1
|
Rapid Detection of Antimicrobial Resistance in Mycoplasma genitalium by High-Resolution Melting Analysis with Unlabeled Probes. Microbiol Spectr 2022; 10:e0101422. [PMID: 35880894 PMCID: PMC9430336 DOI: 10.1128/spectrum.01014-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With looming resistance to fluoroquinolones in Mycoplasma genitalium, public health control strategies require effective antimicrobial resistance (AMR) diagnostic methods for clinical and phenotypic AMR surveillance. We developed a novel AMR detection method, MGparC-AsyHRM, based on the combination of asymmetric high-resolution melting (HRM) technology and unlabeled probes, which simultaneously performs M. genitalium identification and genotypes eight mutations in the parC gene that are responsible for most cases of fluoroquinolone resistance. These enhancements expand the traditional HRM from the conventional detection of single-position mutations to a method capable of detecting short fragments with closely located AMR positions with a high diversity of mutations. Based on the results of clinical sample testing, this method produces an accordance of 98.7% with the Sanger sequencing method. Furthermore, the specificity for detecting S83I, S83N, S83R, and D87Y variants, the most frequently detected mutations in fluoroquinolone resistance, was 100%. This method maintained a stable and accurate performance for genomic copies at rates of ≥20 copies per reaction, demonstrating high sensitivity. Additionally, no specific cross-reactions were observed when testing eight common sexually transmitted infection (STI)-related agents. Notably, this work highlights the significant potential of our method in the field of AMR testing, with the results suggesting that our method can be applied in a range of scenarios and to additional pathogens. In summary, our method enables high throughput, provides excellent specificity and sensitivity, and is cost-effective, suggesting that this method can be used to rapidly monitor the molecular AMR status and complement current AMR surveillance. IMPORTANCE Mycoplasma genitalium was recently added to the antimicrobial-resistant (AMR) threats "watch list" of the U.S. Centers for Disease Control and Prevention because this pathogen has become extremely difficult to treat as a result of increased resistance. M. genitalium is also difficult to culture, and therefore, molecule detection is the only method available for AMR testing. In this work, we developed a novel AMR detection method, MGparC-AsyHRM, based on the combination of asymmetrical HRM technology and unlabeled probes, and it simultaneously performs M. genitalium identification and genotypes eight mutations in the parC gene that are responsible for most cases of fluoroquinolone resistance. The MGparC-AsyHRM method is a high-throughput, low-cost, simple, and culture-free procedure that can enhance public health and management of M. genitalium infections and AMR control, providing a strong complement to phenotypic AMR surveillance to address the spread of fluoroquinolone resistance.
Collapse
|
2
|
Teal CN, Coykendall DK, Campbell MR, Eardley DL, Delomas TA, Shira JT, Schill DJ, Bonar SA, Culver M. Sex-specific markers undetected in green sunfish Lepomis cyanellus using restriction-site associated DNA sequencing. JOURNAL OF FISH BIOLOGY 2022; 100:1528-1540. [PMID: 35439326 DOI: 10.1111/jfb.15063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
We used restriction-site associated DNA sequencing for SNP discovery and genotyping of known-sex green sunfish Lepomis cyanellus DNA samples to search for sex-diagnostic single nucleotide polymorphisms (SNPs) and restriction-site associated sequences present in one sex and absent in the other. The bioinformatic analyses discovered candidate SNPs and sex-specific restriction-site associated sequences that fit patterns of male or female heterogametic sex determination systems. However, when primers were developed and tested, no candidates reliably identified phenotypic sex. The top performing SNP candidate (ZW_218) correlated with phenotypic sex 63.0% of the time and the presence-absence loci universally amplified in both sexes. We recommend further investigations that interrogate a larger fraction of the L. cyanellus genome. Additionally, studies on the effect of temperature and rearing density on sex determination, as well as breeding of sex-reversed individuals, could provide more insights into the sex determination system of L. cyanellus.
