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Traglia GM, Betancor L, Yim L, Iriarte A, Chabalgoity JA. Genotypic and phenotypic analysis of Salmonella enterica serovar Derby, looking for clues explaining the impairment of egg isolates to cause human disease. Front Microbiol 2024; 15:1357881. [PMID: 38903793 PMCID: PMC11186997 DOI: 10.3389/fmicb.2024.1357881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
Salmonella enterica serovar Derby causes foodborne disease (FBD) outbreaks worldwide, mainly from contaminated pork but also from chickens. During a major epidemic of FBD in Uruguay due to S. enteritidis from poultry, we conducted a large survey of commercially available eggs, where we isolated many S. enteritidis strains but surprisingly also a much larger number (ratio 5:1) of S. Derby strains. No single case of S. Derby infection was detected in that period, suggesting that the S. Derby egg strains were impaired for human infection. We sequenced fourteen of these egg isolates, as well as fifteen isolates from pork or human infection that were isolated in Uruguay before and after that period, and all sequenced strains had the same sequence type (ST40). Phylogenomic analysis was conducted using more than 3,500 genomes from the same sequence type (ST), revealing that Uruguayan isolates clustered into four distantly related lineages. Population structure analysis (BAPS) suggested the division of the analyzed genomes into nine different BAPS1 groups, with Uruguayan strains clustering within four of them. All egg isolates clustered together as a monophyletic group and showed differences in gene content with the strains in the other clusters. Differences included variations in the composition of mobile genetic elements, such as plasmids, insertion sequences, transposons, and phages, between egg isolates and human/pork isolates. Egg isolates showed an acid susceptibility phenotype, reduced ability to reach the intestine after oral inoculation of mice, and reduced induction of SPI-2 ssaG gene, compared to human isolates from other monophyletic groups. Mice challenge experiments showed that mice infected intraperitoneally with human/pork isolates died between 1-7 days p.i., while all animals infected with the egg strain survived the challenge. Altogether, our results suggest that loss of genes functions, the insertion of phages and the absence of plasmids in egg isolates may explain why these S. Derby were not capable of producing human infection despite being at that time, the main serovar recovered from eggs countrywide.
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Affiliation(s)
| | | | | | - Andrés Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - José Alejandro Chabalgoity
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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Wang BX, Leshchiner D, Luo L, Tuncel M, Hokamp K, Hinton JCD, Monack DM. High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection. Nat Genet 2024; 56:1288-1299. [PMID: 38831009 PMCID: PMC11176087 DOI: 10.1038/s41588-024-01779-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/25/2024] [Indexed: 06/05/2024]
Abstract
Salmonella enterica is comprised of genetically distinct 'serovars' that together provide an intriguing model for exploring the genetic basis of pathogen evolution. Although the genomes of numerous Salmonella isolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. Here, we conduct high-throughput functional genomics on both generalist (Typhimurium) and human-restricted (Typhi and Paratyphi A) Salmonella at unprecedented scale in the study of this enteric pathogen. Using a comprehensive systems biology approach, we identify gene networks with serovar-specific fitness effects across 25 host-associated stresses encountered at key stages of human infection. By experimentally perturbing these networks, we characterize previously undescribed pseudogenes in human-adapted Salmonella. Overall, this work highlights specific vulnerabilities encoded within human-restricted Salmonella that are linked to the degradation of their genomes, shedding light into the evolution of this enteric pathogen.
