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Petano-Duque JM, Rueda-García V, Rondón-Barragán IS. Virulence genes identification in Salmonella enterica isolates from humans, crocodiles, and poultry farms from two regions in Colombia. Vet World 2023; 16:2096-2103. [PMID: 38023281 PMCID: PMC10668553 DOI: 10.14202/vetworld.2023.2096-2103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background and Aim Salmonella spp. is frequently found in the digestive tract of birds and reptiles and transmitted to humans through food. Salmonellosis is a public health problem because of pathogenicity variability in strains for virulence factors. This study aimed to identify the virulence genes in Salmonella isolates from humans, crocodiles, broiler cloacas, and broiler carcasses from two departments of Colombia. Materials and Methods This study was conducted on 31 Salmonella enterica strains from humans with gastroenteritis (seven), crocodiles (seven), broiler cloacas (six), and broiler carcasses (12) from Tolima and Santander departments of Colombia, belonging to 21 serotypes. All samples were tested for Salmonella spp. using culture method on selective and non-selective mediums. Extraction of genomic DNA was performed from fresh colonies, DNA quality was verified by spectrophotometry and confirmed by amplification of InvA gene using conventional polymerase chain reaction (PCR). bapA, fimA, icmF, IroB, marT, mgtC, nlpI, oafA, pagN, siiD, spvC, spvR, spvB, Stn, and vexA genes were amplified by PCR. Results The most prevalent gene was bapA (100%), followed by marT (96.77%), mgtC (93.55%), and fimA (83.87%). Likewise, IroB (70.97%), Stn (67.74%), spvR (61.29%), pagN (54.84%), icmF (54.8%), and SiiD (45.16%) were positive for more than 50% of the strains. Furthermore, none of the isolates tested positive for the vexA gene. Salmonella isolates presented 26 virulence profiles. Conclusion This study reported 14 virulence genes in Salmonella spp. isolates from humans with gastroenteritis, crocodiles, and broiler cloacas and carcasses. The distribution of virulence genes differed among sources. This study could help in decision-making by health and sanitary authorities.
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Affiliation(s)
- Julieth Michel Petano-Duque
- Poultry Research Group, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
| | - Valentina Rueda-García
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
| | - Iang Schroniltgen Rondón-Barragán
- Poultry Research Group, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
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Hockenberry A, Slack E, Stadtmueller BM. License to Clump: Secretory IgA Structure-Function Relationships Across Scales. Annu Rev Microbiol 2023; 77:645-668. [PMID: 37713459 DOI: 10.1146/annurev-micro-032521-041803] [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] [Indexed: 09/17/2023]
Abstract
Secretory antibodies are the only component of our adaptive immune system capable of attacking mucosal pathogens topologically outside of our bodies. All secretory antibody classes are (a) relatively resistant to harsh proteolytic environments and (b) polymeric. Recent elucidation of the structure of secretory IgA (SIgA) has begun to shed light on SIgA functions at the nanoscale. We can now begin to unravel the structure-function relationships of these molecules, for example, by understanding how the bent conformation of SIgA enables robust cross-linking between adjacent growing bacteria. Many mysteries remain, such as the structural basis of protease resistance and the role of noncanonical bacteria-IgA interactions. In this review, we explore the structure-function relationships of IgA from the nano- to the metascale, with a strong focus on how the seemingly banal "license to clump" can have potent effects on bacterial physiology and colonization.
