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Yamin D, Uskoković V, Wakil AM, Goni MD, Shamsuddin SH, Mustafa FH, Alfouzan WA, Alissa M, Alshengeti A, Almaghrabi RH, Fares MAA, Garout M, Al Kaabi NA, Alshehri AA, Ali HM, Rabaan AA, Aldubisi FA, Yean CY, Yusof NY. Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria. Diagnostics (Basel) 2023; 13:3246. [PMID: 37892067 PMCID: PMC10606640 DOI: 10.3390/diagnostics13203246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.
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Affiliation(s)
- Dina Yamin
- Al-Karak Public Hospital, Karak 61210, Jordan;
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
| | - Vuk Uskoković
- TardigradeNano LLC., Irvine, CA 92604, USA;
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Abubakar Muhammad Wakil
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Maiduguri, Maiduguri 600104, Borno, Nigeria
| | - Mohammed Dauda Goni
- Public Health and Zoonoses Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia;
| | - Shazana Hilda Shamsuddin
- Department of Pathology, School of Medical Sciences, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fatin Hamimi Mustafa
- Department of Electronic & Computer Engineering, Faculty of Electrical Engineering, University Teknologi Malaysia, Johor Bharu 81310, Johor, Malaysia;
| | - Wadha A. Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait;
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia;
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Rana H. Almaghrabi
- Pediatric Department, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia;
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Hamza M. Ali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia;
| | - Ali A. Rabaan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | | | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, University Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
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Qiao J, Chen X, Xu X, Fan B, Guan YS, Yang H, Li Q. A metal-organic framework-based fluorescence resonance energy transfer nanoprobe for highly selective detection of Staphylococcus Aureus. J Mater Chem B 2023; 11:8519-8527. [PMID: 37606203 DOI: 10.1039/d3tb01428b] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Survival and infection of pathogenic bacteria, such as Staphylococcus aureus (S. aureus), pose a serious threat to human health. Efficient methods for recognizing and quantifying low levels of bacteria are imperiously needed. Herein, we introduce a metal-organic framework (MOF)-based fluorescence resonance energy transfer (FRET) nanoprobe for ratiometric detection of S. aureus. The nanoprobe utilizes blue-emitting 7-hydroxycoumarin-4-acetic acid (HCAA) encapsulated inside zirconium (Zr)-based MOFs as the energy donor and green-emitting fluorescein isothiocyanate (FITC) as the energy acceptor. Especially, vancomycin (VAN) is employed as the recognition moiety to bind to the cell wall of S. aureus, leading to the disassembly of VAN-PEG-FITC from MOF HCAA@UiO-66. As the distance between the donor and acceptor increases, the donor signal correspondingly increases as the FRET signal decreases. By calculating the fluorescence intensity ratio, S. aureus can be quantified with a dynamic range of 1.05 × 103-1.05 × 107 CFU mL-1 and a detection limit of 12 CFU mL-1. Due to the unique high affinity of VAN to S. aureus, the nanoprobe shows high selectivity and sensitivity to S. aureus, even in real samples like lake water, orange juice, and saliva. The FRET-based ratiometric fluorescence bacterial detection method demonstrated in this work has a prospect in portable application and may reduce the potential threat of pathogens to human health.
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Affiliation(s)
- Jing Qiao
- Institute of Advanced Materials and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Xuanbo Chen
- Institute of Advanced Materials and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Xingliang Xu
- Institute of Advanced Materials and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Ben Fan
- Institute of Advanced Materials and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Ying-Shi Guan
- Institute of Advanced Materials and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Hong Yang
- Institute of Advanced Materials and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Quan Li
- Institute of Advanced Materials and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
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Wang J, Kong K, Guo C, Yin G, Meng S, Lan L, Luo L, Song Y. Cultureless enumeration of live bacteria in urinary tract infection by single-cell Raman spectroscopy. Front Microbiol 2023; 14:1144607. [PMID: 37032883 PMCID: PMC10076591 DOI: 10.3389/fmicb.2023.1144607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Urinary tract infections (UTIs) are the most common outpatient infections. Obtaining the concentration of live pathogens in the sample is crucial for the treatment. Still, the enumeration depends on urine culture and plate counting, which requires days of turn-around time (TAT). Single-cell Raman spectra combined with deuterium isotope probing (Raman-DIP) has been proven to identify the metabolic-active bacteria with high accuracy but is not able to reveal the number of live pathogens due to bacteria replication during the Raman-DIP process. In this study, we established a new approach of using sodium acetate to inhibit the replication of the pathogen and applying Raman-DIP to identify the active single cells. By combining microscopic image stitching and recognition, we could further improve the efficiency of the new method. Validation of the new method on nine artificial urine samples indicated that the exact number of live pathogens obtained with Raman-DIP is consistent with plate-counting while shortening the TAT from 18 h to within 3 h, and the potential of applying Raman-DIP for pathogen enumeration in clinics is promising.
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Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Kang Kong
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Chen Guo
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China
| | - Guangyao Yin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Lu Lan
- VibroniX, Inc., Suzhou, China
| | - Liqiang Luo
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China
- Chongqing Guoke Medical Technology Development Co., Ltd., Chongqing, China
- *Correspondence: Yizhi Song,
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Duong HT, Williams B, White D, Burgess TI, Hardy GESJ. qPCR Assays for Sensitive and Rapid Detection of Quambalaria Species from Plant Tissues. PLANT DISEASE 2022; 106:107-113. [PMID: 34261359 DOI: 10.1094/pdis-04-21-0816-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Several species from the genus Quambalaria (order Microstromatales) cause diseases on eucalypts (Eucalyptus and related genera) both in plantations and natural ecosystems. We developed real-time quantitative PCR (qPCR) assays to rapidly detect and distinguish five Quambalaria species. The design of the species-specific qPCR assay for each species, Q. pitereka (PIT), Q. coyrecup (COR), Q. cyanescens (CYN), Q. pusilla (PUS), and Q. eucalypti (EUC), was based on the ITS region and was evaluated for specificity and sensitivity. The PIT, COR, and CYN qPCR assays could amplify as little as 10 fg µl-1 from pure cultures, whereas PUS and EUC qPCR assays could amplify 100 fg µl-1 of their target species. The PIT, COR, and CYN qPCR assays were further validated using naturally and artificially infected samples of their plant host Corymbia calophylla. These assays will be used for rapid diagnostics and future experiments on the infection process.
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Affiliation(s)
- Hoa T Duong
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, 6150 Perth, Western Australia, Australia
- Institute of Forest Tree Improvement and Biotechnology, Hanoi 10000, Vietnam
| | - Briony Williams
- ArborCarbon, PO Box 1065, Willagee Central 6163, Western Australia, Australia
| | - Diane White
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, 6150 Perth, Western Australia, Australia
| | - Treena I Burgess
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, 6150 Perth, Western Australia, Australia
| | - Giles E St J Hardy
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, 6150 Perth, Western Australia, Australia
- ArborCarbon, PO Box 1065, Willagee Central 6163, Western Australia, Australia
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Kisat MT, Odenheimer-Bergman A, Markus H, Joseph B, Srivatsan SN, Contente-Cuomo T, Khalpey Z, Keim P, O'Keeffe T, Askari R, Salim A, Rhee P, Murtaza M. Plasma metagenomic sequencing to detect and quantify bacterial DNA in ICU patients suspected of sepsis: A proof-of-principle study. J Trauma Acute Care Surg 2021; 91:988-994. [PMID: 34510074 DOI: 10.1097/ta.0000000000003396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Timely recognition of sepsis and identification of pathogens can improve outcomes in critical care patients but microbial cultures have low accuracy and long turnaround times. In this proof-of-principle study, we describe metagenomic sequencing and analysis of nonhuman DNA in plasma. We hypothesized that quantitative analysis of bacterial DNA (bDNA) levels in plasma can enable detection and monitoring of pathogens. METHODS We enrolled 30 patients suspected of sepsis in the surgical trauma intensive care unit and collected plasma samples at the time of diagnostic workup for sepsis (baseline), and 7 days and 14 days later. We performed metagenomic sequencing of plasma DNA and used computational classification of sequencing reads to detect and quantify total and pathogen-specific bDNA fraction. To improve assay sensitivity, we developed an enrichment method for bDNA based on size selection for shorter fragment lengths. Differences in bDNA fractions between samples were evaluated using t test and linear mixed-effects model, following log transformation. RESULTS We analyzed 72 plasma samples from 30 patients. Twenty-seven samples (37.5%) were collected at the time of infection. Median total bDNA fraction was 1.6 times higher in these samples compared with samples with no infection (0.011% and 0.0068%, respectively, p < 0.001). In 17 patients who had active infection at enrollment and at least one follow-up sample collected, total bDNA fractions were higher at baseline compared with the next sample (p < 0.001). Following enrichment, bDNA fractions increased in paired samples by a mean of 16.9-fold. Of 17 samples collected at the time when bacterial pathogens were identified, we detected pathogen-specific DNA in 13 plasma samples (76.5%). CONCLUSION Bacterial DNA levels in plasma are elevated in critically ill patients with active infection. Pathogen-specific DNA is detectable in plasma, particularly after enrichment using selection for shorter fragments. Serial changes in bDNA levels may be informative of treatment response. LEVEL OF EVIDENCE Epidemiologic/Prognostic, Level V.
