Category Archives: C. diff. Research Community

Researchers From Loyola Medicine Retrospectively Studied 100 Vancomycin Taper and Pulse Treatment Patients Treated For Recurrent C. difficile Infection

A tapered and pulsed regimen with vancomycin — with diligent follow-up — can achieve significant cure rates in recurrent Clostridium difficile (C. difficile) infected patients, according to a new study.

Researchers from Loyola Medicine retrospectively studied 100 vancomycin taper and pulse treatment patients treated for recurrent C. difficile infection between January 1, 2009 and December 31, 2014. Their clinic, the study authors wrote, has been a referral center for the infection for the past decade.

To read the article in its entirety please click on the following link:

http://www.mdmag.com/medical-news/pulsed-and-tapered-vancomycin-likely-route-to-recurrent-clostridium-difficile-cure

However, despite the guidelines for treatment of recurrent C. difficile infection being not too different than recurrent episodes – except for the use of vancomycin when the case is severe – there have not been many studies on this vancomycin taper and pulsed dosing. 

The researchers observed that after a referral, the confirmed recurrent C. difficile patients were treated with a vancomycin taper and pulse regimen: a taper of vancomycin to once-daily, followed by alternate day dosing; or once-daily followed by alternate day dosing; followed by every third day, for at least 2 weeks. After this regimen, all patients had 90-day follow-up documentation.

On average, the patients in the clinic were on their third C. difficile diarrhea episode. Half of the patients had also received a standard course of vancomycin, while another third had received some type of vancomycin taper regimen, the researchers said.

Despite the fact that many of these patients were a “treatment experienced” population, 75% of the patients who received a supervised vancomycin taper and pulsed regimen achieved a cure,  study author Stuart Johnson  MD, . He added that the results were further improved for patients who received the expended pulse phase: 81% achieved a cure.

“The findings were not unexpected to us, but I think that many clinicians will be surprised how well a deliberate, prolonged vancomycin taper and pulse regimen – with careful follow up – works,” Johnson said.

There were no significant differences among the patients in terms of gender, age, concomitant antibiotics, proton pump inhibitor use, histamine receptor-2 blocker use, or patients with a regimen greater than 10 weeks in length, the researchers continued.

The researchers added that their finding of improved cure rates with alternate-day dosing plus every third day dosing over strictly alternate-day dosing is consistent with the hypothesis that pulsed dosing can promote a cyclical decrease in spore burden, they wrote. This can also permit the resetting of normal microbiota in the gut.

Johnson concluded that the clinical implications of the study show most recurrent C. difficile patients do not need fecal microbiota transplant (FMT).

“FMT has received an enormous amount of press and this procedure is now widely available throughout the US,” Johnson said. “FMT is attractive because it addresses one of the primary mechanisms involved with recurrent C. difficile infection, a marked disruption of the resident bacteria that populate the intestine and provide an important host defense against C. difficile.

Although physicians screen donor feces for “known pathogens,” not all is known of the potential complications to come from FMT, Johnson said.

“In addition, it appears that efficacy with a carefully supervised vancomycin taper and pulse regimen compare to that achieved with FMT,” Johnson said.

The study, “Vancomycin Taper and Pulsed Regimen with careful Follow up for Patients with Recurrent Clostridium difficile Infection,” was published in the journal Clinical Infectious Diseases.

Norman B. Javitt, M.D. Is Welcomed As a Member Of the C Diff Foundation, R & D Committee

We are pleased to welcome
Norman B. Javitt, M.D. to the
C Diff Foundation.

Dr. Javitt has an extensive professional career in health care.  New York University Medical Center: Instructor, then Assistant Professor Medicine where his career was devoted mostly to research in liver disease, specifically in inborn errors of cholesterol metabolism affecting newborns, and to teaching medical students.

Cornell University Medical School-New York Hospital:  Associate Professor of Medicine, then Professor of medicine and Chief, Division of Gastroenterology the research program continued to grow, attracting many fellows from all over the world.  Also provided care for private patients, both children and adults, with difficult liver problems.

New York University Medical Center:  Professor of Medicine and of Pediatrics, Division chairman Hepatic Diseases April, Research professor 2015-presnt.  At NYUMC Dr. Javitt has been focusing on C. difficile research  and teaching medical students and house staff.  His research interest has also expand to many areas of cholesterol synthesis and metabolism other than just liver disease.

Dr. Javitt has published research papers in age-related macular degeneration, in vitro fertilization, and Alzheimer’s disease.  He has also published more than 150 research papers, in addition to several books and review articles, and presented work at numerous professional meetings and symposia throughout the world.  His work has been supported by the National Institutes of Health, by private foundations and Pharmaceutical companies.  Dr. Javitt is welcomed by fellow researchers in the Research and Development Committee Chaired by Professor Simon M. Cutting, Ph.D…

C. diff. May Carry Risks in Preoperative and Postoperative Patients

 

There are risks for acquiring a C. difficile infection (CDI).

The risks range from the overuse of Antibiotics, Immunosuppressed patients, prolonged hospital stays, being a patient in a long-term care facility, and for the senior population.

There may also be a risk for the surgical patients and the following study explains the study and the results:

To read the article in its entirety please click on the following link: https://cdifffoundation.wordpress.com/wp-admin/post-new.php

A lengthy study of four surgical specialties has determined that Clostridium difficile infection (CDI) is a major risk factor for postoperative patients, although incidences varied.

