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Kajdanek A, Kluska M, Matusiak R, Kazimierczak J, Dastych J. A Rapid and Inexpensive PCR Test for Mastitis Diagnosis Based on NGS Data. Pathogens 2024; 13:423. [PMID: 38787275 DOI: 10.3390/pathogens13050423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/02/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Mastitis is a common mammary gland disease of dairy cattle caused by a wide range of organisms including bacteria, fungi and algae. Mastitis contributes to economic losses of dairy farms due to reduced yield and poor quality of milk. Since the correct identification of pathogens responsible for the development of mastitis is crucial to the success of treatment, it is necessary to develop a quick and accurate test to distinguish the main pathogens causing this disease. In this paper, we describe the development of a test based on the multiplex polymerase chain reaction (PCR) method allowing for the identification of Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus uberis and Staphylococcus aureus. When creating our test, we relied on the results from new generation sequencing (NGS) for accurate determination of species affiliation. The multiplex PCR test was verified on 100 strains including veterinary samples, ATCC and Polish Collection of Microorganisms (PCM) reference strains. The obtained results indicate that this test is accurate and displays high specificity. It may serve as a valuable molecular tool for the detection of major mastitis pathogens.
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2
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Huggins LG, Colella V, Young ND, Traub RJ. Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites. Mol Ecol Resour 2024; 24:e13878. [PMID: 37837372 DOI: 10.1111/1755-0998.13878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/07/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023]
Abstract
Apicomplexan haemoparasites generate significant morbidity and mortality in humans and other animals, particularly in many low-to-middle income countries. Malaria caused by Plasmodium remains responsible for some of the highest numbers of annual deaths of any human pathogen, whilst piroplasmids, such as Babesia and Theileria can have immense negative economic effects through livestock loss. Diagnosing haemoparasites via traditional methods like microscopy is challenging due to low-level and transient parasitaemia. PCR-based diagnostics overcome these limitations by being both highly sensitive and specific, but they may be unable to accurately detect coinfections or identify novel species. In contrast, next-generation sequencing (NGS)-based methods can characterize all pathogens from a group of interest concurrently, although, the short-read platforms previously used have been limited in the taxonomic resolution achievable. Here, we used Oxford Nanopore Technologies' (ONT) long-read MinION™ sequencer to conduct apicomplexan haemoparasite metabarcoding via sequencing the near full-length 18S ribosomal RNA gene, demonstrating its ability to detect Babesia, Hepatozoon, Neospora, Plasmodium, Theileria and Toxoplasma species. This method was tested on blood-extracted DNA from 100 dogs and the results benchmarked against qPCR and Illumina-based metabarcoding. For two common haemoparasites, nanopore sequencing performed as well as qPCR (kappa agreement statistics > 0.98), whilst also detecting one pathogen, Hepatozoon felis, missed by the other techniques. The long-reads obtained by nanopore sequencing provide an improved species-level taxonomic resolution whilst the method's broad applicability mean it can be used to explore apicomplexan communities from diverse mammalian hosts, on a portable sequencer that easily permits adaptation to field use.
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Affiliation(s)
- Lucas G Huggins
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Vito Colella
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J Traub
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
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3
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Abera D, Mossie T. A review on pneumonic pasteurellosis in small ruminants. JOURNAL OF APPLIED ANIMAL RESEARCH 2023. [DOI: 10.1080/09712119.2022.2146123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Dessie Abera
- Debre markos Agricultural Research Center, Debre markos, Ethiopia
| | - Tesfa Mossie
- Jimma Agricultural Research Center, Jimma, Ethiopia
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4
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Wilkes RP. Next-Generation Diagnostics for Pathogens. Vet Clin North Am Food Anim Pract 2023; 39:165-173. [PMID: 36731996 DOI: 10.1016/j.cvfa.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Next-generation sequencing (NGS) was initially developed to aid sequencing of the human genome. This molecular method is cost effective for sequencing and characterizing genomes, not only those of humans or animals but also those of bacteria and other pathogens. However, rather than sequencing a single organism, a targeted NGS method can be used to specifically amplify pathogens of interest in a clinical sample for detection and characterization by sequencing. Targeted NGS is an ideal method for ruminant syndromic testing due to its ability to detect a variety of pathogens in a sample with a single test.
