Tag Archives: Clostridium difficile

Patients Diagnosed With C. difficile Infection (CDI) Have Higher Readmission Rates

Elijah Verheyen, MD'Correspondence information about the author MD Elijah Verheyen

,

Vijay Dalapathi, MD

,

Shilpkumar Arora, MD

,

Kalpesh Patel, MD

,

Pavan Kumar Mankal, MD

,

Varun Kumar, MD

,

Edward Lung, MD

,

Donald P. Kotler, MD

,

Ari Grinspan, MD

Highlights

  • One in five patients admitted with C. difficile is readmitted within 30 days.
  • Recurrent C difficile is the leading cause of readmission.
  • Female sex, renal disease, and anemia increase C difficile readmission risk.
  • Discharge home, as opposed to facility, increases C difficile readmission risk.

Background

Clostridium difficile infection (CDI) is a leading cause of community-onset and healthcare–associated infection, with high recurrence rates, and associated high morbidity and mortality. We report national rates, leading causes, and predictors of hospital readmission for CDI.

Methods

Retrospective study of data from the 2013 Nationwide Readmissions Database of patients with a primary diagnosis of CDI and re-hospitalization within 30-days. A multivariate regression model was used to identify predictors of readmission.

Results

Of 38,409 patients admitted with a primary diagnosis of CDI, 21% were readmitted within 30-days, and 27% of those patients were readmitted with a primary diagnosis of CDI. Infections accounted for 47% of all readmissions. Female sex, anemia/coagulation defects, renal failure/electrolyte abnormalities and discharge to home (versus facility) were 12%, 13%, 15%, 36%, respectively, more likely to be readmitted with CDI.

Conclusions

We found that 1-in-5 patients hospitalized with CDI were readmitted to the hospital within 30-days. Infection comprised nearly half of these readmissions, with CDI being the most common etiology.

Predictors of readmission with CDI include female sex, history of renal failure/electrolyte imbalances, anemia/coagulation defects, and being discharged home. CDI is associated with a high readmission risk, with evidence of several predictive risks for readmission.

SOURCEhttps://www.ajicjournal.org/article/S0196-6553(19)30026-4/fulltext?utm_source=dlvr.it&utm_medium=twitter

Study Investigators Find Combination of Vancomycin and FMT Superior In Treating Recurrent C.difficile Infection (rCDI)

The combination of vancomycin and fecal microbiota transplantation was found to be superior to fidaxomicin or vancomycin in the treatment of patients with recurrent Clostridium difficile infection (rCDI), according to a study published in Gastroenterology.

This randomized, single-center trial was designed to compare the efficacy of fecal microbiota transplantation with that of fidaxomicin and vancomycin.

Sixty-four adults with recurrent CDI seen at a gastroenterology clinic in Denmark between April 5, 2016 and June 10, 2018 were randomly assigned to a group receiving fecal microbiota transplantation applied by colonoscopy or nasojejunal tube after 4 to 10 days of 125 mg vancomycin 4 times daily (n=24), or 10 days of 200 mg fidaxomicin 2 times daily (n=24), or 10 days of 125 mg vancomycin 4 times daily (n=16).

Patients experiencing a CDI recurrence after this course of treatment, and those who could not be randomly assigned were provided rescue fecal microbiota transplantation. The primary study outcome was combined clinical resolution and negative polymerase chain reaction test for C difficile toxin at 8 weeks post-treatment, and secondary end points included week 8 clinical resolution.

The combination of negative C difficile test results and clinical resolution was observed in 71% of the 24 participants who received fecal microbiota transplantation (95% CI, 49-87%; n=17), 33% of the 24 participants who received fidaxomicin (95% CI, 16-55%; n=8), and 19% of the 16 participants (95% CI, 5-46%; n=3) who received vancomycin (fecal microbiota transplantation vs fidaxomicinP=.009; fecal microbiota transplantation vs vancomycin, P=.001; fidaxomicin vs vancomycin, P=.31). Clinical resolution was observed in 92% of participants who received fecal microbiota transplantation (n=22; P=.0002), 42% of participants who were treated with fidaxomicin (n=10; <.0001), and 19% of participants who were treated with vancomycin (n=3; P=.13). No significant differences in results were seen between patients receiving initial fecal microbiota transplantation therapy and those who received rescue treatment with such a transplant.

Of note, adverse events (transient abdominal pain, constipation, bloating and diarrhea) were observed in 10 of the participants who received a fecal microbiota transplant, 1 of which was classified as severe.

Researchers noted limitation of a lack of patients with C difficile ribotype 027, such that results may not be generalizable to settings with a high ribotype 027 frequency. Study interventions were also unblinded, introducing the possibility of observer bias, although the C difficile toxin test was applied to all patients at all time points in an effort to obtain objective outcome measures.

Study investigators concluded, “[fecal microbiota transplantation] was superior to both fidaxomicin and vancomycin monotherapies for [recurrent] CDI, with regard to both combined clinical and microbiological resolution and clinical resolution alone.”

Reference

https://www.infectiousdiseaseadvisor.com/respiratory/new-powder-formulation-tuberculosis-vaccine-candidate-is-in-human-trial/article/829508/

Hvas CL, Jørgensen SMD, Jørgensen SP, et al. Fecal microbiota transplantation is superior to fidaxomicin for treatment of recurrent Clostridium difficile infection [published online January 2, 2019]. Gastroenterology. doi: 10.1053/j.gastro.2018.12.019

Ribotypes and Prevalence of Clostridium difficile (C. diff) Hypervirulent Strain: NAP1/B1/027

The Hypervirulent Strain of Clostridium Difficile: NAP1/B1/027

– A Brief Overview



Abstract

Clostridium difficile is a gram-positive bacterium notorious for causing epidemic diarrhea globally with a significant health burden. The pathogen is clinically challenging with increasing antibiotic resistance and recurrence rate. We provide here an in-depth review of one particular strain/ribotype 027, commonly known as NAP1/B1/027 or North American pulsed-field gel electrophoresis type 1, restriction endonuclease analysis type B1, polymerase chain reaction ribotype 027, which has shown a much higher recurrence rate than other strains.

Introduction & Background

Clostridium difficile (C. diff) is a gram-positive, anaerobic, motile, spore-forming, rod-shaped bacteria [1-2]. It has been isolated from almost all mammals, including pigs, cows, horses, elephants, and Kodiak bears, as well as in poultry and ostriches. It has also been found in the soil and feces of humans and animals. It is transmitted from person to person by the fecal-oral route. The C. diff isolates found in animals are similar to the ones found in humans, but according to Hensgens et al., this similarity does not mean that interspecies transmission occurs. However, immunocompromised people are still at risk for interspecies transmission [1]. Its pathogenicity is dependent on the two toxins that it produces: enterotoxin A (Toxin A or TcdA) and cytotoxin B (Toxin B or TcdB). Enterotoxin damages the actin in target cells which leads to neutrophil infiltration, inflammation, and necrosis of epithelial cells. Cytotoxin B has been shown to damage tight junctions of epithelial cells, which increases vascular permeability and causes hemorrhage [2-3]. These toxins form the basis of stool analysis when diagnosing people with the suspected infection. Despite all the virulence characters described, C. diff is a poor competitor against other gut flora in the human colon. In a healthy colon, this pathogen is not in sufficient quantity to produce a clinically significant disease. Risk factors that disrupt this balance include antibiotics exposure, health care environment, acid suppressants, and elemental diet. The bacterium can cause severe watery diarrhea that can progress to pseudomembranous colitis [3-8]. It has been named as one of the three microorganisms with an ‘urgent’ threat level by the Centers for Disease Control and Prevention (CDC) based on its public health impact in the United States (US) with an estimated $1.5 billion US in annual health care expenditures [8]. Patients who have more than three episodes of unexplained and new onset unformed stools in 24 hours should be referred for testing for a Clostridium difficile infection (CDI). Also, patients with risk factors described previously should undergo testing for this pathogen [9]. The ribotype 027 strain of C. diff is particularly noteworthy as contradicting evidence in the literature is present regarding the disease severity it causes. We provide here a brief overview of the epidemiology, pathophysiology, and treatment of this particular strain.

