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Williamson ED, Kilgore PB, Hendrix EK, Neil BH, Sha J, Chopra AK. Progress on the research and development of plague vaccines with a call to action. NPJ Vaccines 2024; 9:162. [PMID: 39242587 PMCID: PMC11379892 DOI: 10.1038/s41541-024-00958-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/21/2024] [Indexed: 09/09/2024] Open
Abstract
There is a compelling demand for approved plague vaccines due to the endemicity of Yersinia pestis and its potential for pandemic spread. Whilst substantial progress has been made, we recommend that the global funding and health security systems should work urgently to translate some of the efficacious vaccines reviewed herein to expedite clinical development and to prevent future disastrous plague outbreaks, particularly caused by antimicrobial resistant Y. pestis strains.Content includes material subject to Crown Copyright © 2024.This is an open access article under the Open Government License ( http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/ ).
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Affiliation(s)
- E Diane Williamson
- Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK.
| | - Paul B Kilgore
- Department of Microbiology and Immunology, UTMB, Galveston, TX, 77555, USA
| | - Emily K Hendrix
- Department of Microbiology and Immunology, UTMB, Galveston, TX, 77555, USA
| | - Blake H Neil
- Department of Microbiology and Immunology, UTMB, Galveston, TX, 77555, USA
| | - Jian Sha
- Department of Microbiology and Immunology, UTMB, Galveston, TX, 77555, USA
| | - Ashok K Chopra
- Department of Microbiology and Immunology, UTMB, Galveston, TX, 77555, USA.
- Sealy Institute for Vaccine Sciences, UTMB, Galveston, TX, 77555, USA.
- Institute for Human Infections and Immunity, UTMB, Galveston, TX, 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, UTMB, Galveston, TX, 77555, USA.
- Galveston National Laboratory, UTMB, Galveston, TX, 77555, USA.
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2
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Dias RA. Towards a Comprehensive Definition of Pandemics and Strategies for Prevention: A Historical Review and Future Perspectives. Microorganisms 2024; 12:1802. [PMID: 39338476 PMCID: PMC11433773 DOI: 10.3390/microorganisms12091802] [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: 08/12/2024] [Revised: 08/22/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
The lack of a universally accepted definition of a pandemic hinders a comprehensive understanding of and effective response to these global health crises. Current definitions often lack quantitative criteria, rendering them vague and limiting their utility. Here, we propose a refined definition that considers the likelihood of susceptible individuals contracting an infectious disease that culminates in widespread global transmission, increased morbidity and mortality, and profound societal, economic, and political consequences. Applying this definition retrospectively, we identify 22 pandemics that occurred between 165 and 2024 AD and were caused by a variety of diseases, including smallpox (Antonine and American), plague (Justinian, Black Death, and Third Plague), cholera (seven pandemics), influenza (two Russian, Spanish, Asian, Hong Kong, and swine), AIDS, and coronaviruses (SARS, MERS, and COVID-19). This work presents a comprehensive analysis of past pandemics caused by both emerging and re-emerging pathogens, along with their epidemiological characteristics, societal impact, and evolution of public health responses. We also highlight the need for proactive measures to reduce the risk of future pandemics. These strategies include prioritizing surveillance of emerging zoonotic pathogens, conserving biodiversity to counter wildlife trafficking, and minimizing the potential for zoonotic spillover events. In addition, interventions such as promoting alternative protein sources, enforcing the closure of live animal markets in biodiversity-rich regions, and fostering global collaboration among diverse stakeholders are critical to preventing future pandemics. Crucially, improving wildlife surveillance systems will require the concerted efforts of local, national and international entities, including laboratories, field researchers, wildlife conservationists, government agencies and other stakeholders. By fostering collaborative networks and establishing robust biorepositories, we can strengthen our collective capacity to detect, monitor, and mitigate the emergence and transmission of zoonotic pathogens.
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Affiliation(s)
- Ricardo Augusto Dias
- School of Veterinary Medicine, University of Sao Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo 05508-270, Brazil
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3
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Wang W, Li X, Wu J, Fu X, Li B. Imaging analysis of pneumonic plague infection in Xizang, China: a case report and literature review. BMC Pulm Med 2024; 24:378. [PMID: 39090583 PMCID: PMC11295852 DOI: 10.1186/s12890-024-03187-3] [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] [Received: 02/16/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Plague is an acute infectious disease caused by the Yersinia pestis. Historically, it has been a major pandemic with high mortality rates, known as the "Black Death" in the 14th century, which resulted in millions of deaths in Europe. With increasing economic prosperity, more and more people are traveling to Xizang. However, this trend also hides significant safety hazards. Currently, there are few recent reports on plague, especially those with imaging manifestations available. In this study, we report the detailed clinical and radiological data of the patient with pneumonic plague in Xizang, China, in 2023. CASE PRESENTATION We report a case of pneumonic plague in Xizang, which occurred in a herdsman living in an area where dead marmots were found. The patient presented with symptoms such as fever, hemoptysis, dyspnea and coma. Chest computed tomography (CT) scans showed multiple nodules distributed in the central regions of lung lobes, consolidation distributed in secondary pulmonary lobules, and had a gravity-dependent distribution pattern. These imaging findings were consistent with pulmonary hemorrhage and diffuse alveolar damage. Despite emergency treatment, the patient died within 48 h of admission. Through retrospective medical history investigation, laboratory examination and autopsy, the final diagnosis was confirmed as pneumonic plague. CONCLUSION Pneumonic plague is the most deadly infectious disease, and its pathological features mainly include damage to the alveoli, pulmonary hemorrhage, and pulmonary edema. Corresponding to CT, it manifests as acute and rapidly progressing pneumonia, alveolar damage, and pulmonary hemorrhage. The value of this article lies in the completeness and typicality of the imaging data, vivid hand-drawn illustrations of transmission pathways, and comprehensive literature review, all of which serve to enhance public understanding of plague and play an important warning role.
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Affiliation(s)
- Wei Wang
- Department of Radiology, Dongsheng People's Hospital, Erdos, Inner Mongolia, China
| | - Xiaoran Li
- Department of Radiology, Nanjing Gaochun People's Hospital, No.53, Maoshan Road, Nanjing, Jiangsu, 211300, China
| | - Jing Wu
- Department of Radiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoming Fu
- Department of Radiology, Nanjing Gaochun People's Hospital, No.53, Maoshan Road, Nanjing, Jiangsu, 211300, China.
| | - Binjie Li
- Department of Radiology, Shannan People's Hospital, No.16, Zedang Road, Naidong District, Shannan, Xizang, 856000, China.
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4
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Mongillo J, Zedda N, Rinaldo N, Bellini T, Manfrinato MC, Du Z, Yang R, Stenseth NC, Bramanti B. Differential pathogenicity and lethality of bubonic plague (1720-1945) by sex, age and place. Proc Biol Sci 2024; 291:20240724. [PMID: 39045692 PMCID: PMC11267469 DOI: 10.1098/rspb.2024.0724] [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: 12/15/2023] [Revised: 06/05/2024] [Accepted: 06/17/2024] [Indexed: 07/25/2024] Open
Abstract
COVID-19 brought back to the attention of the scientific community that males are more susceptible to infectious diseases. What is clear for other infections-that sex and gender differences influence both risk of infection and mortality-is not yet fully elucidated for plague, particularly bubonic plague, although this knowledge can help find specific defences against a disease for which a vaccine is not yet available. To address this question, we analysed data on plague from hospitals in different parts of the world since the early eighteenth century, which provide demographic information on individual patients, diagnosis and course of the disease in the pre-antibiotic era. Assuming that the two sexes were equally represented, we observe a worldwide prevalence of male cases hospitalized at any age, a result which seems better explained by gender-biased (thus cultural) behaviours than biological sex-related factors. Conversely, case fatality rates differ among countries and geographic macro-areas, while globally, lethality appears slightly prevalent in young females and older adults (regardless of sex). Logistic regression models confirm that the main risk factor for bubonic plague death was the geographical location of the cases and being older than 50 years, whereas sex only showcased a slight trend.
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Affiliation(s)
- J. Mongillo
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara44121, Italy
| | - N. Zedda
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara44121, Italy
| | - N. Rinaldo
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara44121, Italy
| | - T. Bellini
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara44121, Italy
- University Strategic Center for Studies on Gender Medicine, University of Ferrara, Ferrara44121, Italy
| | - M. C. Manfrinato
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara44121, Italy
| | - Z. Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People‘s Republic of China
| | - R. Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People‘s Republic of China
| | - N. C. Stenseth
- Center for Pandemics and One Health Research, Sustainable Health Unit (SUSTAINIT), Faculty of Medicine, University of Oslo, Oslo0316, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo0316, Norway
- Vanke School of Public Health, Tsinghua University, Beijing100084, People‘s Republic of China
| | - B. Bramanti
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara44121, Italy
- University Strategic Center for Studies on Gender Medicine, University of Ferrara, Ferrara44121, Italy
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo0316, Norway
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Velappan N, Biryukov SS, Rill NO, Klimko CP, Rosario-Acevedo R, Shoe JL, Hunter M, Dankmeyer JL, Fetterer DP, Bedinger D, Phipps ME, Watt AJ, Abergel RJ, Dichosa A, Kozimor SA, Cote CK, Lillo AM. Characterization of two affinity matured Anti-Yersinia pestis F1 human antibodies with medical countermeasure potential. PLoS One 2024; 19:e0305034. [PMID: 38954719 PMCID: PMC11218954 DOI: 10.1371/journal.pone.0305034] [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: 11/03/2023] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
Yersinia pestis, the causative agent of plague and a biological threat agent, presents an urgent need for novel medical countermeasures due to documented cases of naturally acquired antibiotic resistance and potential person-to-person spread during a pneumonic infection. Immunotherapy has been proposed as a way to circumvent current and future antibiotic resistance. Here, we describe the development and characterization of two affinity matured human antibodies (αF1Ig AM2 and αF1Ig AM8) that promote survival of mice after exposure to aerosolized Y. pestis. We share details of the error prone PCR and yeast display technology-based affinity maturation process that we used. The resultant matured antibodies have nanomolar affinity for Y. pestis F1 antigen, are produced in high yield, and are resilient to 37°C stress for up to 6 months. Importantly, in vitro assays using a murine macrophage cell line demonstrated that αF1Ig AM2 and αF1Ig AM8 are opsonic. Even more importantly, in vivo studies using pneumonic plague mouse models showed that 100% of the mice receiving 500 μg of IgGs αF1Ig AM2 and αF1Ig AM8 survived lethal challenge with aerosolized Y. pestis CO92. Combined, these results provide evidence of the quality and robustness of αF1Ig AM2 and αF1Ig AM8 and support their development as potential medical countermeasures against plague.
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Affiliation(s)
- Nileena Velappan
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Sergei S. Biryukov
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Nathaniel O. Rill
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Christopher P. Klimko
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Raysa Rosario-Acevedo
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Jennifer L. Shoe
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Melissa Hunter
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Jennifer L. Dankmeyer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - David P. Fetterer
- Biostatisitics Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | | | - Mary E. Phipps
- Los Alamos National Laboratory, Center Alamos for Integrated Nanotechnologies, Los Alamos, NM, United States of America
| | - Austin J. Watt
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Rebecca J. Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Nuclear Engineering, University of California, Berkeley, CA, United States of America
| | - Armand Dichosa
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Stosh A. Kozimor
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Christopher K. Cote
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Antonietta M. Lillo
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
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6
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Sasiene ZJ, LeBrun ES, Velappan N, Anderson AR, Patterson NH, Dufresne M, Farrow MA, Norris JL, Caprioli RM, Mach PM, McBride EM, Glaros TG. Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers. Analyst 2024; 149:3564-3574. [PMID: 38717518 DOI: 10.1039/d4an00325j] [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: 06/25/2024]
Abstract
Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.
