- Open Access
Microbiome mediation of infections in the cancer setting
Genome Medicinevolume 8, Article number: 40 (2016)
Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic barriers, and exposure to nosocomial (hospital-acquired) pathogens. Consequently, cancer-related infections are unique and epidemiologically distinct from those in other patient populations and may be particularly challenging for clinicians to treat. There is increasing evidence that the microbiome is a crucial factor in the cancer patient’s risk for infectious complications. Frequently encountered pathogens with observed ties to the microbiome include vancomycin-resistant Enterococcus, Enterobacteriaceae, and Clostridium difficile; these organisms can exist in the human body without disease under normal circumstances, but all can arise as infections when the microbiome is disrupted. In the cancer patient, such disruptions may result from interventions such as chemotherapy, broad-spectrum antibiotics, or anatomic alteration through surgery. In this review, we discuss evidence of the significant role of the microbiome in cancer-related infections; how a better understanding of the role of the microbiome can facilitate our understanding of these complications; and how this knowledge might be exploited to improve outcomes in cancer patients and reduce risk of infection.
Many patients with neoplastic disease are at increased risk for a variety of infections, either because of adverse effects from cancer treatment or because of the underlying cancer itself. The nature of these infections is frequently related to host insults such as immune suppression, anatomic defects, and epithelial barrier damage. Intensive treatments such as chemotherapy, radiation, and major surgery may each give rise to specific infectious risks. In response, broad-spectrum antimicrobials are commonly administered, which in turn have further shaped and altered the epidemiologic profile of cancer-related infections. As a result, management of infectious complications in patients with cancer is a unique and dynamic challenge for clinicians.
It is increasingly being recognized that the microbiome may be particularly relevant in many cancer-related infections. For example, infections in cancer patients more frequently involve or originate from the intestinal tract than those of non-cancer patients. Typical pathogens seen in cancer patients consist largely of microorganisms originating from the intestinal tract, such as Escherichia coli, Klebsiella spp., Enterococcus, viridans streptococci, and Candida albicans [1, 2]. This contrasts sharply with general hospitals, where Staphylococcus aureus is more typically the most common pathogen encountered, which preferably colonizes skin .
In this review, we examine the role of the microbiome in cancer-related infections. Many non-infectious ties have been made between cancer and the microbiome but will not be discussed here specifically, though some concepts may be overlapping. These include carcinogenesis [4–7], metabolism of immunosuppressants , and graft-versus-host disease in hematopoietic stem cell transplantation (HSCT) [9–11]. Here we focus on the microbiome’s relevance to cancer patients in terms of infectious complications and how the microbiome might be exploited to improve outcomes for these patients.
Significance of the gut microbiome in cancer and infectious implications of a disrupted microbiome
In the intestinal tract, significant disruption of microbial populations due to cancer treatment may explain why the microbiome may be central to understanding the development of infectious complications. One patient group in which the microbiome has been well studied is patients undergoing allogeneic HSCT (allo-HSCT), a cancer treatment that simultaneously exposes patients to cytotoxic chemotherapy, total body irradiation, immunosuppressants, and broad-spectrum antibiotics. Examination of the intestinal microbiome of such patients through serially collected stool specimens at one cancer center demonstrated significant changes in the microbial population, marked by an overall reduction of microbial diversity . Subsequent study of these patients showed that recipients with decreased gut microbial diversity soon after stem cell transplantation were, on average, more likely to die over the next 3 years than those with high gut microbial diversity, independent of other known mortality predictors in allo-HSCT, such as disease status, pre-transplant comorbidity, organ dysfunction, myeloablative intensity of treatment, and even antibiotic administration . More specifically, low gut microbial diversity was primarily associated with transplant-related deaths (death not related to relapse or recurrence of the malignancy), suggesting that the gut microbiome’s association with overall mortality is largely related to complications of transplantation, namely opportunistic infections and graft-versus-host disease, where lymphocytes derived from transplanted stem cells attack host recipient tissues.
Significant disruption of gut inhabitants may explain the observed importance of the microbiome in allo-HSCT. Under normal circumstances, a healthy intestinal microbiome is maintained and prevents infection by promoting colonization resistance, thus blocking overgrowth and expansion of rogue pathobionts, which typically exist as minority members in the microbiota (Fig. 1). This concept is not necessarily a new one and in fact was realized to have important implications for cancer treatment over four decades ago. The term colonization resistance was first used in 1971 by van der Waaij , who observed that intestinal flora containing anaerobic bacteria can resist colonization by E. coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa.
