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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Ann Epidemiol. Author manuscript; available in PMC 2017 May 1.
Published in final edited form as:
PMCID: PMC4892961

The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance

Melinda M. Pettigrew, PhD,1 J. Kristie Johnson, PhD, D(ABMM),2 and Anthony D. Harris, MD MPH2



Hospital-acquired infections (HAIs) are increasing in frequency due to multi-drug resistant organisms (MDROs) and the spread of MDROs has eroded our ability to treat infections. Healthcare professionals cannot rely solely on traditional infection control measures and antimicrobial stewardship to prevent MDRO transmission. We review research on the microbiota as a target for infection control interventions.


We performed a literature review of key research findings related to the microbiota as a target for infection control interventions. These data are summarized and used to outline challenges, opportunities, and unanswered questions in the field.


The healthy microbiota provides protective functions including colonization resistance, which refers to the microbiota's ability to prevent colonization and/or expansion of pathogens. Antibiotic use and other exposures in hospitalized patients are associated with disruptions of the microbiota that may reduce colonization resistance and select for antibiotic resistance. Novel methods to exploit protective mechanisms provided by an intact microbiota may provide the key to preventing the spread of MDROs in the healthcare setting.


Research on the microbiota as a target for infection control has been limited. Epidemiologic studies will facilitate progress towards the goal of manipulating the microbiota for control of MDROs in the healthcare setting.

Keywords: Microbiota, hospital-acquired infection, antibiotic resistance, infection control, antimicrobial stewardship, Clostridium difficile, vancomycin resistant enterococcus


Hospital-acquired infections (HAIs) cause approximately 100,000 deaths per year in the US and the five most common HAIs cost the US healthcare system $9.8 billion annually [1,2]. Approximately 20% of HAIs are due to multi-drug resistant organisms (MDROs) [3]. Colonization of the gastrointestinal tract or other body sites by MDROs is often a first step in the establishment of infection [4]; of patients colonized with MDROs in the intensive care unit (ICU), approximately 20% will develop clinical infection with the same MDRO during their ICU stay [5-7]. Importantly, colonized patients also serve as a reservoir for transmission to others. MDRO's colonize the gastrointestinal tract, respiratory tract, and skin within the context of the microbiota, which is the community of microorganisms that inhabits our bodies. In healthy individuals, the microbiota provides protective functions including prevention of colonization by pathogens and/or expansion of low-density pathogens, (i.e., colonization resistance). Antibiotics and other hospital-associated exposures (e.g., dietary changes) alter the composition, diversity, and density of the microbiota and select for antibiotic resistance [8-10]. Hospitalization-related disruptions of the microbiota may reduce colonization resistance and increase risk for acquisition and expansion of MDRO. Thus, the microbiota may provide a critical target for prevention strategies to limit colonization and spread of MDROs in the healthcare setting.

Research on the potential of the microbiota as a target for infection control has been limited to mechanistic studies in murine models and clinical studies with small numbers of patients and/or highly restricted patient populations. Epidemiologic studies will inform the development of novel interventions to exploit the protective mechanisms provided by an intact microbiota. The goals of this review are to describe limitations of traditional infection control interventions, to summarize key research findings related to the microbiota as a target for infection control interventions, and to outline challenges, opportunities, and unanswered questions in the field.

Limitations of traditional measures to prevent HAIs with MDROs

Traditional infection control measures include barrier precautions, hand hygiene, decolonization of patients and environmental decontamination [11], and can reduce the incidence of HAI [12-14]. However, various infection control interventions have produced inconsistent results and it is clear that infection control measures alone cannot prevent the spread of MDRO since MDRO rates continue to increase [13, 15, 16]. Antimicrobial stewardship programs are also critical for achieving reductions in the prevalence and spread of MDROs. The successes that are achieved by antimicrobial stewardship programs may be difficult to sustain because increases in the prevalence of MDRO's often lead to increases in empiric prescribing of broad-spectrum antibiotics, which then leads to a cycle of increased antibiotic use and increased resistance [17, 18]. Controlling the spread of MDROs in the healthcare setting will require novel and multifaceted approaches above and beyond the current infection control and antimicrobial stewardship interventions.

