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Dillon L, Dimonaco NJ, Creevey CJ. Accessory genes define species-specific routes to antibiotic resistance. Life Sci Alliance 2024; 7:e202302420. [PMID: 38228374 DOI: 10.26508/lsa.202302420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
A deeper understanding of the relationship between the antimicrobial resistance (AMR) gene carriage and phenotype is necessary to develop effective response strategies against this global burden. AMR phenotype is often a result of multi-gene interactions; therefore, we need approaches that go beyond current simple AMR gene identification tools. Machine-learning (ML) methods may meet this challenge and allow the development of rapid computational approaches for AMR phenotype classification. To examine this, we applied multiple ML techniques to 16,950 bacterial genomes across 28 genera, with corresponding MICs for 23 antibiotics with the aim of training models to accurately determine the AMR phenotype from sequenced genomes. This resulted in a >1.5-fold increase in AMR phenotype prediction accuracy over AMR gene identification alone. Furthermore, we revealed 528 unique (often species-specific) genomic routes to antibiotic resistance, including genes not previously linked to the AMR phenotype. Our study demonstrates the utility of ML in predicting AMR phenotypes across diverse clinically relevant organisms and antibiotics. This research proposes a rapid computational method to support laboratory-based identification of the AMR phenotype in pathogens.
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Affiliation(s)
- Lucy Dillon
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Nicholas J Dimonaco
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
- https://ror.org/02fa3aq29 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- https://ror.org/02fa3aq29 Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
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2
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Chakrawarti A, Eckstrom K, Laaguiby P, Barlow JW. Hybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies. Access Microbiol 2024; 6:000766.v3. [PMID: 38725589 PMCID: PMC11077346 DOI: 10.1099/acmi.0.000766.v3] [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: 01/10/2024] [Accepted: 02/23/2024] [Indexed: 05/12/2024] Open
Abstract
Antimicrobial resistance (AMR) in Staphylococcus aureus is a pressing public health challenge with significant implications for the dairy industry, encompassing bovine mastitis concerns and potential zoonotic threats. To delve deeper into the resistance mechanisms of S. aureus, this study employed a hybrid whole genome assembly approach that synergized the precision of Illumina with the continuity of Oxford Nanopore. A total of 62 isolates, collected from multiple sources from Vermont dairy farms, were sequenced using the GridION Oxford Nanopore R9.4.1 platform and the Illumina platform, and subsequently processed through our long-read first bioinformatics pipeline. Our analyses showcased the hybrid-assembled genome's superior completeness compared to Oxford Nanopore (R9.4.1)-only or Illumina-only assembled genomes. Furthermore, the hybrid assembly accurately determined multilocus sequence typing (MLST) strain types across all isolates. The comprehensive probe for antibiotic resistance genes (ARGs) using databases like CARD, Resfinder, and MEGARES 2.0 characterized AMR in S. aureus isolates from Vermont dairy farms, and revealed the presence of notable resistance genes, including beta-lactam genes blaZ, blaI, and blaR. In conclusion, the hybrid assembly approach emerged as a tool for uncovering the genomic nuances of S. aureus isolates collected from multiple sources on dairy farms. Our findings offer a pathway for detecting AMR gene prevalence and shaping AMR management strategies crucial for safeguarding human and animal health.
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Affiliation(s)
- Ashma Chakrawarti
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Pheobe Laaguiby
- Advanced Genome Technologies Core, Vermont Integrative Genomics Resource, The Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - John W. Barlow
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
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3
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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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4
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Wu X, Luo H, Ge C, Xu F, Deng X, Wiedmann M, Baker RC, Stevenson AE, Zhang G, Tang S. Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection. Front Microbiol 2023; 13:1073057. [PMID: 36817104 PMCID: PMC9930645 DOI: 10.3389/fmicb.2022.1073057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/22/2022] [Indexed: 02/04/2023] Open
Abstract
In a previous study, Multiplex-nanopore-sequencing based whole genome sequencing (WGS) allowed for accurate in silico serotype prediction of Salmonella within one day for five multiplexed isolates, using both SISTR and SeqSero2. Since only ten serotypes were tested in our previous study, the conclusions above were yet to be evaluated in a larger scale test. In the current study we evaluated this workflow with 69 Salmonella serotypes and also explored the feasibility of using multiplex-nanopore-sequencing based WGS for antimicrobial resistance gene (AMR) and virulence gene detection. We found that accurate in silico serotype prediction with nanopore-WGS data was achieved within about five hours of sequencing at a minimum of 30× Salmonella genome coverage, with SeqSero2 as the serotype prediction tool. For each tested isolate, small variations were observed between the AMR/virulence gene profiles from the Illumina and Nanopore sequencing platforms. Taking results generated using Illumina data as the benchmark, the average precision value per isolate was 0.99 for both AMR and virulence gene detection. We found that the resistance gene identifier - RGI identified AMR genes with nanopore data at a much lower accuracy compared to Abricate, possibly due to RGI's less stringent minimum similarity and coverage by default for database matching. This study is an evaluation of multiplex-nanopore-sequencing based WGS as a cost-efficient and rapid Salmonella classification method, and a starting point for future validation and verification of using it as a AMR/virulence gene profiling tool for the food industry. This study paves the way for the application of nanopore sequencing in surveillance, tracking, and risk assessment of Salmonella across the food supply chain.