At the time, patients with leukemia and other malignancies were being treated with increasingly effective but intensive chemotherapeutic regimens. Patients were highly susceptible to infectious complications and prevention of these infections became an important focus. This led to the use of strict protective isolation of patients in sterile systems and routine decontamination of the gastrointestinal tract and skin. These programs attempted to keep patients under strict gnotobiotic conditions: sterile isolation rooms with laminar air flow units were used, all food and water were sterilized, and skin and gut decontamination was routinely performed using topical and non-absorbable antibiotics . Although there seemed to be some initial evidence of benefit, subsequent larger studies examining these measures failed to demonstrate sufficient benefit to warrant continuation of these massive efforts [16, 17], and these measures fell out of favor at most cancer institutions.
The concept of colonization resistance gave rise to the notion that infections related to cancer treatment could be better prevented by a more judicious, selective inhibition of microbes, rather than total decontamination. Attempts at prevention of infection turned to selective decontamination of the digestive tract, in which more targeted antibiotics were administered that could selectively remove potential aerobic pathogens yet retain colonization resistance against new pathogens. This approach made use of antibiotics that have little impact on anaerobic bacteria, such as nalidixic acid, trimethoprim-sulfamethoxazole, or polymyxin B . Later, fluoroquinolones such as ciprofloxacin and levofloxacin were also widely used for selective prevention of infection during cancer treatment . These prophylactic approaches provided more effective protection and continue to be practiced today.
More recent work suggests that promotion of colonization resistance occurs through a variety of mechanisms. These include direct inhibition of pathogens by beneficial microbes, through the production of bacteriocins, and indirect mechanisms involving the host, such as activation of immune defenses (for example, nucleotide-binding oligomerization domain-containing protein 2 (NOD2), which is involved in the immune response to bacterial infection) or enhancement of epithelium-derived antimicrobial peptides (for example, regenerating islet-derived III gamma (RegIIIγ)) . In cancer, damage is incurred to commensal bacteria, the immune system, and gut epithelium, which explains the observed loss of colonization resistance and subsequent enhanced susceptibility to infection in afflicted patients.
Chemotherapy and bloodstream infections due to mucosal barrier injury
Cytotoxic chemotherapy remains one of the mainstays of treatment for a variety of cancers and may be given either alone or as part of HSCT. As an adverse effect, it causes varying degrees of damage to hematopoietic cells, which commonly leads to neutropenia, which places the patient at risk for certain infections. Although various sources are possible, concurrent damage to the intestinal mucosa is the singular most common source of infection in neutropenic patients. Mucosal barrier injury by chemotherapy is the earliest and most frequently encountered breach in host defenses against pathogenic microorganisms.
Sonis  described the dynamics of mucosal barrier injury (also known as mucositis) as a sequential series of stages, involving free radical generation, induction of inflammation and apoptosis, signal amplification leading to more inflammation and apoptosis, discontinuity of the epithelial barrier leading to translocation of microorganisms, and subsequent spontaneous healing through cell proliferation. Translocation of intestinal microorganisms to the systemic circulation manifests as bloodstream infection, which can be life-threatening if sepsis ensues. Mucosal barrier injury and exposure to antimicrobial agents probably explains the emergence of most infections arising in neutropenic patients.
Despite the extensive damage to the gastrointestinal tract, symptoms are frequently not localized; fever may often be the only symptom manifested. In current clinical practice, fever in the setting of neutropenia is sufficient to warrant prompt initiation of empiric systemic antibiotics. Antibiotics are primarily selected to target potentially pathogenic bacteria and fungi that may reside in the gut. These include aerobic Gram-negative bacteria such as E. coli, K. pneumoniae, or P. aeruginosa, Gram-positive bacteria such as viridans streptococci and Enterococcus spp., and fungi such as Candida albicans. Although these oxygen-tolerant pathobionts are thought to originate from the intestinal tract, they exist in low relative abundance within the gut lumen under normal circumstances. Notably, obligate anaerobic bacteria, which are typically far more abundant in the large intestine and other parts of the intestinal tract, are rarely seen as bloodstream infections in this setting. Antibiotics with anti-anaerobic activity are therefore not required in the empiric treatment of fever and neutropenia, which is reflected in current clinical practice standards .
