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Atta S, Zhao Y, Sanchez S, Seedial D, Devadhasan JP, Summers AJ, Gates-Hollingsworth MA, Pflughoeft KJ, Gu J, Montgomery DC, AuCoin DP, Zenhausern F, Vo-Dinh T. Plasmonic-Enhanced Colorimetric Lateral Flow Immunoassays Using Bimetallic Silver-Coated Gold Nanostars. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39342509 DOI: 10.1021/acsami.4c13086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
The colorimetric lateral flow immunoassay (cLFIA) has gained widespread attention as a point-of-care testing (POCT) technique due to its low cost, short analysis time, portability, and capability of being performed by unskilled operators with minimal requirement of reagents. However, the low analytical sensitivity of conventional LFIA based on colloidal gold nanospheres limits their applications for sensitive detection of trace amounts of target analytes. In this study, we introduced a novel plasmonic-enhanced colorimetric LFIA (PE-cLFIA) platform featuring bimetallic silver-coated gold nanostars (BGNS) with exceptional optical properties, leading to ultrahigh visual color brightness. The BGNS-based PE-cLFIA was successfully applied to detect a model analyte, low-calcium response V (LcrV), a virulence protein factor found in Yersinia pestis, the causative agent of bubonic plague. The PE-cLFIA sensing using BGNS-3 composed of 45 nm silver thickness showed a high visual colorimetric sensitivity with a detection limit as low as 13.7 pg/mL, which was around 50 times more sensitive than that of a traditional gold nanoparticle-based LFIA. In addition, the antibody-conjugated BGNS-3 showed excellent stability over 6 months. To illustrate the potential for clinical applications, we demonstrated that our LFIA platform for detecting LcrV spiked in human serum without any sample preprocessing exhibited a detection limit of 22.8 pg/mL. These results open up new opportunities for developing hybrid nanoparticle systems for sensitive POCT PE-cLFIA screening for infectious disease detection.
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Affiliation(s)
- Supriya Atta
- Fitzpatrick Institute for Photonics, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Yuanhao Zhao
- Fitzpatrick Institute for Photonics, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sanchez
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Deven Seedial
- Fitzpatrick Institute for Photonics, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Jasmine Pramila Devadhasan
- Center for Applied Nano Bioscience and Medicine, College of Medicine, University of Arizona, Phoenix, Arizona 85004, United States
| | - Alexander Jarrett Summers
- Center for Applied Nano Bioscience and Medicine, College of Medicine, University of Arizona, Phoenix, Arizona 85004, United States
| | | | - Kathryn J Pflughoeft
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, United States
| | - Jian Gu
- Center for Applied Nano Bioscience and Medicine, College of Medicine, University of Arizona, Phoenix, Arizona 85004, United States
- Department of Basic Medical Sciences, The University of Arizona, College of Medicine, 475 North Fifth Street, Phoenix, Arizona 85004, United States
| | - Douglas C Montgomery
- Center for Applied Nano Bioscience and Medicine, College of Medicine, University of Arizona, Phoenix, Arizona 85004, United States
- School of Computing and Augmented Intelligence, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - David P AuCoin
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, United States
| | - Frederic Zenhausern
- Center for Applied Nano Bioscience and Medicine, College of Medicine, University of Arizona, Phoenix, Arizona 85004, United States
- Department of Basic Medical Sciences, The University of Arizona, College of Medicine, 475 North Fifth Street, Phoenix, Arizona 85004, United States
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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2
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Chen L, Zhang L, Li Y, Qiao L, Kumar S. Screening of promising molecules against potential drug targets in Yersinia pestis by integrative pan and subtractive genomics, docking and simulation approach. Arch Microbiol 2024; 206:415. [PMID: 39320535 DOI: 10.1007/s00203-024-04140-y] [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: 07/19/2024] [Revised: 09/02/2024] [Accepted: 09/10/2024] [Indexed: 09/26/2024]
Abstract
This study focuses on Yersinia pestis, the bacterium responsible for plague, which posed a severe threat to public health in history. Despite the availability of antibiotics treatment, the emergence of antibiotic resistance in this pathogen has increased challenges of controlling the infections and plague outbreaks. The development of new drug targets and therapies is urgently needed. This research aims to identify novel protein targets from 28 Y. pestis strains by the integrative pan-genomic and subtractive genomics approach. Additionally, it seeks to screen out potential safe and effective alternative therapies against these targets via high-throughput virtual screening. Targets should lack homology to human, gut microbiota, and known human 'anti-targets', while should exhibit essentiality for pathogen's survival and virulence, druggability, antibiotic resistance, and broad spectrum across multiple pathogenic bacteria. We identified two promising targets: the aminotransferase class I/class II domain-containing protein and 3-oxoacyl-[acyl-carrier-protein] synthase 2. These proteins were modeled using AlphaFold2, validated through several structural analyses, and were subjected to molecular docking and ADMET analysis. Molecular dynamics simulations determined the stability of the ligand-target complexes, providing potential therapeutic options against Y. pestis.
