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Clostridioides difficile is an urgent antimicrobial-resistant bacterium, causing mild to moderate and sometimes life-threatening disease. Commensal gut microbes are critical for providing colonization resistance against C difficile and can be leveraged as non-antibiotic alternative therapeutics for the prevention and treatment of C difficile infection.

An imbalance in our microbiota may contribute to many human diseases, but the mechanistic underpinnings of dysbiosis remain poorly understood. We argue that dysbiosis is secondary to a defect in microbiota-nourishing immunity, a part of our immune system that balances the microbiota to attain colonization resistance against environmental exposure to microorganisms. We discuss this new hypothesis and its implications for ulcerative colitis, an inflammatory bowel disease of the large intestine.

Campylobacter jejuni is a major cause of food-borne human bacterial gastroenteritis but animal models for C. jejuni mediated disease remain limited because C. jejuni poorly colonizes immunocompetent, conventionally-reared (Conv-R) mice. Thus, a reliable rodent model (i.e. persistent colonization) is desirable in order to evaluate C. jejuni-mediated gastrointestinal disease and mechanisms of pathogenicity. As the nature and complexity of the microbiota likely impacts colonization resistance for C. jejuni, Conv-R and gnotobiotic C3H/HeN mice were used to evaluate the persistence of C. jejuni colonization and development of disease. A total of four C. jejuni isolates readily and persistently colonized ASF mice and induced mild mucosal inflammation in the proximal colon, but C. jejuni did not stably colonize nor induce lesions in Conv-R mice. This suggests that the pathogenesis of C. jejuni is influenced by the microbiota, and that ASF mice offer a reproducible model to study the influence of the microbiota on the ability of C. jejuni to colonize the gut and to mediate gastroenteritis.

International audience; AIM: To observe the transfer of the digestive microbiota from sow to piglet, describe the impact of the sow's Salmonella shedding on this transfer and identify transferred populations that could be associated with the future Salmonella status of the piglets.METHODS AND RESULTS: Salmonella shedding status of 19 sows was determined at the beginning and end of gestation. Four piglets were randomly selected from each sow. Using MiSeq, the microbiotas of the sows at the end of gestation and of their piglets 1 day before weaning were described. Results showed that the Salmonella shedding of the sows, the birth mother, the lairage room, the parity and the contamination of the lairage environment were associated to the microbiota of the piglets (permanova P < 0·05). Several genera were associated with piglets born from negative or positive sows.CONCLUSION: There is a link between the microbiota of the sows at the end of gestation and the microbiota of their piglets at weaning, and the Salmonella shedding of the sow is associated with the microbiota of the piglets.SIGNIFICANCE AND IMPACT OF THE STUDY: Salmonella status of the sows affects the microbiota of their piglets and could affect the long-term Salmonella colonization resistance of these animals and their health.

Background The prevention and treatment of bacterial infections is a human health challenge. A disadvantage of antibiotics is that they often kill beneficial commensal, bacteria in addition to, pathogenic bacteria. Indiscriminate killing disrupts the homeostasis between commensal bacteria and the host gut epithelium allowing colonization of the gut by pathogenic bacteria and increases susceptibility to infections. This research was done to develop a non-antibiotic modality to prevent bacterial infections by growing, rather than killing, commensal bacteria in the gut. Gut commensal bacteria grown on carbohydrates produce short-chain fatty acids (SCFAs) that support gut homeostasis maintenance and promote resistance to bacterial colonization. SCFAs have direct and indirect effects on the gut and lung mucosal immune system. They have also been linked to respiratory viral infection reduction and shown to influence macrophage function to mitigate pro-inflammatory neutrophil-mediated tissue damage. Methods A library of over 1,500 synthetic proprietary glycans, termed Microbiome Metabolic Therapies (MMT™), was synthesized using different chemical and enzymatic approaches. An ex vivo platform using fecal bacterial communities from human subjects was devised to screen MMTs for their abilities to deplete pathogenic bacteria, and modulate multiple aspects of bacterial metabolism. Results KB109 was identified based on its ability to reduce the relative abundance of a diversity of pathogens including clinically relevant Gram-negative and Gram-positive bacteria in human fecal communities. KB109 also increased the relative abundance of prevalent commensal bacteria. Monoculture experiments demonstrated that KB109 promotes the growth of commensal bacteria, but not pathogens. Ex vivo screening revealed that KB109 consistently increased SFCA production across multiple fecal communities. Conclusion KB109 represents an appealing activity profile and offers an opportunity to prevent enteric and systemic bacterial infections by promoting gut homeostasis and colonization resistance, and ameliorating respiratory viral infections by stimulating immune homeostasis. KB109 is under evaluation in two COVID-19 clinical studies. Disclosures Jeffrey Meisner, PhD, Kaleido Biosciences (Employee, Shareholder) Jackson Lee, PhD, Kaleido Biosciences (Employee, Shareholder) Jonathan Lawrence, PhD, Kaleido Biosciences (Employee, Shareholder) Megan Roed, BA, Kaleido Biosciences (Employee, Shareholder) Johan van Hylckama Vlieg, PhD, Kaleido Biosciences (Employee, Shareholder)