Review

Ribotypes and prevalence of Clostridium difficile (C. diff)

Clostridium difficile can be characterized according to its ribotyping which is performed using the polymerase chain reaction. Several different ribotypes have been associated with CDI. The ribotypes 001, 002, 014, 046, 078, 126, and 140 have been found to be prevalent in the Middle East [10-12]. In Asia, ribotypes 001, 002, 014, 017, and 018 are more prevalent [13-15]. The predominant strains in Europe and North America include ribotypes 001, 014, 020, 027, and 078 [6]. The ribotype 027 (also referred to as NAP1/B1/027) has emerged in the last decade. Studies have underlined antimicrobial resistance as one of the causes of its epidemic outbreaks. Capillary electrophoresis (CE) ribotyping is used as the standard for characterization of C. diff isolates. This method relies on the intergeneric region variability between 16S and 23S ribosomal deoxyribonucleic acid (DNA) [16]. Ribotype 027 was found to have reduced susceptibility to metronidazole, rifampicin, moxifloxacin, clindamycin, imipenem, and chloramphenicol [17-18]. It is clinically and financially concerning as it leads to severe disease presentation, as well as antimicrobial resistance with high morbidity and mortality rates as compared to other strains [19]. Strains, such as ribotype 027 (especially its spores), spread more easily within the hospital because they can resist the hospital environment, cleaning, and disinfectants [1]. An observational study conducted on patients admitted with diarrhea in a Veteran Affairs Medical Center showed that around 22% of the patients were positive for the NAP1/B1/027 strain out of all the people who tested positive for CDI. Further, a reduction in the rate of diarrhea caused by the NAP1/B1/027 strain was observed with a prevalence of 16.9% in 2016, down from 26.2% in 2013. An increase in the level of awareness and education was thought to be the reason for this decline [20]. The prevalence of this strain in North America is reportedly around 22% – 36%. Ribotype 027 was identified as the most prevalent strain causing CDI with recent outbreaks in North America [20-22]. The prevalence of this strain was shown to be 48% in hospitals in Poland with an outbreak of CDI during September 2011 to August 2013 [21].

NAP1/B1/027 strain

Toxigenicity and Pathogenesis

The North American pulsed-field gel electrophoresis type 1, restriction endonuclease analysis type B1, polymerase chain reaction ribotype 027 (NAP1/B1/027) strain has been shown to contain a gene locus, CdtLoc, that encodes for CD196 ADP-ribosyltransferase (CDT) or binary toxin. The bacterium also produces Toxin A and Toxin B, similar to non-027 ribotypes, through the PaLoc gene locus [23-24]. CDT was first isolated by Popoff et al. [25]. The toxin comprises two separate toxin components: CDTa and CDTb. CDTa, which is an ADP-ribosyltransferase enzyme, modifies actin which results in depolymerization and destruction of the actin cytoskeleton in the gut. CDTb binds to gut cells and increases uptake of CDTa. The destruction caused by CDT favors adherence of bacteria and increased uptake of Toxin A and Toxin B [26].

In addition to the toxins, this strain (along with few others) carries a base pair frameshift deletion at nucleotide 117 of the TcdC gene, which is a negative regulator of Toxins A and B. A mutation in this gene thus causes hyperexpression of toxins by this particular strain. Warny et al. showed that NAP1/B1/027 produces Toxin A approximately 16 times and Toxin B approximately 23 times more than the control strains [27]. One study also proposed that increased sporulation by this strain may also be associated with the increased spread of CDI [28]. The virulent factors associated with NAP1/B1/027 strain have been summarized in Table 1.

Virulent factor Mechanism
1. Toxin A (Enterotoxin A or TcdA) Damages the actin in target cells which leads to neutrophil infiltration, inflammation, and necrosis of epithelial cells [24].
2. Toxin B (Cytotoxin B or TcdB) Damages tight junctions of epithelial cells, which increases vascular permeability and causes hemorrhage [24].
3. CDTa toxin Modification of actin with ADP-ribosylation that results in actin depolymerization and destruction of the cytoskeleton that assists in adherence of bacteria to gut epithelial cells [25-26].
4. CDTb toxin Facilitates uptake of CDTa toxin into the gut epithelial lining [25-26].
5. Hypersporulation Increases reproduction and spread of bacteria [28].
6. TcdC gene mutation (18-bp deletion) Increases the production of Toxin A and Toxin B by down-regulation of feedback inhibitor involved in suppressing toxin production [27].

Previous studies have shown contradicting evidence regarding the severity of disease caused by this particular strain. A recent retrospective analysis by Bauer et al. concluded that NAP1/B1/027 was associated with a decreased odds of severe disease (odds ratio (OR): 0.35, 95% confidence interval (CI) 0.13 – 0.93) and did not increase in-hospital mortality (OR: 1.02, 95% CI 0.53 – 1.96) or recurrence rate (OR: 1.16, 95% CI 0.36 – 3.77) [23]. Several other studies conducted (including cross-sectional, case-control, and cohort studies) did not show any worse outcomes compared to other strains [29-31]. Sirad et al. demonstrated that although NAP1/B1/027 strain may produce more toxins compared to other strains, they produced fewer spores and were not always associated with severe disease [32]. On the contrary, Rao et al. conducted a cohort study and concluded that ribotype 027 was associated with severe CDI (OR: 1.73, 95% CI 1.03 – 2.89; p = 0.037) and increased mortality (OR: 2.02, 95% CI 1.19 – 3.43; p = 0.009) compared to other ribotypes [24]. Another study showed similar results with the North American pulsed-field gel electrophoresis type 1 (NAP1) strain. Multivariate regression analysis exhibited an increase in the severity of CDI with the NAP1 strain (OR: 1.66, 95% CI: 1.90 – 2.54) and increased mortality (OR: 2.12, 95% CI: 1.22 – 3.68) [33]. One study from Quebec labeled this strain to be responsible for severe diseases twice as frequently as compared to other strains [34].

The basis for these contradictory findings can be explained by several reasons, including study design, study population, sample size, the method of detection for C. diff, study setting, and unmeasured confounders. Given these contradictory results, healthcare providers should focus on treating this infection based on their clinical judgment and markers of severe infection, including the number of diarrheal episodes, signs of dehydration, creatinine level, albumin level, white blood cell count, associated co-morbidities, immunocompromised state, etc.

