Alcohol flush does not aid in endoscope channel drying but may serve as an adjunctive microbiocidal measure: A new take on an old assumption.

BACKGROUND: Alcohol is perceived to aid flexible endoscope channel drying, however we previously showed alcohol increased the time required to dry some channels with forced air versus water alone. Yet, alcohol may prevent microorganism outgrowth during storage. Drying endoscope channels has been shown to prevent outgrowth, but it is unknown if incomplete drying (<10 µL remaining) provides similar protection. METHODS: Endoscope channel test articles were used to determine the efficacy of 70%-30% alcohol flush for prevention of Pseudomonas aeruginosa outgrowth and drying efficiency. For non-alcohol flushed channels, the impact of forced air drying on outgrowth of P. aeruginosa was determined. RESULTS: Alcohol flush (70%-30%) prevented outgrowth with little to no recovery of P. aeruginosa during ambient storage. 70% alcohol increased channel drying time by 1.5 or 3-fold compared to 50% alcohol or water, respectively. Forced air drying of non-alcohol flushed channels greatly reduced the initial contamination level and prevented outgrowth. Incomplete drying of contaminated channels was akin to no application of forced air. Applying forced air for more time than necessary to remove residual liquid did not completely eliminate the low level recovery of P. aeruginosa. CONCLUSIONS: Flushing with reduced concentrations of alcohol may provide a strategy to prevent microbial outgrowth while reducing drying time.

Efficacy of flexible endoscope drying using novel endoscope test articles that allow direct visualization of the internal channel systems.

BACKGROUND: Thorough drying of flexible endoscope channels has been identified as an essential reprocessing step. Yet, instructions are not specific on how to dry endoscopes. There is lack of data supporting efficacy of current drying practices, due to limitations in determining channel dryness. METHODS: Novel endoscope test articles were used to evaluate the effectiveness of alcohol flush and hanging in an ambient endoscope storage cabinet. Prepared test articles were hung in a storage cabinet for 5 days and visually inspected for residual liquid. The procedure for preoperative inspection of endoscopic systems was performed to determine the procedure's efficacy for removing residual liquid. Then, testing was performed to assess the impact of pressure, residual liquid type and route of air application on time to dry using compressed air. RESULTS: Alcohol flush followed by hanging in an ambient storage cabinet was not effective for drying endoscope channels, and residual liquid was not completely removed after performing the steps of the preoperative inspection of endoscopic channels. The factors impacting effective compressed air drying were channel dependent. For some channels, alcohol increased the time to dry. CONCLUSIONS: Endoscope drying is complex; borescope evaluation does not ensure a dry device.

Tapering Courses of Oral Vancomycin Induce Persistent Disruption of the Microbiota That Provide Colonization Resistance to Clostridium difficile and Vancomycin-Resistant Enterococci in Mice.

Vancomycin taper regimens are commonly used for the treatment of recurrent Clostridium difficile infections. One rationale for tapering and pulsing of the dose at the end of therapy is to reduce the selective pressure of vancomycin on the indigenous intestinal microbiota. Here, we used a mouse model to test the hypothesis that the indigenous microbiota that provide colonization resistance against C. difficile and vancomycin-resistant enterococci (VRE) is repopulated during tapering courses of vancomycin. Mice were treated orally with vancomycin daily for 10 days, vancomycin in a tapering dose for 42 days, fidaxomicin for 10 days, or saline. To assess colonization resistance, subsets of mice were challenged with 104 CFU of C. difficile or VRE at multiple time points during and after completion of treatment. The impact of the treatments on the microbiome was measured by cultures, real-time PCR for selected anaerobic bacteria, and deep sequencing. Vancomycin taper-treated mice developed alterations of the microbiota and disruption of colonization resistance that was persistent 18 days after treatment. In contrast, mice treated with a 10-day course of vancomycin exhibited recovery of the microbiota and of colonization resistance by 15 days after treatment, and fidaxomicin-treated mice maintained intact colonization resistance. These findings demonstrate that alteration of the indigenous microbiota responsible for colonization resistance to C. difficile and VRE persist during and after completion of tapering courses of vancomycin.

Sensitizing Clostridium difficile Spores with Germinants on Skin and Environmental Surfaces Represents a New Strategy for Reducing Spores via Ambient Mechanisms.

