1
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High-throughput fitness screens link genes to unique phenotypes in human-restricted Salmonella. Nat Genet 2024:10.1038/s41588-024-01780-0. [PMID: 38849614 DOI: 10.1038/s41588-024-01780-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
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2
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Wang BX, Leshchiner D, Luo L, Tuncel M, Hokamp K, Hinton JCD, Monack DM. High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection. Nat Genet 2024:10.1038/s41588-024-01779-7. [PMID: 38831009 DOI: 10.1038/s41588-024-01779-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/25/2024] [Indexed: 06/05/2024]
Abstract
Salmonella enterica is comprised of genetically distinct 'serovars' that together provide an intriguing model for exploring the genetic basis of pathogen evolution. Although the genomes of numerous Salmonella isolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. Here, we conduct high-throughput functional genomics on both generalist (Typhimurium) and human-restricted (Typhi and Paratyphi A) Salmonella at unprecedented scale in the study of this enteric pathogen. Using a comprehensive systems biology approach, we identify gene networks with serovar-specific fitness effects across 25 host-associated stresses encountered at key stages of human infection. By experimentally perturbing these networks, we characterize previously undescribed pseudogenes in human-adapted Salmonella. Overall, this work highlights specific vulnerabilities encoded within human-restricted Salmonella that are linked to the degradation of their genomes, shedding light into the evolution of this enteric pathogen.
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Affiliation(s)
- Benjamin X Wang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Lijuan Luo
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Miles Tuncel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Denise M Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Hanke DM, Wang Y, Dagan T. Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility. Nucleic Acids Res 2024:gkae430. [PMID: 38808675 DOI: 10.1093/nar/gkae430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare in prokaryote chromosomes, with the exception of lineages that underwent an extreme genome reduction (e.g. obligatory symbionts). Much less is known about the frequency of pseudogenes in prokaryotic plasmids; those are genetic elements that can transfer between cells and may encode beneficial traits for their host. Non-functionalization of plasmid-encoded genes may alter the plasmid characteristics, e.g. mobility, or their effect on the host. Analyzing 10 832 prokaryotic genomes, we find that plasmid genomes are characterized by threefold-higher pseudogene density compared to chromosomes. The majority of plasmid pseudogenes correspond to deteriorated transposable elements. A detailed analysis of enterobacterial plasmids furthermore reveals frequent gene non-functionalization events associated with the loss of plasmid self-transmissibility. Reconstructing the evolution of closely related plasmids reveals that non-functionalization of the conjugation machinery led to the emergence of non-mobilizable plasmid types. Examples are virulence plasmids in Escherichia and Salmonella. Our study highlights non-functionalization of core plasmid mobility functions as one route for the evolution of domesticated plasmids. Pseudogenes in plasmids supply insights into past transitions in plasmid mobility that are akin to transitions in bacterial lifestyle.
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Affiliation(s)
- Dustin M Hanke
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
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4
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Yang Y, Wang P, Qaidi SE, Hardwidge PR, Huang J, Zhu G. Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance. Appl Microbiol Biotechnol 2024; 108:328. [PMID: 38717672 PMCID: PMC11078800 DOI: 10.1007/s00253-023-12971-w] [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: 09/26/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 05/12/2024]
Abstract
Pseudogenes are defined as "non-functional" copies of corresponding parent genes. The cognition of pseudogenes continues to be refreshed through accumulating and updating research findings. Previous studies have predominantly focused on mammals, but pseudogenes have received relatively less attention in the field of microbiology. Given the increasing recognition on the importance of pseudogenes, in this review, we focus on several aspects of microorganism pseudogenes, including their classification and characteristics, their generation and fate, their identification, their abundance and distribution, their impact on virulence, their ability to recombine with functional genes, the extent to which some pseudogenes are transcribed and translated, and the relationship between pseudogenes and viruses. By summarizing and organizing the latest research progress, this review will provide a comprehensive perspective and improved understanding on pseudogenes in microorganisms. KEY POINTS: • Concept, classification and characteristics, identification and databases, content, and distribution of microbial pseudogenes are presented. • How pseudogenization contribute to pathogen virulence is highlighted. • Pseudogenes with potential functions in microorganisms are discussed.
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Affiliation(s)
- Yi Yang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Pengzhi Wang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Key Lab of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- College of Bioscience and Biotechnology, Yangzhou University, 12 East Wenhui Road Yangzhou, Jiangsu, 225009, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China.
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5
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Machado LFM, Galán JE. Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradation. mBio 2024; 15:e0060724. [PMID: 38572992 PMCID: PMC11077982 DOI: 10.1128/mbio.00607-24] [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: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Salmonella enterica serovar Typhi and Paratyphi A are the cause of typhoid and paratyphoid fever in humans, which are systemic life-threatening illnesses. Both serovars are exclusively adapted to the human host, where they can cause life-long persistent infection. A distinct feature of these serovars is the presence of a relatively high number of degraded coding sequences coding for metabolic pathways, most likely a consequence of their adaptation to a single host. As a result of convergent evolution, these serovars shared many of the degraded coding sequences although often affecting different genes in the same metabolic pathway. However, there are several coding sequences that appear intact in one serovar while clearly degraded in the other, suggesting differences in their metabolic capabilities. Here, we examined the functionality of metabolic pathways that appear intact in S. Typhi but that show clear signs of degradation in S. Paratyphi A. We found that, in all cases, the existence of single amino acid substitutions in S. Typhi metabolic enzymes, transporters, or transcription regulators resulted in the inactivation of these metabolic pathways. Thus, the inability of S. Typhi to metabolize Glucose-6-Phosphate or 3-phosphoglyceric acid is due to the silencing of the expression of the genes encoding the transporters for these compounds due to point mutations in the transcriptional regulatory proteins. In contrast, its inability to utilize glucarate or galactarate is due to the presence of point mutations in the transporter and enzymes necessary for the metabolism of these sugars. These studies provide additional support for the concept of adaptive convergent evolution of these two human-adapted S. enterica serovars and highlight a limitation of bioinformatic approaches to predict metabolic capabilities. IMPORTANCE Salmonella enterica serovar Typhi and Paratyphi A are the cause of typhoid and paratyphoid fever in humans, which are systemic life-threatening illnesses. Both serovars can only infect the human host, where they can cause life-long persistent infection. Because of their adaptation to the human host, these bacterial pathogens have changed their metabolism, leading to the loss of their ability to utilize certain nutrients. In this study we examined the functionality of metabolic pathways that appear intact in S. Typhi but that show clear signs of degradation in S. Paratyphi A. We found that, in all cases, the existence of single amino acid substitutions in S. Typhi metabolic enzymes, transporters, or transcription regulators resulted in the inactivation of these metabolic pathways. These studies provide additional support for the concept of adaptive convergent evolution of these two human-adapted S. enterica serovars.
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Affiliation(s)
- Leopoldo F. M. Machado
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jorge E. Galán
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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6
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Oke MT, D’Costa VM. Functional Divergence of the Paralog Salmonella Effector Proteins SopD and SopD2 and Their Contributions to Infection. Int J Mol Sci 2024; 25:4191. [PMID: 38673776 PMCID: PMC11050076 DOI: 10.3390/ijms25084191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Salmonella enterica is a leading cause of bacterial food-borne illness in humans and is responsible for millions of cases annually. A critical strategy for the survival of this pathogen is the translocation of bacterial virulence factors termed effectors into host cells, which primarily function via protein-protein interactions with host proteins. The Salmonella genome encodes several paralogous effectors believed to have arisen from duplication events throughout the course of evolution. These paralogs can share structural similarities and enzymatic activities but have also demonstrated divergence in host cell targets or interaction partners and contributions to the intracellular lifecycle of Salmonella. The paralog effectors SopD and SopD2 share 63% amino acid sequence similarity and extensive structural homology yet have demonstrated divergence in secretion kinetics, intracellular localization, host targets, and roles in infection. SopD and SopD2 target host Rab GTPases, which represent critical regulators of intracellular trafficking that mediate diverse cellular functions. While SopD and SopD2 both manipulate Rab function, these paralogs display differences in Rab specificity, and the effectors have also evolved multiple mechanisms of action for GTPase manipulation. Here, we highlight this intriguing pair of paralog effectors in the context of host-pathogen interactions and discuss how this research has presented valuable insights into effector evolution.
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Affiliation(s)
- Mosopefoluwa T. Oke
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Vanessa M. D’Costa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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7
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Stepien TA, Singletary LA, Guerra FE, Karlinsey JE, Libby SJ, Jaslow SL, Gaggioli MR, Gibbs KD, Ko DC, Brehm MA, Greiner DL, Shultz LD, Fang FC. Nuclear factor kappa B-dependent persistence of Salmonella Typhi and Paratyphi in human macrophages. mBio 2024; 15:e0045424. [PMID: 38497655 PMCID: PMC11005419 DOI: 10.1128/mbio.00454-24] [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: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
Salmonella serovars Typhi and Paratyphi cause a prolonged illness known as enteric fever, whereas other serovars cause acute gastroenteritis. Mechanisms responsible for the divergent clinical manifestations of nontyphoidal and enteric fever Salmonella infections have remained elusive. Here, we show that S. Typhi and S. Paratyphi A can persist within human macrophages, whereas S. Typhimurium rapidly induces apoptotic macrophage cell death that is dependent on Salmonella pathogenicity island 2 (SPI2). S. Typhi and S. Paratyphi A lack 12 specific SPI2 effectors with pro-apoptotic functions, including nine that target nuclear factor κB (NF-κB). Pharmacologic inhibition of NF-κB or heterologous expression of the SPI2 effectors GogA or GtgA restores apoptosis of S. Typhi-infected macrophages. In addition, the absence of the SPI2 effector SarA results in deficient signal transducer and activator of transcription 1 (STAT1) activation and interleukin 12 production, leading to impaired TH1 responses in macrophages and humanized mice. The absence of specific nontyphoidal SPI2 effectors may allow S. Typhi and S. Paratyphi A to cause chronic infections. IMPORTANCE Salmonella enterica is a common cause of gastrointestinal infections worldwide. The serovars Salmonella Typhi and Salmonella Paratyphi A cause a distinctive systemic illness called enteric fever, whose pathogenesis is incompletely understood. Here, we show that enteric fever Salmonella serovars lack 12 specific virulence factors possessed by nontyphoidal Salmonella serovars, which allow the enteric fever serovars to persist within human macrophages. We propose that this fundamental difference in the interaction of Salmonella with human macrophages is responsible for the chronicity of typhoid and paratyphoid fever, suggesting that targeting the nuclear factor κB (NF-κB) complex responsible for macrophage survival could facilitate the clearance of persistent bacterial infections.
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Affiliation(s)
- Taylor A. Stepien
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - Fermin E. Guerra
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Joyce E. Karlinsey
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Stephen J. Libby
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Sarah L. Jaslow
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Margaret R. Gaggioli
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Kyle D. Gibbs
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Michael A. Brehm
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Dale L. Greiner
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Ferric C. Fang
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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8
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Kim JS, Liu L, Kant S, Orlicky DJ, Uppalapati S, Margolis A, Davenport BJ, Morrison TE, Matsuda J, McClelland M, Jones-Carson J, Vazquez-Torres A. Anaerobic respiration of host-derived methionine sulfoxide protects intracellular Salmonella from the phagocyte NADPH oxidase. Cell Host Microbe 2024; 32:411-424.e10. [PMID: 38307020 DOI: 10.1016/j.chom.2024.01.004] [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: 09/22/2023] [Revised: 12/06/2023] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
Intracellular Salmonella experiencing oxidative stress downregulates aerobic respiration. To maintain cellular energetics during periods of oxidative stress, intracellular Salmonella must utilize terminal electron acceptors of lower energetic value than molecular oxygen. We show here that intracellular Salmonella undergoes anaerobic respiration during adaptation to the respiratory burst of the phagocyte NADPH oxidase in macrophages and in mice. Reactive oxygen species generated by phagocytes oxidize methionine, generating methionine sulfoxide. Anaerobic Salmonella uses the molybdenum cofactor-containing DmsABC enzymatic complex to reduce methionine sulfoxide. The enzymatic activity of the methionine sulfoxide reductase DmsABC helps Salmonella maintain an alkaline cytoplasm that supports the synthesis of the antioxidant hydrogen sulfide via cysteine desulfuration while providing a source of methionine and fostering redox balancing by associated dehydrogenases. Our investigations demonstrate that nontyphoidal Salmonella responding to oxidative stress exploits the anaerobic metabolism associated with dmsABC gene products, a pathway that has accrued inactivating mutations in human-adapted typhoidal serovars.