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Affiliation(s)
- Lei Chen
- Jiangsu Vocational College of Medicine, Yancheng, China
- School of Graduate Studies, Management and Science University, Shah Alam, Malaysia
| | - Lihu Zhang
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Yanping Li
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Liang Qiao
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, University Drive, Off Persiaran Olahraga, 40100, Shah Alam, Selangor, Malaysia.
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3
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Powell J, Daly M, O'Connell NH, Dunne CP. Seek and you shall find: Yersinia enterocolitica in Ireland's drinking water. Ir J Med Sci 2024; 193:1885-1890. [PMID: 38381378 PMCID: PMC11294261 DOI: 10.1007/s11845-024-03641-5] [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: 01/25/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
INTRODUCTION Three Yersinia species were identified from samples of drinking water from diverse geographic regions of Ireland. Conventional commercial biochemical identification systems classified them as Yersinia enterocolitica. Since this organism is the most common cause of bacterial gastroenteritis in some countries, further investigation was warranted. The aim of the study was to provide a microbial characterisation of three Yersinia species, to determine their pathogenicity, and to review the incidence rate of Yersinia enterocolitica detection in our region. METHODS Organism identification was performed using conventional commercial diagnostic systems MALDI-TOF, API 20E, API 50CHE, TREK Sensititre GNID and Vitek 2 GN, and whole genome sequencing (WGS) was performed. Historical data for detections was extracted from the lab system for 2008 to 2023. RESULTS All three isolates gave "good" identifications of Yersinia enterocolitica on conventional systems. Further analysis by WGS matched two of the isolates with recently described Yersinia proxima, and the third was a member of the non-pathogenic Yersinia enterocolitica clade 1Aa. DISCUSSION Our analysis of these three isolates deemed them to be Yersinia species not known currently to be pathogenic, but determining this necessitated the use of next-generation sequencing and advanced bioinformatics. Our work highlights the importance of having this technology available to public laboratories, either locally or in a national reference laboratory. The introduction of molecular technologies for the detection of Yersinia species may increase the rate of detections. Accurate identification of significant pathogens in environmental, public health and clinical microbiology laboratories is critically important for the protection of society.
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Affiliation(s)
- James Powell
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland
| | - Maureen Daly
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Nuala H O'Connell
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland
| | - Colum P Dunne
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland.
- School of Medicine, University of Limerick, Limerick, Ireland.
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4
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Ristori MV, Guarrasi V, Soda P, Petrosillo N, Gurrieri F, Longo UG, Ciccozzi M, Riva E, Angeletti S. Emerging Microorganisms and Infectious Diseases: One Health Approach for Health Shared Vision. Genes (Basel) 2024; 15:908. [PMID: 39062687 PMCID: PMC11275270 DOI: 10.3390/genes15070908] [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: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Emerging infectious diseases (EIDs) are newly emerging and reemerging infectious diseases. The National Institute of Allergy and Infectious Diseases identifies the following as emerging infectious diseases: SARS, MERS, COVID-19, influenza, fungal diseases, plague, schistosomiasis, smallpox, tick-borne diseases, and West Nile fever. The factors that should be taken into consideration are the genetic adaptation of microbial agents and the characteristics of the human host or environment. The new approach to identifying new possible pathogens will have to go through the One Health approach and omics integration data, which are capable of identifying high-priority microorganisms in a short period of time. New bioinformatics technologies enable global integration and sharing of surveillance data for rapid public health decision-making to detect and prevent epidemics and pandemics, ensuring timely response and effective prevention measures. Machine learning tools are being more frequently utilized in the realm of infectious diseases to predict sepsis in patients, diagnose infectious diseases early, and forecast the effectiveness of treatment or the appropriate choice of antibiotic regimen based on clinical data. We will discuss emerging microorganisms, omics techniques applied to infectious diseases, new computational solutions to evaluate biomarkers, and innovative tools that are useful for integrating omics data and electronic medical records data for the clinical management of emerging infectious diseases.