Purpose The pharmacology, clinical efficacy, safety, dosage and administration, and place in therapy of fidaxomicin for the treatment of Clostridium difficile infection (CDI) are reviewed. Summary Fidaxomicin, a macrocyclic antibiotic, has a narrow spectrum of activity against gram-positive anaerobes and is bactericidal against C. difficile . It has no activity against gram-negative bacteria. Fidaxomicin has minimal activity against Bacteroides species, which may be advantageous in maintaining colonization resistance and protecting the gastrointestinal tract from colonization by C. difficile . The minimum inhibitory concentration for 90% of organisms for fidaxomicin against C. difficile ranged from 0.0078 to 2 μg/mL in in vitro studies. After oral administration, fecal concentrations are detected and are directly proportional to the dose administered. Fidaxomicin resistance in vivo has not been reported. In clinical trials, fidaxomicin has been shown to be noninferior to vancomycin in the management of mild-to-moderately severe CDI. The adverse-effect profile of fidaxomicin is comparable to that of vancomycin. The recommended dosage for treatment of CDI is fidaxomicin 200 mg orally twice daily for 10 days. Fidaxomicin should be considered for patients who previously received treatment with metronidazole or vancomycin for CDI and who are diagnosed with recurrent CDI in which a non-NAP1/BI/027 strain is isolated. At institutions where strain typing is not available, fidaxomicin may be considered in patients with recurrent CDI who have not responded to treatment with the regimen used for the first episode of CDI. Conclusion Fidaxomicin is a well-tolerated agent for the treatment of CDI and has been shown to be noninferior to vancomycin in the management of mild-to-moderately severe CDI.

Objectives: Clostridium difficile infection (CDI) is a major cause of morbidity in the nosocomial environment. Antimicrobial agents such as the third-generation cephalosporins, lincosamides and aminopenicillins are well known for their propensity to induce CDI, but the definitive reasons why remain to be elucidated. Despite their broad spectrum of activity against both aerobic and anaerobic bacteria, the ureidopenicillins remain a class of antimicrobials infrequently associated with the development of CDI. Methods: We used a triple-stage chemostat model that simulates the human gut to study the effects of the ureidopenicillin/b-lactamase inhibitor combination piperacillin/tazobactam on gut bacterial populations and C. difficile. Results: Piperacillin/tazobactam rapidly reduced all enumerated gut bacterial populations (including bacteroides, bifidobacteria and lactobacilli) below the limits of detection by the end of the piperacillin/ tazobactam instillation period. Despite such widespread disruption of gut bacterial populations, C. difficile populations remained principally as spores, with no sustained proliferation or high-level cytotoxin production observed. Conclusions: Factors other than reduced colonization resistance must be responsible for determining whether CDI develops following antimicrobial administration. We believe the gut model is a promising approach for the study of C. difficile pathogenesis reflecting in vivo events likely to occur in CDI.

We hypothesized that orally administered, recombinant class A beta-lactamase would inactivate the portion of parenteral piperacillin excreted into the intestinal tract, preserving colonization resistance of mice against nosocomial pathogens. Subcutaneous piperacillin or piperacillin plus oral beta-lactamase were administered 24 and 12 h before orogastric inoculation of piperacillin-resistant pathogens. Oral administration of beta-lactamase reduced piperacillin-associated alteration of the indigenous microflora and prevented overgrowth of pathogens.