Although it has been shown that CDI is associated with increased cost, morbidity and mortality in patients after surgery, this is the first to examine C. difficile rates across multiple surgical specialties (Infect Control Hosp Epidemiol 2017:1-4. doi: 10.1017/ice.2017.158).

“This study has great importance as the landscape of repayment for elective surgical procedures changes,” said the study’s lead author, James Bernatz, MD, a surgeon with the Department of Orthopedics and Rehabilitative Medicine at University of Wisconsin Hospital and Clinics, in Madison. “With more surgeries being reimbursed as bundled payments, hospitals are pressured to limit costs. As C. diff infection has been found to increase length of stay by one week and double the cost of care, it is clearly a postoperative complication to be avoided.”

Dr. Bernatz and his colleagues conducted the study at a 592-bed tertiary care academic center. They used the hospital’s quality improvement database to review admissions to the orthopedic surgery, neurosurgery, trauma surgery and general surgery units from January 2014 through July 2016. Those patients who underwent an inpatient surgical procedure, and did not meet the exclusion criteria, were surveyed.

Case patients were defined as those who underwent an inpatient procedure and subsequently developed a health care–associated CDI, which was defined as a positive polymerase chain reaction (PCR) test result for C. difficile toxin gene recorded more than 72 hours after admission and within 12 weeks of discharge.

They found 52 cases of CDI among 11,310 surgical admissions to four hospital units: general surgery, neurology, orthopedics and trauma. In all 52 cases, patients had a PCR-positive test result more than 72 hours after admission and within 12 weeks of discharge, making the incidence rate 0.80 cases per 1,000 patient-days. The trauma unit had the highest rate at 9.5 CDI cases per 1,000 admissions (11 cases over 1.160 admissions during the study period). General surgery had 30 cases among 3,447 admissions for a rate of 8.7; orthopedics had six cases among 4,339 admissions for a rate of 1.4; and neurology had five cases among 2,364 admissions for a rate of 2.1.

A number of risk factors were surveyed, including the use of antibiotics.

Regarding antibiotic use, the researchers found that the odds of CDI increased 3.34-fold when the perioperative antibiotic is continued more than 24 hours after surgery, outside of the perioperative window. Antibiotic use, other than the perioperative antibiotic, while in the hospital also was associated with 2.2 times greater odds of CDI. And exposure to antibiotics as long as six months before surgery increases the odds of CDI more than threefold.

“Although the surgeon cannot necessarily control the antibiotics prescribed to their patients in the year leading up to surgery, they can control antibiotic administration in the perioperative and postoperative period,” Dr. Bernatz said. “Antibiotics should be limited to one prophylactic preoperative dose, unless 24 hours of antibiotics are indicated. In the immediate postoperative period, antibiotics should be used judiciously.”

Other significant risk factors included number of hospital admissions in the past year and proton pump inhibitor or histamine type 2 receptor blocker use in the previous six months. “Previous studies have shown a correlation between CDI and hospital admission in the previous 3 months,” the researchers wrote. “Our study reports that this association extends to 12 months. We found that the number of hospital admissions in the past year increases the odds of CDI by 133% for each admission.”

A higher American Society of Anesthesiologists (ASA) physical status classification also was a significant risk factor for CDI; ASA IV or V patients were 15 times more likely to develop CDI than those with ASA class I or II disease, according to the researchers.

Dr. Bernatz said additional research is needed to further reveal these links. “Other studies could examine the rate of C. diff infection between operations within one subspecialty to determine if certain operative variables or patient characteristics affect the postoperative risk of C. diff infection,” he said.

The Latest Developments in C. diff Research and Treatment

 

 

 

 

 

The Program Podcast is Now Available —

Listen at your leisure as our guest, Dr Mary Beth Dorr, PhD, Clinical Director, Clinical Research, Infectious Diseases, and he product development team lead for bezlotoxumab, Merck & Co., Inc.  provided us with an overview of a C. diff. infection, the challenges of recurrence, the latest clinical research overview, current treatment landscape, and pending new C. diff infection treatment guidelines from the Infectious Diseases Society of America (IDSA) that are anticipated to be released fall of 2017.

Click on the C. diff. Spores and More Logo to be connected to the podcast

Researchers Find Key Role of Excess Calcium In the Gut In C. difficile infections (CDI)

New research shows, it can’t make this last, crucial move without enough of a humble nutrient: calcium.

And that new knowledge about Clostridium difficile (a bacterium also known as “C. diff“) may lead to better treatment for the most vulnerable patients.

The discovery, made in research laboratories at the University of Michigan Medical School and the U.S. Food and Drug Administration, is published in the online journal PLoS Pathogens.

It helps solve a key mystery about C. diff: What triggers it to germinate, or break its dormancy, from its hard spore form when it reaches the gut.

Though the findings were made in mice, not humans, the researchers say the crucial role of calcium may help explain another mystery: Why some hospital patients and nursing home residents have a much higher risk of contracting C. diff infections and the resulting diarrhea that carries its spores out of the body.

That group includes people whose guts are flooded with extra calcium because they’re taking certain medications or supplements, have low levels of Vitamin D in their blood or have gut diseases that keep them from absorbing calcium.

The new discovery shows that C. diff can recognize this extra calcium, along with a substance called bile salt produced in the liver, to trigger its awakening and the breaking of its shell.