Prevention

Preventive strategies employed for NAP1/B1/027 strain are similar to strategies taken for other strains. These include barrier methods (gloves and gown while examining patient), use of disposable equipment, handwashing with soap and water, disinfecting the environment, and antimicrobial stewardship [35]. Further vaccines are being developed targeting the toxins, including TcdA and TcdB, for simultaneous prevention and treatment of CDI. Actoxumab and bezlotoxumab, which are monoclonal antibodies against TcdA and TcdB, are being investigated for this purpose. A combined Phase III trial (MODIFY I (NCT01241552) and MODIFY II (NCT01513239)) showed benefit from bezlotoxumab, but the combination of actoxumab and bezlotoxumab did not yield any further benefit [36]. Bezlotoxumab has received Food and Drug Administration (FDA) approval in October 2016 and is to be used in patients more than 18 years of age, who are at high risk of recurrence from CDI, and are receiving antibiotics [37]. A novel tetravalent vaccine against TcdA, TcdB, CDTa, and CDTb has been proposed by Secore et al. using a hamster model which has shown promising results [38].

A novel drug, SYN-004 (ribaxamase), is under investigation that has shown promising results for preventing CDI. This drug, which is a β-lactamase, is excreted into the gut and degrades the excess antibiotic that prevents disruption of normal gut flora, ultimately preventing CDI [39]. The Phase IIa clinical trial of this drug showed that ribaxamase at a dose of 150 mg every six hours results in an undetectable concentration of ceftriaxone in the intestine which can potentially decrease the likelihood of a C. diff infection, given the less probability of disruption of the gut bacteria.

Resistance to Antibiotics and Treatment

Cases of NAP1/B1/027 reported in Panama were found to be highly resistant to clindamycin, moxifloxacin, levofloxacin, ciprofloxacin, and rifampin but were susceptible to metronidazole and vancomycin [40]. Susceptibility of ribotype 027 and non-027 ribotypes to different antibiotics was tested in a study in Canada. Ribotype 027 showed a resistance of 92.2% to moxifloxacin compared to 11.2% for other strains. Similarly, 78.2% of ribotype 027 strains were resistant to ceftriaxone compared to 15.7% of other strains. Ribotype 027 demonstrated a greater than four-fold higher minimum inhibitory concentration (MIC) to metronidazole (4 vs. 1 μg/ml) and two-fold higher MIC for fidaxomicin (1 vs. 2 μg/ml). For clindamycin and vancomycin, the resistance was similar in both groups [41].

Resistance to erythromycin is linked to mutations in the ribosomal methylase genes, whereas resistance to fluoroquinolones is due to a mutation in DNA gyrase. Resistance to rifamycin and fidaxomicin is attributed to ribonucleic acid (RNA) polymerase methylation. The presence of phenicol and lincosamide genes has been shown to cause resistance to linezolid. A study conducted in hospitals of Mexico showed some isolates of ribotype 027 to have reduced susceptibility to fidaxomicin despite the unavailability of this drug in Mexico and the patients being unexposed to it [42]. Antibiotics form the basis of treatment for the NAP1/B1/027 strain. Currently, no specific Infectious Diseases Society of America (IDSA) guidelines are available to guide treatment for this particular strain, and hence, the treatment is similar to a non-NAP1/B1/027 strain [9]. Based on the current guidelines for treating CDI overall, we propose the following table for treating infection caused by the NAP1/B1/027 strain (Table 2).

First line treatment Alternative treatment
Initial non-severe infection Oral vancomycin, 125 mg four times daily for 10 days Fidaxomicin, 200 mg twice daily for 10 days; If neither is available, then use metronidazole, 500 mg three times daily for 10 days
First non-severe recurrence Repeat oral vancomycin, 125 mg four times daily for 10 days Fidaxomicin, 200 mg twice daily for 10 days
Second non-severe recurrence Oral vancomycin taper as follow: 125 mg four times daily for seven to 14 days, 125 mg twice daily for seven days, 125 mg twice once daily for seven days, 125 mg once every other day for seven days, 125 mg once every three days for 14 days Fidaxomicin, 200 mg orally twice daily for 10 days, or a fecal microbiota transplant
Subsequent non-severe recurrence Fecal microbiota transplant Tapering oral vancomycin with probiotics, IVIG, fidaxomicin
Severe disease Oral vancomycin, 125 mg four times daily, increase to 500 mg four times daily if no improvement noted in 24-48 hours or associated complications, including renal failure, ileus, etc. Fidaxomicin if the patient cannot tolerate oral vancomycin for any reason
Ileus Add IV metronidazole, 500 mg every eight hours, to oral vancomycin or fidaxomicin therapy; consider general surgery consult as needed Intracolonic vancomycin, IVIG

This strain has not shown any resistance to fidaxomicin, but there has been some contradicting evidence to this. A case report was published in 2017 in which the NAP1 C. diff infection, resistant to treatment with fidaxomicin and fecal transplants, was effectively treated with intravenous immunoglobulin (IVIG) [43]. Given the emerging threat of antibiotic resistance, increasing awareness, controlling infections, and antimicrobial stewardship can be effective measures to reduce this threat [17].

Currently, several novel antibiotics are under investigation which have gone through various randomized controlled trials for CDI treatment. Ridinilazole and cadazolid have completed Phase II trials, while surotomycin has completed two Phase III trials which have shown promising results [44-47].

Conclusions

The data regarding the NAP1/B1/027 strain is inconclusive with ongoing debates whether this particular strain is associated with severe disease. Further research, including meta-analyses, are needed to solve this enigma. Clinicians should guide treatment based on their judgment and objective evidence of disease severity.