Collapse
Affiliation(s)
- Chad N Teal
- Arizona Cooperative Fish and Wildlife Research Unit, School of Natural Resources and the Environment, Tucson, Arizona, USA
| | - D Katharine Coykendall
- Pacific States Marine Fisheries Commission, Eagle Fish Genetics Lab, Eagle, Idaho, USA
- Idaho Department of Fish and Game, Eagle Fish Genetics Lab, Eagle, Idaho, USA
| | - Matthew R Campbell
- Idaho Department of Fish and Game, Eagle Fish Genetics Lab, Eagle, Idaho, USA
| | - Daniel L Eardley
- Pacific States Marine Fisheries Commission, Eagle Fish Genetics Lab, Eagle, Idaho, USA
- Idaho Department of Fish and Game, Eagle Fish Genetics Lab, Eagle, Idaho, USA
| | - Thomas A Delomas
- Pacific States Marine Fisheries Commission, Eagle Fish Genetics Lab, Eagle, Idaho, USA
- Idaho Department of Fish and Game, Eagle Fish Genetics Lab, Eagle, Idaho, USA
| | - James T Shira
- University of Arizona Genetics Core, Tucson, Arizona, USA
| | | | - Scott A Bonar
- US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, School of Natural Resources and the Environment, University of Arizona, ENR2, Tucson, Arizona, USA
| | - Melanie Culver
- US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, School of Natural Resources and the Environment, University of Arizona, ENR2, Tucson, Arizona, USA
| |
Collapse
|
3
|
Li E, Zhang H, Jiang H, Pieterse CMJ, Jousset A, Bakker PAHM, de Jonge R. Experimental-Evolution-Driven Identification of Arabidopsis Rhizosphere Competence Genes in Pseudomonas protegens. mBio 2021; 12:e0092721. [PMID: 34101491 PMCID: PMC8262913 DOI: 10.1128/mbio.00927-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/30/2021] [Indexed: 11/20/2022] Open
Abstract
Beneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including competition with neighboring microorganisms and host immunity. Forward and reverse genetics have led to the identification of mechanisms that are used by beneficial microorganisms to overcome these challenges, such as the production of iron-chelating compounds, the formation of strong biofilms, or the concealment of characteristic microbial molecular patterns that trigger the host immune system. However, how such mechanisms arose from an evolutionary perspective is much less understood. To study bacterial adaptation in the rhizosphere, we employed experimental evolution to track the physiological and genetic dynamics of root-dwelling Pseudomonas protegens in the Arabidopsis thaliana rhizosphere under axenic conditions. This simplified binary one plant/one bacterium system allows for the amplification of key adaptive mechanisms for bacterial rhizosphere colonization. We identified 35 mutations, including single-nucleotide polymorphisms, insertions, and deletions, distributed over 28 genes. We found that mutations in genes encoding global regulators and in genes for siderophore production, cell surface decoration, attachment, and motility accumulated in parallel, underlining the finding that bacterial adaptation to the rhizosphere follows multiple strategies. Notably, we observed that motility increased in parallel across multiple independent evolutionary lines. All together, these results underscore the strength of experimental evolution in identifying key genes, pathways, and processes for bacterial rhizosphere colonization and a methodology for the development of elite beneficial microorganisms with enhanced root-colonizing capacities that can support sustainable agriculture in the future. IMPORTANCE Beneficial root-associated microorganisms carry out many functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming many challenges. Previously, diverse mechanisms that are used by beneficial microorganisms to overcome these challenges were identified. However, how such mechanisms have developed from an evolutionary perspective is much less understood. Here, we employed experimental evolution to track the evolutionary dynamics of a root-dwelling pseudomonad on the root of Arabidopsis. We found that mutations in global regulators, as well as in genes for siderophore production, cell surface decoration, attachment, and motility, accumulate in parallel, emphasizing these strategies for bacterial adaptation to the rhizosphere. We identified 35 mutations distributed over 28 genes. All together, our results demonstrate the power of experimental evolution in identifying key pathways for rhizosphere colonization and a methodology for the development of elite beneficial microorganisms that can support sustainable agriculture.
