCR assay by aligning those sequences against 1730 MPV complete genomes reported in 2022 worldwide. Sequence mismatches were found in 99.08% and 97.46% of genomes for the MPV generic forward and reverse primers, respectively. Mismatch-corrected primers were synthetized and compared to the generic assay for MPV detection. Results showed that the two primer-template mismatches resulted in a ~11-fold underestimation of initial template DNA in the reaction and 4-fold increase in the 95% LOD. We further evaluated the specificity of seven other real-time PCR assays used for MPV and orthopoxvirus (OPV) detection and identified two assays with the highest matching score (>99.6%) to the global MPV genome database in 2022. Genetic variations in the primer-probe regions across MPV genomes could indicate the temporal and spatial emergence pattern of monkeypox disease. Our results show that the current MPV real-time generic assay may not be optimal to accurately detect MPV, and the mismatch-corrected assay with full complementarity between primers and current MPV genomes could provide a more sensitive and accurate detection of MPV.
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Affiliation(s)
- Fuqing Wu
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jeremiah Oghuan
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Anna Gitter
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Kristina D Mena
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Eric L Brown
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
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154
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Crim MJ, Hart ML. Health Monitoring for Laboratory Salamanders. Methods Mol Biol 2023; 2562:41-74. [PMID: 36272067 DOI: 10.1007/978-1-0716-2659-7_3] [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] [Indexed: 06/16/2023]
Abstract
Laboratory animal health monitoring programs are necessary to protect animal health and welfare, the validity of experimental data, and human health against zoonotic infections. Health monitoring programs should be designed based on a risk assessment and knowledge about the biology and transmission of salamander pathogens. Both traditional and molecular diagnostic platforms are available for salamanders, and they provide complementary information. A comprehensive approach to health monitoring leverages the advantages of multiple platforms to provide a more complete picture of colony health and pathogen status. This chapter presents key considerations in the design and implementation of a colony health monitoring program for laboratory salamanders, including protocols for necropsy and sample collection.
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155
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Rapid identification and absolute quantitation of zero tolerance-Salmonella enterica subsp. enterica serovar Thompson using droplet digital polymerase chain reaction. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2022.114333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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156
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Costa-Ribeiro A, Azinheiro S, Roumani F, Prado M, Lamas A, Garrido-Maestu A. Multiplex Real-Time PCR for the Detection of Shiga Toxin-Producing Escherichia coli in Foods. Methods Mol Biol 2023; 2967:63-73. [PMID: 37608103 DOI: 10.1007/978-1-0716-3358-8_6] [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] [Indexed: 08/24/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a group of human foodborne pathogens transmitted to humans through the consumption of different types of food. Their detection is mainly performed by targeting specific serogroups by classical microbiological methods and, later, by molecular typing with different techniques. The application of multiplex real-time PCR (qPCR) can significantly improve the turnaround time of the existing methodologies as in one single run it is possible to detect and characterize specific microorganisms. In the present chapter, a pentaplex qPCR assay is described for the identification of STEC which may also be applied for the rapid screening of these pathogens in different types of foods. The assay targets the most important virulence factors of these microorganisms, the genes stx1, stx2, and eae, along with the rfbE gene which encodes for the "O157" antigen as this is the most prevalent serogroup among all STEC, as well as an internal amplification control to rule out false-negative results due to qPCR inhibition.
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Affiliation(s)
- Ana Costa-Ribeiro
- International Iberian Nanotechnology Laboratory, Food Quality and Safety Research Group, Braga, Portugal
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Sarah Azinheiro
- International Iberian Nanotechnology Laboratory, Food Quality and Safety Research Group, Braga, Portugal
- Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Veterinary Science, University of Santiago de Compostela, Lugo, Spain
| | - Foteini Roumani
- International Iberian Nanotechnology Laboratory, Food Quality and Safety Research Group, Braga, Portugal
- Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Veterinary Science, University of Santiago de Compostela, Lugo, Spain
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Food Quality and Safety Research Group, Braga, Portugal
| | - Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory, Department of Analytical Chemistry, Nutrition and Bromatology, Universidad de Santiago de Compostela, Lugo, Spain
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Food Quality and Safety Research Group, Braga, Portugal.
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157
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Osemeke OH, VanKley N, LeFevre C, Peterson C, Linhares DCL. Evaluating oral swab samples for PRRSV surveillance in weaning-age pigs under field conditions. Front Vet Sci 2023; 10:1072682. [PMID: 36876004 PMCID: PMC9976936 DOI: 10.3389/fvets.2023.1072682] [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: 10/17/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction The use of serum and family oral fluids for porcine reproductive and respiratory syndrome virus (PRRSV) surveillance in weaning-age pigs has been previously characterized. Characterizing more sample types similarly offers veterinarians and producers additional validated sample options for PRRSV surveillance in this subpopulation of pigs. Oral swab sampling is relatively easy and convenient; however, there is sparse information on how it compares to the reference sample type for PRRSV surveillance under field conditions. Therefore, this study's objective was to compare the PRRSV reverse-transcription real-time polymerase chain reaction (RT-rtPCR) test outcomes of oral swabs (OS) and sera samples obtained from weaning-age pig litters. Method At an eligible breeding herd, six hundred twenty-three weaning-age piglets from 51 litters were each sampled for serum and OS and tested for PRRSV RNA by RT-rtPCR. Results and Discussion PRRSV RT-rtPCR positivity rate was higher in serum samples (24 of 51 litters, 83 of 623 pigs, with a mean cycle threshold (Ct) value of RT-rtPCR-positive samples per litter ranging from 18.9 to 32.0) compared to OS samples (15 of 51 litters, 33 of 623 pigs, with a mean Ct of RT-rtPCR positive samples per litter ranging from 28.2 to 36.9); this highlights the importance of interpreting negative RT-rtPCR results from OS samples with caution. Every litter with a positive PRRSV RT-rtPCR OS had at least one viremic piglet, highlighting the authenticity of positive PRRSV RT-rtPCR tests using OS; in other words, there was no evidence of environmental PRRSV RNA being detected in OS. Cohen's kappa analysis (Ck = 0.638) indicated a substantial agreement between both sample types for identifying the true PRRSV status of weaning-age pigs.
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Affiliation(s)
| | - Nathan VanKley
- College of Veterinary Medicine, Michigan State University, Lansing, MI, United States
| | - Claire LeFevre
- Carthage Veterinary Service, Carthage, IL, United States
| | - Christina Peterson
- Fieldepi, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Daniel C L Linhares
- Fieldepi, Iowa State University College of Veterinary Medicine, Ames, IA, United States
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158
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Buonavoglia A, Pellegrini F, Lanave G, Diakoudi G, Lucente MS, Zamparini F, Camero M, Gandolfi MG, Martella V, Prati C. Analysis of oral microbiota in non-vital teeth and clinically intact external surface from patients with severe periodontitis using Nanopore sequencing: a case study. J Oral Microbiol 2023; 15:2185341. [PMID: 36891191 PMCID: PMC9987744 DOI: 10.1080/20002297.2023.2185341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Periodontal diseases include a wide range of pathological conditions, damaging the supporting structures of the teeth. Origin and propagation of periodontal disease is believed to be caused by dysbiosis of the commensal oral microbiota. The aim of this study was to evaluate the presence of bacteria in the pulp cavity of teeth with severe periodontal disease with clinically intact external surface. Periodontal (P) and endodontic (E) tissue samples of root canals from six intact teeth of three patients were sampled for analysis of microbial population using Nanopore technology. Streptococcus was the predominant genus in E samples. Porphyromonas (33.4%, p = 0.047), Tannerella (41.7%, p = 0.042), and Treponema (50.0%, p = 0.0064) were significantly more present in P than in E samples. Some samples (E6 and E1) exhibited a remarkable difference in terms of microbial composition, whilst Streptococcus was a common signature in samples E2 to E5, all which were obtained from the same patient. In conclusion, bacteria were identified on both the root surface and the root canal system, thus demonstrating the possibility of bacteria to spread directly from the periodontal pocket to the root canal system even in the absence of crown's loss of integrity.