Clostridium difficile is recognized as an important nosocomial pathogen. C. difficile infection (CDI) is thought to arise as a result of depletion of the normal gut flora by antimicrobial agents. Cefotaxime (CTX) is well-known for its propensity to cause CDI, but the reasons behind its particular predisposition to the disease remain unclear. Previous investigations have so far relied upon the hamster model of CDI or human volunteers. We have used a triple-stage chemostat model of the human gut to investigate the behaviour of C. difficile and components of the normal gut flora, in response to exposure to CTX alone, and in combina- tion with its active metabolite desacetylcefotaxime (dCTX). C. difficile remained in a steady state during non- antibiotic exposed periods, with no detectable cytotoxin. During both antibiotic exposure regimens, prolifer- ation of C. difficile and elevated cytotoxin levels were observed. Cessation of antibiotic instillation produced a reduction in cytotoxin levels and viable counts. Decreases in bacterial counts were observed in response to both antibiotic exposure regimens, notably for bifidobacteria and bacteroides. Numbers of bacteroides were profoundly affected by exposure to the CTX/dCTX combination, and this may indicate a possible role for bacteroides in colonization resistance. We believe that the gut model is a promising method for studying C. difficile pathogenesis in conditions analogous to the in vivo situation.

Oral administration of antibiotics for treatment of urinary tract infections (UTIs) can cause ecological disturbances in the normal intestinal microflora. Poorly absorbed drugs can reach the colon in active form, suppress susceptible microorganisms and disturb the ecological balance. Suppression of the normal microflora may lead to reduced colonization resistance with subsequent overgrowth of pre-existing, naturally resistant microorganisms, such as yeasts and Clostridium difficile. New colonization by resistant potential pathogens may also occur and may spread within the body or to other patients and cause severe infections. It is therefore important to learn more about the ecological effects of antibacterial agents on the human microflora. The impact on intestinal microorganisms of oral antibiotics used for the treatment of UTIs is reviewed here. Ampicillin, amoxycillin and co-amoxiclav suppress both the aerobic and anaerobic intestinal microflora with overgrowth of ampicillin-resistant Enterobacteriaceae. Pivmecillinam also affects the intestinal microflora, suppressing Escherichia coli, but does not have a major effect on the anaerobic microflora. Several orally administered cephalosporins, such as cefixime, cefpodoxime, cefprozil and ceftibuten, reduce the number of Enterobacteriaceae and increase the number of enterococci. Colonization with C. difficile has also been observed. Fluoroquinolones eliminate or strongly suppress intestinal Enterobacteriaceae, but affect enterococci and anaerobic bacteria only slightly. When antimicrobial agents are prescribed for the treatment of UTIs, not only the antimicrobial spectrum of the agent but also the potential ecological disturbances, including the risk of emergence of resistant strains, should be considered.

Sixteen Lactobacillus fermentum strains were isolated from the fecal microflora of pigs. They were challenged in vivo, in gnotobiotic mice harboring a porcine flora devoid of lactobacilli. Some of the strains were able to colonize the digestive tract of the mice at high population levels, whilst other strains were eliminated. Chromosomal DNA restriction analysis performed on both colonizing (C-type) and non-colonizing (NC-type) strains were analyzed by pulsed-field gel electrophoresis. Strains LEMPL9 (C-type) and LEM1.16A (NC-type) exhibited a high degree of homology. When challenged in mice harboring a simplified anaerobic flora, LEMPL9 was able to colonize the digestive tract of the animals whereas LEM1.16A was again eliminated. Mutagenesis performed on LEM1.16A allowed the isolation of a mutant able to colonize the gut of mice harboring the simplified anaerobic flora or a complex human flora, suggesting that genes involved in colonization process might have been affected to enhance the bacterium's colonization ability.