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Affiliation(s)
- Xingwen Wu
- Mars Global Food Safety Center, Beijing, China
| | - Hao Luo
- Mars Global Food Safety Center, Beijing, China
| | - Chongtao Ge
- Mars Global Food Safety Center, Beijing, China
| | - Feng Xu
- Mars Global Food Safety Center, Beijing, China
| | - Xiangyu Deng
- Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | | | | | | | - Silin Tang
- Mars Global Food Safety Center, Beijing, China,*Correspondence: Silin Tang, ✉
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Nowlan JP, Sies AN, Britney SR, Cameron ADS, Siah A, Lumsden JS, Russell S. Genomics of Tenacibaculum Species in British Columbia, Canada. Pathogens 2023; 12:pathogens12010101. [PMID: 36678448 PMCID: PMC9864904 DOI: 10.3390/pathogens12010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Tenacibaculum is a genus of Gram-negative filamentous bacteria with a cosmopolitan distribution. The research describing Tenacibaculum genomes stems primarily from Norway and Chile due to their impacts on salmon aquaculture. Canadian salmon aquaculture also experiences mortality events related to the presence of Tenacibaculum spp., yet no Canadian Tenacibaculum genomes are publicly available. Ribosomal DNA sequencing of 16S and four species-specific 16S quantitative-PCR assays were used to select isolates cultured from Atlantic salmon with mouthrot in British Columbia (BC), Canada. Ten isolates representing four known and two unknown species of Tenacibaculum were selected for shotgun whole genome sequencing using the Oxford Nanopore's MinION platform. The genome assemblies achieved closed circular chromosomes for seven isolates and long contigs for the remaining three isolates. Average nucleotide identity analysis identified T. ovolyticum, T. maritimum, T. dicentrarchi, two genomovars of T. finnmarkense, and two proposed novel species T. pacificus sp. nov. type strain 18-2881-AT and T. retecalamus sp. nov. type strain 18-3228-7BT. Annotation in most of the isolates predicted putative virulence and antimicrobial resistance genes, most-notably toxins (i.e., hemolysins), type-IX secretion systems, and oxytetracycline resistance. Comparative analysis with the T. maritimum type-strain predicted additional toxins and numerous C-terminal secretion proteins, including an M12B family metalloprotease in the T. maritimum isolates from BC. The genomic prediction of virulence-associated genes provides important targets for studies of mouthrot disease, and the annotation of the antimicrobial resistance genes provides targets for surveillance and diagnosis in veterinary medicine.
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Affiliation(s)
- Joseph P. Nowlan
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
| | - Ashton N. Sies
- Department of Biology, University of Regina, Regina, SK S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Scott R. Britney
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Andrew D. S. Cameron
- Department of Biology, University of Regina, Regina, SK S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Ahmed Siah
- BC Center for Aquatic Health Sciences, Campbell River, BC V9W 2C2, Canada
| | - John S. Lumsden
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Spencer Russell
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada
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Mahdi I, Fahsi N, Hijri M, Sobeh M. Antibiotic resistance in plant growth promoting bacteria: A comprehensive review and future perspectives to mitigate potential gene invasion risks. Front Microbiol 2022; 13:999988. [PMID: 36204627 PMCID: PMC9530320 DOI: 10.3389/fmicb.2022.999988] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) are endowed with several attributes that can be beneficial for host plants. They opened myriad doors toward green technology approach to reduce the use of chemical inputs, improve soil fertility, and promote plants’ health. However, many of these PGPB harbor antibiotic resistance genes (ARGs). Less attention has been given to multi-resistant bacterial bioinoculants which may transfer their ARGs to native soil microbial communities and other environmental reservoirs including animals, waters, and humans. Therefore, large-scale inoculation of crops by ARGs-harboring bacteria could worsen the evolution and dissemination of antibiotic resistance and aggravate the negative impacts on such ecosystem and ultimately public health. Their introduction into the soil could serve as ARGs invasion which may inter into the food chain. In this review, we underscore the antibiotic resistance of plant-associated bacteria, criticize the lack of consideration for this phenomenon in the screening and application processes, and provide some recommendations as well as a regulation framework relating to the development of bacteria-based biofertilizers to aid maximizing their value and applications in crop improvement while reducing the risks of ARGs invasion.