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Affiliation(s)
- Alessio Buonavoglia
- Department of Biomedical and Neuromotor Sciences, Dental School, University of Bologna, Bologna, Italy
| | | | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Maria Stella Lucente
- Department of Biomedical and Neuromotor Sciences, Dental School, University of Bologna, Bologna, Italy
| | - Fausto Zamparini
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Michele Camero
- Department of Biomedical and Neuromotor Sciences, Dental School, University of Bologna, Bologna, Italy
| | | | - Vito Martella
- Department of Biomedical and Neuromotor Sciences, Dental School, University of Bologna, Bologna, Italy
| | - Carlo Prati
- Department of Biomedical and Neuromotor Sciences, Dental School, University of Bologna, Bologna, Italy
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159
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Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022; 15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
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Affiliation(s)
- Enespa
- Department of Plant Pathology, School of Agriculture, SMPDC, University of Lucknow, Lucknow, India
| | - Prem Chandra
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, India
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160
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Detection of Salmonella enterica subsp. enterica via Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification. ScientificWorldJournal 2022; 2022:4567817. [PMID: 36619257 PMCID: PMC9822744 DOI: 10.1155/2022/4567817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/31/2022] Open
Abstract
Salmonella enterica is a major cause of diarrheal diseases in developing countries where timely surveillance and proper clinical management are inadequate. In this study, a rapid and cheap method of detecting S. enterica DNA was developed by employing the Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification (QUASR LAMP) platform. QUASR LAMP provides a closed-tube, target-specific endpoint detection of pathogens, wherein results can be analyzed visually through an LED transilluminator and verified through agarose gel electrophoresis. Based on the chromosomal SopD gene, primers and probes were first designed, then screened. The assay was subsequently optimized so that the presence of S. enterica is determined by incubating the extracted DNA at 65°C for only 60 minutes. The assay was repeatable and can be performed by simply using a thermal cycler or even a dry bath incubator. S. enterica positives appear bright yellow green when viewed through a yellow filter excited with blue LED. The developed assay had an in silico and in vitro specificity towards Salmonella enterica subsp. enterica serovars with a limit of detection of 104 copies per microliter. The Salmonella QUASR LAMP assay has the potential for food and environmental applications. Chiefly, as an alternative to traditional microbiology and PCR, this QUASR LAMP assay can be used for point-of-care salmonellosis testing of clinical specimens in low-resource settings.
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161
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Jiménez-Zapata DL, Quiroga-Pérez M, Quiroz-Yepes M, Marulanda-Tobón A, Álvarez JC, Mosquera-López S. Development of a Method for Detecting and Estimating Moniliophthora roreri Spore Loads Based on Spore Traps and qPCR. J Fungi (Basel) 2022; 9:jof9010047. [PMID: 36675868 PMCID: PMC9862605 DOI: 10.3390/jof9010047] [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: 09/19/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022] Open
Abstract
Frosty pod rot, caused by Moniliophthora roreri, is the most damaging disease of cacao in Latin America and, to better comprehend its epidemiology, we must understand its dissemination and proliferation. However, we do not know how M. roreri spores loads fluctuate in time and space due to the lack of a reliable technique to quantify M. roreri spores in the fields. Therefore, we developed a method that relies on spore traps and qPCR to detect and quantify M. roreri spore loads. This study demonstrated that the qPCR protocol can detect down to 0.025 ng of M. roreri DNA and quantify between 0.006 ng and 60 ng. Moreover, it demonstrated that qPCR protocol can detect and quantify DNA extracted from spore suspension and spore traps containing at least 2.9 × 104 M. roreri spores. However, the variability of the estimates for spore samples was high. Finally, we described a spore-trap device designed to carry spore traps in the field. The qPCR protocol and spore-trap device here developed will help in the understanding of the M. roreri dissemination patterns since they can be used to assess the environmental loads of M. roreri spore in cacao fields.
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Affiliation(s)
- Diana L. Jiménez-Zapata
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Manuela Quiroga-Pérez
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Manuela Quiroz-Yepes
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- GEMA Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Alejandro Marulanda-Tobón
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- GEMA Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Javier C. Álvarez
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- Correspondence:
| | - Sandra Mosquera-López
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
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162
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Praia AB, Herkenhoff ME, Broedel O, Frohme M, Saad SMI. Sour Beer with Lacticaseibacillus paracasei subsp. paracasei F19: Feasibility and Influence of Supplementation with Spondias mombin L. Juice and/or By-Product. Foods 2022; 11:foods11244068. [PMID: 36553809 PMCID: PMC9778371 DOI: 10.3390/foods11244068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/30/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
This study aimed to evaluate the probiotic strain Lacticaseibacillus (L.) paracasei subsp. paracasei F19 (F19) with the yeast Saccharomyces cerevisiae US-05 (US-05), using Spondias mombin L. ('taperebá' or 'cajá') juice and by-product, in four sour-type beer formulations: control, with bagasse, juice, and juice and bagasse. The viability of F19 was evaluated by pour-plating and PMA-qPCR. Fermentability, in addition to physicochemical and sensory parameters, and aroma and flavor, were evaluated during brewery by using Headspace Solid-Phase Microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS). F19 was successful in fermenting bagasse in a MRS medium (9.28 log CFU/mL in 24 h) but had a low viability in hopped wort, growing better in formulations without bagasse or juice. No difference between formulations was observed regarding sensory acceptability, and the HS-SPME/GC-MS revealed different flavors and aroma compounds. In conclusion, the production of a potential probiotic sour beer with F19 and US-05 is feasible regarding probiotic viability. However, S. mombin, as juice or bagasse, threatened probiotic survival. Different flavors and aroma compounds were detected, whereas no difference between formulations was found regarding sensory acceptability. The moderate alcohol content achieved is important for bacterial survival and for the development of a probiotic beer with health claims.
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Affiliation(s)
- Ana Beatriz Praia
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Professor Lineu Prestes, 580, São Paulo 05508-000, SP, Brazil
- Food Research Center FoRC, University of São Paulo (USP), Av. Professor Lineu Prestes, 580, São Paulo 05508-000, SP, Brazil
| | - Marcos Edgar Herkenhoff
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Professor Lineu Prestes, 580, São Paulo 05508-000, SP, Brazil
- Food Research Center FoRC, University of São Paulo (USP), Av. Professor Lineu Prestes, 580, São Paulo 05508-000, SP, Brazil
| | - Oliver Broedel
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, 15745 Wildau, Germany
| | - Marcus Frohme
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, 15745 Wildau, Germany
| | - Susana Marta Isay Saad
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Professor Lineu Prestes, 580, São Paulo 05508-000, SP, Brazil
- Food Research Center FoRC, University of São Paulo (USP), Av. Professor Lineu Prestes, 580, São Paulo 05508-000, SP, Brazil
- Correspondence:
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163
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Leong NKC, Gu H, Ng DYM, Chang LDJ, Krishnan P, Cheng SSM, Peiris M, Poon LLM. Development of multiplex RT-ddPCR assays for detection of SARS-CoV-2 and other common respiratory virus infections. Influenza Other Respir Viruses 2022; 17:e13084. [PMID: 36517993 PMCID: PMC9835441 DOI: 10.1111/irv.13084] [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: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Measures for mitigation of Coronavirus Disease 2019 (COVID-19) were set to reduce the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 and other respiratory viruses share similar transmission routes and some common clinical manifestations. Co-circulation of SARS-CoV-2 and other common respiratory viruses is imminent. Therefore, development of multiplex assays for detecting these respiratory viruses is essential for being prepared for future outbreaks of respiratory viruses. METHODS A panel of three reverse transcription droplet digital PCR (RT-ddPCR) assays were developed to detect 15 different human respiratory viruses. Evaluations of its performance were demonstrated. A total of 100 local and 98 imported COVID-19 cases in Hong Kong were screened for co-infection with other common respiratory viruses. RESULTS All detected viral targets showed distinct signal clusters using the multiplex RT-ddPCR assays. These assays have a broad range of linearity and good intra-/inter-assay reproducibility for each target. The lower limits of quantification for all targets were ≤46 copies per reaction. Six imported cases of COVID-19 were found to be co-infected with other respiratory viruses, whereas no local case of co-infection was observed. CONCLUSIONS The multiplex RT-ddPCR assays were demonstrated to be useful for screening of respiratory virus co-infections. The strict preventive measures applied in Hong Kong may be effective in limiting the circulation of other human respiratory viruses. The multiplex assays developed in this study can achieve a robust detection method for clinical and research purposes.
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Affiliation(s)
- Nathaniel K. C. Leong
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Haogao Gu
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Daisy Y. M. Ng
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Lydia D. J. Chang
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Samuel S. M. Cheng
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Malik Peiris
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong,Centre for Immunology and InfectionHong Kong Science and Technology ParkHong Kong,HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Leo L. M. Poon
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong,Centre for Immunology and InfectionHong Kong Science and Technology ParkHong Kong,HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
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164
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Ghorbanian F, Seo H, Tajdozian H, Lee Y, Rahim MDA, Kim S, Jung IY, Lee S, Song HY. In Vivo Efficacy of Bacillus velezensis Isolated from Korean Gochang Bokbunja Vinegar against Carbapenem-Resistant Klebsiella pneumoniae Infections. Pol J Microbiol 2022; 71:553-562. [PMID: 36515501 PMCID: PMC9944968 DOI: 10.33073/pjm-2022-051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/03/2022] [Indexed: 12/15/2022] Open
Abstract
Outbreaks of carbapenem-resistant Enterobacteriaceae (CRE), especially Klebsiella pneumoniae (CRKP), are commonly reported as severe infections in hospitals and long-term care settings, and their occurrence is increasing globally. Conventional antibiotics used for treating CRE have become ineffective due to resistance development. Furthermore, their safety issues restrict their availability and use for CRE treatment. Therefore, developing new drugs different from existing drugs to combat this deadly menace is urgently needed. Probiotics can be a potential option in this context, as probiotics' efficacy against a variety of infectious illnesses has already been well established. Here, we report the effect of the Bacillus velezensis strain isolated from Gochang Bokbunja vinegar in Korea on CRE infection using two mouse models. Data showed that pretreatment with B. velezensis significantly reduced body weight loss and mortality of CRKP-infected mice in the preventive model. The oral administration of B. velezensis in a therapeutic model also decreased the mortality and illness severity in CRKP-infected mice. Moreover, a two-week oral acute toxicity assay in guinea pigs did not reveal any aberrant clinical signs. Our findings demonstrate the potential effectiveness of our candidate probiotic strain, B. velezensis, against CRKP, suggesting that it could be used as an antimicrobial agent for treating CRKP-related infections.
