An SNP is a spontaneous genetic change having a potential to modify the functions of the original genes and to lead to phenotypic diversity of bacteria in nature. In this study, a phylogenetic analysis of Salmonella enterica serovar Enteritidis, a major food-borne pathogen, showed that eight strains of S. Enteritidis isolated in South Korea, including FORC_075 and FORC_078, have almost identical genome sequences. Interestingly, however, the abilities of FORC_075 to form biofilms and red, dry and rough (RDAR) colonies were significantly impaired, resulting in phenotypic differences among the eight strains. Comparative genomic analyses revealed that one of the non-synonymous SNPs unique to FORC_075 has occurred in envZ, which encodes a sensor kinase of the EnvZ/OmpR two-component system. The SNP in envZ leads to an amino acid change from Pro248 (CCG) in other strains including FORC_078 to Leu248 (CTG) in FORC_075. Allelic exchange of envZ between FORC_075 and FORC_078 identified that the SNP in envZ is responsible for the impaired biofilm- and RDAR colony-forming abilities of S. Enteritidis. Biochemical analyses demonstrated that the SNP in envZ significantly increases the phosphorylated status of OmpR in S. Enteritidis and alters the expression of the OmpR regulon. Phenotypic analyses further identified that the SNP in envZ decreases motility of S. Enteritidis but increases its adhesion and invasion to both human epithelial cells and murine macrophage cells. In addition to an enhancement of infectivity to the host cells, survival under acid stress was also elevated by the SNP in envZ. Together, these results suggest that the natural occurrence of the SNP in envZ could contribute to phenotypic diversity of S. Enteritidis, possibly improving its fitness and pathogenesis.
YangL, JelsbakL, MarvigRL, DamkiærS, WorkmanCT et al. Evolutionary dynamics of bacteria in a human host environment. Proc Natl Acad Sci U S A2011; 108:7481–7486 [View Article][PubMed]
KellyBG, VespermannA, BoltonDJ. The role of horizontal gene transfer in the evolution of selected foodborne bacterial pathogens. Food Chem Toxicol2009; 47:951–968 [View Article][PubMed]
ColleryMM, KuehneSA, McBrideSM, KellyML, MonotM et al. What’s a SNP between friends: The influence of single nucleotide polymorphisms on virulence and phenotypes of Clostridium difficile strain 630 and derivatives. Virulence2017; 8:767–781
MikheechevaNE, ZaychikovaMV, MelerzanovAV, DanilenkoVN. A nonsynonymous SNP catalog of Mycobacterium tuberculosis virulence genes and its use for detecting new potentially virulent sublineages. Gen Biol Evol2017; 9:887–899
ScaltritiE, SasseraD, ComandatoreF, MorgantiM, MandalariC et al. Differential single nucleotide polymorphism-based analysis of an outbreak caused by Salmonella enterica serovar Manhattan reveals epidemiological details missed by standard pulsed-field gel electrophoresis. J Clin Microbiol2015; 53:1227–1238 [View Article][PubMed]
European Food Safety Authority and European Centre for Disease Prevention and Control (EFSA and ECDC) The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2017. Efsa J2018; 16:e05500 [View Article][PubMed]
DelgadoJ, ForstS, HarlockerS, InouyeM. Identification of a phosphorylation site and functional analysis of conserved aspartic acid residues of OmpR, a transcriptional activator for ompF and ompC in Escherichia coli. Mol Microbiol1993; 10:1037–1047 [View Article][PubMed]
HeadCG, TardyA, KenneyLJ. Relative binding affinities of OmpR and OmpR-phosphate at the ompF and ompC regulatory sites. J Mol Biol1998; 281:857–870 [View Article][PubMed]