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Affiliation(s)
- Zachary J Sasiene
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Erick S LeBrun
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nileena Velappan
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Austin R Anderson
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nathan H Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Melissa A Farrow
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Phillip M Mach
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Ethan M McBride
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Trevor G Glaros
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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7
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Shafiei N, Mahmoodzadeh Hosseini H, Amani J, Mirhosseini SA, Jafary H. Screening and identification of DNA nucleic acid aptamers against F1 protein of Yersinia pestis using SELEX method. Mol Biol Rep 2024; 51:722. [PMID: 38829419 DOI: 10.1007/s11033-024-09561-y] [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] [Received: 11/19/2023] [Accepted: 04/16/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Yersinia pestis is a bacterium that causes the disease plague. It has caused the deaths of many people throughout history. The bacterium possesses several virulence factors (pPla, pFra, and PYV). PFra plasmid encodes fraction 1 (F1) capsular antigen. F1 protein protects the bacterium against host immune cells through phagocytosis process. This protein is specific for Y. pestis. Many diagnostic techniques are based on molecular and serological detection and quantification of F1 protein in different food and clinical samples. Aptamers are small nucleic acid sequences that can act as specific ligands for many targets.This study, aimed to isolate the high-affinity ssDNA aptamers against F1 protein. METHODS AND RESULTS In this study, SELEX was used as the main strategy in screening aptamers. Moreover, enzyme-linked aptamer sorbent assay (ELASA) and surface plasmon resonance (SPR) were used to determine the affinity and specificity of obtained aptamers to F1 protein. The analysis showed that among the obtained aptamers, the three aptamers of Yer 21, Yer 24, and Yer 25 were selected with a KD value of 1.344E - 7, 2.004E - 8, and 1.68E - 8 M, respectively. The limit of detection (LoD) was found to be 0.05, 0.076, and 0.033 μg/ml for Yer 21, Yer 24, and Yer 25, respectively. CONCLUSION This study demonstrated that the synthesized aptamers could serve as effective tools for detecting and analyzing the F1 protein, indicating their potential value in future diagnostic applications.
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Affiliation(s)
- Nafiseh Shafiei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamideh Mahmoodzadeh Hosseini
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Jafar Amani
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hanieh Jafary
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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8
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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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9
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Sarfraz A, Qurrat-Ul-Ain Fatima S, Shehroz M, Ahmad I, Zaman A, Nishan U, Tayyab M, Sheheryar, Moura AA, Ullah R, Ali EA, Shah M. Decrypting the multi-genome data for chimeric vaccine designing against the antibiotic resistant Yersinia pestis. Int Immunopharmacol 2024; 132:111952. [PMID: 38555818 DOI: 10.1016/j.intimp.2024.111952] [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] [Received: 01/03/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Yersinia pestis, the causative agent of plague, is a gram-negative bacterium that can be fatal if not treated properly. Three types of plague are currently known: bubonic, septicemic, and pneumonic plague, among which the fatality rate of septicemic and pneumonic plague is very high. Bubonic plague can be treated, but only if antibiotics are used at the initial stage of the infection. But unfortunately, Y. pestis has also shown resistance to certain antibiotics such as kanamycin, minocycline, tetracycline, streptomycin, sulfonamides, spectinomycin, and chloramphenicol. Despite tremendous progress in vaccine development against Y. pestis, there is no proper FDA-approved vaccine available to protect people from its infections. Therefore, effective broad-spectrum vaccine development against Y. pestis is indispensable. In this study, vaccinomics-assisted immunoinformatics techniques were used to find possible vaccine candidates by utilizing the core proteome prepared from 58 complete genomes of Y. pestis. Human non-homologous, pathogen-essential, virulent, and extracellular and membrane proteins are potential vaccine targets. Two antigenic proteins were prioritized for the prediction of lead epitopes by utilizing reverse vaccinology approaches. Four vaccine designs were formulated using the selected B- and T-cell epitopes coupled with appropriate linkers and adjuvant sequences capable of inducing potent immune responses. The HLA allele population coverage of the T-cell epitopes selected for vaccine construction was also analyzed. The V2 constructs were top-ranked and selected for further analysis on the basis of immunological, physicochemical, and immune-receptor docking interactions and scores. Docking and molecular dynamic simulations confirmed the stability of construct V2 interactions with the host immune receptors. Immune simulation analysis anticipated the strong immune profile of the prioritized construct. In silico restriction cloning ensured the feasible cloning ability of the V2 construct in the expression system of E. coli strain K12. It is anticipated that the designed vaccine construct may be safe, effective, and able to elicit strong immune responses against Y. pestis infections and may, therefore, merit investigation using in vitro and in vivo assays.
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Affiliation(s)
- Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | | | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree 47150, Pakistan
| | - Iqra Ahmad
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Muhammad Tayyab
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture Peshawar, Pakistan
| | - Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | | | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan.
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10
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Lê-Bury P, Echenique-Rivera H, Pizarro-Cerdá J, Dussurget O. Determinants of bacterial survival and proliferation in blood. FEMS Microbiol Rev 2024; 48:fuae013. [PMID: 38734892 PMCID: PMC11163986 DOI: 10.1093/femsre/fuae013] [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: 11/06/2023] [Revised: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 05/13/2024] Open
Abstract
Bloodstream infection is a major public health concern associated with high mortality and high healthcare costs worldwide. Bacteremia can trigger fatal sepsis whose prevention, diagnosis, and management have been recognized as a global health priority by the World Health Organization. Additionally, infection control is increasingly threatened by antimicrobial resistance, which is the focus of global action plans in the framework of a One Health response. In-depth knowledge of the infection process is needed to develop efficient preventive and therapeutic measures. The pathogenesis of bloodstream infection is a dynamic process resulting from the invasion of the vascular system by bacteria, which finely regulate their metabolic pathways and virulence factors to overcome the blood immune defenses and proliferate. In this review, we highlight our current understanding of determinants of bacterial survival and proliferation in the bloodstream and discuss their interactions with the molecular and cellular components of blood.
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Affiliation(s)
- Pierre Lê-Bury
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Autoimmune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), 18 route du Panorama, 92260 Fontenay-aux-Roses, France
| | - Hebert Echenique-Rivera
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-146, 28 rue du Dr Roux, 75015 Paris, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
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11
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Guo J, Zhong Y, Wang Y, Liu P, Jin H, Wang Y, Shi L, Wang P, Li W. Phylogenetic Relationships and Evolution of the Genus Eganvirus (186-Type) Yersinia pestis Bacteriophages. Viruses 2024; 16:748. [PMID: 38793629 PMCID: PMC11126057 DOI: 10.3390/v16050748] [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: 03/18/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Plague is an endemic infectious disease caused by Yersinia pestis. In this study, we isolated fourteen phages with similar sequence arrangements to phage 186; these phages exhibited different lytic abilities in Enterobacteriaceae strains. To illustrate the phylogenetic relationships and evolutionary relationships between previously designated 186-type phages, we analysed the complete sequences and important genes of the phages, including whole-genome average nucleotide identity (ANI) and collinearity comparison, evolutionary analysis of four conserved structural genes (V, T, R, and Q genes), and analysis of the regulatory genes (cI, apl, and cII) and integrase gene (int). Phylogenetic analysis revealed that thirteen of the newly isolated phages belong to the genus Eganvirus and one belongs to the genus Felsduovirus in the family Peduoviridae, and these Eganvirus phages can be roughly clustered into three subgroups. The topological relationships exhibited by the whole-genome and structural genes seemed similar and stable, while the regulatory genes presented different topological relationships with the structural genes, and these results indicated that there was some homologous recombination in the regulatory genes. These newly isolated 186-type phages were mostly isolated from dogs, suggesting that the resistance of Canidae to Y. pestis infection may be related to the wide distribution of phages with lytic capability.
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Affiliation(s)
- Jin Guo
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Youhong Zhong
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Yiting Wang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Pan Liu
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Haixiao Jin
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Yumeng Wang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Liyuan Shi
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Peng Wang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
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12
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Oakley R, Hedrich N, Walker A, Dinkita HM, Tschopp R, Abongomera C, Paris DH. Status of zoonotic disease research in refugees, asylum seekers and internally displaced people, globally: A scoping review of forty clinically important zoonotic pathogens. PLoS Negl Trop Dis 2024; 18:e0012164. [PMID: 38768252 PMCID: PMC11142688 DOI: 10.1371/journal.pntd.0012164] [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: 06/27/2023] [Revised: 05/31/2024] [Accepted: 04/23/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND At the end of 2022, there were over 108 million forcibly displaced people globally, including refugees, asylum seekers (AS) and internally displaced people (IDPs). Forced migration increases the risk of infectious disease transmission, and zoonotic pathogens account for 61% of emerging and re-emerging infectious diseases. Zoonoses create a high burden of disease and have the potential to cause large-scale outbreaks. This scoping review aimed to assess the state of research on a range of clinically relevant zoonotic pathogens in displaced populations in order to identify the gaps in literature and guide future research. METHODOLOGY / PRINCIPAL FINDINGS Literature was systematically searched to identify original research related to 40 selected zoonotic pathogens of interest in refugees, AS and IDPs. We included only peer-reviewed original research in English, with no publication date restrictions. Demographic data, migration pathways, health factors, associated outbreaks, predictive factors and preventative measures were extracted and synthesized. We identified 4,295 articles, of which 347 were included; dates of publications ranged from 1937 to 2022. Refugees were the most common population investigated (75%). Migration pathways of displaced populations increased over time towards a more complex web, involving migration in dual directions. The most frequent pathogen investigated was Schistosoma spp. (n = 99 articles). Disease outbreaks were reported in 46 publications (13.3%), with viruses being the most commonly reported pathogen type. Limited access to hygiene/sanitation, crowding and refugee status were the most commonly discussed predictors of infection. Vaccination/prophylaxis drug administration, surveillance/screening and improved hygiene/sanitation were the most commonly discussed preventative measures. CONCLUSIONS / SIGNIFICANCE The current research on zoonoses in displaced populations displays gaps in the spectrum of pathogens studied, as well as in the (sub)populations investigated. Future studies should be more inclusive of One Health approaches to adequately investigate the impact of zoonotic pathogens and identify transmission pathways as a basis for designing interventions for displaced populations.
