Less Is Best in the Convergent Evolution of Typhoidal Salmonella
Authors: Andrés Vázquez-Torres
Journal: Cell Host & Microbe (2018)

Related works in this issue of Cell Host & Microbe (Bronner et al., 2018Bronner D.N. Faber F. Olsan E.E. Byndloss M.X. Sayed N.A. Xu G. Yoo W. Kim D. Ryu S. Lebrilla C.B. Baumler A.J. Genetic ablation of butyrate utilization attenuated gastrointestinal Salmonella disease.Cell Host Microbe. 2018; 23 (this issue): 266-273Abstract Full Text Full Text PDF PubMed Google Scholar) and in a recent issue of Cell Reports (Hiyoshi et al., 2018Hiyoshi H. Wangdi T. Lock G. Saechao C. Raffatellu M. Cobb B.A. Baumler A.J. Mechanisms to evade the phagocytic respiratory burst arose by convergent evolution in typhoidal Salmonella serovars.Cell Rep. 2018; 22https://doi.org/10.1016/j.chom.2018.01.004Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar) demonstrate how loss-of-function mutations in butyrate utilization and lipopolysaccharide O-antigen processing contribute to evasion of innate host defenses and the convergent evolution of distinct typhoidal Salmonella lineages. Related works in this issue of Cell Host & Microbe (Bronner et al., 2018Bronner D.N. Faber F. Olsan E.E. Byndloss M.X. Sayed N.A. Xu G. Yoo W. Kim D. Ryu S. Lebrilla C.B. Baumler A.J. Genetic ablation of butyrate utilization attenuated gastrointestinal Salmonella disease.Cell Host Microbe. 2018; 23 (this issue): 266-273Abstract Full Text Full Text PDF PubMed Google Scholar) and in a recent issue of Cell Reports (Hiyoshi et al., 2018Hiyoshi H. Wangdi T. Lock G. Saechao C. Raffatellu M. Cobb B.A. Baumler A.J. Mechanisms to evade the phagocytic respiratory burst arose by convergent evolution in typhoidal Salmonella serovars.Cell Rep. 2018; 22https://doi.org/10.1016/j.chom.2018.01.004Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar) demonstrate how loss-of-function mutations in butyrate utilization and lipopolysaccharide O-antigen processing contribute to evasion of innate host defenses and the convergent evolution of distinct typhoidal Salmonella lineages. Salmonella enterica subspecies I includes about 2,300 different serovars, representing more than 99% of all Salmonella infections in warm-blooded animals (Porwollik et al., 2004Porwollik S. Boyd E.F. Choy C. Cheng P. Florea L. Proctor E. McClelland M. Characterization of Salmonella enterica subspecies I genovars by use of microarrays.J. Bacteriol. 2004; 186: 5883-5898Crossref PubMed Scopus (187) Google Scholar). Medically relevant Salmonella can be categorized as either zoonotic nontyphoidal generalists, which are common causes of self-limiting gastroenteritis, or human-adapted typhoidal specialists, which are the etiology of a life-threatening systemic syndrome commonly known as enteric or typhoid fever. Within 24 hr of infection, nontyphoidal Salmonella elicit robust inflammatory responses that are dominated by the massive infiltration of neutrophils into the gastrointestinal mucosa. Conversely, typhoidal strains avoid early inflammation but elicit late fever, leukopenia, and monocytosis, causing about 200,000 casualties per year worldwide. Typhoid fever can be caused by either Typhi or Paratyphi A serovars that independently evolved in recent human history from nontyphoidal ancestral strains (McClelland et al., 2004McClelland M. Sanderson K.E. Clifton S.W. Latreille P. Porwollik S. Sabo A. Meyer R. Bieri T. Ozersky P. McLellan M. et al.Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid.Nat. Genet. 2004; 36: 1268-1274Crossref PubMed Scopus (306) Google Scholar). The evolution of Typhi and Paratyphi A has been marked by the horizontal acquisition of novel loci. For example, cytolethal distending toxin, a virulence factor that cleaves the DNA of host cell nuclei (Galán, 2016Galán J.E. Typhoid toxin provides a window into typhoid fever and the biology of Salmonella Typhi.Proc. Natl. Acad. Sci. USA. 2016; 113: 6338-6344Crossref PubMed Scopus (57) Google Scholar), is responsible for the leukopenia that affects approximately 20% of patients with typhoid fever. Typhi also carries the viaB locus encoding the Vi capsule, a major carbohydrate determinant that suppresses complement activation, provides serum resistance, and inhibits phagocytosis and the respiratory burst (Sabbagh et al., 2010Sabbagh S.C. Forest C.G. Lepage C. Leclerc J.M. Daigle F. So similar, yet so different: uncovering distinctive features in the genomes of Salmonella enterica serovars Typhimurium and Typhi.FEMS Microbiol. Lett. 2010; 305: 1-13Crossref PubMed Scopus (162) Google Scholar). The Vi capsule is nonetheless absent from human-specific Paratyphi A (McClelland et al., 2004McClelland M. Sanderson K.E. Clifton S.W. Latreille P. Porwollik S. Sabo A. Meyer R. Bieri T. Ozersky P. McLellan M. et al.Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid.Nat. Genet. 2004; 36: 1268-1274Crossref PubMed Scopus (306) Google Scholar), suggesting that this serovar must rely on so far unidentified virulence factors to elicit a syndrome that is clinically indistinguishable from that triggered by Typhi. As much as they have been sculpted by the horizontal acquisition of novel genes, Typhi and Paratyphi A genomes have also been chiseled by the gradual loss of genetic information (Sabbagh et al., 2010Sabbagh S.C. Forest C.G. Lepage C. Leclerc J.M. Daigle F. So similar, yet so different: uncovering distinctive features in the genomes of Salmonella enterica serovars Typhimurium and Typhi.FEMS Microbiol. Lett. 2010; 305: 1-13Crossref PubMed Scopus (162) Google Scholar). The genomes of Typhi and Paratyphi A harbor 210 and 173 pseudogenes, respectively, of which only 30 are common to both serovars (McClelland et al., 2004McClelland M. Sanderson K.E. Clifton S.W. Latreille P. Porwollik S. Sabo A. Meyer R. Bieri T. Ozersky P. McLellan M. et al.Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid.Nat. Genet. 2004; 36: 1268-1274Crossref PubMed Scopus (306) Google Scholar). Typhi and Paratyphi A have lost loci associated with colonization of the gut, elicitation of diarrhea, utilization of iron, and synthesis of cobalamin. Differences in the number and nature of the mutations giving rise to pseudogene formation suggest that Typhi and Paratyphi A arose independently during the natural history of typhoidal Salmonella. Despite the uniqueness of some of their pathoadaptive mutations, Typhi and Paratyphi A still trigger the same clinical syndrome, providing a clear example of convergent evolution. Recent papers published in Cell Host & Microbe (Bronner et al., 2018Bronner D.N. Faber F. Olsan E.E. Byndloss M.X. Sayed N.A. Xu G. Yoo W. Kim D. Ryu S. Lebrilla C.B. Baumler A.J. Genetic ablation of butyrate utilization attenuated gastrointestinal Salmonella disease.Cell Host Microbe. 2018; 23 (this issue): 266-273Abstract Full Text Full Text PDF PubMed Google Scholar) and Cell Reports (Hiyoshi et al., 2018Hiyoshi H. Wangdi T. Lock G. Saechao C. Raffatellu M. Cobb B.A. Baumler A.J. Mechanisms to evade the phagocytic respiratory burst arose by convergent evolution in typhoidal Salmonella serovars.Cell Rep. 2018; 22https://doi.org/10.1016/j.chom.2018.01.004Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar) have investigated how pseudogene formation contributes to the biology of Typhi and Paratyphi A. In the current issue of Cell Host & Microbe, Bronner et al., 2018Bronner D.N. Faber F. Olsan E.E. Byndloss M.X. Sayed N.A. Xu G. Yoo W. Kim D. Ryu S. Lebrilla C.B. Baumler A.J. Genetic ablation of butyrate utilization attenuated gastrointestinal Salmonella disease.Cell Host Microbe. 2018; 23 (this issue): 266-273Abstract Full Text Full Text PDF PubMed Google Scholar have evaluated the clinical importance of the ydiQRSTD locus, an operon that encodes a pathway for β-oxidation of butyrate (Campbell et al., 2003Campbell J.W. Morgan-Kiss R.M. Cronan Jr., J.E. A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic β-oxidation pathway.Mol. Microbiol. 2003; 47: 793-805Crossref PubMed Scopus (154) Google Scholar) and that is present in nontyphoidal Salmonella but absent in Typhi and Paratyphi A. A ΔydiD S. Typhimurium strain induced less colitis than wild-type controls as measured by reduced production of lipocalin-2, edema, epithelial erosion, and infiltration of inflammatory phagocytes into the gut mucosa (Figure 1). The differences in pathology between wild-type and ΔydiD S. Typhimurium disappeared in germ-free mice but were evident in gnotobiotic mice colonized with 17 human Clostridia isolates or germ-free mice fed a diet rich in butyrate. Collectively, these investigations suggest that utilization of Clostridia-derived