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Affiliation(s)
- Ju-Sim Kim
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Lin Liu
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sashi Kant
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David J Orlicky
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Siva Uppalapati
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Alyssa Margolis
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Bennett J Davenport
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Thomas E Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Michael McClelland
- University of California Irvine School of Medicine, Department of Microbiology and Molecular Genetics, Irvine, CA, USA
| | - Jessica Jones-Carson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Andres Vazquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Veterans Affairs, Eastern Colorado Health Care System, Aurora, CO 80045, USA.
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Scharte F, Franzkoch R, Hensel M. Flagella-mediated cytosolic motility of Salmonella enterica Paratyphi A aids in evasion of xenophagy but does not impact egress from host cells. Mol Microbiol 2024; 121:413-430. [PMID: 37278220 DOI: 10.1111/mmi.15104] [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: 04/29/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
Salmonella enterica is a common foodborne, facultative intracellular enteropathogen. Typhoidal serovars like Paratyphi A (SPA) are human restricted and cause severe systemic diseases, while many serovars like Typhimurium (STM) have a broad host range, and usually lead to self-limiting gastroenteritis. There are key differences between typhoidal and non-typhoidal Salmonella in pathogenesis, but underlying mechanisms remain largely unknown. Transcriptomes and phenotypes in epithelial cells revealed induction of motility, flagella and chemotaxis genes for SPA but not STM. SPA exhibited cytosolic motility mediated by flagella. In this study, we applied single-cell microscopy to analyze triggers and cellular consequences of cytosolic motility. Live-cell imaging (LCI) revealed that SPA invades host cells in a highly cooperative manner. Extensive membrane ruffling at invasion sites led to increased membrane damage in nascent Salmonella-containing vacuole, and subsequent cytosolic release. After release into the cytosol, motile bacteria showed the same velocity as under culture conditions in media. Reduced capture of SPA by autophagosomal membranes was observed by LCI and electron microscopy. Prior work showed that SPA does not use flagella-mediated motility for cell exit via the intercellular spread. However, cytosolic motile SPA was invasion-primed if released from host cells. Our results reveal flagella-mediated cytosolic motility as a possible xenophagy evasion mechanism that could drive disease progression and contributes to the dissemination of systemic infection.
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Affiliation(s)
- Felix Scharte
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Rico Franzkoch
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- Universität Osnabrück, iBiOs-Integrated Bioimaging Facility, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- Universität Osnabrück, CellNanOs-Center of Cellular Nanoanalytics, Osnabrück, Germany
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10
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Machado LFM, Galán JE. Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580360. [PMID: 38405738 PMCID: PMC10888927 DOI: 10.1101/2024.02.14.580360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Salmonella enterica serovar Typhi and Paratyphi A are the cause of typhoid and paratyphoid fever in humans, which are systemic life-threatening illnesses. Both serovars are exclusively adapted to the human host, where they can cause life-long persistent infection. A distinct feature of these serovars is the presence of a relatively high number of degraded coding sequences coding for metabolic pathways, most likely a consequence of their adaptation to a single host. As a result of convergent evolution, these serovars shared many of the degraded coding sequences although often affecting different genes in the same metabolic pathway. However, there are several coding sequences that appear intact in one serovar while clearly degraded in the other, suggesting differences in their metabolic capabilities. Here, we examined the functionality of metabolic pathways that appear intact in S . Typhi but that show clear signs of degradation in S . Paratyphi A. We found that, in all cases, the existence of single amino acid substitutions in S. Typhi metabolic enzymes, transporters, or transcription regulators resulted in the inactivation of these metabolic pathways. Thus, the inability of S . Typhi to metabolize Glucose-6-Phosphate or 3-phosphoglyceric acid is due to the silencing of the expression of the genes encoding the transporters for these compounds due to point mutations in the transcriptional regulatory proteins. In contrast, its inability to utilize glucarate or galactarate is due to the presence of point mutations in the transporter and enzymes necessary for the metabolism of these sugars. These studies provide additional support for the concept of adaptive convergent evolution of these two human-adapted Salmonella enterica serovars and highlight a limitation of bioinformatic approaches to predict metabolic capabilities.
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11
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Meiring JE, Khanam F, Basnyat B, Charles RC, Crump JA, Debellut F, Holt KE, Kariuki S, Mugisha E, Neuzil KM, Parry CM, Pitzer VE, Pollard AJ, Qadri F, Gordon MA. Typhoid fever. Nat Rev Dis Primers 2023; 9:71. [PMID: 38097589 DOI: 10.1038/s41572-023-00480-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Typhoid fever is an invasive bacterial disease associated with bloodstream infection that causes a high burden of disease in Africa and Asia. Typhoid primarily affects individuals ranging from infants through to young adults. The causative organism, Salmonella enterica subsp. enterica serovar Typhi is transmitted via the faecal-oral route, crossing the intestinal epithelium and disseminating to systemic and intracellular sites, causing an undifferentiated febrile illness. Blood culture remains the practical reference standard for diagnosis of typhoid fever, where culture testing is available, but novel diagnostic modalities are an important priority under investigation. Since 2017, remarkable progress has been made in defining the global burden of both typhoid fever and antimicrobial resistance; in understanding disease pathogenesis and immunological protection through the use of controlled human infection; and in advancing effective vaccination programmes through strategic multipartner collaboration and targeted clinical trials in multiple high-incidence priority settings. This Primer thus offers a timely update of progress and perspective on future priorities for the global scientific community.
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Affiliation(s)
- James E Meiring
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
| | - Farhana Khanam
- International Centre for Diarrhoel Disease Research, Dhaka, Bangladesh
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Richelle C Charles
- Massachusetts General Hospital, Harvard Medical School, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | | | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Emmanuel Mugisha
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Christopher M Parry
- Department of Clinical Sciences and Education, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases and Public Health Modelling Unit, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Firdausi Qadri
- International Centre for Diarrhoel Disease Research, Dhaka, Bangladesh
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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12
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Hajra D, Nair AV, Chakravortty D. Decoding the invasive nature of a tropical pathogen of concern: The invasive non-Typhoidal Salmonella strains causing host-restricted extraintestinal infections worldwide. Microbiol Res 2023; 277:127488. [PMID: 37716125 DOI: 10.1016/j.micres.2023.127488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Invasive-Non-Typhoidal Salmonella (iNTS) are the major cause of health concern in the low-income, under-developed nations in Africa and Asia that lack proper sanitation facilities. Around 5% of the NTS cases give rise to invasive, extraintestinal diseases leading to focal infections like osteomyelitis, meningitis, osteoarthritis, endocarditis and neonatal sepsis. iNTS serovars like S. Typhimurium, S. Enteritidis, S. Dublin, S. Choleraesuis show a greater propensity to become invasive than others which hints at the genetic basis of their emergence. The major risk factors attributing to the invasive diseases include immune-compromised individuals having co-infection with malaria or HIV, or suffering from malnutrition. The rampant use of antibiotics leading to the emergence of multi-drug resistant strains poses a great challenge in disease management. An extensive understanding of the iNTS pathogenesis and its epidemiology will open up avenues for the development of new vaccination and therapeutic strategies to restrict the spread of this neglected disease.
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Affiliation(s)
- Dipasree Hajra
- Department of Microbiology & Cell Biology, Indian Institute of Science, India
| | - Abhilash Vijay Nair
- Department of Microbiology & Cell Biology, Indian Institute of Science, India
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13
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Zhou X, Kang X, Chen J, Song Y, Jia C, Teng L, Tang Y, Jiang Z, Peng X, Tao X, Xu Y, Huang L, Xu X, Xu Y, Zhang T, Yu S, Gong J, Wang S, Liu Y, Zhu G, Kehrenberg C, Weill FX, Barrow P, Li Y, Zhao G, Yue M. Genome degradation promotes Salmonella pathoadaptation by remodeling fimbriae-mediated proinflammatory response. Natl Sci Rev 2023; 10:nwad228. [PMID: 37965675 PMCID: PMC10642762 DOI: 10.1093/nsr/nwad228] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/07/2023] [Accepted: 08/08/2023] [Indexed: 11/16/2023] Open
Abstract
Understanding changes in pathogen behavior (e.g. increased virulence, a shift in transmission channel) is critical for the public health management of emerging infectious diseases. Genome degradation via gene depletion or inactivation is recognized as a pathoadaptive feature of the pathogen evolving with the host. However, little is known about the exact role of genome degradation in affecting pathogenic behavior, and the underlying molecular detail has yet to be examined. Using large-scale global avian-restricted Salmonella genomes spanning more than a century, we projected the genetic diversity of Salmonella Pullorum (bvSP) by showing increasingly antimicrobial-resistant ST92 prevalent in Chinese flocks. The phylogenomic analysis identified three lineages in bvSP, with an enhancement of virulence in the two recently emerged lineages (L2/L3), as evidenced in chicken and embryo infection assays. Notably, the ancestor L1 lineage resembles the Salmonella serovars with higher metabolic flexibilities and more robust environmental tolerance, indicating stepwise evolutionary trajectories towards avian-restricted lineages. Pan-genome analysis pinpointed fimbrial degradation from a virulent lineage. The later engineered fim-deletion mutant, and all other five fimbrial systems, revealed behavior switching that restricted horizontal fecal-oral transmission but boosted virulence in chicks. By depleting fimbrial appendages, bvSP established persistent replication with less proinflammation in chick macrophages and adopted vertical transovarial transmission, accompanied by ever-increasing intensification in the poultry industry. Together, we uncovered a previously unseen paradigm for remodeling bacterial surface appendages that supplements virulence-enhanced evolution with increased vertical transmission.
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Affiliation(s)
- Xiao Zhou
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Xiamei Kang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Jiaqi Chen
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yan Song
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Chenghao Jia
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lin Teng
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yanting Tang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Zhijie Jiang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xianqi Peng
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xiaoxi Tao
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yiwei Xu
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Linlin Huang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xuebin Xu
- Department of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Yaohui Xu
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450053, China
| | - Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Shenye Yu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
| | - Shaohui Wang
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, Giessen 35392, Germany
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des bactéries pathogènes entériques, Paris 75724, France
| | - Paul Barrow
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK
| | - Yan Li
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Guoping Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
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14
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Thurston TLM, Holden DW. The Salmonella Typhi SPI-2 injectisome enigma. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001405. [PMID: 37862087 PMCID: PMC10634361 DOI: 10.1099/mic.0.001405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023]
Abstract
The Salmonella pathogenicity island 2 (SPI-2)-encoded type III secretion system (injectisome) is assembled following uptake of bacteria into vacuoles in mammalian cells. The injectisome translocates virulence proteins (effectors) into infected cells. Numerous studies have established the requirement for a functional SPI-2 injectisome for growth of Salmonella Typhimurium in mouse macrophages, but the results of similar studies involving Salmonella Typhi and human-derived macrophages are not consistent. It is important to clarify the functions of the S. Typhi SPI-2 injectisome, not least because an inactivated SPI-2 injectisome forms the basis for live attenuated S. Typhi vaccines that have undergone extensive trials in humans. Intracellular expression of injectisome genes and effector delivery take longer in the S. Typhi/human macrophage model than for S. Typhimurium and we propose that this could explain the conflicting results. Furthermore, strains of both S. Typhimurium and S. Typhi contain intact genes for several 'core' effectors. In S. Typhimurium these cooperate to regulate the vacuole membrane and contribute to intracellular bacterial replication; similar functions are therefore likely in S. Typhi.
