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Yeager J, Gómez-Jaramillo AM, Ortiz-Prado E, Calvopiña M, Chan BK. Phage therapy: resurrecting a historical solution for the contemporary challenge of rising antibiotic resistance in Latin America. Expert Rev Anti Infect Ther 2024; 22:19-23. [PMID: 38217395 DOI: 10.1080/14787210.2024.2305842] [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: 07/17/2023] [Accepted: 01/11/2024] [Indexed: 01/15/2024]
Abstract
INTRODUCTION Antimicrobial resistance in Latin America is a growing concern in both human and non-human animal populations. The economic burden that is likely to be imposed through increased resistance will cause further strains on public health systems and the population at large. AREAS COVERED We propose the rapid adoption and implementation of phage therapy as a necessary addition to the medical arsenal to help mitigate antimicrobial resistance, with an emphasis on considering the potential benefits that highly biodiverse countries such as Ecuador may have on phage discovery. However, programs may count on limited government support and/or facilitation, which could slow progress. EXPERT OPINION We highlight the need for educational campaigns to be implemented in parallel with the development of phage therapy programs, particularly to implement these novel treatments in rural and indigenous communities.
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Affiliation(s)
- Justin Yeager
- Biodiversidad Medio Ambiente y Salud, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Ana María Gómez-Jaramillo
- Postgraduate Program in Infectious Diseases, School of Medicine, Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Esteban Ortiz-Prado
- OneHealth Research Group, Facultad de Ciencias de la Salud, Universidad De Las Américas (UDLA), Quito, Ecuador
| | - Manuel Calvopiña
- OneHealth Research Group, Facultad de Ciencias de la Salud, Universidad De Las Américas (UDLA), Quito, Ecuador
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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Understanding quantitative polymerase chain reaction bioanalysis issues before validation planning: Japan Bioanalysis Forum discussion group. Bioanalysis 2022; 14:1391-1405. [PMID: 36621859 DOI: 10.4155/bio-2022-0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Investigating the biodistribution of cell and gene therapy products may play an important role in evaluating their safety and pharmacology. As quantitative polymerase chain reaction (qPCR) is often used for these analyses, it is essential to improve the reliability of bioanalysis performed using qPCR. In this report, the authors discuss the use of qPCR in nonclinical studies, as it can be used to detect target DNA/RNA and it is quantitative and applicable for long-term analysis. The authors also discuss points to consider during bioanalysis using qPCR and present appropriate validation items and their criteria. The authors anticipate the discussion provided herein to contribute to the development of validation and sample analysis for pharmaceuticals analyzed using qPCR.
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Boutal H, Moguet C, Pommiès L, Simon S, Naas T, Volland H. The Revolution of Lateral Flow Assay in the Field of AMR Detection. Diagnostics (Basel) 2022; 12:1744. [PMID: 35885647 PMCID: PMC9317642 DOI: 10.3390/diagnostics12071744] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
The global spread of antimicrobial resistant (AMR) bacteria represents a considerable public health concern, yet their detection and identification of their resistance mechanisms remain challenging. Optimal diagnostic tests should provide rapid results at low cost to enable implementation in any microbiology laboratory. Lateral flow assays (LFA) meet these requirements and have become essential tools to combat AMR. This review presents the versatility of LFA developed for the AMR detection field, with particular attention to those directly triggering β-lactamases, their performances, and specific limitations. It considers how LFA can be modified by detecting not only the enzyme, but also its β-lactamase activity for a broader clinical sensitivity. Moreover, although LFA allow a short time-to-result, they are generally only implemented after fastidious and time-consuming techniques. We present a sample processing device that shortens and simplifies the handling of clinical samples before the use of LFA. Finally, the capacity of LFA to detect amplified genetic determinants of AMR by isothermal PCR will be discussed. LFA are inexpensive, rapid, and efficient tools that are easy to implement in the routine workflow of laboratories as new first-line tests against AMR with bacterial colonies, and in the near future directly with biological media.