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Affiliation(s)
- Rebecca P Wilkes
- Department of Comparative Pathobiology and Molecular Section Head, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, 406 South University St., West Lafayette, IN 47907-2065, USA.
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5
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Loy JD, Monday JD, Smith DR. Future Directions for Ruminant Diagnostics. Vet Clin North Am Food Anim Pract 2023; 39:175-183. [PMID: 36731997 DOI: 10.1016/j.cvfa.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Diagnostic advances such as next-generation sequencing, highly multiplexed real-time PCR tests, and MALDI-TOF mass spectrometry have provided a tremendous increase in the amount of diagnostic information to clinicians. However, interpretation and application of these results to both individual and herd-level diagnostics still require the necessary skills in critical thinking and diagnostic interpretation to maximize benefit. This article provides a summary of advancements in diagnostic medicine and interpretation, as well as identifies gaps in knowledge that can be targeted to continue to build on best practices and application of diagnostic tools to improve ruminant health.
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Affiliation(s)
- John Dustin Loy
- College of Veterinary Medicine, Mississippi State University, 240 Wise Center Drive, PO Box 6100, Mississippi State, MS 39762, USA.
| | - Jessie D Monday
- Texas A&M Veterinary Medical Diagnostic Laboratory - Canyon, WT Box 60818, 3209 Russell Long Boulevard, Canyon, TX 79016, USA
| | - David R Smith
- College of Veterinary Medicine, Mississippi State University, 240 Wise Center Drive, PO Box 6100, Mississippi State, MS 39762, USA
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6
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Park DG, Ha ES, Kang B, Choi I, Kwak JE, Choi J, Park J, Lee W, Kim SH, Kim SH, Lee JH. Development and Evaluation of a Next-Generation Sequencing Panel for the Multiple Detection and Identification of Pathogens in Fermented Foods. J Microbiol Biotechnol 2023; 33:83-95. [PMID: 36457187 PMCID: PMC9895999 DOI: 10.4014/jmb.2211.11009] [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: 11/07/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/03/2022]
Abstract
These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 108-105 CFU of target strains. However, a few false-positive results were shown at 106-105 CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.
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Affiliation(s)
- Dong-Geun Park
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Su Ha
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Byungcheol Kang
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Iseul Choi
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Jeong-Eun Kwak
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinho Choi
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Jeongwoong Park
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea,Corresponding author Phone: +82-2-880-4854 Fax: +82-2-873-5095 E-mail:
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Huggins LG, Colella V, Atapattu U, Koehler AV, Traub RJ. Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma. Microbiol Spectr 2022; 10:e0308822. [PMID: 36250862 PMCID: PMC9769565 DOI: 10.1128/spectrum.03088-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/26/2022] [Indexed: 01/09/2023] Open
Abstract
Dogs across the globe are afflicted by diverse blood- and vector-borne bacteria (VBB), many of which cause severe disease and can be fatal. Diagnosis of VBB infections can be challenging due to the low concentration of bacteria in the blood, the frequent occurrence of coinfections, and the wide range of known, emerging, and potentially novel VBB species encounterable. Therefore, there is a need for diagnostics that address these challenges by being both sensitive and capable of detecting all VBB simultaneously. We detail the first employment of a nanopore-based sequencing methodology conducted on the Oxford Nanopore Technologies (ONT) MinION device to accurately elucidate the "hemobacteriome" from canine blood through sequencing of the full-length 16S rRNA gene. We detected a diverse range of important canine VBB, including Ehrlichia canis, Anaplasma platys, Mycoplasma haemocanis, Bartonella clarridgeiae, "Candidatus Mycoplasma haematoparvum", a novel species of hemotropic mycoplasma, and Wolbachia endosymbionts of filarial worms, indicative of filariasis. Our nanopore-based protocol was equivalent in sensitivity to both quantitative PCR (qPCR) and Illumina sequencing when benchmarked against these methods, achieving high agreement as defined by the kappa statistics (k > 0.81) for three key VBB. Utilizing the ability of the ONT' MinION device to sequence long read lengths provides an excellent alternative diagnostic method by which the hemobacteriome can be accurately characterized to the species level in a way previously unachievable using short reads. We envision our method to be translatable to multiple contexts, such as the detection of VBB in other vertebrate hosts, including humans, while the small size of the MinION device is highly amenable to field use. IMPORTANCE Blood- and vector-borne bacteria (VBB) can cause severe pathology and even be lethal for dogs in many regions across the globe. Accurate characterization of all the bacterial pathogens infecting a canine host is critical, as coinfections are common and emerging and novel pathogens that may go undetected by traditional diagnostics frequently arise. Deep sequencing using devices from Oxford Nanopore Technologies (ONT) provides a solution, as the long read lengths achievable provide species-level taxonomic identification of pathogens that previous short-read technologies could not accomplish. We developed a protocol using ONT' MinION sequencer to accurately detect and classify a wide spectrum of VBB from canine blood at a sensitivity comparable to that of regularly used diagnostics, such as qPCR. This protocol demonstrates great potential for use in biosurveillance and biosecurity operations for the detection of VBB in a range of vertebrate hosts, while the MinION sequencer's portability allows this method to be used easily in the field.