Role of the microbiota in preventing acquisition and/or expansion of potential HAI-associated pathogens

In healthy individuals, the gastrointestinal microbiota provides several important immunologic, metabolic, and protective functions including colonization resistance [19, 20]. Colonization resistance was first described in a series of seminal papers dating back to the 1970s [21, 22]. These studies examined the impact of antibiotics on the gastrointestinal flora and showed that 1) a lower infectious dose of pathogens (e.g., Escherichia coli, Pseudomonas aeruginosa) was needed to establish colonization in mice who had received antibiotics, 2) antibiotic treatment resulted in overgrowth/expansion of exogenous pathogens, and 3) the extent of colonization resistance differed by the antibiotic used [21, 22]. Colonization resistance was attributed to anaerobic bacteria that were abolished by antimicrobial treatment [21]. Colonization resistance may be preserved in the presence of some antibiotics, for example, β-lactamase producing anaerobes help preserve colonization resistance in the gut by inactivating β-lactam antibiotics [23, 24]. Murine studies also indicate that in addition to colonization resistance, an intact microbiota can mediate clearance of gastrointestinal pathogens once infection has been established [25].

Mechanisms that mediate colonization resistance include competition for nutrients and adherence sites, direct inhibition of pathogens via substances excreted by members of the microbiota, and innate and adaptive immune responses induced by commensals [26, 27]. Antibiotic induced changes in the composition and diversity of the gastrointestinal microbiome may also lead to the disruption of carbohydrate and bile metabolism and the loss of anaerobes that produce short chain fatty acids [28, 29]. Short chain fatty acids help regulate regulatory T cells and promote homeostasis within the gastrointestinal tract and may play a critical role in colonization resistance [30] although some studies were unable to correlate short chain fatty acid production with lower levels of pathogen colonization [31, 32].

Impact of antibiotics on the microbiota

Antibiotics have a profound impact on the gastrointestinal and upper respiratory tract microbiota. Specific antibiotics favor survival of non-pathogenic and pathogenic species within the microbiota if they are resistant to the prescribed antibiotic. Antibiotics can alter bacterial loads, relative abundance of commensals, and lead to lower levels of diversity in the microbiota [8, 9, 33]. Dethlefsen et al. studied three healthy volunteers receiving two courses of ciprofloxacin separated by six months and followed them for over ten months [33]. They observed a rapid loss of diversity within 3-4 days of ciprofloxacin exposure. Rebounds in bacterial diversity were observed after approximately one week but the microbiota did not return to its original composition. Other authors have shown that the impact of antibiotics can persist for years after the original treatment [9].

Antibiotics exert a powerful selective pressure on the microbiota that extends beyond altering the prevalence of specific taxa. The microbiota provides a reservoir of resistance genes, termed the antibiotic resistome, which can be horizontally transferred within and across species and lead to the emergence of antibiotic resistance in pathogens [34, 35]. Sommer et al. characterized the reservoir of antibiotic resistance genes in the oral and gut microbiota in two healthy individuals who had no previous antibiotic exposure in the prior year [36]. Of concern, close to half of the resistance genes from 572 cultured gastrointestinal bacteria strains were identical at the nucleotide level to antibiotic resistance genes previously identified in human pathogens. Hu et al. examined the gut microbiota of 162 individuals from Spain, China, and the Netherlands and identified a total of 1,093 antibiotic resistance genes [37]. The high level of diverse antibiotic resistance determinants represents a substantial reservoir of genes that could potentially be transferred to, and emerge in, human pathogens. The antibiotic resistome also contains cryptic resistance genes that may evolve into resistance genes under appropriate conditions [34]. Some genes within the antibiotic resistome may have sequence matches to known resistance genes but may not be functional [38]. Moreover, there may be barriers to gene exchange with human pathogens in the case of certain resistance genes. Epidemiologic studies, including randomized controlled trials, can address questions regarding the differential impact of different classes of antibiotics on the antibiotic resistome and track how resistance determinants spread in the healthcare setting.

Factors affecting the microbiota and risk of colonization and disease in hospitalized patients

To this point, studies of the impact of antibiotics on the microbiota have most often focused on healthy individuals [9, 33]. Exposures are quite different in hospitalized patients. In addition to receiving multiple courses of antibiotics, hospitalized patients are exposed to other factors such as stress, intravenous nutrition, and other medications, which all may impact the microbiota. Zaborin et al. examined fecal samples from 14 ICU patients and five healthy controls [39]. The flora of healthy volunteers contained approximately 40 genera and high relative abundances of Firmicutes and Bacteroidetes. In contrast, 36% of the ICU patients had extremely low levels of diversity, defined as having >90% abundance of one bacterial taxon. These patients also experienced rapid fluctuations in the flora and replacement of one dominant taxon by another. The microbiota of hospitalized patients was dominated by Enterococcus, Staphylococcus and Enterobacteriacea, phylogenetic groups that include potential HAI-associated pathogens and MDROs [39]. These data provide important insights into the potential differences in the microbiota between healthy individuals and hospitalized patients. However, the study contained a small number of subjects presenting with a diverse range of medical conditions and length of hospital stay. Individuals respond differently to antibiotic treatment [9, 33]. Factors such as age, presence of comorbid conditions, types of medical interventions, and length of stay can also impact the risk of MDRO acquisition [3, 40-43]. Thus, it is reasonable to assume that patient demographics and clinical characteristics will have differing impacts on the microbiota.