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Affiliation(s)
- Alyson Hockenberry
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
- Department of Environmental Systems Science (D-USYS), ETH Zürich, Zürich, Switzerland;
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland;
- Botnar Research Centre for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Beth M Stadtmueller
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA;
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois, Urbana, Illinois, USA
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3
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Genetic and Structural Variation in the O-Antigen of Salmonella enterica Serovar Typhimurium Isolates Causing Bloodstream Infections in the Democratic Republic of the Congo. mBio 2022; 13:e0037422. [PMID: 35862803 PMCID: PMC9426603 DOI: 10.1128/mbio.00374-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Salmonella enterica serovar Typhimurium causes a devastating burden of invasive disease in sub-Saharan Africa with high levels of antimicrobial resistance. No licensed vaccine is available, but O-antigen-based candidates are in development, as the O-antigen moiety of lipopolysaccharides is the principal target of protective immunity. The vaccines under development are designed based on isolates with O-antigen O-acetylated at position C-2 of abequose, giving the O:5 antigen. Serotyping data on recent Salmonella Typhimurium clinical isolates from the Democratic Republic of the Congo (DRC), however, indicate increasing levels of isolates without O:5. The importance and distribution of this loss of O:5 antigen in the population as well as the genetic mechanism responsible for the loss and chemical characteristics of the O-antigen are poorly understood. In this study, we Illumina whole-genome sequenced 354 Salmonella Typhimurium isolates from the DRC, which were isolated between 2002 and 2017. We used genomics and phylogenetics combined with chemical approaches (1H nuclear magnetic resonance [NMR], high-performance anion-exchange chromatography with pulsed amperometric detection [HPAEC-PAD], high-performance liquid chromatography–PAD [HPLC-PAD], and HPLC-size exclusion chromatography [HPLC-SEC]) to characterize the O-antigen features within the bacterial population. We observed convergent evolution toward the loss of the O:5 epitope predominantly caused by recombination events in a single gene, the O-acetyltransferase gene oafA. In addition, we observe further O-antigen variations, including O-acetylation of the rhamnose residue, different levels of glucosylation, and the absence of O-antigen repeating units. Large recombination events underlying O-antigen variation were resolved using long-read MinION sequencing. Our study suggests evolutionary pressure toward O-antigen variants in a region where invasive disease by Salmonella Typhimurium is highly endemic. This needs to be taken into account when developing O-antigen-based vaccines, as it might impact the breadth of coverage in such regions.
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4
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Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat Microbiol 2021; 6:830-841. [PMID: 34045711 PMCID: PMC7611113 DOI: 10.1038/s41564-021-00911-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune clearance1. However, not all variants are equally fit in all environments2,3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here, we demonstrate this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm). A dominant surface antigen of S.Tm is its O-antigen: a long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase variation4,5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen-specific immunoglobulin A and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naive mice. Through the use of rationally designed oral vaccines, we induced immunoglobulin A responses blocking all of these trajectories. This selected for Salmonella mutants carrying deletions of the O-antigen polymerase gene wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents or complement) and predation (bacteriophages) and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.
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Affiliation(s)
- Médéric Diard
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Zoology, University of Oxford, Oxford, UK
| | - Verena Lentsch
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | | | | | - Daniel Hoces
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Selma Aslani
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Markus Arnoldini
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Flurina Böhi
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zürich, Zürich, Switzerland
| | - Kathrin Schumann-Moor
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Division of Surgical Research, University Hospital of Zürich, Zürich, Switzerland
| | - Jozef Adamcik
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas Donohue
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK.,Department of Orthopedics and Trauma, Medical University of Graz, Graz, Austria
| | - Marjan W van der Woude
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Alyson Hockenberry
- Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland.,Department of Environmental Sciences, ETH Zürich, Zürich, Switzerland
| | - Patrick H Viollier
- Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wüthrich
- Infection Biology, University Hospital of Basel, Basel, Switzerland
| | | | - Claude Loverdo
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Adrian Egli
- Infection Biology, University Hospital of Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Raffaele Mezzenga
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.,Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Otto Holst
- Forschungszentrum Borstel, Borstel, Germany
| | - Beat H Meier
- Institute for Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Emma Slack
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland. .,Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.
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5
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Wu X, Luo H, Xu F, Ge C, Li S, Deng X, Wiedmann M, Baker RC, Stevenson A, Zhang G, Tang S. Evaluation of Salmonella Serotype Prediction With Multiplex Nanopore Sequencing. Front Microbiol 2021; 12:637771. [PMID: 33776971 PMCID: PMC7987803 DOI: 10.3389/fmicb.2021.637771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
The use of whole genome sequencing (WGS) data generated by the long-read sequencing platform Oxford Nanopore Technologies (ONT) has been shown to provide reliable results for Salmonella serotype prediction in a previous study. To further meet the needs of industry for accurate, rapid, and cost-efficient Salmonella confirmation and serotype classification, we evaluated the serotype prediction accuracy of using WGS data from multiplex ONT sequencing with three, four, five, seven, or ten Salmonella isolates (each isolate represented one Salmonella serotype) pooled in one R9.4.1 flow cell. Each multiplexing strategy was repeated with five flow cells, and the loaded samples were sequenced simultaneously in a GridION sequencer for 48 h. In silico serotype prediction was performed using both SeqSero2 (for raw reads and genome assemblies) and SISTR (for genome assemblies) software suites. An average of 10.63 Gbp of clean sequencing data was obtained per flow cell. We found that the unevenness of data yield among each multiplexed isolate was a major barrier for shortening sequencing time. Using genome assemblies, both SeqSero2 and SISTR accurately predicted all the multiplexed isolates under each multiplexing strategy when depth of genome coverage ≥50× for each isolate. We identified that cross-sample barcode assignment was a major cause of prediction errors when raw sequencing data were used for prediction. This study also demonstrated that, (i) sequence data generated by ONT multiplex sequencing can be used to simultaneously predict serotype for three to ten Salmonella isolates, (ii) with three to ten Salmonella isolates multiplexed, genome coverage at ≥50× per isolate was obtained within an average of 6 h of ONT multiplex sequencing, and (iii) with five isolates multiplexed, the cost per isolate might be reduced to 23% of that incurred with single ONT sequencing. This study is a starting point for future validation of multiplex ONT WGS as a cost-efficient and rapid Salmonella confirmation and serotype classification tool for the food industry.