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Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Vito Colella
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ushani Atapattu
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
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8
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Dai Y, Sheng K, Hu L. Diagnostic efficacy of targeted high-throughput sequencing for lower respiratory infection in preterm infants. Am J Transl Res 2022; 14:8204-8214. [PMID: 36505277 PMCID: PMC9730095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/26/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To examine the pathogen diagnostic performance of targeted high-throughput next-gen sequencing (tNGS) in respiratory infectious diseases in preterm infants using dynamic follow-up. METHODS Clinical samples of respiratory secretions were consecutively collected from 20 preterm infants weekly for 5 weeks, during which 10 developed bronchopulmonary dysplasia. Pathogen identification from these collected specimens was performed by both conventional cultivation and tNGS. RESULTS We found that targeted next-generation sequencing shared a 90.9% full or partial consistency for lower respiratory pathogen detection with the traditional culture-based approach, and increased the detection rate by 105.9%. Moreover, most of the pathogens identified by tNGS were diminished in patients after treatment. CONCLUSION This study reveals the high sensitivity and performance of targeted high-throughput sequencing for respiratory infectious disease diagnosis and pathogen identification. The trial registry number is NCT03850457, and the trial URL is https://clinicaltrials.gov/ct2/show/NCT03850457.
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Affiliation(s)
- Yi Dai
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical CenterShanghai, China
| | - Kai Sheng
- Geriatrics Department, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Lan Hu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical CenterShanghai, China
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9
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Neculai-Valeanu AS, Ariton AM. Udder Health Monitoring for Prevention of Bovine Mastitis and Improvement of Milk Quality. Bioengineering (Basel) 2022; 9:608. [PMID: 36354519 PMCID: PMC9687184 DOI: 10.3390/bioengineering9110608] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 08/05/2023] Open
Abstract
To maximize milk production, efficiency, and profits, modern dairy cows are genetically selected and bred to produce more and more milk and are fed copious quantities of high-energy feed to support ever-increasing milk volumes. As demands for increased milk yield and milking efficiency continue to rise to provide for the growing world population, more significant stress is placed on the dairy cow's productive capacity. In this climate, which is becoming increasingly hotter, millions of people depend on the capacity of cattle to respond to new environments and to cope with temperature shocks as well as additional stress factors such as solar radiation, animal crowding, insect pests, and poor ventilation, which are often associated with an increased risk of mastitis, resulting in lower milk quality and reduced production. This article reviews the impact of heat stress on milk production and quality and emphasizes the importance of udder health monitoring, with a focus on the use of emergent methods for monitoring udder health, such as infrared thermography, biosensors, and lab-on-chip devices, which may promote animal health and welfare, as well as the quality and safety of dairy products, without hindering the technological flow, while providing significant benefits to farmers, manufacturers, and consumers.
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10
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Mastitis: What It Is, Current Diagnostics, and the Potential of Metabolomics to Identify New Predictive Biomarkers. DAIRY 2022. [DOI: 10.3390/dairy3040050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Periparturient diseases continue to be the greatest challenge to both farmers and dairy cows. They are associated with a decrease in productivity, lower profitability, and a negative impact on cows’ health as well as public health. This review article discusses the pathophysiology and diagnostic opportunities of mastitis, the most common disease of dairy cows. To better understand the disease, we dive deep into the causative agents, traditional paradigms, and the use of new technologies for diagnosis, treatment, and prevention of mastitis. This paper takes a systems biology approach by highlighting the relationship of mastitis with other diseases and introduces the use of omics sciences, specifically metabolomics and its analytical techniques. Concluding, this review is backed up by multiple studies that show how earlier identification of mastitis through predictive biomarkers can benefit the dairy industry and improve the overall animal health.
