-
- 2.
Lessa, F. C. et al. Burden of Clostridium difficile infection in the United States. N. Engl. J. Med. 372, 825–834 (2015).
- 3.
Surawicz, C. M. et al. Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections. Am. J. Gastroenterol. 108, 478–498 (2013).
- 4.
Pepin, J. et al. Increasing risk of relapse after treatment of Clostridium difficile colitis in Quebec, Canada. Clin. Infect. Dis. 40, 1591–1597 (2005).
- 5.
Vincent, Y., Manji, A., Gregory-Miller, K. & Lee, C. A review of management of Clostridium difficile Infection: primary and recurrence. Antibiotics 4, 411–423 (2015).
-
- 6.
Seekatz, A. M. & Young, V. B. Clostridium difficile and the microbiota. J. Clin. Invest. 124, 4182–4189 (2014).
- 7.
Kelly, C. R. et al. Update on fecal microbiota transplantation 2015: indications, methodologies, mechanisms, and outlook. Gastroenterology 149, 223–237 (2015).
- 8.
Lynch, S. V. & Pedersen, O. The human intestinal microbiome in health and disease. N. Engl. J. Med. 375, 2369–2379 (2016).
- 9.
Seekatz, A. M. et al. Recovery of the gut microbiome following fecal microbiota transplantation. MBio 5, e00893–00814 (2014).
- 10.
Seekatz, A. M., Rao, K., Santhosh, K. & Young, V. B. Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection. Genome Med. 8, 47 (2016).
- 11.
Seekatz, A. M. et al. Fecal microbiota transplantation eliminates Clostridium difficile in a murine model of relapsing disease. Infect. Immun. 83, 3838–3846 (2015).
- 12.
Zackular, J. P. et al. Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection. Nat. Med. 22, 1330–1334 (2016).
- 13.
Theriot, C. M. et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat. Commun. 5, 3114 (2014).
- 14.
Weingarden, A. R. et al. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am. J. Physiol. Gastrointest. Liver Physiol. 306, G310–G319 (2014).
- 15.
Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).
- 16.
Davis, M. Y., Zhang, H., Brannan, L. E., Carman, R. J. & Boone, J. H. Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk. Microbiome 4, 53 (2016).
- 17.
Schubert, A. M., Sinani, H. & Schloss, P. D. Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile. MBio 6, e00974 (2015).
- 18.
Ottesen, A. et al. Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak. BMC Microbiol. 16, 275 (2016).
- 19.
Daquigan, N., Grim, C. J., White, J. R., Hanes, D. E. & Jarvis, K. G. Early recovery of Salmonella from food using a 6-hour non-selective pre-enrichment and reformulation of tetrathionate broth. Front. Microbiol. 7, 2103 (2016).
- 20.
Grim, C. J. et al. High-resolution microbiome profiling for detection and tracking of Salmonella enterica. Front. Microbiol. 8, 1587 (2017).
- 21.
Khanna, S. et al. Gut microbiome predictors of treatment response and recurrence in primary Clostridium difficile infection. Aliment. Pharmacol. Ther. 44, 715–727 (2016).
- 22.
Cohen, S. H. et al. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA). Infect. Control Hosp. Epidemiol. 31, 431–455 (2010).
- 23.
Zhou, Y. et al. Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. PLoS One 10, e0118632 (2015).
- 24.
Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell. Host. Microbe 15, 382–392 (2014).
- 25.
Furuya-Kanamori, L. et al. Asymptomatic Clostridium difficile colonization: epidemiology and clinical implications. BMC Infect. Dis. 15, 516 (2015).
- 26.
McNamara, S. E. et al. Carriage of Clostridium difficile and other enteric pathogens among a 4-H avocational cohort. Zoonoses Public Health 58, 192–199 (2011).
- 27.
Miyajima, F. et al. Characterisation and carriage ratio of Clostridium difficile strains isolated from a community-dwelling elderly population in the United Kingdom. PLoS One 6, e22804 (2011).
- 28.
Ozaki, E. et al. Clostridium difficile colonization in healthy adults: transient colonization and correlation with enterococcal colonization. J. Med. Microbiol. 53, 167–172 (2004).
- 29.