BACKGROUND: Clostridium difficile is a leading cause of healthcare-associated infections worldwide. Prevention of C. difficile transmission is challenging because spores are not killed by alcohol-based hand sanitizers or many commonly used disinfectants. One strategy to control spores is to induce germination, thereby rendering the spores more susceptible to benign disinfection measures and ambient stressors. METHODS/RESULTS: C. difficile spores germinated on skin after a single application of cholic acid-class bile salts and co-germinants; for 4 C. difficile strains, recovery of viable spores from skin was reduced by ~0.3 log10CFU to 2 log10CFU after 2 hours and ~1 log10CFU to > 2.5 log10CFU after 24 hours. The addition of taurocholic acid to 70% and 30% ethanol significantly enhanced reduction of viable spores on skin and on surfaces. Desiccation, and to a lesser extent the presence of oxygen, were identified as the stressors responsible for reductions of germinated spores on skin and surfaces. Additionally, germinated spores became susceptible to killing by pH 1.5 hydrochloric acid, suggesting that germinated spores that remain viable on skin and surfaces might be killed by gastric acid after ingestion. Antibiotic-treated mice did not become colonized after exposure to germinated spores, whereas 100% of mice became colonized after exposure to the same quantity of dormant spores. CONCLUSIONS: Germination could provide a new approach to reduce C. difficile spores on skin and in the environment and to render surviving spores less capable of causing infection. Our findings suggest that it may be feasible to develop alcohol-based hand sanitizers containing germinants that reduce spores on hands.

Acquisition of Clostridium difficile Colonization and Infection After Transfer From a Veterans Affairs Hospital to an Affiliated Long-Term Care Facility.

BACKGROUND Clostridium difficile infection (CDI) and asymptomatic carriage of toxigenic C. difficile are common in long-term care facilities (LTCFs). However, whether C. difficile is frequently acquired in the LTCF versus during acute-care admissions remains unknown. OBJECTIVE To test the hypothesis that LTCF residents often acquire C. difficile colonization and infection in the LTCF DESIGN This 5-month cohort study was conducted to determine the incidence of acquisition of C. difficile colonization and infection in asymptomatic patients transferred from a Veterans Affairs hospital to an affiliated LTCF. METHODS Rectal swabs were cultured for toxigenic C. difficile at the time of transfer to the LTCF and weekly for up to 6 weeks. We calculated the proportion of LTCF-onset CDI cases within 1 month of transfer that occurred in residents colonized on admission versus those with new acquisition in the LTCF. RESULTS Of 110 patients transferred to the LTCF, 12 (11%) were asymptomatically colonized with toxigenic C. difficile upon admission, and 4 of these 12 patients (33%) developed CDI within 1 month, including 3 recurrent and 1 initial CDI episode. Of 82 patients with negative cultures on transfer and at least 1 follow-up culture, 22 (27%) acquired toxigenic C. difficile colonization, and 4 developed CDI within 1 month, including 1 recurrent and 3 initial CDI episodes. CONCLUSION LTCF residents frequently acquired colonization with toxigenic C. difficile after transfer from the hospital, and 3 of 4 initial CDI cases with onset within 1 month of transfer occurred in residents who acquired colonization in the LTCF. Infect Control Hosp Epidemiol 2017;38:1070-1076.

An Increase in Healthcare-Associated Clostridium difficile Infection Associated with Use of a Defective Peracetic Acid-Based Surface Disinfectant.

BACKGROUND We investigated an increase in the incidence of healthcare-associated Clostridium difficile infection (CDI) that occurred following a change from a bleach disinfectant to a peracetic acid-based disinfectant. OBJECTIVE To evaluate the efficacy of the peracetic acid-based disinfectant. DESIGN Laboratory-based product evaluation. METHODS The commercial peracetic acid-based product is activated on site by mixing a small volume of concentrated hydrogen peroxide and peracetic acid present in a "SmartCap" reservoir with the remaining contents of the container. We measured concentrations of peracetic acid in newly activated and in-use product and determined the stability of nonactivated and activated product. We tested the efficacy of the product against C. difficile spores using the American Society for Testing and Materials standard quantitative carrier disk test method. RESULTS Measured concentrations of peracetic acid (50-800 parts per million [ppm]) were significantly lower than the level stated on the product label (1,500 ppm), and similar results were obtained for containers from multiple lot numbers and from another hospital. Product with peracetic acid levels below 600 ppm had significantly reduced activity against C. difficile spores. Peracetic acid concentrations were reduced markedly after storage of either activated or nonactivated product for several weeks. The Environmental Protection Agency confirmed the finding of low disinfectant levels and ordered discontinuation of sale of the product. CONCLUSION Use of a defective peracetic acid-based surface disinfectant may have contributed to an increase in healthcare-associated CDI. Our findings highlight the importance of evaluating the efficacy of liquid disinfectants in healthcare settings. Infect Control Hosp Epidemiol 2017;38:300-305.