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Affiliation(s)
- Fatemeh Ghorbanian
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnam, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Hoonhee Seo
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnam, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Hanieh Tajdozian
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnam, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Youngkyoung Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnam, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - MD Abdur Rahim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnam, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Il-Yun Jung
- Korea Balsamic Vinegar Association, Gochang, Jeonbuk, Republic of Korea
| | - Saebim Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnam, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnam, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea, H.-Y. Song, Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnam, Republic of Korea; Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, Chungnam, Republic of Korea
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165
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Lauro ML, Bowman AM, Smith JP, Gaye SN, Acevedo-Skrip J, DePhillips PA, Loughney JW. Overcoming Biopharmaceutical Interferents for Quantitation of Host Cell DNA Using an Automated, High-Throughput Methodology. AAPS J 2022; 25:10. [PMID: 36482268 PMCID: PMC9735023 DOI: 10.1208/s12248-022-00764-4] [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: 06/27/2022] [Accepted: 10/21/2022] [Indexed: 12/13/2022] Open
Abstract
The rapid development of biologics and vaccines in response to the current pandemic has highlighted the need for robust platform assays to characterize diverse biopharmaceuticals. A critical aspect of biopharmaceutical development is achieving a highly pure product, especially with respect to residual host cell material. Specifically, two important host cell impurities of focus within biopharmaceuticals are residual DNA and protein. In this work, a novel high-throughput host cell DNA quantitation assay was developed for rapid screening of complex vaccine drug substance samples. The developed assay utilizes the commercially available, fluorescent-sensitive Picogreen dye within a 96-well plate configuration to allow for a cost effective and rapid analysis. The assay was applied to in-process biopharmaceutical samples with known interferences to the dye, including RNA and protein. An enzymatic digestion pre-treatment was found to overcome these interferences and thus allow this method to be applied to wide-ranging, diverse analyses. In addition, the use of deoxycholate in the digestion treatment allowed for disruption of interactions in a given sample matrix in order to more accurately and selectively quantitate DNA. Critical analytical figures of merit for assay performance, such as precision and spike recovery, were evaluated and successfully demonstrated. This new analytical method can thus be successfully applied to both upstream and downstream process analysis for biologics and vaccines using an innovative and automated high-throughput approach.
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Affiliation(s)
- Mackenzie L. Lauro
- grid.417993.10000 0001 2260 0793Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486 USA
| | - Amy M. Bowman
- grid.417993.10000 0001 2260 0793Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486 USA
| | - Joseph P. Smith
- grid.417993.10000 0001 2260 0793Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486 USA
| | - Susannah N. Gaye
- grid.417993.10000 0001 2260 0793Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486 USA
| | - Jillian Acevedo-Skrip
- grid.417993.10000 0001 2260 0793Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486 USA
| | - Pete A. DePhillips
- grid.417993.10000 0001 2260 0793Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486 USA
| | - John W. Loughney
- grid.417993.10000 0001 2260 0793Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486 USA
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166
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The conundrum of breast cancer and microbiome - A comprehensive review of the current evidence. Cancer Treat Rev 2022; 111:102470. [DOI: 10.1016/j.ctrv.2022.102470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
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167
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Cheng TY, Zimmerman JJ, Giménez-Lirola LG. Internal reference genes with the potential for normalizing quantitative PCR results for oral fluid specimens. Anim Health Res Rev 2022; 23:147-156. [PMID: 36330795 DOI: 10.1017/s1466252322000044] [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] [Indexed: 11/06/2022]
Abstract
In basic research, testing of oral fluid specimens by real-time quantitative polymerase chain reaction (qPCR) has been used to evaluate changes in gene expression levels following experimental treatments. In diagnostic medicine, qPCR has been used to detect DNA/RNA transcripts indicative of bacterial or viral infections. Normalization of qPCR using endogenous and exogenous reference genes is a well-established strategy for ensuring result comparability by controlling sample-to-sample variation introduced during sampling, storage, and qPCR testing. In this review, the majority of recent publications in human (n = 136) and veterinary (n = 179) medicine did not describe the use of internal reference genes in qPCRs for oral fluid specimens (52.9% animal studies; 57.0% human studies). However, the use of endogenous reference genes has not been fully explored or validated for oral fluid specimens. The lack of valid internal reference genes inherent to the oral fluid matrix will continue to hamper the reliability, reproducibility, and generalizability of oral fluid qPCR assays until this issue is addressed.
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Affiliation(s)
- Ting-Yu Cheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jeffrey J Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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168
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Lima A, França A, Muzny CA, Taylor CM, Cerca N. DNA extraction leads to bias in bacterial quantification by qPCR. Appl Microbiol Biotechnol 2022; 106:7993-8006. [PMID: 36374332 PMCID: PMC10493044 DOI: 10.1007/s00253-022-12276-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Quantitative PCR (qPCR) has become a widely used technique for bacterial quantification. The affordability, ease of experimental design, reproducibility, and robustness of qPCR experiments contribute to its success. The establishment of guidelines for minimum information for publication of qPCR experiments, now more than 10 years ago, aimed to mitigate the publication of contradictory data. Unfortunately, there are still a significant number of recent research articles that do not consider the main pitfalls of qPCR for quantification of biological samples, which undoubtedly leads to biased experimental conclusions. qPCR experiments have two main issues that need to be properly tackled: those related to the extraction and purification of genomic DNA and those related to the thermal amplification process. This mini-review provides an updated literature survey that critically analyzes the following key aspects of bacterial quantification by qPCR: (i) the normalization of qPCR results by using exogenous controls, (ii) the construction of adequate calibration curves, and (iii) the determination of qPCR reaction efficiency. It is primarily focused on original papers published last year, where qPCR was applied to quantify bacterial species in different types of biological samples, including multi-species biofilms, human fluids, and water and soil samples. KEY POINTS: • qPCR is a widely used technique used for absolute bacterial quantification. • Recently published papers lack proper qPCR methodologies. • Not including proper qPCR controls significantly affect experimental conclusions.
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Affiliation(s)
- Angela Lima
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Angela França
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology & Microbial Genomics Resource Group, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal.
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
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169
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Argyropoulos CD, Skoulou V, Efthimiou G, Michopoulos AK. Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review. AIR QUALITY, ATMOSPHERE, & HEALTH 2022; 16:477-533. [PMID: 36467894 PMCID: PMC9703444 DOI: 10.1007/s11869-022-01286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.
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Affiliation(s)
| | - Vasiliki Skoulou
- B3 Challenge Group, Chemical Engineering, School of Engineering, University of Hull, Cottingham Road, Hull, HU6 7RX UK
| | - Georgios Efthimiou
- Centre for Biomedicine, Hull York Medical School, University of Hull, Cottingham Road, Hull, HU6 7RX UK
| | - Apostolos K. Michopoulos
- Energy & Environmental Design of Buildings Research Laboratory, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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170
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Masri A, Brown DM, Smith DGE, Stone V, Johnston HJ. Comparison of In Vitro Approaches to Assess the Antibacterial Effects of Nanomaterials. J Funct Biomater 2022; 13:255. [PMID: 36412895 PMCID: PMC9703965 DOI: 10.3390/jfb13040255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/04/2022] [Accepted: 11/17/2022] [Indexed: 07/24/2023] Open
Abstract
The antibacterial properties of nanomaterials (NMs) can be exploited in a range of consumer products (e.g., wound dressings, food packaging, textiles, medicines). There is also interest in the exploitation of NMs as treatments for infectious diseases to help combat antibiotic resistance. Whilst the antibacterial activity of NMs has been assessed in vitro and in vivo in numerous studies, the methodology used is very varied. Indeed, while numerous approaches are available to assess the antibacterial effect of NMs in vitro, they have not yet been systematically assessed for their suitability and sensitivity for testing NMs. It is therefore timely to consider what assays should be prioritised to screen the antibacterial properties of NMs. The majority of existing in vitro studies have focused on investigating the antibacterial effects exhibited by silver (Ag) NMs and have employed a limited range of assays. We therefore compared the antibacterial effects of copper oxide (CuO) NMs to Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis at various concentrations (12.5-200 µg/mL) using a battery of tests (well and disc diffusion, plate counts-time-kill method, optical density measurement-OD, Alamar Blue and live/dead viability assays, and quantitative polymerase chain reaction). CuO NMs were most toxic to B. subtilis and E. coli, while P. aeruginosa was the least sensitive strain. All assays employed detected the antibacterial activity of CuO NMs; however, they varied in their sensitivity, time, cost, technical difficulty and requirement for specialized equipment. In the future, we suggest that a combination of approaches is used to provide a robust assessment of the antibacterial activity of NMs. In particular, we recommend that the time-kill and OD assays are prioritised due to their greater sensitivity. We also suggest that standard operating protocols are developed so that the antibacterial activity of NMs can be assessed using a harmonised approach.
