Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing

Using whole genome sequencing to characterize Clostridioides difficile isolates at a tertiary center in Melbourne, Australia

Objective

Clostridioides difficile infection (CDI) is the commonest cause of healthcare-associated diarrhea and undergoes standardized surveillance and mandatory reporting in most Australian states and territories. Historically attributed to nosocomial spread, local and international whole genome sequencing (WGS) data suggest varied sources of acquisition. This study describes C. difficile genotypes isolated at a tertiary center in Melbourne, Australia, their likely source of acquisition, and common risk factors.

Design

Retrospective observational study.

Setting

The Royal Melbourne Hospital (RMH), a 570-bed tertiary center in Victoria, Australia.

Methods

Short-read whole genome sequencing was performed on 75 out of 137 C. difficile isolates obtained from 1/5/2021 to 28/2/2022 and compared to previous data from 8/11/2015 to 1/11/2016. Existing data from infection control surveillance and electronic medical records were used for epidemiological and risk factor analysis.

Results

Eighty-five (62.1%) of the 137 cases were defined as healthcare-associated from epidemiological data. On genome sequencing, 33 different multi-locus sequence type (MLST) subtypes were identified, with changes in population structure compared to the 2015-16 period. Risk factors for CDI were present in 130 (94.9%) cases, including 108 (78.8%) on antibiotics, 86 (62.8%) on acid suppression therapy, and 25 (18.2) on chemotherapy.

Conclusion

In both study periods, most C. difficile isolates were not closely related, suggesting varied sources of acquisition and that spread of C. difficile within the hospital was unlikely. Current infection control precautions may therefore warrant review. Underlying risk factors for CDI were common and may contribute to the proportion of healthcare-associated infections in the absence of proven hospital transmission.

A genomic survey of Clostridioides difficile isolates from hospitalized patients in Melbourne, Australia

IMPORTANCE

There has been a decrease in healthcare-associated Clostridioides difficile infection in Australia, but an increase in the genetic diversity of infecting strains, and an increase in community-associated cases. Here, we studied the genetic relatedness of C. difficile isolated from patients at a major hospital in Melbourne, Australia. Diverse ribotypes were detected, including those associated with community and environmental sources. Some types of isolates were more likely to carry antimicrobial resistance determinants, and many of these were associated with mobile genetic elements. These results correlate with those of other recent investigations, supporting the observed increase in genetic diversity and prevalence of community-associated C. difficile, and consequently the importance of sources of transmission other than symptomatic patients. Thus, they reinforce the importance of surveillance for in both hospital and community settings, including asymptomatic carriage, food, animals, and other environmental sources to identify and circumvent important sources of C. difficile transmission.

Antibiotics and antibiotic-associated diarrhea: a real-world disproportionality study of the FDA adverse event reporting system from 2004 to 2022

BACKGROUND

Our study aimed to assess the risk signals of antibiotic-associated diarrhea (AAD) caused by various antibiotics using real-world data and provide references for safe clinical applications.

METHODS

We analyzed data extracted from the FDA Adverse Event Reporting System (FAERS) database, covering the period from the first quarter of 2004 to the third quarter of 2022. We computed the reporting odds ratio (ROR) for each antibiotic or antibiotic class to compare the signal difference. Furthermore, we also examined the differences in the onset times and outcomes of AAD caused by various antibiotics.

RESULTS

A total of 5,397 reports met the inclusion requirements. Almost all antibiotics, except tobramycin and minocycline (ROR 0.98; 95%CI: 0.64-1.51 and 0.42; 95%CI: 0.16-1.11, respectively), showed a significant correlation with AAD. The analysis of the correlation between different classes of antibiotics and AAD revealed that lincomycins (ROR 29.19; 95%CI: 27.06-31.50), third-generation cephalosporins (ROR 15.96; 95%CI: 14.58-17.47), and first/second generation cephalosporins (ROR 15.29; 95%CI: 13.74-17.01) ranked the top three. The ROR values for antibiotics from the same class of antibiotics also varied greatly, with the ROR values for third-generation cephalosporins ranging from 9.97 to 58.59. There were also differences in ROR values between β-lactamase inhibitors and their corresponding β-lactamase drugs, such as amoxicillin-clavulanate (ROR = 13.31; 95%CI: 12.09-14.65) and amoxicillin (ROR = 6.50; 95%CI: 5.69-7.44). 91.35% of antibiotics have an onset time of less than four weeks.