Do piperacillin/tazobactam and other antibiotics with inhibitory activity against Clostridium difficile reduce the risk for acquisition of C. difficile colonization?

BACKGROUND: Systemic antibiotics vary widely in in vitro activity against Clostridium difficile. Some agents with activity against C. difficile (e.g., piperacillin/tazobactam) inhibit establishment of colonization in mice. We tested the hypothesis that piperacillin/tazobactam and other agents with activity against C. difficile achieve sufficient concentrations in the intestinal tract to inhibit colonization in patients. METHODS: Point-prevalence culture surveys were conducted to compare the frequency of asymptomatic rectal carriage of toxigenic C. difficile among patients receiving piperacillin/tazobactam or other inhibitory antibiotics (e.g. ampicillin, linezolid, carbapenems) versus antibiotics lacking activity against C. difficile (e.g., cephalosporins, ciprofloxacin). For a subset of patients, in vitro inhibition of C. difficile (defined as a reduction in concentration after inoculation of vegetative C. difficile into fresh stool suspensions) was compared among antibiotic treatment groups. RESULTS: Of 250 patients, 32 (13 %) were asymptomatic carriers of C. difficile. In comparison to patients receiving non-inhibitory antibiotics or prior antibiotics within 90 days, patients currently receiving piperacillin/tazobactam were less likely to be asymptomatic carriers (1/36, 3 versus 7/36, 19 and 15/69, 22 %, respectively; P = 0.024) and more likely to have fecal suspensions with in vitro inhibitory activity against C. difficile (20/28, 71 versus 3/11, 27 and 4/26, 15 %; P = 0.03). Patients receiving other inhibitory antibiotics were not less likely to be asymptomatic carriers than those receiving non-inhibitory antibiotics. CONCLUSIONS: Our findings suggest that piperacillin/tazobactam achieves sufficient concentrations in the intestinal tract to inhibit C. difficile colonization during therapy.

A Cumulative Spore Killing Approach: Synergistic Sporicidal Activity of Dilute Peracetic Acid and Ethanol at Low pH Against Clostridium difficile and Bacillus subtilis Spores.

Background. Alcohol-based hand sanitizers are the primary method of hand hygiene in healthcare settings, but they lack activity against bacterial spores produced by pathogens such as Clostridium difficile and Bacillus anthracis. We previously demonstrated that acidification of ethanol induced rapid sporicidal activity, resulting in ethanol formulations with pH 1.5-2 that were as effective as soap and water washing in reducing levels of C difficile spores on hands. We hypothesized that the addition of dilute peracetic acid (PAA) to acidified ethanol would enhance sporicidal activity while allowing elevation of the pH to a level likely to be well tolerated on skin (ie, >3). Methods. We tested the efficacy of acidified ethanol solutions alone or in combination with PAA against C difficile and Bacillus subtilis spores in vitro and against nontoxigenic C difficile spores on hands of volunteers. Results. Acidification of ethanol induced rapid sporicidal activity against C difficile and to a lesser extent B subtilis. The addition of dilute PAA to acidified ethanol resulted in synergistic enhancement of sporicidal activity in a dose-dependent fashion in vitro. On hands, the addition of 1200-2000 ppm PAA enhanced the effectiveness of acidified ethanol formulations, resulting in formulations with pH >3 that were as effective as soap and water washing. Conclusions. Acidification and the addition of dilute PAA induced rapid sporicidal activity in ethanol. Our findings suggest that it may be feasible to develop effective sporicidal ethanol formulations that are safe and tolerable on skin.

Acquisition of Clostridium difficile on Hands of Healthcare Personnel Caring for Patients with Resolved C. difficile Infection.