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Affiliation(s)
- Regina Oakley
- Department of Medicine, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Nadja Hedrich
- Epidemiology, Biostatistics and Prevention Institute, University of Zürich, Zürich, Switzerland
| | - Alexandra Walker
- Department of Medicine, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Rea Tschopp
- University of Basel, Basel, Switzerland
- One Health Division, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Charles Abongomera
- Department of Medicine, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniel H. Paris
- Department of Medicine, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
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13
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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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14
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Galloway DR, Li J, Nguyen NX, Falkenberg FW, Henning L, Krile R, Chou YL, Herron JN, Hale JS, Williamson ED. Co-formulation of the rF1V plague vaccine with depot-formulated cytokines enhances immunogenicity and efficacy to elicit protective responses against aerosol challenge in mice. Front Immunol 2024; 15:1277526. [PMID: 38605961 PMCID: PMC11007139 DOI: 10.3389/fimmu.2024.1277526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/05/2024] [Indexed: 04/13/2024] Open
Abstract
This study evaluated a depot-formulated cytokine-based adjuvant to improve the efficacy of the recombinant F1V (rF1V) plague vaccine and examined the protective response following aerosol challenge in a murine model. The results of this study showed that co-formulation of the Alhydrogel-adsorbed rF1V plague fusion vaccine with the depot-formulated cytokines recombinant human interleukin 2 (rhuIL-2) and/or recombinant murine granulocyte macrophage colony-stimulating factor (rmGM-CSF) significantly enhances immunogenicity and significant protection at lower antigen doses against a lethal aerosol challenge. These results provide additional support for the co-application of the depot-formulated IL-2 and/or GM-CSF cytokines to enhance vaccine efficacy.
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Affiliation(s)
- Darrell R. Galloway
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT, United States
| | - Jiahui Li
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT, United States
| | - Nguyen X. Nguyen
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | | | - Lisa Henning
- Battelle Biomedical Research Center, Columbus, OH, United States
| | - Robert Krile
- Battelle Biomedical Research Center, Columbus, OH, United States
| | - Ying-Liang Chou
- Battelle Biomedical Research Center, Columbus, OH, United States
| | - James N. Herron
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT, United States
| | - J. Scott Hale
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - E. Diane Williamson
- Chemical Biological Radiological Division, Defense Science and Technology Laboratory (DSTL), Porton Down, Salisbury, United Kingdom
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15
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Rocha IV, Bezerra MF, Sobreira M, Leal NC, de Almeida AMP. Lyophilization for bacteria preservation: a promising approach for Yersinia pestis strains from an unique collection in Brazil (Fiocruz-CYP). Antonie Van Leeuwenhoek 2024; 117:61. [PMID: 38520511 DOI: 10.1007/s10482-024-01949-x] [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: 08/30/2023] [Accepted: 02/12/2024] [Indexed: 03/25/2024]
Abstract
Yersinia pestis, the causative agent of plague, is a highly virulent bacterium that poses a significant threat to human health. Preserving this bacterium in a viable state is crucial for research and diagnostic purposes. This paper presents and evaluates a simple lyophilization protocol for the long-term storage of Y. pestis strains from Fiocruz-CYP, aiming to explore its impact on viability and long-term stability, while replacing the currently used methodologies. The lyophilization tests were conducted using the non-virulent Y. pestis strain EV76, subjected to the lyophilization process under vacuum conditions. Viability assessment was performed to evaluate the effects of lyophilization and storage conditions on Y. pestis under multiple temperature conditions (- 80 °C, - 20 °C, 4-8 °C and room temperature). The lyophilization protocol employed in this study consistently demonstrated its efficacy in maintaining high viability rates for Y. pestis samples in a up to one year follow-up. The storage temperature that consistently exhibited the highest recovery rates was - 80 °C, followed by - 20 °C and 4-8 °C. Microscopic analysis of the post-lyophilized cultures revealed preserved morphological features, consistent with viable bacteria. The high viability rates observed in the preserved samples indicate the successful preservation of Y. pestis using this protocol. Overall, the presented lyophilization protocol provides a valuable tool for the long-term storage of Y. pestis, offering stability, viability, and functionality. By refining the currently used methods of lyophilization, this protocol can improve long-term preservation for Y. pestis strains collections, facilitating research efforts, diagnostic procedures, and the development of preventive and therapeutic strategies against plague.
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Affiliation(s)
- Igor Vasconcelos Rocha
- Department of Microbiology, Aggeu Magalhães Institute - IAM, Oswaldo Cruz Foundation - Fiocruz-PE, Recife, Pernambuco, Brazil.
| | - Matheus Filgueira Bezerra
- Department of Microbiology, Aggeu Magalhães Institute - IAM, Oswaldo Cruz Foundation - Fiocruz-PE, Recife, Pernambuco, Brazil
| | - Marise Sobreira
- Department of Microbiology, Aggeu Magalhães Institute - IAM, Oswaldo Cruz Foundation - Fiocruz-PE, Recife, Pernambuco, Brazil
| | - Nilma Cintra Leal
- Department of Microbiology, Aggeu Magalhães Institute - IAM, Oswaldo Cruz Foundation - Fiocruz-PE, Recife, Pernambuco, Brazil
| | - Alzira Maria Paiva de Almeida
- Department of Microbiology, Aggeu Magalhães Institute - IAM, Oswaldo Cruz Foundation - Fiocruz-PE, Recife, Pernambuco, Brazil
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16
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Mikucki A, Kahler CM. Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis. Microorganisms 2023; 11:3005. [PMID: 38138149 PMCID: PMC10745880 DOI: 10.3390/microorganisms11123005] [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: 11/06/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored.
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Affiliation(s)
- August Mikucki
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
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17
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Suntsov VV. Molecular phylogenies of the plague microbe Yersinia pestis: an environmental assessment. AIMS Microbiol 2023; 9:712-723. [PMID: 38173967 PMCID: PMC10758575 DOI: 10.3934/microbiol.2023036] [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: 07/13/2023] [Revised: 09/26/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Two approaches are applied to studies of the phylogeny of the plague microbe Yersinia pestis, i.e., the reconstruction of its history: Molecular genetic (MG) and ecological (ECO). The MG approach dominates. Phylogenies created with MG and ECO methods are not congruent. MG conclusions contradict the known facts and patterns of ecology, biogeography, paleontology, etc. We discuss some obvious contradictions and inconsistencies and suggest that real phylogenies of the plague microbe can be constructed only on the basis of the integration of MG and ECO approaches.
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Affiliation(s)
- Victor V. Suntsov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow 119071, Russia
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18
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Warren ME, Pickett BE, Adams BJ, Villalva C, Applegate A, Robison RA. Comparative sequence analysis elucidates the evolutionary patterns of Yersinia pestis in New Mexico over thirty-two years. PeerJ 2023; 11:e16007. [PMID: 37780382 PMCID: PMC10541020 DOI: 10.7717/peerj.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/09/2023] [Indexed: 10/03/2023] Open
Abstract
Background Yersinia pestis, a Gram-negative bacterium, is the causative agent of plague. Y. pestis is a zoonotic pathogen that occasionally infects humans and became endemic in the western United States after spreading from California in 1899. Methods To better understand evolutionary patterns in Y. pestis from the southwestern United States, we sequenced and analyzed 22 novel genomes from New Mexico. Analytical methods included, assembly, multiple sequences alignment, phylogenetic tree reconstruction, genotype-phenotype correlation, and selection pressure. Results We identified four genes, including Yscp and locus tag YPO3944, which contained codons undergoing negative selection. We also observed 42 nucleotide sites displaying a statistically significant skew in the observed residue distribution based on the year of isolation. Overall, the three genes with the most statistically significant variations that associated with metadata for these isolates were sapA, fliC, and argD. Phylogenetic analyses point to a single introduction of Y. pestis into the United States with two subsequent, independent movements into New Mexico. Taken together, these analyses shed light on the evolutionary history of this pathogen in the southwestern US over a focused time range and confirm a single origin and introduction into North America.
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Affiliation(s)
- Mary E. Warren
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Byron J. Adams
- Department of Biology, Brigham Young University, Provo, UT, United States
- Monte L. Bean Life Science Museum, Provo, UT, United States
| | - Crystal Villalva
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Alyssa Applegate
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
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19
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Abdel Z, Abdeliyev B, Yessimseit D, Begimbayeva E, Mussagalieva R. Natural foci of plague in Kazakhstan in the space-time continuum. Comp Immunol Microbiol Infect Dis 2023; 100:102025. [PMID: 37523875 DOI: 10.1016/j.cimid.2023.102025] [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] [Received: 06/01/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 08/02/2023]
Abstract
The relevance of the problem of the stated topic lies in the fact that the causative agent of the plague infection demonstrates high survival while maintaining high virulence in the territories, which are enzootic in terms of the plague. The study aimed to investigate the geographic distribution and genetic diversity of the plague pathogen in endemic regions through molecular genetic research. The work included the results of laboratory studies of 3058 samples, including soil - 1154, burrow substrates - 549, the contents of the feeding chamber - 349, bone remains - 18, biological objects - 988 samples of sera and suspensions from carriers and vectors of plague infection collected from 14 autonomous plague foci of Kazakhstan for the period 2021-2022. The leading method in the study was a laboratory experiment, thanks to which, using a new advanced technology on a microbiological analyser VITEK 2 COMPACT 30, it was possible to study pathogenic and non-pathogenic strains of the genus Yersinia isolated during field experiment. As a result of experimental work, it was shown that during a long inter-epizootic period, the plague pathogen can persist in the soil in symbiosis with soil microorganisms, and in this area, it chooses soil with a low-quality index of 10 points, where soils with a low total microbial number and species landscape prevail.
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Affiliation(s)
- Ziyat Abdel
- Laboratory of Plague, Masgut Aikimbayev National Scientific Center for Especially Dangerous Infections of the Ministry of Healthcare of the Republic of Kazakhstan, Almaty, Republic of Kazakhstan
| | - Beck Abdeliyev
- Department of Express Diagnostics and Indication of Especially Dangerous Infections, Masgut Aikimbayev National Scientific Center for Especially Dangerous Infections of the Ministry of Healthcare of the Republic of Kazakhstan, Almaty, Republic of Kazakhstan.
| | - Duman Yessimseit
- Department of Express Diagnostics and Indication of Especially Dangerous Infections, Masgut Aikimbayev National Scientific Center for Especially Dangerous Infections of the Ministry of Healthcare of the Republic of Kazakhstan, Almaty, Republic of Kazakhstan
| | - Elmira Begimbayeva
- Department of the National and Working Collection of Microorganisms, Masgut Aikimbayev National Scientific Center for Especially Dangerous Infections of the Ministry of Healthcare of the Republic of Kazakhstan, Almaty, Republic of Kazakhstan
| | - Raikhan Mussagalieva
- Department of Organizational, Advisory and Methodological Work, Masgut Aikimbayev National Scientific Center for Especially Dangerous Infections of the Ministry of Healthcare of the Republic of Kazakhstan, Almaty, Republic of Kazakhstan
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20
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Ali H, Samad A, Ajmal A, Ali A, Ali I, Danial M, Kamal M, Ullah M, Ullah R, Kalim M. Identification of Drug Targets and Their Inhibitors in Yersinia pestis Strain 91001 through Subtractive Genomics, Machine Learning, and MD Simulation Approaches. Pharmaceuticals (Basel) 2023; 16:1124. [PMID: 37631039 PMCID: PMC10459760 DOI: 10.3390/ph16081124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Yersinia pestis, the causative agent of plague, is a Gram-negative bacterium. If the plague is not properly treated it can cause rapid death of the host. Bubonic, pneumonic, and septicemic are the three types of plague described. Bubonic plague can progress to septicemic plague, if not diagnosed and treated on time. The mortality rate of pneumonic and septicemic plague is quite high. The symptom-defining disease is the bubo, which is a painful lymph node swelling. Almost 50% of bubonic plague leads to sepsis and death if not treated immediately with antibiotics. The host immune response is slow as compared to other bacterial infections. Clinical isolates of Yersinia pestis revealed resistance to many antibiotics such as tetracycline, spectinomycin, kanamycin, streptomycin, minocycline, chloramphenicol, and sulfonamides. Drug discovery is a time-consuming process. It always takes ten to fifteen years to bring a single drug to the market. In this regard, in silico subtractive proteomics is an accurate, rapid, and cost-effective approach for the discovery of drug targets. An ideal drug target must be essential to the pathogen's survival and must be absent in the host. Machine learning approaches are more accurate as compared to traditional virtual screening. In this study, k-nearest neighbor (kNN) and support vector machine (SVM) were used to predict the active hits against the beta-ketoacyl-ACP synthase III drug target predicted by the subtractive genomics approach. Among the 1012 compounds of the South African Natural Products database, 11 hits were predicted as active. Further, the active hits were docked against the active site of beta-ketoacyl-ACP synthase III. Out of the total 11 active hits, the 3 lowest docking score hits that showed strong interaction with the drug target were shortlisted along with the standard drug and were simulated for 100 ns. The MD simulation revealed that all the shortlisted compounds display stable behavior and the compounds formed stable complexes with the drug target. These compounds may have the potential to inhibit the beta-ketoacyl-ACP synthase III drug target and can help to combat Yersinia pestis-related infections. The dataset and the source codes are freely available on GitHub.