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Affiliation(s)
- Ismail Mahdi
- Agrobiosciences Research Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Nidal Fahsi
- Agrobiosciences Research Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- *Correspondence: Mohamed Hijri,
| | - Mansour Sobeh
- Agrobiosciences Research Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- Mansour Sobeh,
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7
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Hayashi K, Doi Y, Suzuki M. Rapid phylogenetic analysis using open reading frame content patterns acquired by Oxford Nanopore sequencing. J Appl Microbiol 2022; 133:3699-3707. [PMID: 36073316 DOI: 10.1111/jam.15807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
AIMS Phylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) using whole-genome sequencing (WGS) is increasingly used in epidemiological investigations of bacteria. The approach, however, is both resource intensive and time-consuming. Oxford Nanopore Technologies (ONT) sequencing is capable of real-time data analysis but the high error rate hampers its application in cgSNP-based phylogenetic analysis. Here, we developed a cgSNP-independent phylogenetic analysis method using ONT read assemblies by focusing on open reading frame (ORF) content patterns. METHODS AND RESULTS WGS data of 66 Enterobacter hormaechei strains acquired by both ONT and Illumina sequencing and 162 strains obtained from NCBI database were converted to binary sequences based on the presence or absence of ORFs using BLASTn. Phylogenetic trees calculated from binary sequences (ORF trees) were compared with cgSNP trees derived from Illumina sequences. Clusters of closely related strains in the cgSNP trees formed comparable clusters in the ORF trees built with binary sequences, and the tree topologies between them were similar based on Fowlkes-Mallows index. CONCLUSIONS The ORF-based phylogenetic analysis using ONT sequencing may be useful in epidemiological investigations and offer advantages over the cgSNP-based approach. SIGNIFICANCE AND IMPACT OF THE STUDY Conversion of assembled WGS data to binary sequences based on the presence or absence of ORFs circumvents read error concerns with ONT sequencing. Since ONT sequencing generates data in real-time and does not require major investment, this ORF-based phylogenetic analysis method has the potential to enable phylogenetic and epidemiological analysis at the point of care.
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Affiliation(s)
- Kengo Hayashi
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.,Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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Ju Y, Pu M, Sun K, Song G, Geng J. Nanopore Electrochemistry for Pathogen Detection. Chem Asian J 2022; 17:e202200774. [PMID: 36069587 DOI: 10.1002/asia.202200774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Pathogen infections have seriously threatened human health, and there is an urgent demand for rapid and efficient pathogen identification to provide instructions in clinical diagnosis and therapeutic intervention. Recently, nanopore technology, a rapidly maturing technology which delivers ultrasensitive sensing and high throughput in real-time and at low cost, has achieved success in pathogen detection. Furthermore, the remarkable development of nanopore sequencing, for example, the MinION sequencer from Oxford Nanopore Technologies (ONT) as a competitive sequencing technology, has facilitated the rapid analysis of disease-related microbiomes at the whole-genome level and on a large scale. Here, we highlighted recent advances in nanopore approaches for pathogen detection at the single-molecule level. We also overviewed the applications of nanopore sequencing in pathogenic bacteria identification and diagnosis. In the end, we discussed the challenges and future developments of nanopore technology as promising tools for the management of infections, which may be helpful to aid understanding as well as decision-making.
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Affiliation(s)
- Yuan Ju
- Sichuan University, Sichuan University Library, CHINA
| | - Mengjun Pu
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Ke Sun
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Guiqin Song
- North Sichuan Medical College [Search North Sichuan Medical College]: North Sichuan Medical University, Shool of Basic Medical Sciences and Forensic Medicine, CHINA
| | - Jia Geng
- Sichuan University, State Key Laboratory of Biotherapy, No 17 Section 3 of South Renmin Rd, 610040, Chengdu, CHINA
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Suminda GGD, Bhandari S, Won Y, Goutam U, Kanth Pulicherla K, Son YO, Ghosh M. High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance. Comput Struct Biotechnol J 2022; 20:5378-5392. [PMID: 36212529 PMCID: PMC9526013 DOI: 10.1016/j.csbj.2022.09.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.
