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Kumwenda B, Canals R, Predeus AV, Zhu X, Kröger C, Pulford C, Wenner N, Lora LL, Li Y, Owen SV, Everett D, Hokamp K, Heyderman RS, Ashton PM, Gordon MA, Msefula CL, Hinton JCD. Salmonella enterica serovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage. MICROLIFE 2024; 5:uqae005. [PMID: 38623411 PMCID: PMC11018118 DOI: 10.1093/femsml/uqae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024]
Abstract
Invasive non-typhoidal Salmonella (iNTS) disease is a serious bloodstream infection that targets immune-compromised individuals, and causes significant mortality in sub-Saharan Africa. Salmonella enterica serovar Typhimurium ST313 causes the majority of iNTS in Malawi. We performed an intensive comparative genomic analysis of 608 S. Typhimurium ST313 isolates dating between 1996 and 2018 from Blantyre, Malawi. We discovered that following the arrival of the well-characterized S. Typhimurium ST313 lineage 2 in 1999, two multidrug-resistant variants emerged in Malawi in 2006 and 2008, designated sublineages 2.2 and 2.3, respectively. The majority of S. Typhimurium isolates from human bloodstream infections in Malawi now belong to sublineages 2.2 or 2.3. To understand the emergence of the prevalent ST313 sublineage 2.2, we studied two representative strains, D23580 (lineage 2) and D37712 (sublineage 2.2). The chromosome of ST313 lineage 2 and sublineage 2.2 only differed by 29 SNPs/small indels and a 3 kb deletion of a Gifsy-2 prophage region including the sseI pseudogene. Lineage 2 and sublineage 2.2 had distinctive plasmid profiles. The transcriptome was investigated in 15 infection-relevant in vitro conditions and within macrophages. During growth in physiological conditions that do not usually trigger S. Typhimurium SPI2 gene expression, the SPI2 genes of D37712 were transcriptionally active. We identified down-regulation of flagellar genes in D37712 compared with D23580. Following phenotypic confirmation of transcriptomic differences, we discovered that sublineage 2.2 had increased fitness compared with lineage 2 during mixed growth in minimal media. We speculate that this competitive advantage is contributing to the emergence of sublineage 2.2 in Malawi.
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Affiliation(s)
- Benjamin Kumwenda
- School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences Blantyre, Blantyre, 265, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Rocío Canals
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Alexander V Predeus
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Xiaojun Zhu
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Carsten Kröger
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Caisey Pulford
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Lizeth Lacharme Lora
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Yan Li
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Siân V Owen
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Dean Everett
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, P.O. Box 127788, United Arab Emirates
| | - Karsten Hokamp
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Robert S Heyderman
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
- Research Department of Infection, Division of Infection & Immunity, University College London, London, WC1E 6BT, United Kingdom
| | | | - Melita A Gordon
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Chisomo L Msefula
- School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences Blantyre, Blantyre, 265, Malawi
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
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Tsai S, Tikekar RV. The effect of emulsifier type and oil inclusion on stress-related gene expression of Salmonella typhimurium in oil-in-water emulsion. J Food Sci 2024; 89:1211-1224. [PMID: 38224194 DOI: 10.1111/1750-3841.16908] [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: 07/27/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
Salmonella has been associated with numerous outbreaks from contaminated food products, including emulsions. Emulsions are influenced by emulsifier type and oil presence, which can have varying degrees of stress or protection on bacteria. Although our previous research has shown that emulsifier solutions, rather than emulsions, provide a protective effect on Salmonella typhimurium after thermal treatment, the underlying mechanism remains unclear. This study selected S. typhimurium as the model microorganism and utilized the same emulsifiers (Tween 20, Tween 80, Triton X-100) to create emulsifier solutions and emulsions with the same oil fraction (60% (v/v)) to examine their effect on the expression of nine selected genes (rpoE, rpoH, otsB, proV, fadA, fabA, dnaK, ibpA, ompC) associated with stress response. Specifically, the study observed variations in gene expression under normal and thermal stress at 55°C. After 20-h incubation, Triton X-100 emulsion caused an upregulation of stress-related genes, rpoE, otsB, and fabA, suggesting stressful environment. After thermal treatment, S. typhimurium in Triton X-100 solution showed a longer 5-log reduction time with increased proV and decreased fabA and ompC expression, suggesting enhanced thermal protection compared to its emulsion. Conversely, Tween 80 solution increased fabA and ompC expression, indicating greater membrane fluidity and passive diffusion, potentially reducing thermal resistance. However, according to the upregulation of ibpA, this effect was likely mitigated by the overproduction of heat shock proteins. Notably, Triton X-100 environments exhibited the most significant gene expression changes after heat treatment, whereas Tween 80 without oil was the most inhospitable for bacterial survival. These findings inform bacterial responses under various conditions, aiding food safety strategies.
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Affiliation(s)
- Shawn Tsai
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Rohan V Tikekar
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
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Browning KR, Merrikh H. Pathogenic bacteria experience pervasive RNA polymerase backtracking during infection. mBio 2024; 15:e0273723. [PMID: 38095872 PMCID: PMC10790778 DOI: 10.1128/mbio.02737-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/06/2023] [Indexed: 12/26/2023] Open
Abstract
IMPORTANCE Eukaryotic hosts have defense mechanisms that may disrupt molecular transactions along the pathogen's chromosome through excessive DNA damage. Given that DNA damage stalls RNA polymerase (RNAP) thereby increasing mutagenesis, investigating how host defense mechanisms impact the movement of the transcription machinery on the pathogen chromosome is crucial. Using a new methodology we developed, we elucidated the dynamics of RNAP movement and association with the chromosome in the pathogenic bacterium Salmonella enterica during infection. We found that dynamics of RNAP movement on the chromosome change significantly during infection genome-wide, including at regions that encode for key virulence genes. In particular, we found that there is pervasive RNAP backtracking on the bacterial chromosome during infections and that anti-backtracking factors are critical for pathogenesis. Altogether, our results suggest that, interestingly, the host environment can promote the development of antimicrobial resistance and hypervirulence as stalled RNAPs can accelerate evolution through increased mutagenesis.
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Affiliation(s)
- Kaitlyn R. Browning
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Houra Merrikh
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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Smith C, Smith E, Rydlova A, Varro R, Hinton JCD, Gordon MA, Choy RKM, Liu X, Pollard AJ, Chiu C, Cooke GS, Gibani MM. Protocol for the challenge non-typhoidal Salmonella (CHANTS) study: a first-in-human, in-patient, double-blind, randomised, safety and dose-escalation controlled human infection model in the UK. BMJ Open 2024; 14:e076477. [PMID: 38199617 PMCID: PMC10806722 DOI: 10.1136/bmjopen-2023-076477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION Invasive non-typhoidal Salmonella (iNTS) serovars are a major cause of community-acquired bloodstream infections in sub-Saharan Africa (SSA). In this setting, Salmonella enterica serovar Typhimurium accounts for two-thirds of infections and is associated with an estimated case fatality rate of 15%-20%. Several iNTS vaccine candidates are in early-stage assessment which-if found effective-would provide a valuable public health tool to reduce iNTS disease burden. The CHANTS study aims to develop a first-in-human Salmonella Typhimurium controlled human infection model, which can act as a platform for future vaccine evaluation, in addition to providing novel insights into iNTS disease pathogenesis. METHODS AND ANALYSIS This double-blind, safety and dose-escalation study will randomise 40-80 healthy UK participants aged 18-50 to receive oral challenge with one of two strains of S. Typhimurium belonging to the ST19 (strain 4/74) or ST313 (strain D23580) lineages. 4/74 is a global strain often associated with diarrhoeal illness predominantly in high-income settings, while D23580 is an archetypal strain representing invasive disease-causing isolates found in SSA. The primary objective is to determine the minimum infectious dose (colony-forming unit) required for 60%-75% of participants to develop clinical or microbiological features of systemic salmonellosis. Secondary endpoints are to describe and compare the clinical, microbiological and immunological responses following challenge. Dose escalation or de-escalation will be undertaken by continual-reassessment methodology and limited within prespecified safety thresholds. Exploratory objectives are to describe mechanisms of iNTS virulence, identify putative immune correlates of protection and describe host-pathogen interactions in response to infection. ETHICS AND DISSEMINATION Ethical approval has been obtained from the NHS Health Research Authority (London-Fulham Research Ethics Committee 21/PR/0051; IRAS Project ID 301659). The study findings will be disseminated in international peer-reviewed journals and presented at national/international stakeholder meetings. Study outcome summaries will be provided to both funders and participants. TRIAL REGISTRATION NUMBER NCT05870150.
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Affiliation(s)
- Christopher Smith
- Department of Infectious Disease, Imperial College London, London, UK
| | - Emma Smith
- Department of Infectious Disease, Imperial College London, London, UK
| | - Anna Rydlova
- Department of Infectious Disease, Imperial College London, London, UK
| | - Robert Varro
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Southern Region, Malawi
| | | | - Xinxue Liu
- Oxford Vaccine Group, Department of Paediatrics, Oxford University, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, Oxford University, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham S Cooke
- Department of Infectious Disease, Imperial College London, London, UK
| | - Malick M Gibani
- Department of Infectious Disease, Imperial College London, London, UK
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Yang J, Barrila J, Nauman EA, Nydam SD, Yang S, Park J, Gutierrez-Jensen AD, Castro CL, Ott CM, Buss K, Steel J, Zakrajsek AD, Schuff MM, Nickerson CA. Incremental increases in physiological fluid shear progressively alter pathogenic phenotypes and gene expression in multidrug resistant Salmonella. Gut Microbes 2024; 16:2357767. [PMID: 38783686 PMCID: PMC11135960 DOI: 10.1080/19490976.2024.2357767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
The ability of bacteria to sense and respond to mechanical forces has important implications for pathogens during infection, as they experience wide fluid shear fluctuations in the host. However, little is known about how mechanical forces encountered in the infected host drive microbial pathogenesis. Herein, we combined mathematical modeling with hydrodynamic bacterial culture to profile transcriptomic and pathogenesis-related phenotypes of multidrug resistant S. Typhimurium (ST313 D23580) under different fluid shear conditions relevant to its transition from the intestinal tract to the bloodstream. We report that D23580 exhibited incremental changes in transcriptomic profiles that correlated with its pathogenic phenotypes in response to these progressive increases in fluid shear. This is the first demonstration that incremental changes in fluid shear forces alter stress responses and gene expression in any ST313 strain and offers mechanistic insight into how forces encountered by bacteria during infection might impact their disease-causing ability in unexpected ways.