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171
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Wang KL, Zhang JX, Min D, Lv JL, Liu DF, Yu HQ. Detection and Quantification of Antimicrobial-Resistant Cells in Aquatic Environments by Bioorthogonal Noncanonical Amino Acid Tagging. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15685-15694. [PMID: 36251006 DOI: 10.1021/acs.est.2c05024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aquatic environments are important reservoirs of antibiotic wastes, antibiotic resistance genes, and bacteria, enabling the persistence and proliferation of antibiotic resistance in different bacterial populations. To prevent the spread of antibiotic resistance, effective approaches to detect antimicrobial susceptibility in aquatic environments are highly desired. In this work, we adopt a metabolism-based bioorthogonal noncanonical amino acid tagging (BONCAT) method to detect, visualize, and quantify active antimicrobial-resistant bacteria in water samples by exploiting the differences in bacterial metabolic responses to antibiotics. The BONCAT approach can be applied to rapidly detect bacterial resistance to multiple antibiotics within 20 min of incubation, regardless of whether they act on proteins or DNA. In addition, the combination of BONCAT with the microscope enables the intuitive characterization of antibiotic-resistant bacteria in mixed systems at single-cell resolution. Furthermore, BONCAT coupled with flow cytometry exhibits good performance in determining bacterial resistance ratios to chloramphenicol and population heterogeneity in hospital wastewater samples. In addition, this approach is also effective in detecting antibiotic-resistant bacteria in natural water samples. Therefore, such a simple, fast, and efficient BONCAT-based approach will be valuable in monitoring the increase and spread of antibiotic resistance within natural and engineered aquatic environments.
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Affiliation(s)
- Kai-Li Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jia-Xin Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jun-Lu Lv
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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172
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Genital Microbiota and Outcome of Assisted Reproductive Treatment-A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111867. [PMID: 36431002 PMCID: PMC9693990 DOI: 10.3390/life12111867] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
The balance between different bacterial species is essential for optimal vaginal health. Microbiome includes the host genome along with microorganism genomes and incorporates the biotic and abiotic factors, reflecting the habitat as a whole. A significant difference exists in the composition and number of the human microbiota in healthy individuals. About one-tenth of the total body microbiota exists in the urogenital tract and these can be identified by microscopy and culture-based methods, quantitative PCR, next generation and whole genome sequencing. The trend of delaying the planning of pregnancy to a later age nowadays has resulted in magnifying the use of assisted reproductive treatment (ART). Hence, genital microbiota and its impact on fertility has generated immense interest in recent years. In this systematic review, we searched the available evidence on the microbiota of the genital tract in women undergoing ART and studied the outcomes of IVF in different microbial compositions. Despite the inconsistency of the studies, it is evident that vaginal, cervical and endometrial microbiota might play a role in predicting ART outcomes. However, there is no clear evidence yet on whether the diversity, richness, quantity, or composition of species in the maternal genital tract significantly affects the outcomes in ARTs.
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173
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Ma D, Straathof J, Liu Y, Hull NM. Monitoring SARS-CoV-2 RNA in Wastewater with RT-qPCR and Chip-Based RT-dPCR: Sewershed-Level Trends and Relationships to COVID-19. ACS ES&T WATER 2022; 2:2084-2093. [PMID: 37552751 PMCID: PMC9173673 DOI: 10.1021/acsestwater.2c00055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 08/10/2023]
Abstract
We evaluated the performance of reverse transcription quantitative PCR (uniplex and duplex RT-qPCR) and chip-based digital PCR (duplex RT-dPCR) using CDC N1 and CDC N2 assays for longitudinal monitoring of SARS-CoV-2 RNA in influent wastewater samples (n = 281) from three wastewater plants in Ohio from January 2021 to January 2022. Human fecal virus (PMMoV) and wastewater flow rate were used to normalize SARS-CoV-2 concentrations. SARS-CoV-2 measurements and COVID-19 cases were strongly correlated, but normalization effects on correlations varied between sewersheds. SARS-CoV-2 measurements by RT-qPCR were strongly correlated with 7-day moving average COVID-19 cases (average Spearman's ρ = 0.58, p < 0.05). SARS-CoV-2 was detected more frequently in samples with duplex RT-dPCR than with duplex RT-qPCR during periods of low COVID-19 cases. Duplex and uniplex RT-qPCR N1 concentrations were more strongly correlated with cases (ρ = 0.62) than N2 (ρ = 0.52). RT-dPCR correlations (average ρ = 0.21) were weaker than those of RT-qPCR (average ρ = 0.58). We also share practical experience from establishing wastewater surveillance. Per sample, RT-qPCR had a lower cost ($6 vs $18) and sample turnaround time (3-4 h vs 7-9 h) than RT-dPCR. These findings reinforce selection and use of PCR-based wastewater surveillance tools.
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Affiliation(s)
- Daniel Ma
- Department of Civil, Environmental and Geodetic
Engineering, The Ohio State University, Columbus, Ohio 43210,
United States
| | - Judith Straathof
- Department of Civil, Environmental and Geodetic
Engineering, The Ohio State University, Columbus, Ohio 43210,
United States
| | - Yijing Liu
- Department of Civil, Environmental and Geodetic
Engineering, The Ohio State University, Columbus, Ohio 43210,
United States
| | - Natalie Marie Hull
- Department of Civil, Environmental and Geodetic
Engineering, The Ohio State University, Columbus, Ohio 43210,
United States
- The Sustainability Institute, The Ohio
State University, Columbus, Ohio 43210, United
States
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174
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Safford H, Zuniga-Montanez RE, Kim M, Wu X, Wei L, Sharpnack J, Shapiro K, Bischel HN. Wastewater-Based Epidemiology for COVID-19: Handling qPCR Nondetects and Comparing Spatially Granular Wastewater and Clinical Data Trends. ACS ES&T WATER 2022; 2:2114-2124. [PMID: 37552742 PMCID: PMC9397567 DOI: 10.1021/acsestwater.2c00053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 05/28/2023]
Abstract
Wastewater-based epidemiology (WBE) is a useful complement to clinical testing for managing COVID-19. While community-scale wastewater and clinical data frequently correlate, less is known about subcommunity relationships between the two data types. Moreover, nondetects in qPCR wastewater data are typically handled through methods known to bias results, overlooking perhaps better alternatives. We address these knowledge gaps using data collected from September 2020-June 2021 in Davis, California (USA). We hypothesize that coupling the expectation maximization (EM) algorithm with the Markov Chain Monte Carlo (MCMC) method could improve estimation of "missing" values in wastewater qPCR data. We test this hypothesis by applying EM-MCMC to city wastewater treatment plant data and comparing output to more conventional nondetect handling methods. Dissimilarities in results (i) underscore the importance of specifying nondetect handling method in reporting and (ii) suggest that using EM-MCMC may yield better agreement between community-scale clinical and wastewater data. We also present a novel framework for spatially aligning clinical data with wastewater data collected upstream of a treatment plant (i.e., distributed across a sewershed). Applying the framework to data from Davis reveals reasonable agreement between wastewater and clinical data at highly granular spatial scales-further underscoring the public-health value of WBE.
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Affiliation(s)
- Hannah Safford
- Department of Civil and Environmental Engineering,
University of California Davis, 3109 Ghausi Hall, 480 Bainer
Hall Drive, Davis, California 95616, United States
| | - Rogelio E. Zuniga-Montanez
- Department of Civil and Environmental Engineering,
University of California Davis, 3109 Ghausi Hall, 480 Bainer
Hall Drive, Davis, California 95616, United States
| | - Minji Kim
- School of Veterinary Medicine, University
of California Davis, Davis, California 95616, United
States
| | - Xiaoliu Wu
- Department of Statistics, University of
California Davis, Davis, California 95616, United
States
| | - Lifeng Wei
- Department of Statistics, University of
California Davis, Davis, California 95616, United
States
| | - James Sharpnack
- Department of Statistics, University of
California Davis, Davis, California 95616, United
States
| | - Karen Shapiro
- School of Veterinary Medicine, University
of California Davis, Davis, California 95616, United
States
| | - Heather N. Bischel
- Department of Civil and Environmental Engineering,
University of California Davis, 3109 Ghausi Hall, 480 Bainer
Hall Drive, Davis, California 95616, United States
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175
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Arulmoorthy MP, Vijayan R, Sinduja K, Suresh E, Vasudevan S. Infection with Decapod iridescent virus 1: an emerging disease in shrimp culture. Arch Microbiol 2022; 204:685. [DOI: 10.1007/s00203-022-03289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
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176
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Schuster CJ, Kent ML, Peterson JT, Sanders JL. MULTI-STATE OCCUPANCY MODEL ESTIMATES PROBABILITY OF DETECTION OF AN AQUATIC PARASITE USING ENVIRONMENTAL DNA: PSEUDOLOMA NEUROPHILIA IN ZEBRAFISH AQUARIA. J Parasitol 2022; 108:527-538. [PMID: 36326809 PMCID: PMC9811945 DOI: 10.1645/22-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Detecting the presence of important parasites within a host and its environment is critical to understanding the dynamics that influence a pathogen's ability to persist, while accurate detection is also essential for the implementation of effective control strategies. Pseudoloma neurophilia is the most common pathogen reported in zebrafish (Danio rerio) research facilities. The only assays currently available for P. neurophilia are through lethal sampling, often requiring euthanasia of the entire population for accurate estimates of prevalence in small populations. We present a non-lethal screening method to detect P. neurophilia in tank water based on the detection of environmental DNA (eDNA) from this microsporidium, using a previously developed qPCR assay that was adapted to the digital PCR (dPCR) platform to complement current surveillance protocols. Using the generated dPCR data, a multi-state occupancy model was also implemented to predict the probability of detecting the microsporidium in tank water under different flow regimes and pathogen prevalence. The occupancy model revealed that samples collected in static conditions were more informative than samples collected from flow-through conditions, with a probability of detection at 80% and 47%, respectively. There was also a positive correlation between the frequency of detection in water and prevalence in fish based on qPCR.