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Affiliation(s)
- Hervé Boutal
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Christian Moguet
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Lilas Pommiès
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Stéphanie Simon
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Thierry Naas
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France;
- Team Resist, UMR1184, Université Paris-Saclay—INSERM—CEA, LabEx Lermit, 91190 Gif-sur-Yvette, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Hervé Volland
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
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Trinh TND, Lee NY. Nucleic acid amplification-based microfluidic approaches for antimicrobial susceptibility testing. Analyst 2021; 146:3101-3113. [PMID: 33876805 DOI: 10.1039/d1an00180a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Because of the global spread of antimicrobials, there is an urgent need to develop rapid and effective tools for antimicrobial susceptibility testing to help clinicians prescribe accurate and appropriate antibiotic doses sooner. The conventional methods for antimicrobial susceptibility testing are usually based on bacterial culture methods, which are time-consuming, complicated, and labor-intensive. Therefore, other approaches are needed to address these issues. Recently, microfluidic technology has gained significant attention in infection management due to its advantages including rapid detection, high sensitivity and specificity, highly automated assay, simplicity, low cost, and potential for point-of-care testing in low-resource areas. Microfluidic advances for antimicrobial susceptibility testing can be classified into phenotypic (usually culture-based) and genotypic tests. Genotypic antimicrobial susceptibility testing is the detection of resistant genes in a microorganism using methods such as nucleic acid amplification. This review (with 107 references) surveys the different forms of nucleic acid amplification-based microdevices used for genotypic antimicrobial susceptibility testing. The first section reviews the serious threat of antimicrobial-resistant microorganisms and the urgent need for fast check-ups. Next, several conventional antimicrobial susceptibility testing methods are discussed, and microfluidic technology as a promising candidate for rapid detection of antimicrobial-resistant microorganisms is briefly introduced. The next section highlights several advancements of microdevices, with an emphasis on their working principles and performance. The review concludes with the importance of fully integrated microdevices and a discussion on future perspectives.
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Affiliation(s)
- Thi Ngoc Diep Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea.
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Zhang X, Yang Q, Zhang Q, Jiang X, Wang X, Li Y, Zhao J, Qu K. Rapid detection of cytochrome cd1-containing nitrite reductase encoding gene nirS of denitrifying bacteria with loop-mediated isothermal amplification assay. Sci Rep 2020; 10:16484. [PMID: 33020497 PMCID: PMC7536394 DOI: 10.1038/s41598-020-73304-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/15/2020] [Indexed: 12/26/2022] Open
Abstract
The cytochrome cd1-containing nitrite reductase, nirS, plays an important role in biological denitrification. Consequently, investigating the presence and abundance of nirS is a commonly used approach to understand the distribution and potential activity of denitrifying bacteria, in addition to denitrifier communities. Herein, a rapid method for detecting nirS gene with loop-mediated isothermal amplification (LAMP) was developed, using Pseudomonas aeruginosa PAO1 (P. aeruginosa PAO1) as model microorganism to optimize the assay. The LAMP assay relied on a set of four primers that were designed to recognize six target sequence sites, resulting in high target specificity. The limit of detection for the LAMP assay under optimized conditions was 1.87 pg/reaction of genomic DNA, which was an order of magnitude lower than that required by conventional PCR assays. Moreover, it was validated that P. aeruginosa PAO1 cells as well as genomic DNA could be directly used as template. Only 1 h was needed from the addition of bacterial cells to the reaction to the verification of amplification success. The nirS gene of P. aeruginosa PAO1 in spiked seawater samples could be detected with both DNA-template based LAMP assay and cell-template based LAMP assay, demonstrating the practicality of in-field use.
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Affiliation(s)
- Xuzhi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China
| | - Qianqian Yang
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Qingli Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiaoyu Jiang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaochun Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yang Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Jun Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Keming Qu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China.
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6
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Simmons MD, Miller LM, Sundström MO, Johnson S. Aptamer-Based Detection of Ampicillin in Urine Samples. Antibiotics (Basel) 2020; 9:E655. [PMID: 33003560 PMCID: PMC7601551 DOI: 10.3390/antibiotics9100655] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
The misuse of antibiotics in health care has led to increasing levels of drug resistant infections (DRI's) occurring in the general population. Most technologies developed for the detection of DRI's typically focus on phenotyping or genotyping bacterial resistance rather than on the underlying cause and spread of DRI's; namely the misuse of antibiotics. An aptameric based assay has been developed for the monitoring of ampicillin in urine samples, for use in determining optimal antibiotic dosage and monitoring patient compliance with treatment. The fluorescently labelled aptamers were shown to perform optimally at pH 7, ideal for buffered clinical urine samples, with limits of detection as low as 20.6 nM, allowing for determination of ampicillin in urine in the clinically relevant range of concentrations (100 nM to 100 µM). As the assay requires incubation for only 1 h with a small sample volume, 50 to 150 µL, the test would fit within current healthcare pathways, simplifying the adoption of the technology.