Taur and colleagues characterized the fecal microbiota of 94 patients undergoing allogenic hematopoietic stem cell transplant using 16S rRNA gene sequencing [44]. The authors evaluated temporal trends in microbiota diversity and intestinal domination by a particular taxon to determine whether the composition of the microbiota was related to clinical outcomes. A given taxon was considered dominant if they were the most abundant taxon and comprised ≥ 30% of the sequence reads. Enterococcus was the most frequent dominating taxon followed by Streptococcus and Proteobacteria in 40.4%, 37.2%, and 12.8% of patients, respectively. Intestinal domination by members of the genus Enterococcus was associated with an increased risk of vancomycin-resistant Enterococcus (VRE) bacteremia (Hazard Ratio (HR) 9.35, 95% confidence interval (CI)= 2.43-45.44) and Proteobacteria domination was associated with an increased risk of gram-negative bacteremia (HR 5.46, 95% CI=1.03-19.91) [44]. This important study lends credence to the idea that microbiota related methods to prevent initial colonization and expansion by VRE would provide an additional tool to prevent HAI due to VRE.

The aforementioned studies by Zaborin et al. [39] and Taur et al. [44] greatly advance our understanding of the impact of hospitalization on the microbiota. The stem cell transplant patients studied by Taur et al. are a very special patient population that undergoes chemotherapy, radiation, and high levels of antibiotic use. The study by Zaborin et al., while based on a limited number of patients, suggests that extreme shifts in the flora may also be observed in ICU patients with other underlying medical conditions. In order to accurately understand how hospital associated risk factors impact on the microbiota, future studies must include sufficient sample sizes, detailed patient demographic and clinical data, and appropriate comparison groups.

Potential reduction of risk of HAI associated with reconstituted/transplanted microbiota

The potential translational value of microbiome studies is exemplified by the use of fecal microbiota transplants (FMT) to treat Clostridium difficile infections, and several studies of the microbiota and HAI have focused on this pathogen. C. difficile is an anaerobic spore-forming bacterium that is the leading cause of hospital-acquired diarrhea in the United States [45]. In 2011, C. difficile was associated with an estimated 453,000 infections [46]. Of these, 293,300 (65.8%) were associated with healthcare and 104,400 (24.2%) had an onset in the hospital. A randomized controlled trial showed that 94% of patients who received FMT resolved infection without relapse compared to 31% who received vancomycin alone (P<0.001) [47].

A mathematical model was developed to evaluate the impact of FMT on transmission of C. difficile in the ICU [48]. Lofgren et al. modeled a series of scenarios including widespread use of FMT after C. difficile and prophylactic use of FMT in high-risk patients (e.g., patients who received antibiotics) to prevent incident C. difficile infections. FMT after C. difficile was not associated with a reduction in incident HAIs. Prophylactically treating patients had a statistically significant but minimal impact on incident infections. The model necessarily used simplifying assumptions that may not be correct [49]. However, this model provides a framework for analyzing microbiota-based interventions for control of HAIs.

Critical protective taxa in the gastrointestinal microbiota

Concerns regarding the unpleasant nature of FMT and risks of pathogen transfer, which are especially acute in immune compromised patients, have led researchers to focus on identification of mechanisms and key species to prevent acquisition and infection with C. difficile. Successful treatment of C. difficile infection by FMT is associated with shifts in the microbiota from a low-diversity diseased state characterized by high abundance of Proteobacteria and Bacilli, to a more diverse microbial community with higher levels of Bacteroidetes and Clostridium [50, 51]. A study of 338 individuals examined the microbiota in hospitalized patients with and without C. difficile associated diarrhea and healthy controls [52]. Low abundance or absence of Bacteroides, Porphyromonadaceae, Lachnospiraceae, and Ruminococcaceae was associated with C. difficile diarrhea. Buffie et al. used a combination of human, murine and mathematical modeling studies to identify individual taxa associated with protection from C.difficile infection and the mechanisms involved [53]. These investigators compared the microbiota in mice and hospitalized patients and identified four bacteria species, Clostridium scindens, Barnesiella intestihominis, Pseudoflavonifractor capillosus and Blautia hansenii, that were potentially protective for C. difficile infection. Adoptive fecal transfer experiments in mice showed that C. scindens alone and a cocktail of the four bacterial species inhibited growth of C. difficile and toxin production. C. scindens is a 7 α-dehydroxylating intestinal bacterium that can convert stimulatory combinations of bile acids into inhibitory combinations of bile acids. Specific bile acids in the gut promote spore germination, and secondary bile acids inhibit the growth of vegetative C. difficile [54]. The adoptive fecal transfer results need to be confirmed in humans but are an important step in identifying multi-species probiotics that could be used to treat infections.