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Affiliation(s)
- Hamid Ali
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 44000, Pakistan
| | - Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan; (A.S.); (A.A.); (M.D.); (M.K.)
| | - Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan; (A.S.); (A.A.); (M.D.); (M.K.)
| | - Amjad Ali
- Faculty of Biological Sciences, Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Ijaz Ali
- Centre for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, Hawally 32093, Kuwait;
| | - Muhammad Danial
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan; (A.S.); (A.A.); (M.D.); (M.K.)
| | - Masroor Kamal
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan; (A.S.); (A.A.); (M.D.); (M.K.)
| | - Midrar Ullah
- Department of Biotechnology, Shaheed Benazir Bhutto University Sheringal, Dir Upper 18050, Pakistan;
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy King Saud University, Riyadh 11451, Saudi Arabia;
| | - Muhammad Kalim
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA;
- Houston Methodist Cancer Center/Weill Cornel Medicine, Houston, TX 77030, USA
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21
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Pitta JLDLP, Bezerra MF, Fernandes DLRDS, de Block T, Novaes ADS, de Almeida AMP, Rezende AM. Genomic Analysis of Yersinia pestis Strains from Brazil: Search for Virulence Factors and Association with Epidemiological Data. Pathogens 2023; 12:991. [PMID: 37623951 PMCID: PMC10459997 DOI: 10.3390/pathogens12080991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/13/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023] Open
Abstract
Yersinia pestis, the etiological agent of the plague, is considered a genetically homogeneous species. Brazil is currently in a period of epidemiological silence but plague antibodies are still detected in sentinel animals, suggesting disease activity in the sylvatic cycle. The present study deployed an in silico approach to analyze virulence factors among 407 Brazilian genomes of Y. pestis belonging to the Fiocruz Collection (1966-1997). The pangenome analysis associated several known virulence factors of Y. pestis in clades according to the presence or absence of genes. Four main strain clades (C, E, G, and H) exhibited the absence of various virulence genes. Notably, clade G displayed the highest number of absent genes, while clade E showed a significant absence of genes related to the T6SS secretion system and clade H predominantly demonstrated the absence of plasmid-related genes. These results suggest attenuation of virulence in these strains over time. The cgMLST analysis associated genomic and epidemiological data highlighting evolutionary patterns related to the isolation years and outbreaks of Y. pestis in Brazil. Thus, the results contribute to the understanding of the genetic diversity and virulence within Y. pestis and the potential for utilizing genomic data in epidemiological investigations.
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Affiliation(s)
- João Luiz de Lemos Padilha Pitta
- Microbiology Department of Aggeu Magalhães Institute—FIOCRUZ PE, Recife 50740-465, PE, Brazil; (M.F.B.); (D.L.R.d.S.F.); (A.M.P.d.A.)
- Bioinformatics Platform of Aggeu Magalhães Institute—FIOCRUZ PE, Recife 50740-465, PE, Brazil
| | - Matheus Filgueira Bezerra
- Microbiology Department of Aggeu Magalhães Institute—FIOCRUZ PE, Recife 50740-465, PE, Brazil; (M.F.B.); (D.L.R.d.S.F.); (A.M.P.d.A.)
| | | | - Tessa de Block
- Department of Clinical Sciences—Institute of Tropical Medicine, 2000 Antwerp, Belgium;
| | - Ane de Souza Novaes
- Department of Biological Sciences—Federal University of Vale do São Francisco—UNIVASF, Petrolina 56300-000, PE, Brazil;
| | - Alzira Maria Paiva de Almeida
- Microbiology Department of Aggeu Magalhães Institute—FIOCRUZ PE, Recife 50740-465, PE, Brazil; (M.F.B.); (D.L.R.d.S.F.); (A.M.P.d.A.)
| | - Antonio Mauro Rezende
- Microbiology Department of Aggeu Magalhães Institute—FIOCRUZ PE, Recife 50740-465, PE, Brazil; (M.F.B.); (D.L.R.d.S.F.); (A.M.P.d.A.)
- Bioinformatics Platform of Aggeu Magalhães Institute—FIOCRUZ PE, Recife 50740-465, PE, Brazil
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22
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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 PMCID: PMC10354491 DOI: 10.1098/rspb.2023.0622] [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: 05/15/2023] [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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23
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Kambouris ME, Patrinos GP, Velegraki A, Manoussopoulos Y. Historical microbiology: researching past bioevents by integrating scholarship (re)sources with paleomicrobiology assets. Future Microbiol 2023; 18:681-693. [PMID: 37584528 DOI: 10.2217/fmb-2023-0031] [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: 08/17/2023] Open
Abstract
The analysis of past epidemics and pandemics, either spontaneous or of human origin, may revise the physical history of microbiota and create a temporal context in our understanding regarding pathogen attributes like virulence, evolution, transmission and disease dynamics. The data of high-tech scientific methods seem reliable, but their interpretation may still be biased when tackling events of the distant past. Such endeavors should be adjusted to other cognitive resources including historical accounts reporting the events of interest and references in alien medical cultures and terminologies; the latter may contextualize them differently from current practices. Thus 'historical microbiology' emerges. Validating such resources requires utmost care, as these may be susceptible to different biases regarding the interpretation of facts and phenomena; biases partly due to methodological limitations.
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Affiliation(s)
| | - George P Patrinos
- Department of Pharmacy, University of Patras, Rio Patras, 26504, Greece
- Department of Genetics & Genomics, College of Medicine & Health Sciences & Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | | | - Yiannis Manoussopoulos
- Plant Protection Division of Patras, Institute of Industrial & Forage Plants, NEO & Amerikis, Patras, 26004, Greece
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24
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Erly B, Fleck-Derderian S, Cooley KM, Meyer-Lee K, House J, VinHatton E, Nelson CA. A Perilous Combination: Streptococcus Coinfection with Human Plague-Report of Two Cases and Review of the Literature, 1937-2022. Vector Borne Zoonotic Dis 2023; 23:371-377. [PMID: 37352427 PMCID: PMC10512700 DOI: 10.1089/vbz.2022.0084] [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: 06/25/2023] Open
Abstract
Background: Plague in humans and animals is caused by Yersinia pestis, a zoonotic gram-negative bacterium endemic in certain regions of Asia, Africa, and the United States. Coinfection with both Y. pestis and Streptococci species has been anecdotally reported in humans and associated with severe and rapidly fatal disease. Methods: This report presents two cases of patients who died following Y. pestis and Streptococcus coinfection. Additional cases of previously published Y. pestis-Streptococcus coinfection were identified and reviewed using a search of electronic databases. Results: The first case patient developed cough and dyspnea following 4 days of fever, malaise, and back pain and died before receiving medical care. Postmortem blood cultures were positive for Y. pestis, Streptococcus pyogenes, and Streptococcus dysgalactiae. The second case patient was hospitalized with fever, vomiting, diarrhea, and dyspnea and died of sepsis and respiratory failure on the day of admission. Y. pestis and Streptococcus pneumoniae were isolated from blood cultures drawn on admission. Seven additional cases of Y. pestis and Streptococcus coinfection were identified, dating between 1948 and 2009. These patients were healthy overall before their illness, with ages ranging from 9 to 60 years. The majority of patients had primary bubonic plague with associated pneumonia or septicemia. None of the patients who died received timely antimicrobial therapy directed against gram-negative pathogens. In every case but one, an occupational or environmental risk factor for plague was later identified. Conclusion: Y. pestis infection begins with a pre-inflammatory phase, during which Y. pestis and other pathogens can rapidly proliferate. Streptococci, which are frequently asymptomatic colonizers, may become invasive in this environment, leading to coinfection. The challenges of diagnosing Y. pestis in the context of coinfection may delay effective treatment. This case series and literature review illustrate the importance of clinicians remaining alert to environmental and occupational exposures in patients presenting with an infectious syndrome, especially in those who have an unexpectedly severe clinical presentation.
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Affiliation(s)
- Brian Erly
- Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Shannon Fleck-Derderian
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Katharine M. Cooley
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Kim Meyer-Lee
- Larimer County Department of Health and Environment, Fort Collins, Colorado, USA
| | - Jennifer House
- Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | | | - Christina A. Nelson
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
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25
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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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26
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Suntsov VV. Parallelism in Speciation and Intraspecific Diversification of the Plague Microbe Yersinia pestis. BIOL BULL+ 2023; 50:103-109. [PMID: 37251308 PMCID: PMC10196287 DOI: 10.1134/s1062359023010120] [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: 03/09/2022] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 05/31/2023]
Abstract
Modern "molecular genetic (MG) phylogenies" of the plague microbe Yersinia pestis, built on models of neutral evolution using statistical methods of phylogenetic analysis, contradict numerous obvious environmental (ECO) patterns and are not consistent with the concept of adaptatiogenesis. The reason for the discrepancy between MG and ECO phylogenies is seen in the underestimation by the MG approach of parallelisms in the processes of speciation and intraspecific diversification of the plague microbe. ECO methods showed the parallel tritope (almost) simultaneous speciation of three primary genovariants (populations, subspecies) Y. pestis 2.ANT3, 3.ANT2, and 4.ANT1 in three geographical populations of the Mongolian marmot (Marmota sibirica), which in the MG approach is mistaken for polytomy ("Big Bang"), caused by unknown natural phenomena on the eve of the first pandemic (Justinian's plague, 6th-8th centuries AD). The discrepancy between the MG and ECO interpretations of the evolution of intraspecifically-derived phylogenetic subbranches 0.PE and 2.MED is also associated with parallel evolutionary processes in independent lines, based on genovariants 2.ANT3, 3.ANT2, and 4.ANT1. The independence of these phylogenetic lines and parallelisms of sub-branches 0.PE and 2.MED associated with them are not taken into account in the MG approach. The prospect of creating a real phylogenetic tree for Y. pestis depends on a creative synthesis of the two approaches-MG and ECO.