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Dechêne-Tempier M, Marois-Créhan C, Libante V, Jouy E, Leblond-Bourget N, Payot S. Update on the Mechanisms of Antibiotic Resistance and the Mobile Resistome in the Emerging Zoonotic Pathogen Streptococcus suis. Microorganisms 2021; 9:microorganisms9081765. [PMID: 34442843 PMCID: PMC8401462 DOI: 10.3390/microorganisms9081765] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as well as resistance to aminoglycosides, fluoroquinolones, amphenicols, and glycopeptides. Most of the resistance mechanisms are encoded by antibiotic resistance genes, and a large part are carried by mobile genetic elements (MGEs) that can be transferred through horizontal gene transfer. This review provides an update of the resistance genes, their combination in multidrug isolates, and their localization on MGEs in S. suis. It also includes an overview of the contribution of biofilm to antimicrobial resistance in this bacterial species. The identification of resistance genes and study of their localization in S. suis as well as the environmental factors that can modulate their dissemination appear essential in order to decipher the role of this bacterium as a reservoir of antibiotic genes for other species.
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Affiliation(s)
- Manon Dechêne-Tempier
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
| | - Corinne Marois-Créhan
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
| | - Virginie Libante
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
| | - Eric Jouy
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
| | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
- Correspondence:
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11
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Chen Z, Erickson DL, Meng J. Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses. Genomics 2021; 113:1366-1377. [PMID: 33716184 DOI: 10.1016/j.ygeno.2021.03.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/18/2021] [Accepted: 03/08/2021] [Indexed: 11/18/2022]
Abstract
Oxford Nanopore sequencing has been widely used to achieve complete genomes of bacterial pathogens. However, the error rates of Oxford Nanopore long reads are high. Various polishing algorithms using Illumina short reads to correct the errors in Oxford Nanopore long-read assemblies have been developed. The impact of polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads on improving genomic analyses was evaluated using both simulated and real reads. Ten species (10 strains) were selected for simulated reads, while real reads were tested on 11 species (11 strains). Oxford Nanopore long reads were assembled with Unicycler to produce a draft assembly, followed by three rounds of polishing with Illumina short reads using two polishing tools, Pilon and NextPolish. One round of NextPolish polishing generated genome completeness and accuracy parameters similar to the reference genomes, whereas two or three rounds of Pilon polishing were needed, though contiguity remained unchanged after polishing. The polished assemblies of Escherichia coli O157:H7, Salmonella Typhimurium, and Cronobacter sakazakii with simulated reads did not provide accurate plasmid identifications. One round of NextPolish polishing was needed for accurately identifying plasmids in Staphylococcus aureus and E. coli O26:H11 with real reads, whereas one and two rounds of Pilon polishing were necessary for these two strains, respectively. Polishing failed to provide an accurate antimicrobial resistance (AMR) genotype for S. aureus with real reads. One round of polishing recovered an accurate AMR genotype for Klebsiella pneumoniae with real reads. The reference genome and draft assembly of Citrobacter braakii with real reads differed, which carried blaCMY-83 and fosA6, respectively, while both genes were present after one round of polishing. However, polishing did not improve the assembly of E. coli O26:H11 with real reads to achieve numbers of virulence genes similar to the reference genome. The draft and polished assemblies showed a phylogenetic tree topology comparable with the reference genomes. For multilocus sequence typing and pan-genome analyses, one round of NextPolish polishing was sufficient to obtain accurate results, while two or three rounds of Pilon polishing were needed. Overall, NextPolish outperformed Pilon for polishing the Oxford Nanopore long-read assemblies of bacterial pathogens, though both polishing strategies improved genomic analyses compared to the draft assemblies.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - David L Erickson
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA; Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
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Wang G, Gao Y, Xu X, Zhang P, Wang J, Li G, Lv Q, Niu X, Liu H. Mode of action and structural modelling of the interaction of formononetin with suilysin. J Appl Microbiol 2021; 131:2010-2018. [PMID: 33639036 DOI: 10.1111/jam.15051] [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: 10/28/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 11/28/2022]
Abstract