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11
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Kattoor JJ, Nikolai E, Qurollo B, Wilkes RP. Targeted Next-Generation Sequencing for Comprehensive Testing for Selected Vector-Borne Pathogens in Canines. Pathogens 2022; 11:pathogens11090964. [PMID: 36145396 PMCID: PMC9503002 DOI: 10.3390/pathogens11090964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The standard for detecting vector-borne pathogens is real-time PCR (rtPCR). However, this requires many individual tests to obtain an accurate diagnosis. The purpose of this study was to develop and validate a targeted next-generation sequencing (NGS) assay for vector-borne pathogens. Pathogen target regions were amplified via PCR using two primer pools that were developed in conjunction with ThermoFisher Scientific, and barcoded DNA libraries were prepared and sequenced with the Ion Torrent S5 system. Data were assembled using SPAdes and mapped to a reference file containing sequences from the pathogens. The raw reads were analyzed to confirm the results. Test feasibility and analytical specificity were evaluated with type strains or validated positive clinical samples from dogs. The analytical sensitivity of the method was compared to Ct values obtained by rtPCR testing. Diagnostic sensitivity and specificity were assessed with a set of known positive and negative clinical samples based on rtPCR testing. Positive and negative percent agreements and Cohen’s kappa were calculated. The primer sets were specific for the intended targets, based on sequence analysis of the amplified products, and the method detected 17 different pathogens. Analytical sensitivity was equivalent to an rtPCR Ct value of approximately 35–36. The positive percent agreement was 92%, and the negative percent agreement was 88%. Cohen’s kappa was 0.804, which indicates almost perfect agreement between the rtPCR assays and the targeted NGS assay. Using a targeted method reduces the costs associated with NGS sequencing and allows for a 2–3 day turn-around time, making this a viable method for detection of vector-borne pathogens in canine whole blood samples.
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Affiliation(s)
- Jobin J. Kattoor
- Animal Disease Diagnostic Laboratory, Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | - Emma Nikolai
- Animal Disease Diagnostic Laboratory, Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | - Barbara Qurollo
- Vector Borne Disease Diagnostic Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
| | - Rebecca P. Wilkes
- Animal Disease Diagnostic Laboratory, Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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12
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DNA Microarray-based Detection of Bacteria in Samples Containing Antibiotics: Effect of Antibiotics on the Performance of Pathogen Detection Assays. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0342-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Fan T, Zhang Y, Lv Y, Chang J, Bauer BA, Yang J, Wang CW. Cutaneous myiasis with eosinophilic pleural effusion: A case report. World J Clin Cases 2021; 9:4803-4809. [PMID: 34222451 PMCID: PMC8223839 DOI: 10.12998/wjcc.v9.i18.4803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cutaneous myiasis is frequently observed; however, eosinophilic pleural effusion induced by this condition is rare.
CASE SUMMARY We report the case of a 65-year-old female Tibetan patient from Qinghai Province, who presented to West China Hospital of Sichuan University around mid-November 2011 with a chief complaint of recurrent cough, occasional hemoptysis, and right chest pain. There was no past medical and surgical history of note, except for occasional dietary habit of eating raw meat. Clinical examination revealed a left lung collapse and diminished breathing sounds in her left lung, with moist rales heard in both lungs. Chest X-rays demonstrated a left hydropneumothorax and a right lung infection. Chest computed tomography revealed a left hydropneumothorax with partial compressive atelectasis and patchy consolidation on the right lung. Laboratory data revealed peripheral blood eosinophilia of 37.2%, with a white blood cell count of 10.4 × 109/L. Serum immunoglobulin E levels were elevated (1650 unit/mL). Serum parasite antibodies were negative except for cysticercosis immunoglobulin G. Bone marrow aspirates were hypercellular, with a marked increase in the number of mature eosinophils and eosinophilic myelocytes. An ultrasound-guided left-sided thoracentesis produced a yellow-cloudy exudative fluid. Failure to respond to antibiotic treatment during hospitalization for her symptoms and persistent blood eosinophilia led the team to start oral albendazole (400 mg/d) for presumed parasitic infestation for three consecutive days after the ninth day of hospitalization. Intermittent migratory stabbing pain and swelling sensation on both her upper arms and shoulders were reported; tender nodules and worm-like live organisms were observed in the responding sites 1 wk later. After the removal of the live organisms, they were subsequently identified as first stage hypodermal larvae by the Sichuan Institute of Parasites. The patient’s symptoms were relieved soon afterwards. Telephonic follow-up 1 mo later indicated that the blood eosinophilia and pleural effusion were resolved.