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Affiliation(s)
- Corbin J Schuster
- Department of Microbiology, Oregon State University, 2820 SW Campus Way, Corvallis, Oregon 97331
- Zebrafish International Resource Center, University of Oregon, 1100 Johnson Lane, Eugene, Oregon 97403
| | - Michael L Kent
- Department of Microbiology, Oregon State University, 2820 SW Campus Way, Corvallis, Oregon 97331
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, 700 SW 30th St., Corvallis, Oregon 97331
| | - James T Peterson
- U.S. Geological Survey, Oregon Cooperative Fish and Wildlife Unit, Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, 2820 SW Campus Way, Corvallis, Oregon 97331
| | - Justin L Sanders
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, 700 SW 30th St., Corvallis, Oregon 97331
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177
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Performance Evaluation and Validation of Air Samplers To Detect Aerosolized Coxiella burnetii. Microbiol Spectr 2022; 10:e0065522. [PMID: 36073825 PMCID: PMC9602806 DOI: 10.1128/spectrum.00655-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Coxiella burnetii, the etiological agent of Q fever, is an intracellular zoonotic pathogen transmitted via the respiratory route. Once released from infected animals, C. burnetii can travel long distances through air before infecting another host. As such, the ability to detect the presence of C. burnetii in air is important. In this study, three air samplers, AirPort MD8, BioSampler, and the Coriolis Micro, were assessed against a set of predetermined criteria in the presence of three different aerosolized C. burnetii concentrations. Two liquid collection media, phosphate-buffered saline (PBS) and alkaline polyethylene glycol (Alk PEG), were tested with devices requiring a collection liquid. Samples were tested by quantitative polymerase chain reaction assay (qPCR) targeting the single-copy com1 gene or multicopy insertion element IS1111. All air samplers performed well at detecting airborne C. burnetii across the range of concentrations tested. At high nebulized concentrations, AirPort MD8 showed higher, but variable, recovery probabilities. While the BioSampler and Coriolis Micro recovered C. burnetii at lower concentrations, the replicates were far more repeatable. At low and intermediate nebulized concentrations, results were comparable in the trials between air samplers, although the AirPort MD8 had consistently higher recovery probabilities. In this first study validating air samplers for their ability to detect aerosolized C. burnetii, we found that while all samplers performed well, not all samplers were equal. It is important that these results are further validated under field conditions. These findings will further inform efforts to detect airborne C. burnetii around known point sources of infection. IMPORTANCE Coxiella burnetii causes Q fever in humans and coxiellosis in animals. It is important to know if C. burnetii is present in the air around putative sources as it is transmitted via inhalation. This study assessed air samplers (AirPort MD8, BioSampler, and Coriolis Micro) for their efficacy in detecting C. burnetii. Our results show that all three devices could detect aerosolized bacteria effectively; however, at high concentrations the AirPort performed better than the other two devices, showing higher percent recovery. At intermediate and low concentrations AirPort detected at a level higher than or similar to that of other samplers. Quantification of samples was hindered by the limit of quantitation of the qPCR assay. Compared with the other two devices, the AirPort was easier to handle and clean in the field. Testing air around likely sources (e.g., farms, abattoirs, and livestock saleyards) using validated sampling devices will help better estimate the risk of Q fever to nearby communities.
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178
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Schmitz JE, Stratton CW, Persing DH, Tang YW. Forty Years of Molecular Diagnostics for Infectious Diseases. J Clin Microbiol 2022; 60:e0244621. [PMID: 35852340 PMCID: PMC9580468 DOI: 10.1128/jcm.02446-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.
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Affiliation(s)
- Jonathan E. Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David H. Persing
- Medical and Scientific Affairs, Cepheid, Sunnyvale, California, USA
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
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179
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Ultrafast PCR Detection of COVID-19 by Using a Microfluidic Chip-Based System. Bioengineering (Basel) 2022; 9:bioengineering9100548. [PMID: 36290516 PMCID: PMC9598518 DOI: 10.3390/bioengineering9100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
With the evolution of the pandemic caused by the Coronavirus disease of 2019 (COVID-19), reverse transcriptase-polymerase chain reactions (RT-PCR) have invariably been a golden standard in clinical diagnosis. Nevertheless, the traditional polymerase chain reaction (PCR) is not feasible for field application due to its drawbacks, such as time-consuming and laboratory-based dependence. To overcome these challenges, a microchip-based ultrafast PCR system called SWM-02 was proposed to make PCR assay in a rapid, portable, and low-cost strategy. This novel platform can perform 6-sample detection per run using multiple fluorescent channels and complete an ultrafast COVID-19 RT-PCR test within 40 min. Here, we evaluated the performance of the microdevice using the gradient-diluted COVID-19 reference samples and commercial PCR kit and determined its limit-of-detection (LoD) as 500 copies/mL, whose variation coefficients for the nucleocapsid (N) gene and open reading frame 1 ab region (ORF1ab) gene are 1.427% and 0.7872%, respectively. The system also revealed an excellent linear correlation between cycle threshold (Ct) values and dilution factors (R2 > 0.99). Additionally, we successfully detected the target RNAs and internal gene in the clinical samples by fast PCR, which shows strong consistency with conventional PCR protocol. Hence, with compact dimension, user-friendly design, and fast processing time, SWM-02 has the capability of offering timely and sensitive on-site molecular diagnosis for prevention and control of pathogen transmission.
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180
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Chen Z, Yin G, Wei J, Qi T, Qian Z, Wang Z, Zong S, Cui Y. Quantitative analysis of multiple breast cancer biomarkers using DNA-PAINT. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:3671-3679. [PMID: 36063064 DOI: 10.1039/d2ay00670g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Immunotherapy has become an efficient treatment method of breast cancer. Detection of proteins such as PD-L1 and CTLA-4, which are important immune checkpoint molecules, is attracting more and more attention as they play key roles in immunotherapy. Here, by combining the high resolution of DNA-PAINT (DNA points accumulation for imaging in nanoscale topography) with the qPAINT quantitative analysis method, accurate spatial localization and absolute quantification of PD-L1 and CTLA-4 on the membrane of breast cancer cells could be achieved. Meanwhile, exchange-PAINT was also conducted to count three other biomarkers (EpCAM, EGFR, and HER2). Simultaneous analysis of these biomarkers can greatly facilitate the differentiation of different kinds of breast cancer. Such a simple quantitative analysis method holds great potential in diagnosis and immunotherapy of cancers.
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Affiliation(s)
- Zengwei Chen
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Gaoqiang Yin
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Jinxiu Wei
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Tongsheng Qi
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Ziting Qian
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Zhuyuan Wang
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Shenfei Zong
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Yiping Cui
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
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181
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Ansari S, Yamaoka Y. Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance. Clin Microbiol Rev 2022; 35:e0025821. [PMID: 35404105 PMCID: PMC9491184 DOI: 10.1128/cmr.00258-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.
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Affiliation(s)
- Shamshul Ansari
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, USA
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
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182
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Guo S, Toth CRA, Luo F, Chen X, Xiao J, Edwards EA. Transient Oxygen Exposure Causes Profound and Lasting Changes to a Benzene-Degrading Methanogenic Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13036-13045. [PMID: 36083837 PMCID: PMC9496526 DOI: 10.1021/acs.est.2c02624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
We investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A one-time injection of 0.1 mL air , simulating a small leak into 30 mL batch culture bottle, had no measurable impact on benzene degradation rates, although retrospectively, a tiny enrichment of aerobic taxa was detected. A subsequent 100 times larger injection of air stalled methanogenesis and caused drastic perturbation of the microbial community. A benzene-degrading Pseudomonas became highly enriched and consumed all available oxygen. Anaerobic benzene-degrading ORM2 cell numbers plummeted during this time; re-growth and associated recovery of methanogenic benzene degradation took almost 1 year. These results highlight the oxygen sensitivity of this methanogenic culture and confirm that the mechanism for anaerobic biotransformation of benzene is independent of oxygen, fundamentally different from established aerobic pathways, and is carried out by distinct microbial communities. The study also highlights the importance of including microbial decay in characterizing and modeling mixed microbial communities.