butyrate promotes intestinal colonization by nontyphoidal Salmonella. The inability of Salmonella to utilize butyrate prevented Salmonella pathogenicity island-1 (SPI1) gene transcription by an as-of-yet unknown mechanism. Because the SPI1 type III secretion system stimulates electrolyte secretion and signals recruitment of polymorphonuclear cells into the mucosa, butyrate-dependent repression of SPI1 expression may be an important aspect contributing to the immunosuppressive nature of ydiQRSTD-deficient Salmonella serovars Typhi and Paratyphi A. Bronner et al., 2018Bronner D.N. Faber F. Olsan E.E. Byndloss M.X. Sayed N.A. Xu G. Yoo W. Kim D. Ryu S. Lebrilla C.B. Baumler A.J. Genetic ablation of butyrate utilization attenuated gastrointestinal Salmonella disease.Cell Host Microbe. 2018; 23 (this issue): 266-273Abstract Full Text Full Text PDF PubMed Google Scholar also noted that the intestinal mucosa of mice infected with a ΔydiD S. Typhimurium strain heterologously expressing the viaB-encoded capsule while simultaneously bearing a loss-of-function mutation in the fepE regulatory gene completely lacked any histopathological signs of inflammation. Previous work by Baumler’s lab had shown that the Vi capsule and a fepE mutation, whose product enables the formation of lipopolysaccharide very long O antigens, help Typhi evade antibody-mediated complement activation (Crawford et al., 2013Crawford R.W. Wangdi T. Spees A.M. Xavier M.N. Tsolis R.M. Bäumler A.J. Loss of very-long O-antigen chains optimizes capsule-mediated immune evasion by Salmonella enterica serovar Typhi.MBio. 2013; 4: 4Crossref Scopus (40) Google Scholar). The study by Bronner et al., 2018Bronner D.N. Faber F. Olsan E.E. Byndloss M.X. Sayed N.A. Xu G. Yoo W. Kim D. Ryu S. Lebrilla C.B. Baumler A.J. Genetic ablation of butyrate utilization attenuated gastrointestinal Salmonella disease.Cell Host Microbe. 2018; 23 (this issue): 266-273Abstract Full Text Full Text PDF PubMed Google Scholar adds significant insight into the evolution of Typhi and indicates that only three genetic changes (i.e., acquisition of the Vi capsule and two loss-of-function mutations) cooperate to suppress gastrointestinal inflammation during the early stages of Typhi infection (Figure 1). Paratyphi A and Typhi cause an indistinguishable clinical presentation in humans. However, these two serovars appear to achieve their goals by different means. Paratyphi A lacks the SPI-7-encoded immunosuppressive Vi capsular antigen that is used by Typhi to prevent antibody-mediated complement activation (Crawford et al., 2013Crawford R.W. Wangdi T. Spees A.M. Xavier M.N. Tsolis R.M. Bäumler A.J. Loss of very-long O-antigen chains optimizes capsule-mediated immune evasion by Salmonella enterica serovar Typhi.MBio. 2013; 4: 4Crossref Scopus (40) Google Scholar). A paper recently published in Cell Reports (Hiyoshi et al., 2018Hiyoshi H. Wangdi T. Lock G. Saechao C. Raffatellu M. Cobb B.A. Baumler A.J. Mechanisms to evade the phagocytic respiratory burst arose by convergent evolution in typhoidal Salmonella serovars.Cell Rep. 2018; 22https://doi.org/10.1016/j.chom.2018.01.004Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar) indicates that lipopolysaccharide very long O2 antigen of Paratyphi A assumes the immunosuppressive properties of Typhi’s Vi capsule (Figure 1). Hiyoshi et al., 2018Hiyoshi H. Wangdi T. Lock G. Saechao C. Raffatellu M. Cobb B.A. Baumler A.J. Mechanisms to evade the phagocytic respiratory burst arose by convergent evolution in typhoidal Salmonella serovars.Cell Rep. 2018; 22https://doi.org/10.1016/j.chom.2018.01.004Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar noted that both Typhi and Paratyphi A evade the respiratory burst engendered by the NADPH phagocyte oxidase of human neutrophils. A combination of the Vi capsule and a mutation in fepE, which prevents formation of very long O9 antigens, suppressed the activation of the respiratory burst. However, Paratyphi A not only lacks the Vi antigen, but also expresses a functional fepE gene, indicating that very long O antigens, per se, are not proinflammatory. As expected, Paratyphi A strains bearing mutations in fepE were devoid of very long O antigen. Surprisingly, ΔfepE Paratyphi A bound to natural IgM antibodies and activated a respiratory burst from human neutrophils. These findings suggest that, in analogy to Typhi’s Vi antigen, very long O2 antigen contributes to the immunosuppression associated with Paratyphi A infection. The locus responsible for the immunosuppressive characteristics of Paratyphi A’s very long O2 antigen mapped to a frameshift or premature codon in the rfbE gene encoding a CDP-tyvelose epimerase that typically converts CDP-paratose to CDP-tyvelose in group D Salmonella strains such as Typhi (Verma and Reeves, 1989Verma N. Reeves P. Identification and sequence of rfbS and rfbE, which determine antigenic specificity of group A and group D salmonellae.J. Bacteriol. 