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de Graaf M, Beck R, Caccio SM, Duim B, Fraaij PLA, Le Guyader FS, Lecuit M, Le Pendu J, de Wit E, Schultsz C. Sustained fecal-oral human-to-human transmission following a zoonotic event. Curr Opin Virol 2016; 22:1-6. [PMID: 27888698 PMCID: PMC7102779 DOI: 10.1016/j.coviro.2016.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 12/28/2022]
Abstract
Bacterial, viral and parasitic zoonotic pathogens that transmit via the fecal-oral route have a major impact on global health. However, the mechanisms underlying the emergence of such pathogens from the animal reservoir and their persistence in the human population are poorly understood. Here, we present a framework of human-to-human transmission of zoonotic pathogens that considers the factors relevant for fecal-oral human-to-human transmission route at the levels of host, pathogen, and environment. We discuss current data gaps and propose future research directions.
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Affiliation(s)
- Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Relja Beck
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Simone M Caccio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Pieter LA Fraaij
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Pediatrics, Erasmus Medical Center-Sophia, Rotterdam, The Netherlands
| | | | - Marc Lecuit
- Institut Pasteur, Inserm U1117, Biology of Infection Unit, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Necker-Pasteur Centre for Infectiology, Necker-Enfants Malades University Hospital, Institut Imagine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Emmie de Wit
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Constance Schultsz
- Department of Global Health and Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands.
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Lokken KL, Walker GT, Tsolis RM. Disseminated infections with antibiotic-resistant non-typhoidal Salmonella strains: contributions of host and pathogen factors. Pathog Dis 2016; 74:ftw103. [PMID: 27765795 DOI: 10.1093/femspd/ftw103] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2016] [Indexed: 11/14/2022] Open
Abstract
Non-typhoidal Salmonella enterica serovars (NTS) are generally associated with gastroenteritis; however, the very young and elderly, as well as individuals with compromised immunity, are at risk of developing disseminated infection that can manifest as bacteremia or focal infections at systemic sites. Disseminated NTS infections can be fatal and are responsible for over 600 000 deaths annually. Most of these deaths are in sub-Saharan Africa, where multidrug-resistant NTS clones are currently circulating in a population with a high proportion of individuals that are susceptible to disseminated disease. This review considers how genome degradation observed in African NTS isolates has resulted in phenotypic differences in traits related to environmental persistence and host-pathogen interactions. Further, it discusses host mechanisms promoting susceptibility to invasive infection with NTS in individuals with immunocompromising conditions. We conclude that mechanistic knowledge of how risk factors compromise immunity to disseminated NTS infection will be important for the design of interventions to protect against systemic disease.
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Affiliation(s)
- Kristen L Lokken
- Medical Microbiology and Immunology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Gregory T Walker
- Medical Microbiology and Immunology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Renée M Tsolis
- Medical Microbiology and Immunology, University of California, One Shields Avenue, Davis, CA 95616, USA
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Wheeler NE, Barquist L, Kingsley RA, Gardner PP. A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. Bioinformatics 2016; 32:3566-3574. [PMID: 27503221 PMCID: PMC5181535 DOI: 10.1093/bioinformatics/btw518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/17/2016] [Accepted: 08/02/2016] [Indexed: 02/04/2023] Open
Abstract
Motivation: Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics. Results: We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms. Availability and Implementation: A program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/deltaBS. Contact:nicole.wheeler@pg.canterbury.ac.nz or lars.barquist@uni-wuerzburg.de Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicole E Wheeler
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Robert A Kingsley
- Institute of Food Research, Norwich Research Park, Norwich, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Paul P Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Bio-protection Research Centre, University of Canterbury, Christchurch, New Zealand
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Ramachandran G, Aheto K, Shirtliff ME, Tennant SM. Poor biofilm-forming ability and long-term survival of invasive Salmonella Typhimurium ST313. Pathog Dis 2016; 74:ftw049. [PMID: 27222487 DOI: 10.1093/femspd/ftw049] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2016] [Indexed: 11/12/2022] Open
Abstract
Salmonella enterica serovar Typhimurium, an enteric pathogen that causes a self-limiting gastroenteritis, forms biofilms on different surfaces. In sub-Saharan Africa, Salmonella Typhimurium of a novel sequence type (ST) 313 was identified and produces septicemia in the absence of gastroenteritis. No animal reservoir has been identified, and it is hypothesized that transmission occurs via human to human. In this study, we show that invasive Salmonella Typhimurium ST313 strains from Mali are poor biofilm producers compared to Salmonella Typhimurium ST19 strains, which are found worldwide and are known to be associated with gastroenteritis. We evaluated biofilms using crystal violet staining, examination of the red, dry and rough morphotype, pellicle formation and a continuous flow system. One month-old Salmonella Typhimurium ST19 colonies survived in the absence of exogenous nutrients and were highly resistant to sodium hypochlorite treatment compared to Salmonella Typhimurium ST313. This study for the first time demonstrates the comparative biofilm-forming ability and long-term survival of clinical Salmonella Typhimurium ST19 and ST313 isolates. Salmonella Typhimurium ST19 strains are strong biofilm producers and can survive desiccation compared to Salmonella Typhimurium ST313 that form weak biofilms and survive poorly following desiccation. Our data suggest that like Salmonella Typhi, Salmonella Typhimurium ST313 lack mechanisms that allow it to persist in the environment.
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Affiliation(s)
- Girish Ramachandran
- Center for Vaccine Development, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
| | - Komi Aheto
- Center for Vaccine Development, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
| | - Mark E Shirtliff
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Sharon M Tennant
- Center for Vaccine Development, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
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