AibaH, MizunoT. Phosphorylation of a bacterial activator protein, OmpR, by a protein kinase, EnvZ, stimulates the transcription of the ompF and ompC genes in Escherichia coli. FEBS Lett1990; 261:19–22 [View Article][PubMed]
DormanCJ, ChatfieldS, HigginsCF, HaywardC, DouganG. Characterization of porin and ompR mutants of a virulent strain of Salmonella typhimurium: ompR mutants are attenuated in vivo. Infect Immun1989; 57:2136–2140 [View Article][PubMed]
QuinnHJ, CameronADS, DormanCJ. Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella typhimurium and Escherichia coli in the acid stress response. PLoS Genet2014; 10:e1004215 [View Article][PubMed]
HammarM, ArnqvistA, BianZ, OlsenA, NormarkS. Expression of two csg operons is required for production of fibronectin- and Congo red-binding curli polymers in Escherichia coli K-12. Mol Microbiol1995; 18:661–670
RomlingU, RohdeM, OlsenA, NormarkS, AgfDRJ. the checkpoint of multicellular and aggregative behaviour in Salmonella typhimurium regulates at least two independent pathways. Mol Microbiol2000; 36:10–23
RömlingU. Characterization of the rdar morphotype, a multicellular behaviour in Enterobacteriaceae. Cell Mol Life Sci2005; 62:1234–1246 [View Article][PubMed]
XuS, ZouX, ShengX, ZhangH, MaoL et al. Expression of fljB:z66 on a linear plasmid of Salmonella enterica serovar Typhi is dependent on fliA and flhDC and regulated by OmpR. Braz J Microbiol2010; 41:729–740 [View Article][PubMed]
EllermeierCD, EllermeierJR, SlauchJM. Hild, HilC and RtsA constitute a feed forward loop that controls expression of the SPI1 type three secretion system regulator hilA in Salmonella enterica serovar typhimurium. Mol Microbiol2005; 57:691–705 [View Article][PubMed]
GroismanEA, OchmanH. Cognate gene clusters govern invasion of host epithelial-cells by Salmonella typhimurium and Shigella flexneri. Embo J1993; 12:3779–3787
SheaJE, HenselM, GleesonC, HoldenDW. Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium. Proc Natl Acad Sci U S A1996; 93:2593–2597 [View Article][PubMed]
ChakrabortyS, MizusakiH, KenneyLJ. A FRET-based DNA biosensor tracks OmpR-dependent acidification of Salmonella during macrophage infection. Plos Biology2015; 13:
RichterM, Rosselló-MóraR. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A2009; 106:19126–19131 [View Article][PubMed]
CroucherNJ, PageAJ, ConnorTR, DelaneyAJ, KeaneJA et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res2015; 43:e15
NeigerMR, GonzalezJF, Gonzalez-EscobedoG, KuckH, WhiteP et al. Pathoadaptive alteration of Salmonella biofilm formation in response to the gallbladder environment. J Bacteriol2019; 201:
ParkJH, JoY, JangSY, KwonH, IriecurrencyY et al. The cabABC operon essential for biofilm and rugose colony development in Vibrio vulnificus. Plos Pathog2015; 11:
DatsenkoKA, WannerBL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A2000; 97:6640–6645
PhilippeN, AlcarazJP, CoursangeE, GeiselmannJ, SchneiderD. Improvement of pCVD442, a suicide plasmid for gene allele exchange in bacteria. Plasmid2004; 51:246–255
LeeZW, HwangSH, ChoiG, JangKK, LeeTH et al. A MARTX Toxin rtxA Gene Is Controlled by Host Environmental Signals through a CRP-Coordinated Regulatory Network in Vibrio vulnificus. mBio.2020; 11:
KimSM, LeeDH, ChoiSH. Evidence that the Vibrio vulnificus flagellar regulator FlhF is regulated by a quorum sensing master regulator SmcR. Microbiology-Sgm2012; 158:2017–2025
YoshidaCE, KruczkiewiczP, LaingCR, LingohrEJ, GannonVPJ et al. The Salmonella in silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. PLoS One2016; 11:1 [View Article][PubMed]
MacKenzieKD, PalmerMB, KosterWL, WhiteAP. Examining the link between biofilm formation and the ability of pathogenic Salmonella strains to colonize multiple host species. Front Vet Sci2017; 4:
DesaiSK, KenneyLJ. Switching lifestyles is an in vivo adaptive strategy of bacterial pathogens. Front Cell Infect Microbiol2019; 9:421 [View Article][PubMed]
SerraDO, RichterAM, HenggeR. Cellulose as an architectural element in spatially structured Escherichia coli biofilms. J Bacteriol2013; 195:5540–5554 [View Article][PubMed]
KlumppJ, FuchsTM. Identification of novel genes in genomic islands that contribute to Salmonella typhimurium replication in macrophages. Microbiology2007; 153:1207–1220
Gal-MorO, GibsonDL, BalutaD, VallanceBA, FinlayBB. A novel secretion pathway of Salmonella enterica acts as an antivirulence modulator during salmonellosis. Plos Pathog2008; 4:
TheoretJR, CooperKK, ZekariasB, RolandKL, LawBF et al. The Campylobacter jejuni Dps homologue is important for in vitro biofilm formation and cecal colonization of poultry and may serve as a protective antigen for vaccination. Clin Vaccine Immunol2012; 19:1426–1431 [View Article][PubMed]
Prigent-CombaretC, BrombacherE, VidalO, AmbertA, LejeuneP et al. Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene. J Bacteriol2001; 183:7213–7223
GerstelU, KolbA, RomlingU. Regulatory components at the csgD promoter-additional roles for OmpR and integration host factor and role of the 5 ' untranslated region. Fems Microbiol Lett2006; 261:109–117
StablerRA, HeM, DawsonL, MartinM, ValienteE et al. Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol2009; 10:R102 [View Article][PubMed]
HorstmannN, SaldanaM, SahasrabhojaneP, YaoH, XPS et al. Dual-Site phosphorylation of the control of virulence regulator impacts group A streptococcal global gene expression and pathogenesis. Plos Pathog2014; 10:
IchikawaM, MinamiM, IsakaM, TatsunoI, HasegawaT. Analysis of two-component sensor proteins involved in the response to acid stimuli in Streptococcus pyogenes. Microbiology-Sgm2011; 157:3187–3194
FloresAR, JewellBE, YelamanchiliD, OlsenRJ, MusserJM. A single amino acid replacement in the sensor kinase LiaS contributes to a carrier phenotype in Group A Streptococcus. Infect Immun2015; 83:4237–4246 [View Article][PubMed]
HorstmannN, TranCN, BrumlowC, DebRoyS, YaoH et al. Phosphatase activity of the control of virulence sensor kinase CovS is critical for the pathogenesis of group A streptococcus. Plos Pathog2018; 14:
WhiteAP, GibsonDL, GrasslGA, KayWW, FinlayBB et al. Aggregation via the red, dry, and rough morphotype is not a virulence adaptation in Salmonella enterica serovar typhimurium. Infect Immun2008; 76:1048–1058 [View Article][PubMed]
TükelC, NishimoriJH, WilsonRP, WinterMG, KeestraAM et al. Toll-like receptors 1 and 2 cooperatively mediate immune responses to curli, a common amyloid from enterobacterial biofilms. Cell Microbiol2010; 12:1495–1505 [View Article][PubMed]
WinterSE, WinterMG, GodinezI, YangHJ, RussmannH et al. A rapid change in virulence gene expression during the transition from the intestinal lumen into tissue promotes systemic dissemination of Salmonella. Plos Pathog2010; 6:
YukHG, SchneiderKR. Adaptation of Salmonella spp. in juice stored under refrigerated and room temperature enhances acid resistance to simulated gastric fluid. Food Microbiol2006; 23:694–700
Álvarez-OrdóñezA, PrietoM, BernardoA, HillC, LópezM. The acid tolerance response of Salmonella spp.: an adaptive strategy to survive in stressful environments prevailing in foods and the host. Food Res Int2012; 45:482–492 [View Article]
HammarlofDL, KrogerC, OwenSV, CanalsR, Lacharme-LoraL et al. Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella. Proc Natl Acad Sci U S A2018; 115:E2614–E23
LetunicI, BorkP. Interactive tree of life (iTOL) V3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res2016; 44:W242–W5