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Affiliation(s)
- Xingwen Wu
- Mars Global Food Safety Center, Beijing, China
| | - Hao Luo
- Mars Global Food Safety Center, Beijing, China
| | - Feng Xu
- Mars Global Food Safety Center, Beijing, China
| | - Chongtao Ge
- Mars Global Food Safety Center, Beijing, China
| | - Shaoting Li
- Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Xiangyu Deng
- Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | | | | | | | - Silin Tang
- Mars Global Food Safety Center, Beijing, China
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6
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Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase. mBio 2020; 11:mBio.01364-20. [PMID: 32843546 PMCID: PMC7448272 DOI: 10.1128/mbio.01364-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Acyltransferase-3 (AT3) domain-containing membrane proteins are involved in O-acetylation of a diverse range of carbohydrates across all domains of life. In bacteria they are essential in processes including symbiosis, resistance to antimicrobials, and biosynthesis of antibiotics. Their mechanism of action, however, is poorly characterized. We analyzed two acetyltransferases as models for this important family of membrane proteins, which modify carbohydrates on the surface of the pathogen Salmonella enterica, affecting immunogenicity, virulence, and bacteriophage resistance. We show that when these AT3 domains are fused to a periplasmic partner domain, both domains are required for substrate acetylation. The data show conserved elements in the AT3 domain and unique structural features of the periplasmic domain. Our data provide a working model to probe the mechanism and function of the diverse and important members of the widespread AT3 protein family, which are required for biologically significant modifications of cell-surface carbohydrates. Membrane bound acyltransferase-3 (AT3) domain-containing proteins are implicated in a wide range of carbohydrate O-acyl modifications, but their mechanism of action is largely unknown. O-antigen acetylation by AT3 domain-containing acetyltransferases of Salmonella spp. can generate a specific immune response upon infection and can influence bacteriophage interactions. This study integrates in situ and in vitro functional analyses of two of these proteins, OafA and OafB (formerly F2GtrC), which display an “AT3-SGNH fused” domain architecture, where an integral membrane AT3 domain is fused to an extracytoplasmic SGNH domain. An in silico-inspired mutagenesis approach of the AT3 domain identified seven residues which are fundamental for the mechanism of action of OafA, with a particularly conserved motif in TMH1 indicating a potential acyl donor interaction site. Genetic and in vitro evidence demonstrate that the SGNH domain is both necessary and sufficient for lipopolysaccharide acetylation. The structure of the periplasmic SGNH domain of OafB identified features not previously reported for SGNH proteins. In particular, the periplasmic portion of the interdomain linking region is structured. Significantly, this region constrains acceptor substrate specificity, apparently by limiting access to the active site. Coevolution analysis of the two domains suggests possible interdomain interactions. Combining these data, we propose a refined model of the AT3-SGNH proteins, with structurally constrained orientations of the two domains. These findings enhance our understanding of how cells can transfer acyl groups from the cytoplasm to specific extracellular carbohydrates.
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7
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Xu F, Ge C, Luo H, Li S, Wiedmann M, Deng X, Zhang G, Stevenson A, Baker RC, Tang S. Evaluation of real-time nanopore sequencing for Salmonella serotype prediction. Food Microbiol 2020; 89:103452. [DOI: 10.1016/j.fm.2020.103452] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/02/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022]
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8
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The protective capacity of anti-O4 antigen antibodies against Salmonella infection is influenced by the presence or absence of the O5 antigen. Vaccine 2020; 38:5408-5412. [PMID: 32616326 DOI: 10.1016/j.vaccine.2020.06.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/22/2020] [Accepted: 06/18/2020] [Indexed: 01/29/2023]
Abstract
Anti-O-antigen antibodies, such as anti-O4 antigen IgG, induce protective immunity against Salmonella enterica serovar Typhimurium (S. Typhimurium) infection. S. Typhimurium belongs to the group O4, which can be classified into two serological variants, namely factor O5 antigen positive (O5+) and factor O5 antigen negative (O5-). In this study, we determined the protective immunity induced by anti-O4 antigen IgG against O5+ and O5- S. Typhimurium infection in a mouse model. Unexpectedly, anti-O4 antigen IgG induced protection against O5- of S. Typhimurium, but not against O5+ of S. Typhimurium. We suggest that the affinity of the O4 antigen with anti-O4 antigen IgG is stronger in the O5- S. Typhimurium compared to the O5+ S. Typhimurium. Although anti-O4 antigen IgG has the potential to protect against S. Typhimurium infection, the effects of anti-O4 antigen IgG in protection against Salmonella infection differ depending on the presence or absence of the O5 antigen.