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Affiliation(s)
- Mehreen T Kisat
- From the Center for Noninvasive Diagnostics (M.T.K., A.O.-B., H.M., S.N.S., T.C.-C., M.M.), Translational Genomics Research Institute, Phoenix; Department of Surgery (M.T.K., B.J., Z.K., T.O., P.R.), University of Arizona, Tucson, Arizona; Department of Surgery (M.T.K., R.A., A.S.), Brigham and Women's Hospital, Boston, Massachusetts; and Pathogen and Microbiome Institute, Northern Arizona University (P.K.), Flagstaff, Arizona
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Evaluation of Nanopore Sequencing as a Diagnostic Tool for the Rapid Identification of Mycoplasma bovis from Individual and Pooled Respiratory Tract Samples. J Clin Microbiol 2021; 59:e0111021. [PMID: 34550807 DOI: 10.1128/jcm.01110-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Rapid identification of Mycoplasma bovis infections in cattle is a key factor to guide antimicrobial therapy and biosecurity measures. Recently, Nanopore sequencing became an affordable diagnostic tool for both clinically relevant viruses and bacteria, but the diagnostic accuracy for M. bovis identification is undocumented. Therefore, in this study Nanopore sequencing was compared to rapid identification of M. bovis with matrix-assisted laser desorption ionization-time of flight mass spectrometry (RIMM) and a triplex real-time PCR assay in a Bayesian latent class model (BLCM) for M. bovis in bronchoalveolar lavage fluid (BALf) samples obtained from calves. In practice, pooling of samples is often used to save money, but the influence on diagnostic accuracy has not been described for M. bovis. Therefore, a convenience sample of 17 pooled samples containing 5 individual BALf samples per farm was analyzed as well. The results for the pooled samples were compared with those for the individual samples to determine sensitivity and specificity. The BLCM showed good sensitivity (77.3% [95% credible interval, 57.8 to 92.8%]) and high specificity (97.4% [91.5 to 99.7%]) for Nanopore sequencing, compared to RIMM (sensitivity, 93.0% [76.8 to 99.5%]; specificity, 91.3% [82.5 to 97.0%]) and real-time PCR (sensitivity, 94.6% [89.7 to 97.7%]; specificity, 86.0% [76.1 to 93.6%]). Sensitivity and specificity of pooled analysis for M. bovis were 85.7% (95% confidence interval, 59.8 to 111.6%) and 90.0% (71.4 to 108.6%%), respectively, for Nanopore sequencing and 100% (100% to 100%) and 88.9% (68.4 to 109.4%) for RIMM. In conclusion, Nanopore sequencing is a rapid, reliable tool for the identification of M. bovis. To reduce costs and increase the chance of M. bovis identification, pooling of 5 samples for Nanopore sequencing and RIMM is possible.
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LoopTag FRET Probe System for Multiplex qPCR Detection of Borrelia Species. Life (Basel) 2021; 11:life11111163. [PMID: 34833039 PMCID: PMC8624210 DOI: 10.3390/life11111163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Laboratory diagnosis of Lyme borreliosis refers to some methods with known limitations. Molecular diagnostics using specific nucleic acid probes may overcome some of these limitations. Methods: We describe the novel reporter fluorescence real-time polymerase chain reaction (PCR) probe system LoopTag for detection of Borrelia species. Advantages of the LoopTag system include having cheap conventional fluorescence dyes, easy primer design, no restrictions for PCR product lengths, robustness, high sequence specificity, applicability for multiplex real-time PCRs, melting curve analysis (single nucleotide polymorphism analysis) over a large temperature range, high sensitivity, and easy adaptation of conventional PCRs. Results: Using the LoopTag probe system we were able to detect all nine tested European species belonging to the Borrelia burgdorferi (sensu lato) complex and differentiated them from relapsing fever Borrelia species. As few as 10 copies of Borrelia in one PCR reaction were detectable. Conclusion: We established a novel multiplex probe real-time PCR system, designated LoopTag, that is simple, robust, and incorporates melting curve analysis for the detection and in the differentiation of European species belonging to the Borrelia burgdorferi s.l. complex.
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Li S, Renick P, Senkowsky J, Nair A, Tang L. Diagnostics for Wound Infections. Adv Wound Care (New Rochelle) 2021; 10:317-327. [PMID: 32496977 DOI: 10.1089/wound.2019.1103] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Significance: Infections can significantly delay the healing process in chronic wounds, placing an enormous economic burden on health care resources. Identification of infection biomarkers and imaging modalities to observe and quantify them has seen progress over the years. Recent Advances: Traditionally, clinicians determine the presence of infection through visual observation of wounds and confirm their diagnosis through wound culture. Many laboratory markers, including C-reactive protein, procalcitonin, presepsin, and bacterial protease activity, have been quantified to assist diagnosis of infection. Moreover, imaging modalities like plain radiography, computed tomography, magnetic resonance imaging, ultrasound imaging, spatial frequency domain imaging, thermography, autofluorescence imaging, and biosensors have emerged for real-time wound infection diagnosis and showed their unique advantages in deeper wound infection diagnosis. Critical Issues: While traditional diagnostic approaches provide valuable information, they are time-consuming and depend on clinicians' experiences. There is a need for noninvasive wound infection diagnostics that are highly specific, rapid, and accurate, and do not require extensive training. Future Directions: While innovative diagnostics utilizing various imaging instrumentation are being developed, new biomarkers have been investigated as potential indicators for wound infection. Products may be developed to either qualitatively or quantitatively measure these biomarkers. This review summarizes and compares all available diagnostics for wound infection, including those currently used in clinics and still under development. This review could serve as a valuable resource for clinicians treating wound infections as well as patients and wound care providers who would like to be informed of the recent developments.
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Affiliation(s)
- Shuxin Li
- Department of Bioengineering, The University of Texas at Arlington, Arlington, Texas, USA
| | - Paul Renick
- Department of Bioengineering, The University of Texas at Arlington, Arlington, Texas, USA
| | - Jon Senkowsky
- Texas Health Physician's Group, Arlington, Texas, USA
| | | | - Liping Tang
- Department of Bioengineering, The University of Texas at Arlington, Arlington, Texas, USA
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Novel High-Throughput Multiplex qPCRs for the Detection of Canine Vector-Borne Pathogens in the Asia-Pacific. Microorganisms 2021; 9:microorganisms9051092. [PMID: 34069665 PMCID: PMC8161336 DOI: 10.3390/microorganisms9051092] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/10/2023] Open
Abstract
The Asia-Pacific hosts a large diversity of canine vector-borne pathogens (VBPs) with some of the most common and most pathogenic, generating significant mortality as well as a spectrum of health impacts on local dog populations. The VBPs Anaplasma platys, Babesia gibsoni, Babesia vogeli, Ehrlichia canis, Hepatozoon canis and haemotropic Mycoplasma spp. are all endemic throughout the region, with many exhibiting shifting geographical distributions that warrant urgent attention. Moreover, many of these species cause similar clinical signs when parasitising canine hosts, whilst knowledge of the exact pathogen is critical to ensure treatment is effective. This is complicated by frequent coinfection that can exacerbate pathology. Here, we describe the development, optimisation and validation of two novel quadruplex Taq-Man based real-time PCRs (qPCRs) for the specific and sensitive detection of the aforementioned VBPs. To ensure accurate evaluation of diagnostic performance, results of our qPCRs were evaluated on field samples from Thai dogs and compared with both conventional PCR (cPCR) results and next-generation sequencing (NGS) metabarcoding. Our qPCRs were found to be more sensitive at detecting canine VBP than cPCR and generated results similar to those achieved by NGS. These qPCRs will provide a valuable high-throughput diagnostic tool available to epidemiologists, researchers and clinicians for the diagnosis of key canine VBPs in the Asia-Pacific and further afield.
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Monitoring microbial growth on a microfluidic lab-on-chip with electrochemical impedance spectroscopic technique. Biomed Microdevices 2021; 23:26. [PMID: 33885989 DOI: 10.1007/s10544-021-00564-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/17/2022]
Abstract
A continuous rise in the wastes from industrial effluents, bio-waste, and pharmaceuticals has deteriorated surface water and drinking water sources. Standard laboratory tests of total coliform are time-consuming and logistically inefficient for field data generation. Better and portable sensing technologies are needed. This paper reports an electrical impedance spectroscopic technique incorporated in a micro-fluidic chip with interdigitated microelectrodes to monitor the growth of microbial cells. Lag, log, and stationary phases of Escherichia coli cell growth with an integrated electrode are successfully detected, for samples of reverse osmosis water, standard treated tap water, and recycled water respectively. The results indicate that reverse osmosis water has a higher probability of contamination with bacterial pathogens compared to the other two types of water samples when subjected to the same amount of added nutrients. The statistical analysis shows a possible single detection range with higher-order regression, and repeat use of a single chip with the electrode was found to be within an acceptable limit. The interdigitated electrodes exposed to in-situ cell growth conditions and repeated electrical measurements have shown a promise for possible periodic or continuous monitoring. The paper further identifies several complimentary analysis methodologies that are robust towards phase noise in the measured impedance and are suited particularly for early-stage detection of bacterial contamination. The cell adhesion tendencies over the microelectrode due to the electric field need to be further analyzed.
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Gutierrez-Millan C, Calvo Díaz C, Lanao JM, Colino CI. Advances in Exosomes-Based Drug Delivery Systems. Macromol Biosci 2020; 21:e2000269. [PMID: 33094544 DOI: 10.1002/mabi.202000269] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/10/2020] [Indexed: 12/12/2022]
Abstract
Exosomes, a subgroup of extracellular vesicles, are important mediators of long-distance intercellular communication and are involved in a diverse range of biological processes such as the transport of lipids, proteins, and nucleic acids. Researchers, seeing the problems caused by the toxic effects and clearance of synthetic nanoparticles, consider exosomes as an interesting alternative to such nanoparticles in the specific and controlled transport of drugs. In recent years, there have been remarkable advances in the use of exosomes in cancer therapeutics or for treating neurological diseases, among other applications. The objective of this work is to analyze studies focused on exosomes used in drug delivery system, present and future applications in this field of research are discussed based on the results obtained.