The microbiota may provide an optimal target for control of other MDROs that are common causes of HAI. Research has also focused on identifying taxa associated with colonization and expansion of VRE. Murine studies have correlated VRE clearance with intestinal recolonization by bacteria of the genus Barnesiella [55]. Barnesiella was also associated with lower levels of VRE in allogenic hematopoietic stem cell transplant patients; patients with VRE domination had significantly lower levels of Barnesiella compared to patients without VRE domination [55].

Stiefel et al. developed a potential strategy to prevent colonization and expansion by VRE and C. difficile [56]. Mice were colonized with a cephalosporinase-producing strain of Bacteroides thetaiotaomicron, which prevented overgrowth of VRE and C. difficile in the presence of systemic therapy with ceftriaxone [56]. While these data are promising, the investigators had to pretreat mice with piperacillin-tazobactam to create a favorable environment for B. thetaiotaomicron to establish colonization. It is not clear that single species transfers, with bacteria such as B. thetaiotaomicron, would effectively establish in the human gastrointestinal tract. Moreover, such a strategy would only work for patients receiving β-lactam therapy and raises ethical concerns regarding introduction of a bacteria species that carries a horizontally transmissible resistance determinant.

The microbiota and prevention of acquisition and spread of MDROs at non-gastrointestinal sites

Many microbiome-related studies focus on the gastrointestinal tract although pneumonia is the most common HAI, representing approximately 20% of all infections [43]. The microbiota differs across body sites and data from one anatomic site likely cannot be generalized to another site [57]. Several hundred bacterial taxa colonize the upper respiratory tract [58, 59]. The upper and lower respiratory tracts are a complex and connected ecosystem and there is growing recognition that pneumonia may occur as a consequence of disruptions in homeostasis in the respiratory tract microbiota [19, 60, 61]. A few culture-independent studies have examined the respiratory tract microbiota in hospitalized patients [62-65]. Reductions in microbial diversity have been associated with P. aeruginosa colonization in cystic fibrosis patients, which indicates that the respiratory tract flora also plays a role in mediating colonization resistance [66]. In contrast, murine studies indicate that a normal, healthy nasal microbiota does not prevent colonization by Klebsiella pneumoniae while a normal, healthy gastrointestinal microbiota does [67]. Bousbia et al. described the microbiota in bronchoalveolar lavage samples from pneumonia patients in the ICU and controls. The microbiota was unexpectedly complex; the investigators identified 160 different bacteria species and up to 16 different microorganisms in a single sample. Pathogens such as P. aeruginosa and Streptococcus species were commonly detected in both patients and controls [67]. Further studies, especially longitudinal studies, are required to evaluate the role of the respiratory microbiota in facilitating colonization resistance and to determine causality. These data could then be used to design interventions to prevent HAIs in the respiratory tract and other non-gastrointestinal sites.

Challenges, opportunities, and unanswered questions

With recent technologic advances, the ability to characterize the microbiota has increased dramatically. Model animal systems have provided great insights and the influence of genetics and environmental factors can be studied under controlled conditions [27, 68, 69]. However, the microbiota and immune systems of mice and humans differ, and although murine models can show proof of concept, they are not a substitute for epidemiologic human studies [53, 70, 71].

The composition, diversity and taxonomy of the microbiota varies greatly between individuals [57]. The diversity and composition of microbiota samples can represent the normal variation between people or temporal fluctuations that are independent of the disease state [72, 73]. Adequately powered longitudinal studies are needed to capture the transition from homeostatic to dysbiotic states [73-75]. Such studies may require complex study designs and large datasets. Analyses of the microbiota can be added to ongoing epidemiologic studies and may be feasible as sample processing and high-throughput sequencing costs go down. However, researchers are increasingly recognizing the potential for contamination with environmental bacterial DNA despite the use of molecular biology grade water and commercial kits [76]. The problem is especially acute when low biomass samples are examined using platforms with high depth of coverage [76, 77]. Recommendations to mitigate contamination include collecting and sequencing controls from each batch of storage medium, DNA extraction, and PCR kits along with the study samples. The need to sequence reagent controls may present challenges when pre-existing collections are used for microbiota and metagenomic analyses in epidemiologic studies.