Previous research had suggested it couldn’t do this without another key component, an amino acid called glycine. But the new findings show calcium and the bile salt called taurochlorate alone are enough. Mouse gut contents that were depleted of gut calcium had a 90 percent lower rate of C. diff spore germination.

“These spores are like armored seeds, and they can pass through the gut’s acidic environment intact,” says Philip Hanna, Ph.D., senior author of the new paper and a professor of microbiology and immunology at U-M. “Much of the spore’s own weight is made of calcium, but we’ve shown that calcium from the gut can work with bile salts to trigger the enzyme needed to activate the spore and start the germination process.”

Ironically, the researchers say, one way to use this new knowledge in human patients might be to add even more calcium to the system.

That could awaken all the dormant C. diff spores in a patient’s gut at once, and make them vulnerable to antibiotics that can only kill the germinated form. That could also prevent the transmission of more spores through diarrhea to the patient’s room. That could slow or stop the cycle of transmission that could threaten them or other patients in the future.

Hanna’s graduate student, Travis Kochan, made a key observation that led to the discovery. He noted that the fluid “growth medium” that the researchers typically grow C. diff in for their studies had calcium in it. He realized this could artificially alter the results of their experiments about what caused C. diff spores to germinate.

So, he used a chemical to remove the calcium while leaving all the other nutrients that                  keep C. diff growing. The result: no new spore germination happened in the calcium-free growth medium.

FDA’s Center for Biologics Evaluation and Research conducted further research in laboratory dishes and in the guts of mice. FDA’s Paul Carlson, Ph.D., a former U-M research fellow, and fellow FDA scientists in his laboratory found that C. diff spores that were mutated so that glycine couldn’t act on them could still germinate and colonize mice. This suggested that calcium, and not glycine, was critical for this process.

Both mutant and regular forms of the bacteria could still activate an enzyme inside the C. diff spore that led the bacteria to start dissolving their hard shell. This released the store of calcium that the spore had been harboring inside itself, and increases the local level of the nutrient even further.

“These spores don’t want to germinate in the wrong place,” says Kochan, whose grandfather suffered from a severe C. diff infection which ultimately led to his death. “C. diff spores have specialized to germinate in the gut environment, especially in the environment of the small intestine, where calcium and the bile salt injection from the liver comes in.”

Hanna notes that the bile salt connection to C. diff spore germination was first discovered at U-M in 1982 by a team led by Ken Wilson, M.D.

Calcium and the gut

Certain ailments and treatments cause defects in calcium absorption, but are also risk factors for C. diff infections. For example, patients with vitamin D deficiency are five times more likely to get C. diff.

Medications aimed at calming acid reflux – such as proton pump inhibitors – and steroids can increase the amount of calcium in the gut. A Vitamin D deficiency can keep the body from reabsorbing calcium through the gut wall, allowing it to build up.

And people with inflammatory bowel diseases such as Crohn’s and colitis also have a harder time absorbing calcium from food through their gut walls.

Older adults are also often counseled to take calcium supplements to compensate for lower calcium levels and protect their bones from fracturing.

Hanna cautions that the new findings should not cause any patients to stop taking their medications or doctor-recommended supplements, or to start taking new ones. But he hopes to work with clinicians at U-M and beyond to test the new knowledge in a clinical setting. Meanwhile, he and Kochan and their FDA and U-M colleagues will continue to study C. diff germination in mice and look for ways to block the enzymes crucial to spore germination.

 

To read the article in its entirety – please click on the following link to be re-directed:

http://www.news-medical.net/news/20170713/Scientists-reveal-key-role-of-excess-gut-calcium-in-C-diffc2a0infections.aspx?utm_source=dlvr.it&utm_medium=twitter

Inquire and Consider Becoming A Candidate In a C. difficile Infection Clinical Trial To Help You – Help Them – Help Others

Every scientific research and development, every clinical trial in progress is a glimmer of hope………..HOPE for clinically safe and approved avenues to prevent and treat a
C. difficile infection
.

 

 

Listed below you will find a web link that will redirect you to obtain information that pertains to organizations who have on-going
C. difficile Prevention and Treatment clinical trials in progress.  

Click on each organization’s website link to review their research and clinical trial study opportunities — Inquire if you or your loved one qualify to participate in a study. Please direct all clinical trial questions to the companies offering the clinical trials.  Thank you.

To Learn More About Clinical Trials —

ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. Learn more About Clinical Studies and About This Site, including relevant History, Policies, and Laws.  Click on the link below to be redirected to the clinicaltrials.gov website:

https://clinicaltrials.gov/

 

Clinical Studies In Progress To

Help You — Help Them — Help Others  ♥

 

 

Here is a list of Clinical Trial Phases:

Clinical trials are conducted in a series of steps, called phases – each phase is designed to answer a separate research question.

  • Phase I: Researchers test a new drug or treatment in a small group of people for the first time to evaluate its safety, determine a safe dosage range, and identify side effects.
  • Phase II: The drug or treatment is given to a larger group of people to see if it is effective and to further evaluate its safety.
  • Phase III: The drug or treatment is given to large groups of people to confirm its effectiveness, monitor side effects, compare it to commonly used treatments, and collect information that will allow the drug or treatment to be used safely.
  • Phase IV: Studies are done after the drug or treatment has been marketed to gather information on the drug’s effect in various populations and any side effects associated with long-term use.