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Affiliation(s)
- Carmen Gutierrez-Millan
- Area of Pharmacy and Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Salamanca, Salamanca, 37007, Spain
- The Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, 37007, Spain
| | - Clara Calvo Díaz
- Area of Pharmacy and Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Salamanca, Salamanca, 37007, Spain
| | - José M Lanao
- Area of Pharmacy and Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Salamanca, Salamanca, 37007, Spain
- The Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, 37007, Spain
| | - Clara I Colino
- Area of Pharmacy and Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Salamanca, Salamanca, 37007, Spain
- The Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, 37007, Spain
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Deckert A, Bärnighausen T, Kyei NN. Simulation of pooled-sample analysis strategies for COVID-19 mass testing. Bull World Health Organ 2020; 98:590-598. [PMID: 33012859 PMCID: PMC7463190 DOI: 10.2471/blt.20.257188] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 01/24/2023] Open
Abstract
OBJECTIVE To evaluate two pooled-sample analysis strategies (a routine high-throughput approach and a novel context-sensitive approach) for mass testing during the coronavirus disease 2019 (COVID-19) pandemic, with an emphasis on the number of tests required to screen a population. METHODS We used Monte Carlo simulations to compare the two testing strategies for different infection prevalences and pooled group sizes. With the routine high-throughput approach, heterogeneous sample pools are formed randomly for polymerase chain reaction (PCR) analysis. With the novel context-sensitive approach, PCR analysis is performed on pooled samples from homogeneous groups of similar people that have been purposively formed in the field. In both approaches, all samples contributing to pools that tested positive are subsequently analysed individually. FINDINGS Both pooled-sample strategies would save substantial resources compared to individual analysis during surge testing and enhanced epidemic surveillance. The context-sensitive approach offers the greatest savings: for instance, 58-89% fewer tests would be required for a pooled group size of 3 to 25 samples in a population of 150 000 with an infection prevalence of 1% or 5%. Correspondingly, the routine high-throughput strategy would require 24-80% fewer tests than individual testing. CONCLUSION Pooled-sample PCR screening could save resources during COVID-19 mass testing. In particular, the novel context-sensitive approach, which uses pooled samples from homogeneous population groups, could substantially reduce the number of tests required to screen a population. Pooled-sample approaches could help countries sustain population screening over extended periods of time and thereby help contain foreseeable second-wave outbreaks.
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Affiliation(s)
- Andreas Deckert
- Heidelberg Institute of Global Health, Heidelberg University, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Till Bärnighausen
- Heidelberg Institute of Global Health, Heidelberg University, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Nicholas Na Kyei
- Heidelberg Institute of Global Health, Heidelberg University, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
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Bradhurst P, Wong A, Gunaratne S, Anandacoomarasamy A. Pseudoseptic arthritis of the hip as the initial presentation of ankylosing spondylitis. Intern Med J 2020; 50:255-256. [DOI: 10.1111/imj.14664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/24/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Bradhurst
- Department of RheumatologyConcord Repatriation General Hospital Sydney New South Wales Australia
| | - Arthur Wong
- Department of RheumatologyConcord Repatriation General Hospital Sydney New South Wales Australia
| | - Shyamini Gunaratne
- Department of RheumatologyConcord Repatriation General Hospital Sydney New South Wales Australia
| | - Ana Anandacoomarasamy
- Department of RheumatologyConcord Repatriation General Hospital Sydney New South Wales Australia
- Sydney Medical SchoolThe University of Sydney Sydney New South Wales Australia
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14
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Rapid PCR identification of Prevotella copri in an Australian cohort of pregnant women. J Dev Orig Health Dis 2019; 11:228-234. [PMID: 31843036 DOI: 10.1017/s2040174419000849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Gut bacteria from the genus Prevotella are found in high abundance in faeces of non-industrialised communities but low abundance in industrialised, Westernised communities. Prevotella copri is one of the principal Prevotella species within the human gut. As it has been associated with developmental health and disease states, we sought to (i) develop a real-time polymerase chain reaction (PCR) to rapidly determine P. copri abundance and (ii) investigate its abundance in a large group of Australian pregnant mothers.The Barwon Infant Study is a pre-birth cohort study (n = 1074). Faecal samples were collected from mothers at 36 weeks gestation. Primers with a probe specific to the V3 region of P. copri 16S rRNA gene were designed and optimised for real-time PCR. Universal 16S rRNA gene primers amplified pan-bacterial DNA in parallel. Relative abundance of P. copri was calculated using a 2-ΔCt method.Relative abundance of P. copri by PCR was observed in 165/605 (27.3%) women. The distribution was distinctly bimodal, defining women with substantial (n = 115/165, 69.7%) versus very low P. copri expression (n = 50/165, 30.3%). In addition, abundance of P. copri by PCR correlated with 16S rRNA gene MiSeq sequencing data (r2 = 0.67, P < 0.0001, n = 61).We have developed a rapid and cost-effective technique for identifying the relative abundance of P. copri using real-time PCR. The expression of P. copri was evident in only a quarter of the mothers, and either at substantial or very low levels. PCR detection of P. copri may facilitate assessment of this species in large, longitudinal studies across multiple populations and in various clinical settings.
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15
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Targeted transcript quantification in single disseminated cancer cells after whole transcriptome amplification. PLoS One 2019; 14:e0216442. [PMID: 31430289 PMCID: PMC6701776 DOI: 10.1371/journal.pone.0216442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Gene expression analysis of rare or heterogeneous cell populations such as disseminated cancer cells (DCCs) requires a sensitive method allowing reliable analysis of single cells. Therefore, we developed and explored the feasibility of a quantitative PCR (qPCR) assay to analyze single-cell cDNA pre-amplified using a previously established whole transcriptome amplification (WTA) protocol. We carefully selected and optimized multiple steps of the protocol, e.g. re-amplification of WTA products, quantification of amplified cDNA yields and final qPCR quantification, to identify the most reliable and accurate workflow for quantitation of gene expression of the ERBB2 gene in DCCs. We found that absolute quantification outperforms relative quantification. We then validated the performance of our method on single cells of established breast cancer cell lines displaying distinct levels of HER2 protein. The different protein levels were faithfully reflected by transcript expression across the tested cell lines thereby proving the accuracy of our approach. Finally, we applied our method to breast cancer DCCs of a patient undergoing anti-HER2-directed therapy. Here, we were able to measure ERBB2 expression levels in all HER2-protein-positive DCCs. In summary, we developed a reliable single-cell qPCR assay applicable to measure distinct levels of ERBB2 in DCCs.
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16
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Kazi M, Khot R, Shetty A, Rodrigues C. Rapid detection of the commonly encountered carbapenemases (New Delhi metallo-β-lactamase, OXA-48/181) directly from various clinical samples using multiplex real-time polymerase chain reaction assay. Indian J Med Microbiol 2019; 36:369-375. [PMID: 30429389 DOI: 10.4103/ijmm.ijmm_18_324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Resistance due to New Delhi metallo-β-lactamase (NDM) and OXA-48/181 continues to emerge as a threat which is associated with nosocomial outbreaks and is a serious healthcare concern. Phenotypic detection being laborious and time-consuming requires rapid detection of NDM and OXA-48/181, which is achieved through real-time polymerase chain reaction (RT-PCR). Materials and Methods In this study, RT-PCR assay was developed to simultaneously detect NDM and OXA-48/181. The assay was validated on 102 non-duplicate, phenotypically characterised clinical samples. Results The assay showed a sensitivity and specificity of 97% and 100% for the detection of carbapenemases in comparison to conventional PCR. The in-house developed multiplex RT-PCR would help to rule-in the presence of NDM and OXA-48/181. Conclusions Rapid detection of these carbapenemases would be assist in better patient management, in terms of accurate antimicrobial treatment, help in cohorting infected from uninfected patient to prevent spread.
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Affiliation(s)
- Mubin Kazi
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Rukhsar Khot
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Anjali Shetty
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Camilla Rodrigues
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre, Mumbai, Maharashtra, India
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17
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Affiliation(s)
- Marilynn Ransom Fairfax
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA.
| | - Martin H Bluth
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Pathology Laboratories, Michigan Surgical Hospital, 21230 Dequindre Road, Warren, MI 48091, USA
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA
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18
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Webb JR, Price EP, Somprasong N, Schweizer HP, Baird RW, Currie BJ, Sarovich DS. Development and validation of a triplex quantitative real-time PCR assay to detect efflux pump-mediated antibiotic resistance in Burkholderia pseudomallei. Future Microbiol 2018; 13:1403-1418. [PMID: 30256166 PMCID: PMC6190177 DOI: 10.2217/fmb-2018-0155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/23/2018] [Indexed: 01/12/2023] Open
Abstract
AIM To develop a probe-based triplex quantitative real-time PCR assay to simultaneously detect the upregulation of the efflux pumps AmrAB-OprA, BpeAB-OprB and BpeEF-OprC in Burkholderia pseudomallei strains exhibiting increased minimum inhibitory concentrations toward meropenem, doxycycline or trimethoprim-sulfamethoxazole. METHODS The triplex assay was developed and subsequently tested on RNA isolated from eight clinical and eight laboratory-generated B. pseudomallei mutants harboring efflux pump regulator mutations. RESULTS The triplex assay accurately detected efflux pump upregulation in all clinical and laboratory mutants, which corresponded with decreased antibiotic susceptibility or antibiotic resistance. CONCLUSION Rapid detection of antibiotic resistance provides clinicians with a tool to identify potential treatment failure in near real time, enabling informed alteration of treatment during an infection and improved patient outcomes.