Systemic bloodstream infection due to mucosal barrier injury and subsequent bacterial translocation has been shown more recently to be closely related to dynamic changes in the intestinal microbiome. In one study of 94 patients undergoing allo-HSCT at a transplant center, serial fecal specimens showing loss of microbial diversity demonstrated a concurrent increased abundance and overgrowth of certain pathogenic bacteria . The most common bacteria observed were vancomycin-resistant Enterococcus (VRE), Enterobacteriaceae such as E. coli and Klebsiella spp., and viridans streptococci. Interestingly, these organisms were the most common bloodstream isolates recovered from patients undergoing allo-HSCT at this institution [22–24]. Expansion and domination of these pathogens in the gut was associated with subsequent systemic infection with the corresponding pathogen in blood; patients who developed VRE bloodstream infection had a preceding domination of the intestinal microbiome by VRE and patients who developed Gram-negative bloodstream infections had a preceding domination by proteobacteria (the phylum of bacteria containing many known aerobic Gram-negative pathogens).
This provided confirmation that bloodstream infections during neutropenia arise largely from a gut source and that translocation of bacteria is preceded by a transformative process in the gut microbiome, in which colonization resistance is promptly lost, leading to overgrowth by a single species (Fig. 1). This provides a potential explanation for why anaerobes are not commonly encountered in systemic infections, despite their overwhelming presence in the gut under normal circumstances. If bloodstream infections during fever and neutropenia occurred merely because of a cancer-treatment-related breach in the intestinal mucosa, one might have expected a greater predominance of anaerobic infections.
These microbial changes took place a median of 7 days before the onset of detectable bacteremia, raising the question of whether examination of the fecal microbiota could forewarn of impending systemic infection in these patients. Perhaps not surprisingly, administration of antibiotics, specifically those with anti-anaerobic activity, was correlated with subsequent expansion of pathogenic bacteria . Other factors, such as chemotherapy, may contribute to disruption of the microbiota, either by damaging host mechanisms that would normally help to maintain microbial populations and enhance colonization resistance or through direct killing of bacteria. Although currently not known, it may be the case that preservation or repair of a functionally intact microbiota may help to prevent the progression of mucosal barrier injury. Van Vliet and colleagues  proposed several mechanisms by which intestinal bacteria might serve to interfere with damage to intestinal tissues, building on the original Sonis  model of mucositis. These proposed mechanisms include: (1) modulation of inflammation and oxidative stress through a variety of mechanisms by beneficial members such as Bacteroides thetaiotaomicron, Clostridium cluster XIVa, and Faecalibacterium prausnitzii; (2) attenuation of intestinal permeability by members such as bifidobacteria and lactobacilli, which increase tight junction expression; (3) maintenance of the mucus layer, for example, by various Lactobacillus species, which upregulate mucin production; (4) stimulation of epithelial repair through butyrate and other factors generated by symbiotic bacteria; and (5) regulation of immune effector molecules such as RegIIIγ and IgA, which promote intestinal homeostasis and colonization resistance.
Clostridium difficile infection
C. difficile infection has perhaps one of the clearest ties to the microbiome, as it is known to result from disruption of normal intestinal bacteria following antibiotic administration and other perturbations of the gut flora. In certain cancer patient populations, rates of C. difficile infection are particularly high. This may be related to a combination of factors, including frequent use of broad-spectrum antibiotics, immune suppression, prolonged or frequent hospitalizations, and chemotherapy, which has been observed to cause C. difficile infection by itself [26, 27].
In patients undergoing treatment with HSCT, high rates of C. difficile infection have been observed, typically ranging from 12 to 30 % [28–32]. These rates far exceed those in the general patient population, where incidence is generally less than 1 % . This may be a reflection of the extreme degree of microbial dysbiosis experienced by these patients over the course of transplantation.
In one study of C. difficile infection in patients hospitalized to undergo HSCT, examination of fecal samples revealed that about 40 % of patients were asymptomatically colonized with toxigenic C. difficile at the start of transplant hospitalization . C. difficile infection occurred in this subset of pre-colonized patients, suggesting that the high rates of infection are not well explained by nosocomial (hospital-acquired) transmission.
