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Zhuang L, Gong J, Zhao Y, Yang J, Liu G, Zhao B, Song C, Zhang Y, Shen Q. Progress in methods for the detection of viable Escherichia coli. Analyst 2024; 149:1022-1049. [PMID: 38273740 DOI: 10.1039/d3an01750h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Escherichia coli (E. coli) is a prevalent enteric bacterium and a necessary organism to monitor for food safety and environmental purposes. Developing efficient and specific methods is critical for detecting and monitoring viable E. coli due to its high prevalence. Conventional culture methods are often laborious and time-consuming, and they offer limited capability in detecting potentially harmful viable but non-culturable E. coli in the tested sample, which highlights the need for improved approaches. Hence, there is a growing demand for accurate and sensitive methods to determine the presence of viable E. coli. This paper scrutinizes various methods for detecting viable E. coli, including culture-based methods, molecular methods that target DNAs and RNAs, bacteriophage-based methods, biosensors, and other emerging technologies. The review serves as a guide for researchers seeking additional methodological options and aiding in the development of rapid and precise assays. Moving forward, it is anticipated that methods for detecting E. coli will become more stable and robust, ultimately contributing significantly to the improvement of food safety and public health.
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Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, P. R. China
| | - Ying Zhao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Guofang Liu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Bin Zhao
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Chunlei Song
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
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Delannoy S, Hoffer C, Tran ML, Madec JY, Brisabois A, Fach P, Haenni M. High throughput qPCR analyses suggest that Enterobacterales of French sheep and cow cheese rarely carry genes conferring resistances to critically important antibiotics for human medicine. Int J Food Microbiol 2023; 403:110303. [PMID: 37384974 DOI: 10.1016/j.ijfoodmicro.2023.110303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023]
Abstract
Bacteria present in raw milk can carry acquired or intrinsic antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, only a few studies have evaluated raw milk cheese as a potential reservoir of ARGs. This study thus aimed at providing new data regarding resistance markers present in raw milk cheese. Sheep (n = 360) and cow (n = 360) cheese samples produced in France were incubated in buffered peptone water supplemented with acriflavin or novobiocin; as corroborated by 16S metabarcoding, samples were enriched in Gram-negative bacteria since Escherichia coli and Hafnia alvei respectively accounted for 40 % and 20 % of the samples' microbiota. Screening of the samples for the presence of 30 ARGs and 16 MGEs by high throughput qPCR array showed that nine ARGs conferring resistances to 1st-generation beta-lactams, aminoglycosides, trimethoprim/sulfonamides and tetracyclines occurred in >75 % of both sheep and cow samples. This is neither surprising nor alarming since these resistance genes are widely spread across the One Health human, animal and environmental sectors. Conversely, genes conferring resistances to last-generations cephalosporins were rarely identified, while those conferring resistances to carbapenems or amikacin, which are restricted to human use, were never detected. Multiple MGEs were detected, the most frequent ones being IncF plasmids, confirming the potential transmission of ARGs. Our results are in line with the few studies of the resistome of milk or milk cheese showing that genes conferring resistances to 1st-generation beta-lactams, aminoglycosides and tetracyclines families are widespread, while those conferring resistances to critically important antibiotics are rare or absent.
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Affiliation(s)
- Sabine Delannoy
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France.
| | - Corine Hoffer
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Maï-Lan Tran
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, 69007 Lyon, France
| | - Anne Brisabois
- Strategy and Programs Department, ANSES, 94700 Maisons-Alfort, France
| | - Patrick Fach
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, 69007 Lyon, France
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PALOMINO-KOBAYASHI LA, PONS MJ, RUIZ J. Estimation of inherent bacterial DNA contamination in a qPCR master mix: concerns about background DNA of reagents. MINERVA BIOTECHNOLOGY AND BIOMOLECULAR RESEARCH 2022. [DOI: 10.23736/s2724-542x.22.02925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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The ratio of nicotinic acid to nicotinamide as a microbial biomarker for assessing cell therapy product sterility. Mol Ther Methods Clin Dev 2022; 25:410-424. [PMID: 35573051 PMCID: PMC9065052 DOI: 10.1016/j.omtm.2022.04.006] [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: 10/06/2021] [Accepted: 04/10/2022] [Indexed: 11/20/2022]
Abstract
Controlling microbial risks in cell therapy products (CTPs) is important for product safety. Here, we identified the nicotinic acid (NA) to nicotinamide (NAM) ratio as a biomarker that detects a broad spectrum of microbial contaminants in cell cultures. We separately added six different bacterial species into mesenchymal stromal cell and T cell culture and found that NA was uniquely present in these bacteria-contaminated CTPs due to the conversion from NAM by microbial nicotinamidases, which mammals lack. In cells inoculated with 1 × 104 CFUs/mL of different microorganisms, including USP <71> defined organisms, the increase in NA to NAM ratio ranged from 72 to 15,000 times higher than the uncontaminated controls after 24 h. Importantly, only live microorganisms caused increases in this ratio. In cells inoculated with 18 CFUs/mL of Escherichia coli, 20 CFUs/mL of Bacillus subtilis, and 10 CFUs/mL of Candida albicans, significant increase of NA to NAM ratio was detected using LC-MS after 18.5, 12.5, and 24.5 h, respectively. In contrast, compendial sterility test required >24 h to detect the same amount of these three organisms. In conclusion, the NA to NAM ratio is a useful biomarker for detection of early-stage microbial contaminations in CTPs.