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Affiliation(s)
- Matthew D. Simmons
- Department of Electronic Engineering, University of York, Heslington, York, North Yorkshire YO10 5DD, UK;
| | - Lisa M. Miller
- Department of Chemistry, University of York, Heslington, York, North Yorkshire YO10 5DD, UK;
| | - Malin O. Sundström
- Department of Electronic Engineering, University of York, Heslington, York, North Yorkshire YO10 5DD, UK;
| | - Steven Johnson
- Department of Electronic Engineering, University of York, Heslington, York, North Yorkshire YO10 5DD, UK;
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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8
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Amalfitano S, Levantesi C, Copetti D, Stefani F, Locantore I, Guarnieri V, Lobascio C, Bersani F, Giacosa D, Detsis E, Rossetti S. Water and microbial monitoring technologies towards the near future space exploration. WATER RESEARCH 2020; 177:115787. [PMID: 32315899 DOI: 10.1016/j.watres.2020.115787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Space exploration is demanding longer lasting human missions and water resupply from Earth will become increasingly unrealistic. In a near future, the spacecraft water monitoring systems will require technological advances to promptly identify and counteract contingent events of waterborne microbial contamination, posing health risks to astronauts with lowered immune responsiveness. The search for bio-analytical approaches, alternative to those applied on Earth by cultivation-dependent methods, is pushed by the compelling need to limit waste disposal and avoid microbial regrowth from analytical carryovers. Prospective technologies will be selected only if first validated in a flight-like environment, by following basic principles, advantages, and limitations beyond their current applications on Earth. Starting from the water monitoring activities applied on the International Space Station, we provide a critical overview of the nucleic acid amplification-based approaches (i.e., loop-mediated isothermal amplification, quantitative PCR, and high-throughput sequencing) and early-warning methods for total microbial load assessments (i.e., ATP-metry, flow cytometry), already used at a high readiness level aboard crewed space vehicles. Our findings suggest that the forthcoming space applications of mature technologies will be necessarily bounded by a compromise between analytical performances (e.g., speed to results, identification depth, reproducibility, multiparametricity) and detrimental technical requirements (e.g., reagent usage, waste production, operator skills, crew time). As space exploration progresses toward extended missions to Moon and Mars, miniaturized systems that also minimize crew involvement in their end-to-end operation are likely applicable on the long-term and suitable for the in-flight water and microbiological research.
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Affiliation(s)
- Stefano Amalfitano
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy.
| | - Caterina Levantesi
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy
| | - Diego Copetti
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via del Mulino 19, 20861, Brugherio, Monza-Brianza, Italy
| | - Fabrizio Stefani
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via del Mulino 19, 20861, Brugherio, Monza-Brianza, Italy
| | - Ilaria Locantore
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Vincenzo Guarnieri
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Cesare Lobascio
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Francesca Bersani
- Centro Ricerche SMAT, Società Metropolitana Acque Torino S.p.A., C.so Unità d'Italia 235/3, 10127, Torino, Italy
| | - Donatella Giacosa
- Centro Ricerche SMAT, Società Metropolitana Acque Torino S.p.A., C.so Unità d'Italia 235/3, 10127, Torino, Italy
| | - Emmanouil Detsis
- European Science Foundation, 1 quai Lezay Marnésia, BP 90015, 67080, Strasbourg Cedex, France
| | - Simona Rossetti
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy
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Kumar SS, Ghosh AR. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology (Reading) 2019; 165:593-610. [DOI: 10.1099/mic.0.000786] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shravanthi S. Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
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Banerjee I, Aralaguppe SG, Lapins N, Zhang W, Kazemzadeh A, Sönnerborg A, Neogi U, Russom A. Microfluidic centrifugation assisted precipitation based DNA quantification. LAB ON A CHIP 2019; 19:1657-1664. [PMID: 30931470 DOI: 10.1039/c9lc00196d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleic acid amplification methods are increasingly being used to detect trace quantities of DNA in samples for various diagnostic applications. However, quantifying the amount of DNA from such methods often requires time consuming purification, washing or labeling steps. Here, we report a novel microfluidic centrifugation assisted precipitation (μCAP) method for single-step DNA quantification. The method is based on formation of a visible precipitate, which can be quantified, when an intercalating dye (GelRed) is added to the DNA sample and centrifuged for a few seconds. We describe the mechanism leading to the precipitation phenomenon. We utilize centrifugal microfluidics to precisely control the formation of the visible and quantifiable mass. Using a standard CMOS sensor for imaging, we report a detection limit of 45 ng μl-1. Furthermore, using an integrated lab-on-DVD platform we recently developed, the detection limit is lowered to 10 ng μl-1, which is comparable to those of current commercially available instruments for DNA quantification. As a proof of principle, we demonstrate the quantification of LAMP products for a HIV-1B type genome containing plasmid on the lab-on-DVD platform. The simple DNA quantification system could facilitate advanced point of care molecular diagnostics.