AIMS Suilysin is a critical pore-forming virulence factor of Streptococcus suis that has been demonstrated to substantially contribute to its pathogenicity. We have demonstrated that formononetin alleviates S. suis infection both in vivo and in vitro by targeting suilysin. However, the molecular mechanism of the effect is unclear. Our aim was to determine the molecular mechanism of the effect of formononetin on suilysin. METHODS AND RESULTS The mechanism of interaction between formononetin and suilysin was investigated by molecular modelling. The results indicated that formononetin was bound at the junction of domain two and domain four of suilysin. The binding free energy values indicated that the A415, Y412, E414, N413, T61, T62 and G416 residues are critical for this binding, this observation was confirmed by the changes in the flexibility of these residues and the distances between these residues and formononetin. The inhibitory effect of formononetin on the pore-forming activity of suilysin, binding constant and binding free energy were significantly decreased by site-specific mutagenesis of Y412 and N413. Finally, we analysed the spatial configuration of suilysin before and after formononetin binding, the results indicated that the binding changed the conformation of suilysin, especially the angle between domain two and domain four, resulting in the disruption of cholesterol binding to suilysin and in the loss of pore-forming activity. CONCLUSIONS Formononetin is located at the junction of domain two and domain four of suilysin, and Y412 and N413 play critical roles in the binding. Formononetin binding changes the angle between domain two and domain four of suilysin, resulting in the loss of the pore-inducing activity of suilysin. SIGNIFICANCE AND IMPACT OF THE STUDY This work will promote the application of formononetin to combat S. suis infections and may contribute to the development of new inhibitors or modification of existing inhibitors.
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Affiliation(s)
- G Wang
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Food Engineering, Jilin Engineering Normal University, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Y Gao
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - X Xu
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - P Zhang
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - J Wang
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - G Li
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Q Lv
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - X Niu
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - H Liu
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China
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Kaprou GD, Bergšpica I, Alexa EA, Alvarez-Ordóñez A, Prieto M. Rapid Methods for Antimicrobial Resistance Diagnostics. Antibiotics (Basel) 2021; 10:209. [PMID: 33672677 PMCID: PMC7924329 DOI: 10.3390/antibiotics10020209] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus, there is a growing demand for methods and technologies that enable rapid antimicrobial susceptibility testing (AST). The conventional methods and technologies addressing AMR diagnostics and AST employed in clinical microbiology are tedious, with high turnaround times (TAT), and are usually expensive. As a result, empirical antimicrobial therapies are prescribed leading to AMR spread, which in turn causes higher mortality rates and increased healthcare costs. This review describes the developments in current cutting-edge methods and technologies, organized by key enabling research domains, towards fighting the looming AMR menace by employing recent advances in AMR diagnostic tools. First, we summarize the conventional methods addressing AMR detection, surveillance, and AST. Thereafter, we examine more recent non-conventional methods and the advancements in each field, including whole genome sequencing (WGS), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and microfluidics technology. Following, we provide examples of commercially available diagnostic platforms for AST. Finally, perspectives on the implementation of emerging concepts towards developing paradigm-changing technologies and methodologies for AMR diagnostics are discussed.
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Affiliation(s)
- Georgia D. Kaprou
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Ieva Bergšpica
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia
| | - Elena A. Alexa
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
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14
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Yongkiettrakul S, Wongsurawat T, Jenjaroenpun P, Acheampong DA, Srimanote P, Maneerat K, Visessanguan W, Nookaew I. Genome sequences of antibiotic-resistant Streptococcus suis strains isolated from human patients and diseased and asymptomatic pigs in Thailand. INFECTION GENETICS AND EVOLUTION 2020; 87:104674. [PMID: 33316429 DOI: 10.1016/j.meegid.2020.104674] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
Streptococcus suis, a zoonotic bacterial pathogen, has negative economic impacts on both intensive swine production and human health worldwide. Whole-genome sequencing and comparative genomic analysis have been widely used for comprehensive classification and investigation of the genetic basis of several S. suis strains obtained from distinct hosts in different geographic areas, revealing great genetic diversity of this zoonotic pathogen. In this study, whole-genome sequences of antibiotic-resistant S. suis strains isolated from human patients (2 strains), diseased pigs (4 strains), and asymptomatic pigs (3 strains) in Thailand were compared with known genomes of 1186 S. suis strains. Single-nucleotide polymorphism-based phylogenetic analysis indicated that the Thai-isolated S. suis strains have close genetic relatedness to S. suis strains isolated from Canada, China, Denmark, Netherlands, United Kingdom, and United States of America. The genome analysis revealed genes conferring antibiotic resistance (aad(6), ant(6)-Ia, ermB, tet(O), patB, and sat4) and gene clusters (aph(3')-IIIa and aac(6')-Ie-aph(2″)-Ia) associated with aminoglycoside, macrolide, and fluoroquinolone resistance in S. suis in Thailand. This work provides additional resources for future genomic epidemiology investigation of S. suis.
