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Seabaugh JA, Anderson DM. Pathogenicity and virulence of Yersinia. Virulence 2024; 15:2316439. [PMID: 38389313 PMCID: PMC10896167 DOI: 10.1080/21505594.2024.2316439] [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: 10/05/2023] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
The genus Yersinia includes human, animal, insect, and plant pathogens as well as many symbionts and harmless bacteria. Within this genus are Yersinia enterocolitica and the Yersinia pseudotuberculosis complex, with four human pathogenic species that are highly related at the genomic level including the causative agent of plague, Yersinia pestis. Extensive laboratory, field work, and clinical research have been conducted to understand the underlying pathogenesis and zoonotic transmission of these pathogens. There are presently more than 500 whole genome sequences from which an evolutionary footprint can be developed that details shared and unique virulence properties. Whereas the virulence of Y. pestis now seems in apparent homoeostasis within its flea transmission cycle, substantial evolutionary changes that affect transmission and disease severity continue to ndergo apparent selective pressure within the other Yersiniae that cause intestinal diseases. In this review, we will summarize the present understanding of the virulence and pathogenesis of Yersinia, highlighting shared mechanisms of virulence and the differences that determine the infection niche and disease severity.
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Affiliation(s)
- Jarett A. Seabaugh
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
| | - Deborah M. Anderson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
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Wang B, Wang C, Li B, Yang J, Lin P, Jin X, Niu Y, Zhang W, Zhang X, Huang Y. Isolation of camel single domain antibodies against Yersinia pestis V270 antigen based on a semi-synthetic single domain antibody library and development of a VHH-based lateral flow assay. Vet Med Sci 2024; 10:e1532. [PMID: 38952277 PMCID: PMC11217587 DOI: 10.1002/vms3.1532] [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: 11/13/2023] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Antibodies have been proven effective as diagnostic agents for detecting zoonotic diseases. The variable domain of camel heavy chain antibody (VHH), as an antibody derivative, may be used as an alternative for traditional antibodies in existing immunodiagnostic reagents for detecting rapidly spreading infectious diseases. OBJECTIVES To expedite the isolation of specific antibodies for diagnostic purposes, we constructed a semi-synthetic camel single domain antibody library based on the phage display technique platform (PDT) and verified the validity of this study. METHODS The semi-synthetic single domain antibody sequences consist of two parts: one is the FR1-FR3 region amplified by RT-PCR from healthy camel peripheral blood lymphocytes (PBLs), and the other part is the CDR3-FR4 region synthesised as an oligonucleotide containing CDR3 randomised region. The two parts were fused by overlapping PCR, resulting in the rearranged variable domain of heavy-chain antibodies (VHHs). Y. pestis low-calcium response V protein (LcrV) is an optional biomarker to detect the Y. pestis infection. The semi-synthetic library herein was screened using recombinant (LcrV) as a target antigen. RESULTS After four cycles of panning the library, four VHH binders targeting 1-270 aa residues of LcrV were isolated. The four VHH genes with unique sequences were recloned into an expression vector and expressed as VHH-hFc chimeric antibodies. The purified antibodies were identified and used to develop a lateral flow immunoassay (LFA) test strip using latex microspheres (LM) for the rapid and visual detection of Y. pestis infection. CONCLUSIONS These data demonstrate the great potential of the semi-synthetic library for use in isolation of antigen-specific nanobodies and the isolated specific VHHs can be used in antigen-capture immunoassays.
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Affiliation(s)
- Bo Wang
- Beijing Uncover Biotech Limited Liability CompanyBeijingChina
- Ordos Uncover Biotech Limited Liability CompanyDalad QiInner MongoliaChina
| | - Chunsheng Wang
- Department of VaccineOrdos Dalad Animal Disease Prevention and Control CenterDalad QiInner MongoliaChina
| | - Bo Li
- Department of Veterinary MedicineDaren Traditional Chinese Medicine HospitalDalad QiInner MongoliaChina
| | - Jin Yang
- Beijing Uncover Biotech Limited Liability CompanyBeijingChina
- Ordos Uncover Biotech Limited Liability CompanyDalad QiInner MongoliaChina
| | - Pengfei Lin
- Department of VaccineOrdos Dalad Animal Disease Prevention and Control CenterDalad QiInner MongoliaChina
| | - Xuefeng Jin
- Department of VaccineOrdos Dalad Animal Disease Prevention and Control CenterDalad QiInner MongoliaChina
| | - Yaojie Niu
- Department of Veterinary MedicineDaren Traditional Chinese Medicine HospitalDalad QiInner MongoliaChina
| | - Wei Zhang
- Department of VaccineOrdos Dalad Animal Disease Prevention and Control CenterDalad QiInner MongoliaChina
| | - Xinshi Zhang
- Department of Veterinary MedicineDaren Traditional Chinese Medicine HospitalDalad QiInner MongoliaChina
| | - Ying Huang
- Beijing Uncover Biotech Limited Liability CompanyBeijingChina
- Ordos Uncover Biotech Limited Liability CompanyDalad QiInner MongoliaChina
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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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Randriantseheno LN, Andrianaivoarimanana V, Pizarro-Cerdá J, Wagner DM, Rajerison M. Review of genotyping methods for Yersinia pestis in Madagascar. PLoS Negl Trop Dis 2024; 18:e0012252. [PMID: 38935608 PMCID: PMC11210753 DOI: 10.1371/journal.pntd.0012252] [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: 06/29/2024] Open
Abstract
BACKGROUND Plague, a zoonotic disease caused by Yersinia pestis, was responsible for 3 historical human pandemics that killed millions of people. It remains endemic in rodent populations in Africa, Asia, North America, and South America but human plague is rare in most of these locations. However, human plague is still highly prevalent in Madagascar, which typically records a significant part of all annual global cases. This has afforded an opportunity to study contemporary human plague in detail using various typing methods for Y. pestis. AIM This review aims to summarize the methods that have been used to type Y. pestis in Madagascar along with the major discoveries that have been made using these approaches. METHODS Pubmed and Google Scholar were used to search for the keywords: "typing Yersinia pestis Madagascar," "evolution Yersinia pestis Madagascar," and "diversity Yersinia pestis Madagascar." Eleven publications were relevant to our topic and further information was retrieved from references cited in those publications. RESULTS The history of Y. pestis typing in Madagascar can be divided in 2 periods: the pre-genomics and genomics eras. During the pre-genomics era, ribotyping, direct observation of plasmid content and plasmid restriction fragment length polymorphisms (RFLP) were employed but only revealed a limited amount of diversity among Malagasy Y. pestis strains. Extensive diversity only started to be revealed in the genomics era with the use of clustered regularly interspaced palindromic repeats (CRISPR), multiple-locus variable number tandem repeats (VNTR) analysis (MLVA), and single-nucleotide polymorphisms (SNPs) discovered from whole genome sequences. These higher-resolution genotyping methods have made it possible to highlight the distribution and persistence of genotypes in the different plague foci of Madagascar (Mahajanga and the Central and Northern Highlands) by genotyping strains from the same locations across years, to detect transfers between foci, to date the emergence of genotypes, and even to document the transmission of antimicrobial resistant (AMR) strains during a pneumonic plague outbreak. Despite these discoveries, there still remain topics that deserve to be explored, such as the contribution of horizontal gene transfer to the evolution of Malagasy Y. pestis strains and the evolutionary history of Y. pestis in Madagascar. CONCLUSIONS Genotyping of Y. pestis has yielded important insights on plague in Madagascar, particularly since the advent of whole-genome sequencing (WGS). These include a better understanding of plague persistence in the environment, antimicrobial AMR and multi-drug resistance in Y. pestis, and the person-to-person spread of pneumonic plague. Considering that human plague is still a significant public health threat in Madagascar, these insights can be useful for controlling and preventing human plague in Madagascar and elsewhere, and also are relevant for understanding the historical pandemics and the possible use of Y. pestis as a biological weapon.
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Affiliation(s)
- Lovasoa Nomena Randriantseheno
- Plague Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Ecole doctorale Sciences de la Vie et de l’Environnement, Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | | | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
- Institut Pasteur, French National Reference Laboratory ‘Plague & Other Yersiniosis’, WHO Collaborating Centre for Plague FRA-140, Paris, France
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Bennasar-Figueras A. The Natural and Clinical History of Plague: From the Ancient Pandemics to Modern Insights. Microorganisms 2024; 12:146. [PMID: 38257973 PMCID: PMC10818976 DOI: 10.3390/microorganisms12010146] [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: 12/19/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The human pathogen Yersinia pestis is responsible for bubonic, septicemic, and pneumonic plague. A deeply comprehensive overview of its historical context, bacteriological characteristics, genomic analysis based on ancient DNA (aDNA) and modern strains, and its impact on historical and actual human populations, is explored. The results from multiple studies have been synthesized to investigate the origins of plague, its transmission, and effects on different populations. Additionally, molecular interactions of Y. pestis, from its evolutionary origins to its adaptation to flea-born transmission, and its impact on human and wild populations are considered. The characteristic combinations of aDNA patterns, which plays a decisive role in the reconstruction and analysis of ancient genomes, are reviewed. Bioinformatics is fundamental in identifying specific Y. pestis lineages, and automated pipelines are among the valuable tools in implementing such studies. Plague, which remains among human history's most lethal infectious diseases, but also other zoonotic diseases, requires the continuous investigation of plague topics. This can be achieved by improving molecular and genetic screening of animal populations, identifying ecological and social determinants of outbreaks, increasing interdisciplinary collaborations among scientists and public healthcare providers, and continued research into the characterization, diagnosis, and treatment of these diseases.