CONCLUSIONS

There is a significant correlation between almost all antibiotics and AAD, particularly lincomycins and β-lactam antibiotics, as well as a different correlation within the same class. These findings offer valuable evidence for selecting antibiotics appropriately.

Core genome multilocus sequence typing of Clostridioides difficile to investigate transmission in the hospital setting

PURPOSE

Traditional epidemiological investigations of healthcare-associated Clostridioides difficile infection (HA-CDI) are often insufficient. This study aimed to evaluate a procedure that includes secondary isolation and genomic typing of single toxigenic colonies using core genome multilocus sequence typing (cgMLST) for the investigation of C. difficile transmission.

METHODS

We analyzed retrospectively all toxigenic C. difficile-positive stool samples stored at the Lausanne University Hospital over 6 consecutive months. All isolates were initially typed and classified using a modified double-locus sequence typing (DLST) method. Genome comparison of isolates with the same DLST and clustering were subsequently performed using cgMLST. The electronic administrative records of patients with CDI were investigated for spatiotemporal epidemiological links supporting hospital transmission. A comparative descriptive analysis between genomic and epidemiological data was then performed.

RESULTS

From January to June 2021, 86 C. difficile isolates were recovered from thawed samples of 71 patients. Thirteen different DLST types were shared by > 1 patient, and 13 were observed in single patients. A genomic cluster was defined as a set of isolates from different patients with ≤ 3 locus differences, determined by cgMLST. Seven genomic clusters were identified, among which plausible epidemiological links were identified in only 4/7 clusters.

CONCLUSION

Among clusters determined by cgMLST analysis, roughly 40% included unexplained HA-CDI acquisitions, which may be explained by unidentified epidemiological links, asymptomatic colonization, and/or shared common community reservoirs. The use of DLST, followed by whole genome sequencing analysis, is a promising and cost-effective stepwise approach for the investigation of CDI transmission in the hospital setting.

Clostridioides difficile outbreak detection: Evaluation by ribotyping and whole-genome sequencing of a surveillance algorithm based on ward-specific cutoffs

OBJECTIVE

We evaluated the performance of an early-warning algorithm, based on ward-specific incidence cutoffs for detecting Clostridioides difficile transmission in hospitals. We also sought to determine the frequency of intrahospital Clostridioides difficile transmission in our setting.

DESIGN

Diagnostic performance of the algorithm was tested with confirmed transmission events as the comparison criterion. Transmission events were identified by a combination of high-molecular-weight typing, ward history, ribotyping, and whole-genome sequencing (WGS).

SETTING

The study was conducted in 2 major and 2 minor secondary-care hospitals with adjacent catchment areas in western Sweden, comprising a total population of ∼480,000 and ∼1,000 hospital beds.

PATIENTS

All patients with a positive PCR test for Clostridioides difficile toxin B during 2020 and 2021.

METHODS

We conducted culturing and high-molecular-weight typing of all positive clinical samples. Ward history was determined for each patient to find possible epidemiological links between patients with the same type. Transmission events were determined by PCR ribotyping followed by WGS.

RESULTS

We identified 4 clusters comprising a total of 10 patients (1.5%) among 673 positive samples that were able to be cultured and then typed by high-molecular-weight typing. The early-warning algorithm performed no better than chance; patient diagnoses were made at wards other than those where the transmission events likely occurred.

CONCLUSIONS

In surveillance of potential transmission, it is insufficient to consider only the ward where diagnosis is made, especially in settings with high strain diversity. Transmission within wards occurs sporadically in our setting.

Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit

Despite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States. Current prevention strategies are limited by their failure to account for patients who carry C. difficile asymptomatically, who may act as hidden reservoirs transmitting infections to other patients. To improve the understanding of asymptomatic carriers' contribution to C. difficile spread, we conducted admission and daily longitudinal culture-based screening for C. difficile in a US-based intensive care unit over nine months and performed whole-genome sequencing on all recovered isolates. Despite a high burden of carriage, with 9.3% of admissions having toxigenic C. difficile detected in at least one sample, only 1% of patients culturing negative on admission to the unit acquired C. difficile via cross-transmission. While patients who carried toxigenic C. difficile on admission posed minimal risk to others, they themselves had a 24-times greater risk for developing a healthcare-onset C. difficile infection than noncarriers. Together, these findings suggest that current infection prevention practices can be effective in preventing nosocomial cross-transmission of C. difficile, and that decreasing C. difficile infections in hospitals further will require interventions targeting the transition from asymptomatic carriage to infection.