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Alexandrino F, Malgarin JS, Krieger MA, Morello LG. Optimized broad-range real-time PCR-based method for bacterial screening of platelet concentrates. BRAZ J BIOL 2020; 81:692-700. [PMID: 32876173 DOI: 10.1590/1519-6984.229893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/08/2020] [Indexed: 11/22/2022] Open
Abstract
Bacterial contamination of blood components remains a major challenge in transfusion medicine, particularly, platelet concentrates (PCs) due to the storage conditions that support bacterial proliferation. In this study, we develop a rapid, sensitive and specific real-time PCR protocol for bacterial screening of PCs. An internally controlled real-time PCR-based method was optimized and validated with our proprietary 16S Universal PCR Master Mix (IBMP/Fiocruz), which targets a conserved region of the bacterial 16S rRNA gene. Nonspecific background DNA was completely eliminated by treating the PCR Master Mix with ethidium monoazide (EMA). A lower limit of detection was observed for 10 genome equivalents with an observed Ct value of 34±1.07 in calibration curve generated with 10-fold serial dilutions of E. coli DNA. The turnaround time for processing, including microbial DNA purification, was approximately 4 hours. The developed method showed a high sensitivity with no non-specific amplification and a lower time-to-detection than traditional microbiological methods, demonstrating it to be an efficient means of screening pre-transfusion PCs.
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Affiliation(s)
- F Alexandrino
- Instituto de Biologia Molecular do Paraná - IBMP, Rua Prof. Algacyr Munhoz Mader, 3775, CEP 81350-010, Curitiba, PR, Brasil
| | - J S Malgarin
- Instituto de Biologia Molecular do Paraná - IBMP, Rua Prof. Algacyr Munhoz Mader, 3775, CEP 81350-010, Curitiba, PR, Brasil
| | - M A Krieger
- Instituto de Biologia Molecular do Paraná - IBMP, Rua Prof. Algacyr Munhoz Mader, 3775, CEP 81350-010, Curitiba, PR, Brasil
| | - L G Morello
- Instituto de Biologia Molecular do Paraná - IBMP, Rua Prof. Algacyr Munhoz Mader, 3775, CEP 81350-010, Curitiba, PR, Brasil
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Abstract
Increasing antibiotic resistance has resulted in infections that are life-threatening and difficult to treat. Interventions that prevent these infections, particularly without using antibiotics, could save lives. Intestinal colonization by pathogens, including vancomycin-resistant Enterococcus and carbapenem-resistant Enterobacteriaceae (part of the order Enterobacterales) is associated with subsequent infection, and increased colonization density is associated with increased infection risk. Therefore, colonization offers a window of opportunity for infection prevention if (i) there are rapid and inexpensive assays to detect colonization, (ii) there are safe and effective interventions, and (iii) the risk of infection outweighs the risk of the treatment. Fecal transplants are proof of principle that manipulating the microbiome can reduce such colonization and prevent infections. This study demonstrates the feasibility of implementing rapid and inexpensive assays to quantify colonization and measures the strength of association between Enterobacterales dominance and subsequent infection. The approach described here could be a valuable tool in the prevention of antibiotic-resistant infections. The Enterobacterales order of Gram-negative bacteria includes the common nosocomial pathogens Klebsiella pneumoniae, Escherichia coli, Serratia marcescens, and Enterobacter species. Intestinal domination by some colonizing bacterial taxa is associated with subsequent infection, but 16S rRNA gene sequencing is too costly and slow to be used in a clinical setting. The objectives of this study were to develop a PCR-based assay that can measure Enterobacterales density, validate it against 16S rRNA gene sequencing, and measure the association between Enterobacterales dominance and subsequent infection. Two quantitative PCR (qPCR) assays that were developed to quantify the absolute and relative abundance of Enterobacterales had good correlation with 16S rRNA sequence analysis (P < 0.0001). Using both PCR assays and 16S sequencing, a matched case-control study was performed comparing rectal swabs from hospitalized patients who later developed bloodstream, urinary tract, or respiratory Enterobacterales infections (n = 95) to swabs from patients who remained uninfected (n = 189). Enterobacterales abundance measured by sequencing was high in both cases and controls (means, 31.1% and 27.5%, respectively; P = 0.322). We observed an increased risk of infection that depended on both the absolute and relative abundance of Enterobacterales as measured by qPCR assay A (P = 0.012). After adjustment for albumin levels, central venous catheter presence, and use of cephalosporins at the time of swab collection, this association still approached significance (P = 0.061). These results demonstrate that using qPCR to measure intestinal colonization dominance is feasible, indicate that hospitalized patients have high levels of Enterobacterales colonization, and suggest that both relative and absolute abundance may be associated with subsequent infection. IMPORTANCE Increasing antibiotic resistance has resulted in infections that are life-threatening and difficult to treat. Interventions that prevent these infections, particularly without using antibiotics, could save lives. Intestinal colonization by pathogens, including vancomycin-resistant Enterococcus and carbapenem-resistant Enterobacteriaceae (part of the order Enterobacterales) is associated with subsequent infection, and increased colonization density is associated with increased infection risk. Therefore, colonization offers a window of opportunity for infection prevention if (i) there are rapid and inexpensive assays to detect colonization, (ii) there are safe and effective interventions, and (iii) the risk of infection outweighs the risk of the treatment. Fecal transplants are proof of principle that manipulating the microbiome can reduce such colonization and prevent infections. This study demonstrates the feasibility of implementing rapid and inexpensive assays to quantify colonization and measures the strength of association between Enterobacterales dominance and subsequent infection. The approach described here could be a valuable tool in the prevention of antibiotic-resistant infections.