Collapse
Affiliation(s)
- Erqin Li
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Hao Zhang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Henan Jiang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Ecology and Biodiversity, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Peter A. H. M. Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
4
|
Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CMJ, Bakker PAHM, Jousset A. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun 2021; 12:3829. [PMID: 34158504 PMCID: PMC8219802 DOI: 10.1038/s41467-021-24005-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
Collapse
Affiliation(s)
- Erqin Li
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands ,grid.14095.390000 0000 9116 4836Freie Universität Berlin, Institut für Biologie, Berlin, Germany ,grid.452299.1Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ronnie de Jonge
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
| | - Chen Liu
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Henan Jiang
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Ville-Petri Friman
- grid.5685.e0000 0004 1936 9668University of York, Department of Biology, York, UK
| | - Corné M. J. Pieterse
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Peter A. H. M. Bakker
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Alexandre Jousset
- grid.5477.10000000120346234Utrecht University, Department of Biology, Ecology and Biodiversity, Utrecht, The Netherlands
| |
Collapse
|
5
|
Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CMJ, Bakker PAHM, Jousset A. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun 2021. [PMID: 34158504 DOI: 10.1038/s41467-012-24005-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
Collapse
Affiliation(s)
- Erqin Li
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ronnie de Jonge
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
| | - Chen Liu
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Henan Jiang
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | | | - Corné M J Pieterse
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Peter A H M Bakker
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Alexandre Jousset
- Utrecht University, Department of Biology, Ecology and Biodiversity, Utrecht, The Netherlands.
| |
Collapse
|
6
|
Lope P, Maribel H, Egma M, Henri B, Carlos P. Characterization of influenza A(H1N1)pdm09 isolates of Peru using HRM, a post PCR molecular biology method. Bioinformation 2019; 15:640-645. [PMID: 31787813 PMCID: PMC6859703 DOI: 10.6026/97320630015640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/06/2019] [Accepted: 10/07/2019] [Indexed: 11/23/2022] Open
Abstract
Influenza caused by A(H1N1)pdm09 is a public health issue with severe conditions in vulnerable populations leading to death. Therefore, it is of interest to characterize and monitor influenza A(H1N1)pdm09 genotypes using High Resolution Melting (HRM), a post PCR molecular biology method. We used HRM analysis (using RotorGene Q thermocycler) to characterize A(H1N1)pdm09 genotypes from several places of Peru. RNA was purified from nasal and pharyngeal swab samples referred to LRNVR-INS, synthesized cDNA, and then the hemagglutinin gene and matrix fragment were amplified. Thus, 287 samples positive for influenza A(H1N1)pdm09 were identified across Peru where places like Lima, Piura, and Arequipa documented highest number of cases. The HRM data was analyzed and results showed different profiles which were further grouped into four genotypes for the HA (A, B, C, D) and 3 for the M (a, b, c) genes. We also report ten genotypes (I-X) of virus using combined HA (hemagglutinin) and M gene profiles representing a national geography. The prevalent genotypes are I and II with a frequency of 35.89% (103) and 29.27% (84), respectively linking with severe acute respiratory infection.
Collapse
Affiliation(s)
- Priscila Lope
- Laboratorio de Referencia Nacional de Virus Respiratorio, Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
- Laboratorio de virologia. Universidad Nacional Mayor de San Marcos. Lima. Peru
| | - Huaringa Maribel
- Laboratorio de Referencia Nacional de Virus Respiratorio, Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
| | - Mayta Egma
- Laboratorio de virologia. Universidad Nacional Mayor de San Marcos. Lima. Peru
| | - Bailon Henri
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular. Centro Nacional de Salud Publica. Instituto Nacional de Salud. Lima. Peru
| | - Padilla Carlos
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular. Centro Nacional de Salud Publica. Instituto Nacional de Salud. Lima. Peru
| |
Collapse
|
7
|
Synthesis and biological evaluation of a library of hybrid derivatives as inhibitors of influenza virus PA-PB1 interaction. Eur J Med Chem 2018; 157:743-758. [PMID: 30142611 DOI: 10.1016/j.ejmech.2018.08.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/03/2018] [Accepted: 08/11/2018] [Indexed: 11/21/2022]
Abstract
The limited treatment options against influenza virus along with the growing public health concerns regarding the continuous emergence of drug-resistant viruses make essential the development of new anti-flu agents with novel mechanisms of action. One of the most attractive targets is the interaction between two subunits of the RNA-dependent RNA polymerase, PA and PB1. Herein we report the rational design of hybrid compounds starting from a 3-cyano-4,6-diphenylpyridine scaffold recently identified as disruptor of PA-PB1 interactions. Guided by the previously reported SAR data, a library of amino acid derivatives was synthesized. The biological evaluation led to the identification of new PA-PB1 inhibitors, that do not show appreciable toxicity. Molecular modeling shed further lights on the inhibition mechanism of these compounds.