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Affiliation(s)
- V. V. Suntsov
- Severtsov Institute of Problems of Ecology and Evolution, Moscow, 119071 Russia
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27
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Clavel P, Louis L, Sarkissian CD, Thèves C, Gillet C, Chauvey L, Tressières G, Schiavinato S, Calvière-Tonasso L, Telmon N, Clavel B, Jonvel R, Tzortzis S, Bouniol L, Fémolant JM, Klunk J, Poinar H, Signoli M, Costedoat C, Spyrou MA, Seguin-Orlando A, Orlando L. Improving the extraction of ancient Yersinia pestis genomes from the dental pulp. iScience 2023; 26:106787. [PMID: 37250315 PMCID: PMC10214834 DOI: 10.1016/j.isci.2023.106787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/11/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17th and 18th centuries Common Era.
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Affiliation(s)
- Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Lexane Louis
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Clio Der Sarkissian
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Catherine Thèves
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Claudia Gillet
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Gaétan Tressières
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Laure Calvière-Tonasso
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Norbert Telmon
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Benoît Clavel
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), CNRS-UMR7209, Muséum national d’histoire naturelle, 55 Rue Buffon, 75005 Paris, France
| | - Richard Jonvel
- Amiens Métropole Service Archéologie Préventive, 2 rue Colbert, 80000 Amiens, France
| | - Stéfan Tzortzis
- Service Régional de l’Archéologie, 21 allée Claude Forbin, 13100 Aix-en-Provence, France
| | - Laetitia Bouniol
- Service archéologique de la ville de Beauvais, 1 rue Desgroux, 60021 Beauvais, France
| | - Jean-Marc Fémolant
- Service archéologique de la ville de Beauvais, 1 rue Desgroux, 60021 Beauvais, France
| | | | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, ON L8S 4L9, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S, 4L9, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Michel Signoli
- Aix-Marseille Université, CNRS, EFS, ADES, 13005 Marseille, France
| | | | - Maria A. Spyrou
- Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Andaine Seguin-Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
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28
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Chaaban T, Mohsen Y, Ezzeddine Z, Ghssein G. Overview of Yersinia pestis Metallophores: Yersiniabactin and Yersinopine. BIOLOGY 2023; 12:598. [PMID: 37106798 PMCID: PMC10136090 DOI: 10.3390/biology12040598] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
The pathogenic anaerobic bacteria Yersinia pestis (Y. pestis), which is well known as the plague causative agent, has the ability to escape or inhibit innate immune system responses, which can result in host death even before the activation of adaptive responses. Bites from infected fleas in nature transmit Y. pestis between mammalian hosts causing bubonic plague. It was recognized that a host's ability to retain iron is essential in fighting invading pathogens. To proliferate during infection, Y. pestis, like most bacteria, has various iron transporters that enable it to acquire iron from its hosts. The siderophore-dependent iron transport system was found to be crucial for the pathogenesis of this bacterium. Siderophores are low-molecular-weight metabolites with a high affinity for Fe3+. These compounds are produced in the surrounding environment to chelate iron. The siderophore secreted by Y. pestis is yersiniabactin (Ybt). Another metallophore produced by this bacterium, yersinopine, is of the opine type and shows similarities with both staphylopine and pseudopaline produced by Staphylococcus aureus and Pseudomonas aeruginosa, respectively. This paper sheds light on the most important aspects of the two Y. pestis metallophores as well as aerobactin a siderophore no longer secreted by this bacterium due to frameshift mutation in its genome.
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Affiliation(s)
- Taghrid Chaaban
- Nursing Sciences Department, Faculty of Public Health, Islamic University of Lebanon, Khalde P.O. Box 30014, Lebanon
- Nursing Sciences Research Chair, Laboratory Educations and Health Practices (LEPS), (EA 3412), UFR SMBH, University Paris 13, Sorbonne Paris Cite, F-93017 Bobigny, France
| | - Yehya Mohsen
- Department of Medical Laboratory Technology, College of Health and Medical Technologies, Al-Ayen University, Nasiriyah 64001, Iraq
| | - Zeinab Ezzeddine
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
- Faculty of Sciences V, Lebanese University, Nabatieh 1700, Lebanon
| | - Ghassan Ghssein
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
- Faculty of Sciences V, Lebanese University, Nabatieh 1700, Lebanon
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29
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Guo XP, Yan HQ, Yang W, Yin Z, Vadyvaloo V, Zhou D, Sun YC. A frameshift in Yersinia pestis rcsD alters canonical Rcs signalling to preserve flea-mammal plague transmission cycles. eLife 2023; 12:e83946. [PMID: 37010269 PMCID: PMC10191623 DOI: 10.7554/elife.83946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/02/2023] [Indexed: 04/04/2023] Open
Abstract
Multiple genetic changes in the enteric pathogen Yersinia pseudotuberculosis have driven the emergence of Yesinia pestis, the arthropod-borne, etiological agent of plague. These include developing the capacity for biofilm-dependent blockage of the flea foregut to enable transmission by flea bite. Previously, we showed that pseudogenization of rcsA, encoding a component of the Rcs signalling pathway, is an important evolutionary step facilitating Y. pestis flea-borne transmission. Additionally, rcsD, another important gene in the Rcs system, harbours a frameshift mutation. Here, we demonstrated that this rcsD mutation resulted in production of a small protein composing the C-terminal RcsD histidine-phosphotransferase domain (designated RcsD-Hpt) and full-length RcsD. Genetic analysis revealed that the rcsD frameshift mutation followed the emergence of rcsA pseudogenization. It further altered the canonical Rcs phosphorylation signal cascade, fine-tuning biofilm production to be conducive with retention of the pgm locus in modern lineages of Y. pestis. Taken together, our findings suggest that a frameshift mutation in rcsD is an important evolutionary step that fine-tuned biofilm production to ensure perpetuation of flea-mammal plague transmission cycles.
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Affiliation(s)
- Xiao-Peng Guo
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hai-Qin Yan
- Department of Basic Medical Sciences, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical CollegeBengbuChina
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Viveka Vadyvaloo
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yi-Cheng Sun
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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30
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Kambouris ME. Global Catastrophic Biological Risks in the Post-COVID-19 World: Time to Act Is Now. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:153-170. [PMID: 36946656 DOI: 10.1089/omi.2022.0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Global Catastrophic Biological Risks (GCBRs) refer to events with biological agents that can result in unprecedented or catastrophic disasters that are beyond the collective response-abilities of nation-states and the existing governance instruments of global governance and international affairs. This article offers a narrative review, with a view to new hypothesis development to rethink GCBRs after coronavirus disease 2019 (COVID-19) so as to better prepare for future pandemics and ecological crises, if not to completely prevent them. To determine GCBRs' spatiotemporal contexts, define causality, impacts, differentiate the risk and the event, would improve theorization of GCBRs compared to the impact-centric current definition. This could in turn lead to improvements in preparedness, response, allocation of resources, and possibly deterrence, while actively discouraging lack of due biosecurity diligence. Critical governance of GCBRs in ways that unpack the political power-related dimensions could be particularly valuable because the future global catastrophic events might be different in quality, scale, and actors. Theorization of GCBRs remains an important task going forward in the 21st century in ways that draw from experiences in the field, while integrating flexibility, versatility, and critically informed responses to GCBRs.
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Kolodziejek AM, Bearden SW, Maes S, Montenieri JM, Gage KL, Hovde CJ, Minnich SA. Yersinia pestis Δ ail Mutants Are Not Susceptible to Human Complement Bactericidal Activity in the Flea. Appl Environ Microbiol 2023; 89:e0124422. [PMID: 36744930 PMCID: PMC9973026 DOI: 10.1128/aem.01244-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/09/2023] [Indexed: 02/07/2023] Open
Abstract
Ail confers serum resistance in humans and is a critical virulence factor of Y. pestis, the causative agent of plague. Here, the contribution of Ail for Y. pestis survival in the flea vector was examined. Rat or human but not mouse sera were bactericidal against a Y. pestis Δail mutant at 28°C in vitro. Complement components deposited rapidly on the Y. pestis surface as measured by immunofluorescent microscopy. Ail reduced the amount of active C3b on the Y. pestis surface. Human sera retained bactericidal activity against a Y. pestis Δail mutant in the presence of mouse sera. However, in the flea vector, the serum protective properties of Ail were not required. Flea colonization studies using murine sera and Y. pestis KIM6+ wild type, a Δail mutant, and the Δail/ail+ control showed no differences in bacterial prevalence or numbers during the early stage of flea colonization. Similarly, flea studies with human blood showed Ail was not required for serum resistance. Finally, a variant of Ail (AilF100V E108_S109insS) from a human serum-sensitive Y. pestis subsp. microtus bv. Caucasica 1146 conferred resistance to human complement when expressed in the Y. pestis KIM6+ Δail mutant. This indicated that Ail activity was somehow blocked, most likely by lipooligosaccharide, in this serum sensitive strain. IMPORTANCE This work contributes to our understanding of how highly virulent Y. pestis evolved from its innocuous enteric predecessor. Among identified virulence factors is the attachment invasion locus protein, Ail, that is required to protect Y. pestis from serum complement in all mammals tested except mice. Murine sera is not bactericidal. In this study, we asked, is bactericidal sera from humans active in Y. pestis colonized fleas? We found it was not. The importance of this observation is that it identifies a protective niche for the growth of serum sensitive and nonsensitive Y. pestis strains.
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Affiliation(s)
- Anna M. Kolodziejek
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, USA
| | - Scott W. Bearden
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Sarah Maes
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - John M. Montenieri
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Kenneth L. Gage
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Carolyn J. Hovde
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, USA
| | - Scott A. Minnich
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, USA
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Lê-Bury P, Druart K, Savin C, Lechat P, Mas Fiol G, Matondo M, Bécavin C, Dussurget O, Pizarro-Cerdá J. Yersiniomics, a Multi-Omics Interactive Database for Yersinia Species. Microbiol Spectr 2023; 11:e0382622. [PMID: 36847572 PMCID: PMC10100798 DOI: 10.1128/spectrum.03826-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/26/2023] [Indexed: 03/01/2023] Open
Abstract
The genus Yersinia includes a large variety of nonpathogenic and life-threatening pathogenic bacteria, which cause a broad spectrum of diseases in humans and animals, such as plague, enteritis, Far East scarlet-like fever (FESLF), and enteric redmouth disease. Like most clinically relevant microorganisms, Yersinia spp. are currently subjected to intense multi-omics investigations whose numbers have increased extensively in recent years, generating massive amounts of data useful for diagnostic and therapeutic developments. The lack of a simple and centralized way to exploit these data led us to design Yersiniomics, a web-based platform allowing straightforward analysis of Yersinia omics data. Yersiniomics contains a curated multi-omics database at its core, gathering 200 genomic, 317 transcriptomic, and 62 proteomic data sets for Yersinia species. It integrates genomic, transcriptomic, and proteomic browsers, a genome viewer, and a heatmap viewer to navigate within genomes and experimental conditions. For streamlined access to structural and functional properties, it directly links each gene to GenBank, the Kyoto Encyclopedia of Genes and Genomes (KEGG), UniProt, InterPro, IntAct, and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and each experiment to Gene Expression Omnibus (GEO), the European Nucleotide Archive (ENA), or the Proteomics Identifications Database (PRIDE). Yersiniomics provides a powerful tool for microbiologists to assist with investigations ranging from specific gene studies to systems biology studies. IMPORTANCE The expanding genus Yersinia is composed of multiple nonpathogenic species and a few pathogenic species, including the deadly etiologic agent of plague, Yersinia pestis. In 2 decades, the number of genomic, transcriptomic, and proteomic studies on Yersinia grew massively, delivering a wealth of data. We developed Yersiniomics, an interactive web-based platform, to centralize and analyze omics data sets on Yersinia species. The platform allows user-friendly navigation between genomic data, expression data, and experimental conditions. Yersiniomics will be a valuable tool to microbiologists.