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Affiliation(s)
- Jiseon Yang
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Jennifer Barrila
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
| | - Eric A. Nauman
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
| | - Seth D. Nydam
- Department of Animal Care & Technologies, Arizona State University, Tempe, AZ, USA
| | - Shanshan Yang
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, USA
| | - Jin Park
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, USA
| | - Ami D. Gutierrez-Jensen
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Christian L. Castro
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- JES Tech, Houston, TX, USA
| | - C. Mark Ott
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX, USA
| | - Kristina Buss
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, USA
| | - Jason Steel
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, USA
| | - Anne D. Zakrajsek
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
| | - Mary M. Schuff
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
| | - Cheryl A. Nickerson
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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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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Martins IM, Seribelli AA, Machado Ribeiro TR, da Silva P, Lustri BC, Hernandes RT, Falcão JP, Moreira CG. Invasive non-typhoidal Salmonella (iNTS) aminoglycoside-resistant ST313 isolates feature unique pathogenic mechanisms to reach the bloodstream. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105519. [PMID: 37890808 DOI: 10.1016/j.meegid.2023.105519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Invasive non-typhoidal Salmonella (iNTS) from the clonal type ST313 (S. Typhimurium ST313) is the primary cause of invasive salmonellosis in Africa. Recently, in Brazil, iNTS ST313 strains have been isolated from different sources, but there is a lack of understanding of the mechanisms behind how these gut bacteria can break the gut barrier and reach the patient's bloodstream. Here, we compare 13 strains of S. Typhimurium ST313, previously unreported isolates, from human blood cultures, investigating aspects of virulence and mechanisms of resistance. Initially, RNAseq analyses between ST13-blood isolate and SL1344 (ST19) prototype revealed 15 upregulated genes directly related to cellular invasion and replication, such as sopD2, sifB, and pipB. Limited information is available about S. Typhimurium ST313 pathogenesis and epidemiology, especially related to the global distribution of strains. Herein, the correlation of strains isolated from different sources in Brazil was employed to compare clinical and non-clinical isolates, a total of 22 genomes were studied by single nucleotide polymorphism (SNPs). The epidemiological analysis of 22 genomes of S. Typhimurium ST313 strains grouped them into three distinct clusters (A, B, and C) by SNP analysis, where cluster A comprised five, group B six, and group C 11. The 13 clinical blood isolates were all resistant to streptomycin, 92.3% of strains were resistant to ampicillin and 15.39% were resistant to kanamycin. The resistance genes acrA, acrB, mdtK, emrB, emrR, mdsA, and mdsB related to the production of efflux pumps were detected in all (100%) strains studied, similar to pathogenic traits investigated. In conclusion, we evidenced that S. Typhimurium ST313 strains isolated in Brazil have unique epidemiology. The elevated frequencies of virulence genes such as sseJ, sopD2, and pipB are a major concern in these Brazilian isolates, showing a higher pathogenic potential.
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Affiliation(s)
- Isabela Mancini Martins
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil
| | - Amanda Aparecida Seribelli
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo- USP, Ribeirão Preto, SP, Brazil
| | - Tamara R Machado Ribeiro
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil
| | - Patrick da Silva
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil
| | - Bruna Cardinali Lustri
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil
| | - Rodrigo T Hernandes
- Instituto de Biociências, Universidade Estadual Paulista- UNESP, Botucatu, SP, Brazil
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo- USP, Ribeirão Preto, SP, Brazil.
| | - Cristiano Gallina Moreira
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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Chalka A, Dallman TJ, Vohra P, Stevens MP, Gally DL. The advantage of intergenic regions as genomic features for machine-learning-based host attribution of Salmonella Typhimurium from the USA. Microb Genom 2023; 9:001116. [PMID: 37843883 PMCID: PMC10634445 DOI: 10.1099/mgen.0.001116] [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: 03/08/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
Salmonella enterica is a taxonomically diverse pathogen with over 2600 serovars associated with a wide variety of animal hosts including humans, other mammals, birds and reptiles. Some serovars are host-specific or host-restricted and cause disease in distinct host species, while others, such as serovar S. Typhimurium (STm), are generalists and have the potential to colonize a wide variety of species. However, even within generalist serovars such as STm it is becoming clear that pathovariants exist that differ in tropism and virulence. Identifying the genetic factors underlying host specificity is complex, but the availability of thousands of genome sequences and advances in machine learning have made it possible to build specific host prediction models to aid outbreak control and predict the human pathogenic potential of isolates from animals and other reservoirs. We have advanced this area by building host-association prediction models trained on a wide range of genomic features and compared them with predictions based on nearest-neighbour phylogeny. SNPs, protein variants (PVs), antimicrobial resistance (AMR) profiles and intergenic regions (IGRs) were extracted from 3883 high-quality STm assemblies collected from humans, swine, bovine and poultry in the USA, and used to construct Random Forest (RF) machine learning models. An additional 244 recent STm assemblies from farm animals were used as a test set for further validation. The models based on PVs and IGRs had the best performance in terms of predicting the host of origin of isolates and outperformed nearest-neighbour phylogenetic host prediction as well as models based on SNPs or AMR data. However, the models did not yield reliable predictions when tested with isolates that were phylogenetically distinct from the training set. The IGR and PV models were often able to differentiate human isolates in clusters where the majority of isolates were from a single animal source. Notably, IGRs were the feature with the best performance across multiple models which may be due to IGRs acting as both a representation of their flanking genes, equivalent to PVs, while also capturing genomic regulatory variation, such as altered promoter regions. The IGR and PV models predict that ~45 % of the human infections with STm in the USA originate from bovine, ~40 % from poultry and ~14.5 % from swine, although sequences of isolates from other sources were not used for training. In summary, the research demonstrates a significant gain in accuracy for models with IGRs and PVs as features compared to SNP-based and core genome phylogeny predictions when applied within the existing population structure. This article contains data hosted by Microreact.
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Affiliation(s)
- Antonia Chalka
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - Tim J. Dallman
- Institute for Risk Assessment Sciences (IRAS), University of Utrecht, Heidelberglaan, Utrecht, Netherlands
| | - Prerna Vohra
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - Mark P. Stevens
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - David L. Gally
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
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Alves da Silva A, Silva IJ, Arraiano CM. A paradox of bacterial persistence and antibiotic resistance: chloramphenicol acetyl transferase as a double barrel shot gun. MICROLIFE 2023; 4:uqad034. [PMID: 37781689 PMCID: PMC10540939 DOI: 10.1093/femsml/uqad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/04/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
The problematic microbial resistance to antibiotics has led to an increasing interest in bacterial persistence and its impact on infection. Nonetheless, these two mechanisms are often assessed in independent studies, and there is a lack of knowledge about their relation or possible interactions, both at cellular and population levels. This work shows evidence that the insertion of the resistance gene Chloramphenicol Acetyl Transferase (cat) together with its cognate antibiotic chloramphenicol (CAM), is capable to modulate Salmonella Typhimurium persistence to several antibiotics and decrease its survival. This effect is independent of the antibiotics' mechanisms of action or the locus of cat. RelA [p(ppGpp) syntetase] has been shown to be involved in persistence. It was recently proposed that RelA [(p)ppGpp synthetase], binds to uncharged tRNAs, forming RelA.tRNA complexes. These complexes bind to vacant A-sites in the ribosome, and this mechanism is essential for the activation of RelA. In this study, we propose that the antibiotic chloramphenicol blocks the A-site of the ribosome, hindering the binding of RelA.tRNA complexes to the ribosome thus preventing the activation of RelA and (p)ppGpp synthesis, with a consequent decrease in the level of persistence of the population. Our discovery that the concomitant use of chloramphenicol and other antibiotics in chloramphenicol resistant bacteria can decrease the persister levels can be the basis of novel therapeutics aiming to decrease the persisters and recalcitrant infections.
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Affiliation(s)
- Ana Alves da Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Inês Jesus Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cecília Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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Tsai CN, Massicotte MA, MacNair CR, Perry JN, Brown ED, Coombes BK. Screening under infection-relevant conditions reveals chemical sensitivity in multidrug resistant invasive non-typhoidal Salmonella (iNTS). RSC Chem Biol 2023; 4:600-612. [PMID: 37547457 PMCID: PMC10398353 DOI: 10.1039/d3cb00014a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Bloodstream infections caused by invasive, non-typhoidal Salmonella (iNTS) are a major global health concern, particularly in Africa where the pathogenic variant of Salmonella Typhimurium sequence type (ST) 313 is dominant. Unlike S. Typhimurium strains that cause gastroenteritis, iNTS strains cause bloodstream infections and are resistant to multiple first-line antibiotics, thus limiting current treatment options. Here, we developed and implemented multiple small molecule screens under physiological, infection-relevant conditions to reveal chemical sensitivities in ST313 and to identify host-directed therapeutics as entry points to drug discovery to combat the clinical burden of iNTS. Screening ST313 iNTS under host-mimicking growth conditions identified 92 compounds with antimicrobial activity despite inherent multidrug resistance. We characterized the antimicrobial activity of the nucleoside analog 3'-azido-3'-deoxythymidine as an exemplary compound from this screen, which depended on bacterial thymidine kinase activity for antimicrobial activity. In a companion macrophage-based screening platform designed to enrich for host-directed therapeutics, we identified three compounds (amodiaquine, berbamine, and indatraline) as actives that required the presence of host cells for antibacterial activity. These three compounds had antimicrobial activity only in the presence of host cells that significantly inhibited intracellular ST313 iNTS replication in macrophages. This work provides evidence that despite high invasiveness and multidrug resistance, ST313 iNTS remains susceptible to unconventional drug discovery approaches.