Additional Resource Information on clinical trials can be found at http://clinicaltrials.gov/info/resources

 

To review C. difficile Clinical Trials Available Today, please click on the following link to be redirected:

https://cdifffoundation.org/clinical-trials-2/

 

 

 

 

DISCLAIMER
“The C Diff Foundation’s mission is to educate and advocate for Clostridium difficile infection prevention, treatments, support, and environmental safety worldwide.
The C Diff Foundation’s organization is comprised of 100% volunteering members who are dedicated to our mission and adhere to the Foundation’s Code of Ethics
which prohibits paid endorsements and/or paid promotion of products, services, medications, or clinical studies in progress.   All website postings are strictly for
information purposes.
All website entries, public presentations, and workshops are to raise C. diff. infection awareness in all areas of the C Diff Foundation’s mission statement, including infection prevention, diagnostics, sepsis, healthcare-associated infections, antimicrobial resistance, antibiotic stewardship and provide education on all the above.”

C diff Infection Compared Control in 6 United Kingdom Hospitals With Whole-Genome Sequencing (WGS)

David W. Eyre
Warren N. Fawley
Anu Rajgopal
Christopher Settle
Kalani Mortimer
Simon D. Goldenberg
Susan Dawson
Derrick W. Crook
Tim E. A. Peto
A. Sarah Walker

.

Clin Infect Dis cix338.
Published:
29 May 2017 

Abstract

Background Variation in Clostridium difficile infection (CDI) rates between healthcare institutions suggests overall incidence could be reduced if the lowest rates could be achieved more widely.
Methods.

We used whole-genome sequencing (WGS) of consecutive C. difficile isolates from 6 English hospitals over 1 year (2013–14) to compare infection control performance. Fecal samples with a positive initial screen for C. difficile were sequenced. Within each hospital, we estimated the proportion of cases plausibly acquired from previous cases.

Results.

Overall, 851/971 (87.6%) sequenced samples contained toxin genes, and 451 (46.4%) were fecal-toxin-positive. Of 652 potentially toxigenic isolates >90-days after the study started, 128 (20%, 95% confidence interval [CI] 17–23%) were genetically linked (within ≤2 single nucleotide polymorphisms) to a prior patient’s isolate from the previous 90 days. Hospital 2 had the fewest linked isolates, 7/105 (7%, 3–13%), hospital 1, 9/70 (13%, 6–23%), and hospitals 3–6 had similar proportions of linked isolates (22–26%) (P ≤ .002 comparing hospital-2 vs 3–6). Results were similar adjusting for locally circulating ribotypes. Adjusting for hospital, ribotype-027 had the highest proportion of linked isolates (57%, 95% CI 29–81%). Fecal-toxin-positive and toxin-negative patients were similarly likely to be a potential transmission donor, OR = 1.01 (0.68–1.49). There was no association between the estimated proportion of linked cases and testing rates.

Conclusions.

WGS can be used as a novel surveillance tool to identify varying rates of C. difficile transmission between institutions and therefore to allow targeted efforts to reduce CDI incidence.

To view the article in its entirety please click on the following link:

Preventing Clostridium difficile infection (CDI) is a priority for infection control teams, as it remains a major healthcare-associated infection; although the incidence of healthcare-associated CDI in the United Kingdom has fallen to 1.5 per 10000 inpatient bed-days [1], rates across Europe range from 0.7 to 28.7/10000 bed-days [2], and there were an estimated 293000 healthcare-associated cases in the United States in 2011 [3].

Variation in CDI incidence across countries and between healthcare institutions [4] suggests overall incidence could be reduced if the lowest rates could be achieved more widely. Surveillance programs [5] and penalties for healthcare institutions [6] have been implemented to promote reductions. However, robustly identifying the best performing institutions is challenging.

Variations in true incidence can arise from differences in patient risk factors or locally circulating strains. However, testing strategy also influences reported incidence; reported CDI incidence is associated with testing rates [2]. With low testing rates, CDI ascertainment is likely to be suboptimal. Conversely, high testing rates may lead to overdiagnosis, for example, from testing C. difficile colonized patients, who do not have CDI but may have diarrhea of another cause.

The lack of a universally accepted objective CDI case definition means that robust comparisons of infection rates between institutions should ideally also consider independent measures of which patients are being tested to assess the comparability of differing testing strategies [7].

Additionally, assessing potential sources of healthcare- attributed CDI cases [8] is complex, requiring differentiation between lapses in infection control around symptomatic cases or more generally, deviation from optimal antimicrobial stewardship, and external factors, for example, the food chain. Healthcare exposure increases the risk of C. difficile acquisition; both CDI and colonization increase during hospital stay [9]. However, despite this strong association, studies using whole-genome sequencing (WGS) [10–12] and other genotyping schemes [13–15] have shown that, in endemic settings with standard infection control, only the minority of infections are likely to have been acquired from other hospitalized CDI cases. However, the extent to which this proportion of linked cases varies between hospitals is unknown. Furthermore, such potential variance in linkage rates could identify a potentially preventable group of CDIs.

We investigated variation in the proportion of linked cases using WGS of consecutive C. difficile isolates from 6 hospitals in England and explored whether this could be used to assess their infection control effectiveness, by assessing the proportion of cases plausibly acquired from (linked to) previous cases.

METHODS

Samples and Settings

Hospitals in England are recommended to store frozen aliquots of C. difficile–positive fecal samples for 12 months [16]. Stored consecutive hospital and community diarrheal samples submitted for routine C. difficile testing at 6 hospital laboratories were studied, including a tertiary referral center and teaching hospital, and 5 district general hospitals serving a mix of urban and rural populations (see Supplement). Samples were obtained for a one-year period at each hospital between January 2013 and October 2014. Results were anonymized by assigning a computer-generated random identifier, hospital 1 to hospital 6.