CONCLUSION Eosinophilic pleural fluid can be present in a wide array of disorders. Myiasis should be an important consideration for the differential diagnosis when eosinophilic pleural effusion with blood eosinophilia is observed.
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Affiliation(s)
- Tao Fan
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Yu Zhang
- Department of Respiratory and Critical Care Medicine, Chengdu Integrated Traditional Chinese and Western Medicine Hospital, Chengdu 610016, Sichuan Province, China
| | - Yan Lv
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Jing Chang
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Brent A Bauer
- Department of General Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Juan Yang
- Department of General Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Cheng-Wei Wang
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
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14
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LaMontagne MG, Tran PL, Benavidez A, Morano LD. Development of an inexpensive matrix-assisted laser desorption-time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize. PeerJ 2021; 9:e11359. [PMID: 34123583 PMCID: PMC8166240 DOI: 10.7717/peerj.11359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety c ontained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.
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Affiliation(s)
- Michael G LaMontagne
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Phi L Tran
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Alexander Benavidez
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
| | - Lisa D Morano
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
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15
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Novel High-Throughput Multiplex qPCRs for the Detection of Canine Vector-Borne Pathogens in the Asia-Pacific. Microorganisms 2021; 9:microorganisms9051092. [PMID: 34069665 PMCID: PMC8161336 DOI: 10.3390/microorganisms9051092] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/10/2023] Open
Abstract
The Asia-Pacific hosts a large diversity of canine vector-borne pathogens (VBPs) with some of the most common and most pathogenic, generating significant mortality as well as a spectrum of health impacts on local dog populations. The VBPs Anaplasma platys, Babesia gibsoni, Babesia vogeli, Ehrlichia canis, Hepatozoon canis and haemotropic Mycoplasma spp. are all endemic throughout the region, with many exhibiting shifting geographical distributions that warrant urgent attention. Moreover, many of these species cause similar clinical signs when parasitising canine hosts, whilst knowledge of the exact pathogen is critical to ensure treatment is effective. This is complicated by frequent coinfection that can exacerbate pathology. Here, we describe the development, optimisation and validation of two novel quadruplex Taq-Man based real-time PCRs (qPCRs) for the specific and sensitive detection of the aforementioned VBPs. To ensure accurate evaluation of diagnostic performance, results of our qPCRs were evaluated on field samples from Thai dogs and compared with both conventional PCR (cPCR) results and next-generation sequencing (NGS) metabarcoding. Our qPCRs were found to be more sensitive at detecting canine VBP than cPCR and generated results similar to those achieved by NGS. These qPCRs will provide a valuable high-throughput diagnostic tool available to epidemiologists, researchers and clinicians for the diagnosis of key canine VBPs in the Asia-Pacific and further afield.
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Strom M, Crowley T, Shigdar S. Novel Detection of Nasty Bugs, Prevention Is Better than Cure. Int J Mol Sci 2020; 22:E149. [PMID: 33375709 PMCID: PMC7795740 DOI: 10.3390/ijms22010149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
Hospital-acquired infections (HAIs) are a growing concern around the world. They contribute to increasing mortality and morbidity rates and are an economic threat. All hospital patients have the potential to contract an HAI, but those with weakened or inferior immune systems are at highest risk. Most hospital patients will contract at least one HAI, but many will contract multiple ones. Bacteria are the most common cause of HAIs and contribute to 80-90% of all HAIs, with Staphylococcus aureus, Clostridium difficile, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae accounting for the majority. Each of these bacteria are highly resistant to antibiotics and can produce a protective film, known as a biofilm, to further prevent their eradication. It has been shown that by detecting and eradicating bacteria in the environment, infection rates can be reduced. The current methods for detecting bacteria are time consuming, non-specific, and prone to false negatives or false positives. Aptamer-based biosensors have demonstrated specific, time-efficient and simple detection, highlighting the likelihood that they could be used in a similar way to detect HAI-causing bacteria.