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Affiliation(s)
- Caressa N Tsai
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
| | - Marie-Ange Massicotte
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
| | - Craig R MacNair
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
| | - Jordyn N Perry
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
| | - Eric D Brown
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
| | - Brian K Coombes
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
- Farncombe Family Digestive Health Research Institute Hamilton ON Canada
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11
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Bhatia RP, Kirit HA, Lewis CM, Sankaranarayanan K, Bollback JP. Evolutionary barriers to horizontal gene transfer in macrophage-associated Salmonella. Evol Lett 2023; 7:227-239. [PMID: 37475746 PMCID: PMC10355182 DOI: 10.1093/evlett/qrad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/06/2023] [Accepted: 04/20/2023] [Indexed: 07/22/2023] Open
Abstract
Horizontal gene transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack systematic and experimental data supporting these predictions. Here, we address this gap by measuring the relative fitness of 44 genes horizontally transferred from Escherichia coli to Salmonella enterica in infection-relevant environments. We estimated the distribution of fitness effects in each environment and identified that dosage-dependent effects across different environments are a significant barrier to HGT. The majority of genes were found to be deleterious. We also found longer genes had stronger negative fitness consequences than shorter ones, showing that gene length was negatively associated with HGT. Furthermore, fitness effects of transferred genes were found to be environmentally dependent. In summary, a substantial fraction of transferred genes had a significant fitness cost on the recipient, with both gene characteristics and the environment acting as evolutionary barriers to HGT.
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Affiliation(s)
- Rama P Bhatia
- Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Hande Acar Kirit
- Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
- Department of Anthropology, University of Oklahoma, Norman, OK, United States
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jonathan P Bollback
- Corresponding author: Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom.
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12
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Fei X, Li Q, Jiao X, Olsen JE. Identification of Salmonella Pullorum Factors Affecting Immune Reaction in Macrophages from the Avian Host. Microbiol Spectr 2023; 11:e0078623. [PMID: 37191575 PMCID: PMC10269470 DOI: 10.1128/spectrum.00786-23] [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: 02/24/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023] Open
Abstract
The host-specific Salmonella serovar S. Pullorum (SP) modulates the chicken immune response to a Th2-biased response associated with persistent infection. This is different from the Th1-biased immune response induced by the genetically close serovar, S. Enteritidis (SE). Based on core genome differences between SP and SE, we used three complementary bioinformatics approaches to identify SP genes, which may be important for stimulation of the immune response. Defined mutants were constructed in selected genes, and the infection potential and ability of mutants to stimulate cytokine production in avian derived HD11 macrophages were determined. Deletion of large genomic regions unique to SP did not change infection potential nor immune stimulation significantly. Mutants in genes with conserved single nucleotide polymorphisms (SNPs) between the two serovars in the region 100 bp upstream of the start codon (conserved upstream SNPs [CuSNPs]) such as sseE, osmB, tolQ, a putative immune antigen, and a putative persistent infection factor, exhibited differences in induction of inflammatory cytokines compared to wild-type SP, suggesting a possible role of these CuSNPs in immune regulation. Single nucleotide SP mutants correcting for the CuSNP difference were constructed in the upstream region of sifA and pipA. The SNP corrected pipA mutant expressed pipA at a higher level than the wild-type SP strain, and the mutant differentially caused upregulation of proinflammatory cytokines. It suggests that this CuSNP is important for the suppression of proinflammatory responses. In conclusion, this study has identified putative immune stimulating factors of relevance to the difference in infection dynamics between SP and SE in avian macrophages. IMPORTANCE Salmonella Pullorum is host specific to avian species, where it causes life-threatening infection in young birds. It is unknown why it is host restricted and causes systemic disease, rather than gastroenteritis normally seen with Salmonella. In the present study, we identified genes and single nucleotide polymorphisms (SNPs; relative to the broad-host-range type Salmonella Enteritidis), which affected survival and immune induction in macrophages from hens suggesting a role in development of the host specific infection. Further studies of such genes may enable understanding of which genetic factors determine the development of host specific infection by S. Pullorum. In this study, we developed an in silico approach to predict candidate genes and SNPs for development of the host-specific infection and the specific induction of immunity associated with this infection. This study flow can be used in similar studies in other clades of bacteria.
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Affiliation(s)
- Xiao Fei
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, People’s Republic of China
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, People’s Republic of China
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, People’s Republic of China
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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Akinyemi KO, Fakorede CO, Linde J, Methner U, Wareth G, Tomaso H, Neubauer H. Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria. BMC Microbiol 2023; 23:164. [PMID: 37312043 DOI: 10.1186/s12866-023-02901-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/17/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Salmonella infections remain an important public health issue worldwide. Some serovars of non-typhoidal Salmonella (NTS) have been associated with bloodstream infections and gastroenteritis, especially in children in Sub-Saharan Africa with circulating S. enterica serovars with drug resistance and virulence genes. This study identified and verified the clonal relationship of Nigerian NTS strains isolated from humans, animals, and the environment. METHODS In total, 2,522 samples were collected from patients, animals (cattle and poultry), and environmental sources between December 2017 and May 2019. The samples were subjected to a standard microbiological investigation. All the isolates were identified using Microbact 24E, and MALDI-TOF MS. The isolates were serotyped using the Kauffmann-White scheme. Antibiotic susceptibility testing was conducted using the disc diffusion method and the Vitek 2 compact system. Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data. RESULTS Forty-eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified were S. Cotham (n = 17), S. Give (n = 16), S. Mokola (n = 6), S. Abony (n = 4), S. Typhimurium (n = 4), and S. Senftenberg (n = 1). All 48 Salmonella isolates carried intrinsic and acquired resistant genes such as aac.6…Iaa, mdf(A), qnrB, qnrB19 genes and golT, golS, pcoA, and silP, mediated by plasmid Col440I_1, incFIB.B and incFII. Between 100 and 118 virulence gene markers distributed across several Salmonella pathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. WGS revealed that strains of each Salmonella serovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. The dominant sequence types were S. Give ST516 and S. Cotham ST617. CONCLUSION We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. Strategies to control and prevent the spread of NTS in the context of one's health are essential to prevent possible outbreaks.
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Affiliation(s)
| | | | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, PO Box 13736, Toukh, Moshtohor, Egypt
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
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Browning KR, Merrikh H. Pathogenic bacteria experience pervasive RNA polymerase backtracking during infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540596. [PMID: 37215019 PMCID: PMC10197661 DOI: 10.1101/2023.05.12.540596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Pathogenic bacteria and their eukaryotic hosts are in a constant arms race. Hosts have numerous defense mechanisms at their disposal that not only challenge the bacterial invaders, but have the potential to disrupt molecular transactions along the bacterial chromosome. However, it is unclear how the host impacts association of proteins with the bacterial chromosome at the molecular level during infection. This is partially due to the lack of a method that could detect these events in pathogens while they are within host cells. We developed and optimized a system capable of mapping and measuring levels of bacterial proteins associated with the chromosome while they are actively infecting the host (referred to as PIC-seq). Here, we focused on the dynamics of RNA polymerase (RNAP) movement and association with the chromosome in the pathogenic bacterium Salmonella enterica as a model system during infection. Using PIC-seq, we found that RNAP association patterns with the chromosome change during infection genome-wide, including at regions that encode for key virulence genes. Importantly, we found that infection of a host significantly increases RNAP backtracking on the bacterial chromosome. RNAP backtracking is the most common form of disruption to RNAP progress on the chromosome. Interestingly, we found that the resolution of backtracked RNAPs via the anti-backtracking factors GreA and GreB is critical for pathogenesis, revealing a new class of virulence genes. Altogether, our results strongly suggest that infection of a host significantly impacts transcription by disrupting RNAP movement on the chromosome within the bacterial pathogen. The increased backtracking events have important implications not only for efficient transcription, but also for mutation rates as stalled RNAPs increase the levels of mutagenesis.
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Affiliation(s)
- Kaitlyn R. Browning
- Vanderbilt University School of Medicine, Department of Biochemistry, Nashville, TN 37232, USA
| | - Houra Merrikh
- Vanderbilt University School of Medicine, Department of Biochemistry, Nashville, TN 37232, USA
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15
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Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures. mSystems 2022; 7:e0046722. [PMID: 36317888 PMCID: PMC9764980 DOI: 10.1128/msystems.00467-22] [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] [Indexed: 11/07/2022] Open
Abstract
Establishing transcriptional regulatory networks (TRNs) in bacteria has been limited to well-characterized model strains. Using machine learning methods, we established the transcriptional regulatory networks of six Salmonella enterica serovar Typhimurium strains from their transcriptomes. By decomposing a compendia of RNA sequencing (RNA-seq) data with independent component analysis, we obtained 400 independently modulated sets of genes, called iModulons. We (i) performed pan-genome analysis of the phylogroup structure of S. Typhimurium and analyzed the iModulons against this background, (ii) revealed different genetic signatures in pathogenicity islands that explained phenotypes, (iii) discovered three transport iModulons linked to antibiotic resistance, (iv) described concerted responses to cationic antimicrobial peptides, and (v) uncovered new regulons. Thus, by combining pan-genome and transcriptomic analytics, we revealed variations in TRNs across six strains of serovar Typhimurium. IMPORTANCE Salmonella enterica serovar Typhimurium is a pathogen involved in human nontyphoidal infections. Treating S. Typhimurium infections is difficult due to the species's dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN) that is different across strains. In this study, we describe the use of independent component analysis to characterize the differential TRNs across the S. Typhimurium pan-genome using a compendium of high-quality RNA-seq data. This approach provided unprecedented insights into the differences between regulation of key cellular functions and pathogenicity in the different strains. The study provides an impetus to initiate a large-scale effort to reveal the TRN differences between the major phylogroups of the pathogenic bacteria, which could fundamentally impact personalizing treatments of bacterial pathogens.
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16
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Saldaña-Ahuactzi Z, Knodler LA. FoxR is an AraC-like transcriptional regulator of ferrioxamine uptake in Salmonella enterica. Mol Microbiol 2022; 118:369-386. [PMID: 35970762 DOI: 10.1111/mmi.14970] [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: 03/23/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 01/07/2023]
Abstract
Salmonella enterica spp. produce siderophores to bind iron with high affinity and can also use three xenosiderophores secreted by other microorganisms, ferrichrome, coprogen, and ferrioxamine. Here we focused on FoxA, a TonB-dependent transporter of ferrioxamines. Adjacent to foxA is a gene annotated as a helix-turn-helix (HTH) domain-containing protein, SL0358 (foxR), in the Salmonella enterica serovar Typhimurium SL1344 genome. FoxR shares homology with transcriptional regulators belonging to the AraC/XylS family. foxR is syntenic with foxA in the Enterobacteriaceae family, suggesting their functional relatedness. Both foxA and foxR are repressed by the ferric uptake regulator (Fur) under iron-rich growth conditions. When iron is scarce, FoxR acts as a transcriptional activator of foxA by directly binding to its upstream regulatory region. A point mutation in the HTH domain of FoxR abolished this binding, as did mutation of a direct repeat motif in the foxA upstream regulatory region. Desferrioxamine (DFOE) enhanced FoxR protein stability and foxA transcription but did not affect the affinity of FoxR binding to the foxA regulatory region. In summary, we have identified FoxR as a new member of the AraC/XylS family that regulates xenosiderophore-mediated iron uptake by S. Typhimurium and likely other Enterobacteriaceae members.