Each hospital used the United Kingdom-recommended 2-stage C. difficile testing algorithm [17]. Hospital 1 used toxin gene polymerase chain reaction (PCR) as a screening test, hospital 2 both glutamate dehydrogenase (GDH) enzyme immunoassay (EIA) and toxin gene PCR as a combined screening test, and hospitals 3–6 a GDH screen. Screen-positive samples underwent confirmatory fecal-toxin EIA testing. Screen-positive, fecal-toxin-positive patients were regarded as having CDI. Toxin gene PCR was also performed as a third-line test on all GDH-positive samples at hospitals 3 and 6, and on samples from inpatients at hospital 5. PCR-positive, fecal-toxin-negative patients, with a clinical syndrome in keeping with CDI, were regarded as potential cases for treatment and infection control purposes.

All screen-positive fecal samples were sent to Leeds General Infirmary microbiology laboratory, United Kingdom (except hospital 2, which submitted isolates and excluded toxin EIA-negative/PCR-negative samples), where they underwent selective culture for C. difficile [18] and capillary electrophoresis ribotyping [19]. Individual patient consent for use of anonymized bacterial isolates was not required.

Sequencing

DNA was extracted from subculture of a single colony from each culture-positive sample and sequenced using Illumina HiSeq2500. Sequence data were processed as previously (see Supplement) [10, 20], mapping sequenced reads to the C. difficile 630 reference genome [21]. Sequences were compared using single-nucleotide polymorphisms (SNPs) between sequences obtained from maximum-likelihood phylogenies [22], corrected for recombination [23]. Potentially toxigenic strains were identified as those containing toxin genes using BLAST searches of de novo [24] assemblies.

Analysis

For each sample, only the hospital, collection date, and fecal-toxin EIA result were known; no further epidemiological data were available. Within each hospital, sequences were compared with all sequences from samples obtained in the prior 90 days. Samples from the community and hospital were included to increase the chance of identifying transmission events occurring in hospital but leading to CDI onset after discharge. From previous estimates of C. difficile evolution and within-host diversity [10, 25, 26], ≤2 SNPs are expected between isolates linked by transmission within 90 days. Therefore, where ≥1 prior sequences within ≤2 SNPs were identified, a case was considered to have been potentially acquired from another case. A 90 day threshold for linking cases was chosen assuming that cases were rapidly treated and infectiousness declined, and that subsequent cases related by direct transmission occurred within incubation periods implied by surveillance definitions [8] and previous studies [13]. As the sources of cases occurring at the start of the study may themselves have been sampled before the study started, the proportion of cases linked to a prior case was only calculated for cases occurring after the first 90 days, with cases in the first 90 days included only as potential sources for subsequent cases.

Two differing case definitions were considered. Initially, all patients with culture-positive potentially toxigenic C. difficile were considered “cases” to capture possible transmission events involving potentially toxigenic C. difficile irrespective of fecal-toxin status. The analysis was then repeated restricted only to fecal-toxin-positive CDI cases. For comparisons with previously published data, the same definition and analysis approach was applied to fecal-toxin-positive CDI cases occurring within 90 days in Oxford (September 2007 to December 2010, split by calendar year) [10] and Leeds (August 2010 to April 2012) [11].

Risk Factor Analysis

Univariate logistic regression was used to determine whether a case’s toxin status affected the risk of it being genetically related to a prior case, that is, potentially acquired from another case. Similarly, logistic regression was used to determine whether a case’s fecal-toxin status affected the risk of it being genetically linked to a subsequent case, that is, to assess the relative infectiousness of fecal-toxin-positive and toxin-negative patients.

To assess whether the locally circulating strain mix affected transmission estimates, hospital-specific estimates were adjusted for ribotype using multivariate logistic regression (see Supplement).

Simulations

To estimate the impact of missing data (as not all sampled cases were sequenced at some hospitals), we simulated transmission at a theoretical hospital. We subsampled simulated cases and calculated the change in the percentage of cases linked to a prior case as the proportion of missing samples increases (details in Supplement).

METHODS

Samples and Settings

Hospitals in England are recommended to store frozen aliquots of C. difficile–positive fecal samples for 12 months [16]. Stored consecutive hospital and community diarrheal samples submitted for routine C. difficile testing at 6 hospital laboratories were studied, including a tertiary referral center and teaching hospital, and 5 district general hospitals serving a mix of urban and rural populations (see Supplement).

Samples were obtained for a one-year period at each hospital between January 2013 and October 2014. Results were anonymized by assigning a computer-generated random identifier, hospital 1 to hospital 6.

Each hospital used the United Kingdom-recommended 2-stage C. difficile testing algorithm [17].

Hospital 1 used toxin gene polymerase chain reaction (PCR) as a screening test,

Hospital 2 both glutamate dehydrogenase (GDH) enzyme immunoassay (EIA) and toxin gene PCR as a combined screening test, and hospitals 3–6 a GDH screen.

Screen-positive samples underwent confirmatory fecal-toxin EIA testing. Screen-positive, fecal-toxin-positive patients were regarded as having CDI. Toxin gene PCR was also performed as a third-line test on all GDH-positive samples at hospitals 3 and 6, and on samples from inpatients at hospital 5. PCR-positive, fecal-toxin-negative patients, with a clinical syndrome in keeping with CDI, were regarded as potential cases for treatment and infection control purposes.