Rousseau, C. et al. Clostridium difficile carriage in healthy infants in the community: a potential reservoir for pathogenic strains. Clin. Infect. Dis. 55, 1209–1215 (2012).
- 30.
Schutze, G. E. & Willoughby, R. E. Committee on infectious diseases and American academy of pediatrics. Clostridium difficile infection in infants and children. Pediatrics 131, 196–200 (2013).
- 31.
Kim, J. et al. Epidemiological features of Clostridium difficile-associated disease among inpatients at children’s hospitals in the United States, 2001–2006. Pediatrics 122, 1266–1270 (2008).
- 32.
Cerquetti, M., Luzzi, I., Caprioli, A., Sebastianelli, A. & Mastrantonio, P. Role of Clostridium difficile in childhood diarrhea. Pediatr. Infect. Dis. J. 14, 598–603 (1995).
- 33.
Stoesser, N. et al. Epidemiology of Clostridium difficile in infants in Oxfordshire, UK: Risk factors for colonization and carriage, and genetic overlap with regional C. difficile infection strains. PLoS One 12, e0182307 (2017).
- 34.
Chang, T. W., Sullivan, N. M. & Wilkins, T. D. Insusceptibility of fetal intestinal mucosa and fetal cells to Clostridium difficile toxins. Zhongguo Yao Li Xue Bao 7, 448–453 (1986).
- 35.
Eglow, R. et al. Diminished Clostridium difficile toxin A sensitivity in newborn rabbit ileum is associated with decreased toxin A receptor. J. Clin. Invest. 90, 822–829 (1992).
- 36.
Kuiper, G. A. et al. Clostridium difficile infections in young infants: case presentations and literature review. IDCases 10, 7–11 (2017).
- 37.
Nicholson, M. R., Thomsen, I. P. & Edwards, K. M. Controversies surrounding Clostridium difficile infection ininfants and young children. Children. 1, 40–47 (2014).
-
- 38.
El Feghaly, R. E., Stauber, J. L., Tarr, P. I. & Haslam, D. B. Intestinal inflammatory biomarkers and outcome in pediatric Clostridium difficile infections. J. Pediatr. 163, 1697–1704 (2013).
- 39.
Wilson, K. H. & Perini, F. Role of competition for nutrients in suppression of Clostridium difficile by the colonic microflora. Infect. Immun. 56, 2610–2614 (1988).
- 40.
Baumler, A. J. & Sperandio, V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature 535, 85–93 (2016).
- 41.
Greathouse, K. L., Harris, C. C. & Bultman, S. J. Dysfunctional families: Clostridium scindens and secondary bile acids inhibit the growth of Clostridium difficile. Cell. Metab. 21, 9–10 (2015).
- 42.
Ridlon, J. M., Alves, J. M., Hylemon, P. B. & Bajaj, J. S. Cirrhosis, bile acids and gut microbiota: unraveling a complex relationship. Gut Microbes 4, 382–387 (2013).
- 43.
Kakiyama, G. et al. Modulation of the fecal bile acid profile by gut microbiota in cirrhosis. J. Hepatol. 58, 949–955 (2013).
- 44.
Theriot, C. M., Bowman, A. A. & Young, V. B. Antibiotic-induced alterations of the gut microbiota alter secondary bile acid production and allow for Clostridium difficile spore germination and outgrowth in the large intestine. mSphere 1, e00045-15 (2016).
- 45.
Natarajan, M., Walk, S. T., Young, V. B. & Aronoff, D. M. A clinical and epidemiological review of non-toxigenic Clostridium difficile. Anaerobe 22, 1–5 (2013).
- 46.
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
- 47.
Chikhi, R. & Rizk, G. Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms Mol. Biol. 8, 22 (2013).
- 48.
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
- 49.
Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
- 50.
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335–336 (2010).
- 51.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).
- 52.
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
- 53.
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
- 54.
Abernethy, M. G. et al. Urinary microbiome and cytokine levels in women with interstitial cystitis. Obstet. Gynecol. 129, 500–506 (2017).
- 55.
Guerrero-Preston, R. et al. High-resolution microbiome profiling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation. Oncotarget. https://doi.org/10.18632/oncotarget.20677 (2017).