1
|
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; 56:1288-1299. [PMID: 38831009 PMCID: PMC11176087 DOI: 10.1038/s41588-024-01779-7] [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: 09/12/2023] [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.
Collapse
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.
| |
Collapse
|
2
|
Caillava AJ, Ortiz GE, Melli LJ, Ugalde JE, Ciocchini AE, Comerci DJ. Improving bioreactor production of a recombinant glycoprotein in
Escherichia coli
: Effect of specific growth rate on protein glycosylation and specific productivity. Biotechnol Bioeng 2019; 116:1427-1438. [DOI: 10.1002/bit.26953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/30/2018] [Accepted: 02/07/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Ana J. Caillava
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Gastón E. Ortiz
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Luciano J. Melli
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Juan E. Ugalde
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Andrés E. Ciocchini
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Diego J. Comerci
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
- Comisión Nacional de Energía Atómica, Grupo Pecuario, Centro Atómico EzeizaBuenos Aires Argentina
| |
Collapse
|
3
|
Felgner J, Jain A, Nakajima R, Liang L, Jasinskas A, Gotuzzo E, Vinetz JM, Miyajima F, Pirmohamed M, Hassan-Hanga F, Umoru D, Jibir BW, Gambo S, Olateju K, Felgner PL, Obaro S, Davies DH. Development of ELISAs for diagnosis of acute typhoid fever in Nigerian children. PLoS Negl Trop Dis 2017. [PMID: 28640809 PMCID: PMC5498068 DOI: 10.1371/journal.pntd.0005679] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Improved serodiagnostic tests for typhoid fever (TF) are needed for surveillance, to facilitate patient management, curb antibiotic resistance, and inform public health programs. To address this need, IgA, IgM and IgG ELISAs using Salmonella enterica serovar Typhi (S. Typhi) lipopolysaccharide (LPS) and hemolysin E (t1477) protein were conducted on 86 Nigerian pediatric TF and 29 non-typhoidal Salmonella (NTS) cases, 178 culture-negative febrile cases, 28 "other" (i.e., non-Salmonella) pediatric infections, and 48 healthy Nigerian children. The best discrimination was achieved between TF and healthy children. LPS-specific IgA and IgM provided receiver operator characteristic areas under the curve (ROC AUC) values of 0.963 and 0.968, respectively, and 0.978 for IgA+M combined. Similar performance was achieved with t1477-specific IgA and IgM (0.968 and 0.968, respectively; 0.976 combined). IgG against LPS and t1477 was less accurate for discriminating these groups, possibly as a consequence of previous exposure, although ROC AUC values were still high (0.928 and 0.932, respectively). Importantly, discrimination between TF and children with other infections was maintained by LPS-specific IgA and IgM (AUC = 0.903 and 0.934, respectively; 0.938 combined), and slightly reduced for IgG (0.909), while t1477-specific IgG performed best (0.914). A similar pattern was seen when comparing TF with other infections from outside Nigeria. The t1477 may be recognized by cross-reactive antibodies from other acute infections, although a robust IgG response may provide some diagnostic utility in populations where incidence of other infections is low, such as in children. The data are consistent with IgA and IgM against S. Typhi LPS being specific markers of acute TF.
Collapse
Affiliation(s)
- Jiin Felgner
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Aarti Jain
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Rie Nakajima
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Li Liang
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Algis Jasinskas
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Eduardo Gotuzzo
- Alexander von Humboldt Institute of Tropical Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
- Hospital Nacional Cayetano Heredia, Lima, Peru
| | - Joseph M. Vinetz
- Alexander von Humboldt Institute of Tropical Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Fabio Miyajima
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | | | | | | | - Safiya Gambo
- Department of Pediatrics, Murtala Specialist Hospital, Kano, Nigeria
| | | | - Philip L. Felgner
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Stephen Obaro
- Department of Pediatrics, Aminu Kano Teaching Hospital, Kano, Nigeria
- University of Abuja Teaching Hospital, Gwagwalada, Nigeria
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- International Foundation against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - D. Huw Davies
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail:
| |
Collapse
|
4
|
Principi N, Esposito S. Preventing invasive salmonellosis in children through vaccination. Expert Rev Vaccines 2016; 15:897-905. [PMID: 27140662 DOI: 10.1080/14760584.2016.1183484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Vaccination is an important strategy to control endemic enteric fever (EF) and to interrupt transmission during outbreaks. The main aim of this paper is to discuss the efficacy of available EF vaccines in children and to highlight novel vaccination possibilities against EF and non-typhoid invasive salmonelloses. AREAS COVERED Two types of typhoid vaccines are presently available in the industrialized world. One of these vaccines is administered parenterally and is based on the virulence-associated (Vi) capsular polysaccaride of Salmonella typhi. The second vaccine is based on a live attenuated strain of the pathogen and is given orally. In addition, a Vi-tetanus toxoid conjugated vaccine is currently licensed in India; however, it is not available anywhere else. Expert commentary: Unfortunately, only typhoid fever is addressed by the currently licensed typhoid vaccines. Moreover, they are unsuitable for infants and remain a possible aid for reducing the risk of EF only in older subjects. They should be used in developing countries with endemic EF. New vaccines able to confer long-term protection to subjects in the first years of life and those with immature immune systems could significantly reduce incidence rates of EF in younger children. Vi-conjugate preparations are promising solutions in this regard.