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Affiliation(s)
- Teresa L. M. Thurston
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - David W. Holden
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, UK
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15
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Smith C, Smith E, Chiu C, Hinton J, Perez Sepulveda B, Gordon M, Choy RK, Hill PW, Meiring JE, Darton TC, Carey ME, Cooke G, Gibani MM. The Challenge Non-Typhoidal Salmonella (CHANTS) Consortium: Development of a non-typhoidal Salmonella controlled human infection model: Report from a consultation group workshop, 05 July 2022, London, UK. Wellcome Open Res 2023; 8:111. [PMID: 37808389 PMCID: PMC10558987 DOI: 10.12688/wellcomeopenres.19012.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
Invasive non-typhoidal Salmonella disease (iNTS) is a major cause of morbidity and mortality globally, particularly as a cause of bloodstream infection in children and immunocompromised adults in sub-Saharan Africa. Vaccines to prevent non-typhoidal Salmonella (NTS) would represent a valuable public health tool in this setting to avert cases and prevent expansion of antimicrobial resistance. Several NTS and combination typhoidal-NTS vaccine candidates are in early-stage development, although the pathway to licensure is unclear due to challenges in conducting large phase III field trials. Controlled human infection models (CHIM) present an opportunity to accelerate vaccine development for a range of enteric pathogens. Several recent typhoidal Salmonella CHIMs have been conducted safely and have played pivotal roles in progressing vaccine candidates to pre-qualification and licensure. The Challenge Non-Typhoidal Salmonella (CHANTS) consortium has been formed with funding from the Wellcome Trust, to deliver the first NTS CHIM, which can act as a platform for future vaccine evaluation. This paper reports the conclusions of a consultation group workshop convened with key stakeholders. The aims of this meeting were to: (1) define the rationale for an NTS CHIM (2) map the NTS vaccine pipeline (3) refine study design and (4) establish potential future use cases.
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Affiliation(s)
- Christopher Smith
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Emma Smith
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Jay Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Blanca Perez Sepulveda
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Melita Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - Peter W.S. Hill
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - James E. Meiring
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2TN, UK
| | - Thomas C. Darton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2TN, UK
| | - Megan E. Carey
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Malick M. Gibani
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - CHANTS Consortium
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- PATH, Seattle, Washington, 98121, USA
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2TN, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
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16
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Smith C, Smith E, Chiu C, Hinton J, Perez Sepulveda B, Gordon M, Choy RK, Hill PW, Meiring JE, Darton TC, Carey ME, Cooke G, Gibani MM. The Challenge Non-Typhoidal Salmonella (CHANTS) Consortium: Development of a non-typhoidal Salmonella controlled human infection model: Report from a consultation group workshop, 05 July 2022, London, UK. Wellcome Open Res 2023; 8:111. [PMID: 37808389 PMCID: PMC10558987 DOI: 10.12688/wellcomeopenres.19012.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 04/21/2024] Open
Abstract
Invasive non-typhoidal Salmonella disease (iNTS) is a major cause of morbidity and mortality globally, particularly as a cause of bloodstream infection in children and immunocompromised adults in sub-Saharan Africa. Vaccines to prevent non-typhoidal Salmonella (NTS) would represent a valuable public health tool in this setting to avert cases and prevent expansion of antimicrobial resistance. Several NTS and combination typhoidal-NTS vaccine candidates are in early-stage development, although the pathway to licensure is unclear due to challenges in conducting large phase III field trials. Controlled human infection models (CHIM) present an opportunity to accelerate vaccine development for a range of enteric pathogens. Several recent typhoidal Salmonella CHIMs have been conducted safely and have played pivotal roles in progressing vaccine candidates to pre-qualification and licensure. The Challenge Non-Typhoidal Salmonella (CHANTS) consortium has been formed with funding from the Wellcome Trust, to deliver the first NTS CHIM, which can act as a platform for future vaccine evaluation. This paper reports the conclusions of a consultation group workshop convened with key stakeholders. The aims of this meeting were to: (1) define the rationale for an NTS CHIM (2) map the NTS vaccine pipeline (3) refine study design and (4) establish potential future use cases.
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Affiliation(s)
- Christopher Smith
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Emma Smith
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Jay Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Blanca Perez Sepulveda
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Melita Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - Peter W.S. Hill
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - James E. Meiring
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2TN, UK
| | - Thomas C. Darton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2TN, UK
| | - Megan E. Carey
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Malick M. Gibani
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - CHANTS Consortium
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- PATH, Seattle, Washington, 98121, USA
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2TN, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
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17
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Hooda Y, Tanmoy AM, Saha SK, Saha S. Genomic Surveillance of Salmonella Paratyphi A: Neglected No More? Open Forum Infect Dis 2023; 10:S53-S57. [PMID: 37274527 PMCID: PMC10236518 DOI: 10.1093/ofid/ofad077] [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: 01/04/2023] [Accepted: 02/04/2023] [Indexed: 06/06/2023] Open
Abstract
Salmonella enterica serovar Paratyphi A, the causative agent of paratyphoid fever, is a neglected tropical disease with a high burden and mortality in low- and middle-income countries. Limited information is available regarding its genomic diversity, especially from South Asian countries that are collectively responsible for >80% of all paratyphoid cases. At the 2021 International Conference on Typhoid and Other Salmonelloses, researchers from the around the globe presented their work on Salmonella Paratyphi A genomics. Presentations described recent genomic data from South Asia and the development of Paratype, an open-access single-nucleotide polymorphism-based genotyping scheme, to segregate Salmonella Paratyphi A genomes in a systematic and sustainable manner. In this review, we attempt to summarize the progress made thus far on Salmonella Paratyphi A genomics and discuss the questions that remain to better understand the pathogen and develop interventions to fight it.
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Affiliation(s)
- Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
- Department of Microbiology, Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh
| | - Senjuti Saha
- Correspondence: Senjuti Saha, PhD, Child Health Research Foundation, 23/2 Khilji Road, Sel Huq Skypark, Block-B, Mohammadpur, Dhaka 1207, Bangladesh ()
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18
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Irfan S, Hasan Z, Qamar F, Ghanchi N, Ashraf J, Kanji A, Razzak S, Greig D, Nair S, Hasan R. Ceftriaxone resistant Salmonella enterica serovar Paratyphi A identified in a case of enteric fever: first case report from Pakistan. BMC Infect Dis 2023; 23:267. [PMID: 37101111 PMCID: PMC10132421 DOI: 10.1186/s12879-023-08152-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/10/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Enteric fever is an acute systemic infectious disease associated with substantial morbidity and mortality in low- and middle-income countries (LMIC), with a global burden of 14.3 million cases. Cases of enteric fever or paratyphoid fever, caused by Salmonella enterica serovar Paratyphi A (S. Para A) have been found to rise in many endemic and non-endemic countries. Drug resistance is relatively uncommon in S. Para A. Here we report a case of paratyphoid fever caused by ceftriaxone resistant S. Para A from Pakistan. CASE PRESENTATION A 29-year-old female presented with a history of fever, headache, and shivering. Her blood culture revealed a S. Para A isolate (S7), which was resistant to ceftriaxone, cefixime, ampicillin and ciprofloxacin. She was prescribed oral Azithromycin for 10 days, which resulted in resolution of her symptoms. Two other isolates of S. Para A (S1 and S4), resistant to fluoroquinolone were also selected for comparison. DST and whole genome sequencing was performed for all three isolates. Sequence analysis was performed for identification of drug resistance and phylogeny. Whole Genome Sequencing (WGS) of S7 revealed the presence of plasmids, IncX4 and IncFIB(K). blaCTX-M-15 and qnrS1 genes were found on IncFIB(K). The gyrA S83F mutation conferring fluoroquinolone resistance was also found present. Multi-locus sequence typing (MLST) showed the S7 isolate to belong to ST129. S1 and S4 had the gyrA S83Y and S83F mutations respectively. CONCLUSIONS We highlight the occurrence of plasmid-mediated ceftriaxone resistant strain of S. Para A. This is of significance as ceftriaxone is commonly used to treat paratyphoid fever and resistance in S. Para A is not known. Continuous epidemiological surveillance is required to monitor the transmission and spread of antimicrobial resistance (AMR) among Typhoidal Salmonellae. This will guide treatment options and preventive measures including the need for vaccination against S. Para A in the region.
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Affiliation(s)
- Seema Irfan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O Box3500, Karachi, 74800, Pakistan.
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Farah Qamar
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Najia Ghanchi
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Javaria Ashraf
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Safina Razzak
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - David Greig
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Satheesh Nair
- GASTROINTESTINAL PATHOGENS UNIT Gastrointestinal Bacteria Reference Unit National Infection Service, Public Health England, London, UK
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
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19
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Jacob JJ, Pragasam AK, Vasudevan K, Velmurugan A, Priya Teekaraman M, Priya Thirumoorthy T, Ray P, Gupta M, Kapil A, Bai SP, Nagaraj S, Saigal K, Chandola TR, Thomas M, Bavdekar A, Ebenezer SE, Shastri J, De A, Dutta S, Alexander AP, Koshy RM, Jinka DR, Singh A, Srivastava SK, Anandan S, Dougan G, John J, Kang G, Veeraraghavan B, Mutreja A. Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages. PLoS Pathog 2023; 19:e1010650. [PMID: 37115804 PMCID: PMC10171690 DOI: 10.1371/journal.ppat.1010650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 05/10/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Paratyphoid fever caused by S. Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by S. Paratyphi A has substantially increased, yet only limited data is available on the population structure and genetic diversity of this serovar. We examined the phylogenetic distribution and evolutionary trajectory of S. Paratyphi A isolates collected as part of the Indian enteric fever surveillance study "Surveillance of Enteric Fever in India (SEFI)." In the study period (2017-2020), S. Paratyphi A comprised 17.6% (441/2503) of total enteric fever cases in India, with the isolates highly susceptible to all the major antibiotics used for treatment except fluoroquinolones. Phylogenetic analysis clustered the global S. Paratyphi A collection into seven lineages (A-G), and the present study isolates were distributed in lineages A, C and F. Our analysis highlights that the genome degradation events and gene acquisitions or losses are key molecular events in the evolution of new S. Paratyphi A lineages/sub-lineages. A total of 10 hypothetically disrupted coding sequences (HDCS) or pseudogenes-forming mutations possibly associated with the emergence of lineages were identified. The pan-genome analysis identified the insertion of P2/PSP3 phage and acquisition of IncX1 plasmid during the selection in 2.3.2/2.3.3 and 1.2.2 genotypes, respectively. We have identified six characteristic missense mutations associated with lipopolysaccharide (LPS) biosynthesis genes of S. Paratyphi A, however, these mutations confer only a low structural impact and possibly have minimal impact on vaccine effectiveness. Since S. Paratyphi A is human-restricted, high levels of genetic drift are not expected unless these bacteria transmit to naive hosts. However, public-health investigation and monitoring by means of genomic surveillance would be constantly needed to avoid S. Paratyphi A serovar becoming a public health threat similar to the S. Typhi of today.
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Affiliation(s)
| | | | - Karthick Vasudevan
- Christian Medical College, Vellore, India
- REVA University, Bangalore, India
| | | | | | | | - Pallab Ray
- Post Graduate Institute of Medical & Educational Research, Chandigarh, India
| | - Madhu Gupta
- Post Graduate Institute of Medical & Educational Research, Chandigarh, India
| | - Arti Kapil
- All India Institute of Medical Sciences, New Delhi, India
| | | | | | | | | | | | | | | | - Jayanthi Shastri
- Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India
| | - Anuradha De
- Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India
| | - Shantha Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | | | | | | | | | | | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jacob John
- Christian Medical College, Vellore, India
| | | | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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20
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Schindler Y, Rahav G, Nissan I, Treygerman O, Prajgrod G, Attia BZ, Raz R, Valenci GZ, Tekes-Manova D, Maor Y. Group B streptococcus virulence factors associated with different clinical syndromes: Asymptomatic carriage in pregnant women and early-onset disease in the newborn. Front Microbiol 2023; 14:1093288. [PMID: 36860481 PMCID: PMC9968972 DOI: 10.3389/fmicb.2023.1093288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023] Open
Abstract
Background Group B streptococcus (GBS) harbors many virulence factors but there is limited data regarding their importance in colonization in pregnancy and early-onset disease (EOD) in the newborn. We hypothesized that colonization and EOD are associated with different distribution and expression of virulence factors. Methods We studied 36 GBS EOD and 234 GBS isolates collected during routine screening. Virulence genes (pilus-like structures-PI-1, PI-2a, PI-2b; rib and hvgA) presence and expression were identified by PCR and qRT-PCR. Whole genome sequencing (WGS) and comparative genomic analyses were used to compare coding sequences (CDSs) of colonizing and EOD isolates. Results Serotype III (ST17) was significantly associated with EOD and serotype VI (ST1) with colonization. hvgA and rib genes were more prevalent among EOD isolates (58.3 and 77.8%, respectively; p < 0.01). The pilus loci PI-2b and PI-2a were more prevalent among EOD isolates (61.1%, p < 0.01), while the pilus loci PI-2a and PI-1 among colonizing isolates (89.7 and 93.1% vs. 55.6 and 69.4%, p < 0.01). qRT PCR analysis revealed that hvgA was barely expressed in colonizing isolates, even though the gene was detected. Expression of the rib gene and PI-2b was two-fold higher in EOD isolates compared to colonizing isolates. Transcription of PI-2a was three-fold higher in colonizing isolates compared to EOD isolates. ST17 isolates (associated with EOD) had a smaller genome size compared ST1 and the genome was more conserved relative to the reference strain and ST17 isolates. In a multivariate logistic regression analysis virulence factors independently associated with EOD were serotype 3, and PI-1 and PI-2a was protective. Conclusion There was a significant difference in the distribution of hvg A, rib, and PI genes among EOD (serotype III/ST17) and colonizing (serotype VI/ST1) isolates suggesting an association between invasive disease and these virulence factors. Further study is needed to understand the contribution of these genes to GBS virulence.