A subsequent study of this cohort  compared microbiome profiles of patients who developed clinical infection with those of asymptomatic carriers without clinical infection, using a time series modeling approach. Results from this study showed protective effects from Clostridium scindens, a non-pathogenic intestinal species within the bacterial family Lachnospiraceae (Clostridium cluster XIVa). In the same study, colonization of mice with C. scindens conferred protection against C. difficile . It was further shown that the likely mechanism of protection occurs through production of secondary bile acids, which inhibit vegetative growth of C. difficile [36, 37]. Results from other microbiome studies have also provided evidence that Lachnospiraceae confers protective effects against C. difficile infection by promoting colonization resistance .
Bacteria from the Bacteroidetes phylum also appear to have durable protective effects against C. difficile infection; in patients with recurrent C. difficile infection who were cured using fecal microbiota transplantation (FMT), examination of the microbiota before and after FMT revealed that the most obvious microbial change was significant colonization with Bacteroidetes, where it had been previously completely lacking [39, 40]. Further evidence can indirectly be seen with fidaxomicin treatment, which was shown to be non-inferior to oral vancomycin for the treatment of C. difficile infection, but with fewer observed recurrences . This is hypothesized to be related to fidaxomicin’s narrower spectrum of activity; a previous study suggested that this drug spares Bacteroides spp. during treatment .
Given the high rates of C. difficile infection in at-risk populations such as HSCT patients, FMT and fidaxomicin treatment have both been raised as possible therapeutic strategies to prevent this complication during cancer treatment. Therapeutic clinical trials for both are ongoing [43, 44].
Other microbiota links to cancer-related infections
Infections outside the gut
The microbiome may influence risk for cancer-related infections at sites other than the intestinal tract. One recent study examining the impact of the gut microbiome on lung complications in recipients of allogeneic HSCT showed that disruption of the microbiota and overgrowth and domination by Gammaproteobacteria was associated with an increased risk of subsequent pulmonary complications . The reasons for this association are still unclear; these findings may be due to bacterial translocation to the lungs during early HSCT or increased inflammation signaled by an aberrant gut or lung microbiome.
Anatomic disruptions that affect microbiota compositions
In cancer, mechanical defects in intestinal anatomy are not uncommonly encountered. These may be caused by locally infiltrating cancer itself, radiation damage, or surgical interventions performed as part of cancer treatment. The impact of these anatomic derangements on the composition of the microbiota is unknown, but could have relevance to the overall outcome for these patients.
In patients with ileostomy or colostomy, the gut microbial composition has been studied and noted to be much more predominantly aerobic . In small bowel transplant patients, presence of a temporary ileostomy was associated with a more dramatic shift in microbiota than small bowel transplant itself . Beneficial anaerobes such as Bacteroides and Clostridia were largely missing in patients with ileostomy, and instead the gut microbiotas of these patients were dominated by facultative anaerobes . Presumably this is related to increased oxygen content in the bowel following ileostomy. In this study, metabolomic profiling further showed increased metabolites derived from the Krebs cycle. It is unclear what the implications of this compositional shift are; the authors noted cases of sepsis due to enteric pathogens in patients with ileostomy . If it is true that a colonic shift away from obligate anaerobic bacteria imparts increased risk of domination by potential pathogens and subsequent systemic infection in these patients, a re-evaluation of the indications for ileostomy might be considered.
Balancing of antibiotics in cancer
Over the course of cancer treatment, antibiotics are administered frequently. Given the increased susceptibility of cancer patients to infection, antibiotic treatments may entail prolonged courses or may involve agents with a broad spectrum of activity, given either as treatment or as prevention in a high-risk patient. The heavy use of antibiotics in cancer care is likely to make the microbiome particularly clinically relevant in these patients.
The gut microbiome works to prevent infection by contributing to colonization resistance against pathogens and by stimulating host immune responses to infection. Paradoxically, although antibiotics are given to combat infection, these treatments can serve to harm natural host defenses against infection by disrupting beneficial bacteria that previously supported these host defenses. Early microbiome studies of healthy volunteers have suggested that even short courses of antibiotics can have a substantial impact on the gut microbiome . With careful stewardship, however, antibiotics are still an essential part of patient care in current medicine.
Realizing that antibiotics remain a necessary evil, it is useful to note that antibiotics vary greatly in terms of their spectrum of activity not only against pathogens, but also against non-pathogenic beneficial microbes. For example, in recipients of allo-HSCT, metronidazole administration was associated with an increase in the abundance of intestinal VRE, which in turn preceded systemic infection with VRE in the setting of neutropenia and mucosal barrier injury . However, ciprofloxacin administration successfully prevented an increase in the number of pathogenic Gram-negative bacteria such as Enterobacteriaceae, without significant disruption of healthy anaerobes, such as Clostridia or Bacteroides, which contribute to colonization resistance and protection against increasing numbers of pathobionts [12, 49, 50].