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Affiliation(s)
- Zeus Saldaña-Ahuactzi
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Leigh A Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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Falay D, Hardy L, Tanzito J, Lunguya O, Bonebe E, Peeters M, Mattheus W, Van Geet C, Verheyen E, Akaibe D, Katuala P, Ngbonda D, Weill FX, Pardos de la Gandara M, Jacobs J. Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo. PLoS Negl Trop Dis 2022; 16:e0010740. [PMID: 36067238 PMCID: PMC9481155 DOI: 10.1371/journal.pntd.0010740] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/16/2022] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
Background Invasive non-typhoidal Salmonella (iNTS–mainly serotypes Enteritidis and Typhimurium) are major causes of bloodstream infections in children in sub-Saharan Africa, but their reservoir remains unknown. We assessed iNTS carriage in rats in an urban setting endemic for iNTS carriage and compared genetic profiles of iNTS from rats with those isolated from humans. Methodology/Principal findings From April 2016 to December 2018, rats were trapped in five marketplaces and a slaughterhouse in Kisangani, Democratic Republic of the Congo. After euthanasia, blood, liver, spleen, and rectal content were cultured for Salmonella. Genetic relatedness between iNTS from rats and humans—obtained from blood cultures at Kisangani University Hospital—was assessed with multilocus variable-number tandem repeat (VNTR) analysis (MLVA), multilocus sequence typing (MLST) and core-genome MLST (cgMLST). 1650 live-capture traps yielded 566 (34.3%) rats (95.6% Rattus norvegicus, 4.4% Rattus rattus); 46 (8.1%) of them carried Salmonella, of which 13 had more than one serotype. The most common serotypes were II.42:r:- (n = 18 rats), Kapemba (n = 12), Weltevreden and Typhimurium (n = 10, each), and Dublin (n = 8). Salmonella Typhimurium belonged to MLST ST19 (n = 7 rats) and the invasive ST313 (n = 3, isolated from deep organs but not from rectal content). Sixteen human S. Typhimurium isolates (all ST313) were available for comparison: MLVA and cgMLST revealed two distinct rat-human clusters involving both six human isolates, respectively, i.e. in total 12/16 human ST313 isolates. All ST313 Typhimurium isolates from rats and humans clustered with the ST313 Lineage 2 isolates and most were multidrug resistant; the remaining isolates from rats including S. Typhimurium ST19 were pan-susceptible. Conclusion The present study provides evidence of urban rats as potential reservoirs of S. Typhimurium ST313 in an iNTS endemic area in sub-Saharan Africa. Dadi (°1974, DR Congo) is a Medical Doctor (Kisangani University 2005) with a master in pediatrics (Kisangani University 2015) with special interest in infectious diseases and tropical medicine. He has 11 years of field research experience. He was team member of scientific expedition “Boyekoli Ebale Congo” in 2010 as medical support for the researchers. He conducted work field in a multidisciplinary framework with biologists from faculty of sciences (university of Kisangani) exploring zoonotic diseases in several places in the Congo. Currently, he is doing his PhD research at KU Leuven and Institute of Tropical Medicine Antwerp (ITM), Belgium. Passionate about transmissible diseases, Dadi is exploring the potential reservoirs of non-typhoidal Salmonella in Kisangani, DR Congo.
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Affiliation(s)
- Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
| | - Jacques Tanzito
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Octavie Lunguya
- Department of Medical Biology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo
- Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Edmonde Bonebe
- Department of Medical Biology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo
| | - Marjan Peeters
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, Brussels, Belgium
| | - Chris Van Geet
- Department of Cardiovascular Sciences and Pediatrics, KU Leuven and University Hospital Leuven, Leuven, Belgium
| | - Erik Verheyen
- OD Taxonomy & Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Evolutionary Ecology, University of Antwerp, Antwerp, Belgium
| | - Dudu Akaibe
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Pionus Katuala
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Dauly Ngbonda
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des bactéries pathogènes entériques, Paris, France
| | | | - Jan Jacobs
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level. mSystems 2022; 7:e0149321. [PMID: 35913188 PMCID: PMC9426430 DOI: 10.1128/msystems.01493-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens could identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range, and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here, we present SalmoNet2, a major update to SalmoNet1, the first multilayered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory, and enzyme-enzyme interactions. The new version extends the number of Salmonella networks from 11 to 20. We now include a strain from the second species in the Salmonella genus, a strain from the Salmonella enterica subspecies arizonae and additional strains of importance from the subspecies enterica, including S. Typhimurium strain D23580, an epidemic multidrug-resistant strain associated with invasive nontyphoidal salmonellosis (iNTS). The database now uses strain specific metabolic models instead of a generalized model to highlight differences between strains. The update has increased the coverage of high-quality protein-protein interactions, and enhanced interoperability with other computational resources by adopting standardized formats. The resource website has been updated with tutorials to help researchers analyze their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/. IMPORTANCE Multilayered network databases collate interaction information from multiple sources, and are powerful both as a knowledge base and subject of analysis. Here, we present SalmoNet2, an integrated network resource containing protein-protein, transcriptional regulatory, and metabolic interactions for 20 Salmonella strains. Key improvements to the update include expanding the number of strains, strain-specific metabolic networks, an increase in high-quality protein-protein interactions, community standard computational formats to help interoperability, and online tutorials to help users analyze their data using SalmoNet2.
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19
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Transcriptional Organization of the Salmonella Typhimurium Phage P22 pid ORFan Locus. Int J Mol Sci 2022; 23:ijms23031253. [PMID: 35163175 PMCID: PMC8835761 DOI: 10.3390/ijms23031253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
Many phage genes lack sequence similarity to any other open reading frame (ORF) in current databases. These enigmatic ORFan genes can have a tremendous impact on phage propagation and host interactions but often remain experimentally unexplored. We previously revealed a novel interaction between phage P22 and its Salmonella Typhimurium host, instigated by the ORFan gene pid (for phage P22 encoded instigator of dgo expression) and resulting in derepression of the host dgoRKAT operon. The pid gene is highly expressed in phage carrier cells that harbor a polarly located P22 episome that segregates asymmetrically among daughter cells. Here, we discovered that the pid locus is fitted with a weak promoter, has an exceptionally long 5′ untranslated region that is instructive for a secondary pid mRNA species, and has a 3′ Rho-independent termination loop that is responsible for stability of the pid transcript.
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20
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Adler BA, Kazakov AE, Zhong C, Liu H, Kutter E, Lui LM, Nielsen TN, Carion H, Deutschbauer AM, Mutalik VK, Arkin AP. The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34910616 PMCID: PMC8744999 DOI: 10.1099/mic.0.001126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance and host-range is sparse. Here, we employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven diverse lytic phages including four new phages isolated from a therapeutic phage cocktail. We uncovered 301 diverse host factors essential in phage infection, many of which are shared between multiple phages demonstrating potential cross-resistance mechanisms. We validate many of these novel findings and uncover the intricate interplay between RpoS, the virulence-associated general stress response sigma factor and RpoN, the nitrogen starvation sigma factor in phage cross-resistance. Finally, the infectivity pattern of eleven phages across a panel of 23 genome sequenced Salmonella strains indicates that additional constraints and interactions beyond the host factors uncovered here define the phage host range.
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Affiliation(s)
- Benjamin A Adler
- The UC Berkeley-UCSF Graduate Program in Bioengineering, Berkeley, California, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Crystal Zhong
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Heloise Carion
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Vivek K Mutalik
- Innovative Genomics Institute, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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21
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Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe 2021; 29:1620-1633.e8. [PMID: 34597593 PMCID: PMC8585504 DOI: 10.1016/j.chom.2021.09.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 02/23/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022]
Abstract
Temperate phages are pervasive in bacterial genomes, existing as vertically inherited islands termed prophages. Prophages are vulnerable to predation of their host bacterium by exogenous phages. Here, we identify BstA, a family of prophage-encoded phage-defense proteins in diverse Gram-negative bacteria. BstA localizes to sites of exogenous phage DNA replication and mediates abortive infection, suppressing the competing phage epidemic. During lytic replication, the BstA-encoding prophage is not itself inhibited by BstA due to self-immunity conferred by the anti-BstA (aba) element, a short stretch of DNA within the bstA locus. Inhibition of phage replication by distinct BstA proteins from Salmonella, Klebsiella, and Escherichia prophages is generally interchangeable, but each possesses a cognate aba element. The specificity of the aba element ensures that immunity is exclusive to the replicating prophage, preventing exploitation by variant BstA-encoding phages. The BstA protein allows prophages to defend host cells against exogenous phage attack without sacrificing the ability to replicate lytically. BstA is an abortive infection protein found in prophages of Gram-negative bacteria aba, a short DNA sequence within the bstA locus, acts as a self-immunity element aba gives BstA-encoding prophages immunity to BstA-driven abortive infection Variant BstA proteins have distinct and cognate aba elements
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Affiliation(s)
- Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK; Biozentrum, University of Basel, Basel, Switzerland
| | - Charles L Dulberger
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Ella V Rodwell
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Arthur Bowers-Barnard
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Natalia Quinones-Olvera
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.