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Affiliation(s)
- Benjamin X Wang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Lijuan Luo
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Miles Tuncel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Denise M Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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Pereira GDN, Seribelli AA, Gomes CN, Vilela FP, Tonani L, Tiba-Casas MR, Medeiros MIC, Rodrigues DDP, Kress MRVZ, Falcão JP. Virulence potential of Salmonella 1,4, [5],12:i:- strains isolated during decades from different sources in the Southeast region of Brazil. Braz J Microbiol 2023; 54:2827-2843. [PMID: 37817050 PMCID: PMC10689702 DOI: 10.1007/s42770-023-01145-5] [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: 06/01/2023] [Accepted: 09/30/2023] [Indexed: 10/12/2023] Open
Abstract
Salmonella 1,4, [5],12:i:- is one of the most prevalent serovars associated with gastroenteritis in several countries, including Brazil. However, few studies have analyzed the virulence potential of this variant in this country. Therefore, this study aimed to characterize S. 1,4, [5],12:i:- strains isolated in Southeast Brazil. To this end, 113 S. 1,4, [5],12:i:- strains isolated from different sources between 1983 and 2020 were analyzed. For all strains, the frequencies of 11 virulence genes were investigated using PCR and the molecular typing was performed using pulsed-field gel electrophoresis (PFGE). Furthermore, 40 strains isolated from human and non-human sources were characterized by survival under acid and oxidative stress, and virulence analysis in Galleria mellonella was performed for 20 selected strains. All virulence genes were detected in more than 91% of the strains. The studied strains were grouped into four clusters using PFGE. Most strains were present in one cluster, named PFGE-A, with a genetic similarity of ≥ 79.5%. All 40 strains survived acid stress after 10 min and 1 h of exposure. Under oxidative stress, all 40 strains survived after 10 min, and 36 survived after 1 h of exposure. In the G. mellonella assay, nine isolates from non-human sources and six isolates from human showed high-to-intermediate virulence profiles. In conclusion, the pathogenic potential of the strains studied was corroborated by the high frequency of all the virulence genes identified. The PFGE results suggested that most strains belonged to one main cluster that has been prevailing in the São Paulo State, Brazil. The S. 1,4, [5],12:i:- strains isolated from human and non-human sources successfully survived the unfavorable conditions in the human gastrointestinal tract. Finally, strains isolated from non-human sources showed a higher proportion of isolates with high to intermediate virulence profiles in G. mellonella than in human isolates, suggesting a possible difference between isolates from different origins.
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Affiliation(s)
- Giovana do Nascimento Pereira
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, S/N°, Ribeirão Preto, SP, 14040-903, Brasil
| | - Amanda Aparecida Seribelli
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, S/N°, Ribeirão Preto, SP, 14040-903, Brasil
- Departamento de Biologia Celular E Molecular E Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto - USP, Av. Do Café, S/N°, Ribeirão Preto, SP, 14040-903, Brasil
| | - Carolina Nogueira Gomes
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, S/N°, Ribeirão Preto, SP, 14040-903, Brasil
| | - Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, S/N°, Ribeirão Preto, SP, 14040-903, Brasil
| | - Ludmilla Tonani
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, S/N°, Ribeirão Preto, SP, 14040-903, Brasil
| | | | | | | | - Márcia Regina von Zeska Kress
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, S/N°, Ribeirão Preto, SP, 14040-903, Brasil
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, S/N°, Ribeirão Preto, SP, 14040-903, Brasil.
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Schumacher K, Brameyer S, Jung K. Bacterial acid stress response: from cellular changes to antibiotic tolerance and phenotypic heterogeneity. Curr Opin Microbiol 2023; 75:102367. [PMID: 37633223 DOI: 10.1016/j.mib.2023.102367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/28/2023]
Abstract
Most bacteria are neutralophiles but can survive fluctuations in pH in their environment. Herein, we provide an overview of the adaptation of several human, soil, and food bacteria to acid stress, mainly based on next-generation sequencing studies, highlighting common and specific strategies. We also discuss the interplay between acid stress response and antibiotic tolerance, as well as the response of individual cells.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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Baarlen PV. Special Issue "Omics Research of Pathogenic Microorganisms". Genes (Basel) 2023; 14:1229. [PMID: 37372409 DOI: 10.3390/genes14061229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Infectious diseases of plants, animals and humans pose a serious threat to global health and seriously impact ecosystem stability and agriculture, including food security [...].
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Affiliation(s)
- Peter van Baarlen
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
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Han M, Schierstaedt J, Duan Y, Trotereau J, Virlogeux-Payant I, Schikora A. Novel method to recover Salmonella enterica cells for Tn-Seq approaches from lettuce leaves and agricultural environments using combination of sonication, filtration, and dialysis membrane. J Microbiol Methods 2023; 208:106724. [PMID: 37054820 DOI: 10.1016/j.mimet.2023.106724] [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: 11/18/2022] [Revised: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/15/2023]
Abstract
Salmonella enterica in agricultural environments has become an important concern, due to its potential transmission to humans and the associated public health risks. To identify genes contributing to Salmonella adaptation to such environments, transposon sequencing has been used in recent years. However, isolating Salmonella from atypical hosts, such as plant leaves, can pose technical challenges due to low bacterial content and the difficulty to separate an adequate number of bacteria from host tissues. In this study, we describe a modified methodology using a combination of sonication and filtration to recover S. enterica cells from lettuce leaves. We successfully recovered over a total of 3.5 × 106Salmonella cells in each biological replicate from two six-week old lettuce leaves, 7 days after infiltration with a Salmonella suspension of 5 × 107 colony forming units (CFU)/mL. Moreover, we have developed a dialysis membrane system as an alternative method for recovering bacteria from culture medium, mimicking a natural environment. Inoculating 107 CFU/mL of Salmonella into the media based on plant (lettuce and tomato) leaf and diluvial sand soil, a final concentration of 109.5 and 108.5 CFU/mL was obtained, respectively. One millilitre of the bacterial suspension after 24 h incubation at 28 °C using 60 rpm agitation was pelleted, corresponding to 109.5 and 108.5 cells from leaf- or soil-based media. The recovered bacterial population, from both lettuce leaves and environment-mimicking media, can adequately cover a presumptive library density of 106 mutants. In conclusion, this protocol provides an effective method to recover a Salmonella transposon sequencing library from in planta and in vitro systems. We expect this novel technique to foster the study of Salmonella in atypical hosts and environments, as well as other comparable scenarios.