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  39. Kokai-Kun JF, Roberts T, Coughlin O, et al.: The oral β-lactamase SYN-004 (ribaxamase) degrades ceftriaxone excreted into the intestine in phase 2a clinical studies. Antimicrob Agents Chemother. 2017, 61:pii: e02197-16. 10.1128/AAC.02197-16
  40. López-Ureña D, Quesada-Gómez C, Miranda E, Fonseca M, Rodríguez-Cavallini E: Spread of epidemic Clostridium difficile NAP1/027 in Latin America: case reports in Panama. J Med Microbiol. 2014, 63:322-24. 10.1099/jmm.0.066399-0
  41. Karlowsky JA, Adam HJ, Kosowan T, et al.: PCR ribotyping and antimicrobial susceptibility testing of isolates of Clostridium difficile cultured from toxin-positive diarrheal stools of patients receiving medical care in Canadian hospitals: the Canadian Clostridium difficile Surveillance Study (CAN-DIFF) 2013-2015. Diagn Microbiol Infect Dis. 2018, 91:105-11. 10.1016/j.diagmicrobio.2018.01.017
  42. Martínez-Meléndez A, Tijerina-Rodríguez L, Morfin-Otero R, et al.: Circulation of highly drug-resistant Clostridium difficile ribotypes 027 and 001 in two tertiary-care hospitals in Mexico. Microb Drug Resist. 2018, 24:386-92. 10.1089/mdr.2017.0323
  43. Coffman K, Chen XJC, Okamura C, Louie E: IVIG – A cure to severe refractory NAP-1 Clostridium difficile colitis? A case of successful treatment of severe infection, which failed standard therapy including fecal microbiota transplants and fidaxomicin. IDCases. 2017, 8:27-28. 10.1016/j.idcr.2017.03.002
  44. Vickers RJ, Tillotson GS, Nathan R, et al.: Efficacy and safety of ridinilazole compared with vancomycin for the treatment of Clostridium difficile infection: a phase 2, randomised, double-blind, active-controlled, non-inferiority study. Lancet Infect Dis. 2017, 17:735-44. 10.1016/S1473-3099(17)30235-9
  45. Louie T, Nord CE, Talbot GH, et al.: Multicenter, double-blind, randomized, phase 2 study evaluating the novel antibiotic, cadazolid, in patients with Clostridium difficile infection. Antimicrob Agents Chemother. 2015, 59:6266-73. 10.1128/AAC.00504-15
  46. Daley P, Louie T, Lutz JE, et al.: Surotomycin versus vancomycin in adults with Clostridium difficile infection: primary clinical outcomes from the second pivotal, randomized, double-blind, phase 3 trial. J Antimicrob Chemother. 2017, 72:3462-70. 10.1093/jac/dkx299
  47. Aziz M, Chandrasekar VT, Desai M, Fatima R, Jackson M, Sharma P: Sa1858 – surotomycin (a novel antibiotic) vs vancomycin for Clostridium difficile infection: a systematic review and meta analysis. Gastroenterology. 2018, 154:S421.

C Diff Foundation Recognizes Rebiotix CEO Lee Jones with 2019 ‘Above and Beyond’ Award


C Diff Foundation Board presented Rebiotix CEO Lee Jones for Advocacy, Innovation in
C. difficile infection treatment

 

(NEW PORT RICHEY, Fla.) — The C. Diff Foundation Board of Directors announced that the 2019 “Above and Beyond” Award was presented to Rebiotix CEO Lee Jones in Roseville, Minnesota. The award, given to one recipient annually, is given to a person or organization that show extraordinary dedication to C. diff. patient safety, advocacy, and overall drive to improve the lives of those impacted by the infection.

“We are very proud to recognize Ms. Jones with our “Above and Beyond” award,” said C. Diff Foundation Founder and President, Nancy Caralla. “Lee’s dedication to the entire C.diff. community of patients, family members, and physicians hasn’t wavered since the founding of Rebiotix in 2011. She is a true example of what can happen when focusing on patient well-being drives new approaches to healthcare.”

The award was presented by the Foundation’s Vice President, Scott Battles at the Rebiotix office.

 

 

 

 

 

 

“It’s an honor to receive this award from the C. Diff Foundation,” said Ms. Jones. “The purpose of starting Rebiotix was to bring the power of the microbiome to the clinic in a scientifically sound, quality-controlled way to help patients. We stand with the Foundation in believing that patient well-being should be at the core of all that we do, from clinical trials to exploring new scientific landscapes within the microbiome space.”

About Rebiotix Inc.:

Rebiotix Inc., part of the Ferring Pharmaceuticals Group, is a late-stage clinical microbiome company focused on harnessing the power of the human microbiome to revolutionize the treatment of debilitating diseases. Rebiotix possesses a deep and diverse clinical pipeline, with its lead drug candidate, RBX2660, in Phase 3 clinical development for the prevention of recurrent Clostridium difficile (C. diff) infection. RBX2660 has been granted Fast Track, Orphan and Breakthrough Therapy designation from the FDA for its potential to prevent recurrent C. diff infection.

Rebiotix’s clinical pipeline also features RBX7455, a lyophilized, room temperature stable oral capsule formulation. Rebiotix is also targeting several other disease states with drug products built on its pioneering Microbiota Restoration Therapy(tm) platform. For more information on Rebiotix and its pipeline of human microbiome-directed therapies, visit https://www.rebiotix.com/

 

Da Volterra Shared Results From Phase I Clinical Trial of DAV132 to Prevent Gut Microbiome Disruption Caused by Antibiotics and Prevent C. diff. Infections

DAV132 is a first-in-class product to protect the microbiome during antibiotic treatments and prevent Clostridium difficile infections.

French biotech Da Volterra is developing products to fight the rapidly rising rates of antibiotic resistance. During a Phase I study, the company’s medical device, DAV132, was used with the antibiotic, moxifloxacin, and successfully protected the intestinal microbiota from antibiotic residues. Overall, the product managed to reduce exposure of the microbiota to the antibiotic by 99% and maintain 97.8% of the microbiome’s genetic richness without affecting the drugs therapeutic efficacy.

In a randomized, controlled clinical trial performed in 44 healthy human volunteers, DAV132 was used in association with moxifloxacin, a widely used fluoroquinolone antibiotic. It was demonstrated that DAV132 is able to effectively capture residual antibiotics in the colon and reduce their concentration to very low levels. DAV132 reduced exposure of the intestinal microbiota to moxifloxacin by 99%. Meanwhile the plasma concentration of the antibiotic was essentially unaffected by the co-administration DAV132, meaning that its therapeutic efficacy will be maintained.

The ability of DAV132 to protect the intestinal microbiome was explored by identifying changes in bacterial gene richness as well as a detailed statistical analysis of the evolution of bacterial species throughout the study. In volunteers who received moxifloxacin alone, gene richness was drastically diminished to 54.6% of baseline after antibiotic treatment and failed to return to baseline even one month after treatment; 39% of bacterial species identified in the intestinal microbiota were affected. The co-administration of DAV132 with moxifloxacin largely protected the intestinal microbiome from disruption (97.8% of baseline for bacterial gene richness, and 93% of bacterial species protected).

The primary endpoints for the study were fully achieved and DAV132 showed an excellent tolerability profile.

Annie Ducher MD, Chief Medical Officer of Da Volterra, declared: “This clinical study is indicative of the potential of DAV132 to become one of the first preventative solutions to protect the intestinal microbiome and further avoid the detrimental consequences of antibiotic treatments, such as Clostridium difficile infections, for patients. We look forward to advancing the development of DAV132 in a pivotal patient study in 2018.”

Jean de Gunzburg PhD, Chief Scientific Officer of Da Volterra, added: “This study constitutes the first scientific demonstration of the protection of the intestinal microbiome from dysbiosis caused by a fluoroquinolone antibiotic treatment; our data suggests that this effect should be extendable to many different antibiotics from several therapeutic classes. The metagenomics analysis is outstanding and thoroughly convincing that DAV132 is highly effective at protecting the commensal bacteria in the intestines.”

The results are available under the reference: Gunzburg et al. Protection of the human gut microbiome from antibiotics. The Journal of Infectious Diseases, jix604, https://doi.org/10.1093/infdis/jix604.

***

About DAV132:
With a novel and unique mechanism of action, DAV132 is a product candidate aiming to protect the intestinal microbiome from the side effects of antibiotics, hence preventing the onset of C. difficile infections. DAV132 is an adsorbent with a proprietary coating with colon targeted delivery. DAV132 has been tested in four Phase 1 clinical studies with no adverse safety events. DAV132 is currently entering a Phase 2 clinical trial.