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Affiliation(s)
- Antoni Bennasar-Figueras
- Microbiologia—Departament de Biologia, Universitat de les Illes Balears (UIB), Campus UIB, Carretera de Valldemossa, Km 7.5, 07122 Palma de Mallorca, Spain; ; Tel.: +34-971172778
- Facultat de Medicina, Hospital Universitari Son Espases (HUSE), Universitat de les Illes Balears (UIB), Carretera de Valldemossa, 79, 07122 Palma de Mallorca, Spain
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Liang J, Duan R, Qin S, Lv D, He Z, Zhang H, Duan Q, Xi J, Chun H, Fu G, Zheng X, Tang D, Wu W, Han H, Jing H, Wang X. The complex genomic diversity of Yersinia pestis on the long-term plague foci in Qinghai-Tibet plateau. Ecol Evol 2023; 13:e10387. [PMID: 37529582 PMCID: PMC10375460 DOI: 10.1002/ece3.10387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/15/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023] Open
Abstract
Plague is a typical natural focus disease that circulates in different ecology of vectors and reservoir hosts. We conducted genomic population and phylogenetic analyses of the Yersinia pestis collected from the 12 natural plague foci in China with more than 20 kinds of hosts and vectors. Different ecological landscapes with specific hosts, vectors, and habitat which shape various niches for Y. pestis. The phylogeographic diversity of Y. pestis in different kinds plague foci in China showed host niches adaptation. Most natural plague foci strains are region-and focus-specific, with one predominant subpopulation; but the isolates from the Qinghai-Tibet plateau harbor a higher genetic diversity than other foci. The Y. pestis from Marmota himalayana plague foci are defined as the ancestors of different populations at the root of the evolutionary tree, suggesting several different evolutionary paths to other foci. It has the largest pan-genome and widest SNP distances with most accessory genes enriched in mobilome functions (prophages, transposons). Geological barriers play an important role in the maintenance of local Y. pestis species and block the introduction of non-native strains. This study provides new insights into the control of plague outbreaks and epidemics, deepened the understanding of the evolutionary history of MHPF (M. himalayana plague focus) in China. The population structure and identify clades among different natural foci of China renewed the space cognition of the plague.
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Affiliation(s)
- Junrong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Ran Duan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Shuai Qin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Dongyue Lv
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Zhaokai He
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Haoran Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Qun Duan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Jinxiao Xi
- Gansu Provincial Center for Disease Control and PreventionLanzhouChina
| | - Hua Chun
- Subei Mongolian Autonomous County Center for Disease Control and PreventionJiuquanChina
| | - Guoming Fu
- Subei Mongolian Autonomous County Center for Disease Control and PreventionJiuquanChina
| | - Xiaojin Zheng
- Akesai Kazakh Autonomous County Center for Disease Control and PreventionJiuquanChina
| | - Deming Tang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Weiwei Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Haonan Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Huaiqi Jing
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Xin Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
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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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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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<i>Yersinia pestis</i> ssp. <i>pestis</i> Spatial MLVA25 Genotypic Structure in the Transboundary Saylyugem Natural Plague Focus. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2023. [DOI: 10.21055/0370-1069-2022-4-110-116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Advanced molecular-genetic methods for the diagnosis and typing of Yersinia pestis ssp. pestis in the field and clinical material are used for epidemiological surveillance of plague in the Saylyugem natural focus. The aim of the work was to study the spatial genotypic structure of Y. pestis ssp. pestis in the transboundary Saylyugem natural plague focus using MLVA25 typing. Materials and methods. The MLVA25 typing of 160 strains of Y. pestis ssp. Pestis isolated in the Saylyugem natural plague focus in 2012–2021 was carried out. Phylogenetic tree construction was performed with the help of UPGMA and MST methods. Results and discussion. The Y. pestis ssp. pestis strains isolated from the Saylyugem natural plague focus were differentiated into 15 MLVA types by the 25 VNTR loci cluster analysis. The studied strains form a homogeneous complex of MLVA25 types without marked geographical distribution across seven spatial groups. The analysis of the frequency of occurrence of the tandem repeats number for three variable loci of Y. pestis ssp. pestis strains shows the significant differences between the samples from the Mongolian and Russian parts of the Saylyugem natural plague focus. The most pronounced differences in spatial genotypic structure are traced through the yp4280ms62 locus.
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Historical and Modern Classifications of the Plague Agent. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2023. [DOI: 10.21055/0370-1069-2022-4-14-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The review presents the data on domestic and foreign phenotypic classifications of Yersinia pestis strains developed in the XX century; genetic classifications of the XXI century; as well as on the genealogy of ancient strains of the plague microbe, reconstructed using paleogenomic technologies. Since the discovery of the plague agent in 1894, many classifications were created that corresponded to the level of development of microbiology at that time. The intraspecific classification schemes of the XX century were based on three principles: phenotypic differences between strains, features of the species composition of carriers, and geographical affiliation. With the development of molecular microbiology early on in the XXI century, a genetic nomenclature of the branches of the pathogen evolution was developed and a number of classifications based on the analysis of the population structure of Y. pestis were created. Through the prism of the genetic diversity of Y. pestis strains from natural plague foci in Russia, near and far abroad countries, an improved classification with a division into seven subspecies has been developed: pestis, tibetica, caucasica, qinghaica, angolica, central asiatica, ulegeica, which allocates the subspecies according to the phylogenetic principle and epidemic significance. With the advancements in paleomicrobiology, prehistoric lineages of evolution have been included in the genealogy of Y. pestis, which expand the data on the intraspecific diversity of the plague microbe.
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Bacterial Protein Tyrosine Phosphatases as Possible Targets for Antimicrobial Therapies in Response to Antibiotic Resistance. Antioxidants (Basel) 2022; 11:antiox11122397. [PMID: 36552605 PMCID: PMC9774629 DOI: 10.3390/antiox11122397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The review is focused on the bacterial protein tyrosine phosphatases (PTPs) utilized by bacteria as virulence factors necessary for pathogenicity. The inhibition of bacterial PTPs could contribute to the arrest of the bacterial infection process. This mechanism could be utilized in the design of antimicrobial therapy as adjuvants to antibiotics. The review summaries knowledge on pathogenic bacterial protein tyrosine phosphatases (PTPs) involved in infection process, such as: PTPA and PTPB from Staphylococcus aureus and Mycobacterium tuberculosis; SptP from Salmonella typhimurium; YopH from Yersinia sp. and TbpA from Pseudomonas aeruginosa. The review focuses also on the potential inhibitory compounds of bacterial virulence factors and inhibitory mechanisms such as the reversible oxidation of tyrosine phosphatases.
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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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Nilsson P, Ravinet M, Cui Y, Berg PR, Zhang Y, Guo R, Luo T, Song Y, Trucchi E, Hoff SNK, Lv R, Schmid BV, Easterday WR, Jakobsen KS, Stenseth NC, Yang R, Jentoft S. Polygenic plague resistance in the great gerbil uncovered by population sequencing. PNAS NEXUS 2022; 1:pgac211. [PMID: 36712379 PMCID: PMC9802093 DOI: 10.1093/pnasnexus/pgac211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 06/18/2023]
Abstract
Pathogens can elicit high selective pressure on hosts, potentially altering genetic diversity over short evolutionary timescales. Intraspecific variation in immune response is observable as variable survivability from specific infections. The great gerbil (Rhombomys opimus) is a rodent plague host with a heterogenic but highly resistant phenotype. Here, we investigate the genomic basis for plague-resistant phenotypes by exposing wild-caught great gerbils to plague (Yersinia pestis). Whole genome sequencing of 10 survivors and 10 moribund individuals revealed a subset of genomic regions showing elevated differentiation. Gene ontology analysis of candidate genes in these regions demonstrated enrichment of genes directly involved in immune functions, cellular metabolism and the regulation of apoptosis as well as pathways involved in transcription, translation, and gene regulation. Transcriptomic analysis revealed that the early activated great gerbil immune response to plague consisted of classical components of the innate immune system. Our approach combining challenge experiments with transcriptomics and population level sequencing, provides new insight into the genetic background of plague-resistance and confirms its complex nature, most likely involving multiple genes and pathways of both the immune system and regulation of basic cellular functions.