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Affiliation(s)
- Jessica R Webb
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Erin P Price
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Nawarat Somprasong
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Herbert P Schweizer
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Robert W Baird
- Departments of Infectious Diseases & Pathology & Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Bart J Currie
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Departments of Infectious Diseases & Pathology & Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Derek S Sarovich
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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19
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Pathogens and Their Effect on Exosome Biogenesis and Composition. Biomedicines 2018; 6:biomedicines6030079. [PMID: 30041409 PMCID: PMC6164629 DOI: 10.3390/biomedicines6030079] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/17/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
Exosomes are nanosized membrane microvesicles (30⁻100 nm) that have the capability to communicate intercellularly and transport cell components (i.e., miRNA, mRNA, proteins and DNA). Exosomes are found in nearly every cell type (i.e., mast cells, dendritic, tumor, and macrophages). There have been many studies that have shown the importance of exosome function as well as their unique packaging and targeting abilities. These characteristics make exosomes ideal candidates to act as biomarkers and therapeutics for disease. We will discuss the biogenesis, composition, and relationship of exosomes with non-viral microbial infections including gram-negative bacteria, gram-positive bacteria, Leishmania and Trypanosoma cruzi.
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20
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Stakheev AA, Ryazantsev DY, Zvezdina YK, Baranov MS, Zavriev SK. A Novel Fluorescent GFP Chromophore Analog-Based Dye for Quantitative PCR. BIOCHEMISTRY (MOSCOW) 2018; 83:855-860. [DOI: 10.1134/s000629791807009x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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De Neuter N, Bartholomeus E, Elias G, Keersmaekers N, Suls A, Jansens H, Smits E, Hens N, Beutels P, Van Damme P, Mortier G, Van Tendeloo V, Laukens K, Meysman P, Ogunjimi B. Memory CD4 + T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus. Genes Immun 2018; 20:255-260. [PMID: 29904098 DOI: 10.1038/s41435-018-0035-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/18/2018] [Accepted: 04/25/2018] [Indexed: 12/17/2022]
Abstract
Pathogens of past and current infections have been identified directly by means of PCR or indirectly by measuring a specific immune response (e.g., antibody titration). Using a novel approach, Emerson and colleagues showed that the cytomegalovirus serostatus can also be accurately determined by using a T cell receptor repertoire data mining approach. In this study, we have sequenced the CD4+ memory T cell receptor repertoire of a Belgian cohort with known cytomegalovirus serostatus. A random forest classifier was trained on the CMV specific T cell receptor repertoire signature and used to classify individuals in the Belgian cohort. This study shows that the novel approach can be reliably replicated with an equivalent performance as that reported by Emerson and colleagues. Additionally, it provides evidence that the T cell receptor repertoire signature is to a large extent present in the CD4+ memory repertoire.
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Affiliation(s)
- Nicolas De Neuter
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium. .,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium. .,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
| | - Esther Bartholomeus
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - George Elias
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Nina Keersmaekers
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Evelien Smits
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium.,Center for Oncological Research Antwerp, University of Antwerp, Antwerp, Belgium
| | - Niel Hens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.,Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Viggo Van Tendeloo
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium
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22
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Abstract
Microbiological diagnostic procedures have changed rapidly in recent years. This is especially true in the field of molecular diagnostics. Classical culture-based techniques are still the gold standard in many areas; however, they are already complemented by automated and also molecular techniques to guarantee faster and better quality results. The most commonly used techniques include real-time polymerase chain reaction (RT-PCR) based systems and nucleic acid hybridization. These procedures are used most powerfully from direct patient samples or in assays to detect the presence of nonculturable or fastidious organisms. Further techniques such as DNA sequencing are not yet used routinely for urological samples and can be considered experimental. However, in conjunction with dropping prices and further technical developments, these techniques promise to be used much more in the near future. Regarding bacterial identification from culture, mass spectrometry (MALDI-TOF MS) has become the technique of choice in recent years especially in Europe. It has tremendously shortened the time to result. This is now going to be extended to antibiotic susceptibility testing. This is of paramount importance in view of ever rising antimicrobial resistance rates. Techniques described in this review offer a faster and better microbiological diagnosis. Such continuous improvements are critical especially in times of cost pressure and rising antimicrobial resistance rates. It is in our interest to provide the best possible care for patients and in this regard a good and effective communication between the laboratory and the clinician is of vital importance.
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Affiliation(s)
- S Schubert
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, Marchioninistr. 17, 81377, München, Deutschland.
| | - A Wieser
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, Marchioninistr. 17, 81377, München, Deutschland.,Abteilung für Infektions- und Tropenmedizin der LMU, Leopoldstrasse 5, 80802, München, Deutschland.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort München, München, Deutschland
| | - G Bonkat
- alta uro AG, Centralbahnplatz 6, 4051, Basel, Schweiz
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23
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Schlachter S, Chan K, Marras SAE, Parveen N. Detection and Differentiation of Lyme Spirochetes and Other Tick-Borne Pathogens from Blood Using Real-Time PCR with Molecular Beacons. Methods Mol Biol 2018; 1616:155-170. [PMID: 28600768 DOI: 10.1007/978-1-4939-7037-7_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Real-time PCR assays have recently been implemented in diagnostics for many bacterial pathogens, allowing rapid and accurate detection, which ultimately results in improved clinical intervention. Here, we describe a sensitive method of detection for three common tick-borne pathogens Borrelia burgdorferi, Anaplasma phagocytophilum, and Babesia microti since coinfections with these pathogens have started occurring with increasing frequency over the last several years in both North America and Europe. A shared geographic region, the same tick vectors, and similar transmission cycle all favor simultaneous transmission of these three tick-borne pathogens. Furthermore, early symptoms of the diseases are often similar and somewhat nonspecific leading to poor clinical identification. The multiplex real-time PCR assay we describe here utilizes gene-specific primers, molecular beacon probes tagged with different fluorophores, and optimized PCR conditions to detect even small amounts of specific pathogen DNA without interference. Application of this detection method will offer better diagnostics for acute and persistent infection compared to the two-tier serological tests that are currently approved in North America and Europe, which do not necessarily detect active infection.
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Affiliation(s)
- Samantha Schlachter
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, 225 Warren Street, Newark, NJ, 07103-3535, USA
| | - Kamfai Chan
- AI Biosciences, Inc., 1902 Pinon Drive, Suite C, College Station, TX, 77845-5816, USA
| | - Salvatore A E Marras
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, 225 Warren Street, Newark, NJ, 07103-3535, USA
| | - Nikhat Parveen
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, 225 Warren Street, Newark, NJ, 07103-3535, USA.
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24
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Yang Y, Lin Y, Chen Z, Gong T, Yang P, Girault H, Liu B, Qiao L. Bacterial Whole Cell Typing by Mass Spectra Pattern Matching with Bootstrapping Assessment. Anal Chem 2017; 89:12556-12561. [PMID: 29086558 DOI: 10.1021/acs.analchem.7b03820] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Bacterial typing is of great importance in clinical diagnosis, environmental monitoring, food safety analysis, and biological research. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is now widely used to analyze bacterial samples. Identification of bacteria at the species level can be realized by matching the mass spectra of samples against a library of mass spectra of known bacteria. Nevertheless, in order to reasonably type bacteria, identification accuracy should be further improved. Herein, we propose a new framework to the identification and assessment for MALDI-MS based bacterial analysis. Our approach combines new measures for spectra similarity and a novel bootstrapping assessment. We tested our approach on a general data set containing the mass spectra of 1741 strains of bacteria and another challenging data set containing 250 strains, including 40 strains in the Bacillus cereus group that were previously claimed to be impossible to resolve by MALDI-MS. With the bootstrapping assessment, we achieved much more reliable predictions at both the genus and species level, and enabled to resolve the Bacillus cereus group. To the best of the authors' knowledge, our method is the first to provide a statistical assessment to MALDI-MS based bacterial typing that could lead to more reliable bacterial typing.
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Affiliation(s)
- Yi Yang
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University , Shanghai 200000, China
| | - Yu Lin
- Research School of Computer Science, College of Engineering and Computer Science, The Australian National University , Canberra, ACT 0200, Australia
| | - Zhuoxin Chen
- Institutes of Biomedical Sciences, Fudan University , Shanghai 200000, China
| | - Tianqi Gong
- Institutes of Biomedical Sciences, Fudan University , Shanghai 200000, China
| | - Pengyuan Yang
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University , Shanghai 200000, China.,Institutes of Biomedical Sciences, Fudan University , Shanghai 200000, China
| | - Hubert Girault
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne , Industrie 17, CH-1951 Sion, Switzerland
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University , Shanghai 200000, China.,Institutes of Biomedical Sciences, Fudan University , Shanghai 200000, China
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University , Shanghai 200000, China.,Institutes of Biomedical Sciences, Fudan University , Shanghai 200000, China
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25
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Safarkar R, Mehrabadi JF, Noormohammadi Z, Mirnejad R. Development a rapid and accurate multiplex real time PCR method for the detection Chlamydia trachomatis and Mycoplasma hominis. J Clin Lab Anal 2017; 31:e22126. [PMID: 28238212 PMCID: PMC6817121 DOI: 10.1002/jcla.22126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Sexually transmitted diseases easily spread among sexually active people and often have no symptoms. Rapid and accurate method for detecting these infections are necessary in early stages. The traditional detection methods of them are difficult and time-consuming. METHODS In this study, multiplex real time PCR was optimized for rapid identification of Chlamydia trachomatis and Mycoplasma hominis in a single tube and was performed with our designed primers. The sensitivity test was carried out to designed primers with diluted genomic DNA. To defined the specificity, non STD bacteria were used as DNA template. RESULTS This study indicated that the developed multiplex real time PCR can be an effective alternative procedure to the conventional methods for rapid and accurate identification of C Chlamydia trachomatis and Mycoplasma hominis. Multiplex real-time PCR Results of them were checked with melting curves. The sensitivity of our designed primer by multiplex real time PCR for Chlamydia trachomatis and Mycoplasma hominis were 4.78×1010 and 8.35×1010 , respectively, Which the primers did not amplify any product from a non-STD species. CONCLUSIONS Multiplex real time PCR by our new primers and analysis of melting curves were successfully usable for rapid and accurate detection of Chlamydia trachomatis and Mycoplasma hominis. This assay instead of traditional culture method, has considerable potential to be rapid, accurate and highly sensitive molecular diagnostic tool for simultaneous and direct detection.