Collapse
|
8
|
Zhou Z, Liu T, Zhang J, Zhan P, Liu X. Influenza A virus polymerase: an attractive target for next-generation anti-influenza therapeutics. Drug Discov Today 2018; 23:503-518. [PMID: 29339107 DOI: 10.1016/j.drudis.2018.01.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/31/2017] [Accepted: 01/05/2018] [Indexed: 12/20/2022]
Abstract
The influenza RNA-dependent RNA polymerase (RdRP) is conserved among different types of influenza virus, playing an important part in transcription and replication. In this regard, influenza RdRP is an attractive target for novel anti-influenza drug discovery. Herein, we will introduce the structural and functional information of influenza polymerase; and an overview of inhibitors targeting the PA endonuclease and PB2 cap-binding site is provided, along with the approaches utilized for identification of these inhibitors. The protein-protein interactions (PPIs) of the three polymerase subunits: PA, PB1 and PB2, are described based on the published crystal structures, and inhibitors targeting the PA-PB1 interaction are introduced briefly.
Collapse
Affiliation(s)
- Zhongxia Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Tao Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China.
| |
Collapse
|
9
|
Lee E, Kim EJ, Shin YK, Song JY. Design and testing of multiplex RT-PCR primers for the rapid detection of influenza A virus genomic segments: Application to equine influenza virus. J Virol Methods 2015; 228:114-22. [PMID: 26655588 DOI: 10.1016/j.jviromet.2015.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 02/07/2023]
Abstract
The avian influenza A virus causes respiratory infections in animal species. It can undergo genomic recombination with newly obtained genetic material through an interspecies transmission. However, the process is an unpredictable event, making it difficult to predict the emergence of a new pandemic virus and distinguish its origin, especially when the virus is the result of multiple infections. Therefore, identifying a novel influenza is entirely dependent on sequencing its whole genome. Occasionally, however, it can be time-consuming, costly, and labor-intensive when sequencing many influenza viruses. To compensate for the difficulty, we developed a rapid, cost-effective, and simple multiplex RT-PCR to identify the viral genomic segments. As an example to evaluate its performance, H3N8 equine influenza virus (EIV) was studied for the purpose. In developing this protocol to amplify the EIV eight-segments, a series of processes, including phylogenetic analysis based on different influenza hosts, in silico analyses to estimate primer specificity, coverage, and variation scores, and investigation of host-specific amino acids, were progressively conducted to reduce or eliminate the negative factors that might affect PCR amplification. Selectively, EIV specific primers were synthesized with dual priming oligonucleotides (DPO) system to increase primer specificity. As a result, 16 primer pairs were selected to screen the dominantly circulating H3N8 EIV 8 genome segments: PA (3), PB2 (1), PA (3), NP (3), NA8 (2), HA3 (1), NS (1), and M (2). The diagnostic performance of the primers was evaluated with eight sets composing of four segment combinations using viral samples from various influenza hosts. The PCR results suggest that the multiplex RT-PCR has a wide range of applications in detection and diagnosis of newly emerging EIVs. Further, the proposed procedures of designing multiplex primers are expected to be used for detecting other animal influenza A viruses.
Collapse
Affiliation(s)
- EunJung Lee
- Viral Disease Division, Animal and Plant Quarantine Agency, 175 Anyang-ro, Manan-gu, Anyang-si, Gyeonggi-do, Republic of Korea
| | - Eun-Ju Kim
- Viral Disease Division, Animal and Plant Quarantine Agency, 175 Anyang-ro, Manan-gu, Anyang-si, Gyeonggi-do, Republic of Korea
| | - Yeun-Kyung Shin
- Viral Disease Division, Animal and Plant Quarantine Agency, 175 Anyang-ro, Manan-gu, Anyang-si, Gyeonggi-do, Republic of Korea
| | - Jae-Young Song
- Viral Disease Division, Animal and Plant Quarantine Agency, 175 Anyang-ro, Manan-gu, Anyang-si, Gyeonggi-do, Republic of Korea.