About Da Volterra:
Da Volterra is a biopharmaceutical company based in France that develops new strategies aimed at protecting the intestinal microbiome from the deleterious effects of antibiotics, and preventing multi-resistant and life-threatening infections. Da Volterra’s innovative approaches promise a substantial medical progress to combat deadly pathogens. http://www.davolterra.com

(January 2018)

To read the article in its entirety, please click on the following link to be redirected:

https://www.businesswire.com/news/home/20180116005398/en/Da-Volterra-Announces-Publication-Full-Results-Clinical

Gut Microbiome Research High-resolution Profiling Reveals the Extent of Clostridium difficile (C.diff.) Burden

Microbiome profiling through 16S rRNA gene sequencing has proven to be a valuable tool to characterize the diversity and composition of gut microbial communities, including in studies of CDI development and recurrence.8

 

Authors:

  • Ninalynn Daquigan,
  • Anna Maria Seekatz,
  • K. Leigh Greathouse,
  • Vincent B. Young &
  • James Robert White
Published online:

Abstract

Microbiome profiling through 16S rRNA gene sequence analysis has proven to be a useful research tool in the study of C. difficile infection (CDI); however, CDI microbiome studies typically report results at the genus level or higher, thus precluding identification of this pathogen relative to other members of the gut microbiota.

Accurate identification of C. difficile relative to the overall gut microbiome may be useful in assessments of colonization in research studies or as a prognostic indicator for patients with CDI.

To investigate the burden of C. difficile at the species level relative to the overall gut microbiome, we applied a high-resolution method for 16S rRNA sequence assignment to previously published gut microbiome studies of CDI and other patient populations. We identified C. difficile in 131 of 156 index cases of CDI (average abundance 1.78%), and 18 of 211 healthy controls (average abundance 0.008%).

We further detected substantial levels of C. difficile in a subset of infants that persisted over the first two to 12 months of life. Correlation analysis of C. difficile burden compared to other detected species demonstrated consistent negative associations with C. scindens and multiple Blautia species.

These analyses contribute insight into the relative burden of C. difficile in the gut microbiome for multiple patient populations, and indicate that high-resolution 16S rRNA gene sequence analysis may prove useful in the development and evaluation of new therapies for CDI.

Introduction

Clostridium difficile infection (CDI) poses a major healthcare burden to the global population, with an estimated 450,000 cases and 29,000 deaths in the United States annually.1,2 CDI is often associated with antibiotic treatment and is frequently acquired by patients during hospitalization.

Multiple diagnostic tests for CDI are available and hospitals commonly use a combination of enzyme immunoassay (EIA) and glutamate dehydrogenase (GDH) testing in tandem with real-time polymerase chain reaction (PCR) for increased sensitivity and shorter turnaround time.3

After diagnosis, patients with CDI are typically treated with metronidazole and/or vancomycin depending on symptom severity.3 Treatment failure is estimated to occur in 20% of patients, resulting in a recurrent CDI population that may require other treatment strategies.4,5 The development of microbial-based therapeutics, such as fecal microbiota transplantation (FMT) and combinations of selected microbes for the treatment of recurrent CDI suggests that mixtures of commensal microbes may be routinely utilized in the future as an alternative to powerful antibiotics.6,7

Microbiome profiling through 16S rRNA gene sequencing has proven to be a valuable tool to characterize the diversity and composition of gut microbial communities, including in studies of CDI development and recurrence.8

Given the intricate relationship between the gut microbiota and CDI, accurate                                   identification of C. difficile directly from 16S rRNA profiles in patient populations could be a valuable measure in future studies. However, a fundamental challenge to studying C. difficile through these approaches has been the level of taxonomic resolution provided through short 16S rRNA sequences.

As a result, most microbiome sequencing studies of CDI utilize higher aggregate taxonomic categories (e.g., the Clostridium XI cluster, which encompasses many other organisms related to C. difficile) as a proxy for the organism itself or simply avoid quantification altogether.9,10,11,12,13,14,15,16,17

Here we utilize a high-resolution method (Resphera Insight) for assigning species-level context to 16S rRNA gene sequence data to estimate C. difficile burden in different patient populations. This method was recently validated for detection of Listeria monocytogenes18 and Salmonella enterica,19,20 and was applied in this study to determine the relative abundance of C. difficile in several clinically relevant patient groups. Re-examining published 16S rRNA gene sequence datasets has confirmed previous associations of C. difficile with C. scindens, and identified new positive and negative correlations of C. difficile with other species, both of which may help provide insight into community aspects of C. difficile colonization and resistance against CDI.

Results

Evaluation of sensitivity and specificity for C. difficile identification

One of the challenges of 16S rRNA gene sequencing is the limited information available in these short DNA fragments to distinguish related microbial members below the genus-level. To accurately assess C. difficile at the species level from 16S rRNA gene sequence data, we used a method developed specifically for species level characterization (Resphera Insight, see Methods). We first validated this approach by obtaining full-length 16S rRNA gene sequences from 804 novel C. difficile isolates derived from multiple sources, and subsequently simulated noisy 16S rRNA gene sequence reads for taxonomic assignment (see Methods). Performance was measured using the Diagnostic True Positive Rate (DTP), defined as the percentage of sequences with an unambiguous assignment to C. difficile. The method achieved an average DTP of 99.9% (ranging from 98.92 to 100% per isolate, Table S1), indicating sufficient sensitivity to detect C. difficile from short 16S rRNA gene sequence reads.

In addition to establishing sufficient sensitivity to detect C. difficile, we also sought to evaluate false positive rates in which the method incorrectly assigns a sequence to C. difficile. As this species is a member of the Clostridium XI cluster, a false positive assessment was performed based on in silico simulations of 22 other members of this group, including the very similar Clostridium irregulare. Simulating 10,000 16S rRNA gene sequence reads per species with a 0.5% error rate, 20 of 22 species resulted in zero false positive assignments to C. difficile, with the highest false positive rate (0.07%) attributed to Clostridium irregulare (Table 1).

Table 1: False positive rates for 22 related species

Representation of C. difficile relative to the microbiota in adult cases of CDI and healthy individuals

To examine the presence of C. difficile in different human populations, we re-examined existing published 16S rRNA gene sequencing datasets with our validated method. We first compared the relative abundance of C. difficile across a cohort of healthy individuals to two cohorts of patients diagnosed with CDI (symptomatic index cases) from Seekatz et al.10 and Khanna et al.21 (Table S2). The Seekatz protocol for CDI diagnosis followed a two-stage algorithm employing enzyme immunoassay for GDH antigen and toxins A and B, with confirmation of tcdB gene presence via PCR if toxin and GDH results were discordant; the Khanna et al. protocol for CDI diagnosis was not reported in the original publication. The healthy patient cohort and Seekatz CDI datasets were generated using equivalent processing and sequencing methods.10 Average analyzed sequencing depths per sample for CDI and healthy groups were 16,114 and 14,937, respectively.