1989; 171: 5694-5701Crossref PubMed Scopus (79) Google Scholar). In support of this hypothesis, heterologous expression of a functional rfbE gene converted the O2 antigen of Paratyphi A into the O9 antigen of Typhi. Presence of tyvelose at the O antigen branching position in rfbE+ Paratyphi A stimulated binding to human IgM natural antibodies and elicited a productive respiratory burst from human polymorphonuclear phagocytes. Collectively, this work demonstrates that the two distinct lineages of human-adapted Typhi and Paratyphi A avoid recognition of opsonic natural antibodies via two distinct, but functionally analogous, strategies (Figure 1). The Vi capsule of viaB+ fepE− S. Typhi cloaks tyvelose moieties in short-length lipopolysaccharide O9 antigens from IgM recognition. Conversely, a nonopsonic paratose moiety at the branching sugar position of very long O2 antigen helps fepE+ rfbE− Paratyphi A duck immune recognition of surface antigens by human IgM antibodies. In evolutionary terms, only recently has typhoidal Salmonella become a human-adapted specialist (Achtman, 2008Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens.Annu. Rev. Microbiol. 2008; 62: 53-70Crossref PubMed Scopus (328) Google Scholar). Acquisition of a few pathogenicity islands, phages, and plasmids, together with the pathoadaptive advantages provided by a few pseudogenes, drove these genetically monomorphic human pathogens into systemic sites away from the crowded gastrointestinal lumen. The papers by Bronner et al., 2018Bronner D.N. Faber F. Olsan E.E. Byndloss M.X. Sayed N.A. Xu G. Yoo W. Kim D. Ryu S. Lebrilla C.B. Baumler A.J. Genetic ablation of butyrate utilization attenuated gastrointestinal Salmonella disease.Cell Host Microbe. 2018; 23 (this issue): 266-273Abstract Full Text Full Text PDF PubMed Google Scholar and Hiyoshi et al., 2018Hiyoshi H. Wangdi T. Lock G. Saechao C. Raffatellu M. Cobb B.A. Baumler A.J. Mechanisms to evade the phagocytic respiratory burst arose by convergent evolution in typhoidal Salmonella serovars.Cell Rep. 2018; 22https://doi.org/10.1016/j.chom.2018.01.004Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar provide mechanistic insights into how horizontal gene acquisition and the formation of a few pseudogenes shaped the convergent evolution of human-restricted Typhi and Paratyphi A, affording these strict human pathogens with the nocuous ability to evade the antimicrobial actions of the NADPH phagocyte oxidase. These studies were funded by VA Merit Grant BX0002073 and NIH R01 AI54959. The author thanks members of the Vázquez-Torres lab for discussions. Mechanisms to Evade the Phagocyte Respiratory Burst Arose by Convergent Evolution in Typhoidal Salmonella SerovarsHiyoshi et al.Cell ReportsFebruary 13, 2018In BriefThe clinical presentation of typhoid fever differs from gastroenteritis, which has been attributed to the Salmonella enterica serovar (S.) Typhi capsular polysaccharide. Paradoxically, S. Paratyphi A is not capsulated but causes typhoid-like disease. Hiyoshi et al. show that the very long O antigen of S. Paratyphi A functions as a capsule, an example of convergent evolution. Full-Text PDF Open AccessGenetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella DiseaseBronner et al.Cell Host & MicrobeFebruary 14, 2018In BriefBronner et al. show that genes enabling Salmonella enterica serovar (S.) Typhimurium to utilize microbiota-derived butyrate are deleted in the genome of the closely related S. Typhi, thereby moderating intestinal inflammation induced by the pathogen. Thus, gene loss can aid in the transition from gastrointestinal to extraintestinal pathogen. Full-Text PDF Open Archive