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Affiliation(s)
- Maria Vittoria Ristori
- Operative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, Italy; (M.V.R.); (M.C.); (E.R.)
| | - Valerio Guarrasi
- Unit of Computer Systems and Bioinformatics, Department of Engineering, University Campus Bio-Medico of Rome, Via Alvaro del Portillo, 21, 00128 Rome, Italy; (V.G.); (P.S.)
| | - Paolo Soda
- Unit of Computer Systems and Bioinformatics, Department of Engineering, University Campus Bio-Medico of Rome, Via Alvaro del Portillo, 21, 00128 Rome, Italy; (V.G.); (P.S.)
- Department of Diagnostic and Intervention, Radiation Physics, Biomedical Engineering, Umeå University, 901 87 Umeå, Sweden
| | - Nicola Petrosillo
- Infection Prevention Control/Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy;
| | - Fiorella Gurrieri
- Operative Research Unit of Medical Genetics, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy;
- Research Unit of Medical Genetics, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy
| | - Umile Giuseppe Longo
- Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, Italy;
- Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy
| | - Massimo Ciccozzi
- Operative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, Italy; (M.V.R.); (M.C.); (E.R.)
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Via Alvaro del Portillo, 21, 00128 Rome, Italy
| | - Elisabetta Riva
- Operative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, Italy; (M.V.R.); (M.C.); (E.R.)
- Unit of Virology, University Campus Bio-Medico of Rome, Via Alvaro del Portillo, 21, 00128 Rome, Italy
| | - Silvia Angeletti
- Operative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, Italy; (M.V.R.); (M.C.); (E.R.)
- Research Unit of Clinical Laboratory Science, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy
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5
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Mazzanti C, Zedda N, Bramanti B. Antimicrobial therapies administrated during the Third Plague Pandemic in Europe. LE INFEZIONI IN MEDICINA 2024; 32:254-263. [PMID: 38827832 PMCID: PMC11142408 DOI: 10.53854/liim-3202-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/12/2024] [Indexed: 06/05/2024]
Abstract
Plague raged in Europe for over 1400 years and was responsible for three major pandemics. Today, plague still poses a serious threat to global public health and surveillance is imperative. Plague is still present in natural reservoirs on several continents, including Africa, Asia and the Americas, and sometimes causes local cases and epidemics. The Third Plague Pandemic caused millions of deaths worldwide, including in Europe. Plague arrived in Europe in the autumn of 1896 mostly through maritime trade routes, where it spread with several epidemic events until 1945, when, in the port city of Taranto, the last known outbreak was recorded. In this paper, we present an overview of the natural history and pathogenicity of Yersinia pestis, the bacterium responsible for plague, its spread from Asia to Europe during the Third Pandemic, and the therapies used to treat and prevent the disease in Europe, with particular focus on the case of Taranto. In Taranto, the Pasteur Institute's antiserum antimicrobial therapy, and vaccination were used to treat and stop the advance of the bacterium, with mixed results.
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Affiliation(s)
- Carlotta Mazzanti
- Department of Environmental and Prevention Sciences, University of Ferrara, Italy
| | - Nicoletta Zedda
- Department of Environmental and Prevention Sciences, University of Ferrara, Italy
| | - Barbara Bramanti
- Department of Environmental and Prevention Sciences, University of Ferrara, Italy
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6
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Vasseur L, Barbault F, Monari A. Interaction between Yersinia pestis Ail Outer Membrane Protein and the C-Terminal Domain of Human Vitronectin. J Phys Chem B 2024; 128:3929-3936. [PMID: 38619541 DOI: 10.1021/acs.jpcb.4c00965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Yersinia pestis, the causative agent of plague, is capable of evading the human immune system response by recruiting the plasma circulating vitronectin proteins, which act as a shield and avoid its lysis. Vitronectin recruitment is mediated by its interaction with the bacterial transmembrane protein Ail, protruding from the Y. pestis outer membrane. By using all-atom long-scale molecular dynamic simulations of Ail embedded in a realistic model of the bacterial membrane, we have shown that vitronectin forms a stable complex, mediated by interactions between the disordered moieties of the two proteins. The main amino acids driving the complexation have also been evidenced, thus favoring the possible rational design of specific peptides which, by inhibiting vitronectin recruitment, could act as original antibacterial agents.