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Greiling TM, Dehner C, Chen X, Hughes K, Iñiguez AJ, Boccitto M, Ruiz DZ, Renfroe SC, Vieira SM, Ruff WE, Sim S, Kriegel C, Glanternik J, Chen X, Girardi M, Degnan P, Costenbader KH, Goodman AL, Wolin SL, Kriegel MA. Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus. Sci Transl Med 2019; 10:10/434/eaan2306. [PMID: 29593104 DOI: 10.1126/scitranslmed.aan2306] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 11/17/2017] [Accepted: 01/19/2018] [Indexed: 12/14/2022]
Abstract
The earliest autoantibodies in lupus are directed against the RNA binding autoantigen Ro60, but the triggers against this evolutionarily conserved antigen remain elusive. We identified Ro60 orthologs in a subset of human skin, oral, and gut commensal bacterial species and confirmed the presence of these orthologs in patients with lupus and healthy controls. Thus, we hypothesized that commensal Ro60 orthologs may trigger autoimmunity via cross-reactivity in genetically susceptible individuals. Sera from human anti-Ro60-positive lupus patients immunoprecipitated commensal Ro60 ribonucleoproteins. Human Ro60 autoantigen-specific CD4 memory T cell clones from lupus patients were activated by skin and mucosal Ro60-containing bacteria, supporting T cell cross-reactivity in humans. Further, germ-free mice spontaneously initiated anti-human Ro60 T and B cell responses and developed glomerular immune complex deposits after monocolonization with a Ro60 ortholog-containing gut commensal, linking anti-Ro60 commensal responses in vivo with the production of human Ro60 autoantibodies and signs of autoimmunity. Together, these data support that colonization with autoantigen ortholog-producing commensal species may initiate and sustain chronic autoimmunity in genetically predisposed individuals. The concept of commensal ortholog cross-reactivity may apply more broadly to autoimmune diseases and lead to novel treatment approaches aimed at defined commensal species.
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Affiliation(s)
- Teri M Greiling
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA.,Department of Dermatology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carina Dehner
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xinguo Chen
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm SE-171 77, Sweden.,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Kevin Hughes
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm SE-171 77, Sweden.,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Alonso J Iñiguez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Marco Boccitto
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm SE-171 77, Sweden.,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Daniel Zegarra Ruiz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Stephen C Renfroe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Silvio M Vieira
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - William E Ruff
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Soyeong Sim
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm SE-171 77, Sweden.,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Christina Kriegel
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Julia Glanternik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xindi Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Michael Girardi
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Patrick Degnan
- Department of Microbial Pathogenesis and Yale Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Karen H Costenbader
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Yale Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sandra L Wolin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA. .,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Martin A Kriegel
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA. .,Section of Rheumatology, Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
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Abstract
Many studies have shown that the urinary tract harbours its own microbial community known as the urinary microbiota, which have been implicated in urinary tract disorders. This observation contradicts the long-held notion that urine is a sterile biofluid in the absence of acute infection of the urinary tract. In light of this new discovery, many basic questions that are crucial for understanding the role of the urinary microbiota in human health and disease remain unanswered. Given that the urinary microbiota is an emerging area of study, optimized techniques and protocols to identify microorganisms in the urinary tract are still being established. However, the low microbial biomass and close proximity to higher microbial biomass environments (for example, the vagina) present distinct methodological challenges for microbial community profiling of the urinary microbiota. A clear understanding of the unique technical considerations for obtaining and analysing low microbial biomass samples, as well the influence of key elements of experimental design and computational analysis on downstream interpretation, will improve our ability to interpret and compare results across methods and studies and is relevant for studies profiling the urinary microbiota and other sites of low microbial abundance.
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Sun Y, Chang Y, Zhang Q, Liu M. An Origami Paper-Based Device Printed with DNAzyme-Containing DNA Superstructures for Escherichia coli Detection. MICROMACHINES 2019; 10:E531. [PMID: 31408962 PMCID: PMC6722672 DOI: 10.3390/mi10080531] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 11/16/2022]
Abstract
Rapid detection of pathogenic bacteria is extremely important for public health and safety. Here, we describe for the first time an integrated origami paper-based analytical device (PAD) incorporating cell lysis, molecular recognition, amplification and visual detection of Escherichia coli (E. coli). The device features three components: paper for its ability to extract protein molecules nonspecifically from cells, DNA superstructures for their ability to immobilize RNA-cleaving DNAzymes (RCDs) but undergo target-induced RNA cleavage on paper, and isothermal rolling circle amplification (RCA) for its ability to amplify each cleavage event into repetitive sequence units that can be detected by naked eye. This device can achieve detection of E. coli K12 with a detection limit of as low as 103 CFU·mL-1 in a total turnaround time of 35 min. Furthermore, this device allowed the sensitive detection of E. coli in complex sample matrices such as juice and milk. Given that more specific RCDs can be evolved for diverse bacteria, the integrated PAD holds great potential for rapid, sensitive and highly selective detection of pathogenic bacteria in resource-limited settings.