Several important questions can be addressed by epidemiologic studies and include: What are the key protective taxa that facilitate colonization resistance for a given MDRO? How do antibiotic-induced changes in microbiota facilitate or prevent acquisition of potential pathogens? Which antibiotics have the greatest negative impact on the microbiota? Which bacterial taxa and antibiotic resistance genes represent the greatest threat? What are the clinically relevant genes within the antibiotic resistome? What other factors (e.g., stress, steroids, opiates) negatively impact the microbiota?

An improved understanding of the role of the microbiota in preventing or facilitating the spread of MDROs in the healthcare setting may well yield novel approaches towards prevention of HAIs. For example, strategies for selectively introducing commensals (e.g., probiotics) to promote optimal levels of biodiversity in the gastrointestinal tract and other sites may emerge as effective methods for preventing HAIs. Trials of the effectiveness of probiotics for infection control have produced mixed results [78, 79]. Probiotics are highly strain and species specific, and effective probiotics for prevention of HAI would likely have to contain mixtures of multiple species or be targeted towards specific pathogens. Auto-banking of microbiota samples and FMT may also provide viable options for restoration of a healthy microbiota [80]. Greater understanding of colonization resistance and the taxa that play critical roles within the healthy microbiota is needed. Epidemiologists can and should play an important role in creating well designed and adequately powered epidemiologic studies to reach the translational goal of manipulating the microbiota for controlling the spread of MDRO in the healthcare setting. Epidemiologist can also play an important role in translating findings into clinical interventions. Over the long term, such studies will allow investigators to develop preventive measures in the areas of infection control, antibiotic stewardship, and probiotics.


The authors gratefully acknowledge Janneane Gent for critical review of the manuscript. This research was supported by NIH5K24AI079040-07 to A.D.H.