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Affiliation(s)
- Laurine Vasseur
- Université Paris Cité and CNRS, ITODYS, F-75006 Paris, France
| | | | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, F-75006 Paris, France
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7
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Marks KD, Anderson DM. Protection from plague via single dose administration of antibody to neutralize the type I interferon response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584497. [PMID: 38559124 PMCID: PMC10979884 DOI: 10.1101/2024.03.11.584497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Yersinia pestis is a gram-negative bacterium and the causative agent for the plague. Yersinia spp . use effector proteins of the type III secretion system (T3SS) to skew the host immune response toward a bacterial advantage during infection. Previous work established that mice which lack the type I IFN receptor (IFNAR), exhibit resistance to pulmonary infection by Y. pestis . In this work, we addressed the efficacy of a single dose administration of neutralizing antibody to IFNAR (MAR1) as a preventive treatment for plague. We show that single dose administration of MAR1 provides protection from mortality due to secondary septicemic plague where it appears to reduce the production of serum TNFα during the disease phase. We further demonstrate that the T3SS effector protein YopJ is necessary for MAR1-induced protection, however IFNAR-dependent serum TNFα was observed independent of YopJ. We further define tissue-specific anti-bacterial roles of IFNAR that are blocked by YopJ activity indicating that YopJ and IFNAR work in parallel to promote disease. The combined data suggest that therapeutic targeting of IFNAR signaling may reduce the hyper-inflammatory response associated with plague.
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8
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Guo X, Xin Y, Tong Z, Cao S, Zhang Y, Wu G, Chen H, Wang T, Song Y, Zhang Q, Yang R, Du Z. A novel sORF gene mutant strain of Yersinia pestis vaccine EV76 offers enhanced safety and improved protection against plague. PLoS Pathog 2024; 20:e1012129. [PMID: 38547321 PMCID: PMC11020802 DOI: 10.1371/journal.ppat.1012129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 04/16/2024] [Accepted: 03/15/2024] [Indexed: 04/18/2024] Open
Abstract
We recently identified two virulence-associated small open reading frames (sORF) of Yersinia pestis, named yp1 and yp2, and null mutants of each individual genes were highly attenuated in virulence. Plague vaccine strain EV76 is known for strong reactogenicity, making it not suitable for use in humans. To improve the immune safety of EV76, three mutant strains of EV76, Δyp1, Δyp2, and Δyp1&yp2 were constructed and their virulence attenuation, immunogenicity, and protective efficacy in mice were evaluated. All mutant strains were attenuated by the subcutaneous (s.c.) route and exhibited more rapid clearance in tissues than the parental strain EV76. Under iron overload conditions, only the mice infected with EV76Δyp1 survived, accompanied by less draining lymph nodes damage than those infected by EV76. Analysis of cytokines secreted by splenocytes of immunized mice found that EV76Δyp2 induced higher secretion of multiple cytokines including TNF-α, IL-2, and IL-12p70 than EV76. On day 42, EV76Δyp2 or EV76Δyp1&yp2 immunized mice exhibited similar protective efficacy as EV76 when exposed to Y. pestis 201, both via s.c. or intranasal (i.n.) routes of administration. Moreover, when exposed to 200-400 LD50 Y. pestis strain 201Δcaf1 (non-encapsulated Y. pestis), EV76Δyp2 or EV76Δyp1&yp2 are able to afford about 50% protection to i.n. challenges, significantly better than the protection afforded by EV76. On 120 day, mice immunized with EV76Δyp2 or EV76Δyp1&yp2 cleared the i.n. challenge of Y. pestis 201-lux as quickly as those immunized with EV76, demonstrating 90-100% protection. Our results demonstrated that deletion of the yp2 gene is an effective strategy to attenuate virulence of Y. pestis EV76 while improving immunogenicity. Furthermore, EV76Δyp2 is a promising candidate for conferring protection against the pneumonic and bubonic forms of plague.