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Affiliation(s)
- Min Han
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
| | - Jasper Schierstaedt
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany; Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Department Plant-Microbe Systems, Theodor-Echtermeyer Weg 1, Großbeeren 14979, Germany
| | - Yongming Duan
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
| | - Jérôme Trotereau
- INRAE Val de Loire, Université de Tours, UMR ISP, Nouzilly 37380, France
| | | | - Adam Schikora
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany.
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Functional Genomics Identified Novel Genes Involved in Growth at Low Temperatures in Listeria monocytogenes. Microbiol Spectr 2022; 10:e0071022. [PMID: 35735974 PMCID: PMC9431668 DOI: 10.1128/spectrum.00710-22] [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: 12/27/2022] Open
Abstract
Listeria monocytogenes (Lm) is a foodborne pathogen that can cause severe human illness. Standard control measures for restricting bacterial growth, such as refrigeration, are often inadequate as Lm grows well at low temperatures. To identify genes involved in growth at low temperatures, a powerful functional genomics method Tn-seq was performed in this study. This genome-wide screening comprehensively identified the known and novel genetic determinants involved in low-temperature growth. A novel gene lmo1366, encoding rRNA methyltransferase, was identified to play an essential role in Lm growth at 16°C. In contrast, the inactivation of lmo2301, a gene encoding the terminase of phage A118, significantly enhanced the growth of Lm at 16°C. The deletion of lmo1366 or lmo2301 resulted in cell morphology alterations and impaired the growth rate in milk and other conditions at low temperatures. Transcriptomic analysis revealed that the Δlmo1366 and Δlmo2301 mutants exhibited altered transcriptional patterns compared to the wild-type strain at 16°C with significant differences in genes involved in ribosome structural stability and function, and membrane biogenesis, respectively. This work uncovered novel genetic determinants involved in Lm growth at 16°C, which could lead to a better understanding of how bacteria survive and multiply at low temperatures. Furthermore, these findings could potentially contribute to developing novel antibacterial strategies under low-temperature conditions. IMPORTANCEListeria monocytogenes is a Gram-positive pathogen that contributes to foodborne outbreaks due to its ability to survive at low temperatures. However, the genetic determinants of Lm involved in growth at low temperatures have not been fully defined. Here, the genetic determinants involved in the low-temperature growth of Lm were comprehensively identified on a genome-wide scale by Tn-seq. The gene lmo1366, encoding rRNA methyltransferase, was identified essential for growth under low-temperature conditions. On the other hand, the gene lmo2301, encoding terminase of phage A118, plays a negative role in bacterial growth at low temperatures. The transcriptomic analysis revealed the potential mechanisms. These findings lead to a better understanding of how bacteria survive and multiply at low temperatures and could provide unique targets for novel antibacterial strategies under low-temperature conditions.
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Lambré C, Barat Baviera JM, Bolognesi C, Chesson A, Cocconcelli PS, Crebelli R, Gott DM, Grob K, Lampi E, Riviere G, Steffensen I, Tlustos C, Van Loveren H, Vernis L, Zorn H, Bolton D, Bover‐Cid S, de Knecht J, Peixe L, Skandamis P, Martino C, Messens W, Tard A, Mortensen A. Evaluation of the safety and efficacy of lactic acid to reduce microbiological surface contamination on carcases from kangaroos, wild pigs, goats and sheep. EFSA J 2022; 20:e07265. [PMID: 35592024 PMCID: PMC9097752 DOI: 10.2903/j.efsa.2022.7265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Studies evaluating the safety and efficacy of lactic acid to reduce microbiological surface contamination from carcases of wild game (i.e. kangaroos and wild pigs) and small stock (i.e. goats and sheep) before chilling at the slaughterhouse were assessed. Wild pig and kangaroo hide‐on carcases may have been chilled before they arrive at the slaughterhouse and are treated after removal of the hides. Lactic acid solutions (2–5%) are applied to the carcases at temperatures of up to 55°C by spraying or misting. The treatment lasts 6–7 s per carcass side. The Panel concluded that: [1] the treatment is of no safety concern, provided that the lactic acid complies with the European Union specifications for food additives; [2] based on the available evidence, it was not possible to conclude on the efficacy of spraying or misting lactic acid on kangaroo, wild pig, goats and sheep carcases; [3] treatment of the above‐mentioned carcases with lactic acid may induce reduced susceptibility to the same substance, but this can be minimised; there is currently no evidence that prior exposure of food‐borne pathogens to lactic acid leads to the occurrence of resistance levels that compromise antimicrobial therapy; and [4] the release of lactic acid is not of concern for the environment, assuming that wastewaters released by the slaughterhouses are treated on‐site, if necessary, to counter the potentially low pH caused by lactic acid, in compliance with local rules.