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Affiliation(s)
- Pernille Nilsson
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | | | | | | | | | - Rong Guo
- Xinjiang Center for Disease Control and Prevention, Urumqi 830002, China
| | - Tao Luo
- Xinjiang Center for Disease Control and Prevention, Urumqi 830002, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy
| | - Siv N K Hoff
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Ruichen Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - W Ryan Easterday
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | | | | | - Ruifu Yang
- To whom correspondence should be addressed:
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15
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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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16
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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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17
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Li Q, Ye C, Zhao F, Li W, Zhu S, Lv Y, Park CG, Zhang Y, Jiang LY, Yang K, He Y, Cai H, Zhang S, Ding HH, Njiri OA, Tembo JM, Alkraiem AA, Li AY, Sun ZY, Li W, Yan MY, Kan B, Huo X, Klena JD, Skurnik M, Anisimov AP, Gao X, Han Y, Yang RF, Xiamu X, Wang Y, Chen H, Chai B, Sun Y, Yuan J, Chen T. PgtE Enzyme of Salmonella enterica Shares the Similar Biological Roles to Plasminogen Activator (Pla) in Interacting With DEC-205 (CD205), and Enhancing Host Dissemination and Infectivity by Yersinia pestis. Front Immunol 2022; 13:791799. [PMID: 35401532 PMCID: PMC8986990 DOI: 10.3389/fimmu.2022.791799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
Abstract
Yersinia pestis, the cause of plague, is a newly evolved Gram-negative bacterium. Through the acquisition of the plasminogen activator (Pla), Y. pestis gained the means to rapidly disseminate throughout its mammalian hosts. It was suggested that Y. pestis utilizes Pla to interact with the DEC-205 (CD205) receptor on antigen-presenting cells (APCs) to initiate host dissemination and infection. However, the evolutionary origin of Pla has not been fully elucidated. The PgtE enzyme of Salmonella enterica, involved in host dissemination, shows sequence similarity with the Y. pestis Pla. In this study, we demonstrated that both Escherichia coli K-12 and Y. pestis bacteria expressing the PgtE-protein were able to interact with primary alveolar macrophages and DEC-205-transfected CHO cells. The interaction between PgtE-expressing bacteria and DEC-205-expressing transfectants could be inhibited by the application of an anti-DEC-205 antibody. Moreover, PgtE-expressing Y. pestis partially re-gained the ability to promote host dissemination and infection. In conclusion, the DEC-205-PgtE interaction plays a role in promoting the dissemination and infection of Y. pestis, suggesting that Pla and the PgtE of S. enterica might share a common evolutionary origin.
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Affiliation(s)
- Qiao Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Chenglin Ye
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fei Zhao
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Wenjin Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Sizhe Zhu
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yin Lv
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Chae Gyu Park
- Therapeutic Antibody Research Center, Genuv Inc., Seoul, South Korea
- Immune and Vascular Cell Network Research Center, National Creative Initiatives, Department of Life Sciences, Ewha Womans University, Seoul, South Korea
| | - Yingmiao Zhang
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Ling-Yu Jiang
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Kun Yang
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yingxia He
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Huahua Cai
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Song Zhang
- Union Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Hong-Hui Ding
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Olivia Adhiambo Njiri
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - John Mambwe Tembo
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Ayman Ahmad Alkraiem
- Tongji Hospital, Tongji Medical College, Huazhong University, Wuhan, China
- Department of Biology, College of Science, Taibah University, Medina, Saudi Arabia
| | - An-Yi Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Zi-Yong Sun
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Wei Li
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mei-Ying Yan
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xixiang Huo
- Center for Infectious Diseases, Hubei Provincial Centers for Disease Control and Prevention (CDC), Wuhan, China
| | - John D. Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Andrey P. Anisimov
- Laboratory for Plague Microbiology, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Xiaofang Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Rui-Fu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiding Xiamu
- Division of Disease Control and Prevention for Endemic Diseases , Wenquan Center for Disease Control and Prevention, Wenquan, China
| | - Yuanzhi Wang
- Department of Pathogen Biology and Immunology, Shihezi University School of Medicine, Shihezi, China
| | - Hongxiang Chen
- Union Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Bao Chai
- Department of Dermatology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Dermatology, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Yicheng Sun
- Ministry of Health (MOH) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Tie Chen,, ; Jingping Yuan,; Yicheng Sun,
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Tie Chen,, ; Jingping Yuan,; Yicheng Sun,
| | - Tie Chen
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
- *Correspondence: Tie Chen,, ; Jingping Yuan,; Yicheng Sun,
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18
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Suntsov VV. Host Aspect of Territorial Expansion of the Plague Microbe Yersinia pestis from the Populations of the Tarbagan Marmot (Marmota sibirica). BIOL BULL+ 2021. [DOI: 10.1134/s1062359021080288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Dudek CA, Jahn D. PRODORIC: state-of-the-art database of prokaryotic gene regulation. Nucleic Acids Res 2021; 50:D295-D302. [PMID: 34850133 PMCID: PMC8728284 DOI: 10.1093/nar/gkab1110] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/12/2021] [Accepted: 11/01/2021] [Indexed: 11/14/2022] Open
Abstract
PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.
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Affiliation(s)
- Christian-Alexander Dudek
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
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20
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Li J, Wang Y, Liu F, Shen X, Wang Y, Fan M, Peng Y, Wang S, Feng Y, Zhang W, Lv Y, Zhang H, Lu X, Zhang E, Wei J, Chen L, Kan B, Zhang Z, Xu J, Wang W, Li W. Genetic source tracking of human plague cases in Inner Mongolia-Beijing, 2019. PLoS Negl Trop Dis 2021; 15:e0009558. [PMID: 34343197 PMCID: PMC8362994 DOI: 10.1371/journal.pntd.0009558] [Citation(s) in RCA: 3] [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: 06/22/2020] [Revised: 08/13/2021] [Accepted: 06/11/2021] [Indexed: 11/19/2022] Open
Abstract
On 12 November 2019, one couple from the Sonid Left Qi (County) in the Inner Mongolia Autonomous Region was diagnosed with pneumonic plague in Beijing. The wife acquired the infection from her husband. Thereafter, two bubonic plague cases were identified in Inner Mongolia on November 16th and 24th. In this study, genome-wide single nucleotide polymorphism (SNP) analysis was used to identify the phylogenetic relationship of Yersinia pestis strains isolated in Inner Mongolia. Strains isolated from reservoirs in 2018 and 2019 in Inner Mongolia, together with the strain isolated from Patient C, were further clustered into 2.MED3m, and two novel lineages (2.MED3q, 2.MED3r) in the 2.MED3 population. According to the analysis of PCR-based molecular subtyping methods, such as the MLVA 14 scheme and seven SNP allele sequencing, Patients A/B and D were classified as 2.MED3m. In addition, strains from rodents living near the patients' residences were clustered into the same lineage as patients. Such observations indicated that human plague cases originated from local reservoirs. Corresponding phylogenetic analysis also indicated that rodent plague strains in different areas in Inner Mongolia belong to different epizootics rather than being caused by spreading from the same epizootic in Meriones unguiculatus in 2019.
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Affiliation(s)
- Jianyun Li
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, China
| | - Yumeng Wang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Fang Liu
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, China
| | - Xiaona Shen
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Yiting Wang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Mengguang Fan
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, China
| | - Yao Peng
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Shuyi Wang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, China
| | - Yilan Feng
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, China
| | - Wen Zhang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Yanning Lv
- Beijing Center for Disease Control and Prevention, Beijing, China
| | - Huijuan Zhang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Xin Lu
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Enmin Zhang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Jianchun Wei
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Lijuan Chen
- Beijing Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Zhongbing Zhang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, China
| | - Jianguo Xu
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
| | - Wenrui Wang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, China
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Changping, Beijing, China
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21
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Aborode AT, Dos Santos Costa AC, Mohan A, Goyal S, Rabiu AT, Tsagkaris C, Uwishema O, Outani O, Ahmad S, Essar MY. Epidemic of plague amidst COVID-19 in Madagascar: efforts, challenges, and recommendations. Trop Med Health 2021; 49:56. [PMID: 34256858 PMCID: PMC8275634 DOI: 10.1186/s41182-021-00349-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/05/2021] [Indexed: 12/03/2022] Open
Abstract
The plague has been wreaking havoc on people in Madagascar with the COVID-19 pandemic. Madagascar’s healthcare sector is striving to respond to COVID-19 in the face of a plague outbreak that has created a new strain on the country’s public health system. The goal and activities of the gradual epidemic of plague in Madagascar during COVID-19 are described in this research. In order to contain the plague and the COVID-19 pandemic in this country, we have suggested long-term recommendations that can help to contain the outbreak so that it may spread to non-endemic areas.