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1. Zimlichman E, Henderson D, Tamir O, Franz C, Song P, Yamin CK, et al. Health care-associated infections: a meta-analysis of costs and financial impact on the US health care system. JAMA Intern Med. 2013;173(22):2039–46. [PubMed]
2. Zaph C. Which species are in your feces? J Clin Investig. 2010;120(12):4182–5. [PMC free article] [PubMed]
3. Sievert DM, Ricks P, Edwards JR, Schneider A, Patel J, Srinivasan A, et al. Antimicrobial-resistant pathogens associated with healthcare-associated infections: summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2009-2010. Infect Control Hosp Epidemiol. 2013;34(1):1–14. [PubMed]
4. Johnson JK, Smith G, Lee MS, Venezia RA, Stine OC, Nataro JP, et al. The role of patient-to-patient transmission in the acquisition of imipenem-resistant Pseudomonas aeruginosa colonization in the intensive care unit. J Infect Dis. 2009;200(6):900–5. [PMC free article] [PubMed]
5. Harris AD, Furuno JP, Roghmann MC, Johnson JK, Conway LJ, Venezia RA, et al. Targeted surveillance of methicillin-resistant Staphylococcus aureus and its potential use to guide empiric antibiotic therapy. Antimicrob Agents Chemother. 2010;54(8):3143–8. [PMC free article] [PubMed]
6. Thom KA, Hsiao WW, Harris AD, Stine OC, Rasko DA, Johnson JK. Patients with Acinetobacter baumannii bloodstream infections are colonized in the gastrointestinal tract with identical strains. Am J Infect Control. 2010;38(9):751–3. [PMC free article] [PubMed]
7. Thom KA, Johnson JA, Strauss SM, Furuno JP, Perencevich EN, Harris AD. Increasing prevalence of gastrointestinal colonization with ceftazidime-resistant gram-negative bacteria among intensive care unit patients. Infect Control Hosp Epidemiol. 2007;28(11):1240–6. [PubMed]
8. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. Plos Biol. 2007;5(7):e177. [PubMed]
9. Jakobsson HE, Jernberg C, Andersson AF, Sjolund-Karlsson M, Jansson JK, Engstrand L. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS ONE. 2010;5(3):e9836. [PMC free article] [PubMed]
10. 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(26):1925–32. [PMC free article] [PubMed]
11. Yokoe DS, Anderson DJ, Berenholtz SM, Calfee DP, Dubberke ER, Ellingson KD, et al. A compendium of strategies to prevent healthcare-associated infections in acute care hospitals: 2014 updates. Infect Control Hosp Epidemiol. 2014;35(8):967–77. [PMC free article] [PubMed]
12. Harris AD, Pineles L, Belton B, Johnson JK, Shardell M, Loeb M, et al. Universal glove and gown use and acquisition of antibiotic-resistant bacteria in the ICU: a randomized trial. JAMA. 2013;310(15):1571–80. [PMC free article] [PubMed]
13. Gurieva T, Bootsma MC, Bonten MJ. Successful Veterans Affairs initiative to prevent methicillin-resistant Staphylococcus aureus infections revisited. Clin Infect Dis. 2012;54(11):1618–20. [PubMed]
14. Huang SS, Septimus E, Kleinman K, Moody J, Hickok J, Avery TR, et al. Targeted versus universal decolonization to prevent ICU infection. New Engl J Med. 2013;368(24):2255–65. [PubMed]
15. Huskins WC, Huckabee CM, O'Grady NP, Murray P, Kopetskie H, Zimmer L, et al. Intervention to reduce transmission of resistant bacteria in intensive care. New Engl J Med. 2011;364(15):1407–18. [PMC free article] [PubMed]
16. Jain R, Kralovic SM, Evans ME, Ambrose M, Simbartl LA, Obrosky DS, et al. Veterans Affairs initiative to prevent methicillin-resistant Staphylococcus aureus infections. New Engl J Med. 2011;364(15):1419–30. [PubMed]
17. Charani E, Cooke J, Holmes A. Antibiotic stewardship programmes--what's missing? Antimicrob Chemother. 2010;65(11):2275–7. [PubMed]
18. MacDougall C, Polk RE. Antimicrobial stewardship programs in health care systems. Clin Microbiol Rev. 2005;18(4):638–56. [PMC free article] [PubMed]
19. Gao Z, Kang Y, Yu J, Ren L. Human pharyngeal microbiome may play a protective role in respiratory tract infections. Genomics Proteomics & Bioinformatics. 2014;12(3):144–50. [PMC free article] [PubMed]
20. Yurist-Doutsch S, Arrieta MC, Vogt SL, Finlay BB. Gastrointestinal microbiota-mediated control of enteric pathogens. Annual Rev Genet. 48:361–82. [PubMed]
21. van der Waaij D, Berghuis-de Vries JM, Lekkerkerk L-V. Colonization resistance of the digestive tract in conventional and antibiotic-treated mice. J Hyg. 1971;69(3):405–11. [PMC free article] [PubMed]
22. Thijm HA, van der Waaij D. The effect of three frequently applied antibiotics on the colonization resistance of the digestive tract of mice. J Hyg. 1979;82(3):397–405. [PMC free article] [PubMed]
23. Stiefel U, Nerandzic MM, Koski P, Donskey CJ. Orally administered β-lactamase enzymes represent a novel strategy to prevent colonization by Clostridium difficile. J Antimicrob Chemother. 2008;62(5):1105–8. [PubMed]