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Affiliation(s)
| | | | | | - Xu Chen
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Johnny Xiao
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
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183
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DNMT1 Gene Expression in Patients with Helicobacter pylori Infection. ScientificWorldJournal 2022; 2022:2386891. [PMID: 36147796 PMCID: PMC9489387 DOI: 10.1155/2022/2386891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
DNMT1, as a critical enzyme affecting epigenetics through methylation of DNA cytosine-rich sequences, regulates gene expression. Exterior factors including long-term infections, in this study Helicobacter pylori infection, could change host cells' epigenetics by affecting DNMT1 gene expression. This study investigated the statistical correlation between H. pylori virulence genes and DNMT1 gene expression in gastric antral epithelial cells of gastric adenocarcinoma and gastritis patients. In a case-control study, 50 and 53 gastritis and gastric adenocarcinoma antral biopsies, including 23 and 21 patients with H. pylori infection, respectively, were collected from hospitals in the west of Iran. Having extracted total RNA from gastric biopsy samples, cDNA was synthesized and virulence genes of H. pylori were detected by using the PCR method. Relative real-time RT PCR was used to detect ΔΔCt fold changes of the DNMT1 gene expression in divided groups of patients based on H. pylori infection and clinical manifestations. The results showed that along with increasing patients' age, the DNMT1 gene expression will increase in gastric antral epithelial cells of gastric cancer patients (P ≤ 0.05). On the other hand, the biopsy samples with infection of H. pylori cagA, cagY, and cagE genotypes revealed a direct correlation along with increased DNMT1 gene expression. This study revealed the correlations of H. pylori cag pathogenicity island genes with increased DNMT1 gene expression.
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184
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Lindstedt K, Buczek D, Pedersen T, Hjerde E, Raffelsberger N, Suzuki Y, Brisse S, Holt K, Samuelsen Ø, Sundsfjord A. Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods. Gut Microbes 2022; 14:2118500. [PMID: 36045603 PMCID: PMC9450895 DOI: 10.1080/19490976.2022.2118500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Klebsiella pneumoniae is an important opportunistic healthcare-associated pathogen and major contributor to the global spread of antimicrobial resistance. Gastrointestinal colonization with K. pneumoniae is a major predisposing risk factor for infection and forms an important hub for the dispersal of resistance. Current culture-based detection methods are time consuming, give limited intra-sample abundance and strain diversity information, and have uncertain sensitivity. Here we investigated the presence and abundance of K. pneumoniae at the species and strain level within fecal samples from 103 community-based adults by qPCR and whole metagenomic sequencing (WMS) compared to culture-based detection. qPCR demonstrated the highest sensitivity, detecting K. pneumoniae in 61.2% and 75.8% of direct-fecal and culture-enriched sweep samples, respectively, including 52/52 culture-positive samples. WMS displayed lower sensitivity, detecting K. pneumoniae in 71.2% of culture-positive fecal samples at a 0.01% abundance cutoff, and was inclined to false positives in proportion to the relative abundance of other Enterobacterales present. qPCR accurately quantified K. pneumoniae to 16 genome copies/reaction while WMS could estimate relative abundance to at least 0.01%. Quantification by both methods correlated strongly with each other (Spearman's rho = 0.91). WMS also supported accurate intra-sample K. pneumoniae sequence type (ST)-level diversity detection from fecal microbiomes to 0.1% relative abundance, agreeing with the culture-based detected ST in 16/19 samples. Our results show that qPCR and WMS are sensitive and reliable tools for detection, quantification, and strain analysis of K. pneumoniae from fecal samples with potential to support infection control and enhance insights in K. pneumoniae gastrointestinal ecology.
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Affiliation(s)
- Kenneth Lindstedt
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,CONTACT Kenneth Lindstedt
| | - Dorota Buczek
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry, UiT the Arctic University of Norway, Tromsø, Norway
| | - Niclas Raffelsberger
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Kathryn Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Arnfinn Sundsfjord Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, 9038, Norway
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185
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Tiwari A, Ahmed W, Oikarinen S, Sherchan SP, Heikinheimo A, Jiang G, Simpson SL, Greaves J, Bivins A. Application of digital PCR for public health-related water quality monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155663. [PMID: 35523326 DOI: 10.1016/j.scitotenv.2022.155663] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 05/25/2023]
Abstract
Digital polymerase chain reaction (dPCR) is emerging as a reliable platform for quantifying microorganisms in the field of water microbiology. This paper reviews the fundamental principles of dPCR and its application for health-related water microbiology. The relevant literature indicates increasing adoption of dPCR for measuring fecal indicator bacteria, microbial source tracking marker genes, and pathogens in various aquatic environments. The adoption of dPCR has accelerated recently due to increasing use for wastewater surveillance of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) - the virus that causes Coronavirus Disease 2019 (COVID-19). The collective experience in the scientific literature indicates that well-optimized dPCR assays can quantify genetic material from microorganisms without the need for a calibration curve and often with superior analytical performance (i.e., greater sensitivity, precision, and reproducibility) than quantitative polymerase chain reaction (qPCR). Nonetheless, dPCR should not be viewed as a panacea for the fundamental uncertainties and limitations associated with measuring microorganisms in water microbiology. With dPCR platforms, the sample analysis cost and processing time are typically greater than qPCR. However, if improved analytical performance (i.e., sensitivity and accuracy) is critical, dPCR can be an alternative option for quantifying microorganisms, including pathogens, in aquatic environments.
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Affiliation(s)
- Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, Queensland, Australia
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, USA; Department of Biology, Morgan State University, Baltimore, MD 21251, USA; BioEnvironmental Science Program, Department of Biology, Morgan State University, Baltimore, MD 21251, USA
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland; Finnish Food Authority, Seinäjoki, Finland
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | | | - Justin Greaves
- School of Environmental Sustainability, Loyola University Chicago, 6364 N. Sheridan Rd, Chicago, IL 60660, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, LA, USA.
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186
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MacAulay S, Ellison AR, Kille P, Cable J. Moving towards improved surveillance and earlier diagnosis of aquatic pathogens: From traditional methods to emerging technologies. REVIEWS IN AQUACULTURE 2022; 14:1813-1829. [PMID: 36250037 PMCID: PMC9544729 DOI: 10.1111/raq.12674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 06/16/2023]
Abstract
Early and accurate diagnosis is key to mitigating the impact of infectious diseases, along with efficient surveillance. This however is particularly challenging in aquatic environments due to hidden biodiversity and physical constraints. Traditional diagnostics, such as visual diagnosis and histopathology, are still widely used, but increasingly technological advances such as portable next generation sequencing (NGS) and artificial intelligence (AI) are being tested for early diagnosis. The most straightforward methodologies, based on visual diagnosis, rely on specialist knowledge and experience but provide a foundation for surveillance. Future computational remote sensing methods, such as AI image diagnosis and drone surveillance, will ultimately reduce labour costs whilst not compromising on sensitivity, but they require capital and infrastructural investment. Molecular techniques have advanced rapidly in the last 30 years, from standard PCR through loop-mediated isothermal amplification (LAMP) to NGS approaches, providing a range of technologies that support the currently popular eDNA diagnosis. There is now vast potential for transformative change driven by developments in human diagnostics. Here we compare current surveillance and diagnostic technologies with those that could be used or developed for use in the aquatic environment, against three gold standard ideals of high sensitivity, specificity, rapid diagnosis, and cost-effectiveness.
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Affiliation(s)
| | | | - Peter Kille
- School of Biosciences, Cardiff UniversityCardiffUK
| | - Joanne Cable
- School of Biosciences, Cardiff UniversityCardiffUK
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187
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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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188
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What Can Genetics Do for the Control of Infectious Diseases in Aquaculture? Animals (Basel) 2022; 12:ani12172176. [PMID: 36077896 PMCID: PMC9454762 DOI: 10.3390/ani12172176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Infectious diseases place an economic burden on aquaculture and a limitation to its growth. This state-of-the-art review describes the application of genetics and genomics as novel tools to control infectious disease in aquaculture. Abstract Infectious diseases place an economic burden on aquaculture and a limitation to its growth. An innovative approach to mitigate their impact on production is breeding for disease resistance: selection for domestication, family-based selection, marker-assisted selection, and more recently, genomic selection. Advances in genetics and genomics approaches to the control of infectious diseases are key to increasing aquaculture efficiency, profitability, and sustainability and to reducing its environmental footprint. Interaction and co-evolution between a host and pathogen can, however, turn breeding to boost infectious disease resistance into a potential driver of pathogenic change. Parallel molecular characterization of the pathogen and its virulence and antimicrobial resistance genes is therefore essential to understand pathogen evolution over time in response to host immunity, and to apply appropriate mitigation strategies.