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Affiliation(s)
- Roya Safarkar
- Department of Biology, Science and Research BranchIslamic Azad UniversityTehranIran
| | | | - Zahra Noormohammadi
- Department of Biology, Science and Research BranchIslamic Azad UniversityTehranIran
| | - Reza Mirnejad
- Molecular Biology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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26
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Abadi ATB. Resistance to clarithromycin and gastroenterologist’s persistence roles in nomination for Helicobacter pylori as high priority pathogen by World Health Organization. World J Gastroenterol 2017; 23:6379-6384. [PMID: 29085187 PMCID: PMC5643263 DOI: 10.3748/wjg.v23.i35.6379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/06/2017] [Accepted: 08/25/2017] [Indexed: 02/07/2023] Open
Abstract
Due to the increasing prevalence of clarithromycin resistance, future of management of Helicobacter pylori (H. pylori) infections need to be recognized. To now, clarithromycin was the best effective, well-tolerated and safe antibiotic used in treatment of the bacterium, but, increasing trend of resistance reduced efficacy of recommended regimens. Indeed, gastroenterologists are mostly unable to start appropriate therapy-according to the sensitivity profile-due to the certain difficulties in routine H. pylori culture procedure and being time consuming method. This announcement by World Health Organization (WHO) was an onset to reconsider current challenging dilemma about H. pylori clarithromycin resistant isolates. Therefore, investigating of various factors affecting this nomination by WHO is highly welcomed. In fact, WHO enumerated more than 16 pathogens which seriously threats human life and public health, thus better management or effective guidelines are necessary. Here for the first time, we nominated this phenomenon as ‘‘gastroenterologist’s persistence’’ which should be equally investigated as antibiotic resistance. The ability of gastroenterologists to win the game against H. pylori infections is highly influenced by their collaboration with diagnostic laboratories to apply susceptibility patterns before any prescription. In conclusion, closer collaboration between two important partners (gastroenterologists and microbiologists) in management of H. pylori infection may hopefully trigger an era to remedy current crisis in clarithromycin resistance, a later gastric cancer can be practically preventable.
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Affiliation(s)
- Amin Talebi Bezmin Abadi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115, Iran
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27
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A novel quantitative PCR mediated by high-fidelity DNA polymerase. Sci Rep 2017; 7:10365. [PMID: 28871131 PMCID: PMC5583327 DOI: 10.1038/s41598-017-10782-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/14/2017] [Indexed: 01/19/2023] Open
Abstract
The biggest challenge for accurate diagnosis of viral infectious disease is the high genetic variability of involved viruses, which affects amplification efficiency and results in low sensitivity and narrow spectrum. Here, we developed a new simple qPCR mediated by high-fidelity (HF) DNA polymerase. The new method utilizes an HFman probe and one primer. Fluorescent signal was generated from the 3'-5' hydrolysis of HFman probe by HF DNA polymerase before elongation initiation. Mismatches between probe/primer and template have less influence on the amplification efficiency of the new method. The new qPCR exhibited higher sensitivity and better adaptability to sequence variable templates than the conventional TaqMan probe based-qPCR in quantification of HIV-1 viral load. Further comparison with COBAS TaqMan HIV-1 Test (v2.0) showed a good correlation coefficient (R2 = 0.79) between both methods in quantification of HIV-1 viral load among 21 clinical samples. The characteristics of tolerance to variable templates and one probe-one primer system imply that the probe/primer design for the new method will be easier and more flexible than the conventional method for highly heterogeneous viruses. Therefore, the HF DNA polymerase-mediated qPCR method is a simple, sensitive and promising approach for the development of diagnostics for viral infectious diseases.
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Brait M, Izumchenko E, Kagohara LT, Long S, Wysocki PT, Faherty B, Fertig EJ, Khor TO, Bruckheimer E, Baia G, Ciznadija D, Sloma I, Ben-Zvi I, Paz K, Sidransky D. Comparative mutational landscape analysis of patient-derived tumour xenografts. Br J Cancer 2017; 116:515-523. [PMID: 28118322 PMCID: PMC5318980 DOI: 10.1038/bjc.2016.450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/23/2016] [Accepted: 12/14/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Screening of patients for cancer-driving mutations is now used for cancer prognosis, remission scoring and treatment selection. Although recently emerged targeted next-generation sequencing-based approaches offer promising diagnostic capabilities, there are still limitations. There is a pressing clinical need for a well-validated, rapid, cost-effective mutation profiling system in patient specimens. Given their speed and cost-effectiveness, quantitative PCR mutation detection techniques are well suited for the clinical environment. The qBiomarker mutation PCR array has high sensitivity and shorter turnaround times compared with other methods. However, a direct comparison with existing viable alternatives are required to assess its true potential and limitations. METHODS In this study, we evaluated a panel of 117 patient-derived tumour xenografts by the qBiomarker array and compared with other methods for mutation detection, including Ion AmpliSeq sequencing, whole-exome sequencing and droplet digital PCR. RESULTS Our broad analysis demonstrates that the qBiomarker's performance is on par with that of other labour-intensive and expensive methods of cancer mutation detection of frequently altered cancer-associated genes, and provides a foundation for supporting its consideration as an option for molecular diagnostics. CONCLUSIONS This large-scale direct comparison and validation of currently available mutation detection approaches is extremely relevant for the current scenario of precision medicine and will lead to informed choice of screening methodologies, especially in lower budget conditions or time frame limitations.
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Affiliation(s)
- Mariana Brait
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Evgeny Izumchenko
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Luciane T Kagohara
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Samuel Long
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Piotr T Wysocki
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Brian Faherty
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Elana J Fertig
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Tin Oo Khor
- Champions Oncology, Baltimore, MD 21205, USA
| | | | - Gilson Baia
- Champions Oncology, Baltimore, MD 21205, USA
| | | | - Ido Sloma
- Champions Oncology, Baltimore, MD 21205, USA
| | - Ido Ben-Zvi
- Champions Oncology, Baltimore, MD 21205, USA
| | - Keren Paz
- Champions Oncology, Baltimore, MD 21205, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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Darton TC, Zhou L, Blohmke CJ, Jones C, Waddington CS, Baker S, Pollard AJ. Blood culture-PCR to optimise typhoid fever diagnosis after controlled human infection identifies frequent asymptomatic cases and evidence of primary bacteraemia. J Infect 2017; 74:358-366. [PMID: 28130144 PMCID: PMC5345565 DOI: 10.1016/j.jinf.2017.01.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/11/2017] [Accepted: 01/14/2017] [Indexed: 01/09/2023]
Abstract
Background Improved diagnostics for typhoid are needed; a typhoid controlled human infection model may accelerate their development and translation. Here, we evaluated a blood culture-PCR assay for detecting infection after controlled human infection with S. Typhi and compared test performance with optimally performed blood cultures. Methodology/Principal findings Culture-PCR amplification of blood samples was performed alongside daily blood culture in 41 participants undergoing typhoid challenge. Study endpoints for typhoid diagnosis (TD) were fever and/or bacteraemia. Overall, 24/41 (59%) participants reached TD, of whom 21/24 (86%) had ≥1 positive blood culture (53/674, 7.9% of all cultures) or 18/24 (75%) had ≥1 positive culture-PCR assay result (57/684, 8.3%). A further five non-bacteraemic participants produced culture-PCR amplicons indicating infection; overall sensitivity/specificity of the assay compared to the study endpoints were 70%/65%. We found no significant difference between blood culture and culture-PCR methods in ability to identify cases (12 mismatching pairs, p = 0.77, binomial test). Clinical and stool culture metadata demonstrated that additional culture-PCR amplification positive individuals likely represented true cases missed by blood culture, suggesting the overall attack rate may be 30/41 (73%) rather than 24/41 (59%). Several participants had positive culture-PCR results soon after ingesting challenge providing new evidence for occurrence of an early primary bacteraemia. Conclusions/Significance Overall the culture-PCR assay performed well, identifying extra typhoid cases compared with routine blood culture alone. Despite limitations to widespread field-use, the benefits of increased diagnostic yield, reduced blood volume and faster turn-around-time, suggest that this assay could enhance laboratory typhoid diagnostics in research applications and high-incidence settings. Culture in ox-bile/tryptone soy broth selectively enriches for bile-tolerant Salmonella Typhi while lysing human cells. PCR sensitivity for detecting typhoid in clinical blood is limited by very low level bacteraemia during clinical illness. PCR amplification of S. Typhi fliC-d in pre-cultured blood can accurately identify typhoid infection in challenge study participants. Daily culture-PCR of blood collected from challenge study participants suggests primary bacteraemia occurs 12–36 h after S. Typhi ingestion. Additional use of culture-PCR demonstrates the true attack rate after typhoid challenge is markedly higher (75%) than previously assumed (60%).