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Affiliation(s)
| | | | - Anmol Mohan
- Karachi Medical & Dental College, Karachi, Pakistan
| | | | | | | | - Olivier Uwishema
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda. .,Faculty of Medicine, Karadeniz Technical University, 61080, Trabzon, Turkey. .,Clinton Global Initiative University, New York, USA.
| | - Oumaima Outani
- Faculty of Medicine and Pharmacy of Rabat, Mohamed 5 University, Rabat, Morocco
| | - Shoaib Ahmad
- District Head Quarters Teaching Hospital, Faisalabad, Pakistan
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22
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Bose D, Mukhopadhyay S. The hunt for a yet unknown: Common molecular signature in some genetically monomorphic enterobacteria. J Basic Microbiol 2021; 61:524-546. [PMID: 33991346 DOI: 10.1002/jobm.202000630] [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: 11/24/2020] [Revised: 04/04/2021] [Accepted: 04/22/2021] [Indexed: 11/09/2022]
Abstract
Mark Achtman introduced the term "genetically monomorphic bacteria" (GM bacteria) for some human and plant pathogens. They displayed a great uniformity in terms of their "genetic" properties. This "uniformity" poses a challenge to microbiologists. To address these problems, we used CodonW and IslandViewer 3 as analytical tools and took Escherichia coli, Salmonella, and Shigella strains as a model organisms. We hypothesized that GM bacterium contains a common molecular signature among them. We have found a significant correlation regarding the number of protein-coding genes, predicted highly expressed genes, and the highest length of gene in this regard. On the other hand, the correspondence analysis of pathogenicity-related genes identified by IslandViewer 3 displayed a somewhat unique pattern in GM bacteria. The probable pathogenic genes are clustered into two separate groups, which is a hallmark of some pattern. Similar genes of non-monomorphic pathogenic strain clustered almost similarly, but the clusters are joined together, they are not completely separated. These features, in our considered view, may be considered as codon usages signatures of these bacteria, and E. coli in particular.
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Affiliation(s)
- Debadin Bose
- Department of Botany, Kabi Nazrul College, Murarai, West Bengal, India
| | - Subhasis Mukhopadhyay
- Distributed Information Centre for Bioinformatics, Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Calcutta, West Bengal, India
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Pisarenko SV, Evchenko AY, Kovalev DA, Evchenko YМ, Bobrysheva OV, Shapakov NA, Volynkina AS, Kulichenko AN. Yersinia pestis strains isolated in natural plague foci of Caucasus and Transcaucasia in the context of the global evolution of species. Genomics 2021; 113:1952-1961. [PMID: 33862185 DOI: 10.1016/j.ygeno.2021.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/31/2021] [Accepted: 04/11/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Plague is a highly dangerous vector-borne infectious disease that has left a significant mark on history of humankind. There are 13 natural plague foci in the Caucasus, located on the territory of the Russian Federation, Azerbaijan, Armenia and Georgia. We performed whole-genome sequencing of Y. pestis strains, isolated in the natural foci of the Caucasus and Transcaucasia. Using the data of whole-genome SNP analysis and Bayesian phylogeny methods, we carried out an evolutionary-phylogeographic analysis of modern population of the plague pathogen in order to determine the phylogenetic relationships of Y. pestis strains from the Caucasus with the strains from other countries. RESULTS We used 345 Y. pestis genomes to construct a global evolutionary phylogenetic reconstruction of species based on whole-genome SNP analysis. The genomes of 16 isolates were sequenced in this study, the remaining 329 genomes were obtained from the GenBank database. Analysis of the core genome revealed 3315 SNPs that allow differentiation of strains. The evolutionary phylogeographic analysis showed that the studied Y. pestis strains belong to the genetic lineages 0.PE2, 2.MED0, and 2.MED1. It was shown that the Y. pestis strains isolated on the territory of the East Caucasian high-mountain, the Transcaucasian high-mountain and the Priaraksinsky low-mountain plague foci belong to the most ancient of all existing genetic lineages - 0.PE2. CONCLUSIONS On the basis of the whole-genome SNP analysis of 345 Y. pestis strains, we describe the modern population structure of the plague pathogen and specify the place of the strains isolated in the natural foci of the Caucasus and Transcaucasia in the structure of the global population of Y. pestis. As a result of the retrospective evolutionary-phylogeographic analysis of the current population of the pathogen, we determined the probable time frame of the divergence of the genetic lineages of Y. pestis, as well as suggested the possible paths of the historical spread of the plague pathogen.
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Affiliation(s)
- Sergey V Pisarenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | - Anna Yu Evchenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Dmitry A Kovalev
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Yuri М Evchenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Olga V Bobrysheva
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Nikolay A Shapakov
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Anna S Volynkina
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
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24
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Suntsov VV. Genomogenesis of the Plague Bacteria Yersinia pestis as a Process of Mosaic Evolution. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421020113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Cote CK, Biryukov SS, Klimko CP, Shoe JL, Hunter M, Rosario-Acevedo R, Fetterer DP, Moody KL, Meyer JR, Rill NO, Dankmeyer JL, Worsham PL, Bozue JA, Welkos SL. Protection Elicited by Attenuated Live Yersinia pestis Vaccine Strains against Lethal Infection with Virulent Y. pestis. Vaccines (Basel) 2021; 9:vaccines9020161. [PMID: 33669472 PMCID: PMC7920443 DOI: 10.3390/vaccines9020161] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 12/22/2022] Open
Abstract
The etiologic agent of plague, Yersinia pestis, is a globally distributed pathogen which poses both a natural and adversarial threat. Due largely to the rapid course and high mortality of pneumonic plague, vaccines are greatly needed. Two-component protein vaccines have been unreliable and potentially vulnerable to vaccine resistance. We evaluated the safety and efficacy of eight live Y. pestis strains derived from virulent strains CO92 or KIM6+ and mutated in one or more virulence-associated gene(s) or cured of plasmid pPst. Stringent, single-dose vaccination allowed down-selection of the two safest and most protective vaccine candidates, CO92 mutants pgm- pPst- and ΔyscN. Both completely protected BALB/c mice against subcutaneous and aerosol challenge with Y. pestis. Strain CD-1 outbred mice were more resistant to bubonic (but not pneumonic) plague than BALB/c mice, but the vaccines elicited partial protection of CD-1 mice against aerosol challenge, while providing full protection against subcutaneous challenge. A ΔyscN mutant of the nonencapsulated C12 strain was expected to display antigens previously concealed by the capsule. C12 ΔyscN elicited negligible titers to F1 but comparable antibody levels to whole killed bacteria, as did CO92 ΔyscN. Although one dose of C12 ΔyscN was not protective, vaccination with two doses of either CO92 ΔyscN, or a combination of the ΔyscN mutants of C12 and CO92, protected optimally against lethal bubonic or pneumonic plague. Protection against encapsulated Y. pestis required inclusion of F1 in the vaccine and was associated with high anti-F1 titers.
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Hinnebusch BJ, Jarrett CO, Bland DM. Molecular and Genetic Mechanisms That Mediate Transmission of Yersinia pestis by Fleas. Biomolecules 2021; 11:210. [PMID: 33546271 PMCID: PMC7913351 DOI: 10.3390/biom11020210] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/19/2022] Open
Abstract
The ability to cause plague in mammals represents only half of the life history of Yersinia pestis. It is also able to colonize and produce a transmissible infection in the digestive tract of the flea, its insect host. Parallel to studies of the molecular mechanisms by which Y. pestis is able to overcome the immune response of its mammalian hosts, disseminate, and produce septicemia, studies of Y. pestis-flea interactions have led to the identification and characterization of important factors that lead to transmission by flea bite. Y. pestis adapts to the unique conditions in the flea gut by altering its metabolic physiology in ways that promote biofilm development, a common strategy by which bacteria cope with a nutrient-limited environment. Biofilm localization to the flea foregut disrupts normal fluid dynamics of blood feeding, resulting in regurgitative transmission. Many of the important genes, regulatory pathways, and molecules required for this process have been identified and are reviewed here.
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Affiliation(s)
- B. Joseph Hinnebusch
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; (C.O.J.); (D.M.B.)
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27
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Cuéllar-Cruz M. The histo-blood group antigens of the host cell may determine the binding of different viruses such as SARS-CoV-2. Future Microbiol 2021; 16:107-118. [PMID: 33459559 PMCID: PMC7842250 DOI: 10.2217/fmb-2020-0158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/05/2021] [Indexed: 12/18/2022] Open
Abstract
Viruses have caused the death of millions of people worldwide. Specifically, human viruses are grouped into 21 families, including the family of coronaviruses (CoVs). In December 2019, in Wuhan, China, a new human CoV was identified, SARS-CoV-2. The first step of the infection mechanism of the SARS-CoV-2 in the human host is adhesion, which occurs through the S glycoprotein that is found in diverse human organs. Another way through which SARS-CoV-2 could possibly attach to the host's cells is by means of the histo-blood group antigens. In this work, we have reviewed the mechanisms by which some viruses bind to the histo-blood group antigens, which could be related to the susceptibility of the individual and are dependent on the histo-blood group.
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Affiliation(s)
- Mayra Cuéllar-Cruz
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta, C.P. 36050, Guanajuato, Guanajuato, México
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Barbieri R, Signoli M, Chevé D, Costedoat C, Tzortzis S, Aboudharam G, Raoult D, Drancourt M. Yersinia pestis: the Natural History of Plague. Clin Microbiol Rev 2020; 34:e00044-19. [PMID: 33298527 PMCID: PMC7920731 DOI: 10.1128/cmr.00044-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.