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Affiliation(s)
- Yating Sun
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China.
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Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. MICROBIOME 2018; 6:226. [PMID: 30558668 PMCID: PMC6298009 DOI: 10.1186/s40168-018-0605-2] [Citation(s) in RCA: 1297] [Impact Index Per Article: 216.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/25/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants-DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam ( https://github.com/benjjneb/decontam ), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls. RESULTS Decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants. CONCLUSIONS Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.
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Affiliation(s)
- Nicole M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Diana M Proctor
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Orofacial Sciences, University of California, San Francisco School of Dentistry, San Francisco, CA, 94143, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Benjamin J Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 456 Research Building, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.
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11
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Viana JD, Ferreira SC, Matana SR, Rossi F, Patel P, Garson JA, Rocha V, Tedder R, Mendrone-Júnior A, Levi JE. Detection of bacterial contamination in platelet concentrates from Brazilian donors by molecular amplification of the ribosomal 16S gene. Transfus Med 2018; 28:420-426. [PMID: 30304760 DOI: 10.1111/tme.12561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 08/09/2018] [Accepted: 09/12/2018] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The aim of our work was to establish a semi-automated high-throughput DNA amplification method for the universal screening of bacteria in platelet concentrates (PCs). BACKGROUND Among cases of transfusion transmission of infectious agents, bacterial contamination ranks first in the number of events, morbidity and mortality. Transmission occurs mainly by transfused PCs. Automated culture is adopted by some blood banks for screening of bacterial contamination, but this procedure is expensive and has a relatively long turnaround time. METHODS PCs were spiked with suspensions of five different bacterial species in a final concentration of 1 and 10 colony-forming units (CFU) per millilitre. After incubation, the presence of bacteria was investigated by real-time polymerase chain reaction (PCR) and by the Enhanced Bacterial Detection System (eBDS, Pall) assay as a reference method. Real-time PCR amplification was performed with a set of universal primers and probes targeting the 16S rRNA gene. Co-amplification of human mitochondrial DNA served as an internal control. RESULTS Using the real-time PCR method, it was possible to detect the presence of all bacterial species tested with an initial concentration of 10 CFU mL-1 24 h after contamination, except for Staphylococcus hominis. The PCR assay also detected, at 24 h, the presence of Serratia marcescens and Enterobacter cloacae with an initial concentration of 1 CFU mL-1 . CONCLUSIONS The real-time PCR assay may be a reliable alternative to conventional culture methods in the screening of bacterial contamination of PCs, enabling bacterial detection even with a low initial concentration of microorganisms.
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Affiliation(s)
- J D Viana
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - S C Ferreira
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - S R Matana
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - F Rossi
- Departamento de Microbiologia do Laboratório Central, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - P Patel
- Microbiology Services, NHS Blood and Transplant, London, UK
| | - J A Garson
- Microbiology Services, NHS Blood and Transplant, London, UK.,Division of Infection and Immunity, University College London, London, UK
| | - V Rocha
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - R Tedder
- Microbiology Services, NHS Blood and Transplant, London, UK.,Division of Infection and Immunity, University College London, London, UK
| | | | - J E Levi
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
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12
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Somerville TF, Corless CE, Neal T, Kaye SB. Effect of storage time and temperature on the detection of Pseudomonas aeruginosa, Acanthamoeba and Herpes Simplex Virus from corneal impression membranes. J Med Microbiol 2018; 67:1321-1325. [PMID: 30051806 DOI: 10.1099/jmm.0.000812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The effect of storage time and temperature on the recovery of pathogen DNA from polytetrafluorethylene (PTFE) was investigated. PTFE impression membranes were inoculated with Pseudomonas aeruginosa, Herpes Simplex Virus-1 (HSV-1) or Acanthamoeba and stored at -70 °C, -20 °C, +4 °C or +35 °C. PCR was performed on days 0, 1, 2, 3, 7 and months 1, 3 and 10 post-inoculation. We found no reduction in the DNA recovery of any of the studied microorganisms for the first 3 days of storage up to +35 °C. For HSV-1 and P. aeruginosa, storage for 3 months at +35 °C was associated with a significant reduction in DNA recovery (P<0.001), but not at +4 °C, -20 °C or -70 °C for 1 month for P. aeruginosa and for 10 months for HSV-1. Acanthamoeba DNA recovery was not affected by any storage parameters (P=0.203). These results will inform the investigation of microbial keratitis where access to microbiological testing is not readily available.