Overall, C. difficile was detected in 58 of 70 CDI index patients (82.9%) in the Seekatz study with an average abundance of 3.04% (Fig. 1a). In the Khanna dataset, C. difficile was detected in 73 of 86 CDI index patients (84.9%) with an average abundance of 0.76% (Fig. 1b). Among healthy controls, only 18 of 211 (8.5%) harbored detectable levels of C. difficile, with an average abundance of 0.008%, significantly less than both Seekatz and Khanna index cases (P < 2e-16; Mann–Whitney test).

Fig. 1
Fig. 1

Relative burden of C. difficile in the gut microbiome of two cohorts of CDI index patients and healthy controls. a Index cases of recurrent CDI (Seekatz et al.) and b CDI index patients (Khanna et al.) frequently harbored moderate to high levels of C. difficile. c Healthy controls. Overall 91.5% of controls had no detectable C. difficile and 0.9% maintained C. difficile levels higher than 0.1%

We were further interested in determining whether the ability to detect C. difficile or varying levels of C. difficile relative abundance from 16S rRNA gene sequences was related to disease outcome. The Seekatz dataset included samples collected from patients that went on to develop recurrent CDI, a serious outcome following primary diagnosis, or from patients who were later reinfected with CDI beyond the standard time recurrence window.10 Additionally, a severity score22 was available for some of the patients. Across the full Seekatz CDI positive sample set, our method detected C. difficile above 0.1% abundance in 59.2% of samples (Table 2). On average, patients with CDI for index (at primary diagnosis), recurrence or reinfection events had C. difficile abundances greater than 1% regardless of the calculated severity status using Infectious Diseases Society of America (IDSA) standards. We found no significant associations of C. difficile abundance with IDSA severity status among index samples or at the time of recurrence or reinfection (P > 0.05, Mann–Whitney test).

Table 2: C. difficile relative abundances in cases of CDI from Seekatz et al.10 compared to healthy controls

Representation of C. difficile relative to the microbiota in infants

To assess the levels of C. difficile carriage among infants relative to the total gut microbiome, we re-examined 16S rRNA gene sequence datasets describing longitudinal studies of pre-term infants in the neonatal intensive care unit (NICU) by Zhou et al.23 and a single infant profiled during the first 18 months of life by Davis et al.16 In the Zhao dataset, 12 necrotizing enterocolitis (NEC) cases and 26 age-matched controls (all treated at Brigham and Women’s Hospital NICU, Boston, MA) were sequenced with an average of seven samples per subject. The Davis asymptomatic case study consisted of profiling 50 fecal samples over time, during which researchers noted colonization switching between toxigenic and non-toxigenic strains and observed 100,000-fold fluctuations of C. difficile spore counts.16

In these two 16S rRNA gene sequence datasets, moderate levels of C. difficile (>1.0% abundance) appeared consistently within infants over time. In the Zhao dataset, C. difficile was detected in 25 of 38 (66%) infants, including 6 of 12 (50%) infants with NEC, and 19 of 26 (73%) normal infants. There was no significant difference in overall C. difficile presence between NEC and normal infants (P = 0.27, Fisher’s exact test), and both groups maintained statistically similar C. difficile abundance distributions relative to their total gut microbial communities under multivariate regression after adjustment for patient source (Fig. 2a). As the original Davis case study determined C. difficile carriage using spore counts and GDH concentration, we detected substantial representation of C. difficile (up to 7.1% abundance) until the time of weaning and transition to cow’s milk (Fig. 2b). We further found a statistically significant correlation between our C. difficile relative abundance estimates and GDH concentration measurements from the Davis study (Spearman correlation = 0.817; P = 5e-13).

Fig. 2
Fig. 2

Distribution of C. difficile during longitudinal gut microbiome sampling of infants. a Pre-term infants in a NICU, including those developing necrotizing enterocolitis (purple) and normal (grey). Each boxplot reflects a single patient with multiple time points (total samples per patient shown along the x-axis). b A longitudinal case study of an infant before (red) and after (blue) weaning during the first 18 months of life. During the transition to cow’s milk, C. difficile relative abundance fell to undetectable levels

Correlations of C. difficile with other bacterial species

Recent studies in animal models have indicated that certain species may generate metabolites that inhibit C. difficile, such as the production of secondary bile acids by C. scindens.15 However, previous studies correlating the abundance of C. difficile with other taxa did not utilize the microbiome-based abundances directly, but rather quantified C. difficile abundance through other means such as real-time PCR, colony forming units through culture, measuring GDH concentration or spore counts.15,16,17

We sought to determine whether high-resolution analysis of the 16S rRNA gene sequence data itself could reveal the same associations, and perhaps other relevant species. Computing correlations using Compositionality Corrected by REnormalization and PErmutation (CCREPE)24 across our re-analyzed cohorts, we found a significant negative association between C. difficile and C. scindens for the Khanna CDI patient cohort and the Davis infant longitudinal study (P < 0.02 for both datasets), with a supporting trend in the other studies (Fig. 3, Table S3). Additionally, multiple members of Blautia spp. displayed a consistent negative correlation like that of C. scindens (Fig. 3, Table S3). In contrast, other Clostridia such as C. neonatale and C. paraputrificum and members of Veillonella showed strong positive associations with C. difficile abundance. In silico simulations of noisy 16S rRNA gene sequence reads from these species confirmed a low mis-assignment rate (average 0.08%; see Table S4).

Fig. 3
Fig. 3

Correlation analysis identifies species positively or negatively associated with C. difficile. The CCREPE N-dimensional checkerboard score (y-axis) incorporates the ratio of co-variation to co-exclusion patterns normalized to a range of (−1, +1). In addition to C. scindens, we identify significant negative correlations with C. difficile for members of Blautia and positive correlations with other Clostridia and Veillonella spp. (*P ≤ 0.05). Ambiguous species level assignments are denoted by slashes. Key for re-analyzed datasets from the following studies: Recurrent CDI=10, Index CDI=21, FMT=9, Infant longitudinal=16, NICU=23 (Table S2)

Discussion

In this study, we sought to identify species-level abundances of C. difficile in 16S rRNA gene sequence datasets from different patient populations using a validated algorithm (Resphera Insight). Similar to previous studies of Listeria monocytogenes18 and Salmonella enterica,19,20 validation using a high-resolution taxonomic assignment method from 804 novel C. difficile isolates established an overall sensitivity of 99.9% with a marginal false positive rate less than 0.1%, suggesting that C. difficile could be distinguished from other related microbiota members.

Compared to the microbiota of healthy individuals, we observed a higher presence and relative abundance of C. difficile in microbiota data collected from two CDI patient cohorts. 8.5% of healthy individuals were positive for C. difficile using our approach, supporting previous epidemiological assessments of asymptomatic carriage rates.25,26,27,28 Although analysis of CDI datasets revealed a wide distribution of C. difficile relative abundances (ranging from virtually undetectable to above 50% of total sequences), the relative abundance of detected C. difficile in relation to other members of the microbiota was significantly lower in healthy individuals than that of CDI patients. The ability to assess C. difficile levels as part of the microbiota community is potentially more important within population surveys compared to diagnosis using traditional PCR or GDH/EIA tests that merely account for the presence of C. difficile using toxin B or GDH as a proxy.