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Affiliation(s)
- R Barbieri
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Signoli
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - D Chevé
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - C Costedoat
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - S Tzortzis
- Ministère de la Culture, Direction Régionale des Affaires Culturelles de Provence-Alpes-Côte d'Azur, Service Régional de l'Archéologie, Aix-en-Provence, France
| | - G Aboudharam
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, Faculty of Odontology, Marseille, France
| | - D Raoult
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Drancourt
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
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Susat J, Bonczarowska JH, Pētersone-Gordina E, Immel A, Nebel A, Gerhards G, Krause-Kyora B. Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic. Sci Rep 2020; 10:14628. [PMID: 32884081 PMCID: PMC7471286 DOI: 10.1038/s41598-020-71530-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/04/2020] [Indexed: 11/28/2022] Open
Abstract
Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing the pla gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the pla gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. The pla gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread of pla-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.
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Affiliation(s)
- Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Joanna H Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | | | - Alexander Immel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Guntis Gerhards
- Institute of Latvian History, University of Latvia, Kalpaka bulvāris 4, Riga, 1050, Latvia
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany.
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Lemon A, Sagawa J, Gravelle K, Vadyvaloo V. Biovar-related differences apparent in the flea foregut colonization phenotype of distinct Yersinia pestis strains do not impact transmission efficiency. Parasit Vectors 2020; 13:335. [PMID: 32611387 PMCID: PMC7329463 DOI: 10.1186/s13071-020-04207-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/24/2020] [Indexed: 12/25/2022] Open
Abstract
Background Yersinia pestis is the flea-transmitted etiological agent of bubonic plague. Sylvatic plague consists of complex tripartite interactions between diverse flea and wild rodent species, and pathogen strains. Transmission by flea bite occurs primarily by the Y. pestis biofilm-mediated foregut blockage and regurgitation mechanism, which has been largely detailed by studies in the model interaction between Y. pestis KIM6+ and Xenopsylla cheopis. Here, we test if pathogen-specific traits influence this interaction by determining the dynamics of foregut blockage development in X. cheopis fleas among extant avirulent pCD1-Y. pestis strains, KIM6+ and CO92, belonging to distinct biovars, and a non-circulating mutant CO92 strain (CO92gly), restored for glycerol fermentation; a key biochemical difference between the two biovars. Methods Separate flea cohorts infected with distinct strains were evaluated for (i) blockage development, bacterial burdens and flea foregut blockage pathology, and (ii) for the number of bacteria transmitted by regurgitation during membrane feeding. Strain burdens per flea was determined for fleas co-infected with CO92 and KIM6+ strains at a ratio of 1:1. Results Strains KIM6+ and CO92 developed foregut blockage at similar rates and peak temporal incidences, but the CO92gly strain showed significantly greater blockage rates that peak earlier post-infection. The KIM6+ strain, however, exhibited a distinctive foregut pathology wherein bacterial colonization extended the length of the esophagus up to the feeding mouthparts in ~65% of blocked fleas; in contrast to 32% and 26%, respectively, in fleas blocked with CO92 and CO92gly. The proximity of KIM6+ to the flea mouthparts in blocked fleas did not result in higher regurgitative transmission efficiencies as all strains transmitted variable numbers of Y. pestis, albeit slightly lower for CO92gly. During competitive co-infection, strains KIM6+ and CO92 were equally fit maintaining equivalent infection proportions in fleas over time. Conclusions We demonstrate that disparate foregut blockage pathologies exhibited by distinct extant Y. pestis strain genotypes do not influence transmission efficiency from X. cheopis fleas. In fact, distinct extant Y. pestis genotypes maintain equivalently effective blockage and transmission efficiencies which is likely advantageous to maintaining continued successful plague spread and establishment of new plague foci.![]()
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Affiliation(s)
- Athena Lemon
- Paul G Allen School for Global Animal Health, Washington State University, Washington, 99164, USA
| | - Janelle Sagawa
- Paul G Allen School for Global Animal Health, Washington State University, Washington, 99164, USA
| | - Kameron Gravelle
- Paul G Allen School for Global Animal Health, Washington State University, Washington, 99164, USA
| | - Viveka Vadyvaloo
- Paul G Allen School for Global Animal Health, Washington State University, Washington, 99164, USA.
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31
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Putative Horizontally Acquired Genes, Highly Transcribed during Yersinia pestis Flea Infection, Are Induced by Hyperosmotic Stress and Function in Aromatic Amino Acid Metabolism. J Bacteriol 2020; 202:JB.00733-19. [PMID: 32205462 PMCID: PMC7221256 DOI: 10.1128/jb.00733-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/17/2020] [Indexed: 11/20/2022] Open
Abstract
Distinct gene repertoires are expressed during Y. pestis infection of its flea and mammalian hosts. The functions of many of these genes remain predicted or unknown, necessitating their characterization, as this may provide a better understanding of Y. pestis specialized biological adaptations to the discrete environments of its two hosts. This study provides functional context to adjacently clustered horizontally acquired genes predominantly expressed in the flea host by deciphering their fundamental processes with regard to (i) transcriptional organization, (ii) transcription activation signals, and (iii) biochemical function. Our data support a role for these genes in osmoadaptation and aromatic amino acid metabolism, highlighting these as preferential processes by which Y. pestis gene expression is modulated during flea infection. While alternating between insects and mammals during its life cycle, Yersinia pestis, the flea-transmitted bacterium that causes plague, regulates its gene expression appropriately to adapt to these two physiologically disparate host environments. In fleas competent to transmit Y. pestis, low-GC-content genes y3555, y3551, and y3550 are highly transcribed, suggesting that these genes have a highly prioritized role in flea infection. Here, we demonstrate that y3555, y3551, and y3550 are transcribed as part of a single polycistronic mRNA comprising the y3555, y3554, y3553, y355x, y3551, and y3550 genes. Additionally, y355x-y3551-y3550 compose another operon, while y3550 can be also transcribed as a monocistronic mRNA. The expression of these genes is induced by hyperosmotic salinity stress, which serves as an explicit environmental stimulus that initiates transcriptional activity from the predicted y3550 promoter. Y3555 has homology to pyridoxal 5′-phosphate (PLP)-dependent aromatic aminotransferases, while Y3550 and Y3551 are homologous to the Rid protein superfamily (YjgF/YER057c/UK114) members that forestall damage caused by reactive intermediates formed during PLP-dependent enzymatic activity. We demonstrate that y3551 specifically encodes an archetypal RidA protein with 2-aminoacrylate deaminase activity but Y3550 lacks Rid deaminase function. Heterologous expression of y3555 generates a critical aspartate requirement in a Salmonella entericaaspC mutant, while its in vitro expression, and specifically its heterologous coexpression with y3550, enhances the growth rate of an Escherichia coli ΔaspC ΔtyrB mutant in a defined minimal amino acid-supplemented medium. Our data suggest that the y3555, y3551, and y3550 genes operate cooperatively to optimize aromatic amino acid metabolism and are induced under conditions of hyperosmotic salinity stress. IMPORTANCE Distinct gene repertoires are expressed during Y. pestis infection of its flea and mammalian hosts. The functions of many of these genes remain predicted or unknown, necessitating their characterization, as this may provide a better understanding of Y. pestis specialized biological adaptations to the discrete environments of its two hosts. This study provides functional context to adjacently clustered horizontally acquired genes predominantly expressed in the flea host by deciphering their fundamental processes with regard to (i) transcriptional organization, (ii) transcription activation signals, and (iii) biochemical function. Our data support a role for these genes in osmoadaptation and aromatic amino acid metabolism, highlighting these as preferential processes by which Y. pestis gene expression is modulated during flea infection.
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Epidemiological and Epizootic Situation on Plague in the Russian Federation and Forecast for Its Development for 2020–2025. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2020. [DOI: 10.21055/0370-1069-2020-1-43-50] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Objective of the investigation was to assess epidemiological and epizootiological conditions in natural plague foci of the Russian Federation, neighboring states and foreign countries in 2019. Negative effect of the current climate warming on the state of parasitic systems of natural foci with circulation of plague microbe of the main subspecies, medieval biovar, phylogenetic branch 2.MED1 is emphasized. In 2019, local plague epizooties were registered in the territory of two (Gorno-Altai high-mountain and Tuva mountain) out of 11 natural plague foci of the Russian Federation. The total area of epizooty covered 2248.5 km2 . All in all, 31 cultures of Y. pestis of the main subspecies, antique biovar, phylogenetic branch 4.ANT and 5 cultures of Altai biovar, central-asian subspecies, phylogenetic branch 0.PE4a were isolated. The forecast for continuing tense epidemiological situation, both for 2020 and for 2021–2025, has been substantiated for natural foci with circulation of the main subspecies of antique biovar, phyologenetic branch 4.ANT: Gorno-Altai high-mountain and Tuva mountain ones. In the remaining nine natural foci in the territory of the Russian Federation epizootic manifestations of plague in 2020 are highly improbable. This prognosis is an indication to optimize the deployment of human and logistical resources of plague control institutions through concentrated preventive activities in the territories of epizootically active natural plague foci. Otlined is the necessity to put a new enhanced classification of Y. pestis into practice.