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Affiliation(s)
- Tobi F Somerville
- 1St Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, UK.,2Department of Eye and Vision Sciences, University of Liverpool, Liverpool, UK
| | - Caroline E Corless
- 3Department of Infection and Immunity, Liverpool Clinical Laboratories, Royal Liverpool University Hospital, Liverpool, UK
| | - Timothy Neal
- 3Department of Infection and Immunity, Liverpool Clinical Laboratories, Royal Liverpool University Hospital, Liverpool, UK
| | - Stephen B Kaye
- 1St Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, UK.,2Department of Eye and Vision Sciences, University of Liverpool, Liverpool, UK
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Kleinschmidt K, Wilkens E, Glaeser SP, Kaempfer P, Staerk A, Roesti D. Development of a qualitative real-time PCR for microbiological quality control testing in mammalian cell culture production. J Appl Microbiol 2017; 122:997-1008. [PMID: 28028873 DOI: 10.1111/jam.13387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/12/2016] [Accepted: 12/22/2016] [Indexed: 12/28/2022]
Abstract
AIMS The aim of this study was to develop and evaluate a real-time PCR technology for microbiological control methods to examine individualized cell therapeutics, an emerging class of pharmaceutical formulations. METHODS AND RESULTS Oligonucleotide primers and hybridization probe for bacterial detection targeting the 16SrRNA gene were adapted based on Nadkarni et al. [Microbiology148 (2002) 257]. For detection of yeast and moulds, primers and probe were designed from conserved sequences of the 18SrRNA gene in this study. The real-time PCR assays were tested on genomic DNA of Escherichia coli and Candida albicans to assess efficiency and linear dynamic range. After successful establishment of robust real-time PCRs, applicability of the assays was evaluated by extracting microbial target DNA from cell-based preparations. Different commercial DNA extraction methods were compared identifying the MagNA Pure DNA Isolation Kit III as the method of choice. Sensitivity was examined for different strains and a detection limit of 102 -103 CFU per ml in a sample containing ~106 mammalian cells per ml was achieved. CONCLUSIONS This study reports the successful establishment of two qualitative real-time PCR assays, enabling in general the broad-range detection of microbial contaminants in a cell-based sample matrix. SIGNIFICANCE AND IMPACT OF THE STUDY Individualized cell therapeutics tend to have a short shelf life. Due to lengthy incubation periods, compendial testing according to current pharmacopoeial guidelines may not be applicable. We report a suitable alternative method upon which future microbiological quality control methods for such products could be based on. However, to implement valid rapid microbiological testing methods using real-time PCR technology, further challenges need to be addressed.
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Affiliation(s)
- K Kleinschmidt
- Microbiological Quality Control Unit, Novartis Pharma Stein AG, Stein, Switzerland
| | - E Wilkens
- Microbiological Quality Control Unit, Novartis Pharma Stein AG, Stein, Switzerland
| | - S P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - P Kaempfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - A Staerk
- Microbiological Quality Control Unit, Novartis Pharma Stein AG, Stein, Switzerland
| | - D Roesti
- Microbiological Quality Control Unit, Novartis Pharma Stein AG, Stein, Switzerland
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Li T, Zhu F, Guo W, Gu H, Zhao J, Yan M, Liu S. Selective capture and rapid identification of E. coli O157:H7 by carbon nanotube multilayer biosensors and microfluidic chip-based LAMP. RSC Adv 2017. [DOI: 10.1039/c7ra04583b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A combination of CNT multilayer biosensors and microfluidic chip-based LAMP was developed for the capture and visual detection of E. coli O157:H7.
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Affiliation(s)
- Tianchan Li
- School of Life Science and Technology
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin 150080
- China
| | - Fanjiao Zhu
- School of Life Science and Technology
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin 150080
- China
| | - Wei Guo
- School of Life Science and Technology
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin 150080
- China
| | - Hongxi Gu
- School of Life Science and Technology
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin 150080
- China
| | - Jing Zhao
- School of Life Science and Technology
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin 150080
- China
| | - Mei Yan
- School of Life Science and Technology
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin 150080
- China
| | - Shaoqin Liu
- School of Life Science and Technology
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin 150080
- China
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Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathog 2016; 8:24. [PMID: 27239228 PMCID: PMC4882852 DOI: 10.1186/s13099-016-0103-7] [Citation(s) in RCA: 323] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 05/10/2016] [Indexed: 12/12/2022] Open
Abstract
Background The advent and use of highly sensitive molecular biology techniques to explore the microbiota and microbiome in environmental and tissue samples have detected the presence of contaminating microbial DNA within reagents. These microbial DNA contaminants may distort taxonomic distributions and relative frequencies in microbial datasets, as well as contribute to erroneous interpretations and identifications. Results We herein report on the occurrence of bacterial DNA contamination within commonly used DNA extraction kits and PCR reagents and the effect of these contaminates on data interpretation. When compared to previous reports, we identified an additional 88 bacterial genera as potential contaminants of molecular biology grade reagents, bringing the total number of known contaminating microbes to 181 genera. Many of the contaminants detected are considered normal inhabitants of the human gastrointestinal tract and the environment and are often indistinguishable from those genuinely present in the sample. Conclusions Laboratories working on bacterial populations need to define contaminants present in all extraction kits and reagents used in the processing of DNA. Any unusual and/or unexpected findings need to be viewed as possible contamination as opposed to unique findings. Electronic supplementary material The online version of this article (doi:10.1186/s13099-016-0103-7) contains supplementary material, which is available to authorized users.