24. Stiefel U, Pultz NJ, Harmoinen J, Koski P, Lindevall K, Helfand MS, et al. Oral administration of β-lactamase preserves colonization resistance of piperacillin-treated mice. J Infect Dis. 2003;188(10):1605–9. [PubMed]
25. Endt K, Stecher B, Chaffron S, Slack E, Tchitchek N, Benecke A, et al. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog. 2010;6(9):e1001097. [PMC free article] [PubMed]
26. Stecher B, Hardt WD. Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol. 2011;14(1):82–91. [PubMed]
27. Yoon MY, Lee K, Yoon SS. Protective role of gut commensal microbes against intestinal infections. J Microbiol. 52(12):983–9. [PubMed]
28. Young VB, Schmidt TM. Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J Clin Microbiol. 2004;42(3):1203–6. [PMC free article] [PubMed]
29. Hogenauer C, Hammer HF, Krejs GJ, Reisinger EC. Mechanisms and management of antibiotic-associated diarrhea. Clin Infect Dis. 1998;27(4):702–10. [PubMed]
30. Rolfe RD. Role of volatile fatty acids in colonization resistance to Clostridium difficile. Infect Immun. 1984;45(1):185–91. [PMC free article] [PubMed]
31. Reeves AE, Koenigsknecht MJ, Bergin IL, Young VB. Suppression of Clostridium difficilein the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae. Infect Immun. 2012;80(11):3786–94. [PMC free article] [PubMed]
32. Su WJ, Waechter MJ, Bourlioux P, Dolegeal M, Fourniat J, Mahuzier G. Role of volatile fatty acids in colonization resistance to Clostridium difficile in gnotobiotic mice. Infect Immun. 1987;55(7):1686–91. [PMC free article] [PubMed]
33. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA. 2011;108(Suppl 1):4554–61. [PubMed]
34. Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol. 2007;5(3):175–86. [PubMed]
35. Perry JA, Westman EL, Wright GD. The antibiotic resistome: what's new? Curr Opin Microbiol. 2014;21:45–50. [PubMed]
36. Sommer MO, Dantas G, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science. 2009;325(5944):1128–31. [PMC free article] [PubMed]
37. Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nature Commun. 2013;4:2151. [PubMed]
38. Draker KA, Boehr DD, Elowe NH, Noga TJ, Wright GD. Functional annotation of putative aminoglycoside antibiotic modifying proteins in Mycobacterium tuberculosis H37Rv. J Antibiotics. 2003;56(2):135–42. [PubMed]
39. Zaborin A, Smith D, Garfield K, Quensen J, Shakhsheer B, Kade M, et al. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. mBio. 2014;5(5):e01361–14. [PMC free article] [PubMed]
40. Chen LF, Arduino JM, Sheng S, Muhlbaier LH, Kanafani ZA, Harris AD, et al. Epidemiology and outcome of major postoperative infections following cardiac surgery: risk factors and impact of pathogen type. Am J Infect Control. 2012;40(10):963–8. [PMC free article] [PubMed]
41. Harris AD, Johnson JK, Thom KA, Morgan DJ, McGregor JC, Ajao AO, et al. Risk factors for development of intestinal colonization with imipenem-resistant Pseudomonas aeruginosa in the intensive care unit setting. Infect Control Hosp Epidemiol. 2011;32(7):719–22. [PMC free article] [PubMed]
42. Vindigni SM, Surawicz CM. C. difficile infection: Changing epidemiology and management paradigms. Clin Transl Gastroenterol. 2015;6:e99. [PMC free article] [PubMed]
43. Magill SS, Edwards JR, Bamberg W, Beldavs ZG, Dumyati G, Kainer MA, et al. Multistate point-prevalence survey of health care-associated infections. New Engl J Med. 2014;370(13):1198–208. [PMC free article] [PubMed]
44. 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(7):905–14. [PMC free article] [PubMed]
45. Leffler DA, Lamont JT. Clostridium difficile infection. New Engl J Med. 2015;372(16):1539–48. [PubMed]
46. Lessa FC, Mu Y, Bamberg WM, Beldavs ZG, Dumyati GK, Dunn JR, et al. Burden of Clostridium difficile infection in the United States. New Engl J Med. 2015;372(9):825–34. [PubMed]
47. 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. New Engl J Med. 2013;368(5):407–15. [PubMed]
48. Lofgren ET, Moehring RW, Anderson DJ, Weber DJ, Fefferman NH. A mathematical model to evaluate the routine use of fecal microbiota transplantation to prevent incident and recurrent Clostridium difficile infection. Infect Control Hosp Epidemiol. 2014;35(1):18–27. [PMC free article] [PubMed]
49. Rao K, Young VB, Aronoff DM. Fecal microbiota therapy: ready for prime time? Infect Control Hosp Epidemiol. 2014;35(1):28–30. [PMC free article] [PubMed]
50. Fuentes S, van Nood E, Tims S, Heikamp-de Jong I, ter Braak CJ, Keller JJ, et al. Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection. ISME J. 2014;8(8):1621–33. [PMC free article] [PubMed]
51. Seekatz AM, Aas J, Gessert CE, Rubin TA, Saman DM, Bakken JS, et al. Recovery of the gut microbiome following fecal microbiota transplantation. mBio. 2014;5(3):e00893–14. [PMC free article] [PubMed]
52. Schubert AM, Rogers MA, Ring C, Mogle J, Petrosino JP, Young VB, et al. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. mBio. 2014;5(3):e01021–14. [PMC free article] [PubMed]