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Affiliation(s)
- Thomas C Darton
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom; The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam.
| | - Liqing Zhou
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Christoph J Blohmke
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Claire Jones
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Claire S Waddington
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
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De Novo RNA Sequencing and Transcriptome Analysis of Monascus purpureus and Analysis of Key Genes Involved in Monacolin K Biosynthesis. PLoS One 2017; 12:e0170149. [PMID: 28114365 PMCID: PMC5256959 DOI: 10.1371/journal.pone.0170149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/29/2016] [Indexed: 12/25/2022] Open
Abstract
Monascus purpureus is an important medicinal and edible microbial resource. To facilitate biological, biochemical, and molecular research on medicinal components of M. purpureus, we investigated the M. purpureus transcriptome by RNA sequencing (RNA-seq). An RNA-seq library was created using RNA extracted from a mixed sample of M. purpureus expressing different levels of monacolin K output. In total 29,713 unigenes were assembled from more than 60 million high-quality short reads. A BLAST search revealed hits for 21,331 unigenes in at least one of the protein or nucleotide databases used in this study. The 22,365 unigenes were categorized into 48 functional groups based on Gene Ontology classification. Owing to the economic and medicinal importance of M. purpureus, most studies on this organism have focused on the pharmacological activity of chemical components and the molecular function of genes involved in their biogenesis. In this study, we performed quantitative real-time PCR to detect the expression of genes related to monacolin K (mokA-mokI) at different phases (2, 5, 8, and 12 days) of M. purpureus M1 and M1-36. Our study found that mokF modulates monacolin K biogenesis in M. purpureus. Nine genes were suggested to be associated with the monacolin K biosynthesis. Studies on these genes could provide useful information on secondary metabolic processes in M. purpureus. These results indicate a detailed resource through genetic engineering of monacolin K biosynthesis in M. purpureus and related species.
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Bian X, Lan Y, Wang B, Zhang YS, Liu B, Yang P, Zhang W, Qiao L. Microfluidic Air Sampler for Highly Efficient Bacterial Aerosol Collection and Identification. Anal Chem 2016; 88:11504-11512. [DOI: 10.1021/acs.analchem.6b02708] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Xiaojun Bian
- College
of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, P. R. China
| | - Ying Lan
- College
of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, P. R. China
| | - Bing Wang
- College
of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, P. R. China
| | - Yu Shrike Zhang
- Division
of Engineering in Medicine, Department of Medicine, Brigham and Women’s
Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, United States
| | - Baohong Liu
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
- Institutes
of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Pengyuan Yang
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
- Institutes
of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Weijia Zhang
- College
of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, P. R. China
- Institutes
of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Liang Qiao
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
- Institutes
of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
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Fernández-Álvarez C, González SF, Santos Y. Development of a SYBR green I real-time PCR assay for specific identification of the fish pathogen Aeromonas salmonicida subspecies salmonicida. Appl Microbiol Biotechnol 2016; 100:10585-10595. [PMID: 27838837 DOI: 10.1007/s00253-016-7929-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/03/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
A SYBR Green I real-time polymerase chain reaction protocol for specific detection of the fish pathogen Aeromonas salmonicida subsp. salmonicida was developed and validated for rapid diagnosis of typical furunculosis. The sequence of the aopO gene of A. salmonicida subsp. salmonicida, which encodes for a serine/threonine protein kinase linked to virulence, was chosen for primer design. The selected primers amplified a 119-bp internal fragment of the aopO gene. The specificity test proved that 100 % (40/40) of the A. salmonicida subsp. salmonicida strains tested showed a positive amplification with subspecies-specific melting temperatures (Tm) of 80.75 ± 0.35 °C. Atypical A. salmonicida subspecies and other non-related bacterial fish pathogens did not amplify or showed unspecific melting profiles, except for one strain of A. salmonicida subsp. achromogenes and one strain of A. salmonicida subsp. smithia. The detection sensitivity was 21 fg of purified bacterial DNA per reaction, corresponding to 1-2 bacterial cells and 6-60 bacteria per reaction for seeded kidney and blood. The assay was highly reproducible with low variation coefficient values for intra-run and inter-run assays. The assay also allowed the specific detection of A. salmonicida subsp. salmonicida in tissues of fish naturally and experimentally infected. No amplification was detected when tissues from healthy fish or fish affected by other diseases were tested. The SYBR Green real-time PCR and melt curve analysis developed in this study is a rapid and accurate method for the specific identification of A. salmonicida subsp. salmonicida isolates and its detection on tissues of fish affected by furunculosis.
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Affiliation(s)
- Clara Fernández-Álvarez
- Departamento de Microbiología y Parasitología, Edificio CIBUS Facultad de Biología and Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
| | - Santiago F González
- Institute for Research in Biomedicine, Università della Suvizzera Italiana, 6500, Bellinzona, Switzerland
| | - Ysabel Santos
- Departamento de Microbiología y Parasitología, Edificio CIBUS Facultad de Biología and Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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Maertzdorf J, McEwen G, Weiner J, Tian S, Lader E, Schriek U, Mayanja-Kizza H, Ota M, Kenneth J, Kaufmann SH. Concise gene signature for point-of-care classification of tuberculosis. EMBO Mol Med 2016; 8:86-95. [PMID: 26682570 PMCID: PMC4734838 DOI: 10.15252/emmm.201505790] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
There is an urgent need for new tools to combat the ongoing tuberculosis (TB) pandemic. Gene expression profiles based on blood signatures have proved useful in identifying genes that enable classification of TB patients, but have thus far been complex. Using real‐time PCR analysis, we evaluated the expression profiles from a large panel of genes in TB patients and healthy individuals in an Indian cohort. Classification models were built and validated for their capacity to discriminate samples from TB patients and controls within this cohort and on external independent gene expression datasets. A combination of only four genes distinguished TB patients from healthy individuals in both cross‐validations and on separate validation datasets with very high accuracy. An external validation on two distinct cohorts using a real‐time PCR setting confirmed the predictive power of this 4‐gene tool reaching sensitivity scores of 88% with a specificity of around 75%. Moreover, this gene signature demonstrated good classification power in HIV+ populations and also between TB and several other pulmonary diseases. Here we present proof of concept that our 4‐gene signature and the top classifier genes from our models provide excellent candidates for the development of molecular point‐of‐care TB diagnosis in endemic areas.
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Affiliation(s)
| | - Gayle McEwen
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - January Weiner
- Max Planck Institute for Infection Biology, Berlin, Germany
| | | | | | | | | | - Martin Ota
- Medical Research Council, Banjul, The Gambia
| | - John Kenneth
- St. John's Research Institute, Bangalore, Karnataka, India
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Wen AM, Steinmetz NF. Design of virus-based nanomaterials for medicine, biotechnology, and energy. Chem Soc Rev 2016; 45:4074-126. [PMID: 27152673 PMCID: PMC5068136 DOI: 10.1039/c5cs00287g] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review provides an overview of recent developments in "chemical virology." Viruses, as materials, provide unique nanoscale scaffolds that have relevance in chemical biology and nanotechnology, with diverse areas of applications. Some fundamental advantages of viruses, compared to synthetically programmed materials, include the highly precise spatial arrangement of their subunits into a diverse array of shapes and sizes and many available avenues for easy and reproducible modification. Here, we will first survey the broad distribution of viruses and various methods for producing virus-based nanoparticles, as well as engineering principles used to impart new functionalities. We will then examine the broad range of applications and implications of virus-based materials, focusing on the medical, biotechnology, and energy sectors. We anticipate that this field will continue to evolve and grow, with exciting new possibilities stemming from advancements in the rational design of virus-based nanomaterials.
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Affiliation(s)
- Amy M Wen
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA. and Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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35
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Kuhn P, Fühner V, Unkauf T, Moreira GMSG, Frenzel A, Miethe S, Hust M. Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display. Proteomics Clin Appl 2016; 10:922-948. [PMID: 27198131 PMCID: PMC7168043 DOI: 10.1002/prca.201600002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/30/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022]
Abstract
Antibodies are valuable molecules for the diagnostic and treatment of diseases caused by pathogens and toxins. Traditionally, these antibodies are generated by hybridoma technology. An alternative to hybridoma technology is the use of antibody phage display to generate recombinant antibodies. This in vitro technology circumvents the limitations of the immune system and allows—in theory—the generation of antibodies against all conceivable molecules. Phage display technology enables obtaining human antibodies from naïve antibody gene libraries when either patients are not available or immunization is not ethically feasible. On the other hand, if patients or immunized/infected animals are available, it is common to construct immune phage display libraries to select in vivo affinity‐matured antibodies. Because the phage packaged DNA sequence encoding the antibodies is directly available, the antibodies can be smoothly engineered according to the requirements of the final application. In this review, an overview of phage display derived recombinant antibodies against bacterial, viral, and eukaryotic pathogens as well as toxins for diagnostics and therapy is given.
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Affiliation(s)
- Philipp Kuhn
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Viola Fühner
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Tobias Unkauf
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | | | - André Frenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany.,YUMAB GmbH, Braunschweig, Germany
| | - Sebastian Miethe
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany.