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Affiliation(s)
- Yulia Schindler
- Laboratory of Microbiology, Mayanei Hayeshua Medical Center, Bnei Brak, Israel,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Galia Rahav
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel,Infectious Disease Unit, Sheba Medical Center, Tel HaShomer, Israel
| | - Israel Nissan
- Infectious Disease Unit, Sheba Medical Center, Tel HaShomer, Israel,National Public Health Laboratory, Ministry of Health, Tel Aviv, Israel
| | - Orit Treygerman
- Laboratory of Microbiology, Meuhedet Health Maintenance Organization, Lod, Israel
| | - George Prajgrod
- Laboratory of Microbiology, Meuhedet Health Maintenance Organization, Lod, Israel
| | | | - Ronit Raz
- Laboratory of Microbiology, Mayanei Hayeshua Medical Center, Bnei Brak, Israel
| | | | - Dorit Tekes-Manova
- Laboratory of Microbiology, Mayanei Hayeshua Medical Center, Bnei Brak, Israel
| | - Yasmin Maor
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel,Infectious Disease Unit, Wolfson Medical Center, Holon, Israel,*Correspondence: Yasmin Maor, ,
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Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity. Nat Commun 2022; 13:7912. [PMID: 36564386 PMCID: PMC9782287 DOI: 10.1038/s41467-022-35587-6] [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: 12/09/2021] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Salmonella Paratyphi A, the primary etiology of paratyphoid, is estimated to cause 3.4 million infections annually, worldwide. With rising antimicrobial resistance and no licensed vaccines, genomic surveillance is key to track and monitor transmission, but there is currently no reliable genotyping framework for this pathogen. Here, we sequence 817 isolates from South Asia and add 562 publicly available genomes to build a global database representing 37 countries, covering 1917-2019. We develop a single nucleotide polymorphism-based genotyping scheme, Paratype, that segregates Salmonella Paratyphi A population into three primary and nine secondary clades, and 18 genotypes. Each genotype is assigned a unique allele definition located on an essential gene. Using Paratype, we identify spatiotemporal genomic variation and antimicrobial resistance markers. We release Paratype as an open-access tool that can use raw read files from both Illumina and Nanopore platforms, and thus can assist surveillance studies tracking Salmonella Paratyphi A across the globe.
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Aiemjoy K, Rumunu J, Hassen JJ, Wiens KE, Garrett D, Kamenskaya P, Harris JB, Azman AS, Teunis P, Seidman JC, Wamala JF, Andrews JR, Charles RC. Seroincidence of Enteric Fever, Juba, South Sudan. Emerg Infect Dis 2022; 28. [PMID: 36286224 PMCID: PMC9622235 DOI: 10.3201/eid2811.220239] [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] [Indexed: 11/25/2022] Open
Abstract
We applied a new serosurveillance tool to estimate typhoidal Salmonella burden using samples collected during 2020 from a population in Juba, South Sudan. By using dried blood spot testing, we found an enteric fever seroincidence rate of 30/100 person-years and cumulative incidence of 74% over a 4-year period.
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Ur Rehman Safi A, Mansour Salih M, Rahman H, Khattak B, El Askary A, Hussain Khalifa E, Qasim M. Immunoaffinity-based mass spectrometric characterization of immunoreactive proteins of Salmonella Typhi. Saudi J Biol Sci 2022; 30:103502. [DOI: 10.1016/j.sjbs.2022.103502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/14/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
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Aiemjoy K, Seidman JC, Saha S, Munira SJ, Islam Sajib MS, Sium SMA, Sarkar A, Alam N, Zahan FN, Kabir MS, Tamrakar D, Vaidya K, Shrestha R, Shakya J, Katuwal N, Shrestha S, Yousafzai MT, Iqbal J, Dehraj IF, Ladak Y, Maria N, Adnan M, Pervaiz S, Carter AS, Longley AT, Fraser C, Ryan ET, Nodoushani A, Fasano A, Leonard MM, Kenyon V, Bogoch II, Jeon HJ, Haselbeck A, Park SE, Zellweger RM, Marks F, Owusu-Dabo E, Adu-Sarkodie Y, Owusu M, Teunis P, Luby SP, Garrett DO, Qamar FN, Saha SK, Charles RC, Andrews JR. Estimating typhoid incidence from community-based serosurveys: a multicohort study. THE LANCET. MICROBE 2022; 3:e578-e587. [PMID: 35750069 PMCID: PMC9329131 DOI: 10.1016/s2666-5247(22)00114-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The incidence of enteric fever, an invasive bacterial infection caused by typhoidal Salmonellae (Salmonella enterica serovars Typhi and Paratyphi), is largely unknown in regions without blood culture surveillance. The aim of this study was to evaluate whether new diagnostic serological markers for typhoidal Salmonella can reliably estimate population-level incidence. METHODS We collected longitudinal blood samples from patients with blood culture-confirmed enteric fever enrolled from surveillance studies in Bangladesh, Nepal, Pakistan, and Ghana between 2016 and 2021 and conducted cross-sectional serosurveys in the catchment areas of each surveillance site. We used ELISAs to measure quantitative IgA and IgG antibody responses to hemolysin E and S Typhi lipopolysaccharide. We used Bayesian hierarchical models to fit two-phase power-function decay models to the longitudinal antibody responses among enteric fever cases and used the joint distributions of the peak antibody titres and decay rate to estimate population-level incidence rates from cross-sectional serosurveys. FINDINGS The longitudinal antibody kinetics for all antigen-isotypes were similar across countries and did not vary by clinical severity. The seroincidence of typhoidal Salmonella infection among children younger than 5 years ranged between 58·5 per 100 person-years (95% CI 42·1-81·4) in Dhaka, Bangladesh, to 6·6 per 100 person-years (4·3-9·9) in Kavrepalanchok, Nepal, and followed the same rank order as clinical incidence estimates. INTERPRETATION The approach described here has the potential to expand the geographical scope of typhoidal Salmonella surveillance and generate incidence estimates that are comparable across geographical regions and time. FUNDING Bill & Melinda Gates Foundation. TRANSLATIONS For the Nepali, Bengali and Urdu translations of the abstract see Supplementary Materials section.
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Affiliation(s)
- Kristen Aiemjoy
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA; Division of Epidemiology, Department of Public Health Sciences, University of California Davis School of Medicine, Davis, CA, USA.
| | | | - Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | | | - Syed Muktadir Al Sium
- Child Health Research Foundation, Dhaka, Bangladesh; Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Anik Sarkar
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Nusrat Alam
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | | | - Dipesh Tamrakar
- Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal
| | - Krista Vaidya
- Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal
| | - Rajeev Shrestha
- Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal
| | - Jivan Shakya
- Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal
| | - Nishan Katuwal
- Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal
| | - Sony Shrestha
- Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal
| | | | - Junaid Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Irum Fatima Dehraj
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Yasmin Ladak
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Noshi Maria
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Mehreen Adnan
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sadaf Pervaiz
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Ashley T Longley
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clare Fraser
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Ariana Nodoushani
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Alessio Fasano
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Boston, MA, USA; Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA
| | - Maureen M Leonard
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Boston, MA, USA; Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA
| | - Victoria Kenyon
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Boston, MA, USA
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, South Korea; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Se Eun Park
- International Vaccine Institute, Seoul, South Korea
| | | | - Florian Marks
- International Vaccine Institute, Seoul, South Korea; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK; Department of Microbiology and Parasitology, University of Antananarivo, Antananarivo, Madagascar; Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
| | - Ellis Owusu-Dabo
- School of Medical Sciences, Kwame Nkrumah University for Science and Technology, Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- School of Medical Sciences, Kwame Nkrumah University for Science and Technology, Kumasi, Ghana
| | - Michael Owusu
- School of Medical Sciences, Kwame Nkrumah University for Science and Technology, Kumasi, Ghana
| | - Peter Teunis
- Center for Global Safe Water, Sanitation and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Farah Naz Qamar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
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Xie L, Ming L, Ding M, Deng L, Liu M, Cong Y. Paratyphoid Fever A: Infection and Prevention. Front Microbiol 2022; 13:945235. [PMID: 35875577 PMCID: PMC9304857 DOI: 10.3389/fmicb.2022.945235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Enteric fever is caused by Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi A, B, and C. While S. Typhi remains the primary causative agent of enteric fever, S. Paratyphi A is responsible for an increasing portion of enteric fever incidence. However, the current available vaccines for enteric fever are all developed from S. Typhi, and lack adequate cross immune protection against paratyphoid fever A. Therefore, paratyphoid A vaccines are urgently needed. The present paper reviews the latest progresses in pathogenesis, global burden, infection features of paratyphoid fever A, as well as the status of vaccine development, highlighting the necessity for the development of vaccines against paratyphoid fever A.
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Affiliation(s)
- Lei Xie
- Precision Medicine Center, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Lan Ming
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Manlin Ding
- Precision Medicine Center, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Luxin Deng
- Department of Clinical Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Miao Liu
- Precision Medicine Center, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Yanguang Cong
- Precision Medicine Center, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Yanguang Cong,
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Cheng RA, Orsi RH, Wiedmann M. The Number and Type of Chaperone-Usher Fimbriae Reflect Phylogenetic Clade Rather than Host Range in Salmonella. mSystems 2022; 7:e0011522. [PMID: 35467401 PMCID: PMC9238391 DOI: 10.1128/msystems.00115-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/03/2022] [Indexed: 01/21/2023] Open
Abstract
Salmonella is one of the most successful foodborne pathogens worldwide, owing in part to its ability to colonize or infect a wide range of hosts. Salmonella serovars are known to encode a variety of different fimbriae (hairlike organelles that facilitate binding to surfaces); however, the distribution, number, and sequence diversity of fimbriae encoded across different lineages of Salmonella were unknown. We queried whole-genome sequence (WGS) data for 242 Salmonella enterica subsp. enterica (subspecies enterica) isolates from the top 217 serovars associated with isolation from humans and agricultural animals; this effort identified 2,894 chaperone-usher (CU)-type fimbrial usher sequences, representing the most conserved component of CU fimbriae. On average, isolates encoded 12 different CU fimbrial ushers (6 to 18 per genome), although the distribution varied significantly (P = 1.328E-08) by phylogenetic clade, with isolates in section Typhi having significantly fewer fimbrial ushers than isolates in clade A2 (medians = 10 and 12 ushers, respectively). Characterization of fimbriae in additional non-enterica subspecies genomes suggested that 8 fimbrial ushers were classified as being unique to subspecies enterica isolates, suggesting that the majority of fimbriae were most likely acquired prior to the divergence of subspecies enterica. Characterization of mobile elements suggested that plasmids represent an important vehicle facilitating the acquisition of a wide range of fimbrial ushers, particularly for the acquisition of fimbriae from other Gram-negative genera. Overall, our results suggest that differences in the number and type of fimbriae encoded most likely reflect differences in phylogenetic clade rather than differences in host range. IMPORTANCE Fimbriae of the CU assembly pathway represent important organelles that mediate Salmonella's interactions with host tissues and abiotic surfaces. Our analyses provide a comprehensive overview of the diversity of CU fimbriae in Salmonella spp., highlighting that the majority of CU fimbriae are distributed broadly across multiple subspecies and suggesting that acquisition most likely occurred prior to the divergence of subspecies enterica. Our data also suggest that plasmids represent the primary vehicles facilitating the horizontal transfer of diverse CU fimbriae in Salmonella. Finally, the observed high sequence similarity between some ushers suggests that different names may have been assigned to closely related fimbrial ushers that likely should be represented by a single designation. This highlights the need to establish standard criteria for fimbria classification and nomenclature, which will also facilitate future studies seeking to associate virulence factors with adaptation to or differences in the likelihood of causing disease in a given host.