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22
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Molecular determinants of peaceful coexistence versus invasiveness of non-Typhoidal Salmonella: Implications in long-term side-effects. Mol Aspects Med 2021; 81:100997. [PMID: 34311996 DOI: 10.1016/j.mam.2021.100997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/02/2021] [Accepted: 07/16/2021] [Indexed: 01/28/2023]
Abstract
The genus Salmonella represents a wide range of strains including Typhoidal and Non-Typhoidal Salmonella (NTS) isolates that exhibit illnesses of varied pathophysiologies. The more frequent NTS ensues a self-limiting enterocolitis with rare occasions of bacteremia or systemic infections. These self-limiting Salmonella strains are capable of subverting and dampening the host immune system to achieve a more prolonged survival inside the host system thus leading to chronic manifestations. Notably, emergence of new invasive NTS isolates known as invasive Non-Typhoidal Salmonella (iNTS) have worsened the disease burden significantly in some parts of the world. NTS strains adapt to attain persister phenotype intracellularly and cause relapsing infections. These chronic infections, in susceptible hosts, are also capable of causing diseases like IBS, IBD, reactive arthritis, gallbladder cancer and colorectal cancer. The present understanding of molecular mechanism of how these chronic infections are manifested is quite limited. The current work is an effort to review the prevailing knowledge emanating from a large volume of research focusing on various forms of NTS infections including those that cause localized, systemic and persistent disease. The review will further dwell into the understanding of how this pathogen contributes to the associated long term sequelae.
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23
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Schultz BM, Melo-Gonzalez F, Salazar GA, Porto BN, Riedel CA, Kalergis AM, Bueno SM. New Insights on the Early Interaction Between Typhoid and Non-typhoid Salmonella Serovars and the Host Cells. Front Microbiol 2021; 12:647044. [PMID: 34276584 PMCID: PMC8282409 DOI: 10.3389/fmicb.2021.647044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is a common source of food and water-borne infections, causing a wide range of clinical ailments in both human and animal hosts. Immunity to Salmonella involves an interplay between different immune responses, which are rapidly initiated to control bacterial burden. However, Salmonella has developed several strategies to evade and modulate the host immune responses. In this sense, the main knowledge about the pathogenicity of this bacterium has been obtained by the study of mouse models with non-typhoidal serovars. However, this knowledge is not representative of all the pathologies caused by non-typhoidal serovars in the human. Here we review the most important features of typhoidal and non-typhoidal serovars and the diseases they cause in the human host, describing the virulence mechanisms used by these pathogens that have been identified in different models of infection.
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Affiliation(s)
- Bárbara M Schultz
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Melo-Gonzalez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Geraldyne A Salazar
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bárbara N Porto
- Laboratory of Clinical and Experimental Immunology, School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil.,Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Claudia A Riedel
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Millennium Institute on Immunology and Immunotherapy, Universidad Andrés Bello, Santiago, Chile
| | - Alexis M Kalergis
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M Bueno
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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24
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Hu Y, Nguyen SV, Wang W, Gan X, Dong Y, Liu C, Cui X, Xu J, Li F, Fanning S. Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016. Front Microbiol 2021; 12:636284. [PMID: 34211439 PMCID: PMC8239406 DOI: 10.3389/fmicb.2021.636284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The mcr-1 gene mediating mobile colistin resistance in Escherichia coli was first reported in China in 2016 followed by reports among different species worldwide, especially in E. coli and Klebsiella. However, data on its transmission in Salmonella are still lacking. This study analyzed the antimicrobial resistance (AMR) profiles and the mcr-1 gene presence in 755 foodborne Salmonella from 26 provinces of mainland, China in 2016. Genomic features of two mcr-1-carrying isolates, genome sequencing, serotypes and further resistance profiles were studied. Among the 755 Salmonella tested, 72.6% were found to be resistant to at least one antimicrobial agent and 10% were defined as multi-drug resistant (MDR). Salmonella Derby CFSA231 and Salmonella Typhimurium CFSA629 were mcr-1-harboring isolates. Both expressed an MDR phenotype and included a single circular chromosome and one plasmid. Among the 22 AMR genes identified in S. Derby CFSA231, only the mcr-1 gene was localized on the IncX4 type plasmid pCFSA231 while 20 chromosomal AMR genes, including four plasmid-mediated quinolone resistance (PMQR) genes, were mapped within a 64 kb Salmonella genomic island (SGI) like region. S. Typhimurium CFSA629 possessed 11 resistance genes including an mcr-1.19 variant and two ESBL genes. Two IS26-flanked composite-like transposons were identified. Additionally, 153 and 152 virulence factors were separately identified in these two isolates with secretion system and fimbrial adherence determinants as the dominant virulence classes. Our study extends our concern on mcr-1-carrying Salmonella in regards to antimicrobial resistance and virulence factors, and highlight the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella.
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Affiliation(s)
- Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Scott V Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland.,Public Health Laboratory, District of Columbia Department of Forensic Sciences, Washington, DC, United States
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Chang Liu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
| | - Xinnan Cui
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China.,China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
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25
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26
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Spiegelhauer MR, García V, Guerra PR, Olsen JE, Herrero-Fresno A. Association of the prophage BTP1 and the prophage-encoded gene, bstA, with antivirulence of Salmonella Typhimurium ST313. Pathog Dis 2021; 78:5813262. [PMID: 32221584 DOI: 10.1093/femspd/ftaa019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
The prophage BTP1 is highly conserved among strains of the pathogenic lineage Salmonella Typhimurium ST313. We aimed to analyze the role of BTP1 and the gene bstA(BTP1-encoded) in virulence of S. Typhimurium D23580, the ST313 lineage 2 reference strain. The deletion mutant D23580ΔbstA showed significantly higher replication and survival rates within human-derived THP-1 macrophages than the wild-type (WT) strain, while the mutant isolate ΔBTP1, lacking the full prophage, did not significantly differ from the WT. Interestingly, during mice infection, ΔBTP1 yielded significantly higher counts in all tested organs [spleens, livers and mesenteric lymph nodes (MLN)] than the WT, and organs were significantly enlarged compared to WT-infected animals. D23580ΔbstA significantly outcompeted the WT during competitive infection of mice, and yielded significantly enlarged spleens and MLN compared to WT-infected animals during single strain infection. Moreover, increased cellular infiltration and focal necrosis were observed in the liver samples of mice infected with D23580ΔbstA and ΔBTP1 compared to WT-infected animals. In conclusion, removal of the gene bstA and the prophage BTP1 in S. Typhimurium D23580 led to increased virulence in mice, demonstrating that bstA is an antivirulence gene.
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Affiliation(s)
- Malene R Spiegelhauer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Priscila R Guerra
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.,National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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27
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A SNP in the Cache 1 Signaling Domain of Diguanylate Cyclase STM1987 Leads to Increased In Vivo Fitness of Invasive Salmonella Strains. Infect Immun 2021; 89:IAI.00810-20. [PMID: 33468583 DOI: 10.1128/iai.00810-20] [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: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 02/08/2023] Open
Abstract
Nontyphoidal Salmonella (NTS) strains are associated with gastroenteritis worldwide but are also the leading cause of bacterial bloodstream infections in sub-Saharan Africa. The invasive NTS (iNTS) strains that cause bloodstream infections differ from standard gastroenteritis-causing strains by >700 single-nucleotide polymorphisms (SNPs). These SNPs are known to alter metabolic pathways and biofilm formation and to contribute to serum resistance and are thought to signify iNTS strains becoming human adapted, similar to typhoid fever-causing Salmonella strains. Identifying SNPs that contribute to invasion or increased virulence has been more elusive. In this study, we identified a SNP in the cache 1 signaling domain of diguanylate cyclase STM1987 in the invasive Salmonella enterica serovar Typhimurium type strain D23580. This SNP was conserved in 118 other iNTS strains analyzed and was comparatively absent in global S Typhimurium isolates associated with gastroenteritis. STM1987 catalyzes the formation of bis-(3',5')-cyclic dimeric GMP (c-di-GMP) and is proposed to stimulate production of cellulose independent of the master biofilm regulator CsgD. We show that the amino acid change in STM1987 leads to a 10-fold drop in cellulose production and increased fitness in a mouse model of acute infection. Reduced cellulose production due to the SNP led to enhanced survival in both murine and human macrophage cell lines. In contrast, loss of CsgD-dependent cellulose production did not lead to any measurable change in in vivo fitness. We hypothesize that the SNP in stm1987 represents a pathoadaptive mutation for iNTS strains.
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28
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Rodwell EV, Wenner N, Pulford CV, Cai Y, Bowers-Barnard A, Beckett A, Rigby J, Picton DM, Blower TR, Feasey NA, Hinton JCD, Perez-Sepulveda BM. Isolation and Characterisation of Bacteriophages with Activity against Invasive Non-Typhoidal Salmonella Causing Bloodstream Infection in Malawi. Viruses 2021; 13:478. [PMID: 33804216 PMCID: PMC7999457 DOI: 10.3390/v13030478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/21/2023] Open
Abstract
In recent years, novel lineages of invasive non-typhoidal Salmonella (iNTS) serovars Typhimurium and Enteritidis have been identified in patients with bloodstream infection in Sub-Saharan Africa. Here, we isolated and characterised 32 phages capable of infecting S. Typhimurium and S. Enteritidis, from water sources in Malawi and the UK. The phages were classified in three major phylogenetic clusters that were geographically distributed. In terms of host range, Cluster 1 phages were able to infect all bacterial hosts tested, whereas Clusters 2 and 3 had a more restricted profile. Cluster 3 contained two sub-clusters, and 3.b contained the most novel isolates. This study represents the first exploration of the potential for phages to target the lineages of Salmonella that are responsible for bloodstream infections in Sub-Saharan Africa.
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Affiliation(s)
- Ella V. Rodwell
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (E.V.R.); (N.W.); (C.V.P.); (Y.C.); (A.B.-B.); (J.C.D.H.)
| | - Nicolas Wenner
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (E.V.R.); (N.W.); (C.V.P.); (Y.C.); (A.B.-B.); (J.C.D.H.)
| | - Caisey V. Pulford
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (E.V.R.); (N.W.); (C.V.P.); (Y.C.); (A.B.-B.); (J.C.D.H.)
| | - Yueyi Cai
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (E.V.R.); (N.W.); (C.V.P.); (Y.C.); (A.B.-B.); (J.C.D.H.)
| | - Arthur Bowers-Barnard
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (E.V.R.); (N.W.); (C.V.P.); (Y.C.); (A.B.-B.); (J.C.D.H.)
| | - Alison Beckett
- Biomedical Electron Microscopy Facility, University of Liverpool, Liverpool L69 7ZB, UK;
| | - Jonathan Rigby
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (J.R.); (N.A.F.)
- Malawi Liverpool Wellcome Trust Clinical Research Programme, The College of Medicine, University of Malawi, Blantyre 3, Malawi
| | - David M. Picton
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (D.M.P.); (T.R.B.)
| | - Tim R. Blower
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (D.M.P.); (T.R.B.)
| | - Nicholas A. Feasey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (J.R.); (N.A.F.)