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Affiliation(s)
- Pierre Lê-Bury
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Karen Druart
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Mass Spectrometry for Biology Unit, Proteomic Platform, Paris, France
| | - Cyril Savin
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-140, Paris, France
| | - Pierre Lechat
- Institut Pasteur, Université Paris Cité, ALPS, Bioinformatic Hub, Paris, France
| | - Guillem Mas Fiol
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Mass Spectrometry for Biology Unit, Proteomic Platform, Paris, France
| | | | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-140, Paris, France
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Ma X, Zhang L, Ren Y, Yun H, Cui H, Li Q, Guo Y, Gao S, Zhang F, Wang A, Liang B. Molecular Mechanism of Chloramphenicol and Thiamphenicol Resistance Mediated by a Novel Oxidase, CmO, in Sphingomonadaceae. Appl Environ Microbiol 2023; 89:e0154722. [PMID: 36519886 PMCID: PMC9888274 DOI: 10.1128/aem.01547-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Antibiotic resistance mediated by bacterial enzyme inactivation plays a crucial role in the degradation of antibiotics in the environment. Chloramphenicol (CAP) resistance by enzymatic inactivation comprises nitro reduction, amide bond hydrolysis, and acetylation modification. However, the molecular mechanism of enzymatic oxidation of CAP remains unknown. Here, a novel oxidase gene, cmO, was identified and confirmed biochemically. The encoded CmO oxidase could catalyze the oxidation at the C-1' and C-3' positions of CAP and thiamphenicol (TAP) in Sphingobium sp. strain CAP-1. CmO is highly conserved in members of the family Sphingomonadaceae and shares the highest amino acid similarity of 41.05% with the biochemically identified glucose methanol choline (GMC) oxidoreductases. Molecular docking and site-directed mutagenesis analyses demonstrated that CAP was anchored inside the protein pocket of CmO with the hydrogen bonding of key residues glycine (G) 99, asparagine (N) 518, methionine (M) 474, and tyrosine (Y) 380. CAP sensitivity tests demonstrated that the acetyltransferase and CmO could enable a higher level of resistance to CAP than the amide bond-hydrolyzing esterase and nitroreductase. This study provides a better theoretical basis and a novel diagnostic gene for understanding and assessing the fate and resistance risk of CAP and TAP in the environment. IMPORTANCE Rising levels of antibiotic resistance are undermining ecological and human health as a result of the indiscriminate usage of antibiotics. Various resistance mechanisms have been characterized-for example, genes encoding proteins that degrade antibiotics-and yet, this requires further exploration. In this study, we report a novel gene encoding an oxidase involved in the inactivation of typical amphenicol antibiotics (chloramphenicol and thiamphenicol), and the molecular mechanism is elucidated. The findings provide novel data with which to understand the capabilities of bacteria to tackle antibiotic stress, as well as the complex function of enzymes in the contexts of antibiotic resistance development and antibiotic removal. The reported gene can be further employed as an indicator to monitor amphenicol's fate in the environment, thus benefiting risk assessment in this era of antibiotic resistance.
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Affiliation(s)
- Xiaodan Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
| | - Liying Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
| | - Yijun Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
| | - Hui Yun
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hanlin Cui
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Qian Li
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
| | - Yuanqiang Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Shuhong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
| | - Fengliang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, China
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Abstract
This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.
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Eroshenko GA, Balykova AN, Nikiforov KA, Krasnov YM, Kukleva LM, Naryshkina EA, Kuznetsov AA, Popov NV, Kutyrev VV. Retrospective analysis of dissemination of the 2.MED1 phylogenetic branch of Yersinia pestis in the Caucasus. PLoS One 2023; 18:e0283670. [PMID: 36989240 PMCID: PMC10057742 DOI: 10.1371/journal.pone.0283670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The 2.MED1 phylogenetic branch of Yersinia pestis of the medieval biovar became widespread in the Caspian Sea region, the Caucasus, and the Northern Aral Sea region in the 20th century, causing outbreaks and epizootics of plague there. Some of the formed natural foci of 2.MED1 still show epizootic activity and retain their epidemic potential. In this work, we carried out a phylogenetic analysis of 46 Y. pestis strains of the medieval biovar isolated in the Caucasus, the Caspian Sea, and the Northern Aral Sea regions during epidemic outbreaks and epizootics from 1922-2014. The obtained phylogenetic data, together with epidemiological and epizootological data accumulated over a period of about a hundred years, indicate the presence of two waves of penetration of the 2.MED1 branch into the Caucasus. The first occurred, apparently, in the first half of the 20th century as a result of the penetration of 2.MED1 from the foci of the Northern and North-Western Caspian Sea. The second wave was caused by the spread of 2.MED1 from the Northern Aral to the foci of the North-Western, Northern and Eastern Caspian Sea regions at the beginning of the second half of the 20th century, followed by introduction into the Pre-Caucasus and Transcaucasia. The rapid spread of 2.MED1 could be associated with the transfer of the pathogen by land and sea transport in the process of economic activity of the population.
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Affiliation(s)
- Galina A Eroshenko
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
| | - Alina N Balykova
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
| | - Konstantin A Nikiforov
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
| | - Yaroslav M Krasnov
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
| | - Lyubov M Kukleva
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
| | - Ekaterina A Naryshkina
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
| | - Alexander A Kuznetsov
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
| | - Nikolay V Popov
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
| | - Vladimir V Kutyrev
- Russian Research Anti-Plague Institute "Microbe", Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russian Federation
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Debnath SK, Debnath M, Srivastava R. Opportunistic etiological agents causing lung infections: emerging need to transform lung-targeted delivery. Heliyon 2022; 8:e12620. [PMID: 36619445 PMCID: PMC9816992 DOI: 10.1016/j.heliyon.2022.e12620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 09/03/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
Lung diseases continue to draw considerable attention from biomedical and public health care agencies. The lung with the largest epithelial surface area is continuously exposed to the external environment during exchanging gas. Therefore, the chances of respiratory disorders and lung infections are overgrowing. This review has covered promising and opportunistic etiologic agents responsible for lung infections. These pathogens infect the lungs either directly or indirectly. However, it is difficult to intervene in lung diseases using available oral or parenteral antimicrobial formulations. Many pieces of research have been done in the last two decades to improve inhalable antimicrobial formulations. However, very few have been approved for human use. This review article discusses the approved inhalable antimicrobial agents (AMAs) and identifies why pulmonary delivery is explored. Additionally, the basic anatomy of the respiratory system linked with barriers to AMA delivery has been discussed here. This review opens several new scopes for researchers to work on pulmonary medicines for specific diseases and bring more respiratory medication to market.
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Qi Z, Meng B, Wei X, Li X, Peng H, Li Y, Feng Q, Huang Y, Zhang Q, Xu X, Zhao H, Yang X, Wang C, Zhao X. Identification and characterization of P2-like bacteriophages of Yersinia pestis. Virus Res 2022; 322:198934. [PMID: 36169047 DOI: 10.1016/j.virusres.2022.198934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/09/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022]
Abstract
Yersinia pestis is the cause of plague, historically known as the "Black Death". Marmota himalayana in the Qinghai-Tibet Plateau (QTP) natural plague focus is the primary host in China. Although several phages originating from Y. pestis have been characterized. This is the first report of isolation of P2-like phages of Y. pestis from M. himalayana. In this study, the isolation and characterization of three P2-like phages of Y. pestis were reported, which were named as vB_YpM_22, vB_YpM_46 and vB_YpM_50. Comparative genome analysis revealed that vB_YpM_22, vB_YpM_46 and vB_YpM_50 are members of the nonlambdoid P2 family, and are highly similar and collinear with enterobacteriophage P2, plague diagnostic phage L-413C and enterobacteriophage fiAA91-ss. The role of LPS core structure of Y. pestis in the phages' receptor was pinpointed. The findings of this study contribute an advance in our current knowledge of Y. pestis phages and will also play a key role in understanding the evolution of Y. pestis phages.
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Affiliation(s)
- 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
| | - Biao Meng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China; Institute of Disease Control and Prevention, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xiao Wei
- Institute of Disease Control and Prevention, Chinese PLA Center for Disease Control and Prevention, Beijing, 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 Center for Disease Control and Prevention, Beijing, China
| | - Yan Li
- Institute of Disease Control and Prevention, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Qunling Feng
- PLA 63750 Military Hospital, Xi'an, Shaanxi, China
| | - Yanan Huang
- PLA 63750 Military Hospital, Xi'an, Shaanxi, 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 Center for Disease Control and Prevention, 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 Center for Disease Control and Prevention, Beijing, China.
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Li J, Gao J, Feng B, Jing Y. PlagueKD: a knowledge graph-based plague knowledge database. Database (Oxford) 2022; 2022:baac100. [PMID: 36412326 PMCID: PMC10161524 DOI: 10.1093/database/baac100] [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: 07/22/2022] [Revised: 10/17/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022]
Abstract
Plague has been confirmed as an extremely horrific international quarantine infectious disease attributed to Yersinia pestis. It has an extraordinarily high lethal rate that poses a serious hazard to human and animal lives. With the deepening of research, there has been a considerable amount of literature related to the plague that has never been systematically integrated. Indeed, it makes researchers time-consuming and laborious when they conduct some investigation. Accordingly, integrating and excavating plague-related knowledge from considerable literature takes on a critical significance. Moreover, a comprehensive plague knowledge base should be urgently built. To solve the above issues, the plague knowledge base is built for the first time. A database is built from the literature mining based on knowledge graph, which is capable of storing, retrieving, managing and accessing data. First, 5388 plague-related abstracts that were obtained automatically from PubMed are integrated, and plague entity dictionary and ontology knowledge base are constructed by using text mining technology. Second, the scattered plague-related knowledge is correlated through knowledge graph technology. A multifactor correlation knowledge graph centered on plague is formed, which contains 9633 nodes of 33 types (e.g. disease, gene, protein, species, symptom, treatment and geographic location), as well as 9466 association relations (e.g. disease-gene, gene-protein and disease-species). The Neo4j graph database is adopted to store and manage the relational data in the form of triple. Lastly, a plague knowledge base is built, which can successfully manage and visualize a large amount of structured plague-related data. This knowledge base almost provides an integrated and comprehensive plague-related knowledge. It should not only help researchers to better understand the complex pathogenesis and potential therapeutic approaches of plague but also take on a key significance to reference for exploring potential action mechanisms of corresponding drug candidates and the development of vaccine in the future. Furthermore, it is of great significance to promote the field of plague research. Researchers are enabled to acquire data more easily for more effective research. Database URL: http://39.104.28.169:18095/.