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Affiliation(s)
- Rachel A. Cheng
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Renato H. Orsi
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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Distinct Potentially Adaptive Accumulation of Truncation Mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A. Microbiol Spectr 2022; 10:e0196921. [PMID: 35467366 PMCID: PMC9241588 DOI: 10.1128/spectrum.01969-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gene inactivation through the accumulation of truncation (or premature stop codon) mutations is a common mode of evolution in bacteria. It is frequently believed to result from reductive evolutionary processes allowing purging of superfluous traits. However, several works have demonstrated that, similar to the occurrences of inactivating nonsynonymous (i.e., amino acid replacement) mutations under positive selection pressures, truncation mutations can also be adaptive where specific traits deleterious in particular environmental conditions need to be inactivated for survival. Here, we performed a comparative analysis of genome-wide accumulation of truncation mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A. Considering the known convergent evolutionary trajectories in these two serovars, we expected a strong overlap of truncated genes in S. Typhi and S. Paratyphi A, emerging through either reductive or adaptive dynamics. However, we detected a distinct set of core truncated genes encoding different overrepresented functional clusters in each serovar. In 54% and 28% truncated genes in S. Typhi and S. Paratyphi A, respectively, inactivating mutations were acquired by only different subsets of isolates, instead of all isolates analyzed for that serovar. Importantly, 62% truncated genes (P < 0.001) in S. Typhi and S. Paratyphi A were also targeted by convergent amino acid mutations in different serovars, suggesting those genes to be under selection pressures. Our findings indicate significant presence of potentially adaptive truncation mutations in conjunction with the ones emerging due to reductive evolution. Further experimental and large-scale bioinformatic studies are necessary to better explore the impact of such adaptive footprints of truncation mutations in the evolution of bacterial virulence. IMPORTANCE Detecting the adaptive mutations leading to gene inactivation or loss of function is crucial for understanding their contribution in the evolution of bacterial virulence and antibiotic resistance. Such inactivating mutations, apart from being of nonsynonymous (i.e., amino acid replacement) nature, can also be truncation mutations, abruptly trimming the length of encoded proteins. Importantly, the notion of reductive evolutionary dynamics is primarily accepted toward the accumulation of truncation mutations. However, our case study on S. Typhi and S. Paratyphi A, two human-restricted systemically invasive pathogens exerting similar clinical manifestations, indicated that a significant proportion of truncation mutations emerge from positive selection pressures. The candidate genes from our study will enable directed functional assays for deciphering the adaptive role of truncation mutations in S. Typhi and S. Paratyphi A pathogenesis. Also, our genome-level analytical approach will pave the way to understand the contribution of truncation mutations in the adaptive evolution of other bacterial pathogens.
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Amagliani G, La Guardia ME, Dominici S, Brandi G, Omiccioli E. Salmonella Abortusovis: An Epidemiologically Relevant Pathogen. Curr Microbiol 2021; 79:3. [PMID: 34878615 DOI: 10.1007/s00284-021-02689-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 10/06/2021] [Indexed: 11/28/2022]
Abstract
The ovine pathogen Salmonella enterica serovar Abortusovis (SAO), a pathogen strictly adapted to ovine hosts, is endemic in several European and Asian countries, where it causes significant economic losses due to the high rates of abortion in infected flocks. In some countries (i.e. Switzerland and Croatia), re-emergence of infection by SAO occurred after decades during which the disease has not been reported. The introduction of (SAO) epidemic strains in new areas is difficult to control due to the asymptomatic behaviors in infected adult lambs, rams, and nonpregnant ewes. Culture-based diagnosis may provide false-negative results. Moreover, the retrospective identification of Salmonella infection in ewes is challenging as excretion of the causative agent is transient and the serum antibodies fall to low titres soon after the abortion. Therefore, regular monitoring of pathogen exposure, mainly through seroconversion assessment, is advisable to prevent disease introduction and spread in SAO-free areas, especially in case of animal export, and to reduce abortion risk.
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Affiliation(s)
- Giulia Amagliani
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, via S. Chiara, 27, 61029, Urbino, PU, Italy.
| | | | | | - Giorgio Brandi
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, via S. Chiara, 27, 61029, Urbino, PU, Italy
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Feng Y, Chen CL, Chang YJ, Li YH, Chiou CS, Su LH, Li HC, Yang HP, Chiu CH. Microbiological and genomic investigations of invasive Salmonella enterica serovar Panama from a large outbreak in Taiwan. J Formos Med Assoc 2021; 121:660-669. [PMID: 34294499 DOI: 10.1016/j.jfma.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 07/03/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND/PURPOSE Salmonella Panama was considered an invasive non-typhoidal Salmonella (iNTS) serovar. Comprehensive clinical, microbiological, and genomic studies on S. Panama are scarce. We aimed to characterize the clinical and microbiological characteristics of S. Panama infection. Virulence mechanism of S. Panama and other iNTS serovars were also examined. METHODS Based on data from the longitudinal surveillance system for Salmonella deployed in Taiwan since 2004, a case-control study was undertaken to evaluate clinical characteristics of S. Panama infection during an outbreak in 2015-2016. Cellular experiments were conducted to compare pathogenicity of S. Panama and other iNTS with S. Typhimurium. RESULTS Most patients (41/44, 93.2%) infected by S. Panama were <5 years old (median, 1.3 years). The case-control study showed that 28 out of the 41 (68.3%) manifested as bacteremia, compared to S. Typhimurium (11.1%). Patients infected by S. Panama had longer durations of fever (P = 0.005) and hospitalization (P < 0.001). Genomic analyses split the isolates into three clades: two clones caused the outbreak, whereas another one accounted for the sporadic infections before 2015. Cellular experiments revealed that S. Panama and other iNTS serovars showed higher monolayer penetration and intracellular survival within macrophages, compared to S. Typhimurium. CONCLUSION This study confirmed that S. Panama is a clinically invasive serovar. Different iNTS serovars express common virulence phenotypes, but they may acquire invasiveness through distinct expression or combinations of virulence genes.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Jung Chang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Hua Li
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chien-Shun Chiou
- Center for Research, Diagnostics and Vaccine Development, Taiwan Centers for Disease Control, Taichung, Taiwan
| | - Lin-Hui Su
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hsin-Chieh Li
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hsin-Ping Yang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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Reuter T, Scharte F, Franzkoch R, Liss V, Hensel M. Single cell analyses reveal distinct adaptation of typhoidal and non-typhoidal Salmonella enterica serovars to intracellular lifestyle. PLoS Pathog 2021; 17:e1009319. [PMID: 34143852 PMCID: PMC8244875 DOI: 10.1371/journal.ppat.1009319] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/30/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
Salmonella enterica is a common foodborne, facultative intracellular enteropathogen. Human-restricted typhoidal S. enterica serovars Typhi (STY) or Paratyphi A (SPA) cause severe typhoid or paratyphoid fever, while many S. enterica serovar Typhimurium (STM) strains have a broad host range and in human hosts usually lead to a self-limiting gastroenteritis. Due to restriction of STY and SPA to primate hosts, experimental systems for studying the pathogenesis of typhoid and paratyphoid fever are limited. Therefore, STM infection of susceptible mice is commonly considered as model system for studying these diseases. The type III secretion system encoded by Salmonella pathogenicity island 2 (SPI2-T3SS) is a key factor for intracellular survival of Salmonella. Inside host cells, the pathogen resides within the Salmonella-containing vacuole (SCV) and induces tubular structures extending from the SCV, termed Salmonella-induced filaments (SIF). This study applies single cell analyses approaches, which are flow cytometry of Salmonella harboring dual fluorescent protein reporters, effector translocation, and correlative light and electron microscopy to investigate the fate and activities of intracellular STY and SPA. The SPI2-T3SS of STY and SPA is functional in translocation of effector proteins, SCV and SIF formation. However, only a low proportion of intracellular STY and SPA are actively deploying SPI2-T3SS and STY and SPA exhibited a rapid decline of protein biosynthesis upon experimental induction. A role of SPI2-T3SS for proliferation of STY and SPA in epithelial cells was observed, but not for survival or proliferation in phagocytic host cells. Our results indicate that reduced intracellular activities are factors of the stealth strategy of STY and SPA and facilitate systemic spread and persistence of the typhoidal Salmonella. Typhoidal Salmonella enterica serovars Typhi (STY) and Paratyphi A (SPA) cause a major disease burden to the human population. The restriction of these pathogens to human hosts limits experimental analyses of molecular mechanisms of diseases. S. enterica serovar Typhimurium is commonly used as surrogate model for typhoidal Salmonella (TS), and allowed the identification of virulence factors for intracellular lifestyle of S. enterica in mammalian host cells. If virulence factors, such as the Salmonella Pathogenicity Island 2-encoded type III secretion system (SPI2-T3SS) have similar roles for intracellular lifestyle of TS is largely unknown. We analyzed, on single cell level, the intracellular activities of STY and SPA in comparison to STM. STY and SPA deploy SPI2-T3SS to actively manipulate their host cells, but with far lower frequency than STM. Our work supports a model of TS as stealth pathogens that persist in host cells.
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Affiliation(s)
- Tatjana Reuter
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Felix Scharte
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Rico Franzkoch
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- iBiOs–integrated Bioimaging Facility Osnabrück, Universität Osnabrück, Osnabrück, Germany
| | - Viktoria Liss
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- iBiOs–integrated Bioimaging Facility Osnabrück, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs–Center of Cellular Nanoanalytics Osnabrück, Universität Osnabrück, Osnabrück, Germany
- * E-mail:
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Chandrashekar S, Vijayakumar R, Chelliah R, Daliri EBM, Madar IH, Sultan G, Rubab M, Elahi F, Yeon SJ, Oh DH. In Vitro and In Silico Screening and Characterization of Antimicrobial Napin Bioactive Protein in Brassica juncea and Moringa oleifera. Molecules 2021; 26:2080. [PMID: 33916405 PMCID: PMC8038560 DOI: 10.3390/molecules26072080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
The study aimed to investigate the antibacterial activity of Mustard (Brassica juncea) and Moringa (Moringa oleifera) leaf extracts and coagulant protein for their potential application in water treatment. Bacterial cell aggregation and growth kinetics studies were employed for thirteen bacterial strains with different concentrations of leaf extracts and coagulant protein. Moringa oleifera leaf extract (MOS) and coagulant protein showed cell aggregation against ten bacterial strains, whereas leaf extract alone showed growth inhibition of five bacterial strains for up to 6 h and five bacterial strains for up to 3 h. Brassica juncea leaf extract (BJS) showed growth inhibition for up to 6 h, and three bacterial strains showed inhibition for up to 3 h. The highest inhibition concentration with 2.5 mg/mL was 19 mm, and furthermore, the minimum inhibitory concentration (MIC) (0.5 mg/mL) and MBC (1.5 mg/mL) were determined to have a higher antibacterial effect for <3 KDa peptides. Based on LCMS analysis, napin was identified in both MOS and BJS; furthermore, the mode of action of napin peptide was determined on lipoprotein X complex (LpxC) and four-chained structured binding protein of bacterial type II topoisomerase (4PLB). The docking analysis has exhibited moderate to potent inhibition with a range of dock score -912.9 Kcal/mol. Thus, it possesses antibacterial-coagulant potential bioactive peptides present in the Moringa oleifera purified protein (MOP) and Brassica juncea purified protein (BJP) that could act as an effective antimicrobial agent to replace currently available antibiotics. The result implies that MOP and Brassica juncea purified coagulant (BJP) proteins may perform a wide degree of antibacterial functions against different pathogens.