All screen-positive fecal samples were sent to Leeds General Infirmary microbiology laboratory, United Kingdom (except hospital 2, which submitted isolates and excluded toxin EIA-negative/PCR-negative samples), where they underwent selective culture for C. difficile [18] and capillary electrophoresis ribotyping [19]. Individual patient consent for use of anonymized bacterial isolates was not required.

Sequencing

DNA was extracted from subculture of a single colony from each culture-positive sample and sequenced using Illumina HiSeq2500. Sequence data were processed as previously (see Supplement) [10, 20], mapping sequenced reads to the C. difficile 630 reference genome [21]. Sequences were compared using single-nucleotide polymorphisms (SNPs) between sequences obtained from maximum-likelihood phylogenies [22], corrected for recombination [23]. Potentially toxigenic strains were identified as those containing toxin genes using BLAST searches of de novo [24] assemblies.

Analysis

For each sample, only the hospital, collection date, and fecal-toxin EIA result were known; no further epidemiological data were available. Within each hospital, sequences were compared with all sequences from samples obtained in the prior 90 days. Samples from the community and hospital were included to increase the chance of identifying transmission events occurring in hospital but leading to CDI onset after discharge. From previous estimates of C. difficile evolution and within-host diversity [10, 25, 26], ≤2 SNPs are expected between isolates linked by transmission within 90 days. Therefore, where ≥1 prior sequences within ≤2 SNPs were identified, a case was considered to have been potentially acquired from another case. A 90 day threshold for linking cases was chosen assuming that cases were rapidly treated and infectiousness declined, and that subsequent cases related by direct transmission occurred within incubation periods implied by surveillance definitions [8] and previous studies [13]. As the sources of cases occurring at the start of the study may themselves have been sampled before the study started, the proportion of cases linked to a prior case was only calculated for cases occurring after the first 90 days, with cases in the first 90 days included only as potential sources for subsequent cases.

Two differing case definitions were considered. Initially, all patients with culture-positive potentially toxigenic C. difficile were considered “cases” to capture possible transmission events involving potentially toxigenic C. difficile irrespective of fecal-toxin status. The analysis was then repeated restricted only to fecal-toxin-positive CDI cases. For comparisons with previously published data, the same definition and analysis approach was applied to fecal-toxin-positive CDI cases occurring within 90 days in Oxford (September 2007 to December 2010, split by calendar year) [10] and Leeds (August 2010 to April 2012) [11].

Risk Factor Analysis

Univariate logistic regression was used to determine whether a case’s toxin status affected the risk of it being genetically related to a prior case, that is, potentially acquired from another case. Similarly, logistic regression was used to determine whether a case’s fecal-toxin status affected the risk of it being genetically linked to a subsequent case, that is, to assess the relative infectiousness of fecal-toxin-positive and toxin-negative patients.

To assess whether the locally circulating strain mix affected transmission estimates, hospital-specific estimates were adjusted for ribotype using multivariate logistic regression (see Supplement).

Simulations

To estimate the impact of missing data (as not all sampled cases were sequenced at some hospitals), we simulated transmission at a theoretical hospital. We sub-sampled simulated cases and calculated the change in the percentage of cases linked to a prior case as the proportion of missing samples increases (details in Supplement).

RESULTS

Consecutive samples sent for C. difficile testing at 6 hospitals were studied for 12 months (Table 1). In total, 1052/1098 (96%) of GDH/toxin-PCR screen-positive samples were available: 95/98 (97%) at hospital 1, 144/178 (81%) at hospital 2, 118/127 (93%) at hospital 5 and otherwise 100%. 974/1052 (93%) available samples were confirmed as C. difficile on culture. For the 5 hospitals with available testing data, 887/21539 (4.1%) of samples submitted for testing were culture-positive (Table 1); 971/974 (99.7%) culture-positive samples were successfully sequenced. Of sequenced culture-positive samples, 451/971 (46.4%) were EIA fecal-toxin-positive, 35–71% by hospital. By contrast, 851/971 (87.6%) were potentially toxigenic, that is, had toxin genes detected via sequence data. Hence, 400/851 (47.0%) samples containing potentially toxigenic C. difficile did not have fecal-toxin detected. In the 971 sequenced isolates, the most common ribotypes identified were 014, 015, 005, 002, 020, and 078 (Table 2). Ribotype-027(NAP1/ST-1) only accounted for 16 (2%) cases.

To view graphs and tables, please click the following link:

https://academic.oup.com/cid/article/doi/10.1093/cid/cix338/3857742/Comparison-of-Control-of-Clostridium-difficile

Relatedness to Prior Cases

The proportion of cases plausibly linked to a prior case by recent transmission varied by hospital. Of 851 sequenced potentially toxigenic cases, all were considered as potential sources of infection, but only the 652 obtained after the first 90 days of sampling at each hospital were assessed for linkage to a previous case. Across the 6 hospitals, 128/652 (20%, 95% confidence interval [CI] 17–23%) potentially toxigenic cases were genetically linked to a prior case from the previous 90 days. Hospital 2 had the fewest cases linked to a prior case, 7/105 (7%, 3–13%), hospital 1 had an intermediate number, 9/70 (13%, 6–23%), and hospitals 3–6 had similar numbers of linked cases, 37/153 (24%, 18–32%), 32/134 (24%, 17–32%), 18/76 (24%, 15–35%), and 25/113 (22%, 15–31%), respectively. Hospital 2 had significantly fewer linked cases than hospitals 3–6 (P ≤ .002), with weaker evidence for lower rates in hospital 1 than hospitals 3, 4, and 5 (P = .05, .07, .09, respectively). Overall, 48/128 (38%) of potential transmission recipients were fecal-toxin-negative (11–68% across hospitals, Figure 1A). Fecal-toxin detection in a recipient was associated with increased odds of having a potential transmission donor, odds ratio 1.67 (95% CI 1.12–2.48, P = .01).