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Affiliation(s)
- Xiao Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Youquan Xin
- Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Zehui Tong
- School of Basic Medical Sciences, Anhui Medical University Hefei, China
| | - Shiyang Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Gengshan Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hongyan Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qingwen Zhang
- Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zongmin Du
- School of Basic Medical Sciences, Anhui Medical University Hefei, China
- Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
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9
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Meng B, Qi Z, Li X, Peng H, Bi S, Wei X, Li Y, Zhang Q, Xu X, Zhao H, Yang X, Wang C, Zhao X. Characterization of Mu-Like Yersinia Phages Exhibiting Temperature Dependent Infection. Microbiol Spectr 2023; 11:e0020323. [PMID: 37466430 PMCID: PMC10434027 DOI: 10.1128/spectrum.00203-23] [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: 01/12/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Yersinia pestis is the etiological agent of plague. Marmota himalayana of the Qinghai-Tibetan plateau is the primary host of flea-borne Y. pestis. This study is the report of isolation of Mu-like bacteriophages of Y. pestis from M. himalayana. The isolation and characterization of four Mu-like phages of Y. pestis were reported, which were named as vB_YpM_3, vB_YpM_5, vB_YpM_6, and vB_YpM_23 according to their morphology. Comparative genome analysis revealed that vB_YpM_3, vB_YpM_5, vB_YpM_6, and vB_YpM_23 are phylogenetically closest to Escherichia coli phages Mu, D108 and Shigella flexneri phage SfMu. The role of LPS core structure of Y. pestis in the phages' receptor was pinpointed. All the phages exhibit "temperature dependent infection," which is independent of the growth temperature of the host bacteria and dependent of the temperature of phage infection. The phages lyse the host bacteria at 37°C, but enter the lysogenic cycle and become prophages in the chromosome of the host bacteria at 26°C. IMPORTANCE Mu-like bacteriophages of Y. pestis were isolated from M. himalayana of the Qinghai-Tibetan plateau in China. These bacteriophages have a unique temperature dependent life cycle, follow a lytic cycle at the temperature of warm-blooded mammals (37°С), and enter the lysogenic cycle at the temperature of its flea-vector (26°С). A switch from the lysogenic to the lytic cycle occurred when lysogenic bacteria were incubated from lower temperature to higher temperature (initially incubating at 26°C and shifting to 37°C). It is speculated that the temperature dependent lifestyle of bacteriophages may affect the population dynamics and pathogenicity of Y. pestis.
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Affiliation(s)
- Biao Meng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- Institute of Disease Control and Prevention, Chinese PLA, Beijing, China
| | - Zhizhen Qi
- Qinghai Institute for Endemic Disease Prevention and Control of Qinghai Province, Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining, China
| | - Xiang Li
- Qinghai Institute for Endemic Disease Prevention and Control of Qinghai Province, Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining, China
| | - Hong Peng
- Institute of Disease Control and Prevention, Chinese PLA, Beijing, China
| | - Shanzheng Bi
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- Institute of Disease Control and Prevention, Chinese PLA, Beijing, China
| | - Xiao Wei
- Institute of Disease Control and Prevention, Chinese PLA, Beijing, China
| | - Yan Li
- Institute of Disease Control and Prevention, Chinese PLA, Beijing, China
| | - Qi Zhang
- Qinghai Institute for Endemic Disease Prevention and Control of Qinghai Province, Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining, China
| | - Xiaoqing Xu
- Qinghai Institute for Endemic Disease Prevention and Control of Qinghai Province, Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining, China
| | - Haihong Zhao
- Qinghai Institute for Endemic Disease Prevention and Control of Qinghai Province, Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining, China
| | - Xiaoyan Yang
- Qinghai Institute for Endemic Disease Prevention and Control of Qinghai Province, Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining, China
| | - Changjun Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- Institute of Disease Control and Prevention, Chinese PLA, Beijing, China
| | - Xiangna Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- Institute of Disease Control and Prevention, Chinese PLA, Beijing, China
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10
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Bonczarowska JH, Susat J, Krause-Kyora B, Dangvard Pedersen D, Boldsen J, Larsen LA, Seeberg L, Nebel A, Unterweger D. Ancient Yersinia pestis genomes lack the virulence-associated Ypf Φ prophage present in modern pandemic strains. Proc Biol Sci 2023; 290:20230622. [PMID: 37464758 DOI: 10.1098/rspb.2023.0622] [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: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023] Open
Abstract
Yersinia pestis is the causative agent of at least three major plague pandemics (Justinianic, Medieval and Modern). Previous studies on ancient Y. pestis genomes revealed that several genomic alterations had occurred approximately 5000-3000 years ago and contributed to the remarkable virulence of this pathogen. How a subset of strains evolved to cause the Modern pandemic is less well-understood. Here, we examined the virulence-associated prophage (YpfΦ), which had been postulated to be exclusively present in the genomes of strains associated with the Modern pandemic. The analysis of two new Y. pestis genomes from medieval/early modern Denmark confirmed that the phage is absent from the genome of strains dating to this time period. An extended comparative genome analysis of over 300 strains spanning more than 5000 years showed that the prophage is found in the genomes of modern strains only and suggests an integration into the genome during recent Y. pestis evolution. The phage-encoded Zot protein showed structural homology to a virulence factor of Vibrio cholerae. Similar to modern Y. pestis, we observed phages with a common origin to YpfΦ in individual strains of other bacterial species. Our findings present an updated view on the prevalence of YpfΦ, which might contribute to our understanding of the host spectrum, geographical spread and virulence of Y. pestis responsible for the Modern pandemic.