In addition to the spectrum of activity, antibiotics may differ greatly in terms of impact on gut microbiota because of penetration and route of administration. For instance, vancomycin administered orally remains confined to the gut, with little to no systemic absorption, and it has been observed to have profound inhibitory impact on beneficial gut microbes, including Bacteroidetes and other anaerobic bacteria . In contrast, vancomycin given intravenously penetrates poorly into the gut lumen  and, therefore, has far less impact on the intestinal microbiota than when administered orally. Indeed, both microbiome studies and previous clinical studies have found no association between administration of intravenous vancomycin and colonization or infection with VRE, despite concerns to the contrary [12, 53, 54].
Based on these observations, each antibiotic’s spectrum of activity and pharmacologic distribution in the body clearly are important determinants of its impact on the microbiome. Given that antibiotics can range greatly from having profound deleterious effects on the microbiome to having little to no impact, antibiotics should be more clearly and precisely characterized as to their effect on the microbiota and clinicians should incorporate this knowledge into their therapeutic considerations.
Conclusions and future steps
These studies suggest that the microbiome is an essential mediator in various infections encountered in the cancer setting. A normally functioning microbiota establishes an intricate relationship with its host, creating stability and preventing infection by promoting colonization resistance; however, these microbial populations can be completely disrupted with cancer treatment, giving rise to susceptibility for infection by opportunistic pathobionts.
Microbiome studies of cancer patients will lead to a better understanding of the role of the microbiota in cancer-related infections and will provide insight into how therapeutic interventions might be designed to exploit the benefits of commensal and symbiotic bacteria. For example, further studies should be done to explore the use of ‘microbiota-sparing’ antibiotics, which can effectively prevent or treat infections that arise during cancer treatment but at the same time preserve beneficial microbes that enhance host defenses and promote colonization resistance against infection. In addition, repair of damaged microbial populations through interventions such as FMT or bacteriotherapy should also be further explored to improve defenses in cancer patients where treatment-related disruption of the microbiome may be unavoidable. These approaches have been proposed as interventions that could be performed safely and effectively [55, 56]. An enhanced understanding of the microbiome will allow us to improve our management of cancer-related infectious complications.
allogeneic hematopoietic stem cell transplantation
fecal microbiota transplantation
Velasco E, Byington R, Martins CAS, Schirmer M, Dias LMC, Gonçalves VMSC. Comparative study of clinical characteristics of neutropenic and non-neutropenic adult cancer patients with bloodstream infections. Eur J Clin Microbiol Infect Dis. 2006;25:1–7.
Koll BS, Brown AE. The changing epidemiology of infections at cancer hospitals. Clin Infect Dis. 1993;17:S322–8.
Wisplinghoff H, Bischoff T, Tallent SM, Seifert H, Wenzel RP, Edmond MB. Nosocomial bloodstream infections in US hospitals: analysis of 24,179 cases from a prospective nationwide surveillance study. Clin Infect Dis. 2004;39:309–17.
Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One. 2012;7:e39743.
Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2012;22:292–8.
Rakoff-Nahoum S, Medzhitov R. Toll-like receptors and cancer. Nat Rev Cancer. 2009;9:57–63.
Schwabe RF, Jobin C. The microbiome and cancer. Nat Rev Cancer. 2013;13:800–12.
Lee JR, Muthukumar T, Dadhania D, Taur Y, Jenq RR, Toussaint NC, et al. Gut microbiota and tacrolimus dosing in kidney transplantation. PLoS One. 2015;10:e0122399.
Jenq RR, Van den Brink MR. Allogeneic haematopoietic stem cell transplantation: individualized stem cell and immune therapy of cancer. Nat Rev Cancer. 2010;10:213–21.
Shono Y, Docampo MD, Peled JU, Perobelli SM, Jenq RR. Intestinal microbiota-related effects on graft-versus-host disease. Int J Hematol. 2015;101:428–37.
Jenq RR, Ubeda C, Taur Y, Menezes CC, Khanin R, Dudakov JA, et al. Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation. J Exp Med. 2012;209:903–11.
Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis. 2012;55:905–14.