 

In total, 59/128 (46%) putative transmission recipients were only linked to ≥1 fecal-toxin-positive potential donors, 50 (39%) to only fecal-toxin-negative donors, and 19 (15%) to both toxin-positive and toxin-negative donors. Considering the 667 cases occurring in the first 270 days at each hospital, that is, the cases with an opportunity to transmit to a sampled case within the next 90 days, 120 (18%) were potential donors. Fecal-toxin-positive and -negative cases were similarly infectious: the odds ratio for a fecal-toxin- positive case, compared to a fecal-toxin-negative case, being a potential transmission donor was 1.01 (95% CI 0.68–1.49, P = .97).

When only considering transmission to and from fecal- toxin-positive cases, fewer cases were genetically linked to a previous case within 90 days, 51/335 (15%, 95% CI 12–20%). We observed a different “ranking” of hospitals compared with the above analysis of linkage rates based on potentially toxigenic isolate-positive patients: hospital 3 had the greatest proportion of fecal-toxin-positive cases genetically related to a prior fecal-toxin-positive case, 31% (22–41%), and hospital 6 the lowest, 0% (0–9%) (Figure 1B).

Results were similar to those for all potentially toxigenic C. difficile (Figure 1A) if all C. difficile sequences, nontoxigenic as well as potentially toxigenic, were considered (Figure 1C). Considering only nontoxigenic isolates, very similarly to potentially toxigenic isolates, 19/96 (20%, 95% CI 12–29%) were genetically linked to a prior patient isolate from the previous 90 days.

There was no evidence that the number of linked cases varied during the study at any hospital (Figure 1D). Because different numbers of sequences were obtained from the different hospitals, we investigated how this affected the estimated proportions of cases linked to a prior case. Estimated proportions of linked cases were relatively stable once approximately 50 cases had been sequenced (Figure 2).

Impact of Testing Frequency

The proportion of originally tested samples that were stored and then culture-positive was similar across the 5 hospitals with testing data, 3.8%–4.3% (P = .89, Table 1). In contrast, testing rates ranged from 98 to 239 samples per 10000 bed-days. There was no association between the estimated proportion of cases linked to a previous case within 90 days and testing rates (P = .19 for all potentially toxigenic cases, Figure 3A, and P = .60 for fecal-toxin-positive cases only, Figure 3B). For comparison, Figure 3B also displays rates of linked cases for previously published data from Oxford and Leeds.

Figure 2:  Proportion of potentially toxigenic cases linked to a previous potentially toxigenic case by hospital and number of sequences obtained. Abbreviation: SNP, single-nucleotide polymorphism.

Adjustment for Ribotype

After adjustment for locally circulating ribotypes, estimates of the proportion of potentially toxigenic cases related to a previous potentially toxigenic case within ≤2 SNPs and ≤90 days remained largely unchanged (Figure 4A). Using the same model, per-ribotype estimates for the proportion of related cases, adjusted for differences across hospitals, showed more variation (Figure 4B, Table 2 for unadjusted proportions). Ribotype-027 had significantly more related cases (adjusted proportion, 57%, 95% CI 29–81%, n = 12) than the comparison group of all other ribotypes (11%, 7–18%, P = .002, n = 124), as did ribotype-002 (25%, 15–38%, P = .04, n = 53), 012 (50%, 29–71%, P = .001, n = 22), and 087 (44%, 23–67%, P = .005, n = 18).

Adjustment for Completeness of Testing

As only 144/178 (81%) of GDH-positive samples at hospital 2 were retrievable for culture we assessed the likely impact of these missing samples on the estimated proportion of linked cases by simulating transmission and sampling at a theoretical hospital (Figure S1). As sampling becomes increasingly less complete, the estimated proportion of linked cases declines proportional to the probability of a case being sampled. Applying our simulation to hospital 2 provides a revised estimate of 8% of cases being linked to a prior case (see Supplement for details).

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DISCUSSION

Here, we demonstrate the value of WGS as a tool to estimate different rates of C. difficile transmission across institutions. Sequencing consecutive C. difficile isolates from routine testing over one year, we found transmission rates varied between 6 hospitals. Considering all patients with potentially toxigenic C. difficile, irrespective of fecal-toxin status, in the best performing hospital only 7% of patients’ isolates were sufficiently genetically related to a previous isolate from another patient to support transmission (8% adjusting for incomplete sampling). By contrast, approximately 3–4-fold more isolates (22–26%) were related in 4 of the other hospitals. These results remained similar after adjusting for the locally circulating strains.

Restricting to only patients with fecal-toxin-positive CDI, we confirmed previous findings that only a minority of CDI cases arise from contact with another symptomatic case: 35% in Oxford [10], 35% in Leeds [11], and 37% of ribotype-027 cases in Liverpool [12], were genetically linked to a previous case, with only a subset of these cases sharing time and space on the same hospital ward.