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Affiliation(s)
- Joanna H Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Dorthe Dangvard Pedersen
- Unit of Anthropology, Department of Forensic Medicine, University of Southern Denmark, Odense M, 5230, Denmark
| | - Jesper Boldsen
- Unit of Anthropology, Department of Forensic Medicine, University of Southern Denmark, Odense M, 5230, Denmark
| | | | - Lone Seeberg
- Museum Horsens Arkæologisk Afdeling, Fussingsvej 8, Horsens 8700, Denmark
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, Kiel 24105, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön 24306, Germany
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11
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Suladze T, Jaiani E, Darsavelidze M, Elizbarashvili M, Gorge O, Kusradze I, Kokashvili T, Lashkhi N, Tsertsvadze G, Janelidze N, Chubinidze S, Grdzelidze M, Tsanava S, Valade E, Tediashvili M. New Bacteriophages with Podoviridal Morphotypes Active against Yersinia pestis: Characterization and Application Potential. Viruses 2023; 15:1484. [PMID: 37515171 PMCID: PMC10385128 DOI: 10.3390/v15071484] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Phages of highly pathogenic bacteria represent an area of growing interest for bacterial detection and identification and subspecies typing, as well as for phage therapy and environmental decontamination. Eight new phages-YpEc56, YpEc56D, YpEc57, YpEe58, YpEc1, YpEc2, YpEc11, and YpYeO9-expressing lytic activity towards Yersinia pestis revealed a virion morphology consistent with the Podoviridae morphotype. These phages lyse all 68 strains from 2 different sets of Y. pestis isolates, thus limiting their potential application for subtyping of Y. pestis strains but making them rather promising in terms of infection control. Two phages-YpYeO9 and YpEc11-were selected for detailed studies based on their source of isolation and lytic cross activity towards other Enterobacteriaceae. The full genome sequencing demonstrated the virulent nature of new phages. Phage YpYeO9 was identified as a member of the Teseptimavirus genus and YpEc11 was identified as a member of the Helsettvirus genus, thereby representing new species. A bacterial challenge assay in liquid microcosm with a YpYeO9/YpEc11 phage mixture showed elimination of Y. pestis EV76 during 4 h at a P/B ratio of 1000:1. These results, in combination with high lysis stability results of phages in liquid culture, the low frequency of formation of phage resistant mutants, and their viability under different physical-chemical factors indicate their potential for their practical use as an antibacterial mean.