- Malawi Liverpool Wellcome Trust Clinical Research Programme, The College of Medicine, University of Malawi, Blantyre 3, Malawi
| | - Jay C. D. Hinton
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (E.V.R.); (N.W.); (C.V.P.); (Y.C.); (A.B.-B.); (J.C.D.H.)
| | - Blanca M. Perez-Sepulveda
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (E.V.R.); (N.W.); (C.V.P.); (Y.C.); (A.B.-B.); (J.C.D.H.)
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29
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Pulford CV, Perez-Sepulveda BM, Canals R, Bevington JA, Bengtsson RJ, Wenner N, Rodwell EV, Kumwenda B, Zhu X, Bennett RJ, Stenhouse GE, Malaka De Silva P, Webster HJ, Bengoechea JA, Dumigan A, Tran-Dien A, Prakash R, Banda HC, Alufandika L, Mautanga MP, Bowers-Barnard A, Beliavskaia AY, Predeus AV, Rowe WPM, Darby AC, Hall N, Weill FX, Gordon MA, Feasey NA, Baker KS, Hinton JCD. Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nat Microbiol 2021; 6:327-338. [PMID: 33349664 PMCID: PMC8018540 DOI: 10.1038/s41564-020-00836-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023]
Abstract
Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.
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Affiliation(s)
- Caisey V Pulford
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Blanca M Perez-Sepulveda
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rocío Canals
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jessica A Bevington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rebecca J Bengtsson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Ella V Rodwell
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - Xiaojun Zhu
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rebecca J Bennett
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - George E Stenhouse
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - P Malaka De Silva
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Hermione J Webster
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jose A Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Alicia Tran-Dien
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France
| | - Reenesh Prakash
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Happy C Banda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Lovemore Alufandika
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Mike P Mautanga
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Arthur Bowers-Barnard
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alexandra Y Beliavskaia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alexander V Predeus
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Will P M Rowe
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Melita A Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Kate S Baker
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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30
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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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31
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Wilson CN, Pulford CV, Akoko J, Perez Sepulveda B, Predeus AV, Bevington J, Duncan P, Hall N, Wigley P, Feasey N, Pinchbeck G, Hinton JCD, Gordon MA, Fèvre EM. Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets. PLoS Negl Trop Dis 2020; 14:e0008796. [PMID: 33232324 PMCID: PMC7748489 DOI: 10.1371/journal.pntd.0008796] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 12/18/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Salmonella is a major cause of foodborne disease globally. Pigs can carry and shed non-typhoidal Salmonella (NTS) asymptomatically, representing a significant reservoir for these pathogens. To investigate Salmonella carriage by African domestic pigs, faecal and mesenteric lymph node samples were taken at slaughter in Nairobi, Busia (Kenya) and Chikwawa (Malawi) between October 2016 and May 2017. Selective culture, antisera testing and whole genome sequencing were performed on samples from 647 pigs; the prevalence of NTS carriage was 12.7% in Busia, 9.1% in Nairobi and 24.6% in Chikwawa. Two isolates of S. Typhimurium ST313 were isolated, but were more closely related to ST313 isolates associated with gastroenteritis in the UK than bloodstream infection in Africa. The discovery of porcine NTS carriage in Kenya and Malawi reveals potential for zoonotic transmission of diarrhoeal strains to humans in these countries, but not for transmission of clades specifically associated with invasive NTS disease in Africa.
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Affiliation(s)
- Catherine N. Wilson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- International Livestock Research Institute, Nairobi, Kenya
| | - Caisey V. Pulford
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | - Blanca Perez Sepulveda
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Alexander V. Predeus
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jessica Bevington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Patricia Duncan
- Ministry of Agriculture, Food Security, Irrigation and Water Development, Malawi Government
| | - Neil Hall
- Earlham Institute, Norwich, United Kingdom
| | - Paul Wigley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas Feasey
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Gina Pinchbeck
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Melita A. Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Eric M. Fèvre
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- International Livestock Research Institute, Nairobi, Kenya
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Gerovac M, El Mouali Y, Kuper J, Kisker C, Barquist L, Vogel J. Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. RNA (NEW YORK, N.Y.) 2020; 26:1448-1463. [PMID: 32646969 PMCID: PMC7491321 DOI: 10.1261/rna.076992.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 05/20/2023]
Abstract
RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica, GradR confirms many known RBPs such as CsrA, Hfq, and ProQ by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element in the quest to build a comprehensive catalog of microbial RBPs.
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Affiliation(s)
- Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Youssef El Mouali
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
| | - Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
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33
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Evasion of MAIT cell recognition by the African Salmonella Typhimurium ST313 pathovar that causes invasive disease. Proc Natl Acad Sci U S A 2020; 117:20717-20728. [PMID: 32788367 PMCID: PMC7456131 DOI: 10.1073/pnas.2007472117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are innate T lymphocytes activated by bacteria that produce vitamin B2 metabolites. Mouse models of infection have demonstrated a role for MAIT cells in antimicrobial defense. However, proposed protective roles of MAIT cells in human infections remain unproven and clinical conditions associated with selective absence of MAIT cells have not been identified. We report that typhoidal and nontyphoidal Salmonella enterica strains activate MAIT cells. However, S. Typhimurium sequence type 313 (ST313) lineage 2 strains, which are responsible for the burden of multidrug-resistant nontyphoidal invasive disease in Africa, escape MAIT cell recognition through overexpression of ribB This bacterial gene encodes the 4-dihydroxy-2-butanone-4-phosphate synthase enzyme of the riboflavin biosynthetic pathway. The MAIT cell-specific phenotype did not extend to other innate lymphocytes. We propose that ribB overexpression is an evolved trait that facilitates evasion from immune recognition by MAIT cells and contributes to the invasive pathogenesis of S. Typhimurium ST313 lineage 2.
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Wellawa DH, Allan B, White AP, Köster W. Iron-Uptake Systems of Chicken-Associated Salmonella Serovars and Their Role in Colonizing the Avian Host. Microorganisms 2020; 8:E1203. [PMID: 32784620 PMCID: PMC7465098 DOI: 10.3390/microorganisms8081203] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/09/2023] Open
Abstract
Iron is an essential micronutrient for most bacteria. Salmonella enterica strains, representing human and animal pathogens, have adopted several mechanisms to sequester iron from the environment depending on availability and source. Chickens act as a major reservoir for Salmonella enterica strains which can lead to outbreaks of human salmonellosis. In this review article we summarize the current understanding of the contribution of iron-uptake systems to the virulence of non-typhoidal S. enterica strains in colonizing chickens. We aim to address the gap in knowledge in this field, to help understand and define the interactions between S. enterica and these important hosts, in comparison to mammalian models.
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Affiliation(s)
- Dinesh H. Wellawa
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Brenda Allan
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
| | - Aaron P. White
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Wolfgang Köster
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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35
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Honeycutt JD, Wenner N, Li Y, Brewer SM, Massis LM, Brubaker SW, Chairatana P, Owen SV, Canals R, Hinton JCD, Monack DM. Genetic variation in the MacAB-TolC efflux pump influences pathogenesis of invasive Salmonella isolates from Africa. PLoS Pathog 2020; 16:e1008763. [PMID: 32834002 PMCID: PMC7446830 DOI: 10.1371/journal.ppat.1008763] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/30/2020] [Indexed: 01/23/2023] Open
Abstract
The various sub-species of Salmonella enterica cause a range of disease in human hosts. The human-adapted Salmonella enterica serovar Typhi enters the gastrointestinal tract and invades systemic sites to cause enteric (typhoid) fever. In contrast, most non-typhoidal serovars of Salmonella are primarily restricted to gut tissues. Across Africa, invasive non-typhoidal Salmonella (iNTS) have emerged with an ability to spread beyond the gastrointestinal tract and cause systemic bloodstream infections with increased morbidity and mortality. To investigate this evolution in pathogenesis, we compared the genomes of African iNTS isolates with other Salmonella enterica serovar Typhimurium and identified several macA and macB gene variants unique to African iNTS. MacAB forms a tripartite efflux pump with TolC and is implicated in Salmonella pathogenesis. We show that macAB transcription is upregulated during macrophage infection and after antimicrobial peptide exposure, with macAB transcription being supported by the PhoP/Q two-component system. Constitutive expression of macAB improves survival of Salmonella in the presence of the antimicrobial peptide C18G. Furthermore, these macAB variants affect replication in macrophages and influence fitness during colonization of the murine gastrointestinal tract. Importantly, the infection outcome resulting from these macAB variants depends upon both the Salmonella Typhimurium genetic background and the host gene Nramp1, an important determinant of innate resistance to intracellular bacterial infection. The variations we have identified in the MacAB-TolC efflux pump in African iNTS may reflect evolution within human host populations that are compromised in their ability to clear intracellular Salmonella infections.
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Affiliation(s)
- Jared D. Honeycutt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicolas Wenner
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Yan Li
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Susan M. Brewer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Liliana M. Massis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sky W. Brubaker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Phoom Chairatana
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Siân V. Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Denise M. Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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36
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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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37
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Tsai CN, MacNair CR, Cao MPT, Perry JN, Magolan J, Brown ED, Coombes BK. Targeting Two-Component Systems Uncovers a Small-Molecule Inhibitor of Salmonella Virulence. Cell Chem Biol 2020; 27:793-805.e7. [PMID: 32413287 DOI: 10.1016/j.chembiol.2020.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 12/27/2022]
Abstract
Salmonella serovars are leading causes of gastrointestinal disease and have become increasingly resistant to fluoroquinolone and cephalosporin antibiotics. Overcoming this healthcare crisis requires new approaches in antibiotic discovery and the identification of unique bacterial targets. In this work, we describe a chemical genomics approach to identify inhibitors of Salmonella virulence. From a cell-based, promoter reporter screen of ∼50,000 small molecules, we identified dephostatin as a non-antibiotic compound that inhibits intracellular virulence factors and polymyxin resistance genes. Dephostatin disrupts signaling through both the SsrA-SsrB and PmrB-PmrA two-component regulatory systems and restores sensitivity to the last-resort antibiotic, colistin. Cell-based experiments and mouse models of infection demonstrate that dephostatin attenuates Salmonella virulence in vitro and in vivo, suggesting that perturbing regulatory networks is a promising strategy for the development of anti-infectives.