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9
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SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data. Appl Environ Microbiol 2019; 85:AEM.01746-19. [PMID: 31540993 DOI: 10.1128/aem.01746-19] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022] Open
Abstract
SeqSero, launched in 2015, is a software tool for Salmonella serotype determination from whole-genome sequencing (WGS) data. Despite its routine use in public health and food safety laboratories in the United States and other countries, the original SeqSero pipeline is relatively slow (minutes per genome using sequencing reads), is not optimized for draft genome assemblies, and may assign multiple serotypes for a strain. Here, we present SeqSero2 (github.com/denglab/SeqSero2; denglab.info/SeqSero2), an algorithmic transformation and functional update of the original SeqSero. Major improvements include (i) additional sequence markers for identification of Salmonella species and subspecies and certain serotypes, (ii) a k-mer based algorithm for rapid serotype prediction from raw reads (seconds per genome) and improved serotype prediction from assemblies, and (iii) a targeted assembly approach for specific retrieval of serotype determinants from WGS for serotype prediction, new allele discovery, and prediction troubleshooting. Evaluated using 5,794 genomes representing 364 common U.S. serotypes, including 2,280 human isolates of 117 serotypes from the National Antimicrobial Resistance Monitoring System, SeqSero2 is up to 50 times faster than the original SeqSero while maintaining equivalent accuracy for raw reads and substantially improving accuracy for assemblies. SeqSero2 further suggested that 3% of the tested genomes contained reads from multiple serotypes, indicating a use for contamination detection. In addition to short reads, SeqSero2 demonstrated potential for accurate and rapid serotype prediction directly from long nanopore reads despite base call errors. Testing of 40 nanopore-sequenced genomes of 17 serotypes yielded a single H antigen misidentification.IMPORTANCE Serotyping is the basis of public health surveillance of Salmonella It remains a first-line subtyping method even as surveillance continues to be transformed by whole-genome sequencing. SeqSero allows the integration of Salmonella serotyping into a whole-genome-sequencing-based laboratory workflow while maintaining continuity with the classic serotyping scheme. SeqSero2, informed by extensive testing and application of SeqSero in the United States and other countries, incorporates important improvements and updates that further strengthen its application in routine and large-scale surveillance of Salmonella by whole-genome sequencing.
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10
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Tang S, Orsi RH, Luo H, Ge C, Zhang G, Baker RC, Stevenson A, Wiedmann M. Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella. Front Microbiol 2019; 10:1591. [PMID: 31354679 PMCID: PMC6639432 DOI: 10.3389/fmicb.2019.01591] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/26/2019] [Indexed: 01/26/2023] Open
Abstract
The food industry is facing a major transition regarding methods for confirmation, characterization, and subtyping of Salmonella. Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. To facilitate selection of subtyping methods by the food industry, we present: (i) a comparison between classical serotyping and selected widely used molecular-based subtyping methods including pulsed-field gel electrophoresis, multilocus sequence typing, and WGS (including WGS-based serovar prediction) and (ii) a scoring system to evaluate and compare Salmonella subtyping assays. This literature-based assessment supports the superior discriminatory power of WGS for source tracking and root cause elimination in food safety incident; however, circumstances in which use of other subtyping methods may be warranted were also identified. This review provides practical guidance for the food industry and presents a starting point for further comparative evaluation of Salmonella characterization and subtyping methods.