Selective decontamination of the digestive tract (SDD) is an established form of infection prevention which relies upon local antibiotic action to afford suppression of potential pathogens while preserving 'colonization resistance' (CR). However, CR has never been shown conclusively to play a decisive role in either achieving or maintaining effective prophylaxis in patients and by employing absorbable antimicrobials or parenteral antibiotics, prophylaxis is actually achieved by both local and systemic action. The role of prophylaxis in neutropenic patients is also far from clear since morbidity and mortality remain the same whether or not prophylactic antibacterials are given and most patients still require empirical therapy for fever. In addition, the Gram-positive cocci, rather than Gram-negative bacilli presently predominate as pathogens. There is also an increasing trend towards including fungal and viral infection as targets for prophylaxis. Moreover, current anti-infective strategies are more akin to 'pre-emptive therapy' (PET) since the antimicrobials are available systemically and given at optimum therapeutic doses and there is little to distinguish treatment given to prevent colonization from progressing to infection from that used to arrest incipient infection or effect a cure of established infection. In contrast, SDD as originally conceived may well prove cost-effective for the prevention of infection in intensive care although neither the optimum regimen nor the patient group who would gain most benefit have been defined. None the less, by affording protection against Gram-negative sepsis, both SDD and PET would reduce the pressure on the clinicians to treat empirically and shift the emphasis once more on appropriate investigations which would involve the microbiologist more directly and immediately in patient care. Any savings from lowering the drug usage could then be diverted to improving diagnosis and providing the regular monitoring that is essential to the success of both PET and SDD.

Aspects of selective decontamination as an antibiotic prophylaxis in general surgery are discussed with respect to the respiratory tract and wound infection. The high rate of nosocomial infection encountered in surgical patients, who experience up to 71 per cent of all such infection, is considered. The infection rate increases to 70–80 per cent after 1 week in the surgical intensive care unit, while the infection-related mortality rate rises to up to 60 per cent. The endogenous origin of nosocomial infection suggests the importance of maintaining colonization resistance to prevent colonization with Gram-negative micro-organisms, especially using selective decontamination which eliminates potentially pathogenic micro-organisms while leaving colonization resistance intact. Selective decontamination has proved eflective in decreasing infection rates by 50–80 per cent, and is especially successful in respiratory tract infection. Possible adverse effects and future indications for selective decontamination are discussed.

The influence of co-trimoxazole on colonization resistance of the bowel was investigated in six healthy volunteers, by measuring the numbers of indigenous aerobic flora and of a co-trimoxazole resistant challenge strain of Klebsiella pneumoniae. Impairment of colonization resistance of the bowel was shown by a significant increase in the numbers of yeasts in the faeces of five of six volunteers, by a significant increase in the numbers of Gram-negative bacilli in the faeces of two of six volunteers, and by facilitation of colonization of the bowel by the challenge strain in all volunteers. Impairment of colonization resistance of the mouth was shown by the development of glossitis caused by Candida albicans in two volunteers, and by a significant increase in the numbers of yeasts in mouth washings from four volunteers. It is concluded that co-trimoxazole impairs colonization resistance of the gastro-intestinal tract.

A novel regimen of selective decontamination (SDD) with initial systemic cefotaxime prevented bacterial colonization of the oropharynx and stomach in mechanically ventilated patients. In a three-group study of all patients receiving prolonged mechanical ventilation, patients in control groups A and B received antibiotics only when infection was present. In group A, antibiotics that disturb colonization resistance (CR) were used. In group B, antibiotics use was restricted to antibiotics not affecting CR. Patients in group C received SDD, consisting of norfloxacin, polymyxin E and amphotericin B, administered via a gastric tube and applied to the oropharynx. Group C patients further received an initial five day course of cefotaxime, 500 mg tid. The lower respiratory tract was colonized with microorganisms on admission in about half of the patients, and this persisted in both control groups. In group C, lower respiratory tract colonization was eliminated in all patients after five days. In both control groups about 90% of the patients acquired microbial colonization of the oropharynx and stomach, mostly with Gram-negative bacilli. In group C, only 12% and 24% of the patients acquired colonization of the oropharynx and stomach respectively (P less than 0.001). The oropharynx and stomach were the major sources of microorganisms causing lower respiratory tract infection in both control groups. In group C, elimination of oropharyngeal and gastric colonization completely prevented lower respiratory tract infection from these sources.