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Affiliation(s)
- Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Craig R MacNair
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - My P T Cao
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Jordyn N Perry
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada.
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38
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Decoding the stoichiometric composition and organisation of bacterial metabolosomes. Nat Commun 2020; 11:1976. [PMID: 32332738 PMCID: PMC7181861 DOI: 10.1038/s41467-020-15888-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/31/2020] [Indexed: 01/08/2023] Open
Abstract
Some enteric bacteria including Salmonella have evolved the propanediol-utilising microcompartment (Pdu MCP), a specialised proteinaceous organelle that is essential for 1,2-propanediol degradation and enteric pathogenesis. Pdu MCPs are a family of bacterial microcompartments that are self-assembled from hundreds of proteins within the bacterial cytosol. Here, we seek a comprehensive understanding of the stoichiometric composition and organisation of Pdu MCPs. We obtain accurate stoichiometry of shell proteins and internal enzymes of the natural Pdu MCP by QconCAT-driven quantitative mass spectrometry. Genetic deletion of the major shell protein and absolute quantification reveal the stoichiometric and structural remodelling of metabolically functional Pdu MCPs. Decoding the precise protein stoichiometry allows us to develop an organisational model of the Pdu metabolosome. The structural insights into the Pdu MCP are critical for both delineating the general principles underlying bacterial organelle formation, structural robustness and function, and repurposing natural microcompartments using synthetic biology for biotechnological applications. Enteric pathogens such as Salmonella depend on propanediol-utilising microcompartments (Pdu MCP), which self-assemble from cytosolic proteins. Using mass spectrometry-based absolute quantification, the authors here define the protein stoichiometry and propose an organizational model of a Salmonella Pdu MCP.
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Mohamed A, Taha O, El-Sherif HM, Connerton PL, Hooton SP, Bassim ND, Connerton IF, El-Shibiny A. Bacteriophage ZCSE2 is a Potent Antimicrobial Against Salmonella enterica Serovars: Ultrastructure, Genomics and Efficacy. Viruses 2020; 12:v12040424. [PMID: 32283768 PMCID: PMC7232530 DOI: 10.3390/v12040424] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/22/2020] [Accepted: 04/07/2020] [Indexed: 02/04/2023] Open
Abstract
Developing novel antimicrobials capable of controlling multidrug-resistant bacterial pathogens is essential to restrict the use of antibiotics. Bacteriophages (phages) constitute a major resource that can be harnessed as an alternative to traditional antimicrobial therapies. Phage ZCSE2 was isolated among several others from raw sewage but was distinguished by broad-spectrum activity against Salmonella serovars considered pathogenic to humans and animals. Lytic profiles of ZCSE2 against a panel of Salmonella were determined together with low temperature activity and pH stability. The morphological features of the phage and host infection processes were characterized using a combination of transmission electron and atomic force microscopies. Whole genome sequencing of ZCSE2 produced a complete DNA sequence of 53,965 bp. No known virulence genes were identified in the sequence data, making ZCSE2 a good candidate for phage-mediated biological control purposes. ZCSE2 was further tested against S. Enteritidis in liquid culture and was observed to reduce the target bacterium to below the limits of detection from initial concentrations of 107–108 Colony Forming Units (CFU)/mL. With a broad host-range against pathogenic Salmonella serovars, phage ZCSE2 constitutes a potential tool against a major cause of human and animal disease.
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Affiliation(s)
- Ahmed Mohamed
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt; (A.M.); (O.T.)
| | - Omar Taha
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt; (A.M.); (O.T.)
| | - Hesham M. El-Sherif
- Mechanical Design and Production Engineering Department, Faculty of Engineering, Cairo University, Giza 12613, Egypt;
- Materials Science and Engineering Department, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada;
| | - Phillippa L. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK; (P.L.C.); (S.P.T.H.)
| | - Steven P.T. Hooton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK; (P.L.C.); (S.P.T.H.)
| | - Nabil D. Bassim
- Materials Science and Engineering Department, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada;
| | - Ian F. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK; (P.L.C.); (S.P.T.H.)
- Correspondence: (I.F.C.); (A.E.-S.)
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt; (A.M.); (O.T.)
- Faculty of Environmental Agricultural Sciences, Arish University, Arish 45615, Egypt
- Correspondence: (I.F.C.); (A.E.-S.)
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40
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Owen SV, Canals R, Wenner N, Hammarlöf DL, Kröger C, Hinton JCD. A window into lysogeny: revealing temperate phage biology with transcriptomics. Microb Genom 2020; 6:e000330. [PMID: 32022660 PMCID: PMC7067206 DOI: 10.1099/mgen.0.000330] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/28/2019] [Indexed: 12/17/2022] Open
Abstract
Prophages are integrated phage elements that are a pervasive feature of bacterial genomes. The fitness of bacteria is enhanced by prophages that confer beneficial functions such as virulence, stress tolerance or phage resistance, and these functions are encoded by 'accessory' or 'moron' loci. Whilst the majority of phage-encoded genes are repressed during lysogeny, accessory loci are often highly expressed. However, it is challenging to identify novel prophage accessory loci from DNA sequence data alone. Here, we use bacterial RNA-seq data to examine the transcriptional landscapes of five Salmonella prophages. We show that transcriptomic data can be used to heuristically enrich for prophage features that are highly expressed within bacterial cells and represent functionally important accessory loci. Using this approach, we identify a novel antisense RNA species in prophage BTP1, STnc6030, which mediates superinfection exclusion of phage BTP1. Bacterial transcriptomic datasets are a powerful tool to explore the molecular biology of temperate phages.
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Affiliation(s)
- Siân V. Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
- Present address: GSK Vaccines Institute for Global Health, Siena, Italy
| | - Nicolas Wenner
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Disa L. Hammarlöf
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
- Science for Life Laboratory, KTH, Stockholm, Sweden
| | - Carsten Kröger
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Jay C. D. Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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41
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Lê-Bury G, Deschamps C, Kizilyaprak C, Blanchard W, Daraspe J, Dumas A, Gordon MA, Hinton JCD, Humbel BM, Niedergang F. Increased intracellular survival of Salmonella Typhimurium ST313 in HIV-1-infected primary human macrophages is not associated with Salmonella hijacking the HIV compartment. Biol Cell 2020; 112:92-101. [PMID: 31922615 DOI: 10.1111/boc.201900055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/28/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Non-typhoidal Salmonella (NTS) causes a severe invasive syndrome (iNTS disease) described in HIV-positive adults. The impact of HIV-1 on Salmonella pathogenesis and the molecular basis for the differences between these bacteria and classical diarrhoeal S. Typhimurium remains unclear. RESULTS Here, we show that iNTS-associated S. Typhimurium Sequence Type 313 (ST313) bacteria show greater intracellular survival in primary human macrophages, compared with a 'classical' diarrhoeal S. Typhimurium ST19 isolate. The increased intracellular survival phenotype of ST313 is more pronounced in HIV-infected macrophages. We explored the possibility that the bacteria take advantage of the HIV-associated viral-containing compartments created in human macrophages that have low pH. Confocal fluorescence microscopy and focussed ion beam-scanning electron microscopy tomography showed that Salmonella did not co-localise extensively with HIV-positive compartments. CONCLUSION The capacity of ST313 bacteria to survive better than ST19 bacteria within primary human macrophages is enhanced in cells pre-infected with HIV-1. Our results indicate that the ST313 bacteria do not directly benefit from the niche created by the virus in HIV-1-infected macrophages, and that they might take advantage from a more globally modified host cell. SIGNIFICANCE A better understanding of the interplay between HIV-1 and Salmonella is important not only for these bacteria but also for other opportunistic pathogens.
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Affiliation(s)
- G Lê-Bury
- Institut Cochin, Université de Paris, INSERM, U1016, CNRS, UMR 8104, Paris, F-75014, France
| | - C Deschamps
- Institut Cochin, Université de Paris, INSERM, U1016, CNRS, UMR 8104, Paris, F-75014, France
| | - C Kizilyaprak
- Faculté de Biologie et de Médecine, Electron Microscopy Facility, Université de Lausanne, Lausanne, Switzerland
| | - W Blanchard
- Faculté de Biologie et de Médecine, Electron Microscopy Facility, Université de Lausanne, Lausanne, Switzerland
| | - J Daraspe
- Faculté de Biologie et de Médecine, Electron Microscopy Facility, Université de Lausanne, Lausanne, Switzerland
| | - A Dumas
- Institut Cochin, Université de Paris, INSERM, U1016, CNRS, UMR 8104, Paris, F-75014, France
| | - M A Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.,Malawi-Liverpool-Welcome Trust B=Clinical Research Programme, Malawi
| | - J C D Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - B M Humbel
- Faculté de Biologie et de Médecine, Electron Microscopy Facility, Université de Lausanne, Lausanne, Switzerland.,IMG, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan
| | - F Niedergang
- Institut Cochin, Université de Paris, INSERM, U1016, CNRS, UMR 8104, Paris, F-75014, France
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42
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Silva C, Calva E, Fernández-Mora M, Puente JL, Vinuesa P. Population analysis of D6-like plasmid prophage variants associated with specific IncC plasmid types in the emerging Salmonella Typhimurium ST213 genotype. PLoS One 2019; 14:e0223975. [PMID: 31626639 PMCID: PMC6799933 DOI: 10.1371/journal.pone.0223975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/02/2019] [Indexed: 01/08/2023] Open
Abstract
The Salmonella enterica serovar Typhimurium sequence type 213 (ST213) emerged as a predominant genotype in Mexico. It is characterized by harboring multidrug resistance (MDR) IncC plasmids (previously IncA/C) and the lack of the Salmonella virulence plasmid (pSTV). Here we show that the D6-like plasmid prophage is present in most of the ST213 strains. We used the reported nucleotide sequence of YU39 plasmid (pYU39_89) to design a PCR typing scheme for the D6-like plasmid prophages, and determined the complete nucleotide sequences for the D6-like prophages of three additional ST213 strains (YU07-18, SL26 and SO21). Two prophage variants were described: i) a complete prophage, containing homologous sequences for most of the genetic modules described in P1 and D6 phages, which most likely allow for the lytic and lysogenic lifestyles; and ii) an incomplete prophage, lacking a 15 kb region containing morphogenesis genes, suggesting that it is defective. The tail fiber gene inversion region was the most divergent one between D6 and pYU39_89 genomes, suggesting the production of a distinct set of tail fibers, which could be involved in host range preferences. A glutaminyl-tRNA synthetase gene (glnS), which could be involved in providing host cell increased fitness or plasmid maintenance functions, was found in all D6-like genomes. Population level analysis revealed a biogeographic pattern of distribution of these plasmid-phages and specific associations with variants of MDR IncC plasmids. Statistically significant associations were found between the two prophage variants (p75 or p89), the type of IncC plasmids (I or II) and geographic isolation regions (Sonora, San Luis Potosí, Michoacán and Yucatán). This work integrates results from molecular typing, genomics and epidemiology to provide a broad overview for the evolution of an emergent Salmonella genotype.