While detection of C. difficile from 16S rRNA gene sequence data is limited by sequencing depth, our results suggest that C. difficile does not generally reside in healthy adults. In contrast, we did not detect C. difficile in all patients with CDI. The relative presence of C. difficile in these patients is likely below the detection limit given the available sequencing depth, however some of the samples collected from patients in the Seekatz dataset were collected during antibiotic treatment, thus potentially limiting growth of C. difficile during those time points. Indeed, Seekatz et al. report that they were unable to retrieve C. difficile strains from all patient time points via anaerobic cultivation, generally the gold standard for C. difficile detection and diagnosis.

In a third cohort of 14 recurrent CDI patients receiving fecal microbiota transplantation from nine healthy donors (FMT; Table S2, Fig. 3), C. difficile was less frequently detected than the Seekatz and Khanna index CDI patient groups. Only 4 of 14 FMT patients had any detectable levels of C. difficile before treatment, and 3 of 14 had observations of C. difficile post-FMT. Notably, Resphera Insight detected C. difficile presence in both patients who went on to develop symptomatic CDI post-FMT (recipient IDs 005 and 006).9 Prior to FMT, all patients were treated with vancomycin (125 mg 4× per day) for at least 4 days before and the day of transplantation. Thus, we attribute the reduced detection of C. difficile in this cohort to differences in patient treatment before sampling.

Applying our approach to a longitudinal dataset of 38 premature infants in a single NICU, we identified C. difficile in two-thirds of this patient cohort. Asymptomatic carriage of C. difficile among infants has been observed to be higher than for adults, and it remains unknown whether infant cases of CDI represent true disease.29,30 While CDI testing of infants is not recommended,30 recent epidemiological studies indicate 26% of children hospitalized with CDI are infants under 12 months of age, and 5% are neonates.31 In one study of 753 pediatric patients 0 to 12 years of age, 2.9% of CDI outpatients, 4.6% of CDI inpatients, and 6.6% of healthy controls were positive for C. difficile toxin B.32 Another recent study of C. difficile in 338 healthy infants (<2 yrs) in the United Kingdom found 10% were colonized at enrollment with a toxigenic strain, and 49% became colonized with a toxigenic strain post-enrollment.33 Symptomatic Clostridium difficile infections are believed not to occur in infants due to the expected lack of specific toxin receptors and under-developed signaling pathways in the gut; however, these proposed mechanisms have not been rigorously evaluated in studies of humans.34,35,36 Multiple case studies have argued that CDI can occur in this patient population,36 and there is ongoing debate about the appropriate policy for treatment of symptomatic children who test positive for C. difficile.37,38

Our analysis of an infant case study of asymptomatic colonization during the first 18 months of life identified a reduction in C. difficile relative abundance after abrupt transition from human milk to cow’s milk. Yet in a large longitudinal study by Stoesser and colleagues, multivariate analysis demonstrated that breastfeeding (mixed with formula or exclusively) was protective against asymptomatic C. difficile colonization.33 As noted by Davis and colleagues,16C. difficile does not carry the functional capacity for cleaving monosaccharides from oligosaccharide side chains and thus depends on the generation of monomeric glucose by other commensal members of the gut microbiome.39 Additionally, C. difficile relies on sialic acid as a carbon source for expansion made available by other commensals such as Bifidobacterium species.40 Therefore, the reduction of C. difficile after transition to cow’s milk is potentially the result not of milk source alone, but shifting microbial community composition and the presence of substrates by which C. difficile may thrive.

We were also able to identify a significant negative correlation between the abundance of C. difficile and C. scindens in one of the CDI cohorts, confirming similar trends reported by Buffie et al.15C. scindens, a secondary bile acid producer of deoxycholic acid which has been shown to protect against CDI, may have important translational implications.13,41 New and consistent negative correlations were also identified between C. difficile and multiple species within the Blautia genus including B. faecis, B. luti, B. schinkii, and B. wexlerae. Notably, some members of the Blautia genus are known for 7α-dehydroxylating activity of primary bile acids,42,43,44 however this remains to be evaluated for the species we identified in this study. These data suggest that species other than C. scindens may provide relevant functional capabilities in the context of CDI and prove to be informative in the development of future microbial-based therapeutics. One exception to these findings was the lack of negative correlations identified within the NICU infant cohort, which can be attributed to the very limited observations of these Blautia species and C. scindens in the overall dataset (Table S3). Indeed, among the 322 NICU infant samples analyzed, only B. luti and B. wexlerae were observed at all, and only in 5 (1.6%) and 2 (0.6%) samples, respectively, which precluded their evaluation with the CCREPE method.

While microbiome profiling through 16S rRNA gene sequencing is unlikely to replace existing methods for routine diagnosis of CDI, sequence-based assessment of C. difficile levels in the context of microbiota profiling rather than presence alone may prove valuable in surveillance of C. difficile in patient populations, prediction of disease outcome, or the development of new therapies for CDI. Although our study is limited to 16S rRNA gene-based identification of C. difficile and cannot predict whether a strain produces toxin or carries a functional pathogenicity locus,45 consideration for accurate identification of C. difficile and related members may be useful in assessing clinical outcomes of new microbial therapies that rely on 16S rRNA gene sequencing to validate recovery of the microbiota.

Methods

Validation of Resphera Insight for identification of C. difficile

Whole-genome shotgun sequence datasets available from (i) The Wellcome Trust Sanger Institute and (ii) The University of Maryland Institute for Genome Sciences designated as novel C. difficile isolates were downloaded from the NCBI Sequence Read Archive (see Table S1 for accessions), trimmed for quality using Trimmomatic46 and assembled into contigs using Minia.47 Contigs containing portions of 16S rRNA genes were identified using BLASTN48 and extracted for amplicon simulations. For each isolate, we subsequently simulated 16S rRNA amplicon sequence reads (10,000 per isolate) from the V4 region (the primary amplicon region selected in the real datasets) with a random nucleotide error rate of 0.5%. The Diagnostic True Positive Rate was computed as the percentage of sequences unambiguously assigned by Resphera Insight to C. difficile.

For false positive assessment, simulated V4 sequences were generated from reference 16S rRNA genes for 22 unique species within the Clostridium XI cluster (10,000 per species, 0.5% nucleotide error rate). False positives were defined as unambiguous assignments to C. difficile.


Processing of 16S rRNA gene sequence datasets

Raw 16S rRNA gene sequence datasets were processed as follows: Raw overlapping paired-end reads were merged into consensus fragments by FLASH49 requiring a minimum 20 bp overlap with 5% maximum mismatch density, and subsequently filtered for quality (targeting error rates < 1%) and length (minimum 200 bp) using Trimmomatic46 and QIIME.50 Spurious hits to the PhiX control genome were identified using BLASTN and removed. Sequences were then trimmed of their associated primers, evaluated for chimeras with UCLUST (de novo mode),51 and screened for human-associated contaminants using Bowtie252 searches of NCBI Homo sapiens Annotation Release 106. Mitochondrial contaminants were detected and filtered using the RDP classifier53 with a confidence threshold of 50%, and passing high-quality 16S rRNA gene sequences were subsequently assigned to a high-resolution taxonomic lineage using Resphera Insight (Baltimore, MD).18,19,20,54,55 Briefly, the method relies on (i) a manually curated 16S rRNA gene database including 11,000 unique species and (ii) a hybrid global-local alignment strategy to assign sequences a species-level taxonomic lineage. While the method attempts to achieve species-level resolution, if the internal statistical model indicates uncertainty in final species membership, the tool minimizes false positives by providing “ambiguous assignments” i.e., a list of species reflecting all relevant candidates. For example, if a 16S rRNA gene fragment is ambiguous between Veillonella atypica and Veillonella dispar, the algorithm will provide the ambiguous assignment: “Veillonella_atypica:Veillonella_dispar.”