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189
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Wang D, Jiao X, Jia H, Cheng S, Jin X, Wang Y, Gao Y, Su X. Detection and quantification of Verticillium dahliae and V. longisporum by droplet digital PCR versus quantitative real-time PCR. Front Cell Infect Microbiol 2022; 12:995705. [PMID: 36072220 PMCID: PMC9441566 DOI: 10.3389/fcimb.2022.995705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Vascular wilt, caused by Verticillium dahliae and V. longisporum, limits the quality and yield of agricultural crops. Although quantitative real-time PCR (qPCR) has greatly improved the diagnosis of these two pathogens over traditional, time-consuming isolation methods, the relatively poor detection sensitivity and high measurement bias for traceable matrix-rich samples need to be improved. Here, we thus developed a droplet digital PCR (ddPCR) assay for accurate, sensitive detection and quantification of V. dahliae and V. longisporum. We compared the analytical and diagnostic performance in detail of ddPCR and the corresponding qPCR assay against the genomic DNA (gDNA) of the two fungi from cultures and field samples. In our study, the species specificity, quantification linearity, analytical sensitivity, and measurement viability of the two methods were analyzed. The results indicated that ddPCR using field samples enhanced diagnostic sensitivity, decreased quantification bias, and indicated less susceptibility to inhibitors compared with qPCR. Although ddPCR was as sensitive as qPCR when using gDNA from cultures of V. dahliae and V. longisporum, its detection rates using field samples were much higher than those of qPCR, potentially due to the inhibition from residual matrix in the extracts. The results showed that digital PCR is more sensitive and accurate than qPCR for quantifying trace amounts of V. dahliae and V. longisporum and can facilitate management practices to limit or prevent their prevalence.
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Affiliation(s)
- Di Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xinya Jiao
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Haijiang Jia
- Raw Material Technology Center of Guangxi Tobacco, Nanning, China
| | - Shumei Cheng
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Youhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
- *Correspondence: Xiaofeng Su, ; Yunhua Gao,
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xiaofeng Su, ; Yunhua Gao,
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190
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Warasi MS, Hungerford LL, Lahmers K. Optimizing Pooled Testing for Estimating the Prevalence of Multiple Diseases. JOURNAL OF AGRICULTURAL, BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2022; 27:713-727. [PMID: 35975123 PMCID: PMC9373899 DOI: 10.1007/s13253-022-00511-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/27/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022]
Abstract
Pooled testing can enhance the efficiency of diagnosing individuals with diseases of low prevalence. Often, pooling is implemented using standard groupings (2, 5, 10, etc.). On the other hand, optimization theory can provide specific guidelines in finding the ideal pool size and pooling strategy. This article focuses on optimizing the precision of disease prevalence estimators calculated from multiplex pooled testing data. In the context of a surveillance application of animal diseases, we study the estimation efficiency (i.e., precision) and cost efficiency of the estimators with adjustments for the number of expended tests. This enables us to determine the pooling strategies that offer the highest benefits when jointly estimating the prevalence of multiple diseases, such as theileriosis and anaplasmosis. The outcomes of our work can be used in designing pooled testing protocols, not only in simple pooling scenarios but also in more complex scenarios where individual retesting is performed in order to identify positive cases. A software application using the shiny package in R is provided with this article to facilitate implementation of our methods. Supplementary materials accompanying this paper appear online.
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Affiliation(s)
- Md S. Warasi
- Department of Mathematics and Statistics, Radford University, Whitt Hall 224, Radford, VA 24142 USA
| | - Laura L. Hungerford
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061 USA
| | - Kevin Lahmers
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061 USA
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Yi L, Jin M, Gao M, Wang H, Fan Q, Grenier D, Sun L, Wang S, Wang Y. Specific quantitative detection of Streptococcus suis and Actinobacillus pleuropneumoniae in co-infection and mixed biofilms. Front Cell Infect Microbiol 2022; 12:898412. [PMID: 35992166 PMCID: PMC9381733 DOI: 10.3389/fcimb.2022.898412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Respiratory infections seriously affect the swine industry worldwide. Co-infections of two vital pathogenic bacteria Streptococcus suis (S. suis) and Actinobacillus pleuropneumoniae (A. pleuropneumoniae), colonizing the respiratory tract often occurs in veterinary clinical practice. Moreover, our previous research found that S. suis and A. pleuropneumoniae can form biofilm in vitro. The formation of a mixed biofilm not only causes persistent infections, but also increases the multiple drug resistance of bacteria, which brings difficulties to disease prevention and control. However, the methods for detecting S. suis and A. pleuropneumoniae in co-infection and biofilm are immature. Therefore, in this study, primers and probes were designed based on the conservative sequence of S. suis gdh gene and A. pleuropneumoniae apxIVA gene. Then, a TaqMan duplex real-time PCR method for simultaneous detection of S. suis and A. pleuropneumoniae was successfully established via optimizing the reaction system and conditions. The specificity analysis results showed that this TaqMan real-time PCR method had strong specificity and high reliability. The sensitivity test results showed that the minimum detection concentration of S. suis and A. pleuropneumoniae recombinant plasmid was 10 copies/μL, which is 100 times more sensitive than conventional PCR methods. The amplification efficiencies of S. suis and A. pleuropneumoniae were 95.9% and 104.4% with R2 value greater than 0.995, respectively. The slopes of the calibration curves of absolute cell abundance of S. suis and A. pleuropneumoniae were 1.02 and 1.09, respectively. The assays were applied to cultivated mixed biofilms and approximately 108 CFUs per biofilm were quantified when 108 CFUs planktonic bacteria of either S. suis or A. pleuropneumoniae were added to biofilms. In summary, this study developed a TaqMan real-time PCR assay for specific, accurate quantification of S. suis or A. pleuropneumoniae in mixed biofilms, which may help for the detection, prevention and control of diseases caused by a bacterial mixed infection involving S. suis and A. pleuropneumoniae.
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Affiliation(s)
- Li Yi
- College of Life Science, Luoyang Normal University, Luoyang, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Manyu Jin
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Mengxia Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Haikun Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Qingying Fan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Quebec City, QC, Canada
| | - Liyun Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Yang Wang, ; Shaohui Wang,
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- *Correspondence: Yang Wang, ; Shaohui Wang,
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192
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Russo S, Giorgio G, Leo S, Arrigoni N, Garbarino C, Ricchi M. Validation of IS900- qPCR assay to assess the presence of Mycobacterium avium subs. paratuberculosis in faecal samples according to the OIE procedure. Prev Vet Med 2022; 208:105732. [DOI: 10.1016/j.prevetmed.2022.105732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/19/2022] [Accepted: 07/31/2022] [Indexed: 11/24/2022]
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193
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Nath BK, Das S, Das T, Forwood JK, Raidal SR. Development and applications of a TaqMan based quantitative real-time PCR for the rapid detection of Pigeon circovirus (PiCV). J Virol Methods 2022; 308:114588. [PMID: 35870671 DOI: 10.1016/j.jviromet.2022.114588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
TaqMan probe based quantitative polymerase reaction (TaqMan qPCR) is a robust and reliable technique for detecting and quantifying target DNA copies. Quantitative molecular diagnosis of genetically diverse single stranded DNA (ssDNA) virus such as Pigeon circovirus (PiCV) can be challenging owing to difficulties in primer binding or low abundance of template DNA copies in clinical specimens. Several methods have been described for the detection of PiCV, being qPCR the most simple and reliable. As far as is known, two qPCR systems described until now are based on SYBR green. This study reports development and validation of a highly sensitive TaqMan qPCR targeted to Rep for the detection of highly diverse PiCV in pigeon samples with excellent reproducibility, specificity, and sensitivity. The limit of detection was determined as low as 2 (two) plasmid copies. Estimations of 100 % specificity and 100 % sensitivity were obtained based on the qPCR results with panel of 60 samples (known PiCV positive, n = 30; known PiCV negative, n = 20; samples positive to Beak and feather disease virus (BFDV), n = 5 and samples positive to canine circovirus, n = 5). Co-efficient of variation (CV) for Ct values ranged between 0.27 % and 0.78 % in the same assay and 1.84-2.87 % in different assays.
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Affiliation(s)
- Babu K Nath
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia
| | - Shubhagata Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia
| | - Tridip Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia
| | - Shane R Raidal
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia; School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia.
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194
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Danh K, Karp DG, Singhal M, Tankasala A, Gebhart D, de Jesus Cortez F, Tandel D, Robinson PV, Seftel D, Stone M, Simmons G, Bagri A, Schreiber MA, Buser A, Holbro A, Battegay M, Morris MK, Hanson C, Mills JR, Granger D, Theel ES, Stubbs JR, Corash LM, Tsai CT. Detection of neutralizing antibodies against multiple SARS-CoV-2 strains in dried blood spots using cell-free PCR. Nat Commun 2022; 13:4212. [PMID: 35864104 PMCID: PMC9302227 DOI: 10.1038/s41467-022-31796-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
An easily implementable serological assay to accurately detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibodies is urgently needed to better track herd immunity, vaccine efficacy and vaccination rates. Herein, we report the Split-Oligonucleotide Neighboring Inhibition Assay (SONIA) which uses real-time qPCR to measure the ability of neutralizing antibodies to block binding between DNA-barcoded viral spike protein subunit 1 and the human angiotensin-converting enzyme 2 receptor protein. The SONIA neutralizing antibody assay using finger-prick dried blood spots displays 91-97% sensitivity and 100% specificity in comparison to the live-virus neutralization assays using matched serum specimens for multiple SARS-CoV-2 variants-of-concern. The multiplex version of this neutralizing antibody assay, using easily collectable finger-prick dried blood spots, can be a valuable tool to help reveal the impact of age, pre-existing health conditions, waning immunity, different vaccination schemes and the emergence of new variants-of-concern.