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Affiliation(s)
- Tamar Suladze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Ekaterine Jaiani
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Marina Darsavelidze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Maia Elizbarashvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Olivier Gorge
- French Armed Forces Biomedical Research Institute (IRBA), 1, Place du Général Valérie André-BP 73, 91223 Bretigny-sur-Orge, France
| | - Ia Kusradze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Tamar Kokashvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
- School of Science and Technology, University of Georgia, 77a, Kostava Str., 0171 Tbilisi, Georgia
| | - Nino Lashkhi
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - George Tsertsvadze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Nino Janelidze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
- School of Science and Technology, University of Georgia, 77a, Kostava Str., 0171 Tbilisi, Georgia
| | - Svetlana Chubinidze
- National Center for Disease Control and Pubic Health (NCDC), 99, Kakheti Highway, 0109 Tbilisi, Georgia
| | - Marina Grdzelidze
- National Center for Disease Control and Pubic Health (NCDC), 99, Kakheti Highway, 0109 Tbilisi, Georgia
| | - Shota Tsanava
- National Center for Disease Control and Pubic Health (NCDC), 99, Kakheti Highway, 0109 Tbilisi, Georgia
| | - Eric Valade
- French Armed Forces Biomedical Research Institute (IRBA), 1, Place du Général Valérie André-BP 73, 91223 Bretigny-sur-Orge, France
| | - Marina Tediashvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
- School of Science and Technology, University of Georgia, 77a, Kostava Str., 0171 Tbilisi, Georgia
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12
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Ma’ruf M, Fadli JC, Mahendra MR, Irham LM, Sulistyani N, Adikusuma W, Chong R, Septama AW. A bioinformatic approach to identify pathogenic variants for Stevens-Johnson syndrome. Genomics Inform 2023; 21:e26. [PMID: 37704211 PMCID: PMC10326529 DOI: 10.5808/gi.23010] [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: 02/09/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 07/08/2023] Open
Abstract
Stevens-Johnson syndrome (SJS) produces a severe hypersensitivity reaction caused by Herpes simplex virus or mycoplasma infection, vaccination, systemic disease, or other agents. Several studies have investigated the genetic susceptibility involved in SJS. To provide further genetic insights into the pathogenesis of SJS, this study prioritized high-impact, SJS-associated pathogenic variants through integrating bioinformatic and population genetic data. First, we identified SJS-associated single nucleotide polymorphisms from the genome-wide association studies catalog, followed by genome annotation with HaploReg and variant validation with Ensembl. Subsequently, expression quantitative trait locus (eQTL) from GTEx identified human genetic variants with differential gene expression across human tissues. Our results indicate that two variants, namely rs2074494 and rs5010528, which are encoded by the HLA-C (human leukocyte antigen C) gene, were found to be differentially expressed in skin. The allele frequencies for rs2074494 and rs5010528 also appear to significantly differ across continents. We highlight the utility of these population-specific HLA-C genetic variants for genetic association studies, and aid in early prognosis and disease treatment of SJS.
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Affiliation(s)
- Muhammad Ma’ruf
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
| | | | | | - Lalu Muhammad Irham
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
- Center for Vaccine and Drugs, Research Organization for Health, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
| | - Nanik Sulistyani
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
| | - Wirawan Adikusuma
- Departement of Pharmacy, University of Muhammadiyah Mataram, Mataram 83127, Indonesia
- Center for Vaccine and Drugs, Research Organization for Health, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
| | - Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, CA, USA
| | - Abdi Wira Septama
- Departement of Pharmacy, University of Muhammadiyah Mataram, Mataram 83127, Indonesia
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13
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Biryukov SS, Wu H, Dankmeyer JL, Rill NO, Klimko CP, Egland KA, Shoe JL, Hunter M, Fetterer DP, Qiu J, Davies ML, Bausch CL, Sullivan EJ, Luke T, Cote CK. Polyclonal Antibodies Derived from Transchromosomic Bovines Vaccinated with the Recombinant F1-V Vaccine Increase Bacterial Opsonization In Vitro and Protect Mice from Pneumonic Plague. Antibodies (Basel) 2023; 12:antib12020033. [PMID: 37218899 DOI: 10.3390/antib12020033] [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: 03/10/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Plague is an ancient disease that continues to be of concern to both the public health and biodefense research communities. Pneumonic plague is caused by hematogenous spread of Yersinia pestis bacteria from a ruptured bubo to the lungs or by directly inhaling aerosolized bacteria. The fatality rate associated with pneumonic plague is significant unless effective antibiotic therapy is initiated soon after an early and accurate diagnosis is made. As with all bacterial pathogens, drug resistance is a primary concern when developing strategies to combat these Yersinia pestis infections in the future. While there has been significant progress in vaccine development, no FDA-approved vaccine strategy exists; thus, other medical countermeasures are needed. Antibody treatment has been shown to be effective in animal models of plague. We produced fully human polyclonal antibodies in transchromosomic bovines vaccinated with the recombinant F1-V plague vaccine. The resulting human antibodies opsonized Y. pestis bacteria in the presence of RAW264.7 cells and afforded significant protection to BALB/c mice after exposure to aerosolized Y. pestis. These data demonstrate the utility of this technology to produce large quantities of non-immunogenic anti-plague human antibodies to prevent or possibly treat pneumonic plague in human.