Taur Y, Jenq RR, Perales M-A, Littmann ER, Morjaria S, Ling L, et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood. 2014;124:1174–82.
van der Waaij D, Berghuis-de Vries J, Lekkerkerk-Van der Wees J. Colonization resistance of the digestive tract in conventional and antibiotic-treated mice. J Hygiene. 1971;69:405–11.
Bodey GP. Fever and neutropenia: the early years. J Antimicrob Chemother. 2009;63:i3–13.
Bodey GP, Rodriguez V, Cabanillas F, Freireich EJ. Protected environment-prophylactic antibiotic program for malignant lymphoma. Randomized trial during chemotherapy to induce remission. Am J Med. 1979;66:74–81.
Dietrich M, Gaus W, Vossen J, Van der Waaij D, Wendt F. Protective isolation and antimicrobial decontamination in patients with high susceptibility to infection. Infection. 1977;5:107–14.
Bucaneve G, Micozzi A, Menichetti F, Martino P, Dionisi MS, Martinelli G, et al. Levofloxacin to prevent bacterial infection in patients with cancer and neutropenia. New Engl J Med. 2005;353:977–87.
Buffie CG, Pamer EG. Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol. 2013;13:790–801.
Sonis ST. The pathobiology of mucositis. Nat Rev Cancer. 2004;4:277–84.
Freifeld AG, Bow EJ, Sepkowitz KA, Boeckh MJ, Ito JI, Mullen CA, et al. Clinical practice guideline for the use of antimicrobial agents in neutropenic patients with cancer: 2010 update by the infectious diseases society of America. Clin Infect Dis. 2011;52:e56–93.
Kamboj M, Chung D, Seo SK, Pamer EG, Sepkowitz KA, Jakubowski AA, et al. The changing epidemiology of vancomycin-resistant Enterococcus (VRE) bacteremia in allogeneic hematopoietic stem cell transplant (HSCT) recipients. Biol Blood Marrow Transplant. 2010;16:1576–81.
Almyroudis N, Fuller A, Jakubowski A, Sepkowitz K, Jaffe D, Small T, et al. Pre-and post-engraftment bloodstream infection rates and associated mortality in allogeneic hematopoietic stem cell transplant recipients. Transplant Infect Dis. 2005;7:11–7.
Weinstock DM, Conlon M, Iovino C, Aubrey T, Gudiol C, Riedel E, et al. Colonization, bloodstream infection, and mortality caused by vancomycin-resistant enterococcus early after allogeneic hematopoietic stem cell transplant. Biol Blood Marrow Transplant. 2007;13:615–21.
Van Vliet MJ, Harmsen HJ, de Bont ES, Tissing WJ. The role of intestinal microbiota in the development and severity of chemotherapy-induced mucositis. PLoS Pathog. 2010;6:e1000879.
Anand A, Glatt AE. Clostridium difficile infection associated with antineoplastic chemotherapy: a review. Clin Infect Dis. 1993;17:109–13.
Cudmore MA, Silva J, Fekety R, Liepman MK, Kim K-H. Clostridium difficile colitis associated with cancer chemotherapy. Arch Intern Med. 1982;142:333–5.
Alonso CD, Treadway SB, Hanna DB, Huff CA, Neofytos D, Carroll KC, et al. Epidemiology and outcomes of Clostridium difficile infections in hematopoietic stem cell transplant recipients. Clin Infect Dis. 2012;54:1053–63.
Leung S, Metzger BS, Currie BP. Incidence of Clostridium difficile infection in patients with acute leukemia and lymphoma after allogeneic hematopoietic stem cell transplantation. Infect Control Hosp Epidemiol. 2010;31:313–5.
Chopra T, Chandrasekar P, Salimnia H, Heilbrun LK, Smith D, Alangaden GJ. Recent epidemiology of Clostridium difficile infection during hematopoietic stem cell transplantation. Clin Transplant. 2011;25:E82–7.
Chakrabarti S, Lees A, Jones S, Milligan D. Clostridium difficile infection in allogeneic stem cell transplant recipients is associated with severe graft-versus-host disease and non-relapse mortality. Bone Marrow Transplant. 2000;26:871–6.
Willems L, Porcher R, Lafaurie M, Casin I, Robin M, Xhaard A, et al. Clostridium difficile infection after allogeneic hematopoietic stem cell transplantation: incidence, risk factors, and outcome. Biol Blood Marrow Transplant. 2012;18:1295–301.
Lessa FC, Gould CV, McDonald LC. Current status of Clostridium difficile infection epidemiology. Clin Infect Dis. 2012;55:S65–70.