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Krukonis ES, Thomson JJ. Complement evasion mechanisms of the systemic pathogens Yersiniae and Salmonellae. FEBS Lett 2020; 594:2598-2620. [DOI: 10.1002/1873-3468.13771] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 01/12/2023]
Affiliation(s)
- Eric S. Krukonis
- Division of Integrated Biomedical Sciences University of Detroit Mercy School of Dentistry Detroit MI USA
| | - Joshua J. Thomson
- Division of Integrated Biomedical Sciences University of Detroit Mercy School of Dentistry Detroit MI USA
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Zhang Y, Ying X, He Y, Jiang L, Zhang S, Bartra SS, Plano GV, Klena JD, Skurnik M, Chen H, Cai H, Chen T. Invasiveness of the Yersinia pestis ail protein contributes to host dissemination in pneumonic and oral plague. Microb Pathog 2020; 141:103993. [PMID: 31988008 DOI: 10.1016/j.micpath.2020.103993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/10/2019] [Accepted: 01/21/2020] [Indexed: 11/24/2022]
Abstract
Yersinia pestis, a Gram-negative bacterium, is the etiologic agent of plague. A hallmark of Y. pestis infection is the organism's ability to rapidly disseminate through an animal host. Y. pestis expresses the outer membrane protein, Ail (Attachment invasion locus), which is associated with host invasion and serum resistance. However, whether Ail plays a role in host dissemination remains unclear. In this study, C57BL/6J mice were challenged with a defined Y. pestis strain, KimD27, or an isogenic ail-deleted mutant derived from KimD27 via metacarpal paw pad inoculation, nasal drops, orogastric infection, or tail vein injection to mimic bubonic, pneumonic, oral, or septicemic plague, respectively. Our results showed that ail-deleted Y. pestis KimD27 lost the ability to invade host cells, leading to failed host dissemination in the pneumonic and oral plague models but not in the bubonic or septicemic plague models, which do not require invasiveness. Therefore, this study demonstrated that whether Ail plays a role in Y. pestis pathogenesis depends on the infection route.
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Affiliation(s)
- Yingmiao Zhang
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, Hubei, China
| | - Xiaoling Ying
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, Hubei, China; Translational Medicine Conter, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510000, Guangdong, China
| | - Yingxia He
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, Hubei, China
| | - Lingyu Jiang
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, Hubei, China
| | - Song Zhang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sara Schesser Bartra
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, 33101, USA
| | - Gregory V Plano
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, 33101, USA
| | - John D Klena
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Hongxiang Chen
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huahua Cai
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, Hubei, China.
| | - Tie Chen
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, Hubei, China.
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Bishop AH. The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases. FEMS Microbiol Lett 2019; 366:5303725. [PMID: 30689874 DOI: 10.1093/femsle/fnz021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/26/2019] [Indexed: 12/28/2022] Open
Abstract
The microorganisms with which we share our world go largely unnoticed. We are, however, beginning to be able to exploit their apparently silent presence as witnesses to events that are of legal concern. This information can be used to link forensic samples to criminal events and even perpetrators. Once dead, our bodies are rapidly colonised, internally and externally. The progress of these events can be charted to inform how long and even by what means a person has died. A small number of microbial species could actually be the cause of such deaths as a result of biocrime or bioterrorism. The procedures and techniques to respond to such attacks have matured in the last 20 years. The capability now exists to identify malicious intent, characterise the threat agent to isolate level and potentially link it to perpetrators with a high level of confidence.
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Affiliation(s)
- A H Bishop
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Devon, PL4 8AA, UK
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36
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Kislichkina AA, Platonov ME, Vagaiskaya AS, Bogun AG, Dentovskaya SV, Anisimov AP. Rational Taxonomy of Yersinia pestis. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2019. [DOI: 10.3103/s0891416819020058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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37
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Ye C, Li Q, Li X, Park CG, He Y, Zhang Y, Wu B, Xue Y, Yang K, Lv Y, Ying XL, Ding HH, Cai H, Alkraiem AA, Njiri O, Tembo J, Huang HP, Li AY, Gong J, Qin J, Cheng B, Wei X, Sun Z, Zhang SS, Zhang P, Zheng GX, Li W, Kan B, Yan M, Xiding X, Huo X, Zeng Y, Peng H, Fu Y, Klena JD, Skurnik M, Jiang LY, Chen T. Salmonella enterica Serovar Typhimurium Interacts with CD209 Receptors To Promote Host Dissemination and Infection. Infect Immun 2019; 87:e00100-19. [PMID: 31085704 PMCID: PMC6652768 DOI: 10.1128/iai.00100-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/04/2019] [Indexed: 12/22/2022] Open
Abstract
Salmonella enterica serovar Typhimurium, a Gram-negative bacterium, can cause infectious diseases ranging from gastroenteritis to systemic dissemination and infection. However, the molecular mechanisms underlying this bacterial dissemination have yet to be elucidated. A study indicated that using the lipopolysaccharide (LPS) core as a ligand, S Typhimurium was able to bind human dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (hCD209a), an HIV receptor that promotes viral dissemination by hijacking antigen-presenting cells (APCs). In this study, we showed that S Typhimurium interacted with CD209s, leading to the invasion of APCs and potentially the dissemination to regional lymph nodes, spleen, and liver in mice. Shielding of the exposed LPS core through the expression of O-antigen reduces dissemination and infection. Thus, we propose that similar to HIV, S Typhimurium may also utilize APCs via interactions with CD209s as a way to disseminate to the lymph nodes, spleen, and liver to initiate host infection.
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Affiliation(s)
- Chenglin Ye
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Qiao Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Xinyi Li
- Department of Clinical Laboratory, Jingmen No. 1 People's Hospital, Jingmen, China
| | - Chae Gyu Park
- Laboratory of Immunology, Brain Korea 21 PLUS Project for Medical Science, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yingxia He
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Yingmiao Zhang
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Bicong Wu
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Ying Xue
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Kun Yang
- Department of Pathogen Biology and Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Yin Lv
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Xiao-Ling Ying
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Hong-Hui Ding
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Huahua Cai
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Ayman Ahmad Alkraiem
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
- Department of Biology, College of Science, Taibah University, Medina, Kingdom of Saudi Arabia
| | - Olivia Njiri
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - John Tembo
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Hong-Ping Huang
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - An-Yi Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Jianping Gong
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Jichao Qin
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Bing Cheng
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Xiang Wei
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Ziyong Sun
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Shu-Sheng Zhang
- Department of Biomedical Science, College of Medicine-Rockford, University of Illinois at Chicago, Rockford, Illinois, USA
| | - Pei Zhang
- Department of Biomedical Science, College of Medicine-Rockford, University of Illinois at Chicago, Rockford, Illinois, USA
| | - Guo-Xing Zheng
- Department of Biomedical Science, College of Medicine-Rockford, University of Illinois at Chicago, Rockford, Illinois, USA
| | - Wei Li
- Department of Diarrheal Diseases, National Institute for Communicable Diseases Control and Prevention, Beijing, China
| | - Biao Kan
- Department of Diarrheal Diseases, National Institute for Communicable Diseases Control and Prevention, Beijing, China
| | - Meiying Yan
- Department of Diarrheal Diseases, National Institute for Communicable Diseases Control and Prevention, Beijing, China
| | - Xiamu Xiding
- Division of Disease Control and Prevention for Endemic Diseases, Wenquan Center for Disease Control and Prevention, Xinjiang, China
| | - Xixiang Huo
- Hubei Provincial Center for Disease Control and Prevention (CDC), Wuhan, Hubei, China
| | - Yingchun Zeng
- Hubei Provincial Center for Disease Control and Prevention (CDC), Wuhan, Hubei, China
| | - Hua Peng
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yangxin Fu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John D Klena
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Ling-Yu Jiang
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Tie Chen
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
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Abstract
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.
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Reply to McLean et al.: Collections are critical. Proc Natl Acad Sci U S A 2019; 116:14413. [DOI: 10.1073/pnas.1909035116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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40
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Bos KI, Kühnert D, Herbig A, Esquivel-Gomez LR, Andrades Valtueña A, Barquera R, Giffin K, Kumar Lankapalli A, Nelson EA, Sabin S, Spyrou MA, Krause J. Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annu Rev Microbiol 2019; 73:639-666. [PMID: 31283430 DOI: 10.1146/annurev-micro-090817-062436] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.