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Affiliation(s)
- Jin Li
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Erdos East Street No. 29, Hohhot 010011, China
- Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application of Agriculture and Animal Husbandry, Hohhot, Inner Mongolia Autonomous Region 010018, China
| | - Jing Gao
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Erdos East Street No. 29, Hohhot 010011, China
- Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application of Agriculture and Animal Husbandry, Hohhot, Inner Mongolia Autonomous Region 010018, China
| | - Baiyang Feng
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Erdos East Street No. 29, Hohhot 010011, China
- Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application of Agriculture and Animal Husbandry, Hohhot, Inner Mongolia Autonomous Region 010018, China
| | - Yi Jing
- Faculty of Science, University of New South Wales, Sydney, New Sales Wales 2020, Australia
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Suntsov VV. Ecological scenario of the plague microbe <i>Yersinia pestis</i> speciation underlying adequate molecular evolutionary model. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2022. [DOI: 10.15789/2220-7619-eso-1955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It is known that the psychrophilic pseudotuberculosis microbe serotype 1 (Y. pseudotuberculosis 0:1b) causing Far East scarlet-like fever (FESLF) an intestinal infection found in a wide range of invertebrates and vertebrates inhabiting cold regions in the Northern and Central Asia as well as Far East is direct ancestor of the plague causative agent Yersinia pestis. However, the mechanism of Y. pestis speciation remains poorly elucidated. Numerous Y. pestis phylogenies created by using molecular genetic (MG) technologies are largely contradictory, being not in line with reliable data obtained by natural science approaches (e.g., ecology, epizootology, biogeography, and paleontology), which disagree with current evolutionary doctrine (synthetic theory of evolution). The MG approach provides no definitive answer to the questions of where, when, how, and under what circumstances the species Y. pestis arose. One of the reasons for such situation might be due to inadequacy of using the molecular evolutionary model for Y. pestis phylogenetics. Knowledge of the life cycles for the ancestral pseudotuberculosis and derivative plague microbes as well as related unique environmental features allows to create a reliable ecological model for the plague microbe evolution to be further used for assessing patterns of molecular variability and building proper molecular model that might be accepted for MG-reconstruction of plague microbe history. According to the ecological model, the species Y. pestis was formed in a tritopic manner (almost) simultaneously from FESLF clones (populations) in the three geographical populations of the Mongolian marmot-tarbagan (Marmota sibirica) and the flea Oropsylla silantiewi parasitizing on it. The inducer of speciation was coupled to the last maximum (Sartan) cooling in Central Asia occurred 2215 thousand years ago. Soil cooling and deep freezing resulted in altered behavior of the marmot flea larvae with emergence of facultative hematophagy, which, in turn, led to a unique traumatic (compared to routine alimentary) infection route of sleeping marmots with FESLF and, as a result, a unique way of Y. pestis speciation. The molecular model should predict a Y. pestis peripatric tritope speciation, existing numerous parallelisms in intraspecific variability associated with tritope speciation, and the quantum principle of speciation in the highly variable heterothermic (heteroimmune) stressful marmot-flea (Marmota sibirica Oropsylla silantiewi) host-vector environment involving stress-induced mutagenesis. Such molecular model of evolution may be useful for improving molecular methodology of phylogenetic constructions for a wide range of parasitic microorganisms.
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<i>In silico</i> Research at the Stages of Designing Modern Means for Prevention of Plague (by the Example of Subunit Vaccines). PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2022. [DOI: 10.21055/0370-1069-2022-3-6-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The purpose of this review was to analyze the findings of domestic and foreign researchers on the development of modern drugs for the specific prevention of plague and to illustrate the possibilities of using bioinformatics analysis at the design stages to create an effective and safe vaccine. Work on the creation of an effective new-generation plague vaccine is hampered by several factors associated primarily with the presence of mechanisms of evasion from the immune system of the macroorganism, as well as a large number of pathogenicity determinants in the plague agent. Due to the development of approaches that are based on in silico studies, there is a progressive development of vaccine technologies oriented primarily to the use of the most important immunogens of the plague microbe (F1 and V antigen). Studies aimed at improving the antigenic properties of F1 and LcrV, as well as work on bioinformatic search and analysis of additional promising components to be included in the composition of subunit vaccines are considered as topical applications of bioinformatics data analysis in developing the tools for enhancing the effectiveness of protection through vaccination with subunit preparations.
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Galloway DR, Nguyen NX, Li J, Houston N, Gregersen G, Williamson ED, Falkenberg FW, Herron JN, Hale JS. The magnitude of the germinal center B cell and T follicular helper cell response predicts long-lasting antibody titers to plague vaccination. Front Immunol 2022; 13:1017385. [PMID: 36389793 PMCID: PMC9650111 DOI: 10.3389/fimmu.2022.1017385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/13/2022] [Indexed: 11/27/2022] Open
Abstract
The development of a safe and effective vaccine against Yersinia pestis, the causative organism for plague disease, remains an important global health priority. Studies have demonstrated effective immune-based protection against plague challenge that is induced by plague antigen subunit vaccination in an aqueous alhydrogel formulation; however, whether these candidate vaccines in this formulation and presentation, induce long-lasting immunological memory in the form of durable cellular and antibody recall responses has not been fully demonstrated. In this study, we analyzed germinal center T follicular helper and germinal center B cell responses following F1V and F1 + V plague subunit immunization of mice with vaccines formulated in various adjuvants. Our data demonstrate that recombinant plague protein immunization formulated with IL-2/GM-CSF cytokines bound to alhydrogel adjuvant drive an increase in the magnitude of the germinal center T follicular helper and germinal center B cell responses following primary immunization, compared to vaccines formulated with Alhydrogel adjuvant alone. In contrast, plague protein subunit immunization combined with CpG ODN bound to alhydrogel increased the magnitude and duration of the germinal center Tfh and B cell responses following booster immunization. Importantly, enhanced germinal center Tfh and B cell responses correlated with long-lasting and high F1V-specific antibody titers and more robust antibody recall responses to F1V re-exposure. These findings indicate that vaccine formulations that drive enhancement of the germinal center Tfh and B cell responses are critical for inducing durable plague-specific humoral immunity.
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Affiliation(s)
- Darrell R. Galloway
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT, United States
| | - Nguyen X. Nguyen
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Jiahui Li
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT, United States
| | - Nicholas Houston
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT, United States
| | - Gage Gregersen
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT, United States
| | - E. Diane Williamson
- Chemical Biological Radiological Division, Defense Science and Technology Laboratory (DSTL) Porton Down, Salisbury, United Kingdom
| | | | - James N. Herron
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT, United States
| | - J. Scott Hale
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
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Goldberg AR, Eads DA, Biggins DE. Plague circulation in small mammals elevates extinction risk for the endangered Peñasco least chipmunk. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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Harberts EM, Grubaugh D, Akuma DC, Shin S, Ernst RK, Brodsky IE. Position-Specific Secondary Acylation Determines Detection of Lipid A by Murine TLR4 and Caspase-11. Infect Immun 2022; 90:e0020122. [PMID: 35862717 PMCID: PMC9387250 DOI: 10.1128/iai.00201-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/02/2022] [Indexed: 01/16/2023] Open
Abstract
Immune sensing of the Gram-negative bacterial membrane glycolipid lipopolysaccharide (LPS) is both a critical component of host defense against bacterial infection and a contributor to the hyperinflammatory response, potentially leading to sepsis and death. Innate immune activation by LPS is due to the lipid A moiety, an acylated di-glucosamine molecule that can activate inflammatory responses via the extracellular sensor Toll-like receptor 4 (TLR4)/myeloid differentiation 2 (MD2) or the cytosolic sensor caspase-11 (Casp11). The number and length of acyl chains present on bacterial lipid A structures vary across bacterial species and strains, which affects the magnitude of TLR4 and Casp11 activation. TLR4 and Casp11 are thought to respond similarly to various lipid A structures, as tetra-acylated lipid A structures do not activate either sensor, whereas hexa-acylated structures activate both sensors. However, the precise features of lipid A that determine the differential activation of each receptor remain poorly defined, as direct analysis of extracellular and cytosolic responses to the same sources and preparations of LPS/lipid A structures have been limited. To address this question, we used rationally engineered lipid A isolated from a series of bacterial acyl-transferase mutants that produce novel, structurally defined molecules. Intriguingly, we found that the location of specific secondary acyl chains on lipid A resulted in differential recognition by TLR4 or Casp11, providing new insight into the structural features of lipid A required to activate either TLR4 or Casp11. Our findings indicate that TLR4 and Casp11 sense nonoverlapping areas of lipid A chemical space, thereby constraining the ability of Gram-negative pathogens to evade innate immunity.
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Affiliation(s)
- Erin M. Harberts
- Department of Microbial Pathogenesis, University of Maryland, School of Dentistry, Baltimore, Maryland, USA
| | - Daniel Grubaugh
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Daniel C. Akuma
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Sunny Shin
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland, School of Dentistry, Baltimore, Maryland, USA
| | - Igor E. Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
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Suntsov VV. Climate Changes in Central Asia as a Prerequisite and Trigger of Plague Microbe ( Yersinia pestis) Speciation. CONTEMP PROBL ECOL+ 2022; 15:373-382. [PMID: 35990805 PMCID: PMC9376127 DOI: 10.1134/s1995425522040102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/14/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022]
Abstract
Two physical and climatic factors that were distant and recent prerequisites and a transformation trigger for a clone of the ancestral pseudotuberculous microbe Yersinia pseudotuberculosis O:1b (the causative agent of the Far East scarlet-like fever (FESLF)) into a population of the plague microbe derivative Y. pestis are considered. One remote prerequisite was the aridification of the Central Asian landscapes in the second half of the Cenozoic period and the formation of the Gobi Arid Zone. The arid conditions of Central Asia determined the formation of adaptive species-specific protective behavior in the Tarbagan marmot (Marmota sibirica) when installing the plug of a wintering hole, which later contributed to the massive infection of the animals with FESLF by the aberrant (traumatic, not alimentary) method during hibernation. A recent prerequisite and a real trigger of Y. pestis speciation was the onset of the last maximum (Sartan) ice age in Central Asia at the turn of the Pleistocene and Holocene, 22 000-15 000 years ago. Freezing of the cooling burrows of the Tarbagan marmot caused a behavioral shift in the larval population of the marmot flea Oropsylla silantiewi and the transition to the cold winter-spring months of the year from saprophagy in the nesting litter to hematophagy on the bodies of sleeping animals. Larval scarifications in the oral cavity of sleeping marmots have become the entrance gate for a unique traumatic FESLF infection. The constellation of climatic changes, the heterothermal (and, accordingly, heteroimmune) condition of the family groups of sleeping marmots, and the year-round propagation of marmot fleas in wintering burrows, combined with behavioral shifts in marmots and fleas caused by climatic changes, led to the formation of conditions in the parasitic system M. sibirica-O. silantiewi in which the transformation of the FESLF microbe into the causative agent of the plague occurred according to peripatric speciation. Thus, the climatic changes that happened at different times in the Cenozoic initially led to a shift in behavior of the Tarbagan marmot and, subsequently, to a shift in the behavior of the fleas parasitizing it. Ultimately, the change in the behavior of marmots and fleas caused the transition of the clone(s) of the FESLF causative agent into a new ecological niche and adaptive zone, as well as the transformation into a population(s) of the plague microbe.