In an observational study, we found that healthcare personnel frequently acquired Clostridium difficile on their hands when caring for patients with recently resolved C. difficile infection (CDI) (<6 weeks after treatment) who were no longer under contact precautions. Continuing contact precautions after diarrhea resolves may be useful to reduce transmission.

A Quaternary Ammonium Disinfectant Containing Germinants Reduces Clostridium difficile Spores on Surfaces by Inducing Susceptibility to Environmental Stressors.

Exposing Clostridium difficile spores to germinants in a quaternary ammonium matrix was an effective method to reduce environmental contamination by sensitizing the spores, leaving them susceptible to ambient conditions and enhancing killing by acid, high-intensity visible light, and radiation.

A Novel, Sporicidal Formulation of Ethanol for Glove Decontamination to Prevent Clostridium difficile Hand Contamination During Glove Removal.

Decontamination of gloves before removal could reduce the risk for contamination of hands of personnel caring for patients with Clostridium difficile infection. We demonstrated that a novel sporicidal formulation of ethanol rapidly reduced C. difficile spores on gloved hands without adverse odor, respiratory irritation, or staining of clothing.

Unlocking the Sporicidal Potential of Ethanol: Induced Sporicidal Activity of Ethanol against Clostridium difficile and Bacillus Spores under Altered Physical and Chemical Conditions.

BACKGROUND: Due to their efficacy and convenience, alcohol-based hand sanitizers have been widely adopted as the primary method of hand hygiene in healthcare settings. However, alcohols lack activity against bacterial spores produced by pathogens such as Clostridium difficile and Bacillus anthracis. We hypothesized that sporicidal activity could be induced in alcohols through alteration of physical or chemical conditions that have been shown to degrade or allow penetration of spore coats. PRINCIPAL FINDINGS: Acidification, alkalinization, and heating of ethanol induced rapid sporicidal activity against C. difficile, and to a lesser extent Bacillus thuringiensis and Bacillus subtilis. The sporicidal activity of acidified ethanol was enhanced by increasing ionic strength and mild elevations in temperature. On skin, sporicidal ethanol formulations were as effective as soap and water hand washing in reducing levels of C. difficile spores. CONCLUSIONS: These findings demonstrate that novel ethanol-based sporicidal hand hygiene formulations can be developed through alteration of physical and chemical conditions.

Chlorhexidine Only Works If Applied Correctly: Use of a Simple Colorimetric Assay to Provide Monitoring and Feedback on Effectiveness of Chlorhexidine Application.

We used a colorimetric assay to determine the presence of chlorhexidine on skin, and we identified deficiencies in preoperative bathing and daily bathing in the intensive care unit. Both types of bathing improved with an intervention that included feedback to nursing staff. The assay provides a simple and rapid method of monitoring the performance of chlorhexidine bathing.

The photodynamic antibacterial effects of silicon phthalocyanine (Pc) 4.

The emergence of antibiotic-resistant strains in facultative anaerobic Gram-positive coccal bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), is a global health issue. Typically, MRSA strains are found associated with institutions like hospitals but recent data suggest that they are becoming more prevalent in community-acquired infections. It is thought that the incidence and prevalence of bacterial infections will continue to increase as (a) more frequent use of broad-spectrum antibiotics and immunosuppressive medications; (b) increased number of invasive medical procedures; and (c) higher incidence of neutropenia and HIV infections. Therefore, more optimal treatments, such as photodynamic therapy (PDT), are warranted. PDT requires the interaction of light, a photosensitizing agent, and molecular oxygen to induce cytotoxic effects. In this study, we investigated the efficacy and characterized the mechanism of cytotoxicity induced by photodynamic therapy sensitized by silicon phthalocyanine (Pc) 4 on (a) methicillin-sensitive Staphylococcus aureus (MSSA) (ATCC 25923); (b) community acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) (ATCC 43300); and (c) hospital acquired methicillin-resistant Staphylococcus aureus (HA-MRSA) (PFGE type 300). Our data include confocal image analysis, which confirmed that Pc 4 is taken up by all S. aureus strains, and viable cell recovery assay, which showed that concentrations as low as 1.0 µM Pc 4 incubated for 3 h at 37 °C followed by light at 2.0 J/cm2 can reduce cell survival by 2-5 logs. These results are encouraging, but before PDT can be utilized as an alternative treatment for eradicating resistant strains, we must first characterize the mechanism of cell death that Pc 4-based PDT employs in eliminating these pathogens.