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16
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Loza-Correa M, Perkins H, Kumaran D, Kou Y, Qaisar R, Geelhood S, Ramirez-Arcos S. Noninvasive pH monitoring for bacterial detection in platelet concentrates. Transfusion 2016; 56:1348-55. [PMID: 27028108 DOI: 10.1111/trf.13557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 11/27/2022]
Abstract
BACKGROUND Bacterial contamination of platelet concentrates (PCs) remains the prevalent posttransfusion infectious risk. The pH SAFE system, a noninvasive method used to measure pH of PC for quality control, was evaluated herein as a rapid method to detect bacterial contamination in PCs. STUDY DESIGN AND METHODS Pairs of ABO-D-matched apheresis and buffy coat PCs were pooled and split into two pH SAFE platelet bags. One of the bags served as the control unit, while the other was inoculated with one of nine clinically relevant bacteria (target concentration approx. 1 colony-forming units [CFUs]/mL). The pH of both PCs was measured over 7 days of storage at approximately 4-hour intervals during daytime. One-milliliter samples were taken at the testing points to determine bacterial concentration. RESULTS PCs with pH values of less than 6.6 or with a pH change over time (ΔpH/Δtime) greater or equal than 0.046 pH units/hr are suspected of being contaminated. pH decreased significantly during storage in all bacterially inoculated PC at concentrations of more than 10(7) CFUs/mL (p < 0.0001). A significant decrease in pH (p < 0.0001) was noticed as early as 28 hours in units with Bacillus cereus and as late as 125 hours in units containing Staphylococcus epidermidis. Interestingly, PCs containing Gram-negative species showed a decline in pH followed by a rebound. CONCLUSIONS The pH SAFE system allows for repeated, noninvasive pH screening during PC storage. A significant decrease in pH could serve as an indicator of clinically significant levels of bacterial contamination. Since differences in pH decline were observed among bacterial species, continuous pH monitoring in PCs is recommended.
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Affiliation(s)
| | | | | | - Yuntong Kou
- Canadian Blood Services, Ottawa, Ontario, Canada
| | - Ramie Qaisar
- Canadian Blood Services, Ottawa, Ontario, Canada
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Guo Y, Wang Y, Liu S, Yu J, Wang H, Wang Y, Huang J. Label-free and highly sensitive electrochemical detection of E. coli based on rolling circle amplifications coupled peroxidase-mimicking DNAzyme amplification. Biosens Bioelectron 2016; 75:315-9. [DOI: 10.1016/j.bios.2015.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/04/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022]
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18
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Zhang JJ, Tian JJ, Wei SS, Duan SB, Wang HM, Chen YZ, Ding SH, Zhang C, Meng QL, Li Y. An Internal Reference Control Duplex Real-Time Polymerase Chain Reaction Assay for Detecting Bacterial Contamination in Blood Products. PLoS One 2015; 10:e0134743. [PMID: 26230627 PMCID: PMC4521875 DOI: 10.1371/journal.pone.0134743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 07/13/2015] [Indexed: 11/19/2022] Open
Abstract
Real-time polymerase chain reaction (RT-PCR) enables effective and sensitive screening for infectious risk in the field of blood safety. However, when using RT-PCR to detect bacterial contamination, several intractable points must be considered, one of which is the lack of appropriate quality control. In this study, we developed a simplified RT-PCR assay in which the same primer set and two distinct probes were used to detect both, an internal reference control and the target in a reaction. The copy number of the internal reference control represents the positive detection limit of the assay; therefore, when the threshold-cycle value of the target is less than or equal to that of the internal reference control, the result obtained for the target can be considered to be a true positive. When human gDNA was spiked with Escherichia coli gDNA and the detection limit for the internal reference control was set to five copies, the measured detection limit for E. coli gDNA was two copies. The internal reference control duplex RT-PCR assay showed high efficiency (0.91–1.02), high linearity (R2 > 0.99), and good reproducibility in intra- and inter-assay comparisons. Lastly, when human platelet-rich plasma samples were spiked with E. coli or other bacterial species, all species were detected efficiently, and the results of a two-sample pooled t test showed that the limit of detection for E. coli was 1 cfu/mL. Here, we present a synthetic internal reference control molecule and a new statistical method for improving the reliability of RT-PCR assays when screening for bacterial contamination in blood products.
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Affiliation(s)
- Jin-ju Zhang
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Jing-jing Tian
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Shuang-shi Wei
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Sheng-bao Duan
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Hong-mei Wang
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Ye-zhou Chen
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Shao-hua Ding
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Chun Zhang
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Qing-lin Meng
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
- * E-mail:
| | - Yong Li
- The Chinese Academy of Sciences Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
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Humphrey B, McLeod N, Turner C, Sutton JM, Dark PM, Warhurst G. Removal of Contaminant DNA by Combined UV-EMA Treatment Allows Low Copy Number Detection of Clinically Relevant Bacteria Using Pan-Bacterial Real-Time PCR. PLoS One 2015; 10:e0132954. [PMID: 26172943 PMCID: PMC4501569 DOI: 10.1371/journal.pone.0132954] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/21/2015] [Indexed: 01/12/2023] Open
Abstract
Background More than two decades after its discovery, contaminant microbial DNA in PCR reagents continues to impact the sensitivity and integrity of broad-range PCR diagnostic techniques. This is particularly relevant to their use in the setting of human sepsis, where a successful diagnostic on blood samples needs to combine universal bacterial detection with sensitivity to 1-2 genome copies, because low levels of a broad range of bacteria are implicated. Results We investigated the efficacy of ethidium monoazide (EMA) and propidium monoazide (PMA) treatment as emerging methods for the decontamination of PCR reagents. Both treatments were able to inactivate contaminating microbial DNA but only at concentrations that considerably affected assay sensitivity. Increasing amplicon length improved EMA/PMA decontamination efficiency but at the cost of assay sensitivity. The same was true for UV exposure as an alternative decontamination strategy, likely due to damage sustained by oligonucleotide primers which were a significant source of contamination. However, a simple combination strategy with UV-treated PCR reagents paired with EMA-treated primers produced an assay capable of two genome copy detection and a <5% contamination rate. This decontamination strategy could have important utility in developing improved pan-bacterial assays for rapid diagnosis of low pathogen burden conditions such as in the blood of patients with suspected blood stream infection.