Collapse
Affiliation(s)
- Nicola Principi
- a Paediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation , Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Susanna Esposito
- a Paediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation , Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
| |
Collapse
|
5
|
Storey HL, Huang Y, Crudder C, Golden A, de los Santos T, Hawkins K. A Meta-Analysis of Typhoid Diagnostic Accuracy Studies: A Recommendation to Adopt a Standardized Composite Reference. PLoS One 2015; 10:e0142364. [PMID: 26566275 PMCID: PMC4643909 DOI: 10.1371/journal.pone.0142364] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/21/2015] [Indexed: 01/09/2023] Open
Abstract
Novel typhoid diagnostics currently under development have the potential to improve clinical care, surveillance, and the disease burden estimates that support vaccine introduction. Blood culture is most often used as the reference method to evaluate the accuracy of new typhoid tests; however, it is recognized to be an imperfect gold standard. If no single gold standard test exists, use of a composite reference standard (CRS) can improve estimation of diagnostic accuracy. Numerous studies have used a CRS to evaluate new typhoid diagnostics; however, there is no consensus on an appropriate CRS. In order to evaluate existing tests for use as a reference test or inclusion in a CRS, we performed a systematic review of the typhoid literature to include all index/reference test combinations observed. We described the landscape of comparisons performed, showed results of a meta-analysis on the accuracy of the more common combinations, and evaluated sources of variability based on study quality. This wide-ranging meta-analysis suggests that no single test has sufficiently good performance but some existing diagnostics may be useful as part of a CRS. Additionally, based on findings from the meta-analysis and a constructed numerical example demonstrating the use of CRS, we proposed necessary criteria and potential components of a typhoid CRS to guide future recommendations. Agreement and adoption by all investigators of a standardized CRS is requisite, and would improve comparison of new diagnostics across independent studies, leading to the identification of a better reference test and improved confidence in prevalence estimates.
Collapse
Affiliation(s)
- Helen L. Storey
- Diagnostics Program, PATH, Seattle, Washington, United States of America
- * E-mail:
| | - Ying Huang
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Chris Crudder
- Diagnostics Program, PATH, Seattle, Washington, United States of America
| | - Allison Golden
- Diagnostics Program, PATH, Seattle, Washington, United States of America
| | - Tala de los Santos
- Diagnostics Program, PATH, Seattle, Washington, United States of America
| | - Kenneth Hawkins
- Diagnostics Program, PATH, Seattle, Washington, United States of America
| |
Collapse
|
6
|
Frickmann H, Hänle A, Essig A, Dekker D, Boahen K, Acquah S, Sarpong N, Adu-Sarkodie Y, Schwarz NG, May J, Marks F, Hagen RM, Poppert S. Fluorescence in situ hybridization (FISH) for rapid identification of Salmonella spp. from agar and blood culture broth--an option for the tropics? Int J Med Microbiol 2013; 303:277-84. [PMID: 23642903 DOI: 10.1016/j.ijmm.2013.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/02/2013] [Accepted: 04/07/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Salmonella enterica is an important cause of diarrhea with the potential to cause systemic infection including sepsis, particularly in the tropics. Sepsis in particular requires quick and reliable identification to allow a rapid optimization of antibiotic therapy. We describe the establishment and evaluation of fluorescence in situ hybridization (FISH) as a rapid and easy-to-perform molecular identification procedure from agar and blood culture broths. METHODS Two newly developed FISH probes with specificity for Salmonella spp. were evaluated with 10 reference strains, 448 clinical isolates of Gram-negative bacteria from Germany and Ghana including 316 Salmonella spp. strains, and 39 environmental Salmonella spp. isolates from rivers and streams in Ghana. One FISH probe was further tested with 207 pre-incubated blood culture broths from Germany with Gram-negative rod-shaped bacteria in Gram stain. RESULTS Evaluation of the newly designed FISH probes demonstrated sensitivity of 99.2% and specificity of 98.4% for clinical isolates, sensitivity of 97.4% for environmental Salmonella spp. isolates, and sensitivity of 100% and specificity of 99.5% for blood culture materials. CONCLUSIONS FISH proved to be highly reliable for a rapid identification of Salmonella spp. directly from pre-incubated blood culture broths as well as after growth on agar. The inexpensive and easy-to-perform procedure is particularly suitable for resource-limited areas where more sophisticated procedures are not available.