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Affiliation(s)
- Sangeeta Chandrashekar
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (S.C.); (E.B.-M.D.); (M.R.); (F.E.); (S.-J.Y.)
- Department of Physiology, Bharath Institute of Higher Education and Research, Chennai 600073, India
| | - Raman Vijayakumar
- Department of Physiology, Bharath Institute of Higher Education and Research, Chennai 600073, India
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (S.C.); (E.B.-M.D.); (M.R.); (F.E.); (S.-J.Y.)
| | - Eric Banan-Mwine Daliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (S.C.); (E.B.-M.D.); (M.R.); (F.E.); (S.-J.Y.)
| | - Inamul Hasan Madar
- Department of Biotechnology, School of Biotechnology and Genetic Engineering, Bharathidasan University, Tiruchirappalli 620024, India;
| | - Ghazala Sultan
- Department of Computer Science, Aligarh Muslim University, Aligarh 202002, India;
| | - Momna Rubab
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (S.C.); (E.B.-M.D.); (M.R.); (F.E.); (S.-J.Y.)
- School of Food and Agricultural Sciences, University of Management and Technology, Lahore 54770, Pakistan
| | - Fazle Elahi
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (S.C.); (E.B.-M.D.); (M.R.); (F.E.); (S.-J.Y.)
| | - Su-Jung Yeon
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (S.C.); (E.B.-M.D.); (M.R.); (F.E.); (S.-J.Y.)
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (S.C.); (E.B.-M.D.); (M.R.); (F.E.); (S.-J.Y.)
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32
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Enteric Fever Diagnosis: Current Challenges and Future Directions. Pathogens 2021; 10:pathogens10040410. [PMID: 33915749 PMCID: PMC8065732 DOI: 10.3390/pathogens10040410] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022] Open
Abstract
Enteric fever is a life-threatening systemic febrile disease caused by Salmonella enterica serovars Typhi and Paratyphi (S. Typhi and S. Paratyphi). Unfortunately, the burden of the disease remains high primarily due to the global spread of various drug-resistant Salmonella strains despite continuous advancement in the field. An accurate diagnosis is critical for effective control of the disease. However, enteric fever diagnosis based on clinical presentations is challenging due to overlapping symptoms with other febrile illnesses that are also prevalent in endemic areas. Current laboratory tests display suboptimal sensitivity and specificity, and no diagnostic methods are available for identifying asymptomatic carriers. Several research programs have employed systemic approaches to identify more specific biomarkers for early detection and asymptomatic carrier detection. This review discusses the pros and cons of currently available diagnostic tests for enteric fever, the advancement of research toward improved diagnostic tests, and the challenges of discovering new ideal biomarkers and tests.
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Cohen E, Azriel S, Auster O, Gal A, Zitronblat C, Mikhlin S, Scharte F, Hensel M, Rahav G, Gal-Mor O. Pathoadaptation of the passerine-associated Salmonella enterica serovar Typhimurium lineage to the avian host. PLoS Pathog 2021; 17:e1009451. [PMID: 33739988 PMCID: PMC8011750 DOI: 10.1371/journal.ppat.1009451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/31/2021] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
Salmonella enterica is a diverse bacterial pathogen and a primary cause of human and animal infections. While many S. enterica serovars present a broad host-specificity, several specialized pathotypes have been adapted to colonize and cause disease in one or limited numbers of host species. The underlying mechanisms defining Salmonella host-specificity are far from understood. Here, we present genetic analysis, phenotypic characterization and virulence profiling of a monophasic S. enterica serovar Typhimurium strain that was isolated from several wild sparrows in Israel. Whole genome sequencing and complete assembly of its genome demonstrate a unique genetic signature that includes the integration of the BTP1 prophage, loss of the virulence plasmid, pSLT and pseudogene accumulation in multiple T3SS-2 effectors (sseJ, steC, gogB, sseK2, and sseK3), catalase (katE), tetrathionate respiration (ttrB) and several adhesion/ colonization factors (lpfD, fimH, bigA, ratB, siiC and siiE) encoded genes. Correspondingly, this strain demonstrates impaired biofilm formation, intolerance to oxidative stress and compromised intracellular replication within non-phagocytic host cells. Moreover, while this strain showed attenuated pathogenicity in the mouse, it was highly virulent and caused an inflammatory disease in an avian host. Overall, our findings demonstrate a unique phenotypic profile and genetic makeup of an overlooked S. Typhimurium sparrow-associated lineage and present distinct genetic signatures that are likely to contribute to its pathoadaptation to passerine birds. During Salmonella enterica evolution, many different ecological niches have been effectively occupied by this highly diverse bacterial pathogen. While many S. enterica serovars successfully maintained their ability to infect and colonize in a wide-array of host species, a few biotypes have evolved to colonize and cause a disease in only one or a small group of hosts. The evolutionary dynamic and the mechanisms shaping the host-specificity of Salmonella adapted strains are important to better understand Salmonella pathogenicity and its ecology, but still not fully understood. Here, we report genetic and phenotypic characterization of a S. Typhimurium strain that was isolated from several wild sparrows in Israel. This strain presented unique phenotypic profile that included impaired biofilm formation, high sensitivity to oxidative stress and reduced intracellular replication in non-phagocytic cells. In addition, while this strain was able to cause high inflammatory disease in an avian host, it was highly attenuated in the mouse model. Genome analysis identified that specific genetic signatures found in the sparrow strain are more frequently associated with poultry isolates than clinical isolates of S. Typhimurium. These genetic features are expected to accumulatively contribute toward the adaptation of this strain to birds.
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Affiliation(s)
- Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Shalevet Azriel
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Oren Auster
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Adiv Gal
- Faculty of Sciences, Kibbutzim College, Tel-Aviv Israel
| | | | | | - Felix Scharte
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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34
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J Barton A, Hill J, J Blohmke C, J Pollard A. Host restriction, pathogenesis and chronic carriage of typhoidal Salmonella. FEMS Microbiol Rev 2021; 45:6159486. [PMID: 33733659 PMCID: PMC8498562 DOI: 10.1093/femsre/fuab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/03/2021] [Indexed: 12/16/2022] Open
Abstract
While conjugate vaccines against typhoid fever have recently been recommended by the World Health Organization for deployment, the lack of a vaccine against paratyphoid, multidrug resistance and chronic carriage all present challenges for the elimination of enteric fever. In the past decade, the development of in vitro and human challenge models has resulted in major advances in our understanding of enteric fever pathogenesis. In this review, we summarise these advances, outlining mechanisms of host restriction, intestinal invasion, interactions with innate immunity and chronic carriage, and discuss how this knowledge may progress future vaccines and antimicrobials.
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Affiliation(s)
- Amber J Barton
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK.,Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Jennifer Hill
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Christoph J Blohmke
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
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35
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Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism. Infect Immun 2021; 89:IAI.00606-20. [PMID: 33361201 DOI: 10.1128/iai.00606-20] [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: 09/27/2020] [Accepted: 12/10/2020] [Indexed: 11/20/2022] Open
Abstract
The Enteritidis and Dublin serovars of Salmonella enterica are phylogenetically closely related yet differ significantly in host range and virulence. S Enteritidis is a broad-host-range serovar that commonly causes self-limited gastroenteritis in humans, whereas S Dublin is a cattle-adapted serovar that can infect humans, often resulting in invasive extraintestinal disease. The mechanism underlying the higher invasiveness of S Dublin remains undetermined. In this work, we quantitatively compared the proteomes of clinical isolates of each serovar grown under gut-mimicking conditions. Compared to S Enteritidis, the S Dublin proteome was enriched in proteins linked to response to several stress conditions, such as those encountered during host infection, as well as to virulence. The S Enteritidis proteome contained several proteins related to central anaerobic metabolism pathways that were undetected in S Dublin. In contrast to what has been observed in other extraintestinal serovars, most of the coding genes for these pathways are not degraded in S Dublin. Thus, we provide evidence that S Dublin metabolic functions may be much more affected than previously reported based on genomic studies. Single and double null mutants in stress response proteins Dps, YciF, and YgaU demonstrate their relevance to S Dublin invasiveness in a murine model of invasive salmonellosis. All in all, this work provides a basis for understanding interserovar differences in invasiveness and niche adaptation, underscoring the relevance of using proteomic approaches to complement genomic studies.
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36
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Kubicek-Sutherland JZ, Xie G, Shakya M, Dighe PK, Jacobs LL, Daligault H, Davenport K, Stromberg LR, Stromberg ZR, Cheng Q, Kempaiah P, Ong’echa JM, Otieno V, Raballah E, Anyona S, Ouma C, Chain PSG, Perkins DJ, Mukundan H, McMahon BH, Doggett NA. Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. PLoS Negl Trop Dis 2021; 15:e0008991. [PMID: 33524010 PMCID: PMC7877762 DOI: 10.1371/journal.pntd.0008991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 02/11/2021] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003-2010. Nine isolates were identified as S. Typhimurium sequence type 313 while the other two were S. Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S. Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS.
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Affiliation(s)
| | - Gary Xie
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Migun Shakya
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Priya K. Dighe
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Lindsey L. Jacobs
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | | | - Karen Davenport
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | | | | | - Qiuying Cheng
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Prakasha Kempaiah
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John Michael Ong’echa
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Vincent Otieno
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Evans Raballah
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Medical Laboratory Science, School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Samuel Anyona
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno, Kenya
| | - Collins Ouma
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kenya
| | | | - Douglas J. Perkins
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Harshini Mukundan
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
- * E-mail:
| | | | - Norman A. Doggett
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
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37
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Liu MA, Kidambi A, Reeves PR. The low level of O antigen in Salmonella enterica Paratyphi A is due to inefficiency of the glycosyltransferase WbaV. FEMS Microbiol Lett 2021; 368:6105216. [PMID: 33476372 DOI: 10.1093/femsle/fnab009] [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] [Accepted: 01/18/2021] [Indexed: 11/14/2022] Open
Abstract
The group A O antigen is the major surface polysaccharide of Salmonella enterica serovar Paratyphi A (SPA), and the focal point for most current vaccine development efforts. The SPA O-antigen repeat (O unit) is structurally similar to the group D1 O unit of S. enterica serovar Typhi, differing only in the presence of a terminal side-branch paratose (Par) in place of tyvelose (Tyv), both of which are attached by the glycosyltransferase WbaV. The two O-antigen gene clusters are also highly similar, but with a loss-of-function mutation in the group A tyv gene and the tandem amplification of wbaV in most SPA strains. In this study, we show that SPA strains consistently produce less O antigen than their group D1 counterparts and use an artificial group A strain (D1 Δtyv) to show this is due to inefficient Par attachment by WbaV. We also demonstrate that group A O-antigen production can be increased by overexpression of the wbaV gene in both the D1 Δtyv strain and two multi-wbaV SPA strains. These findings should be broadly applicable in ongoing vaccine development pipelines, where efficient isolation and purification of large quantities of O antigen is of critical importance.
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Affiliation(s)
- Michael A Liu
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Aditi Kidambi
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Peter R Reeves
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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38
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Mylona E, Sanchez-Garrido J, Hoang Thu TN, Dongol S, Karkey A, Baker S, Shenoy AR, Frankel G. Very long O-antigen chains of Salmonella Paratyphi A inhibit inflammasome activation and pyroptotic cell death. Cell Microbiol 2021; 23:e13306. [PMID: 33355403 PMCID: PMC8609438 DOI: 10.1111/cmi.13306] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 11/28/2022]
Abstract
Salmonella Paratyphi A (SPtA) remains one of the leading causes of enteric (typhoid) fever. Yet, despite the recent increased rate of isolation from patients in Asia, our understanding of its pathogenesis is incomplete. Here we investigated inflammasome activation in human macrophages infected with SPtA. We found that SPtA induces GSDMD‐mediated pyroptosis via activation of caspase‐1, caspase‐4 and caspase‐8. Although we observed no cell death in the absence of a functional Salmonella pathogenicity island‐1 (SPI‐1) injectisome, HilA‐mediated overexpression of the SPI‐1 regulon enhances pyroptosis. SPtA expresses FepE, an LPS O‐antigen length regulator, which induces the production of very long O‐antigen chains. Using a ΔfepE mutant we established that the very long O‐antigen chains interfere with bacterial interactions with epithelial cells and impair inflammasome‐mediated macrophage cell death. Salmonella Typhimurium (STm) serovar has a lower FepE expression than SPtA, and triggers higher pyroptosis, conversely, increasing FepE expression in STm reduced pyroptosis. These results suggest that differential expression of FepE results in serovar‐specific inflammasome modulation, which mirrors the pro‐ and anti‐inflammatory strategies employed by STm and SPtA, respectively. Our studies point towards distinct mechanisms of virulence of SPtA, whereby it attenuates inflammasome‐mediated detection through the elaboration of very long LPS O‐polysaccharides.