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Affiliation(s)
- V. V. Suntsov
- Severtsov Institute of Ecology and Evolution, 119071 Moscow, Russia
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Bezerra MF, dos Santos WJT, Rocha IV, Nadaes NR, Dantas-Torres F, Sales KGDS, de Melo Neto OP, Sobreira M, Silva ED, de Almeida AMP, Reis CRDS. Performance assessment of a new indirect rapid diagnostic test for plague detection in humans and other mammalian hosts. Acta Trop 2022; 231:106427. [PMID: 35339434 DOI: 10.1016/j.actatropica.2022.106427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/01/2022]
Abstract
Plague is a flea-borne zoonosis that affects a wide range of mammals and still causes outbreaks in human populations yearly across several countries. While crucial for proper treatment, early diagnosis is still a major challenge in low- and middle-income countries due to poor access to laboratory infrastructure in rural areas. To tackle this issue, we developed and evaluated a new Fraction 1 capsular antigen (F1)-based rapid diagnostic test (RDT) as an alternative method for plague serological diagnosis and surveillance in humans and other mammals. In this study, 187 serum samples from humans, dogs, rodents and rabbits were retrospectively assessed using the plague RDT method. To calculate its performance, results were compared to those obtained by traditional hemagglutination (HA) and ELISA, which are well-established methods in the plague routine serodiagnosis. Remarkably, the results from RDT were in full agreement with those from the ELISA and HA assays, resulting in 100% (CI 95% = 95.5-100%) of sensitivity and 100% (CI 95% = 96.6-100%) of specificity. Accordingly, the Cohen's Kappa test coefficient was 1.0 (almost perfect agreement). Moreover, the RDT showed no cross-reaction when tested with sera from individuals positive to other pathogens, such as Y. pseudotuberculosis, Yersinia enterocolitica, Anaplasma platys, Ehrlichia canis and Leishmania infantum. Although preliminary, this study brings consistent proof-of-concept results with high performance of the Plague RDT when compared to HA and ELISA. Although further human and animal population-based studies will be necessary to validate these findings, the data presented here show that the plague RDT is highly sensitive and specific, polyvalent to several mammal species and simple to use in field surveillance or point-of-care situations with instant results.
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Zhang Y, Wang Z, Wang W, Yu H, Jin M. Applications of polymerase chain reaction‑based methods for the diagnosis of plague (Review). Exp Ther Med 2022; 24:511. [DOI: 10.3892/etm.2022.11438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Yanan Zhang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Zhanli Wang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Wenrui Wang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, Inner Mongolia 010031, P.R. China
| | - Hui Yu
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Min Jin
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
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Kolodziejek AM, Hovde CJ, Minnich SA. Contributions of Yersinia pestis outer membrane protein Ail to plague pathogenesis. Curr Opin Infect Dis 2022; 35:188-195. [PMID: 35665712 PMCID: PMC9186061 DOI: 10.1097/qco.0000000000000830] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Pathogenic Yersinia have been a productive model system for studying bacterial pathogenesis. Hallmark contributions of Yersinia research to medical microbiology are legion and include: (i) the first identification of the role of plasmids in virulence, (ii) the important mechanism of iron acquisition from the host, (iii) the first identification of bacterial surface proteins required for host cell invasion, (iv) the archetypical type III secretion system, and (v) elucidation of the role of genomic reduction in the evolutionary trajectory from a fairly innocuous pathogen to a highly virulent species. RECENT FINDINGS The outer membrane (OM) protein Ail (attachment invasion locus) was identified over 30 years ago as an invasin-like protein. Recent work on Ail continues to provide insights into Gram-negative pathogenesis. This review is a synopsis of the role of Ail in invasion, serum resistance, OM stability, thermosensing, and vaccine development. SUMMARY Ail is shown to be an essential virulence factor with multiple roles in pathogenesis. The recent adaptation of Yersinia pestis to high virulence, which included genomic reduction to eliminate redundant protein functions, is a model to understand the emergence of new bacterial pathogens.
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Affiliation(s)
- Anna M. Kolodziejek
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, Idaho, USA
| | - Carolyn J. Hovde
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, Idaho, USA
| | - Scott A. Minnich
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, Idaho, USA
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48
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Bezerra MF, Xavier CC, de Almeida AMP, Reis CRDS. Evaluation of a multi-species Protein A-ELISA assay for plague serologic diagnosis in humans and other mammal hosts. PLoS Negl Trop Dis 2022; 16:e0009805. [PMID: 35551520 PMCID: PMC9129028 DOI: 10.1371/journal.pntd.0009805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 05/24/2022] [Accepted: 04/11/2022] [Indexed: 11/19/2022] Open
Abstract
Background The Hemagglutination assay (HA) is widely used in plague diagnosis, however, it has a subjective interpretation and demands high amounts of antigen and other immunobiological supplies. On the other hand, the conventional Anti-IgG ELISA is limited by the need of specific conjugates for multiple plague hosts, which leaves a gap for new diagnostic methods able to cover both the diagnosis of human cases and the epidemiological surveillance of multiple sentinel species. Methods We developed an ELISA Protein A-peroxidase method to detect anti-F1 antibodies across several species, including humans. To determine the cut-off and performance rates, HA results from 288 samples (81 rabbits, 64 humans, 66 rodents and 77 dogs) were used as reference. Next, we evaluated the agreement between Protein A-ELISA and Anti-IgG ELISA in an expanded sample set (n = 487). Results Optimal conditions were found with 250ng/well of F1 and 1:500 serum dilution. Protein A-ELISA showed high repeatability and reproducibility. We observed good correlation rates between the Protein A and IgG ELISAs optical densities and a higher positive/negative OD ratio for the Protein A-ELISA method. The overall sensitivity, specificity and area under the curve for Protein A-ELISA were 94%, 99% and 0.99, respectively. Similar results were observed for each species separately. In the analysis of the expanded sample set, there was a strong agreement between Protein A and IgG assays (kappa = 0.97). Furthermore, there was no cross-reaction with other common infectious diseases, such as dengue, Zika, Chagas disease, tuberculosis (humans) and ehrlichiosis, anaplasmosis and leishmaniasis (dogs). Conclusions Altogether, the Protein A-ELISA showed high performance when compared both to HA and Anti-IgG ELISA, with a polyvalent single protocol that requires reduced amounts of antigen and can be employed to any plague hosts. Here, we developed and evaluated an ELISA diagnostic test based on the Protein A-peroxidase conjugate that allows the test to be used for plague laboratorial diagnosis not only in humans, but also in a wide range of mammalian species. This particularity is specifically important for plague epidemiological surveillance, given that Yersinia pestis, the causative agent of plague, have a long list of animal reservoirs across distinct ecosystems. Briefly, we first evaluated the best reaction parameters, such as antigen concentration, serum and protein A-conjugate dilutions. Next, we used serum samples from humans, dogs, rodents and rabbits (n = 288) with known results for plague serology by a conventional method, to evaluate the performance of the new Protein A-ELISA test. We observed a good performance of the novel Protein A-ELISA test, with high sensitivity and specificity rates. Evaluation of the coefficient of variation revealed that the test measurements suffer little variation, and therefore, has high repeatability and reproducibility. Next, by evaluating 487 samples, we observed a high degree of concordance between the Protein A-ELISA with a conventional IgG-based ELISA. Furthermore, this test showed no significant cross-reaction with other common infectious diseases. Altogether, the Protein A-ELISA showed high performance when compared both to HA and Anti-IgG ELISA, with a single protocol that requires reduced amounts of antigen and can be employed to several plague hosts.
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Periago J, Mason C, Griep MA. Theoretical Development of DnaG Primase as a Novel Narrow-Spectrum Antibiotic Target. ACS OMEGA 2022; 7:8420-8428. [PMID: 35309427 PMCID: PMC8928506 DOI: 10.1021/acsomega.1c05928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/01/2022] [Indexed: 06/01/2023]
Abstract
The widespread use of antibiotics to treat infections is one of the reasons that global mortality rates have fallen over the past 80 years. However, antibiotic use is also responsible for the concomitant rise in antibiotic resistance because it results in dysbiosis in which commensal and pathogenic bacteria are both greatly reduced. Therefore, narrow-range antibiotics are a promising direction for reducing antibiotic resistance because they are more discriminate. As a step toward addressing this problem, the goal of this study was to identify sites on DnaG primase that are conserved within Gram-positive bacteria and different from the equivalent sites in Gram-negative bacteria. Based on sequence and structural analysis, the primase C-terminal helicase-binding domain (CTD) was identified as most promising. Although the primase CTD sequences are very poorly conserved, they have highly conserved protein folds, and Gram-positive bacterial primases fold into a compact state that creates a small molecule binding site adjacent to a groove. The small molecule would stabilize the protein in its compact state, which would interfere with the helicase binding. This is important because primase CTD must be in its open conformation to bind to its cognate helicase at the replication fork.
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Deatherage Kaiser BL, Birdsell DN, Hutchison JR, Thelaus J, Jenson SC, Andrianaivoarimanana V, Byström M, Myrtennäs K, McDonough RF, Nottingham RD, Sahl JW, Schweizer HP, Rajerison M, Forsman M, Wunschel DS, Wagner DM. Proteomic Signatures of Antimicrobial Resistance in Yersinia pestis and Francisella tularensis. Front Med (Lausanne) 2022; 9:821071. [PMID: 35223919 PMCID: PMC8866660 DOI: 10.3389/fmed.2022.821071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is a well-recognized, widespread, and growing issue of concern. With increasing incidence of AMR, the ability to respond quickly to infection with or exposure to an AMR pathogen is critical. Approaches that could accurately and more quickly identify whether a pathogen is AMR also are needed to more rapidly respond to existing and emerging biological threats. We examined proteins associated with paired AMR and antimicrobial susceptible (AMS) strains of Yersinia pestis and Francisella tularensis, causative agents of the diseases plague and tularemia, respectively, to identify whether potential existed to use proteins as signatures of AMR. We found that protein expression was significantly impacted by AMR status. Antimicrobial resistance-conferring proteins were expressed even in the absence of antibiotics in growth media, and the abundance of 10–20% of cellular proteins beyond those that directly confer AMR also were significantly changed in both Y. pestis and F. tularensis. Most strikingly, the abundance of proteins involved in specific metabolic pathways and biological functions was altered in all AMR strains examined, independent of species, resistance mechanism, and affected cellular antimicrobial target. We have identified features that distinguish between AMR and AMS strains, including a subset of features shared across species with different resistance mechanisms, which suggest shared biological signatures of resistance. These features could form the basis of novel approaches to identify AMR phenotypes in unknown strains.
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Affiliation(s)
- Brooke L Deatherage Kaiser
- Pacific Northwest National Laboratory, Chemical and Biological Signatures Group, Richland, WA, United States
| | - Dawn N Birdsell
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Janine R Hutchison
- Pacific Northwest National Laboratory, Chemical and Biological Signatures Group, Richland, WA, United States
| | - Johanna Thelaus
- Swedish Defence Research Agency, Chemical, Biological, Radioactive, and Nuclear (CBRN) - Defence and Security, Umeå, Sweden
| | - Sarah C Jenson
- Pacific Northwest National Laboratory, Chemical and Biological Signatures Group, Richland, WA, United States
| | | | - Mona Byström
- Swedish Defence Research Agency, Chemical, Biological, Radioactive, and Nuclear (CBRN) - Defence and Security, Umeå, Sweden
| | - Kerstin Myrtennäs
- Swedish Defence Research Agency, Chemical, Biological, Radioactive, and Nuclear (CBRN) - Defence and Security, Umeå, Sweden
| | - Ryelan F McDonough
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Roxanne D Nottingham
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Herbert P Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Minoarisoa Rajerison
- Plague Unit, Central Laboratory for Plague, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Mats Forsman
- Swedish Defence Research Agency, Chemical, Biological, Radioactive, and Nuclear (CBRN) - Defence and Security, Umeå, Sweden
| | - David S Wunschel
- Pacific Northwest National Laboratory, Chemical and Biological Signatures Group, Richland, WA, United States
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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