| |
Collapse
|
10
|
Chandler DP, Griesemer SB, Knickerbocker C, Golova JB, Lambarqui A, Perov AN, Zimmerman C, Wiles C, Rudy GB, St George K. Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. J Virol Methods 2014; 208:152-9. [PMID: 25066276 PMCID: PMC4175443 DOI: 10.1016/j.jviromet.2014.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 07/09/2014] [Accepted: 07/15/2014] [Indexed: 11/22/2022]
Abstract
The objectives of this study were to develop a user-friendly, gel element microarray test for influenza virus detection, subtyping, and neuraminidase inhibitor resistance detection, assess the performance characteristics of the assay, and perform a clinical evaluation on retrospective nasopharyngeal swab specimens. A streamlined microarray workflow enabled a single user to run up to 24 tests in an 8h shift. The most sensitive components of the test were the primers and probes targeting the A/H1 pdm09 HA gene with an analytical limit of detection (LoD) <100 gene copies (gc) per reaction. LoDs for all targets in nasopharyngeal swab samples were ≤1000 gc, with the exception of one target in the seasonal A/H1N1 subtype. Seasonal H275Y variants were detectable in a mixed population when present at >5% with wild type virus, while the 2009 pandemic H1N1 H275Y variant was detectable at ≤1% in a mixture with pandemic wild type virus. Influenza typing and subtyping results concurred with those obtained with real-time RT-PCR assays on more than 97% of the samples tested. The results demonstrate that a large panel of single-plex, real-time RT-PCR tests can be translated to an easy-to-use, sensitive, and specific microarray test for potential diagnostic use.
Collapse
Affiliation(s)
- Darrell P Chandler
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States.
| | - Sara B Griesemer
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, United States
| | | | - Julia B Golova
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Amine Lambarqui
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Alexander N Perov
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Cynthia Zimmerman
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Cory Wiles
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - George B Rudy
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, United States
| |
Collapse
|
11
|
Abstract
Influenza continues to be a significant health care issue. Although vaccination is the major line of defense, antiviral drugs play an important role in prophylaxis and disease management. Approved drugs for influenza are currently limited to those that target the viral matrix protein or neuraminidase enzyme. Resistance-associated sequence changes in the genes encoding these proteins have been extensively studied. Available methods for genotypic and phenotypic antiviral susceptibility testing have expanded and are being further developed and improved. The sporadic emergence of drug-resistant variants and the global spread of resistant strains have demonstrated the ongoing need for vigilant testing and surveillance.
Collapse
Affiliation(s)
- Jennifer Laplante
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, PO Box 22002, Albany, NY 12201-2002, USA
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, PO Box 22002, Albany, NY 12201-2002, USA.
| |
Collapse
|
12
|
Hata A, Kitajima M, Tajiri-Utagawa E, Katayama H. Development of a high resolution melting analysis for detection and differentiation of human astroviruses. J Virol Methods 2014; 200:29-34. [PMID: 24509176 DOI: 10.1016/j.jviromet.2014.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/16/2014] [Accepted: 01/21/2014] [Indexed: 11/28/2022]
Abstract
Human astroviruses (AstVs), the common causes of viral gastroenteritis, consist of 8 different sero- or genotypes in which a variety of subtypes have been found. In the present study, a rapid and high-throughput method for detection and sequence-discrimination of AstVs by high resolution melting (HRM) analysis was developed. A newly designed primer set for the assay targeting ORF1b-ORF2 junction region of AstVs successfully reacted with all 8 serotypes of AstVs and allowed genotyping using their amplicons. The HRM assay consists of intercalating dye based real time quantitative PCR (qPCR) and melting curve analysis. The qPCR assay was sensitive enough to detect 1.0×10(1) copies/reaction of AstV serotypes. However, 1.0×10(3) copies/reaction of AstVs gene was required to obtain a sequence-specific difference curve, indicating that pre-amplification is necessary to apply the assay to samples containing low numbers of AstVs. AstVs in clinical specimens were subjected to the HRM assay after pre-amplification. The strains possessing same nucleotide sequences at the target region showed an identical difference curve and those possessing different nucleotide sequences showed a distinguishable difference curve. The newly developed HRM assay is an effective technique for screening of AstVs to quantify and discriminate the strains.