Kinnebrew MA, Lee YJ, Jenq RR, Lipuma L, Littmann ER, Gobourne A, et al. Early Clostridium difficile infection during allogeneic hematopoietic stem cell transplantation. PLoS One. 2014;9:e90158.
Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015;517:205–8.
Sorg JA, Sonenshein AL. Bile salts and glycine as cogerminants for Clostridium difficile spores. J Bacteriol. 2008;190:2505–12.
Sorg JA, Sonenshein AL. Chenodeoxycholate is an inhibitor of Clostridium difficile spore germination. J Bacteriol. 2009;191:1115–7.
Reeves AE, Koenigsknecht MJ, Bergin IL, Young VB. Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae. Infect Immun. 2012;80:3786–94.
Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol. 2010;44:354.
Bakken JS, Borody T, Brandt LJ, Brill JV, Demarco DC, Franzos MA, et al. Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol. 2011;9:1044–9.
Louie TJ, Miller MA, Mullane KM, Weiss K, Lentnek A, Golan Y, et al. Fidaxomicin versus vancomycin for Clostridium difficile infection. New Engl J Med. 2011;364:422–31.
Louie TJ, Emery J, Krulicki W, Byrne B, Mah M. OPT-80 eliminates Clostridium difficile and is sparing of bacteroides species during treatment of C. difficile infection. Antimicrob Agents Chemother. 2009;53:261–3.
Memorial Sloan Kettering Cancer Center. Autologous fecal microbiota transplantation (auto-fmt) for prophylaxis of clostridium difficile infection in recipients of allogeneic hematopoietic stem cell transplantation (2000). https://clinicaltrials.gov/ct2/show/NCT02269150.
Sharp M, Corp. D. Safety and efficacy of fidaxomicin versus placebo for prophylaxis against Clostridium Difficile-associated diarrhea in adults undergoing hematopoietic stem cell transplantation (DEFLECT-1) (2000). https://clinicaltrials.gov/ct2/show/NCT01691248.
Harris B, Morjaria SM, Littmann ER, Geyer AI, Stover DE, Barker JN, et al. Gut microbiota predict pulmonary infiltrates after allogeneic hematopoietic cell transplantation. Am J Respir Crit Care Med. 2016. doi: 10.1164/rccm.201507-1491OC.
Finegold SM, Sutter VL, Boyle JD, Shimada K. The normal flora of ileostomy and transverse colostomy effluents. J Infect Dis. 1970;122:376–81.
Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, et al. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci U S A. 2009;106:17187–92.
Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008;6:e280.
Holt H, Lewis D, White L, Bastable S, Reeves D. Effect of oral ciprofloxacin on the faecal flora of healthy volunteers. Eur J Clin Microbiol. 1986;5:201–5.
Donskey CJ, Helfand MS, Pultz NJ, Rice LB. Effect of parenteral fluoroquinolone administration on persistence of vancomycin-resistant Enterococcus faecium in the mouse gastrointestinal tract. Antimicrob Agents Chemother. 2004;48:326–8.
Lewis BB, Buffie CG, Carter R, Leiner I, Toussaint NC, Miller L, et al. Loss of microbiota-mediated colonization resistance to Clostridium difficile infection is greater following oral vancomycin as compared with metronidazole. J Infect Dis. 2015;jiv256.
Moellering RC. Pharmacokinetics of vancomycin. J Antimicrob Chemother. 1984;14:43–52.
Donskey CJ, Chowdhry TK, Hecker MT, Hoyen CK, Hanrahan JA, Hujer AM, et al. Effect of antibiotic therapy on the density of vancomycin-resistant enterococci in the stool of colonized patients. New Engl J Med. 2000;343:1925–32.
Pultz NJ, Stiefel U, Subramanyan S, Helfand MS, Donskey CJ. Mechanisms by which anaerobic microbiota inhibit the establishment in mice of intestinal colonization by vancomycin-resistant Enterococcus. J Infect Dis. 2005;191:949–56.
Van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368:407–15.
Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D, Daigneault MC, et al. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: “RePOOPulating” the gut. Microbiome. 2013;1:1–12.
The authors declare that they have no competing interests.
Both authors read and approved the final manuscript.
About this article
- Hematopoietic Stem Cell Transplantation
- Bloodstream Infection
- Allogeneic Hematopoietic Stem Cell Transplantation
- Fecal Microbiota Transplantation