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Affiliation(s)
- Silin Tang
- Mars Global Food Safety Center, Beijing, China
| | - Renato H. Orsi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
| | - Hao Luo
- Mars Global Food Safety Center, Beijing, China
| | - Chongtao Ge
- Mars Global Food Safety Center, Beijing, China
| | | | | | | | - Martin Wiedmann
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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11
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Boland C, Van Hessche M, Mahillon J, Wattiau P. A liquid bead array for the identification and characterization of fljB-positive and fljB-negative monophasic variants of Salmonella Typhimurium. Food Microbiol 2017; 71:17-24. [PMID: 29366463 DOI: 10.1016/j.fm.2017.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/31/2017] [Accepted: 04/09/2017] [Indexed: 12/13/2022]
Abstract
Salmonella1,4,[5],12:i:- accounts currently for one of the most common serotypes observed worldwide. These isolates do not express the FljB flagellin and mostly derive from Salmonella Typhimurium. They are therefore termed Salmonella Typhimurium monophasic variants (STMV) and are considered of comparable public health risk. Since serological identification of the somatic and flagellar antigens of STMV is not sufficient to demonstrate relatedness with Salmonella Typhimurium, additional assays detecting genetic markers unique to Salmonella Typhimurium are required. In addition, identification of the mutations affecting expression of the flagellar gene fljB can be useful to support the monophasic character observed phenotypically. Finally, genetic subtyping of the various mono- and biphasic Salmonella Typhimurium clonal groups can facilitate their epidemiological follow-up. Here, we present a home-made liquid bead array able to fulfill these requirements. This array confirmed the monophasic character of 240 STMV isolates collected in Belgium during 2014-2015 and identified 10 genetic subtypes. Microevolution in and around the fljB locus linked to IS26 insertions is probably one of the driven force accounting for STMV population diversity. Thanks to its open design, other genetic signatures could later be merged to the assay to subtype additional STMV clonal groups and to detect rare mutations.
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Affiliation(s)
- Cécile Boland
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Operational Direction Bacterial Diseases, Foodborne Bacterial Zoonoses & Antibiotic Resistance Unit, Groeselenbergstr. 99, B-1180 Brussels, Belgium; Université catholique de Louvain (UCL), Faculty of Bioscience Engineering, Earth and Life Institute, Applied Microbiology Cluster (ELIM), Laboratory of Food and Environmental Microbiology, Croix du Sud, 2 - L7.05.12, 1348 Louvain-la-Neuve, Belgium.
| | - Mieke Van Hessche
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Operational Direction Bacterial Diseases, Foodborne Bacterial Zoonoses & Antibiotic Resistance Unit, Groeselenbergstr. 99, B-1180 Brussels, Belgium.
| | - Jacques Mahillon
- Université catholique de Louvain (UCL), Faculty of Bioscience Engineering, Earth and Life Institute, Applied Microbiology Cluster (ELIM), Laboratory of Food and Environmental Microbiology, Croix du Sud, 2 - L7.05.12, 1348 Louvain-la-Neuve, Belgium.
| | - Pierre Wattiau
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Operational Direction Bacterial Diseases, Foodborne Bacterial Zoonoses & Antibiotic Resistance Unit, Groeselenbergstr. 99, B-1180 Brussels, Belgium.
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12
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Szabo I, Grafe M, Kemper N, Junker E, Malorny B. Genetic basis for loss of immuno-reactive O-chain in Salmonella enterica serovar Enteritidis veterinary isolates. Vet Microbiol 2017; 204:165-173. [PMID: 28532797 DOI: 10.1016/j.vetmic.2017.03.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 11/25/2022]
Abstract
Fifty-two rough Salmonella enterica serovar Enteritidis (S. Enteritidis) isolates from broilers and the environment were characterized for their serological and genotypic properties. Under routine diagnostic serotyping methods such isolates lack the immuno-reactivity of the O-chain of the lipopolysaccharide (LPS), and are referred to as non-typeable. Using a modified slide agglutination method, the isolates could be differentiated into three different serological variants. Twenty-six isolates (50%) were defined as semi-rough, nineteen isolates (37%) as deep-rough, four isolates (8%) as rough and three isolates could not be assigned. Genetically, all semi-rough isolates lacked the wzyB gene encoding the O-antigen polymerase. Two isolates carried a frameshift mutation in wzyB. In 15 of 23 cases deep-rough or rough isolates had a single point mutation, a single - or double-nucleotide insert or deletion in the wbaP gene. The mutational changes lead to expression of truncated (premature) protein, resulting in the loss of the immuno-reactive O-chain. Both rough and smooth S. Enteritidis isolates showed identical or highly similar XbaI-PFGE profiles. Our results indicate that the loss of a functional LPS in S. Enteritidis isolates is caused by a variety of different mutation events within the wzyB (semi-rough) or the wbaP (deep-rough) gene and is not a result of a vertical spread of a specific S. Enteritidis subtype. The defect of the LPS may be a common evolutionary mechanism through which host defence can be escaped.