Induced sporicidal activity of chlorhexidine against Clostridium difficile spores under altered physical and chemical conditions.

BACKGROUND: Chlorhexidine is a broad-spectrum antimicrobial commonly used to disinfect the skin of patients to reduce the risk of healthcare-associated infections. Because chlorhexidine is not sporicidal, it is not anticipated that it would have an impact on skin contamination with Clostridium difficile, the most important cause of healthcare-associated diarrhea. However, although chlorhexidine is not sporicidal as it is used in healthcare settings, it has been reported to kill spores of Bacillus species under altered physical and chemical conditions that disrupt the spore's protective barriers (e.g., heat, ultrasonication, alcohol, or elevated pH). Here, we tested the hypothesis that similarly altered physical and chemical conditions result in enhanced sporicidal activity of chlorhexidine against C. difficile spores. PRINCIPAL FINDINGS: C. difficile spores became susceptible to heat killing at 80 °C within 15 minutes in the presence of chlorhexidine, as opposed to spores suspended in water which remained viable. The extent to which the spores were reduced was directly proportional to the concentration of chlorhexidine in solution, with no viable spores recovered after 15 minutes of incubation in 0.04%-0.0004% w/v chlorhexidine solutions at 80 °C. Reduction of spores exposed to 4% w/v chlorhexidine solutions at moderate temperatures (37 °C and 55 °C) was enhanced by the presence of 70% ethanol. However, complete elimination of spores was not achieved until 3 hours of incubation at 55 °C. Elevating the pH to ≥9.5 significantly enhanced the killing of spores in either aqueous or alcoholic chlorhexidine solutions. CONCLUSIONS: Physical and chemical conditions that alter the protective barriers of C. difficile spores convey sporicidal activity to chlorhexidine. Further studies are necessary to identify additional agents that may allow chlorhexidine to reach its target within the spore.

Evaluation of a pulsed xenon ultraviolet disinfection system for reduction of healthcare-associated pathogens in hospital rooms.

OBJECTIVE To determine the effectiveness of a pulsed xenon ultraviolet (PX-UV) disinfection device for reduction in recovery of healthcare-associated pathogens. SETTING Two acute-care hospitals. METHODS We examined the effectiveness of PX-UV for killing of Clostridium difficile spores, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus (VRE) on glass carriers and evaluated the impact of pathogen concentration, distance from the device, organic load, and shading from the direct field of radiation on killing efficacy. We compared the effectiveness of PX-UV and ultraviolet-C (UV-C) irradiation, each delivered for 10 minutes at 4 feet. In hospital rooms, the frequency of native pathogen contamination on high-touch surfaces was assessed before and after 10 minutes of PX-UV irradiation. RESULTS On carriers, irradiation delivered for 10 minutes at 4 feet from the PX-UV device reduced recovery of C. difficile spores, MRSA, and VRE by 0.55±0.34, 1.85±0.49, and 0.6±0.25 log10 colony-forming units (CFU)/cm2, respectively. Increasing distance from the PX-UV device dramatically reduced killing efficacy, whereas pathogen concentration, organic load, and shading did not. Continuous UV-C achieved significantly greater log10CFU reductions than PX-UV irradiation on glass carriers. On frequently touched surfaces, PX-UV significantly reduced the frequency of positive C. difficile, VRE, and MRSA culture results. CONCLUSIONS The PX-UV device reduced recovery of MRSA, C. difficile, and VRE on glass carriers and on frequently touched surfaces in hospital rooms with a 10-minute UV exposure time. PX-UV was not more effective than continuous UV-C in reducing pathogen recovery on glass slides, suggesting that both forms of UV have some effectiveness at relatively short exposure times.

Metallo-ß-lactamase-producing bacteroides species can shield other members of the gut microbiota from antibiotics.

Antibiotics disrupt the intestinal microbiota, rendering patients vulnerable to colonization by exogenous pathogens. Intermicrobial interactions may attenuate this effect. Incubation with ceftriaxone-resistant, ccrA-positive, ß-lactamase-producing Bacteroides strains raised the minimum bactericidal concentration of ceftriaxone required to kill a susceptible Escherichia coli strain (mean change, <0.25 to 29 mg/liter; P = 0.009); incubation with ceftriaxone-resistant but non-ß-lactamase-producing Bacteroides strains had no effect. The production of ß-lactamase by common members of the intestinal microbiota (Bacteroides) can protect susceptible fellow commensals from ß-lactams.