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Affiliation(s)
- Suganya Yongkiettrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand.
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Daniel A Acheampong
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Potjanee Srimanote
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani, Thailand
| | - Krissana Maneerat
- College of Alternative Medicine, Chandrakasem Rajabhat University, Bangkok, Thailand
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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15
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Evaluation of a Highly Efficient DNA Extraction Method for Bacillus anthracis Endospores. Microorganisms 2020; 8:microorganisms8050763. [PMID: 32443768 PMCID: PMC7285266 DOI: 10.3390/microorganisms8050763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 11/19/2022] Open
Abstract
A variety of methods have been established in order to optimize the accessibility of DNA originating from Bacillusanthracis cells and endospores to facilitate highly sensitive molecular diagnostics. However, most endospore lysis techniques have not been evaluated in respect to their quantitative proficiencies. Here, we started by systematically assessing the efficiencies of 20 DNA extraction kits for vegetative B.anthracis cells. Of these, the Epicentre MasterPure kit gave the best DNA yields and quality suitable for further genomic analysis. Yet, none of the kits tested were able to extract reasonable quantities of DNA from cores of the endospores. Thus, we developed a mechanical endospore lysis protocol, facilitating the extraction of high-quality DNA. Transmission electron microscopy or the labelling of spores with the indicator dye propidium monoazide was utilized to assess lysis efficiency. Finally, the yield and quality of genomic spore DNA were quantified by PCR and they were found to be dependent on lysis matrix composition, instrumental parameters, and the method used for subsequent DNA purification. Our final standardized lysis and DNA extraction protocol allows for the quantitative detection of low levels (<50 CFU/mL) of B. anthracis endospores and it is suitable for direct quantification, even under resource-limited field conditions, where culturing is not an option.
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Ramírez-Carreto S, Miranda-Zaragoza B, Rodríguez-Almazán C. Actinoporins: From the Structure and Function to the Generation of Biotechnological and Therapeutic Tools. Biomolecules 2020; 10:E539. [PMID: 32252469 PMCID: PMC7226409 DOI: 10.3390/biom10040539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 12/22/2022] Open
Abstract
Actinoporins (APs) are a family of pore-forming toxins (PFTs) from sea anemones. These biomolecules exhibit the ability to exist as soluble monomers within an aqueous medium or as constitutively open oligomers in biological membranes. Through their conformational plasticity, actinoporins are considered good candidate molecules to be included for the rational design of molecular tools, such as immunotoxins directed against tumor cells and stochastic biosensors based on nanopores to analyze unique DNA or protein molecules. Additionally, the ability of these proteins to bind to sphingomyelin (SM) facilitates their use for the design of molecular probes to identify SM in the cells. The immunomodulatory activity of actinoporins in liposomal formulations for vaccine development has also been evaluated. In this review, we describe the potential of actinoporins for use in the development of molecular tools that could be used for possible medical and biotechnological applications.
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Affiliation(s)
| | | | - Claudia Rodríguez-Almazán
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico; (S.R.-C.); (B.M.-Z.)
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17
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Tools for Molecular Epidemiology of Streptococcus suis. Pathogens 2020; 9:pathogens9020081. [PMID: 32012668 PMCID: PMC7168656 DOI: 10.3390/pathogens9020081] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/04/2022] Open
Abstract
Diseases caused by Streptococcus suis are a significant economic and welfare concern in pigs as well as in humans. Several molecular methods have been applied to investigate S. suis strain diversity and identify phylogenetic groups. Multilocus sequence typing (MLST), commonly used to differentiate between S. suis strains, has been instrumental in identifying that the species is genetically highly diverse. Recent advances in whole-genome analysis have resulted in schemes permitting the classification of S. suis populations as pathogenic or non-pathogenic, or disease-associated or non-disease associated. Here, we review these and other molecular approaches that can be used for surveillance, outbreak tracking, preventative health management, effective treatment and control, as well as vaccine development, including PCR based-assays that are easy to apply in modest diagnostic settings and which allow for the rapid screening of a large number of isolates at relatively low cost, granting the identification of several major clonal complexes of the S. suis population.
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