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Affiliation(s)
- Istvan Szabo
- Federal Institute for Risk Assessment, Department for Biological Safety, National Reference Laboratory for Salmonella, Max-Dohrn-Str 8-10, D-10589 Berlin, Germany.
| | - Marianne Grafe
- Federal Institute for Risk Assessment, Department for Biological Safety, National Reference Laboratory for Salmonella, Max-Dohrn-Str 8-10, D-10589 Berlin, Germany; University of Potsdam, Am Neuen Palais 10, D-14469 Potsdam, Germany
| | - Nicole Kemper
- University of Veterinary Medicine Hannover, Foundation, Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Ernst Junker
- Federal Institute for Risk Assessment, Department for Biological Safety, National Reference Laboratory for Salmonella, Max-Dohrn-Str 8-10, D-10589 Berlin, Germany
| | - Burkhard Malorny
- Federal Institute for Risk Assessment, Department for Biological Safety, National Reference Laboratory for Salmonella, Max-Dohrn-Str 8-10, D-10589 Berlin, Germany
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Nakai Y, Ito A, Ogawa Y, Aribam SD, Elsheimer-Matulova M, Shiraiwa K, Kisaka SMB, Hikono H, Nishikawa S, Akiba M, Kawahara K, Shimoji Y, Eguchi M. Determination of O:4 antigen-antibody affinity level in O:5 antigen positive and negative variants of Salmonella enterica serovar Typhimurium. FEMS Microbiol Lett 2017; 364:3078541. [PMID: 28369258 DOI: 10.1093/femsle/fnx062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/16/2017] [Indexed: 01/05/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) has two serological variants: one that expresses the O:5 antigen (1,4,5,12:i:1,2) and one that lacks O:5 antigen (1,4,12:i:1,2). For serotyping, S. Typhimurium is agglutinated by diagnostic O:4 antigen serum. This study was carried out to compare the antigen-antibody affinity of O:4 antigen in S. Typhimurium χ3306 O:5-positive and S. Typhimurium χ3306 O:5-negative strains. The affinity of O:4 antigen with O:4 antigen serum was found to be stronger in the O:5-negative strains compared to O:5-positive strains. Next, we investigated the antigen-antibody affinity of O:4 antigen with O:4 antigen serum in field strains of S. Typhimurium, which showed the same tendency in affinity as seen with S. Typhimurium χ3306 O:5-positive and negative strains. This study suggests that the presence or absence of O:5 antigen causes differences in O:4 agglutination reactions with different field strains of S. Typhimurium.
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Affiliation(s)
- Yuka Nakai
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Akihisa Ito
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Yohsuke Ogawa
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Swarmistha Devi Aribam
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | | | - Kazumasa Shiraiwa
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Stevens M B Kisaka
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Hirokazu Hikono
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Sayaka Nishikawa
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Masato Akiba
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Kazuyoshi Kawahara
- Department of Biosciences, College of Science and Engineering, Kanto Gakuin University, 1-50-1, Mutsuura-Higashi, Kanazawa-ku, Yokohama 236-8501, Japan
| | - Yoshihiro Shimoji
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Masahiro Eguchi
- National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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14
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Kintz E, Davies MR, Hammarlöf DL, Canals R, Hinton JCD, van der Woude MW. A BTP1 prophage gene present in invasive non-typhoidal Salmonella determines composition and length of the O-antigen of the lipopolysaccharide. Mol Microbiol 2015; 96:263-75. [PMID: 25586744 PMCID: PMC4413052 DOI: 10.1111/mmi.12933] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2015] [Indexed: 12/20/2022]
Abstract
Salmonella Typhimurium isolate D23580 represents a recently identified ST313 lineage of invasive non-typhoidal Salmonellae (iNTS). One of the differences between this lineage and other non-iNTS S. Typhimurium isolates is the presence of prophage BTP1. This prophage encodes a gtrC gene, implicated in O-antigen modification. GtrCBTP1 is essential for maintaining O-antigen length in isolate D23580, since a gtrBTP1 mutant yields a short O-antigen. This phenotype can be complemented by gtrCBTP1 or very closely related gtrC genes. The short O-antigen of the gtrBTP1 mutant was also compensated by deletion of the BTP1 phage tailspike gene in the D23580 chromosome. This tailspike protein has a putative endorhamnosidase domain and thus may mediate O-antigen cleavage. Expression of the gtrCBTP1 gene is, in contrast to expression of many other gtr operons, not subject to phase variation and transcriptional analysis suggests that gtrC is produced under a variety of conditions. Additionally, GtrCBTP1 expression is necessary and sufficient to provide protection against BTP1 phage infection of an otherwise susceptible strain. These data are consistent with a model in which GtrCBTP1 mediates modification of the BTP1 phage O-antigen receptor in lysogenic D23580, and thereby prevents superinfection by itself and other phage that uses the same O-antigen co-receptor.