Collapse
Affiliation(s)
- Hagen Frickmann
- Department of Tropical Medicine at the Bernhard-Nocht Institute, German Armed Forces Hospital of Hamburg, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Abstract
PURPOSE OF REVIEW This review summarizes the recent advances in vaccination against Salmonella enterica serovar Typhi and highlights the data supporting the development of next generation vaccines to address paratyphoid fever and invasive nontyphoidal Salmonella (iNTS) disease. RECENT FINDINGS There has been increasing awareness of the disease burden caused by S. Typhi particularly in Africa and greater recognition of S. Paratyphi A's contribution to enteric fever episodes throughout Asia. Groups have been working to improve the existing typhoid vaccines and provide comprehensive data on the feasibility of their implementation in endemic settings. These data have resulted in modifications to the recommendations for typhoid vaccination in traveller markets and endemic settings, and has also led to the development of S. Paratyphi A vaccine components that can be combined with existing typhoid vaccines to generate bivalent formulations against enteric fever. The epidemiology of iNTS serovars as cause of appreciable morbidity and mortality in Africa, and the need for vaccines, has also become more widely appreciated. SUMMARY Current typhoid vaccines, although moderately effective for short periods of time, cannot be used in all age groups and only target one of the clinically relevant Salmonella serovars. Greater effort must be placed on the development and implementation of improved vaccines for the disease burden resulting from Typhi, Paratyphi A or iNTS infections.
Collapse
|
8
|
Ali A, An SJ, Cui C, Haque A, Carbis R. Preparation and evaluation of immunogenic conjugates of Salmonella enterica serovar Typhi O-specific polysaccharides with diphtheria toxoid. Hum Vaccin Immunother 2012; 8:189-93. [PMID: 22426380 DOI: 10.4161/hv.18350] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a major health problem particularly in developing countries. The available vaccines have certain limitations regarding their efficacy, and inability to induce an immune response especially in individuals under 2 years of age. Conjugate vaccines which consist of a bacteria-specific polysaccharide chemically bound to a carrier protein overcome these problems by inducing a T-cell dependent immune response characterized by enhanced immunogenicity in all ages. In this study, O-specific polysaccharides (OSP) of S. Typhi were conjugated to diphtheria toxoid (DT) using adipic acid dihydrazide (ADH) as a linker. These conjugates (OSP-AH-DT) were then evaluated for their immunogenicity using mice as a model and showed significantly higher levels of IgG ELISA titers (P = 0.0241 and 0.0245) than lipopolysaccharides alone. Different immunization schedules were compared and it was found that schedule-B (three injections with 4-weeks interval) induced higher immune responses than schedule-A (three injections with 2-weeks interval). We showed that diphtheria toxoid can be successfully employed as a carrier protein for conjugation with Salmonella OSP and play an important role in facilitating adequate immune response.
Collapse
Affiliation(s)
- Aamir Ali
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | | | | | | | | |
Collapse
|
9
|
Wang J, Zhao H, Zheng Y, Liu W, Zhou H, Han ARN, Gao X. Monoclonal antibodies to sea cucumber polysaccharide and their use in a sandwich ELISA assay. Hybridoma (Larchmt) 2011; 30:381-5. [PMID: 21851239 DOI: 10.1089/hyb.2011.0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antigen was synthesized with L-SCP, a sea cucumber polysaccharide isolated from Pearsonothuria graeffei (Semper) and bovine serum albumin (BSA) as a carrier protein. Spleen cells with high titer antibody producing ability were removed and fused with myeloma cells of SP2/0-Ag14 origin. Three stable murine monoclonal antibodies (MAb ascites) producing cell lines to L-SCP were generated according to a conventional immunization protocol. Their epitope mapping and binding specificity, which was characterized by blocking and inhibition enzyme-linked immunosorbent assay (ELISA) indicated that these specific MAb ascites have similar binding patterns. A sandwich ELISA was developed on the basis of employing L-SCP specific antibodies including MAb 3G6 as capture antibody and HRP-3G6 as detection antibody. The working range for L-SCP in aqueous solution from this method was 100-10,000 ng/mL with good sensitivity, specificity, and precision (relative standard deviation ≤7.9%). Thus the developed ELISA can be used as a convenient tool for the rapid detection of L-SCP in biological examples in the future.
Collapse
Affiliation(s)
- Junjun Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, P.R. China
| | | | | | | | | | | | | |
Collapse
|
10
|
Osorio-Román IO, Aroca RF, Astudillo J, Matsuhiro B, Vásquez C, Pérez JM. Characterization of bacteria using its O-antigen with surface-enhanced Raman scattering. Analyst 2010; 135:1997-2001. [DOI: 10.1039/c0an00061b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Zhou X, Zhao H, Gao X. Preparation and Characterization of Monoclonal Antibodies Against a Polysaccharide fromFlammulina velutipesMycelium. Hybridoma (Larchmt) 2008; 27:439-44. [DOI: 10.1089/hyb.2008.0033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xuelin Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, P.R. China
| | - Hu Zhao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, P.R. China
| | - Xiangdong Gao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, P.R. China
| |
Collapse
|