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Affiliation(s)
- Sergei S Biryukov
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Hua Wu
- SAB Biotherapeutics, 2100 E 54th St. N, Sioux Falls, SD 57104, USA
| | - Jennifer L Dankmeyer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Nathaniel O Rill
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Christopher P Klimko
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Kristi A Egland
- SAB Biotherapeutics, 2100 E 54th St. N, Sioux Falls, SD 57104, USA
| | - Jennifer L Shoe
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Melissa Hunter
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - David P Fetterer
- Biostatistics Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Ju Qiu
- Biostatistics Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Michael L Davies
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | | | - Eddie J Sullivan
- SAB Biotherapeutics, 2100 E 54th St. N, Sioux Falls, SD 57104, USA
| | - Thomas Luke
- SAB Biotherapeutics, 2100 E 54th St. N, Sioux Falls, SD 57104, USA
| | - Christopher K Cote
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
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14
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Omeershffudin UNM, Kumar S. Antibiotic resistance in Neisseria gonorrhoeae: broad-spectrum drug target identification using subtractive genomics. Genomics Inform 2023; 21:e5. [PMID: 37037463 PMCID: PMC10085745 DOI: 10.5808/gi.22066] [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: 09/29/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 04/03/2023] Open
Abstract
Neisseria gonorrhoeae is a Gram-negative aerobic diplococcus bacterium that primarily causes sexually transmitted infections through direct human sexual contact. It is a major public health threat due to its impact on reproductive health, the widespread presence of antimicrobial resistance, and the lack of a vaccine. In this study, we used a bioinformatics approach and performed subtractive genomic methods to identify potential drug targets against the core proteome of N. gonorrhoeae (12 strains). In total, 12,300 protein sequences were retrieved, and paralogous proteins were removed using CD-HIT. The remaining sequences were analyzed for non-homology against the human proteome and gut microbiota, and screened for broad-spectrum analysis, druggability, and anti-target analysis. The proteins were also characterized for unique interactions between the host and pathogen through metabolic pathway analysis. Based on the subtractive genomic approach and subcellular localization, we identified one cytoplasmic protein, 2Fe-2S iron-sulfur cluster binding domain-containing protein (NGFG RS03485), as a potential drug target. This protein could be further exploited for drug development to create new medications and therapeutic agents for the treatment of N. gonorrhoeae infections.
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Affiliation(s)
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, Seksyen 13, 40100, Shah Alam, Selangor, Malaysia
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15
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Omeershffudin UNM, Kumar S. Antimicrobial resistance in Klebsiella pneumoniae: identification of bacterial DNA adenine methyltransferase as a novel drug target from hypothetical proteins using subtractive genomics. Genomics Inform 2022; 20:e47. [PMID: 36617654 PMCID: PMC9847377 DOI: 10.5808/gi.22067] [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: 10/05/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Klebsiella pneumoniae is a gram-negative bacterium that is known for causing infection innosocomial settings. As reported by the World Health Organization, carbapenem-resistantEnterobacteriaceae, a category that includes K. pneumoniae, are classified as an urgentthreat, and the greatest concern is that these bacterial pathogens may acquire genetictraits that make them resistant towards antibiotics. The last class of antibiotics, carbapenems, are not able to combat these bacterial pathogens, allowing them to clonally expandantibiotic-resistant strains. Most antibiotics target essential pathways of bacterial cells;however, these targets are no longer susceptible to antibiotics. Hence, in our study, we focused on a hypothetical protein in K. pneumoniae that contains a DNA methylation proteindomain, suggesting a new potential site as a drug target. DNA methylation regulates theattenuation of bacterial virulence. We integrated computational-aided drug design by using a bioinformatics approach to perform subtractive genomics, virtual screening, and fingerprint similarity search. We identified a new potential drug, koenimbine, which could bea novel antibiotic.
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Affiliation(s)
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, Shah Alam 40100, Malaysia,Corresponding author E-mail:
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16
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Sah R, Reda A, Mehta R, Mohapatra RK, Dhama K. A situation analysis of the current plague outbreak in the Demographic Republic of Congo and counteracting strategies - Correspondence. Int J Surg 2022; 105:106885. [PMID: 36084808 DOI: 10.1016/j.ijsu.2022.106885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 10/14/2022]
Affiliation(s)
- Ranjit Sah
- Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, 44600, Nepal; Harvard Medical School, Boston, MA, 02115, USA.
| | - Abdullah Reda
- Faculty of Medicine, Al-Azhar University, Cairo, 11651, Egypt
| | - Rachana Mehta
- National Public Health Laboratory, Kathmandu, 44600, Nepal
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, 758002, Odisha, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, 243122, India
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