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Affiliation(s)
- Erica Kintz
- Centre for Immunology and Infection, Hull York Medical School and the Department of Biology, University of York, York, UK
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15
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Arnold ME, Gosling RJ, La Ragione RM, Davies RH, Martelli F. Estimation of the impact of vaccination on faecal shedding and organ and egg contamination forSalmonellaEnteritidis,SalmonellaTyphiumurium and monophasicSalmonellaTyphimurium. Avian Pathol 2014; 43:155-63. [DOI: 10.1080/03079457.2014.896990] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Shi C, Singh P, Ranieri ML, Wiedmann M, Moreno Switt AI. Molecular methods for serovar determination of Salmonella. Crit Rev Microbiol 2013; 41:309-25. [PMID: 24228625 DOI: 10.3109/1040841x.2013.837862] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Salmonella is a diverse foodborne pathogen, which has more than 2600 recognized serovars. Classification of Salmonella isolates into serovars is essential for surveillance and epidemiological investigations; however, determination of Salmonella serovars, by traditional serotyping, has some important limitations (e.g. labor intensive, time consuming). To overcome these limitations, multiple methods have been investigated to develop molecular serotyping schemes. Currently, molecular methods to predict Salmonella serovars include (i) molecular subtyping methods (e.g. PFGE, MLST), (ii) classification using serovar-specific genomic markers and (iii) direct methods, which identify genes encoding antigens or biosynthesis of antigens used for serotyping. Here, we reviewed reported methodologies for Salmonella molecular serotyping and determined the "serovar-prediction accuracy", as the percentage of isolates for which the serovar was correctly classified by a given method. Serovar-prediction accuracy ranged from 0 to 100%, 51 to 100% and 33 to 100% for molecular subtyping, serovar-specific genomic markers and direct methods, respectively. Major limitations of available schemes are errors in predicting closely related serovars (e.g. Typhimurium and 4,5,12:i:-), and polyphyletic serovars (e.g. Newport, Saintpaul). The high diversity of Salmonella serovars represents a considerable challenge for molecular serotyping approaches. With the recent improvement in sequencing technologies, full genome sequencing could be developed into a promising molecular approach to serotype Salmonella.
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Affiliation(s)
- Chunlei Shi
- Department of Food Science, Cornell University , Ithaca, NY , USA and
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17
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Population structure of Salmonella enterica serovar 4,[5],12:b:- strains and likely sources of human infection. Appl Environ Microbiol 2013; 79:5121-9. [PMID: 23793625 DOI: 10.1128/aem.01735-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar 4,[5],12:b:- is a monophasic serovar not able to express the second-phase flagellar antigen (H2 antigen). In Germany, the serovar is occasionally isolated from poultry, reptiles, fish, food, and humans. In this study, a selection of 67 epidemiologically unrelated Salmonella enterica serovar 4,[5],12:b:- strains isolated in Germany between 2000 and 2011 from the environment, animal, food, and humans was investigated by phenotypic and genotypic methods to better understand the population structure and to identify potential sources of human infections. Strains of this monophasic serovar were highly diverse. Within the 67 strains analyzed, we identified 52 different pulsed-field gel electrophoresis XbaI profiles, 12 different multilocus sequence types (STs), and 18 different pathogenicity array types. The relatedness of strains based on the pathogenicity gene repertoire (102 markers tested) was in good agreement with grouping by MLST. S. enterica serovar 4,[5],12:b:- is distributed across multiple unrelated eBurst groups and consequently is highly polyphyletic. Two sequence types (ST88 and ST127) were linked to S. enterica serovar Paratyphi B (d-tartrate positive), two single-locus variants of ST1583 were linked to S. enterica serovar Abony, and one sequence type (ST1484) was associated with S. enterica serovar Mygdal, a recently defined, new serovar. From the characterization of clinical isolates and those of nonhuman origin, it can be concluded that the potential sources of sporadic human infections with S. enterica serovar 4,[5],12:b:- most likely are mushrooms, shellfish/fish, and poultry.