53. 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(7533):205–8. [PMC free article] [PubMed]
54. Giel JL, Sorg JA, Sonenshein AL, Zhu J. Metabolism of bile salts in mice influences spore germination in Clostridium difficile. PLoS ONE. 2010;5(1):e8740. [PMC free article] [PubMed]
55. Ubeda C, Bucci V, Caballero S, Djukovic A, Toussaint NC, Equinda M, et al. Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect Immun. 2013;81(3):965–73. [PMC free article] [PubMed]
56. Stiefel U, Nerandzic MM, Pultz MJ, Donskey CJ. Gastrointestinal colonization with a cephalosporinase-producing bacteroides species preserves colonization resistance against vancomycin-resistant enterococcus and Clostridium difficile in cephalosporin-treated mice. Antimicrob Agents Chemother. 2014;58(8):4535–42. [PMC free article] [PubMed]
57. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14. [PMC free article] [PubMed]
58. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. mBio. 2010;1(3):e00129–10. [PMC free article] [PubMed]
59. Laufer AS, Metlay JP, Gent JF, Fennie KP, Kong Y, Pettigrew MM. Microbial communities of the upper respiratory tract and otitis media in children. mBio. 2011;2(1):e00245–10. [PMC free article] [PubMed]
60. Dickson RP, Erb-Downward JR, Huffnagle GB. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med. 2014;2(3):238–46. [PMC free article] [PubMed]
61. Hasegawa K, Camargo CA., Jr Airway microbiota and acute respiratory infection in children. Expert Rev Clin Immunol. 2015;11(7):789–92. [PMC free article] [PubMed]
62. Lazarevic V, Gaia N, Emonet S, Girard M, Renzi G, Despres L, et al. Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients. Front Cell Infect Microbiol. 2014;4:65. [PMC free article] [PubMed]
63. Bousbia S, Papazian L, Saux P, Forel JM, Auffray JP, Martin C, et al. Repertoire of intensive care unit pneumonia microbiota. PLoS ONE. 2012;7(2):e32486. [PMC free article] [PubMed]
64. Toma I, Siegel MO, Keiser J, Yakovleva A, Kim A, Davenport L, et al. Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia. J Clin Microbiol. 2014;52(11):3913–21. [PMC free article] [PubMed]
65. Lu W, Yu J, Ai Q, Liu D, Song C, Li L. Increased constituent ratios of Klebsiella sp., Acinetobacter sp., and Streptococcus sp. and a decrease in microflora diversity may be indicators of ventilator-associated pneumonia: a prospective study in the respiratory tracts of neonates. PLoS ONE. 2014;9(2):e87504. [PMC free article] [PubMed]
66. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, et al. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol. 2010;12(5):1293–303. [PubMed]
67. Lau HY, Huffnagle GB, Moore TA. Host and microbiota factors that control Klebsiella pneumoniae mucosal colonization in mice. Microbes Infect. 2008;10(12-13):1283–90. [PMC free article] [PubMed]
68. Eloe-Fadrosh EA, Rasko DA. The human microbiome: from symbiosis to pathogenesis. Annu Rev Med. 2013;64:145–63. [PMC free article] [PubMed]
69. Zhao L. The gut microbiota and obesity: from correlation to causality. Nat Rev Microbiol. 2013;11(9):639–47. [PubMed]
70. Nguyen TL, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech. 2015;8(1):1–16. [PMC free article] [PubMed]
71. Seok J, Warren HS, Cuenca AG, Mindrinos MN, Baker HV, Xu W, et al. Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci USA. 2013;110(9):3507–12. [PubMed]
72. Rogers GB, Hoffman LR, Carroll MP, Bruce KD. Interpreting infective microbiota: the importance of an ecological perspective. Trends Microbiol. 2013;21(6):271–6. [PMC free article] [PubMed]
73. Ma B, Forney LJ, Ravel J. Vaginal microbiome: rethinking health and disease. An Rev Microbiol. 2012;66:371–89. [PMC free article] [PubMed]
74. Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, et al. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics. 2015;31(15):2461–8. [PMC free article] [PubMed]
75. La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, Wang Q, et al. Hypothesis testing and power calculations for taxonomic-based human microbiome data. PLoS ONE. 2012;7(12):e52078. [PMC free article] [PubMed]
76. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87. [PMC free article] [PubMed]
77. Degnan PH, Ochman H. Illumina based analysis of microbial community diversity. ISME J. 2011:1–12.
78. Zilberberg MD, Shorr AF. Preventing Clostridium difficile infection in the intensive care unit. Crit Care Clin. 2013;29(1):11–8. [PubMed]
79. Schultz MJ, Haas LE. Antibiotics or probiotics as preventive measures against ventilator-associated pneumonia: a literature review. Crit Care. 2011;15(1):R18. [PMC free article] [PubMed]
80. Tosh PK, McDonald LC. Infection control in the multidrug-resistant era: tending the human microbiome. Clin Infect Dis. 2012;54(5):707–13. [PubMed]