Statistical analyses

Correlations between C. difficile and other species were computed using CCREPE (v.1.10.0)24 (http://huttenhower.sph.harvard.edu/ccrepe). CCREPE (Compositionality Corrected by REnormalization and PErmutation) utilizes an N-dimensional extension of the checkerboard score particularly suited to similarity score calculations between compositions derived from ecological relative abundance measurements of co-occurrence or co-exclusion. Two sample statistical comparisons utilized the Mann-Whitney U test unless otherwise noted.

In silico evaluation for species identified in CCREPE analysis

For single species reported in CCREPE correlation analysis, we simulated noisy 16S rRNA gene sequences (V4 region; 0.5% error rate; 1000 seqs per species), and calculated the frequency of (1) assignments that included the correct species (allowing for ambiguous assignments), (2) unambiguous assignments to the correct species, and (iii) mis-assignments that did not include the correct species (Table S4).


Ethics approvals and consent to participate

IRB approval and patient consent statements from each study: Recurrent CDI (Seekatz et al.10)—All subjects signed written consent to participate in this study. This study was approved by the University of Michigan Institutional Review Board (Study HUM33286; originally approved 8/26/2009).

Index CDI (Khanna et al.21)—We prospectively recruited 88 patients (median age 52.7 years, interquartile range 36.9–65.1; 60.2% female) with their first CDI episode (from 3/2012–9/2013) as identified from the Clinical Microbiology Laboratory at Mayo Clinic, Rochester, Minnesota and collected an aliquot from the stool samples that led to the diagnosis. Clinical data including demographics, hospitalization status, concomitant medications, CDI severity, laboratory parameters, prior and concomitant antibiotic use, initial CDI treatment, treatment response and recurrent CDI were obtained by a review of the electronic medical record.

NICU Infants (Zhou et al.23)—Samples were collected following a protocol that was approved by the Partner’ s Human Research Committee (IRB) for Brigham and Women’ s Hospital. All study procedures were approved by the IRBs at both Brigham and Women’ s Hospital in Boston, MA and at The Genome Institute in St. Louis, MO. The IRB deemed this study to be of minimal risk with no interaction and no intervention with human subjects and thus, was exempt from consent.

Infant Longitudinal (Davis et al.16)—The study was approved by the TechLab Institutional Review Board and included informed consent obtained from the mother.

FMT (Seekatz et al.9)—Informed consent was received from all participants under an approved Institutional Review Board (IRB) protocol at Essentia Health Duluth Clinic (IRB no. SMDC-09068; principal investigator, Timothy Rubin, FDA Investigational New Drug [IND] no. 15460).

Healthy Controls (Seekatz et al. submitted)—All subjects signed written consent to participate in this study. This study was approved by the University of Michigan Institutional Review Board (Study HUM33286; originally approved 8/26/2009).


Data availability

NCBI BioProject accessions of publicly available 16S rRNA gene sequence datasets used in this study: PRJNA307992, PRJNA342347, PRJNA264177, PRJNA331150, PRJNA238042, and PRJNA386260 (Table S2).

Additional Information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Acknowledgements

We thank Cynthia Sears, Karen Carroll, and David Cook for helpful suggestions on this work. This work was supported in part by the ERIN CRC (Enteric Research Investigative Network Cooperative Research Center), (U19AI09087, NIAID), awarded to V.B.Y. A.M.S. supported by the National Center for Advancing Translational Sciences (UL1TR000433).

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https://www.nature.com/articles/s41522-017-0043-0

C diff Infection Control and Hospital Epidemiology Initiative Helps Reduce CDI Rates in VA Facilities

A significant decrease in rates of clinically confirmed long-term care facility onset Clostridium difficile infection (CDI) at 132 Veteran’s Affairs facilities coincided with implementation of a nationwide prevention initiative, researchers report in a new study in Infection Control and Hospital Epidemiology.

The initiative for prevention of CDI in VA long-term care facilities (LTCFs) was implemented in February 2014 following implementation in VA acute care facilities in July 2012. The initiative, which emphasizes environmental management, hand hygiene, contact precautions, and institutional culture change, was extended and tailored to VA LTCFs because they are often linked to VA acute care facilities, where CDI has become the most common healthcare-associated infection. To evaluate the impact of the initiative, the researchers analyzed quarterly CDI trends from the first 33 months of the program and compared them with the 2 years prior to implementation.

The analysis found that there were 137,289 admissions, 9,288,098 resident days, and 1,373 clinically confirmed LTCF-onset CDI cases from April 2014 through December 2016.

The nationwide number of clinically confirmed LTCF-onset CDI cases did not change in the 2 years prior to implementation of the prevention initiative but decreased by 36.1% over the 33-month analysis period.

The results mirror the experience in VA acute care facilities, which saw a 15% drop in hospital-acquired CDI cases over the first 33 months of the prevention initiative, and the authors note that this may have had an impact on their findings, along with strong leadership from the VA Central Office and individual facility accountability.

“The exact reason for the decrease in cases within the VA LTCFs is not known,” they write. “Given the large number of facilities involved and the long observation period, we were not able to collect data on individual facility activities or sustainability of activities; hence, we cannot report a ‘magic bullet’ responsible for the declining trend.”

Study shows substantial burden of primary, recurrent C diff

In another study on CDI, researchers with Merck’s Center for Observational and Real World Evidence estimated the healthcare resource utilization (HCRU) and costs attributable to primary CDI and recurrent CDI (rCDI).

In the retrospective observational study, published in Clinical Infectious Diseases, the researchers analyzed administrative claims data from two commercial databases representing nearly 50 million individuals with private health insurance.

To obtain hospitalized days and costs attributable to primary CDI, patients without CDI were matched 1:1 by propensity score to those with primary CDI but no recurrences. To obtain hospitalized days and costs associated with rCDI, patients with primary CDI but no recurrences were matched 1:1 to those with primary CDI plus one recurrence.

A total of 55,504 CDI patients were identified from July 2010 through June 2014, and among those patients 24.8% had a recurrence. Compared to those patients without CDI, the cumulative hospitalized days and healthcare costs attributable to primary CDI were 5.20 days and $24,205. Compared to those patients with primary CDI only, the cumulative hospitalized days and healthcare costs attributable to rCDI were 1.95 days and $10,580.

“In conclusion, the HCRU and economic burden associated with primary and rCDI are quite substantial,” the authors write. “Better prevention and treatment of CDI, especially rCDI, are needed.”

To read article in its entirety please click on the following link:  http://www.cidrap.umn.edu/news-perspective/2018/01/stewardship-resistance-scan-jan-22-2018