Applying the criteria for linking cases used in the present study to the Oxford and Leeds data sets, 38% of cases in Oxford were linked to a previous case in 2008 falling to 19% in 2010, and 30% of cases were similarly linked in Leeds. Across the 6 study hospitals, serving a range of populations, toxin-positive CDI linkage rates were all <15% with the exception of hospital 3, where 31% of cases were linked. It is likely the lower linkage rates in the current study in part reflect the falling incidence of ribotype-027 [11], associated with more onward transmission in this study, likely as a result of national fluoroquinolone restriction [27] but may also represent changes in infection prevention and control practice.

Our findings also support the recently reported role in transmission of GDH-positive patients with toxigenic C. difficile, but no detected fecal-toxin [28]. By sequencing all GDH-positive cases, we were able to compare the probability of fecal-toxin-positive and toxin-negative patients being potential sources of transmission, that is, having C. difficile genetically linked to a subsequent C. difficile isolate in another patient. Fecal-toxin-negative patients were similarly infectious to fecal-toxin-positive patients: fecal-toxin status did not affect the odds of being a potential transmission source. Strategies to identify and institute infection control measures around patients with potentially toxigenic C. difficile without detected fecal-toxin are therefore likely to reduce overall CDI incidence, although may be more costly, for example if toxin gene PCR is used as an initial screen rather than GDH EIA. Toxin-positive patients, that is, CDI cases, were more likely to have an identified potential transmission donor, than toxin-negative patients. This is in keeping with previous observations that recent C. difficile acquisition is associated with increased risk of disease, whereas long-term carriage is relatively protective [29].

It is likely that differing clinical CDI testing thresholds applied across the study hospitals, despite each being guided by national recommendations; notably, testing rates varied more than 2-fold between hospitals (98–239 tests/10000 bed-days). However, despite this variation, the overall proportion of samples tested that were C. difficile culture-positive was very similar across hospitals (~4%). These 2 findings combined resulted in varying rates of potentially toxigenic C. difficile isolation, 4.2–8.2/10000 bed-days, and varying (fecal-toxin-positive) CDI rates, 1.8–5.7/10000 bed-days. As the proportion of samples that were C. difficile culture-positive was close to reported community asymptomatic C. difficile colonization rates (~4%), and lower than reported colonization rates in asymptomatic hospital inpatients, (~10%) [30], it is possible that the higher reported CDI rates in some study hospitals may reflect overascertainment; independent assessment of which symptomatic patients are tested for CDI would be required to resolve this with certainty [7]. As designed, the study did not measure the extent of transmission involving asymptomatic patients, and therefore it is likely that not all hospital-associated transmission is captured. However, as this was the case for all hospitals, comparisons can still be made between hospitals and with previous studies investigating symptomatic patients.

Interestingly, we did not find any evidence of a relationship between rates of C. difficile testing and proportions of cases that could be linked to a previous case. Differing sampling/testing will likely mean the study populations at each hospital varied, for example with some institutions potentially more likely to include milder CDI cases than others. It should also be noted that differences in the population sampled by a particular testing strategy may affect the proportion of cases linked differently to incomplete sampling of a given population. We quantified the impact of the latter through simulation. Unfortunately, incomplete sampling could appear very similar to the impact of good infection control, as both results in low proportions of linked cases. One study limitation is that we only sequenced 81% GDH-positive samples at hospital 2. However, we demonstrate it may be possible to adjust for incomplete sampling, providing missed cases as assumed missing at random, and the number of onward transmissions from each case was random.

Both a limitation and a strength of our approach is that it relies only on sequencing laboratory samples and sampling dates. We demonstrate this allows comparative hospital surveillance with very limited, and no personal, sensitive or confidential, data. However, without ward admission and patient contact data, it is possible some genetically linked cases do not represent direct transmission from other cases. Genetic links might also arise through indirect healthcare-associated transmission via unsampled hosts or the hospital environment. Additionally, a minority of cases, without healthcare exposure in the last 90 days, may still have been genetically linked. However, there is no obvious reason why genetically related community C. difficile exposures, and therefore the proportion of such cases linked, should vary across England at a population level, even if other CDI risk factors do vary geographically, for example, antimicrobial use. Therefore, although we analyze transmission within the populations served by each hospital, as most CDI cases have recent healthcare exposure, the overall proportion of linked cases is still likely to be a reasonable combined indicator of infection control performance around cases and more generally. Without patient-level identifiers some repeat tests from the same patient may have been wrongly assigned as transmission events; however, we anticipate this was uncommon; repeat testing within 28 days is discouraged in national guidelines [17], and such samples are frequently not routinely processed.

Our method of comparing infection control performance depends on culturing C. difficile, which is not routinely undertaken, and on sequencing at least 6 months of samples, at around US$100 per sample. However, if samples are stored, as recommended in England, C. difficile could be cultured and sequenced retrospectively if increased incidence was noted and then continued prospectively to monitor the impact of any interventions. The cost-effectiveness of such an approach needs further evaluation.

In summary, here we present a novel method that enables assessment of the extent of hospital-acquired infection transmission within healthcare institutions. This approach revealed differences in CDI transmission rates across 6 English hospitals. It demonstrates the potential of whole-genome sequencing as a nationwide tool to identify institutions with excellent and also suboptimal infection control and therefore has the potential to allow targeted efforts to reduce CDI incidence.

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