We investigated the influence of oral administration of amoxycillin, erythromycin and roxithromycin on colonization resistance in healthy volunteers. Antibiotics were administered in a randomized cross-over design. No effect on the colonization resistance of the oropharynx could be demonstrated. Amoxycillin decreased the colonization resistance of the bowel against Enterobacteriaceae and yeasts, whose median concentration in faeces increased 100-fold and 30-fold respectively. Roxithromycin and erythromycin decreased the concentration of Enterobacteriaceae in faeces. Secondary colonization with Enterobacteriaceae was detected as often following roxithromycin as following amoxycillin, but the level of colonization with these bacteria was much higher following amoxycillin. Following roxithromycin and erythromycin the level of secondary colonization did not exceed the original concentration of Enterobacteriaceae, showing that these antibiotics did not decrease the colonization resistance against Enterobacteriaceae. The appearance of secondary colonization in faeces at levels equal to or lower than the concentration of Enterobacteriaceae before administration of antibiotics, should not be regarded as proof of disturbance of colonization resistance.

Six adult volunteers were given 1 g/d of intravenous ceftriaxone for 5 d (consecutive). Ceftriaxone and beta-lactamase activities were assayed in fecal samples obtained before and during drug administration, and anaerobic bacteria, Enterobacteriaceae, and fungi were counted. In two volunteers, no fecal beta-lactamase activity was detected, but ceftriaxone was present during treatment at concentrations of 1.8-2.0 mg/g of feces. Concomitantly, fecal counts of anaerobes in these volunteers dropped from 10.5 to less than 8 log10 colony-forming units (cfu)/g of feces, and those of Candida species increased more than 100-fold. However, in the feces of the four other volunteers, beta-lactamase activity was high during ceftriaxone administration, but no ceftriaxone was detected. In these volunteers, ceftriaxone administration was not followed by any significant change in counts of anaerobes or Candida species. This appeared to be due to the intraintestinal hydrolysis of ceftriaxone by resident beta-lactamase-producing anaerobes. In gnotobiotic mice associated with a human fecal flora containing no beta-lactamase-producing anaerobes, it was possible to prevent the deleterious effects of ceftriaxone on intestinal microbial composition and on colonization resistance (against a strain of Candida albicans and one of ceftriaxone-resistant Enterobacter cloacae) by feeding the animals with an association of four beta-lactamase-producing anaerobic strains.

The influence of oral administration of cefaclor, phenethicillin, co-trimoxazole and doxycycline on colonization resistance (CR) of the oropharynx and colon in healthy volunteers was studied. Antimicrobial agents were administered in a randomized cross-over design. No effect on CR of the oropharynx could be demonstrated. Phenethicillin decreased CR of the colon against Enterobacteriaceae (P = 0.001). Co-trimoxazole significantly decreased the concentration of Enterobacteriaceae in faeces (P = 0.03) but the decrease caused by cefaclor and doxycycline did not reach statistical significance. Administration of antimicrobial agents increased the appearance of secondary colonization by Enterobacteriaceae in faeces, especially when Escherichia coli was eliminated. During administration of phenethicillin, secondary colonization occurred at a concentration exceeding 10(7)/g in some volunteers. Following administration of cefaclor, co-trimoxazole and doxycycline, elimination of E. coli may result in the substitution by resistant Gram-negative bacilli in low concentrations.

The autochthonous anaerobic bacterial flora in the mucosal layer of the gastrointestinal tract limits colonization by aerobic potential pathogens. This effect is called colonization resistance. Colonization of the digestive tract by potentially pathogenic microorganisms precedes infection in patients with leukopenia and in cases of mechanical ventilation and can be prevented by long-term administration of antimicrobial agents that spare the autochthonous anaerobic bacterial flora of the mucous membranes, a concept known as selective decontamination. Antimicrobial agents active against anaerobic flora reduce colonization resistance, permitting colonization by and overgrowth of potentially pathogenic microorganisms and possibly leading to infections with resistant microorganisms. A distinction can be made between antimicrobial agents that reduce colonization resistance and those that leave it intact by examining the effect of antimicrobial agents on aerobic intestinal flora of mice and humans.