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Affiliation(s)
- Bruce Humphrey
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
- * E-mail:
| | - Neil McLeod
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - Carrie Turner
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - J. Mark Sutton
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - Paul M. Dark
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
| | - Geoffrey Warhurst
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
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Tokuno O, Hayakawa A, Yanai T, Mori T, Ohnuma K, Tani A, Minami H, Sugimoto T. Sterility Testing of Stem Cell Products by Broad-Range Bacterial 16S Ribosomal DNA Polymerase Chain Reaction. Lab Med 2015; 46:34-41. [DOI: 10.1309/lmkt4p9ffi2bbsiu] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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21
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Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014; 12:87. [PMID: 25387460 PMCID: PMC4228153 DOI: 10.1186/s12915-014-0087-z] [Citation(s) in RCA: 2006] [Impact Index Per Article: 200.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/13/2014] [Indexed: 12/11/2022] Open
Abstract
Background The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. Results In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Conclusions These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0087-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susannah J Salter
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK.
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El Ichi S, Leon F, Vossier L, Marchandin H, Errachid A, Coste J, Jaffrezic-Renault N, Fournier-Wirth C. Microconductometric immunosensor for label-free and sensitive detection of Gram-negative bacteria. Biosens Bioelectron 2014; 54:378-84. [DOI: 10.1016/j.bios.2013.11.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/18/2013] [Accepted: 11/05/2013] [Indexed: 12/11/2022]
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Takahashi H, Yamazaki H, Akanuma S, Kanahara H, Saito T, Chimuro T, Kobayashi T, Ohtani T, Yamamoto K, Sugiyama S, Kobori T. Preparation of Phi29 DNA polymerase free of amplifiable DNA using ethidium monoazide, an ultraviolet-free light-emitting diode lamp and trehalose. PLoS One 2014; 9:e82624. [PMID: 24505243 PMCID: PMC3915000 DOI: 10.1371/journal.pone.0082624] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/25/2013] [Indexed: 11/25/2022] Open
Abstract
We previously reported that multiply-primed rolling circle amplification (MRPCA) using modified random RNA primers can amplify tiny amounts of circular DNA without producing any byproducts. However, contaminating DNA in recombinant Phi29 DNA polymerase adversely affects the outcome of MPRCA, especially for negative controls such as non-template controls. The amplified DNA in negative control casts doubt on the result of DNA amplification. Since Phi29 DNA polymerase has high affinity for both single-strand and double-stranded DNA, some amount of host DNA will always remain in the recombinant polymerase. Here we describe a procedure for preparing Phi29 DNA polymerase which is essentially free of amplifiable DNA. This procedure is realized by a combination of host DNA removal using appropriate salt concentrations, inactivation of amplifiable DNA using ethidium monoazide, and irradiation with visible light from a light-emitting diode lamp. Any remaining DNA, which likely exists as oligonucleotides captured by the Phi29 DNA polymerase, is degraded by the 3'-5' exonuclease activity of the polymerase itself in the presence of trehalose, used as an anti-aggregation reagent. Phi29 DNA polymerase purified by this procedure has little amplifiable DNA, resulting in reproducible amplification of at least ten copies of plasmid DNA without any byproducts and reducing reaction volume. This procedure could aid the amplification of tiny amounts DNA, thereby providing clear evidence of contamination from laboratory environments, tools and reagents.
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Affiliation(s)
- Hirokazu Takahashi
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Yamazaki
- Isehara Research Laboratory, Technology & Development Division, Kanto Chemical Co., Inc., Isehara, Kanagawa, Japan
| | - Satoshi Akanuma
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hiroko Kanahara
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Toshiyuki Saito
- Transcriptome Profiling Group, National Institute of Radiological Sciences, Chiba, Chiba, Japan
| | - Tomoyuki Chimuro
- Isehara Research Laboratory, Technology & Development Division, Kanto Chemical Co., Inc., Isehara, Kanagawa, Japan
| | - Takayoshi Kobayashi
- Bio-Chemical Department, Reagent Division, Kanto Chemical Co., Inc. Tokyo, Japan
| | - Toshio Ohtani
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kimiko Yamamoto
- Insect Genome Laboratory, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Shigeru Sugiyama
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Toshiro Kobori
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Grigorenko E, Fisher C, Patel S, Chancey C, Rios M, Nakhasi HL, Duncan RC. Multiplex Screening for Blood-Borne Viral, Bacterial, and Protozoan Parasites using an OpenArray Platform. J Mol Diagn 2014; 16:136-44. [DOI: 10.1016/j.jmoldx.2013.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 08/13/2013] [Accepted: 08/22/2013] [Indexed: 02/02/2023] Open
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Affiliation(s)
- C. P. McDonald
- National Bacteriology Laboratory; National Health Service Blood and Transplant; London; UK
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26
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Garson JA, Patel P, McDonald C, Ball J, Rosenberg G, Tettmar KI, Brailsford SR, Pitt T, Tedder RS. Evaluation of an ethidium monoazide-enhanced 16S rDNA real-time polymerase chain reaction assay for bacterial screening of platelet concentrates and comparison with automated culture. Transfusion 2013; 54:870-8. [PMID: 23701338 PMCID: PMC4282358 DOI: 10.1111/trf.12256] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 12/01/2022]