Collapse
Affiliation(s)
- Akihiko Hata
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Masaaki Kitajima
- Center for Environmental Sensing and Modeling Singapore-MIT Alliance for Research and Technology 1 CREATE Way, #09-03 CREATE Tower, Singapore 138602
| | - Etsuko Tajiri-Utagawa
- Second Department of Virology, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0012, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
13
|
Kalthoff D, Beer M, Hoffmann B. High resolution melting analysis: rapid and precise characterisation of recombinant influenza A genomes. Virol J 2013; 10:284. [PMID: 24028349 PMCID: PMC3847122 DOI: 10.1186/1743-422x-10-284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/09/2013] [Indexed: 01/23/2023] Open
Abstract
Background High resolution melting analysis (HRM) is a rapid and cost-effective technique for the characterisation of PCR amplicons. Because the reverse genetics of segmented influenza A viruses allows the generation of numerous influenza A virus reassortants within a short time, methods for the rapid selection of the correct recombinants are very useful. Methods PCR primer pairs covering the single nucleotide polymorphism (SNP) positions of two different influenza A H5N1 strains were designed. Reassortants of the two different H5N1 isolates were used as a model to prove the suitability of HRM for the selection of the correct recombinants. Furthermore, two different cycler instruments were compared. Results Both cycler instruments generated comparable average melting peaks, which allowed the easy identification and selection of the correct cloned segments or reassorted viruses. Conclusions HRM is a highly suitable method for the rapid and precise characterisation of cloned influenza A genomes.
Collapse
Affiliation(s)
- Donata Kalthoff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems, 17493, Germany.
| | | | | |
Collapse
|
14
|
Okomo-Adhiambo M, Sheu TG, Gubareva LV. Assays for monitoring susceptibility of influenza viruses to neuraminidase inhibitors. Influenza Other Respir Viruses 2013; 7 Suppl 1:44-9. [PMID: 23279896 DOI: 10.1111/irv.12051] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Close monitoring of drug susceptibility among human influenza viruses was necessitated by widespread resistance to M2 inhibitors in influenza H1N1 (pre-pandemic and 2009 pandemic) and H3N2 viruses, and of oseltamivir resistance in pre-pandemic H1N1 viruses. The FDA-approved neuraminidase (NA) inhibitors (NAIs), oseltamivir and zanamivir, as well as investigational NAIs, peramivir and laninamivir, are currently the principal treatment options for managing influenza infection. However, there are challenges associated with assessing virus susceptibility to this class of drugs. Traditional cell culture-based assays are not reliable for phenotypic testing of NAI susceptibility due to complexity in interpretation. Two types of laboratory assays are currently available for monitoring NAI susceptibility, phenotypic such as the neuraminidase inhibition (NI) assay and genotypic. The NI assay's requirement for propagated virus lengthens testing turnaround; therefore, the need for timely detection of molecular markers associated with NAI resistance (e.g., H275Y in H1N1) has spurred the development of rapid, high-throughput assays, such as real-time RT-PCR and pyrosequencing. The high sensitivity of genotypic assays allows testing of clinical specimens thus eliminating the need for virus propagation in cell culture. The NI assays are especially valuable when a novel virus emerges or a new NAI becomes available. Modifications continue to be introduced into NI assays, including optimization and data analysis criteria. The optimal assay of choice for monitoring influenza drug susceptibility varies widely depending on the needs of laboratories (e.g., surveillance purposes, clinical settings). Optimally, it is desirable to combine functional and genetic analyses of virus isolates and, when possible, the respective clinical specimens.
Collapse
Affiliation(s)
- Margaret Okomo-Adhiambo
- Virus Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | | |
Collapse
|
15
|
Arvia R, Corcioli F, Azzi A. High resolution melting analysis as a tool to detect molecular markers of antiviral resistance in influenza A viruses. J Virol Methods 2013; 189:265-70. [PMID: 23499313 DOI: 10.1016/j.jviromet.2013.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 11/29/2022]
Abstract
A real-time PCR followed by high resolution melting analysis (HRMA) was developed, for rapid detection of antiviral resistance markers in influenza A viruses, of both H1N1 and H3N2 subtypes. The targets of these assays were the nucleotide substitution G806A (S31N mutation) in the M gene as marker of resistance to adamatanes in influenza viruses A(H3N2), the substitution A356T (E119V mutation) in the N2 gene of influenza viruses A(H3N2) and the substitution C823T (H274Y mutation) in the N1 gene of the pandemic A(H1N1) 2009 virus as markers of oseltamivir resistance. First, the designed primers and the overall protocol of the HRMA were validated using already characterized viral isolates either containing or lacking changes at the tested codons. Then, HRMA was used to search for the marker of oseltamivir resistance in 75 clinical samples, H1N1 2009 positives, analyzed previously by pyrosequencing and Sanger sequencing, and of both adamantane-derivatives and oseltamivir resistance in 57 H3N2 positive clinical samples. The results of HRMA of the H1N1 2009 isolates were in agreement with those obtained by sequencing. As regards the H3N2 isolates, HRMA revealed a widespread resistance to adamantanes with 89.5% nucleotide substitution G806A, while 3% were resistant to oseltamivir (A356T change). HRMA, applied to the detection of markers of resistance to antiviral drugs against influenza A viruses, confirmed to be a procedure flexible, low cost and time-saving, suitable for application to epidemiological surveys and in clinical settings for diagnostic purposes.