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Affiliation(s)
- I Banerjee
- Division of Nanobiotechnology, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Sweden.
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Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review. Molecules 2019; 24:molecules24010163. [PMID: 30609875 PMCID: PMC6337382 DOI: 10.3390/molecules24010163] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/28/2018] [Accepted: 12/29/2018] [Indexed: 12/12/2022] Open
Abstract
Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.
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Kwon SJ, Kim D, Lee I, Nam J, Kim J, Dordick JS. Sensitive multiplex detection of whole bacteria using self-assembled cell binding domain complexes. Anal Chim Acta 2018; 1030:156-165. [PMID: 30032765 DOI: 10.1016/j.aca.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/14/2018] [Accepted: 05/02/2018] [Indexed: 11/29/2022]
Abstract
Detecting bacterial cells at low levels is critical in public health, the food industry and first response. Current processes typically involve laborious cell lysis and genomic DNA extraction to achieve 100-1000 CFU mL-1 levels for detecting gram-positive bacteria. As an alternative to DNA-based methods, cell wall binding domains (CBDs) derived from lysins having a modular structure with an N-terminal catalytic domain and a C-terminal CBD, can be used to detect bacterial pathogens as a result of their exceptionally specific binding to target bacteria with great avidity. We have developed a highly sensitive method for multiplex detection of whole bacterial cells using self-assembled CBD complexes. Self-assembled CBD-SA-reporter complexes were generated using streptavidin (SA), biotin-CBDs, and biotinylated reporters, such as glucose oxidase (GOx) and specific DNA sequences. The simultaneous detection of three test bacteria, Staphylococcus aureus, Bacillus anthracis-Sterne, and Listeria innocua cells in PBS could be accomplished with a 96-well plate-based sandwich method using CBD-SA-GOx complex-coupled spectrophotometric assay to achieve a detection limit of >100 CFU mL-1. To achieve greater detection sensitivity, we used CBD-SA-DNA complexes and qPCR of specific DNA barcodes selectively bound to the surface of target bacterial cells, which resulted in a detection sensitivity as low as 1-10 CFU mL-1 without cross-reactivity. This sensitive multiplex detection of bacterial pathogens using both CBD-SA-GOx and CBD-SA-DNA complexes has the potential to be quickly combined with point-of-care compatible diagnostics for the rapid detection of pathogens in test samples.
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Affiliation(s)
- Seok-Joon Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Domyoung Kim
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Inseon Lee
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jahyun Nam
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.
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Etchebarne BE, Li Z, Stedtfeld RD, Nicholas MC, Williams MR, Johnson TA, Stedtfeld TM, Kostic T, Khalife WT, Tiedje JM, Hashsham SA, Hughes MJ. Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection. Front Microbiol 2017; 8:2211. [PMID: 29312154 PMCID: PMC5732957 DOI: 10.3389/fmicb.2017.02211] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/26/2017] [Indexed: 12/12/2022] Open
Abstract
Battling infection is a major healthcare objective. Untreated infections can rapidly evolve toward the condition of sepsis in which the body begins to fail and resuscitation becomes critical and tenuous. Identification of infection followed by rapid antimicrobial treatment are primary goals of medical care, but precise identification of offending organisms by current methods is slow and broad spectrum empirical therapy is employed to cover most potential pathogens. Current methods for identification of bacterial pathogens in a clinical setting typically require days of time, or a 4- to 8-h growth phase followed by DNA extraction, purification and PCR-based amplification. We demonstrate rapid (70-120 min) genetic diagnostics methods utilizing loop-mediated isothermal amplification (LAMP) to test for 15 common infection pathogen targets, called the Infection Diagnosis Panel (In-Dx). The method utilizes filtration to rapidly concentrate bacteria in sample matrices with lower bacterial loads and direct LAMP amplification without DNA purification from clinical blood, urine, wound, sputum and stool samples. The In-Dx panel was tested using two methods of detection: (1) real-time thermocycler fluorescent detection of LAMP amplification and (2) visual discrimination of color change in the presence of Eriochrome Black T (EBT) dye following amplification. In total, 239 duplicate samples were collected (31 blood, 122 urine, 73 mucocutaneous wound/swab, 11 sputum and two stool) from 229 prospectively enrolled hospital patients with suspected clinical infection and analyzed both at the hospital and by In-Dx. Sensitivity (Se) of the In-Dx panel targets pathogens from urine samples by In-Dx was 91.1% and specificity (Sp) was 97.3%, with a positive predictive value (PPV) of 53.7% and a negative predictive value (NPV) of 99.7% as compared to clinical microbial detection methods. Sensitivity of detection of the In-Dx panel from mucocutaneous swab samples was 65.5% with a Sp of 99.3%, and a PPV of 84% and NPV of 98% as compared to clinical microbial detection methods. Results indicate the LAMP-based In-Dx panel allows rapid and precise diagnosis of clinical infections by targeted pathogens across multiple culture types for point-of-care utilization.