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Diene SM, Bertelli C, Pillonel T, Jacquier N, Croxatto A, Jaton K, Greub G. Comparative genomics of Neisseria meningitidis strains: new targets for molecular diagnostics. Clin Microbiol Infect 2016; 22:568.e1-7. [PMID: 27085725 DOI: 10.1016/j.cmi.2016.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/05/2016] [Accepted: 03/19/2016] [Indexed: 01/19/2023]
Abstract
In 2010, Jaton et al. (False-negative PCR result due to gene polymorphism: the example of Neisseria meningitidis. J Clin Microbiol 2010;48:4590-2) reported an isolate of Neisseria meningitidis serogroup B that was not detected by the ctrA quantitative real-time PCR (qRT-PCR) used in our diagnostic laboratory. Sequence analysis of ctrA revealed several single nucleotide polymorphisms responsible for the negative qRT-PCR. Therefore, we sequenced the genome of this isolate and performed comparative genomics to propose new gene targets for the specific detection of N. meningitidis from clinical specimens. We identified 11 genes as specific to N. meningitidis genomes and common to at least 177 (97%) of the 183 genomes available. Among them, three genes (metA, tauE and shlA) were selected to develop new qRT-PCRs for the detection of N. meningitidis DNA. The three qRT-PCRs were highly sensitive and specific, and they exhibited a good reproducibility when tested on plasmidic positive controls and genomic DNA extracted from strains of N. meningitidis and other relevant bacterial species. The clinical sensitivity and specificity of metA and tauE qRT-PCRs were both 100% based on a testing of cerebrospinal fluid samples positive for N. meningitidis or other clinically relevant bacteria. Despite a 100% specificity, the sensitivity of the shlA qRT-PCR was only 70%. We thus recommend using the metA and/or tauE qRT-PCRs developed here. To prevent PCR failure in the presence of new polymorphic strains, the detection of dual targets by duplex qRT-PCR would be more accurate and suitable for the diagnosis of N. meningitidis from clinical specimens.
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Affiliation(s)
- S M Diene
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - C Bertelli
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - T Pillonel
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - N Jacquier
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - A Croxatto
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - K Jaton
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland.
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Xuan SH, Wu LP, Zhou YG, Xiao MB. Detection of clarithromycin-resistant Helicobacter pylori in clinical specimens by molecular methods: A review. J Glob Antimicrob Resist 2016; 4:35-41. [PMID: 27436390 DOI: 10.1016/j.jgar.2016.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 12/17/2022] Open
Abstract
Various molecular methods have been developed to rapidly detect clarithromycin (CLR) resistance in Helicobacter pylori isolates in clinical specimens. All of these assays for detecting CLR resistance in H. pylori are based on detection of mutations in the 23S rRNA gene. In this article, we summarise current knowledge regarding the detection of H. pylori CLR resistance in clinical specimens by molecular tests. The available data showed that restriction fragment length polymorphism (RFLP), 3'-mismatch PCR, DNA sequencing, the PCR line probe assay (PCR-LiPA) and fluorescence in situ hybridisation assay (FISH) are able to detect CLR-resistant H. pylori in clinical specimens with excellent specificity and sensitivity. However, several factors limit their clinical application, including fastidious, time-consuming preparation and low-throughput as well as carrying a risk of contamination. Furthermore, as an invasive method, FISH is not suitable for children or the elderly. Among the molecular methods, one that is most promising for the future is real-time PCR probe hybridisation technology using fluorescence resonance energy transfer (FRET) probes, which can rapidly detect CLR resistance with high sensitivity and specificity in biopsies and stool specimens, even though mixed infections are present in clinical specimens. Moreover, due to the advantages that this method is simple, rapid and economical, real-time PCR is technically feasible for clinical application in small- and medium-sized hospitals in developing countries. Second, with high sensitivity, specificity and throughput, DNA chips will also be a valuable tool for detecting resistant H. pylori isolates from cultures and clinical specimens.
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Affiliation(s)
- Shi-Hai Xuan
- Department of Clinical Laboratory, The Affiliated Dongtai Hospital of Nantong University, Dongtai 224200, China
| | - Li-Pei Wu
- Department of Clinical Laboratory, The Affiliated Dongtai Hospital of Nantong University, Dongtai 224200, China
| | - Yu-Gui Zhou
- Department of Clinical Laboratory, The Affiliated Dongtai Hospital of Nantong University, Dongtai 224200, China
| | - Ming-Bing Xiao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, China.
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Lehmusvuori A, Soikkeli M, Tuunainen E, Seppä T, Spangar A, Rantakokko-Jalava K, von Lode P, Karhunen U, Soukka T, Wittfooth S. Ready to use dry-reagent PCR assays for the four common bacterial pathogens using switchable lanthanide luminescence probe system. J Microbiol Methods 2015; 118:64-9. [DOI: 10.1016/j.mimet.2015.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 12/23/2022]
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Mor-Reinoso C, Pascual A, Nart J, Quirynen M. Inhibition of de novo plaque growth by a new 0.03 % chlorhexidine mouth rinse formulation applying a non-brushing model: a randomized, double blind clinical trial. Clin Oral Investig 2015; 20:1459-67. [PMID: 26475499 DOI: 10.1007/s00784-015-1625-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVES The aim of this study was to investigate the plaque inhibitory effect of a new 0.03 % chlorhexidine digluconate (CHX) and 0.05 % cetylpyridinium chloride (CPC) mouthrinse formulation and to explore patients' experience and side effects after its use. MATERIALS AND METHODS This short-term, randomized, double blind, parallel, clinical trial enrolled 150 periodontally healthy patients. These volunteers were randomly allocated to one of following mouthrinse groups (n = 50/group): 0.12 % CHX + 0.05 % CPC (Perio-Aid® Treatment alcohol-free), 0.03 % CHX + 0.05 % CPC new test formulation or to the placebo group. Clinical parameters (plaque, gingival, and stain indexes) and microbiological samples were taken at baseline, before supragingival cleaning, and after 4 days of undisturbed plaque growth, rinsing twice/day with one of the mouthrinses. RESULTS Plaque reduction was similar for the 0.12 % CHX (-0.52 ± 0.55) and 0.03 % CHX (-0.47 ± 0.49) groups. Both showed significant reductions in plaque accumulation compared to the placebo (p < 0.001). The new formulation had less of a negative impact on taste perception when compared to the 0.12 % CHX solution. The new CHX mouthrinse was also able to control bacterial loads and reduce some periodontopathogens. CONCLUSIONS This study indicated that the new 0.03 % CHX + 0.05 % CPC formulation exerted clinical efficacy similar to that achieved by an already-marketed 0.12 % CHX + 0.05 % CPC mouthrinse, but with slightly fewer side effects. CLINICAL RELEVANCE Lower CHX mouthrinse formulations could be effective in the inhibition of plaque regrowth with reduced unpleasant subjective side effects.
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Affiliation(s)
- Carolina Mor-Reinoso
- Department of Periodontology, Hospital General de Catalunya, Universitat Internacional de Catalunya, C/ Josep Trueta s/n, C.P. 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Andres Pascual
- Department of Periodontology, Hospital General de Catalunya, Universitat Internacional de Catalunya, C/ Josep Trueta s/n, C.P. 08195, Sant Cugat del Vallès, Barcelona, Spain.
| | - Jose Nart
- Department of Periodontology, Hospital General de Catalunya, Universitat Internacional de Catalunya, C/ Josep Trueta s/n, C.P. 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Marc Quirynen
- Departments of Oral Health Sciences and Periodontology, Katholieke Universiteit Leuven, University Hospitals & Dentistry Leuven, Leuven, Belgium
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Nagamine K, Hung GC, Li B, Lo SC. DNA Sequence Signatures for Rapid Detection of Six Target Bacterial Pathogens Using PCR Assays. Microbiol Insights 2015; 8:7-14. [PMID: 26279626 PMCID: PMC4515919 DOI: 10.4137/mbi.s29736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/05/2022] Open
Abstract
Using Streptococcus pyogenes as a model, we previously established a stepwise computational workflow to effectively identify species-specific DNA signatures that could be used as PCR primer sets to detect target bacteria with high specificity and sensitivity. In this study, we extended the workflow for the rapid development of PCR assays targeting Enterococcus faecalis, Enterococcus faecium, Clostridium perfringens, Clostridium difficile, Clostridium tetani, and Staphylococcus aureus, which are of safety concern for human tissue intended for transplantation. Twenty-one primer sets that had sensitivity of detecting 5-50 fg DNA from target bacteria with high specificity were selected. These selected primer sets can be used in a PCR array for detecting target bacteria with high sensitivity and specificity. The workflow could be widely applicable for the rapid development of PCR-based assays for a wide range of target bacteria, including those of biothreat agents.
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Affiliation(s)
- Kenjiro Nagamine
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies and Division of Human Tissues, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Guo-Chiuan Hung
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies and Division of Human Tissues, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Bingjie Li
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies and Division of Human Tissues, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Shyh-Ching Lo
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies and Division of Human Tissues, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
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Esfandiari B, Pourshafie MR, Gouya MM, Khaki P, Mostafavi E, Darvish J, Bidhendi SM, Hanifi H, Nahrevanian H. An epidemiological comparative study on diagnosis of rodent leptospirosis in Mazandaran Province, northern Iran. Epidemiol Health 2015; 37:e2015012. [PMID: 25773440 PMCID: PMC4430762 DOI: 10.4178/epih/e2015012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 02/22/2015] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES: Leptospirosis is a zoonosis caused by leptospires, in which transmission occurs through contact with contaminated biological fluids from infected animals. Rodents can act as a source of infection for humans and animals. The disease has a global distribution, mainly in humid, tropical and sub-tropical regions. The aim of this study was to compare culture assays, the microscopic agglutination test (MAT), polymerase chain reaction (PCR), and nested PCR (n-PCR), for the diagnosis of leptospirosis in rodents in Mazandaran Province, northern Iran. METHODS: One hundred fifty-one rodents were trapped alive at 10 locations, and their urine and kidney samples were collected and used for the isolation of live Leptospira. The infecting serovars were identified and the antibody titres were measured by MAT, using a panel of 20 strains of live Leptospira species as antigens. The presence of leptospiral DNA was evaluated in urine and kidney samples using PCR and n-PCR. RESULTS: No live leptospires were isolated from the kidney and urine samples of the rodents. Different detection rates of leptospirosis were observed with MAT (21.2%), PCR (11.3%), and n-PCR (3.3%). The dominant strain was Leptospira serjoehardjo (34.4%, p=0.28), although other serotypes were also found. The prevalence of positive leptospirosis tests in rodents was 15.9, 2.6, and 2.6% among Rattus norvegicus, R. rattus, and Apodemus sylvaticus, respectively. CONCLUSIONS: Leptospirosis was prevalent in rodents in Mazandaran Province, northern Iran. MAT was able to detect leptospires more frequently than culture or PCR. The kidney was a more suitable site for identifying leptospiral DNA by n-PCR than urine. Culture was not found to be an appropriate technique for clinical diagnosis.