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18
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Toboldt A, Tietze E, Helmuth R, Fruth A, Junker E, Malorny B. Human infections attributable to the D-tartrate-fermenting variant of Salmonella enterica serovar Paratyphi B in Germany originate in reptiles and, on rare occasions, poultry. Appl Environ Microbiol 2012; 78:7347-57. [PMID: 22885742 PMCID: PMC3457084 DOI: 10.1128/aem.01732-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/01/2012] [Indexed: 11/20/2022] Open
Abstract
In this study, the population structure, incidence, and potential sources of human infection caused by the d-tartrate-fermenting variant of Salmonella enterica serovar Paratyphi B [S. Paratyphi B (dT+)] was investigated. In Germany, the serovar is frequently isolated from broilers. Therefore, a selection of 108 epidemiologically unrelated S. enterica serovar Paratyphi B (dT+) strains isolated in Germany between 2002 and 2010 especially from humans, poultry/poultry meat, and reptiles was investigated by phenotypic and genotypic methods. Strains isolated from poultry and products thereof were strongly associated with multilocus sequence type ST28 and showed antimicrobial multiresistance profiles. Pulsed-field gel electrophoresis XbaI profiles were highly homogeneous, with only a few minor XbaI profile variants. All strains isolated from reptiles, except one, were strongly associated with ST88, another distantly related type. Most of the strains were susceptible to antimicrobial agents, and XbaI profiles were heterogeneous. Strains isolated from humans yielded seven sequence types (STs) clustering in three distantly related lineages. The first lineage, comprising five STs, represented mainly strains belonging to ST43 and ST149. The other two lineages were represented only by one ST each, ST28 and ST88. The relatedness of strains based on the pathogenicity gene repertoire (102 markers tested) was mostly in agreement with the multilocus sequence type. Because ST28 was frequently isolated from poultry but rarely in humans over the 9-year period investigated, overall, this study indicates that in Germany S. enterica serovar Paratyphi B (dT+) poses a health risk preferentially by contact with reptiles and, to a less extent, by exposure to poultry or poultry meat.
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Affiliation(s)
- Anne Toboldt
- Federal Institute for Risk Assessment, National Reference Laboratory for Salmonella, Berlin, Germany
- Free University Berlin, Department of Biology, Chemistry and Pharmacy, Berlin, Germany
| | - Erhard Tietze
- Robert Koch Institute, Wernigerode Branch, Division Bacterial Infections, National Reference Centre for Salmonella and other Enterics, Wernigerode, Germany
| | - Reiner Helmuth
- Federal Institute for Risk Assessment, National Reference Laboratory for Salmonella, Berlin, Germany
| | - Angelika Fruth
- Robert Koch Institute, Wernigerode Branch, Division Bacterial Infections, National Reference Centre for Salmonella and other Enterics, Wernigerode, Germany
| | - Ernst Junker
- Federal Institute for Risk Assessment, National Reference Laboratory for Salmonella, Berlin, Germany
| | - Burkhard Malorny
- Federal Institute for Risk Assessment, National Reference Laboratory for Salmonella, Berlin, Germany
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19
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Calix JJ, Dagan R, Pelton SI, Porat N, Nahm MH. Differential occurrence of Streptococcus pneumoniae serotype 11E between asymptomatic carriage and invasive pneumococcal disease isolates reflects a unique model of pathogen microevolution. Clin Infect Dis 2012; 54:794-9. [PMID: 22267713 DOI: 10.1093/cid/cir953] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Streptococcus pneumoniae is a commensal colonizer of the human nasopharynx (NP) that causes disease after evasion of host defenses and dissemination. Pneumococcal strains expressing the newly identified serotype 11E arise from antigenically similar 11A progenitors by genetic inactivation of the O-acetyltransferase gene wcjE. Each 11E strain contains a distinct mutation to wcjE, suggesting that 11E strains are not transmitted among hosts despite their recovery from multiple patients with pneumococcal disease. We investigated whether the presumed lack of transmission of serotype 11E is consistent with its inability to survive in the NP. METHODS More than 400 pneumococcal carriage, middle ear, conjunctiva, and blood isolates, serotyped as 11A by Quellung reaction, were reexamined for reactivity to 11A- and 11E-specific antibodies. We confirmed serotyping of isolates with sequencing of wcjE alleles. RESULTS Serotype 11E strains were statistically more likely to occur among blood (4 of 15), conjunctiva (1 of 14), or middle ear (2 of 21) isolates than among carriage isolates (2 of 355). All 11E isolates contained unique mutations that putatively decrease wcjE expression. CONCLUSIONS The lack of a circulating 11E clone and the increased occurrence of 11E strains among disease isolates supports the idea that serotype 11E independently arises during infection after initial colonization with a serotype 11A progenitor. Factors encountered in the NP likely contribute to relative rarity of 11E among carriage isolates, whereas selective pressures in deeper tissues possibly promote 11E emergence. These findings illustrate a novel model of microevolution that transpires during the span of a single encounter with serotype 11A, highlighting the adaptability of bacterial pathogens within hosts.
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Affiliation(s)
- Juan J Calix
- Department of Microbiology, Boston University Medical Center, Massachusetts, USA
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