Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens (original) (raw)

• Doorduyn, Y., Van Den Brandhof, W. E., Van Duynhoven, Y. T., Wannet, W. J. & Van Pelt, W. Risk factors for Salmonella Enteritidis and Typhimurium (DT104 and non-DT104) infections in The Netherlands: predominant roles for raw eggs in Enteritidis and sandboxes in Typhimurium infections. Epidemiol. Infect. 134, 617–626 (2006)
  Article CAS Google Scholar
• Pavia, A. T. et al. Epidemiologic evidence that prior antimicrobial exposure decreases resistance to infection by antimicrobial-sensitive Salmonella. J. Infect. Dis. 161, 255–260 (1990)
  Article CAS Google Scholar
• Pépin, J. et al. Emergence of fluoroquinolones as the predominant risk factor for _Clostridium difficile_-associated diarrhea: a cohort study during an epidemic in Quebec. Clin. Infect. Dis. 41, 1254–1260 (2005)
  Article Google Scholar
• Kelly, C. P., Pothoulakis, C. & LaMont, J. T. Clostridium difficile colitis. N. Engl. J. Med. 330, 257–262 (1994)
  Article CAS Google Scholar
• Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A. & Gordon, J. I. Host-bacterial mutualism in the human intestine. Science 307, 1915–1920 (2005)
  Article ADS Google Scholar
• Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010)
  Article CAS Google Scholar
• Stecher, B. et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 6, e1000711 (2010)
  Article Google Scholar
• Chang, D. E. et al. Carbon nutrition of Escherichia coli in the mouse intestine. Proc. Natl Acad. Sci. USA 101, 7427–7432 (2004)
  Article CAS ADS Google Scholar
• Sonnenburg, J. L. et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955–1959 (2005)
  Article CAS ADS Google Scholar
• Martens, E. C., Chiang, H. C. & Gordon, J. I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4, 447–457 (2008)
  Article CAS Google Scholar
• Fabich, A. J. et al. Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect. Immun. 76, 1143–1152 (2008)
  Article CAS Google Scholar
• Kamada, N. et al. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336, 1325–1329 (2012)
  Article CAS ADS Google Scholar
• Pacheco, A. R. et al. Fucose sensing regulates bacterial intestinal colonization. Nature 492, 113–117 (2012)
  Article CAS ADS Google Scholar
• Maltby, R., Leatham-Jensen, M. P., Gibson, T., Cohen, P. S. & Conway, T. Nutritional basis for colonization resistance by human commensal Escherichia coli strains HS and Nissle 1917 against E. coli O157:H7 in the mouse intestine. PLoS ONE 8, e53957 (2013)
  Article CAS ADS Google Scholar
• Dethlefsen, L., Huse, S., Sogin, M. L. & Relman, D. A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6, e280 (2008)
  Article Google Scholar
• Hapfelmeier, S. & Hardt, W. D. A mouse model for S. _typhimurium_-induced enterocolitis. Trends Microbiol. 13, 497–503 (2005)
  Article CAS Google Scholar
• Lawley, T. D. et al. Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota. Infect. Immun. 76, 403–416 (2008)
  Article CAS Google Scholar
• Lawley, T. D. et al. Antibiotic treatment of Clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect. Immun. 77, 3661–3669 (2009)
  Article CAS Google Scholar
• Chen, X. et al. A mouse model of _Clostridium difficile_-associated disease. Gastroenterology 135, 1984–1992 (2008)
  Article Google Scholar
• Vimr, E. R., Kalivoda, K. A., Deszo, E. L. & Steenbergen, S. M. Diversity of microbial sialic acid metabolism. Microbiol. Mol. Biol. Rev. 68, 132–153 (2004)
  Article CAS Google Scholar
• Marcobal, A. et al. Consumption of human milk oligosaccharides by gut-related microbes. J. Agric. Food Chem. 58, 5334–5340 (2010)
  Article CAS Google Scholar
• Hoyer, L. L., Hamilton, A. C., Steenbergen, S. M. & Vimr, E. R. Cloning, sequencing and distribution of the Salmonella typhimurium LT2 sialidase gene, nanH, provides evidence for interspecies gene transfer. Mol. Microbiol. 6, 873–884 (1992)
  Article CAS Google Scholar
• Sebaihia, M. et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nature Genet. 38, 779–786 (2006)
  Article Google Scholar
• Stecher, B. et al. Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol. 5, e244 (2007)
  Article Google Scholar
• Winter, S. E. et al. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467, 426–429 (2010)
  Article CAS ADS Google Scholar
• Lupp, C. et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2, 119–129 (2007)
  Article CAS Google Scholar
• Barman, M. et al. Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract. Infect. Immun. 76, 907–915 (2008)
  Article CAS Google Scholar
• Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000)
  Article CAS ADS Google Scholar
• Vimr, E. R. & Troy, F. A. Identification of an inducible catabolic system for sialic acids (nan) in Escherichia coli. J. Bacteriol. 164, 845–853 (1985)
  CAS PubMed PubMed Central Google Scholar
• Heap, J. T. et al. The ClosTron: mutagenesis in Clostridium refined and streamlined. J. Microbiol. Methods 80, 49–55 (2010)
  Article CAS Google Scholar
• Adams, C. M. et al. Structural and functional studies of the CspB protease required for Clostridium spore germination. PLoS Pathog. 9, e1003165 (2013)
  Article CAS Google Scholar
• O’Connor, J. R. et al. Construction and analysis of chromosomal Clostridium difficile mutants. Mol. Microbiol. 61, 1335–1351 (2006)
  Article Google Scholar
• Sonnenburg, E. D. et al. Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 141, 1241–1252 (2010)
  Article CAS Google Scholar
• Stevens, J. R. et al. Statistical issues in the normalization of multi-species microarray data. Appl. Stat. Agric. Proc. Conf. Appl. Stat. Agric. Kansas State Univ. 47–62 (National Agricultural Library, 2008)
• Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001)
  Article CAS ADS Google Scholar
• Manzi, A. E., Diaz, S. & Varki, A. High-pressure liquid chromatography of sialic acids on a pellicular resin anion-exchange column with pulsed amperometric detection: a comparison with six other systems. Anal. Biochem. 188, 20–32 (1990)
  Article CAS Google Scholar
• Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012)
  Article CAS Google Scholar
• Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335–336 (2010)
  Article CAS Google Scholar
• Lozupone, C., Hamady, M. & Knight, R. UniFrac–an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7, 371 (2006)
  Article Google Scholar