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Mandal RK, Jiang T, Kwon YM. Genetic Determinants in Salmonella enterica Serotype Typhimurium Required for Overcoming In Vitro Stressors in the Mimicking Host Environment. Microbiol Spectr 2021; 9:e0015521. [PMID: 34878334 PMCID: PMC8653844 DOI: 10.1128/spectrum.00155-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/29/2021] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serotype Typhimurium, a nontyphoidal Salmonella (NTS), results in a range of enteric diseases, representing a major disease burden worldwide. There is still a significant portion of Salmonella genes whose mechanistic basis to overcome host innate defense mechanisms largely remains unknown. Here, we have applied transposon insertion sequencing (Tn-seq) method to unveil the genetic factors required for the growth or survival of S. Typhimurium under various host stressors simulated in vitro. A highly saturating Tn5 library of S. Typhimurium 14028s was subjected to selection during growth in the presence of short-chain fatty acid (100 mM propionate), osmotic stress (3% NaCl), or oxidative stress (1 mM H2O2) or survival in extreme acidic pH (30 min in pH 3) or starvation (12 days in 1× phosphate-buffered saline [PBS]). We have identified a total of 339 conditionally essential genes (CEGs) required to overcome at least one of these conditions mimicking host insults. Interestingly, all eight genes encoding FoF1-ATP synthase subunit proteins were required for fitness in all five stresses. Intriguingly, a total of 88 genes in Salmonella pathogenicity islands (SPI), including SPI-1, SPI-2, SPI-3, SPI-5, SPI-6, and SPI-11, are also required for fitness under the in vitro conditions. Additionally, by comparative analysis of the genes identified in this study and the genes previously shown to be required for in vivo fitness, we identified novel genes (marBCT, envF, barA, hscA, rfaQ, rfbI, and the genes encoding putative proteins STM14_1138, STM14_3334, STM14_4825, and STM_5184) that have compelling potential for the development of vaccines and antibacterial drugs to curb Salmonella infection. IMPORTANCE Salmonella enterica serotype Typhimurium is a major human bacterial pathogen that enters the food chain through meat animals asymptomatically carrying this pathogen. Despite the rich genome sequence data, a significant portion of Salmonella genes remain to be characterized for their potential contributions to virulence. In this study, we used transposon insertion sequencing (Tn-seq) to elucidate the genetic factors required for growth or survival under various host stressors, including short-chain fatty acids, osmotic stress, oxidative stress, extreme acid, and starvation. Among the total of 339 conditionally essential genes (CEGs) that are required under at least one of these five stress conditions were 221 previously known virulence genes required for in vivo fitness during infection in at least one of four animal species, including mice, chickens, pigs, and cattle. This comprehensive map of virulence phenotype-genotype in S. Typhimurium provides a roadmap for further interrogation of the biological functions encoded by the genome of this important human pathogen to survive in hostile host environments.
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Affiliation(s)
- Rabindra K. Mandal
- Center of Excellence for Poultry Science, University of Arkansas System Division of Agriculture, Fayetteville, Arkansas, USA
| | - Tieshan Jiang
- Center of Excellence for Poultry Science, University of Arkansas System Division of Agriculture, Fayetteville, Arkansas, USA
| | - Young Min Kwon
- Center of Excellence for Poultry Science, University of Arkansas System Division of Agriculture, Fayetteville, Arkansas, USA
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA
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Liu X, Liu G, Wu Y, Pang X, Wu Y, Qinshu, Niu J, Chen Q, Zhang X. Transposon sequencing: A powerful tool for the functional genomic study of food-borne pathogens. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.06.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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