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Affiliation(s)
| | | | | | - Pejvak Khaki
- Microbiology Department, Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Ehsan Mostafavi
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
| | - Jamshid Darvish
- Department of Biology, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Hamed Hanifi
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
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Cost-effective pooling of DNA from nasopharyngeal swab samples for large-scale detection of bacteria by real-time PCR. J Clin Microbiol 2014; 53:1002-4. [PMID: 25552360 DOI: 10.1128/jcm.03609-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We investigated the potential of pooling DNA from nasopharyngeal specimens to reduce the cost of real-time PCR (RT-PCR) for bacterial detection. Lyophilization is required to reconcentrate DNA. This strategy yields a high specificity (86%) and a high sensitivity (96%). We estimate that compared to individual testing, 37% fewer RT-PCR tests are needed.
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Lee YJ, Kim D, Lee K, Chun JY. Single-channel multiplexing without melting curve analysis in real-time PCR. Sci Rep 2014; 4:7439. [PMID: 25501038 PMCID: PMC4262828 DOI: 10.1038/srep07439] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/21/2014] [Indexed: 01/08/2023] Open
Abstract
Multiplex real-time PCR with quantification of targets in a single fluorescence channel has been the demand in biotechnology industry. Here, we develop a novel analytical real-time PCR technique to detect multiple targets in a single fluorescence channel without melting curve analysis. In this technique, we show the intensity of the fluorescence signals of two discrete Tm targets is different at certain temperatures called detection temperatures, by which a high Tm target can be detected regardless of a low Tm target. We then identify the low Tm target by utilizing a change of the fluorescence signals between two different detection temperatures. Furthermore, it enables us to determine quantification of each target in a single channel, possibly facilitating convenient patient care for drug treatment in clinics.
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Affiliation(s)
- Young-Jo Lee
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Daeyoung Kim
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Kihoon Lee
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Jong-Yoon Chun
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
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Sting R, Molz K, Hoferer M. Creating standards for absolute quantification of Coxiella burnetii in real-time PCR--a comparative study based on transmission electron microscopy. Biologicals 2014; 43:18-22. [PMID: 25465354 DOI: 10.1016/j.biologicals.2014.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/02/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022] Open
Abstract
Quantitative standards are a prerequisite for quality control and quantification of pathogens. In this study the creation of quantitative standards for use in qPCR is described using the pathogen Coxiella burnetii. Quantification of Coxiella burnetii particles by transmission electron microscopy (TEM) was used as primary standard and compared with data obtained by light microscopy as well as genome equivalents (GE) and plasmid units (recombinant plasmid). Based on pathogen quantification using TEM and light microscopy, pathogen detection limits of 6 and 2 C. burnetii particles could be determined per com1 qPCR reaction, respectively. In comparison, the detection limits were 17 and 13 pathogen units using GE and plasmid units, respectively. The standard generated by TEM can be used as gold standard for universal application due to high accuracy, quantitative control of the producing process and supplying intact pathogen particles.
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Affiliation(s)
- Reinhard Sting
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany.
| | - Kerstin Molz
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany
| | - Marc Hoferer
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany
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Emerging rapid resistance testing methods for clinical microbiology laboratories and their potential impact on patient management. BIOMED RESEARCH INTERNATIONAL 2014; 2014:375681. [PMID: 25343142 PMCID: PMC4197867 DOI: 10.1155/2014/375681] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/22/2014] [Accepted: 08/28/2014] [Indexed: 12/25/2022]
Abstract
Atypical and multidrug resistance, especially ESBL and carbapenemase expressing Enterobacteriaceae, is globally spreading. Therefore, it becomes increasingly difficult to achieve therapeutic success by calculated antibiotic therapy. Consequently, rapid antibiotic resistance testing is essential. Various molecular and mass spectrometry-based approaches have been introduced in diagnostic microbiology to speed up the providing of reliable resistance data. PCR- and sequencing-based approaches are the most expensive but the most frequently applied modes of testing, suitable for the detection of resistance genes even from primary material. Next generation sequencing, based either on assessment of allelic single nucleotide polymorphisms or on the detection of nonubiquitous resistance mechanisms might allow for sequence-based bacterial resistance testing comparable to viral resistance testing on the long term. Fluorescence in situ hybridization (FISH), based on specific binding of fluorescence-labeled oligonucleotide probes, provides a less expensive molecular bridging technique. It is particularly useful for detection of resistance mechanisms based on mutations in ribosomal RNA. Approaches based on MALDI-TOF-MS, alone or in combination with molecular techniques, like PCR/electrospray ionization MS or minisequencing provide the fastest resistance results from pure colonies or even primary samples with a growing number of protocols. This review details the various approaches of rapid resistance testing, their pros and cons, and their potential use for the diagnostic laboratory.
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Pabinger S, Rödiger S, Kriegner A, Vierlinger K, Weinhäusel A. A survey of tools for the analysis of quantitative PCR (qPCR) data. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 1:23-33. [PMID: 27920994 PMCID: PMC5129434 DOI: 10.1016/j.bdq.2014.08.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 08/26/2014] [Accepted: 08/26/2014] [Indexed: 01/12/2023]
Abstract
Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.
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Affiliation(s)
- Stephan Pabinger
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Stefan Rödiger
- Faculty of Natural Sciences, InnoProfile Group "Image-based Assays", Brandenburg University of Technology Cottbus - Senftenberg, Großenhainer Straße 57, 01968 Senftenberg, Germany
| | - Albert Kriegner
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Klemens Vierlinger
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Andreas Weinhäusel
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
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Segawa S, Sawai S, Murata S, Nishimura M, Beppu M, Sogawa K, Watanabe M, Satoh M, Matsutani T, Kobayashi M, Iwadate Y, Kuwabara S, Saeki N, Nomura F. Direct application of MALDI-TOF mass spectrometry to cerebrospinal fluid for rapid pathogen identification in a patient with bacterial meningitis. Clin Chim Acta 2014; 435:59-61. [DOI: 10.1016/j.cca.2014.04.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 04/25/2014] [Accepted: 04/25/2014] [Indexed: 11/28/2022]
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Affiliation(s)
- Marilynn Ransom Fairfax
- Department of Pathology, Wayne State University School of Medicine, and Microbiology Division, Detroit Medical Center University Laboratories, 4201 Saint Antoine, Detroit, MI 48201, USA.
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Canier L, Khim N, Kim S, Sluydts V, Heng S, Dourng D, Eam R, Chy S, Khean C, Loch K, Ken M, Lim H, Siv S, Tho S, Masse-Navette P, Gryseels C, Uk S, Van Roey K, Grietens KP, Sokny M, Thavrin B, Chuor CM, Deubel V, Durnez L, Coosemans M, Ménard D. An innovative tool for moving malaria PCR detection of parasite reservoir into the field. Malar J 2013; 12:405. [PMID: 24206649 PMCID: PMC3829804 DOI: 10.1186/1475-2875-12-405] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/05/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND To achieve the goal of malaria elimination in low transmission areas such as in Cambodia, new, inexpensive, high-throughput diagnostic tools for identifying very low parasite densities in asymptomatic carriers are required. This will enable a switch from passive to active malaria case detection in the field. METHODS DNA extraction and real-time PCR assays were implemented in an "in-house" designed mobile laboratory allowing implementation of a robust, sensitive and rapid malaria diagnostic strategy in the field. This tool was employed in a survey organized in the context of the MalaResT project (NCT01663831). RESULTS The real-time PCR screening and species identification assays were performed in the mobile laboratory between October and November 2012, in Rattanakiri Province, to screen approximately 5,000 individuals in less than four weeks and treat parasite carriers within 24-48 hours after sample collection. An average of 240 clinical samples (and 40 quality control samples) was tested every day, six/seven days per week. Some 97.7% of the results were available <24 hours after the collection. A total of 4.9% were positive for malaria. Plasmodium vivax was present in 61.1% of the positive samples, Plasmodium falciparum in 45.9%, Plasmodium malariae in 7.0% and Plasmodium ovale in 2.0%. CONCLUSIONS The operational success of this diagnostic set-up proved that molecular testing and subsequent treatment is logistically achievable in field settings. This will allow the detection of clusters of asymptomatic carriers and to provide useful epidemiological information. Fast results will be of great help for staff in the field to track and treat asymptomatic parasitaemic cases. The concept of the mobile laboratory could be extended to other countries for the molecular detection of malaria or other pathogens, or to culture vivax parasites, which does not support long-time delay between sample collection and culture.
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Affiliation(s)
- Lydie Canier
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Nimol Khim
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Saorin Kim
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | | | - Somony Heng
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Dany Dourng
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Rotha Eam
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sophy Chy
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Chanra Khean
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Kaknika Loch
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Malen Ken
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Hokkean Lim
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sovannaroath Siv
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Sochantha Tho
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | | | | | - Sambunny Uk
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | | | | | - Mao Sokny
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Boukheng Thavrin
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Char Meng Chuor
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | | | - Lies Durnez
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Marc Coosemans
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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