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Affiliation(s)
- Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Luis Roger Esquivel-Gomez
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; .,Faculty of Biological Sciences, Friedrich Schiller University, 07737 Jena, Germany
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41
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Xu L, Stige LC, Leirs H, Neerinckx S, Gage KL, Yang R, Liu Q, Bramanti B, Dean KR, Tang H, Sun Z, Stenseth NC, Zhang Z. Historical and genomic data reveal the influencing factors on global transmission velocity of plague during the Third Pandemic. Proc Natl Acad Sci U S A 2019; 116:11833-11838. [PMID: 31138696 PMCID: PMC6584904 DOI: 10.1073/pnas.1901366116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Quantitative knowledge about which natural and anthropogenic factors influence the global spread of plague remains sparse. We estimated the worldwide spreading velocity of plague during the Third Pandemic, using more than 200 years of extensive human plague case records and genomic data, and analyzed the association of spatiotemporal environmental factors with spreading velocity. Here, we show that two lineages, 2.MED and 1.ORI3, spread significantly faster than others, possibly reflecting differences among strains in transmission mechanisms and virulence. Plague spread fastest in regions with low population density and high proportion of pasture- or forestland, findings that should be taken into account for effective plague monitoring and control. Temperature exhibited a nonlinear, U-shaped association with spread speed, with a minimum around 20 °C, while precipitation showed a positive association. Our results suggest that global warming may accelerate plague spread in warm, tropical regions and that the projected increased precipitation in the Northern Hemisphere may increase plague spread in relevant regions.
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Affiliation(s)
- Lei Xu
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, 100084 Beijing, China
| | - Leif C Stige
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
| | - Simon Neerinckx
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
| | - Kenneth L Gage
- Bacterial Diseases Branch, Division of Vector-Borne Disease, Centers for Disease Control and Prevention, Fort Collins, CO 80523
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071 Beijing, China
| | - Qiyong Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Katharine R Dean
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Hui Tang
- Department of Geosciences, University of Oslo, N-0316 Oslo, Norway
| | - Zhe Sun
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, 100084 Beijing, China
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, 100084 Beijing, China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China;
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Zhang Q, Xin Y, Zhao H, Liu R, Xu X, Yan Y, Kong Z, Wang T, Qi Z, Zhang Q, You Y, Song Y, Cui Y, Yang R, Zhang X, Du Z. Human Macrophages Clear the Biovar Microtus Strain of Yersinia pestis More Efficiently Than Murine Macrophages. Front Cell Infect Microbiol 2019; 9:111. [PMID: 31069175 PMCID: PMC6491462 DOI: 10.3389/fcimb.2019.00111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/29/2019] [Indexed: 12/20/2022] Open
Abstract
Yersinia pestis is the etiological agent of the notorious plague that has claimed millions of deaths in history. Of the four known Y. pestis biovars (Antiqua, Medievalis, Orientalis, and Microtus), Microtus strains are unique for being highly virulent in mice but avirulent in humans. Here, human peripheral lymphocytes were infected with the fully virulent 141 strain or the Microtus strain 201, and their transcriptomes were determined and compared. The most notable finding was that robust responses in the pathways for cytokine-cytokine receptor interaction, chemokine signaling pathway, Toll-like receptor signaling and Jak-STAT signaling were induced at 2 h post infection (hpi) in the 201- but not the 141-infected lymphocytes, suggesting that human lymphocytes might be able to constrain infections caused by strain 201 but not 141. Consistent with the transcriptome results, much higher IFN-γ and IL-1β were present in the supernatants from the 201-infected lymphocytes, while inflammatory inhibitory IL-10 levels were higher in the 141-infected lymphocytes. The expressions of CSTD and SLC11A1, both of which are functional components of the lysosome, increased in the 201-infected human macrophage-like U937 cells. Further assessment of the survival rate of the 201 bacilli in the U937 cells and murine macrophage RAW 264.7 cells revealed no viable bacteria in the U937 cells at 32 hpi.; however, about 5–10% of the bacteria were still alive in the RAW264.7 cells. Our results indicate that human macrophages can clear the intracellular Y. pestis 201 bacilli more efficiently than murine macrophages, probably by interfering with critical host immune responses, and this could partially account for the host-specific pathogenicity of Y. pestis Microtus strains.
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Affiliation(s)
- Qingwen Zhang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Youquan Xin
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Haihong Zhao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Rongjiao Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoqing Xu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhipeng Kong
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Tong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhizhen Qi
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Qi Zhang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Yang You
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xuefei Zhang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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43
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Nikiforov KA, Al’khova ZV, Kukleva LM, Naryshkina EA, Oglodin EG, Eroshenko GA, Kutyrev VV. Phylogenetic Analysis of Yersinia pestis Strains of the Caucasian Subspecies from the Foci of the Caucasus and Transcaucasia according to the Whole Genome Sequencing Data. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419040070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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Yang K, He Y, Park CG, Kang YS, Zhang P, Han Y, Cui Y, Bulgheresi S, Anisimov AP, Dentovskaya SV, Ying X, Jiang L, Ding H, Njiri OA, Zhang S, Zheng G, Xia L, Kan B, Wang X, Jing H, Yan M, Li W, Wang Y, Xiamu X, Chen G, Ma D, Bartra SS, Plano GV, Klena JD, Yang R, Skurnik M, Chen T. Yersinia pestis Interacts With SIGNR1 (CD209b) for Promoting Host Dissemination and Infection. Front Immunol 2019; 10:96. [PMID: 30915064 PMCID: PMC6422942 DOI: 10.3389/fimmu.2019.00096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 01/14/2019] [Indexed: 01/01/2023] Open
Abstract
Yersinia pestis, a Gram-negative bacterium and the etiologic agent of plague, has evolved from Yersinia pseudotuberculosis, a cause of a mild enteric disease. However, the molecular and biological mechanisms of how Y. pseudotuberculosis evolved to such a remarkably virulent pathogen, Y. pestis, are not clear. The ability to initiate a rapid bacterial dissemination is a characteristic hallmark of Y. pestis infection. A distinguishing characteristic between the two Yersinia species is that Y. pseudotuberculosis strains possess an O-antigen of lipopolysaccharide (LPS) while Y. pestis has lost the O-antigen during evolution and therefore exposes its core LPS. In this study, we showed that Y. pestis utilizes its core LPS to interact with SIGNR1 (CD209b), a C-type lectin receptor on antigen presenting cells (APCs), leading to bacterial dissemination to lymph nodes, spleen and liver, and the initiation of a systemic infection. We therefore propose that the loss of O-antigen represents a critical step in the evolution of Y. pseudotuberculosis into Y. pestis in terms of hijacking APCs, promoting bacterial dissemination and causing the plague.
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Affiliation(s)
- Kun Yang
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Pathogen Biology and Immunology, Shihezi University School of Medicine, Shihezi, China
| | - Yingxia He
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chae Gyu Park
- Laboratory of Immunology, Brain Korea 21 PLUS Project for Medical Science, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Young Sun Kang
- Laboratory of Immunology, Brain Korea 21 PLUS Project for Medical Science, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Pei Zhang
- Department of Biomedical Sciences, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Silvia Bulgheresi
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Andrey P Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | | | - Xiaoling Ying
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lingyu Jiang
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Honghui Ding
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Olivia Adhiambo Njiri
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Biological Sciences, Faculty of Science, Technology and Engineering, Chuka University, Chuka, Kenya
| | - Shusheng Zhang
- Department of Biomedical Sciences, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Guoxing Zheng
- Department of Biomedical Sciences, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Lianxu Xia
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Wang
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huaiqi Jing
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meiying Yan
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei Li
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuanzhi Wang
- Department of Pathogen Biology and Immunology, Shihezi University School of Medicine, Shihezi, China
| | - Xiding Xiamu
- Department of Pathogen Biology and Immunology, Shihezi University School of Medicine, Shihezi, China
| | - Gang Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sara Schesser Bartra
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Gregory V Plano
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - John D Klena
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Haartman Institute, Helsinki University Central Hospital Laboratory Diagnostics, University of Helsinki, Helsinki, Finland
| | - Tie Chen
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Pathogen Biology and Immunology, Shihezi University School of Medicine, Shihezi, China
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Yersinia pseudotuberculosis Exploits CD209 Receptors for Promoting Host Dissemination and Infection. Infect Immun 2018; 87:IAI.00654-18. [PMID: 30348825 DOI: 10.1128/iai.00654-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/09/2018] [Indexed: 12/20/2022] Open
Abstract
Yersinia pseudotuberculosis is a Gram-negative enteropathogen and causes gastrointestinal infections. It disseminates from gut to mesenteric lymph nodes (MLNs), spleen, and liver of infected humans and animals. Although the molecular mechanisms for dissemination and infection are unclear, many Gram-negative enteropathogens presumably invade the small intestine via Peyer's patches to initiate dissemination. In this study, we demonstrate that Y. pseudotuberculosis utilizes its lipopolysaccharide (LPS) core to interact with CD209 receptors, leading to invasion of human dendritic cells (DCs) and murine macrophages. These Y. pseudotuberculosis-CD209 interactions result in bacterial dissemination to MLNs, spleens, and livers of both wild-type and Peyer's patch-deficient mice. The blocking of the Y. pseudotuberculosis-CD209 interactions by expression of O-antigen and with oligosaccharides reduces infectivity. Based on the well-documented studies in which HIV-CD209 interaction leads to viral dissemination, we therefore propose an infection route for Y. pseudotuberculosis where this pathogen, after penetrating the intestinal mucosal membrane, hijacks the Y. pseudotuberculosis-CD209 interaction antigen-presenting cells to reach their target destinations, MLNs, spleens, and livers.