Sorting through the wealth of options: comparative evaluation of two ultraviolet disinfection systems.

BACKGROUND: Environmental surfaces play an important role in the transmission of healthcare-associated pathogens. Because environmental cleaning is often suboptimal, there is a growing demand for safe, rapid, and automated disinfection technologies, which has lead to a wealth of novel disinfection options available on the market. Specifically, automated ultraviolet-C (UV-C) devices have grown in number due to the documented efficacy of UV-C for reducing healthcare-acquired pathogens in hospital rooms. Here, we assessed and compared the impact of pathogen concentration, organic load, distance, and radiant dose on the killing efficacy of two analogous UV-C devices. PRINCIPAL FINDINGS: The devices performed equivalently for each impact factor assessed. Irradiation delivered for 41 minutes at 4 feet from the devices consistently reduced C. difficile spores by ∼ 3 log10CFU/cm2, MRSA by>4 log10CFU/cm2, and VRE by >5 log10CFU/cm2. Pathogen concentration did not significantly impact the killing efficacy of the devices. However, both a light and heavy organic load had a significant negative impacted on the killing efficacy of the devices. Additionally, increasing the distance to 10 feet from the devices reduced the killing efficacy to ≤3 log10CFU/cm2 for MRSA and VRE and <2 log10CFU/cm2 for C.difficile spores. Delivery of reduced timed doses of irradiation particularly impacted the ability of the devices to kill C. difficile spores. MRSA and VRE were reduced by >3 log10CFU/cm2 after only 10 minutes of irradiation, while C. difficile spores required 40 minutes of irradiation to achieve a similar reduction. CONCLUSIONS: The UV-C devices were equally effective for killing C. difficile spores, MRSA, and VRE. While neither device would be recommended as a stand-alone disinfection procedure, either device would be a useful adjunctive measure to routine cleaning in healthcare facilities.

Metabolomics analysis identifies intestinal microbiota-derived biomarkers of colonization resistance in clindamycin-treated mice.

BACKGROUND: The intestinal microbiota protect the host against enteric pathogens through a defense mechanism termed colonization resistance. Antibiotics excreted into the intestinal tract may disrupt colonization resistance and alter normal metabolic functions of the microbiota. We used a mouse model to test the hypothesis that alterations in levels of bacterial metabolites in fecal specimens could provide useful biomarkers indicating disrupted or intact colonization resistance after antibiotic treatment. METHODS: To assess in vivo colonization resistance, mice were challenged with oral vancomycin-resistant Enterococcus or Clostridium difficile spores at varying time points after treatment with the lincosamide antibiotic clindamycin. For concurrent groups of antibiotic-treated mice, stool samples were analyzed using quantitative real-time polymerase chain reaction to assess changes in the microbiota and using non-targeted metabolic profiling. To assess whether the findings were applicable to another antibiotic class that suppresses intestinal anaerobes, similar experiments were conducted with piperacillin/tazobactam. RESULTS: Colonization resistance began to recover within 5 days and was intact by 12 days after clindamycin treatment, coinciding with the recovery bacteria from the families Lachnospiraceae and Ruminococcaceae, both part of the phylum Firmicutes. Clindamycin treatment caused marked changes in metabolites present in fecal specimens. Of 484 compounds analyzed, 146 (30%) exhibited a significant increase or decrease in concentration during clindamycin treatment followed by recovery to baseline that coincided with restoration of in vivo colonization resistance. Identified as potential biomarkers of colonization resistance, these compounds included intermediates in carbohydrate or protein metabolism that increased (pentitols, gamma-glutamyl amino acids and inositol metabolites) or decreased (pentoses, dipeptides) with clindamycin treatment. Piperacillin/tazobactam treatment caused similar alterations in the intestinal microbiota and fecal metabolites. CONCLUSIONS: Recovery of colonization resistance after antibiotic treatment coincided with restoration of several fecal bacterial metabolites. These metabolites could provide useful biomarkers indicating intact or disrupted colonization resistance during and after antibiotic treatment.