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Affiliation(s)
- Elli Mylona
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Julia Sanchez-Garrido
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Trang Nguyen Hoang Thu
- Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Avinash R Shenoy
- Department of Infectious Disease, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Gad Frankel
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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39
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Cooper KG, Chong A, Kari L, Jeffrey B, Starr T, Martens C, McClurg M, Posada VR, Laughlin RC, Whitfield-Cargile C, Garry Adams L, Bryan LK, Little SV, Krath M, Lawhon SD, Steele-Mortimer O. Regulatory protein HilD stimulates Salmonella Typhimurium invasiveness by promoting smooth swimming via the methyl-accepting chemotaxis protein McpC. Nat Commun 2021; 12:348. [PMID: 33441540 PMCID: PMC7806825 DOI: 10.1038/s41467-020-20558-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/27/2020] [Indexed: 12/31/2022] Open
Abstract
In the enteric pathogen Salmonella enterica serovar Typhimurium, invasion and motility are coordinated by the master regulator HilD, which induces expression of the type III secretion system 1 (T3SS1) and motility genes. Methyl-accepting chemotaxis proteins (MCPs) detect specific ligands and control the direction of the flagellar motor, promoting tumbling and changes in direction (if a repellent is detected) or smooth swimming (in the presence of an attractant). Here, we show that HilD induces smooth swimming by upregulating an uncharacterized MCP (McpC), and this is important for invasion of epithelial cells. Remarkably, in vitro assays show that McpC can suppress tumbling and increase smooth swimming in the absence of exogenous ligands. Expression of mcpC is repressed by the universal regulator H-NS, which can be displaced by HilD. Our results highlight the importance of smooth swimming for Salmonella Typhimurium invasiveness and indicate that McpC can act via a ligand-independent mechanism when incorporated into the chemotactic receptor array.
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Affiliation(s)
- Kendal G Cooper
- Laboratory of Bacteriology, Rocky Mountain Laboratory, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Audrey Chong
- Laboratory of Bacteriology, Rocky Mountain Laboratory, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Laszlo Kari
- Laboratory of Bacteriology, Rocky Mountain Laboratory, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Brendan Jeffrey
- NIAID Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratory, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Tregei Starr
- Laboratory of Bacteriology, Rocky Mountain Laboratory, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA
- GlaxoSmithKline, Hamilton, MT, 59840, USA
| | - Craig Martens
- NIAID RML Research Technologies Section, Genomics Unit, Rocky Mountain Laboratory, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Molly McClurg
- Department of Biological and Health Sciences, Texas A&M University-Kingsville, Kingsville, TX, 78363, USA
| | - Victoria R Posada
- Department of Biological and Health Sciences, Texas A&M University-Kingsville, Kingsville, TX, 78363, USA
| | - Richard C Laughlin
- Department of Biological and Health Sciences, Texas A&M University-Kingsville, Kingsville, TX, 78363, USA
| | - Canaan Whitfield-Cargile
- Department of Veterinary Large Animal Clinical Sciences, Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, 77843, USA
| | - L Garry Adams
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, 77843, USA
| | - Laura K Bryan
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, 77843, USA
| | - Sara V Little
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, 77843, USA
| | - Mary Krath
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, 77843, USA
| | - Sara D Lawhon
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, 77843, USA
| | - Olivia Steele-Mortimer
- Laboratory of Bacteriology, Rocky Mountain Laboratory, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA.
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40
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Ma S, Liu X, Ma S, Jiang L. SopA inactivation or reduced expression is selected in intracellular Salmonella and contributes to systemic Salmonella infection. Res Microbiol 2020; 172:103795. [PMID: 33347947 DOI: 10.1016/j.resmic.2020.103795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 11/17/2022]
Abstract
Pseudogenes are accumulated in host-restricted Salmonella enterica serovars, while pseudogenization is primarily regarded as a process that purges unnecessary genes from the genome. Here we showed that the inactivation of sopA, which encodes an effector of Salmonella Pathogenicity Island 1, in human-restricted S. enterica serovar Typhi (S. Ty) and Paratyphi A (S. PA) is under positive selection and aimed to reduce bacterial cytotoxicity toward host macrophages. Moreover, we found that the expression of sopA in Salmonella Typhimurium (S. Tm), a broad-host-range serovar which causes systemic disease in mice, was negatively regulated during mice infection and survival in murine macrophages. The sopA repression in S. Tm is mediated by IsrM, a small RNA absent from the genome of S. Ty and S. PA. Due to the lack of IsrM, sopA expression was unregulated in S. Ty and S. PA, which might have facilitated the convergent inactivation of sopA in these two serovars. In conclusion, our findings demonstrate that sopA inactivation or intracellular repression is the target of positive selection during the systemic infection caused by S. enterica serovars.
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Affiliation(s)
- Shuangshuang Ma
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, China.
| | - Xiaoqian Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, China.
| | - Shuai Ma
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, China.
| | - Lingyan Jiang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, China.
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41
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Gallbladder carriage generates genetic variation and genome degradation in Salmonella Typhi. PLoS Pathog 2020; 16:e1008998. [PMID: 33085725 PMCID: PMC7605710 DOI: 10.1371/journal.ppat.1008998] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/02/2020] [Accepted: 09/21/2020] [Indexed: 11/19/2022] Open
Abstract
Despite recent advances in typhoid fever control, asymptomatic carriage of Salmonella Typhi in the gallbladder remains poorly understood. Aiming to understand if S. Typhi becomes genetically adapted for long-term colonisation in the gallbladder, we performed whole genome sequencing on a collection of S. Typhi isolated from the gallbladders of typhoid carriers. These sequences were compared to contemporaneously sampled sequences from organisms isolated from the blood of acute patients within the same population. We found that S. Typhi carriage was not restricted to any particular genotype or conformation of antimicrobial resistance genes, but was largely reflective of S. Typhi circulating in the general population. However, gallbladder isolates showed a higher genetic variability than acute isolates, with median pairwise SNP distances of 21 and 13 SNPs (p = 2.8x10-9), respectively. Within gallbladder isolates of the predominant H58 genotype, variation was associated with a higher prevalence of nonsense mutations. Notably, gallbladder isolates displayed a higher frequency of non-synonymous mutations in genes encoding hypothetical proteins, membrane lipoproteins, transport/binding proteins, surface antigens, and carbohydrate degradation. Specifically, we identified several gallbladder-specific non-synonymous mutations involved in LPS synthesis and modification, with some isolates lacking the Vi capsular polysaccharide vaccine target due to the 134Kb deletion of SPI-7. S. Typhi is under strong selective pressure in the human gallbladder, which may be reflected phylogenetically by long terminal branches that may distinguish organisms from chronic and acute infections. Our work shows that selective pressures asserted by the hostile environment of the human gallbladder generate new antigenic variants and raises questions regarding the role of carriage in the epidemiology of typhoid fever. Salmonella Typhi is the bacterium that causes typhoid. Salmonella Typhi is infamous for being able to be carried in the gallbladder, with Typhoid Mary being the best-known example of a typhoid carrier. Despite having new tools for typhoid control, we have made little progress in understanding this disease process. Aiming to understand if Salmonella Typhi is adapted for long-term survival in the gallbladder, we sequenced the genomes of 24 Salmonella Typhi isolated from the gallbladders of typhoid carriers. We compared these genomes to Salmonella Typhi from acute typhoid patients within the same population. The carriage of Salmonella Typhi was not restricted to any specific genotype or resistance to antibiotics, but reflective of the organisms causing acute disease. However, gallbladder isolates had higher genetic variability than acute isolates, with a higher frequency of mutations changing the amino acid sequences of hypothetical proteins, membrane lipoproteins, transport/binding proteins, surface antigens, and carbohydrate degradation. We identified several gallbladder-specific mutations involved in polysaccharide synthesis on the bacterial surface. Our work shows that selective pressures asserted by the hostile environment of the human gallbladder generates genetic variation, which is not observed in acute isolates, raising questions regarding the role of carriage in the epidemiology of typhoid.
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Suárez-Esquivel M, Chaves-Olarte E, Moreno E, Guzmán-Verri C. Brucella Genomics: Macro and Micro Evolution. Int J Mol Sci 2020; 21:E7749. [PMID: 33092044 PMCID: PMC7589603 DOI: 10.3390/ijms21207749] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 01/25/2023] Open
Abstract
Brucella organisms are responsible for one of the most widespread bacterial zoonoses, named brucellosis. The disease affects several species of animals, including humans. One of the most intriguing aspects of the brucellae is that the various species show a ~97% similarity at the genome level. Still, the distinct Brucella species display different host preferences, zoonotic risk, and virulence. After 133 years of research, there are many aspects of the Brucella biology that remain poorly understood, such as host adaptation and virulence mechanisms. A strategy to understand these characteristics focuses on the relationship between the genomic diversity and host preference of the various Brucella species. Pseudogenization, genome reduction, single nucleotide polymorphism variation, number of tandem repeats, and mobile genetic elements are unveiled markers for host adaptation and virulence. Understanding the mechanisms of genome variability in the Brucella genus is relevant to comprehend the emergence of pathogens.
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Affiliation(s)
- Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José 1180, Costa Rica;
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José 1180, Costa Rica;
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43
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Piccini G, Montomoli E. Pathogenic signature of invasive non-typhoidal Salmonella in Africa: implications for vaccine development. Hum Vaccin Immunother 2020; 16:2056-2071. [PMID: 32692622 PMCID: PMC7553687 DOI: 10.1080/21645515.2020.1785791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Invasive non-typhoidal Salmonella (iNTS) infections are a leading cause of bacteremia in Sub-Saharan Africa (sSA), thereby representing a major public health threat. Salmonella Typhimurium clade ST313 and Salmonella Enteriditis lineages associated with Western and Central/Eastern Africa are among the iNTS serovars which are of the greatest concern due to their case-fatality rate, especially in children and in the immunocompromised population. Identification of pathogen-associated features and host susceptibility factors that increase the risk for invasive non-typhoidal salmonellosis would be instrumental for the design of targeted prevention strategies, which are urgently needed given the increasing spread of multidrug-resistant iNTS in Africa. This review summarizes current knowledge of bacterial traits and host immune responses associated with iNTS infections in sSA, then discusses how this knowledge can guide vaccine development while providing a summary of vaccine candidates in preclinical and early clinical development.
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Affiliation(s)
| | - Emanuele Montomoli
- VisMederi srl , Siena, Italy.,Department of Molecular and Developmental Medicine, University of Siena , Siena, Italy
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44
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Barretto LAF, Fowler CC. Identification of A Putative T6SS Immunity Islet in Salmonella Typhi. Pathogens 2020; 9:pathogens9070559. [PMID: 32664482 PMCID: PMC7400221 DOI: 10.3390/pathogens9070559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Typhoid fever is a major global health problem and is the result of systemic infections caused by the human-adapted bacterial pathogen Salmonella enterica serovar Typhi (S. Typhi). The pathology underlying S. Typhi infections significantly differ from infections caused by broad host range serovars of the same species, which are a common cause of gastroenteritis. Accordingly, identifying S. Typhi genetic factors that impart functionality absent from broad host range serovars offers insights into its unique biology. Here, we used an in-silico approach to explore the function of an uncharacterized 14-gene S. Typhi genomic islet. Our results indicated that this islet was specific to the S. enterica species, where it was encoded by the Typhi and Paratyphi A serovars, but was generally absent from non-typhoidal serovars. Evidence was gathered using comparative genomics and sequence analysis tools, and indicated that this islet was comprised of Type VI secretion system (T6SS) and contact-dependent growth inhibition (CDI) genes, the majority of which appeared to encode orphan immunity proteins that protected against the activities of effectors and toxins absent from the S. Typhi genome. We herein propose that this islet represents an immune system that protects S. Typhi against competing bacteria within the human gut.