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Affiliation(s)
- Kenneth Danh
- Enable Biosciences Inc, South San Francisco, CA, USA
| | | | | | | | - David Gebhart
- Enable Biosciences Inc, South San Francisco, CA, USA
| | | | | | | | - David Seftel
- Enable Biosciences Inc, South San Francisco, CA, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Martin A Schreiber
- Department of Surgery, Oregon Health & Science University, Portland, OR, USA
| | - Andreas Buser
- Regional Blood Transfusion Service, Swiss Red Cross, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Andreas Holbro
- Regional Blood Transfusion Service, Swiss Red Cross, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - John R Mills
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dane Granger
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Elitza S Theel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James R Stubbs
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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195
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Miyazono S, Kodama T, Akamatsu Y, Nakao R, Miyahira H. Application of environmental DNA analysis for detecting potential sources of invasive aquatic plant Egeria densa in a riverine network. LANDSCAPE AND ECOLOGICAL ENGINEERING 2022. [DOI: 10.1007/s11355-022-00517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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196
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Dehghan A, Pourmand MR, Salimi V, Asbagh FA, Foroushani AR, Sadeghi K, Quchani SH. The effects of Chlamydia trachomatis, Mycoplasma hominis, and Ureaplasma urealyticum loads on semen quality: Detection and quantitative analysis. Microb Pathog 2022; 169:105676. [PMID: 35820579 DOI: 10.1016/j.micpath.2022.105676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND The loads of Chlamydia trachomatis (CT), Mycoplasma hominis (MH), and Ureaplasma urealyticum (UU) may impact infertility, as well as cause risk of transmission. The quality and quantity of semen demonstrate male reproductive health. This study aimed to investigate the semen quality affected by CT, MH, and UU loads. MATERIALS AND METHODS 130 semen samples, including infertile and fertile cases, were collected and analyzed. The whole genomic DNA was extracted, and the desired genes' plasmids were constructed. The CT, MH, and UU loads were quantified by real-time PCR. The data were analyzed using SPSS version 24. RESULTS The average age of participants was 35.2 ± 6.8 years. CT, MH, and UU frequency were 9.2% vs. 3.1%, 15.4% vs. 3.1%, and 15.4 vs. 3.1% in infertile and fertile men, respectively. The mean loads of CT, MH, and UU in infertile men were 6.44 log10 copies/ml (range 5.31-7), 4.24 log10 copies/ml (range 3.37-4.7), and 6.94 log10 copies/ml (range 5.08-8.69) respectively, which was significantly higher than fertile men. The findings revealed a significant correlation between CT and UU loads and semen parameters, whereas the load of MH displayed significant effects just on sperm motility, morphology, and the number of leukocytes. CONCLUSION The absence of clinical manifestations may not indicate the quality of semen. The pathogens' loads may significantly influence the quality and properties of male reproductive health.
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Affiliation(s)
- Amin Dehghan
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Firouzeh Akbari Asbagh
- Department of Obstetrics and Gynecology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kaveh Sadeghi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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197
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Nehra M, Kumar V, Kumar R, Dilbaghi N, Kumar S. Current Scenario of Pathogen Detection Techniques in Agro-Food Sector. BIOSENSORS 2022; 12:489. [PMID: 35884292 PMCID: PMC9313409 DOI: 10.3390/bios12070489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 05/05/2023]
Abstract
Over the past-decade, agricultural products (such as vegetables and fruits) have been reported as the major vehicles for foodborne diseases, which are limiting food resources. The spread of infectious diseases due to foodborne pathogens poses a global threat to human health and the economy. The accurate and timely detection of infectious disease and of causative pathogens is crucial in the prevention and treatment of disease. Negligence in the detection of pathogenic substances can be catastrophic and lead to a pandemic. Despite the revolution in health diagnostics, much attention has been paid to the agro-food sector regarding the detection of food contaminants (such as pathogens). The conventional analytical techniques for pathogen detection are reliable and still in operation. However, laborious procedures and time-consuming detection via these approaches emphasize the need for simple, easy-to-use, and affordable detection techniques. The rapid detection of pathogens from food is essential to avoid the morbidity and mortality originating from the suboptimal nature of empiric pathogen treatment. This review critically discusses both the conventional and emerging bio-molecular approaches for pathogen detection in agro-food.
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Affiliation(s)
- Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Virendra Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Rajesh Kumar
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
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198
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Fluorescence-based simultaneous dual oligo sensing of HCV genotypes 1 and 3 using magnetite nanoparticles. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112463. [PMID: 35567883 DOI: 10.1016/j.jphotobiol.2022.112463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/12/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
Nucleic acid tests (NATs) have gained an important position in biosensing in the context of the increasing need to meet the stringent requirements for accurate diagnosis of infectious diseases with high sensitivity and selectivity. Recently, the development of new strategies towards multiplex detection of analytes in a single assay is gaining impetus since such an approach would lead to high throughput analysis, leading to substantial benefits in terms of time, infrastructure, labor, and cost. In this work, we demonstrate a facile fluorescence-based simultaneous dual oligo sensing of genotypes 1 and 3 by employing two target sequences (36-mers each) derived from the NS4B and NS5A regions of HCV genome, respectively. A set of 18-mer amine-tagged probes and another set of 18-mer fluorescently-labeled probes that were complementary to each half of the 36-mer target sequences were designed. The amine-tagged probes were immobilized over aldehyde-derivatized magnetite nanoparticles (NPs) via imine bond formation, which was characterized using X-ray photoelectron spectroscopy (XPS) and energy dispersive spectroscopy (EDS) mapping techniques. The successful hybridization between the two probes with their target followed by magnetic removal of the NPs from the solution enabled quantitative analysis of the target by measuring the fluorescence intensity of the residual concentration of the fluorescently-tagged probe. In this manner, the targets corresponding to genotypes 1 and 3 were simultaneously detected with the detection limit in the range of 10-15 nM. The current strategy can potentially be amalgamated with existing nanotechnology-based techniques towards multiplex oligo sensing of several pathogens.
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199
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Ali A, R.Derar D, A.Mousa H, A.Osman S, Refaai W, I.Almundarij T, A.Al Dubib M, A.Allam S. First report on the isolation of Chlamydia abortus from female dromedary camels with ovarian hydrobursitis. Theriogenology 2022; 191:102-108. [DOI: 10.1016/j.theriogenology.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 11/25/2022]
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200
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Ragothaman KK, Elmarsafi TX, Mobaraki A, Zarick CS, Evans KK, Steinberg JS, Attinger CE, Kim PJ. Evaluation of Polymerase Chain Reaction in the Identification and Quantification of Clinically Relevant Bacterial Species in Lower Extremity Wound Infections. J Foot Ankle Surg 2022; 61:713-718. [PMID: 34895822 DOI: 10.1053/j.jfas.2020.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 02/03/2023]
Abstract
Identification of bacteria by polymerase chain reaction (PCR) is known to be more sensitive than culture, which brings to question the clinical applicability of the results. In this study, we evaluate the ability of PCR to detect clinically relevant bacterial species in lower extremity wound infections requiring operative debridement, as well as the quantitative change in biodiversity and bacterial load reflected by PCR during the course of treatment. Thirty-four infected lower extremity were examined by analysis of 16S ribosomal RNA subunit and by culture. McNemar's test was used to measure the concordance of clinically relevant bacterial species identified by PCR compared to culture during each debridement. Change in wound biodiversity from initial presentation to final closure was evaluated by Wilcoxon signed-rank test. Kaplan-Meier survival curve was used to characterize change in measured bacterial load over the course of operative debridement. A total of 15 and 12 clinically relevant bacterial species were identified by PCR and culture, respectively. The most common bacterial species identified were Coagulase-negative Staphylococcus, Staphylococcus aureus, and Enterococcus spp. PCR was less likely to detect Enterococcus spp. on initial debridement and Coagulase-negative Staphylococcus on closure in this study population. A significant decrease in mean number of clinically relevant species detected from initial debridement to closure was reflected by culture (p = .0188) but not by PCR (p = .1848). Both PCR (p = .0128) and culture (p = .0001) depicted significant reduction in mean bacterial load from initial debridement to closure. PCR is able to identify common clinically relevant bacterial species in lower extremity surgical wound infections. PCR displays increased sensitivity compared to culture with relation to detection of biodiversity, rather than bacterial load. Molecular diagnostics and conventional culture may serve a joint purpose to assist with rendering clinical judgment in complex wound infections.
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Affiliation(s)
- Kevin K Ragothaman
- Foot and Ankle Surgeon, Foot and Ankle Associates, Los Gatos and Cupertino, CA.
| | | | | | - Caitlin S Zarick
- Assistant Professor, Department of Plastic Surgery, Georgetown University School of Medicine, Washington, DC
| | - Karen K Evans
- Professor, Department of Plastic Surgery, Georgetown University School of Medicine, Washington, DC
| | - John S Steinberg
- Assistant Professor, Department of Plastic Surgery, Georgetown University School of Medicine, Washington, DC
| | - Christopher E Attinger
- Professor, Department of Plastic Surgery, Georgetown University School of Medicine, Washington, DC
| | - Paul J Kim
- Professor, Departments of Plastic and Orthopaedic Surgery, University of Texas Southwestern, Dallas, TX
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