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Affiliation(s)
- Claudia Silva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- * E-mail:
| | - Edmundo Calva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Marcos Fernández-Mora
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - José L. Puente
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pablo Vinuesa
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M, Hinton JCD. The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid. PLoS Pathog 2019; 15:e1007948. [PMID: 31560731 PMCID: PMC6785131 DOI: 10.1371/journal.ppat.1007948] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 10/09/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
We have used a transposon insertion sequencing (TIS) approach to establish the fitness landscape of the African Salmonella enterica serovar Typhimurium ST313 strain D23580, to complement our previous comparative genomic and functional transcriptomic studies. We used a genome-wide transposon library with insertions every 10 nucleotides to identify genes required for survival and growth in vitro and during infection of murine macrophages. The analysis revealed genomic regions important for fitness under two in vitro growth conditions. Overall, 724 coding genes were required for optimal growth in LB medium, and 851 coding genes were required for growth in SPI-2-inducing minimal medium. These findings were consistent with the essentiality analyses of other S. Typhimurium ST19 and S. Typhi strains. The global mutagenesis approach also identified 60 sRNAs and 413 intergenic regions required for growth in at least one in vitro growth condition. By infecting murine macrophages with the transposon library, we identified 68 genes that were required for intra-macrophage replication but did not impact fitness in vitro. None of these genes were unique to S. Typhimurium D23580, consistent with a high conservation of gene function between S. Typhimurium ST313 and ST19 and suggesting that novel virulence factors are not involved in the interaction of strain D23580 with murine macrophages. We discovered that transposon insertions rarely occurred in many pBT1 plasmid-encoded genes (36), compared with genes carried by the pSLT-BT virulence plasmid and other bacterial plasmids. The key essential protein encoded by pBT1 is a cysteinyl-tRNA synthetase, and our enzymological analysis revealed that the plasmid-encoded CysRSpBT1 had a lower ability to charge tRNA than the chromosomally-encoded CysRSchr enzyme. The presence of aminoacyl-tRNA synthetases in plasmids from a range of Gram-negative and Gram-positive bacteria suggests that plasmid-encoded essential genes are more common than had been appreciated.
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Affiliation(s)
- Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Roy R Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Rebecca E Steiner
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Siân V Owen
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Melita A Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi, Central Africa
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jay C D Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Lacharme-Lora L, Owen SV, Blundell R, Canals R, Wenner N, Perez-Sepulveda B, Fong WY, Gilroy R, Wigley P, Hinton JCD. The use of chicken and insect infection models to assess the virulence of African Salmonella Typhimurium ST313. PLoS Negl Trop Dis 2019; 13:e0007540. [PMID: 31348776 PMCID: PMC6685681 DOI: 10.1371/journal.pntd.0007540] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/07/2019] [Accepted: 06/11/2019] [Indexed: 11/18/2022] Open
Abstract
Over recent decades, Salmonella infection research has predominantly relied on murine infection models. However, in many cases the infection phenotypes of Salmonella pathovars in mice do not recapitulate human disease. For example, Salmonella Typhimurium ST313 is associated with enhanced invasive infection of immunocompromised people in Africa, but infection of mice and other animal models with ST313 have not consistently reproduced this invasive phenotype. The introduction of alternative infection models could help to improve the quality and reproducibility of pathogenesis research by facilitating larger-scale experiments. To investigate the virulence of S. Typhimurium ST313 in comparison with ST19, a combination of avian and insect disease models were used. We performed experimental infections in five lines of inbred and one line of outbred chickens, as well as in the alternative chick embryo and Galleria mellonella wax moth larvae models. This extensive set of experiments identified broadly similar patterns of disease caused by the African and global pathovariants of Salmonella Typhimurium in the chicken, the chicken embryo and insect models. A comprehensive analysis of all the chicken infection experiments revealed that the African ST313 isolate D23580 had a subtle phenotype of reduced levels of organ colonisation in inbred chickens, relative to ST19 strain 4/74. ST313 isolate D23580 also caused reduced mortality in chicken embryos and insect larvae, when compared with ST19 4/74. We conclude that these three infection models do not reproduce the characteristics of the systemic disease caused by S. Typhimurium ST313 in humans. Salmonella Typhimurium ST313 is associated with systemic infection in human populations in sub-Saharan Africa, and contrasts with the related pathovariant ST19 which causes gastrointestinal disease worldwide. Although the systemic pathology associated with ST313 infection in humans has been comprehensively documented in clinical and epidemiological studies, such pathology has been inconsistently reproduced in animal models of infection. Animal models that reliably recapitulate ST313 infection in humans are needed to study the biological mechanisms underpinning the systemic disease caused by ST313. In this study we performed extensive infection experiments, using several defined and alternative animal infection models to look for robust phenotypes that differentiate infection by S. Typhimurium ST313 from ST19. Large sample sizes and multivariate statistical analysis of infection data for inbred chicken lines allowed us to detect small but consistent differences between the strains. Overall, S. Typhimurium ST313 was associated with a reduced infection burden and pathology relative to ST19. This subtle phenotype may reflect the limitation of animal models to accurately represent infection by pathogens that have adapted to specific host phenotypes, for example, immunodeficiency in humans. Our study demonstrates the challenge of using animal models to differentiate closely-related bacterial pathovariants, and shows that inter-pathovar differences detected in animal models of infection often do not reflect clinical differences in humans at the level of disease mechanism.
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Affiliation(s)
- Lizeth Lacharme-Lora
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Siân V. Owen
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Blundell
- Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, United Kingdom
| | - Rocío Canals
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nicolas Wenner
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Blanca Perez-Sepulveda
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Wai Yee Fong
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Rachel Gilroy
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Paul Wigley
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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45
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Hews CL, Pritchard EJ, Rowley G. The Salmonella Specific, σ E-Regulated, STM1250 and AgsA, Function With the sHsps IbpA and IbpB, to Counter Oxidative Stress and Survive Macrophage Killing. Front Cell Infect Microbiol 2019; 9:263. [PMID: 31396489 PMCID: PMC6663981 DOI: 10.3389/fcimb.2019.00263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/04/2019] [Indexed: 11/13/2022] Open
Abstract
The host presents an array of environments which induce bacterial stress including changes in pH, antimicrobial compounds and reactive oxygen species. The bacterial envelope sits at the interface between the intracellular and extracellular environment and its maintenance is essential for Salmonella cell viability under a range of conditions, including during infection. In this study, we aimed to understand the contribution of the σH- and σE-regulated small heat shock proteins IbpA, IbpB, and AgsA and the putative σE-regulated stress response protein STM1250 to the Salmonella envelope stress response. Due to shared sequence identity, regulatory overlap, and the specificity of STM1250 and AgsA to Salmonella sp., we hypothesized that functional overlap exists between these four stress response proteins, which might afford a selective advantage during Salmonella exposure to stress. We present here new roles for three small heat shock proteins and a putative stress response protein in Salmonella that are not limited to heat shock. We have shown that, compared to WT, a quadruple mutant is significantly more sensitive to hydrogen peroxide, has a lower minimum bactericidal concentration to the cationic antimicrobial peptide polymyxin B, and is attenuated in macrophages.
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Affiliation(s)
- Claire L Hews
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Emily J Pritchard
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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46
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Pulford CV, Wenner N, Redway ML, Rodwell EV, Webster HJ, Escudero R, Kröger C, Canals R, Rowe W, Lopez J, Hall N, Rowley PD, Timofte D, Harrison RA, Baker KS, Hinton JCD. The diversity, evolution and ecology of Salmonella in venomous snakes. PLoS Negl Trop Dis 2019; 13:e0007169. [PMID: 31163033 PMCID: PMC6548357 DOI: 10.1371/journal.pntd.0007169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Reptile-associated Salmonella bacteria are a major, but often neglected cause of both gastrointestinal and bloodstream infection in humans globally. The diversity of Salmonella enterica has not yet been determined in venomous snakes, however other ectothermic animals have been reported to carry a broad range of Salmonella bacteria. We investigated the prevalence and diversity of Salmonella in a collection of venomous snakes and non-venomous reptiles. METHODOLOGY/PRINCIPLE FINDINGS We used a combination of selective enrichment techniques to establish a unique dataset of reptilian isolates to study Salmonella enterica species-level evolution and ecology and used whole-genome sequencing to investigate the relatedness of phylogenetic groups. We observed that 91% of venomous snakes carried Salmonella, and found that a diverse range of serovars (n = 58) were carried by reptiles. The Salmonella serovars belonged to four of the six Salmonella enterica subspecies: diarizonae, enterica, houtanae and salamae. Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, previously described as clade A (52%) and clade B (48%). We identified metabolic differences between S. diarizonae, S. enterica clade A and clade B involving growth on lactose, tartaric acid, dulcitol, myo-inositol and allantoin. SIGNIFICANCE We present the first whole genome-based comparative study of the Salmonella bacteria that colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution. Venomous snakes examined in this study carried a broad range of Salmonella, including serovars which have been associated with disease in humans such as S. Enteritidis. The findings raise the possibility that venomous snakes could be a reservoir for Salmonella serovars associated with human salmonellosis.
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Affiliation(s)
- Caisey V. Pulford
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nicolas Wenner
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Martha L. Redway
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ella V. Rodwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Hermione J. Webster
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Roberta Escudero
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Carsten Kröger
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Rocío Canals
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Will Rowe
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Javier Lopez
- Animal Health Department, Chester Zoo, Cheshire, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Paul D. Rowley
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Dorina Timofte
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Cheshire, United Kingdom
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Robert A. Harrison
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kate S. Baker
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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