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Affiliation(s)
- Mia Strom
- School of Medicine, Deakin University, Geelong 3216, Australia; (M.S.); (T.C.)
| | - Tamsyn Crowley
- School of Medicine, Deakin University, Geelong 3216, Australia; (M.S.); (T.C.)
- Centre for Molecular and Medical Research, Deakin University, Geelong 3216, Australia
| | - Sarah Shigdar
- School of Medicine, Deakin University, Geelong 3216, Australia; (M.S.); (T.C.)
- Centre for Molecular and Medical Research, Deakin University, Geelong 3216, Australia
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Anis E, Ilha MRS, Engiles JB, Wilkes RP. Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples. J Vet Diagn Invest 2020; 33:227-234. [PMID: 33305693 DOI: 10.1177/1040638720978381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Equine infectious disease outbreaks may have profound economic impact, resulting in losses of millions of dollars of revenue as a result of horse loss, quarantine, and cancelled events. Early and accurate diagnosis is essential to limit the spread of infectious diseases. However, laboratory detection of infectious agents, especially the simultaneous detection of multiple agents, can be challenging to the clinician and diagnostic laboratory. Next-generation sequencing (NGS), which allows millions of DNA templates to be sequenced simultaneously in a single reaction, is an ideal technology for comprehensive testing. We conducted a proof-of-concept study of targeted NGS to detect 62 common equine bacterial, viral, and parasitic pathogens in clinical samples. We designed 264 primers and constructed a bioinformatics tool for the detection of targeted pathogens. The designed primers were able to specifically detect the intended pathogens. Results of testing 27 clinical samples with our targeted NGS assay compared with results of routine tests (assessed as a group) yielded positive percent agreement of 81% and negative percent agreement of 83%, overall agreement of 81%, and kappa of 0.56 (moderate agreement). This moderate agreement was likely the result of low sensitivity of some primers. However, our NGS assay successfully detected multiple pathogens in the clinical samples, including some pathogens missed by routine techniques.
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Affiliation(s)
- Eman Anis
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA.,Department of Virology, Faculty of Veterinary Medicine, University of Sadat, El Beheira Governorate, Sadat City, Egypt
| | - Marcia R S Ilha
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA
| | - Julie B Engiles
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA
| | - Rebecca P Wilkes
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN
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Millán J, Di Cataldo S, Volokhov DV, Becker DJ. Worldwide occurrence of haemoplasmas in wildlife: Insights into the patterns of infection, transmission, pathology and zoonotic potential. Transbound Emerg Dis 2020; 68:3236-3256. [PMID: 33210822 DOI: 10.1111/tbed.13932] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 12/17/2022]
Abstract
Haemotropic mycoplasmas (haemoplasmas) have increasingly attracted the attention of wildlife disease researchers due to a combination of wide host range, high prevalence and genetic diversity. A systematic review identified 75 articles that investigated haemoplasma infection in wildlife by molecular methods (chiefly targeting partial 16S rRNA gene sequences), which included 131 host genera across six orders. Studies were less common in the Eastern Hemisphere (especially Africa and Asia) and more frequent in the Artiodactyla and Carnivora. Meta-analysis showed that infection prevalence did not vary by geographic region nor host order, but wild hosts showed significantly higher prevalence than captive hosts. Using a taxonomically flexible machine learning algorithm, we also found vampire bats and cervids to have greater prevalence, whereas mink, a subclade of vesper bats, and true foxes all had lower prevalence compared to the remaining sampled mammal phylogeny. Haemoplasma genotype and nucleotide diversity varied little among wild mammals but were marginally lower in primates and bats. Coinfection with more than one haemoplasma species or genotype was always confirmed when assessed. Risk factors of infection identified were sociality, age, males and high trophic levels, and both prevalence and diversity were often higher in undisturbed environments. Haemoplasmas likely use different and concurrent transmission routes and typically display enzootic dynamics when wild populations are studied longitudinally. Haemoplasma pathology is poorly known in wildlife but appears subclinical. Candidatus Mycoplasma haematohominis, which causes disease in humans, probably has it natural host in bats. Haemoplasmas can serve as a model system in ecological and evolutionary studies, and future research on these pathogens in wildlife must focus on increasing the geographic range and taxa of studies and elucidating pathology, transmission and zoonotic potential. To facilitate such work, we recommend using universal PCR primers or NGS protocols to detect novel haemoplasmas and other genetic markers to differentiate among species and infer cross-species transmission.