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McLaughlin HP, Sue D. Rapid antimicrobial susceptibility testing and β-lactam-induced cell morphology changes of Gram-negative biological threat pathogens by optical screening. BMC Microbiol 2018; 18:218. [PMID: 30563467 PMCID: PMC6299660 DOI: 10.1186/s12866-018-1347-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND For Yersinia pestis, Burkholderia pseudomallei, and Burkholderia mallei, conventional broth microdilution (BMD) is considered the gold standard for antimicrobial susceptibility testing (AST) and, depending on the species, requires an incubation period of 16-20 h, or 24-48 h according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. After a diagnosis of plague, melioidosis or glanders during an outbreak or after an exposure event, the timely distribution of appropriate antibiotics for treatment or post-exposure prophylaxis of affected populations could reduce mortality rates. RESULTS Herein, we developed and evaluated a rapid, automated susceptibility test for these Gram-negative bacterial pathogens based on time-lapse imaging of cells incubating in BMD microtitre drug panels using an optical screening instrument (oCelloScope). In real-time, the instrument screened each inoculated well containing broth with various concentrations of antibiotics published by CLSI for primary testing: ciprofloxacin (CIP), doxycycline (DOX) and gentamicin (GEN) for Y. pestis; imipenem (IPM), ceftazidime (CAZ) and DOX for B. mallei; and IPM, DOX, CAZ, amoxicillin-clavulanic acid (AMC) and trimethoprim-sulfamethoxazole (SXT) for B. pseudomallei. Based on automated growth kinetic data, the time required to accurately determine susceptibility decreased by ≥70% for Y. pestis and ≥ 50% for B. mallei and B. pseudomallei compared to the times required for conventional BMD testing. Susceptibility to GEN, IPM and DOX could be determined in as early as three to six hours. In the presence of CAZ, susceptibility based on instrument-derived growth values could not be determined for the majority of B. pseudomallei and B. mallei strains tested. Time-lapse video imaging of these cultures revealed that the formation of filaments in the presence of this cephalosporin at inhibitory concentrations was detected as growth. Other β-lactam-induced cell morphology changes, such as the formation of spheroplasts and rapid cell lysis, were also observed and appear to be strain- and antibiotic concentration-dependent. CONCLUSIONS A rapid, functional AST was developed and real-time video footage captured β-lactam-induced morphologies of wild-type B. mallei and B. pseudomallei strains in broth. Optical screening reduced the time to results required for AST of three Gram-negative biothreat pathogens using clinically relevant, first-line antibiotics compared to conventional BMD.
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Affiliation(s)
- Heather P. McLaughlin
- Laboratory of Preparedness and Response Branch, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS-H17-5, Atlanta, GA 30333 USA
| | - David Sue
- Laboratory of Preparedness and Response Branch, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS-H17-5, Atlanta, GA 30333 USA
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Abstract
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms. Herein I discuss the potential functions that the genes that are dubbed virulence or antibiotic resistance genes may have in their original hosts in nonclinical, natural ecosystems. In addition, I discuss the potential bottlenecks modulating the transfer of virulence and antibiotic resistance determinants and the consequences in terms of speciation of acquiring one or another of both categories of genes. Finally, I propose that exaptation, a process by which a change of function is achieved by a change of habitat and not by changes in the element with the new functionality, is the basis of the evolution of virulence determinants and of antibiotic resistance genes.
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Noto JM, Chopra A, Loh JT, Romero-Gallo J, Piazuelo MB, Watson M, Leary S, Beckett AC, Wilson KT, Cover TL, Mallal S, Israel DA, Peek RM. Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments. Gut 2018; 67:1793-1804. [PMID: 28924022 PMCID: PMC5857411 DOI: 10.1136/gutjnl-2017-313863] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/30/2017] [Accepted: 07/15/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease. DESIGN Whole genome sequencing of genetically related H. pylori strains that differ in virulence and targeted H. pylori sequencing following prolonged exposure of bacteria to in vitro carcinogenic conditions were performed. RESULTS A total of 180 unique single nucleotide polymorphisms (SNPs) were identified among the collective genomes when compared with a reference H. pylori genome. Importantly, common SNPs were identified in isolates harvested from iron-depleted and high salt carcinogenic microenvironments, including an SNP within fur (FurR88H). To investigate the direct role of low iron and/or high salt, H. pylori was continuously cultured in vitro under low iron or high salt conditions to assess fur genetic variation. Exposure to low iron or high salt selected for the FurR88H variant after only 5 days. To extend these results, fur was sequenced in 339 clinical H. pylori strains. Among the isolates examined, 17% (40/232) of strains isolated from patients with premalignant lesions harboured the FurR88H variant, compared with only 6% (6/107) of strains from patients with non-atrophic gastritis alone (p=0.0034). CONCLUSION These results indicate that specific genetic variation arises within H. pylori strains during in vivo adaptation to conditions conducive for gastric carcinogenesis.
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Affiliation(s)
- Jennifer M Noto
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - John T Loh
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Judith Romero-Gallo
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Blanca Piazuelo
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mark Watson
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Amber C Beckett
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T Wilson
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy L Cover
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA,Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, Tennessee, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia,Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, Tennessee, USA
| | - Dawn A Israel
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard M Peek
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Dai R, Wei B, Xiong H, Yang X, Peng Y, He J, Jin J, Wang Y, Zha X, Zhang Z, Liang Y, Zhang Q, Xu J, Wang Z, Li W. Human plague associated with Tibetan sheep originates in marmots. PLoS Negl Trop Dis 2018; 12:e0006635. [PMID: 30114220 PMCID: PMC6095483 DOI: 10.1371/journal.pntd.0006635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 06/25/2018] [Indexed: 11/21/2022] Open
Abstract
The Qinghai-Tibet plateau is a natural plague focus and is the largest such focus in China. In this area, while Marmota himalayana is the primary host, a total of 18 human plague outbreaks associated with Tibetan sheep (78 cases with 47 deaths) have been reported on the Qinghai-Tibet plateau since 1956. All of the index infectious cases had an exposure history of slaughtering or skinning diseased or dead Tibetan sheep. In this study, we sequenced and compared 38 strains of Yersinia pestis isolated from different hosts, including humans, Tibetan sheep, and M. himalayana. Phylogenetic relationships were reconstructed based on genome-wide single-nucleotide polymorphisms identified from our isolates and reference strains. The phylogenetic relationships illustrated in our study, together with the finding that the Tibetan sheep plague clearly lagged behind the M. himalayana plague, and a previous study that identified the Tibetan sheep as a plague reservoir with high susceptibility and moderate sensitivity, indicated that the human plague was transmitted from Tibetan sheep, while the Tibetan sheep plague originated from marmots. Tibetan sheep may encounter this infection by contact with dead rodents or through being bitten by fleas originating from M. himalayana during local epizootics. Plague is mainly a disease of wild rodents, and their parasitic fleas are considered the transmitting vectors. However, human plague originating from Ovis aries (Tibetan sheep) is found in the Qinghai-Tibet plateau in China, where Marmota. himalayana is the primary plague host. Tibetan sheep-related human plague infection is always associated with slaughtering or skinning diseased or dead Tibetan sheep. The plague in Tibetan sheep clearly lags that in M. himalayana. In this study, we performed a genome-wide single nucleotide polymorphism analysis of Tibetan sheep-related plague events, including pathogens isolated from humans, Tibetan sheep, and marmots. Through genomic analysis, together with the epidemiological connections, we confirmed that human plague came from Tibetan sheep, and the Tibetan sheep plague originated from marmots. Tibetan sheep account for about 1/3 of the total number of sheep in China. Tibetan sheep and goats are important domestic livestock on the Qinghai-Tibet plateau. Therefore, the hazards of Tibetan sheep plague should not be underestimated.
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Affiliation(s)
- Ruixia Dai
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Baiqing Wei
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Haoming Xiong
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Xiaoyan Yang
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Yao Peng
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Jian He
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Juan Jin
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Yumeng Wang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Xi Zha
- Center for Disease Control and Prevention of Tibet Autonomous Region, Lhasa, China
| | - Zhikai Zhang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Ying Liang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Qingwen Zhang
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Jianguo Xu
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Zuyun Wang
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
- * E-mail:
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Suntsov VV. Quantum Speciation of Yersinia pestis Plague Microbe in a Heteroimmune Environment: In the Populations of Hibernating Tarbagan Marmots (Marmota sibirica). CONTEMP PROBL ECOL+ 2018. [DOI: 10.1134/s199542551804008x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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