Collapse
Affiliation(s)
- Rosaria Arvia
- Department of Public Health, University of Florence, Viale Morgagni 48, 50134 Florence, Italy.
| | | | | |
Collapse
|
16
|
Mak PWY, Jayawardena S, Poon LLM. The Evolving Threat of Influenza Viruses of Animal Origin and the Challenges in Developing Appropriate Diagnostics. Clin Chem 2012; 58:1527-33. [DOI: 10.1373/clinchem.2012.182626] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND
An H1N1 subtype of swine origin caused the first influenza pandemic in this century. This pandemic strain was a reassortant of avian, swine, and human influenza viruses. Many diagnostic laboratories were overwhelmed by the testing demands related to this pandemic. Nevertheless, there remains the threat of other animal influenza viruses, such as highly pathogenic H5N1. As a part of pandemic preparedness, it is essential to identify the diagnostic challenges that will accompany the next pandemic.
CONTENT
We discuss the natural reservoir of influenza viruses and the possible role of livestock in the emergence of pandemic strains. The current commonly used molecular tests for influenza diagnosis or surveillance are also briefly reviewed. Some of these approaches are also used to detect animal viruses. Unfortunately, owing to a lack of systematic surveillance of animal influenza viruses, established tests may not be able to detect pandemic strains that have yet to emerge from the animal reservoir. Thus, multiple strategies need to be developed for better identification of influenza viruses. In addition, molecular assays for detection of mutations associated with antiviral resistance and for viral segment reassortments should also be encouraged.
SUMMARY
Influenza viruses are highly dynamic viruses. Regular and systematic influenza surveillance in both humans and animals is essential to provide a more comprehensive picture of the prevalent influenza viruses. To better prepare for the next pandemic, we should develop some simple and easy-to-use tests for characterizing newly emerging influenza viruses.
Collapse
Affiliation(s)
- Polly WY Mak
- Centre of Influenza Research and School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Shanthi Jayawardena
- Centre of Influenza Research and School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Leo LM Poon
- Centre of Influenza Research and School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| |
Collapse
|
17
|
Tang JW, Loh TP, Tambyah PA, Koay ESC. Influenza outbreaks in Singapore: epidemiology, diagnosis, treatment and prevention. Expert Rev Anti Infect Ther 2012; 10:751-60. [PMID: 22943399 DOI: 10.1586/eri.12.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
With the recent influenza A/H1N1 2009 pandemic still spreading through global populations, there has been an increased focus on optimizing the prevention, diagnosis and treatment of influenza infections, as well as the epidemiology of the virus. Clinical and epidemiological data on influenza infections in tropical countries have been relatively sparse until fairly recently, and it is the aim of this review to close some of these gaps by examining the behavior of influenza viruses in the tropical Singaporean population.
Collapse
Affiliation(s)
- Julian W Tang
- Alberta Provincial Laboratory for Public Health, University of Alberta Hospital, Edmonton, 8440-112 Street, Edmonton, AB T6G 2J2, Canada.
| | | | | | | |
Collapse
|
18
|
Tang JWT, Loh TP, Lee CK, Lee HK, Koay ESC, Tambyah PA. Lack of oseltamivir-resistance in A/H1N1p-infected patients, Singapore. J Infect 2012; 65:93-5. [DOI: 10.1016/j.jinf.2012.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 03/02/2012] [Accepted: 03/02/2012] [Indexed: 10/28/2022]
|