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Affiliation(s)
- Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain.,Fundación ARAID, Zaragoza, Spain.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Sophia Di Cataldo
- Programa de Doctorado en Medicina de la Conservación, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
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Malik YS, Verma A, Kumar N, Deol P, Kumar D, Ghosh S, Dhama K. Biotechnological innovations in farm and pet animal disease diagnosis. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7150312 DOI: 10.1016/b978-0-12-816352-8.00013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals.
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Gandhi J, Jayasudha R, Naik P, Sharma S, Dave VP, Joseph J. Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India. Microorganisms 2019; 7:microorganisms7100411. [PMID: 31581465 PMCID: PMC6843429 DOI: 10.3390/microorganisms7100411] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/21/2019] [Accepted: 09/24/2019] [Indexed: 11/30/2022] Open
Abstract
To evaluate the clinical utility of high-throughput sequencing (HTS) approach-based analysis of the bacterial and fungal genome in vitreous fluids from patients clinically diagnosed as endophthalmitis, we subjected 75 vitreous fluids from clinically presumed infectious endophthalmitis patients to high-throughput sequencing (Illumina HiSeq 2500) after DNA extraction and amplification of the 16S rRNA for the detection of bacteria, and ITS 2 region for detection of fungal pathogens. As controls, we included vitreous biopsies from 70 patients diagnosed with other non-infectious retinal disorders. Following the construction of the curated microbial genome database and filtering steps to reduce ambiguousness/contaminants from the environment, the paired reads were analyzed. Our HTS reads revealed in almost all cases the same organism that was grown in culture (bacterial-14/15, fungal 3/3) by conventional microbiological workup. HTS additionally diagnosed the presence of microbes in 42/57 (73.7%) patients who were conventionally negative (fungal pathogens in 36/57, bacterial pathogens in 11/57, including five cases that showed the presence of both bacterial and fungal organisms). Aspergillus sp., Fusarium sp., Exserohilum sp., and Candida sp. were the most predominant genera in our cohort of culture-negative endophthalmitis cases. Heat map based microbial clustering analysis revealed that these organisms were taxonomically similar to the species identified by conventional culture methods. Interestingly, 4/70 control samples also showed the presence of bacterial reads, although their clinical significance is uncertain. HTS is useful in detecting pathogens in endophthalmitis cases that elude conventional attempts at diagnosis and can provide actionable information relevant to management, especially where there is a high index of suspicion of fungal endophthalmitis, particularly in tropical countries. Outcome analyses and clinical trials addressing the success and cost savings of HTS for the diagnosis of endophthalmitis are recommended.
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Affiliation(s)
- Jaishree Gandhi
- Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India.
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India.
| | - Poonam Naik
- Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India.
| | - Savitri Sharma
- Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India.
| | - Vivek Pravin Dave
- Smt. Kannuri Santhamma Centre for vitreoretinal diseases, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India.
| | - Joveeta Joseph
- Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India.
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Martins SAM, Martins VC, Cardoso FA, Germano J, Rodrigues M, Duarte C, Bexiga R, Cardoso S, Freitas PP. Biosensors for On-Farm Diagnosis of Mastitis. Front Bioeng Biotechnol 2019; 7:186. [PMID: 31417901 PMCID: PMC6684749 DOI: 10.3389/fbioe.2019.00186] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022] Open
Abstract
Bovine mastitis is an inflammation of the mammary gland caused by a multitude of pathogens with devastating consequences for the dairy industry. Global annual losses are estimated to be around €30 bn and are caused by significant milk losses, poor milk quality, culling of chronically infected animals, and occasional deaths. Moreover, mastitis management routinely implies the administration of antibiotics to treat and prevent the disease which poses serious risks regarding the emergence of antibiotic resistance. Conventional diagnostic methods based on somatic cell counts (SCC) and plate-culture techniques are accurate in identifying the disease, the respective infectious agents and antibiotic resistant phenotypes. However, pressure exists to develop less lengthy approaches, capable of providing on-site information concerning the infection, and in this way, guide, and hasten the most adequate treatment. Biosensors are analytical tools that convert the presence of biological compounds into an electric signal. Benefitting from high signal-to-noise ratios and fast response times, when properly tuned, they can detect the presence of specific cells and cell markers with high sensitivity. In combination with microfluidics, they provide the means for development of automated and portable diagnostic devices. Still, while biosensors are growing at a fast pace in human diagnostics, applications for the veterinary market, and specifically, for the diagnosis of mastitis remain limited. This review highlights current approaches for mastitis diagnosis and describes the latest outcomes in biosensors and lab-on-chip devices with the potential to become real alternatives to standard practices. Focus is given to those technologies that, in a near future, will enable for an on-farm diagnosis of mastitis.