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Affiliation(s)
- Brett E. Etchebarne
- Department of Osteopathic Medical Specialties, Section of Emergency Medicine, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, United States
| | - Zenggang Li
- Department of Osteopathic Medical Specialties, Section of Emergency Medicine, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, United States
| | - Robert D. Stedtfeld
- Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Michael C. Nicholas
- Department of Osteopathic Medical Specialties, Section of Emergency Medicine, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, United States
| | - Maggie R. Williams
- Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Timothy A. Johnson
- The Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Tiffany M. Stedtfeld
- Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Tanja Kostic
- Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
- Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Walid T. Khalife
- Department of Microbiology, Sparrow Laboratories, Sparrow Health System, Lansing, MI, United States
| | - James M. Tiedje
- The Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Syed A. Hashsham
- Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
- The Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Mary J. Hughes
- Department of Osteopathic Medical Specialties, Section of Emergency Medicine, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, United States
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14
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Samhan FA, Stedtfeld TM, Waseem H, Williams MR, Stedtfeld RD, Hashsham SA. On-filter direct amplification of Legionella pneumophila for rapid assessment of its abundance and viability. WATER RESEARCH 2017; 121:162-170. [PMID: 28527390 PMCID: PMC5525548 DOI: 10.1016/j.watres.2017.05.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 05/14/2023]
Abstract
Guidelines and regulations to control Legionella pneumophila in cooling water systems of large buildings are evolving due to the increasing number of outbreaks. Rapid, on-site, simple, and sensitive quantification methods that are also able to assess viability may be extremely useful in monitoring and control. Culture-based methods for measuring L. pneumophila may take 4-10 days and qPCR-based methods are also slow, requiring at least a day from sample to result, albeit mainly due to the need for sample transport to a centralized laboratory. This study reports a rapid isothermal amplification method for L. pneumophila concentration and detection with live/dead differentiation under field conditions. Using an on-filter direct amplification (i.e., amplification of cells without DNA extraction and purification) approach with propidium monoazide (PMA), and a real time isothermal amplification platform (Gene-Z), L. pneumophila could be detected in 1-2 h at ∼1 cfu/100 ml of tap water. Signature sequences from 16S rRNA and cadA genes were used as genetic markers for L. pneumophila and loop-mediated isothermal amplification (LAMP) primers were designed using Primer Explorer V4. Result were also compared with direct amplification of cells spiked into distilled, tap, and cooling water samples as well as extracted DNA by qPCR. This method may be useful to managers of cooling water systems in large buildings for rapid detection of L. pneumophila. The overall approach of on-site sample concentration, on-filter amplification, and live/dead differentiation may be extended to other organisms where analytical sensitivity and speed are equally important.
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Affiliation(s)
- Farag A Samhan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Hassan Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
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15
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Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae JC, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 198:213-220. [PMID: 28460328 PMCID: PMC5513725 DOI: 10.1016/j.jenvman.2017.04.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 05/05/2023]
Abstract
Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R2 = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Hassen Waseem
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | | | - Xueping Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Trevor Shook
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Amanda Logan
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Ally Graham
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Jong-Chan Chae
- Division of Biotechnology, Chonbuk National University, Iksan, 54596, Republic of Korea
| | - Woo-Jun Sul
- Department of Systems Biotechnology, Chung Ang University, Anseong, 17546, Republic of Korea
| | - Jacob VanHouten
- Science Division, Delta College, University Center, MI, 48710, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Gerben J Zylstra
- Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Brad L Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI, 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA; Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA.
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