Abstract
BACKGROUND Culture-based systems are currently the preferred means for bacterial screening of platelet (PLT) concentrates. Alternative bacterial detection techniques based on nucleic acid amplification have also been developed but these have yet to be fully evaluated. In this study we evaluate a novel 16S rDNA polymerase chain reaction (PCR) assay and compare its performance with automated culture. STUDY DESIGN AND METHODS A total of 2050 time-expired, 176 fresh, and 400 initial-reactive PLT packs were tested by real-time PCR using broadly reactive 16S primers and a "universal" probe (TaqMan, Invitrogen). PLTs were also tested using a microbial detection system (BacT/ALERT, bioMérieux) under aerobic and anaerobic conditions. RESULTS Seven of 2050 (0.34%) time-expired PLTs were found repeat reactive by PCR on the initial nucleic acid extract but none of these was confirmed positive on testing frozen second aliquots. BacT/ALERT testing also failed to confirm any time-expired PLTs positive on repeat testing, although 0.24% were reactive on the first test. Three of the 400 "initial-reactive" PLT packs were found by both PCR and BacT/ALERT to be contaminated (Escherichia coli, Listeria monocytogenes, and Streptococcus vestibularis identified) and 14 additional packs were confirmed positive by BacT/ALERT only. In 13 of these cases the contaminating organisms were identified as anaerobic skin or oral commensals and the remaining pack was contaminated with Streptococcus pneumoniae. CONCLUSION These results demonstrate that the 16S PCR assay is less sensitive than BacT/ALERT and inappropriate for early testing of concentrates. However, rapid PCR assays such as this may be suitable for a strategy of late or prerelease testing.
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Affiliation(s)
- Jeremy A Garson
- National Transfusion Microbiology Laboratories, NHSBT/HPA Epidemiology Unit, NHS Blood and Transplant, Colindale, London; Research Department of Infection, Division of Infection and Immunity, University College London, London; Blood Borne Virus Unit, Viral Reference Department, Centre for Infections, Health Protection Agency, Colindale, London, UK
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Morel P, Naegelen C, Deschaseaux M, Bardiaux L. [Prevention of bacterial risk: pathogen inactivation/detection of bacteria]. Transfus Clin Biol 2013; 20:109-14. [PMID: 23622837 DOI: 10.1016/j.tracli.2013.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/27/2013] [Indexed: 11/30/2022]
Abstract
Bacterial contamination of blood products remains the most important infectious risk of blood transfusion in 2013. Platelet concentrates (PC) are in cause in the majority of the transfusion reaction due to bacterial contaminations. A lot of prevention methods have been developed over the last 10 years (pre-donation interview, skin decontamination, diversion of the first 30 mL of the donation, leuko-reduction...), they have focused on limiting the contamination of the donations and prevent the bacterial growth in donations and/or in the blood products. These measures were effective and led to significantly reducing the risk of adverse effects associated with bacterial growth. However, every year there are about six accidents (with a high level of imputability) and one death. The reduction of the bacterial risk remains a priority for the French Blood Establishment (EFS). The procedure for skin disinfection is going to be improved in order to further strengthen this crucial step to avoid the contamination of donation. Methods of pathogen inactivation applied to plasma and PC are available in France and their effectiveness is demonstrated on the bacterial risk. Methods for bacterial detection of PC are used in many countries now. Automated culture is the most common. Alternatives are now available in the form of rapid tests able to analyze the PC just before the delivery and avoid false negatives observed with automated culture. Assessments are under way to confirm these benefits in 2013.
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Affiliation(s)
- P Morel
- Établissement français du sang (EFS) Bourgogne-Franche-Comté, BP 1937, 1, boulevard Alexander-Fleming, 25020 Besançon cedex, France.
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Liu C, Weber C, Sempek DS, Grossman BJ, Burnham CAD. Sterility testing of apheresis hematopoietic progenitor cell products using an automated blood culture system. Transfusion 2013; 53:2659-66. [DOI: 10.1111/trf.12115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/21/2012] [Accepted: 12/03/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Chang Liu
- Department of Pathology & Immunology; Washington University; St Louis Missouri
- Barnes-Jewish Hospital; St Louis Missouri
| | - Carol Weber
- Department of Pathology & Immunology; Washington University; St Louis Missouri
- Barnes-Jewish Hospital; St Louis Missouri
| | - Diane S. Sempek
- Department of Pathology & Immunology; Washington University; St Louis Missouri
- Barnes-Jewish Hospital; St Louis Missouri
| | - Brenda J. Grossman
- Department of Pathology & Immunology; Washington University; St Louis Missouri
- Barnes-Jewish Hospital; St Louis Missouri
| | - Carey-Ann D. Burnham
- Department of Pathology & Immunology; Washington University; St Louis Missouri
- Barnes-Jewish Hospital; St Louis Missouri
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Schnetzinger F, Pan Y, Nocker A. Use of propidium monoazide and increased amplicon length reduce false-positive signals in quantitative PCR for bioburden analysis. Appl Microbiol Biotechnol 2013; 97:2153-62. [DOI: 10.1007/s00253-013-4711-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/30/2022]
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