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Affiliation(s)
- Sofia A. M. Martins
- Magnomics S.A., Parque Tecnológico de Cantanhede, Cantanhede, Portugal
- INESC Microsistemas e Nanotecnologias Rua Alves Redol, Lisbon, Portugal
| | - Verónica C. Martins
- Magnomics S.A., Parque Tecnológico de Cantanhede, Cantanhede, Portugal
- INESC Microsistemas e Nanotecnologias Rua Alves Redol, Lisbon, Portugal
| | - Filipe A. Cardoso
- Magnomics S.A., Parque Tecnológico de Cantanhede, Cantanhede, Portugal
| | - José Germano
- Magnomics S.A., Parque Tecnológico de Cantanhede, Cantanhede, Portugal
| | - Mónica Rodrigues
- Magnomics S.A., Parque Tecnológico de Cantanhede, Cantanhede, Portugal
- Faculdade de Ciências, CE3C - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisbon, Portugal
| | - Carla Duarte
- INESC Microsistemas e Nanotecnologias Rua Alves Redol, Lisbon, Portugal
- Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, Lisbon, Portugal
| | - Ricardo Bexiga
- Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, Lisbon, Portugal
| | - Susana Cardoso
- INESC Microsistemas e Nanotecnologias Rua Alves Redol, Lisbon, Portugal
| | - Paulo P. Freitas
- INESC Microsistemas e Nanotecnologias Rua Alves Redol, Lisbon, Portugal
- INL- International Iberian Nanotechnology Laboratory, Braga, Portugal
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Li Y, Lee JS. Recent developments in affinity-based selection of aptamers for binding disease-related protein targets. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00842-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Hawkins IK, Rissi DR, Armién AG, Wilkes RP, Anis E. Rabies‐like neuronal inclusions in a dog with meningoencephalomyelitis and neuritis of unknown origin. VETERINARY RECORD CASE REPORTS 2019. [DOI: 10.1136/vetreccr-2018-000759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Ian Keith Hawkins
- Tifton Veterinary Diagnostic and Investigational LaboratoryUniversity of Georgia College of Veterinary MedicineTiftonGeorgiaUSA
| | - Daniel R Rissi
- Athens Veterinary Diagnostic LaboratoryDepartment of PathologyUniversity of Georgia College of Veterinary MedicineAthensGeorgiaUSA
| | - Anibal G Armién
- Veterinary Diagnostic LaboratoryUniversity of Minnesota College of Veterinary MedicineSaint PaulMinnesotaUSA
| | - Rebecca Penrose Wilkes
- Tifton Veterinary Diagnostic and Investigational LaboratoryUniversity of Georgia College of Veterinary MedicineTiftonGeorgiaUSA
- Department of Comparative PathobiologyPurdue University College of Veterinary MedicineWest LafayetteIndianaUSA
| | - Eman Anis
- Tifton Veterinary Diagnostic and Investigational LaboratoryUniversity of Georgia College of Veterinary MedicineTiftonGeorgiaUSA
- Department of VirologyFaculty of Veterinary MedicineUniversity of Sadat CitySadat CityEgypt
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Zhang Y, Hu A, Andini N, Yang S. A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections. Biotechnol Adv 2019; 37:476-490. [PMID: 30797092 PMCID: PMC6447436 DOI: 10.1016/j.biotechadv.2019.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.
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Affiliation(s)
- Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore.
| | - Anne Hu
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Nadya Andini
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California 94305, USA.
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Duncan R, Grigorenko E, Fisher C, Hockman D, Lanning B. Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls - an update. Expert Rev Mol Diagn 2018; 19:15-25. [DOI: 10.1080/14737159.2019.1559055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Robert Duncan
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | | | - Carolyn Fisher
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | | | - Bryan Lanning
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
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