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45
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Alhaj-Qasem DM, Al-Hatamleh MAI, Irekeola AA, Khalid MF, Mohamud R, Ismail A, Mustafa FH. Laboratory Diagnosis of Paratyphoid Fever: Opportunity of Surface Plasmon Resonance. Diagnostics (Basel) 2020; 10:diagnostics10070438. [PMID: 32605310 PMCID: PMC7400347 DOI: 10.3390/diagnostics10070438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/18/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022] Open
Abstract
Paratyphoid fever is caused by the bacterium Salmonellaenterica serovar Paratyphi (A, B and C), and contributes significantly to global disease burden. One of the major challenges in the diagnosis of paratyphoid fever is the lack of a proper gold standard. Given the absence of a licensed vaccine against S. Paratyphi, this diagnostic gap leads to inappropriate antibiotics use, thus, enhancing antimicrobial resistance. In addition, the symptoms of paratyphoid overlap with other infections, including the closely related typhoid fever. Since the development and utilization of a standard, sensitive, and accurate diagnostic method is essential in controlling any disease, this review discusses a new promising approach to aid the diagnosis of paratyphoid fever. This advocated approach is based on the use of surface plasmon resonance (SPR) biosensor and DNA probes to detect specific nucleic acid sequences of S. Paratyphi. We believe that this SPR-based genoassay can be a potent alternative to the current conventional diagnostic methods, and could become a rapid diagnostic tool for paratyphoid fever.
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Affiliation(s)
| | - Mohammad A. I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (M.A.I.A.-H.); (R.M.)
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia;
- Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, Offa PMB 4412, Kwara State, Nigeria
| | - Muhammad Fazli Khalid
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (M.F.K.); (A.I.)
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (M.A.I.A.-H.); (R.M.)
- Hospital Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia
| | - Aziah Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (M.F.K.); (A.I.)
| | - Fatin Hamimi Mustafa
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (M.F.K.); (A.I.)
- Correspondence: ; Tel.: +60-9767-2432
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46
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Sokaribo AS, Hansen EG, McCarthy M, Desin TS, Waldner LL, MacKenzie KD, Mutwiri G, Herman NJ, Herman DJ, Wang Y, White AP. Metabolic Activation of CsgD in the Regulation of Salmonella Biofilms. Microorganisms 2020; 8:E964. [PMID: 32604994 PMCID: PMC7409106 DOI: 10.3390/microorganisms8070964] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/09/2020] [Accepted: 06/20/2020] [Indexed: 12/31/2022] Open
Abstract
Among human food-borne pathogens, gastroenteritis-causing Salmonella strains have the most real-world impact. Like all pathogens, their success relies on efficient transmission. Biofilm formation, a specialized physiology characterized by multicellular aggregation and persistence, is proposed to play an important role in the Salmonella transmission cycle. In this manuscript, we used luciferase reporters to examine the expression of csgD, which encodes the master biofilm regulator. We observed that the CsgD-regulated biofilm system responds differently to regulatory inputs once it is activated. Notably, the CsgD system became unresponsive to repression by Cpx and H-NS in high osmolarity conditions and less responsive to the addition of amino acids. Temperature-mediated regulation of csgD on agar was altered by intracellular levels of RpoS and cyclic-di-GMP. In contrast, the addition of glucose repressed CsgD biofilms seemingly independent of other signals. Understanding the fine-tuned regulation of csgD can help us to piece together how regulation occurs in natural environments, knowing that all Salmonella strains face strong selection pressures both within and outside their hosts. Ultimately, we can use this information to better control Salmonella and develop strategies to break the transmission cycle.
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Affiliation(s)
- Akosiererem S. Sokaribo
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Elizabeth G. Hansen
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Madeline McCarthy
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Taseen S. Desin
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
- Basic Sciences Department, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Landon L. Waldner
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Keith D. MacKenzie
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada;
- Department of Biology, University of Regina, Regina, SK S4S 0A2, Canada
| | - George Mutwiri
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Nancy J. Herman
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Dakoda J. Herman
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medicine, Shenzhen University Health Science, Shenzhen 518060, China;
| | - Aaron P. White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
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Andrews JR, Khanam F, Rahman N, Hossain M, Bogoch II, Vaidya K, Kelly M, Calderwood SB, Bhuiyan TR, Ryan ET, Qadri F, Charles RC. Plasma Immunoglobulin A Responses Against 2 Salmonella Typhi Antigens Identify Patients With Typhoid Fever. Clin Infect Dis 2020; 68:949-955. [PMID: 30020426 PMCID: PMC6399438 DOI: 10.1093/cid/ciy578] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/09/2018] [Indexed: 12/29/2022] Open
Abstract
Background There is a need for a reliable, simple diagnostic assay for typhoid fever. Available commercial serologic assays for typhoid fever have limited sensitivity and specificity. Using high-throughput immunoscreening technologies, we previously identified several immunoreactive Salmonella Typhi antigens that seem promising for possible inclusion in a new diagnostic assay: hemolysin E (HlyE), cytolethal distending toxin, S. Typhi lipopolysaccharide (LPS), and S. Typhi membrane preparation. Methods We assessed plasma antibody responses (immunoglobulin [Ig] M, IgA, and IgG) to these antigens by means of enzyme-linked immunosorbent assay in patients with suspected enteric fever, controls with other febrile illnesses, and healthy controls in Dhaka, Bangladesh and performed Tubex and Typhidot tests, the Widal assay, and the typhoid/paratyphoid test (TPTest) in each patient. Using machine learning methods, we identified a parsimonious serology signature to distinguish acute typhoid cases from controls and then validated our findings in an independent test cohort from Nepal of patients with culture-confirmed S. Typhi and controls with other bacteremic illnesses. Results We demonstrated that the use of 2 antigens (HlyE and LPS) with 1 antibody isotype (IgA) could distinguish typhoid from other invasive bacterial infections (area under the receiver operating characteristic curve [AUC], 0.95; sensitivity, 90%, specificity, 92%). Use of a single antigen (HlyE) and isotype (IgA) had an AUC of 0.93. Conclusion Our results suggest that development of a diagnostic assay for acute typhoid fever focused on detecting IgA responses against HlyE, with or without LPS, is warranted.
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Affiliation(s)
- Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, California
| | - Farhana Khanam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | - Nazia Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | - Motaher Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Ontario, Canada
| | - Krista Vaidya
- Dhulikhel Hospital, Kathmandu University Hospital, Nepal
| | - Meagan Kelly
- Division of Infectious Diseases, Massachusetts General Hospital
| | - Stephen B Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital.,Department of Medicine, Harvard Medical School.,Department of Microbiology and Immunobiology, Harvard Medical School
| | | | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital.,Department of Medicine, Harvard Medical School.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital.,Department of Medicine, Harvard Medical School
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48
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Tang L, Zhou YJ, Zhu S, Liang GD, Zhuang H, Zhao MF, Chang XY, Li HN, Liu Z, Guo ZR, Liu WQ, He X, Wang CX, Zhao DD, Li JJ, Mu XQ, Yao BQ, Li X, Li YG, Duo LB, Wang L, Johnston RN, Zhou J, Zhao JB, Liu GR, Liu SL. E. coli diversity: low in colorectal cancer. BMC Med Genomics 2020; 13:59. [PMID: 32252754 PMCID: PMC7133007 DOI: 10.1186/s12920-020-0704-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Escherichia coli are mostly commensals but also contain pathogenic lineages. It is largely unclear whether the commensal E. coli as the potential origins of pathogenic lineages may consist of monophyletic or polyphyletic populations, elucidation of which is expected to lead to novel insights into the associations of E. coli diversity with human health and diseases. METHODS Using genomic sequencing and pulsed field gel electrophoresis (PFGE) techniques, we analyzed E. coli from the intestinal microbiota of three groups of healthy individuals, including preschool children, university students, and seniors of a longevity village, as well as colorectal cancer (CRC) patients, to probe the commensal E. coli populations for their diversity. RESULTS We delineated the 2280 fresh E. coli isolates from 185 subjects into distinct genome types (genotypes) by PFGE. The genomic diversity of the sampled E. coli populations was so high that a given subject may have multiple genotypes of E. coli, with the general diversity within a host going up from preschool children through university students to seniors. Compared to the healthy subjects, the CRC patients had the lowest diversity level among their E. coli isolates. Notably, E. coli isolates from CRC patients could suppress the growth of E. coli bacteria isolated from healthy controls under nutrient-limited culture conditions. CONCLUSIONS The coexistence of multiple E. coli lineages in a host may help create and maintain a microbial environment that is beneficial to the host. As such, the low diversity of E. coli bacteria may be associated with unhealthy microenvironment in the intestine and hence facilitate the pathogenesis of diseases such as CRC.
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Affiliation(s)
- Le Tang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Departments of Ecosystems and Public Health, University of Calgary, Calgary, Canada
| | - Yu-Jie Zhou
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Present address: Department of Immunology, Capital Medical University, Beijing, China
| | - Songling Zhu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Gong-Da Liang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - He Zhuang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Man-Fei Zhao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - Xiao-Yun Chang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Hai-Ning Li
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Zheng Liu
- Department of Colorectal Surgery of the Second Affiliated Hospital, Harbin Medical University, Harbin, China.,Present address: Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhi-Rong Guo
- Department of Microbiology, Peking University Health Sciences Center, Beijing, China
| | - Wei-Qiao Liu
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.,Present address: Department of Clinical Neurosciences, University of Calgary, Calgary, Canada
| | - Xiaoyan He
- Department of Microbiology, Peking University Health Sciences Center, Beijing, China
| | - Chun-Xiao Wang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Dan-Dan Zhao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Jia-Jing Li
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xiao-Qin Mu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Bing-Qing Yao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xia Li
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yong-Guo Li
- Department of Infectious Diseases of the First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Li-Bo Duo
- Clinical Laboratory of Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Li Wang
- Clinical Laboratory of Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Randal N Johnston
- Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Jin Zhou
- Department of Hematology of the First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jing-Bo Zhao
- Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - Gui-Rong Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China. .,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China. .,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China. .,Department of Microbiology, Peking University Health Sciences Center, Beijing, China. .,Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada. .,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China. .,Department of Infectious Diseases of the First Affiliated Hospital, Harbin Medical University, Harbin, China.
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49
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Abstract
Bacterial genes are sometimes found to be inactivated by mutation. This inactivation may be observable simply because selection for function is intermittent or too weak to eliminate inactive alleles quickly. Here, I investigate cases in Salmonella enterica where inactivation is instead positively selected. These are identified by a rate of introduction of premature stop codons to a gene that is higher than expected under selective neutrality, as assessed by comparison to the rate of synonymous changes. I identify 84 genes that meet this criterion at a 10% false discovery rate. Many of these genes are involved in virulence, motility and chemotaxis, biofilm formation, and resistance to antibiotics or other toxic substances. It is hypothesized that most of these genes are subject to an ongoing process in which inactivation is favored under rare conditions, but the inactivated allele is deleterious under most other conditions and is subsequently driven to extinction by purifying selection.
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Affiliation(s)
- Joshua L Cherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
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50
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O'Boyle N, Turner NCA, Roe AJ, Connolly JPR. Plastic Circuits: Regulatory Flexibility in Fine Tuning Pathogen Success. Trends Microbiol 2020; 28:360-371. [PMID: 32298614 DOI: 10.1016/j.tim.2020.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 12/30/2022]
Abstract
Bacterial pathogens employ diverse fitness and virulence mechanisms to gain an advantage in competitive niches. These lifestyle-specific traits require integration into the regulatory network of the cell and are often controlled by pre-existing transcription factors. In this review, we highlight recent advances that have been made in characterizing this regulatory flexibility in prominent members of the Enterobacteriaceae. We focus on the direct global interactions between transcription factors and their target genes in pathogenic Escherichia coli and Salmonella revealed using chromatin immunoprecipitation coupled with next-generation sequencing. Furthermore, the implications and advantages of such regulatory adaptations in benefiting distinct pathogenic lifestyles are discussed.
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Affiliation(s)
- Nicky O'Boyle
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Natasha C A Turner
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Andrew J Roe
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK.
| | - James P R Connolly
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
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