Screening for Asymptomatic Clostridioides difficile Carriage Among Hospitalized Patients: A Narrative Review

Clostridioides difficile infection (CDI) has become the most common healthcare-associated infection in the United States, with considerable morbidity, mortality, and healthcare costs. Assessing new preventive strategies is vital. We present a literature review of studies evaluating a strategy of screening and isolation of asymptomatic carriers in hospital settings. Asymptomatic detection of C. difficile is reported in ~ 10-20% of admitted patients. Risk factors for carriage include recent hospitalization, previous antibiotics, older age, lower functional capacity, immunosuppression, and others. Asymptomatic C. difficile carriers of toxigenic strains are at higher risk for progression to CDI. They are also shedders of C. difficile spores and may contribute to the persistence and transmission of this bacterium. Screening for asymptomatic carriers at hospital admission can theoretically reduce CDI by isolating carriers to reduce transmission, and implementing antibiotic stewardship measures targeting carriers to prevent progression to clinical illness. Several observational studies, summarized in this review, have reported implementing screening and isolation strategies, and found a reduction in CDI rates. Nevertheless, the data are still limited to a few observational studies, and this strategy is not commonly practiced. Studies supporting screening were performed in North America, coinciding with the period of dominance of the 027/BI/NAP1 strain. Additional studies evaluating screening, followed by infection control and antibiotic stewardship measures, are needed.

Prevalence of Non-Toxigenic Clostridioides difficile in Diarrhoea Patients and Their Clinical Characteristics

Non-toxigenic Clostridioides difficile (NTCD) has been shown to decrease the risk of recurrent C. difficile infection (CDI) in patients following metronidazole or vancomycin treatment for CDI. Limited data on the prevalence of NTCD strains in symptomatic patients and their clinical characteristics are available. We conducted this study to investigate the prevalence of NTCD in diarrhoea patients and their clinical characteristics. Between July 2017 and June 2018, unduplicated stool specimens were collected from patients with diarrhoea. The characteristics and episodes of C. difficile infection in patients with NTCD and toxigenic strains were compared. Among the 1182 stool specimens collected, 236 (18.5%) were identified as growing C. difficile, and 19.5% of the identified isolates were found to be NTCD. Multivariate analysis showed that community-onset diarrhoea (OR = 4.13, 95% CI 1.07-15.97; p = 0.040), underlying diabetes (OR = 3.64, 95% CI 1.46-9.25; p = 0.006), previous use of glycopeptides (OR = 4.75, 95% CI 1.37-16.42; p = 0.014), and the lack of use of proton pump inhibitors (PPIs) (OR = 3.57, 95% CI 1.39-9.09; p = 0.009) were independently associated with the NTCD group. Although there was no statistical significance, the number of CDI episodes occurring after 90 days tended to be lower in the NTCD group (2.2%) than in the toxigenic group (11.2%). A considerable portion of the C. difficile strains isolated from patients with diarrhoea showed NTCD. Further, more extensive studies are needed to clearly define the protective effects of NTCD strains in patients with diarrhoea.

Update on Commonly Used Molecular Typing Methods for Clostridioides difficile

This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.

Clostridioides difficile infection (CDI) in a previous room occupant predicts CDI in subsequent room occupants across different hospital settings

BACKGROUND

Previous single-center studies suggest that exposure to a room previously occupied by a patient with CDI may increase the risk of CDI in subsequent patients. We evaluated the risk of previous room occupant on CDI risk across 5 adult hospitals.

METHODS

This is a non-concurrent cohort study of adult inpatients admitted to 5 hospitals. Exposed rooms were identified as being occupied by a patient diagnosed with CDI and a logistic regression was performed to assess if staying in an exposed room increases the risk of CDI in subsequent patients.

RESULTS

Patients admitted to a room that was previously occupied by a patient with CDI had a 27% increased odds of subsequently being diagnosed with CDI (odds ratio (OR)=1.269; 95% confidence interval (CI)= 1.12-1.44) if exposed within the last 90 days and 40% increased odds (OR=1.401; 95% CI= 1.25-1.57) if exposed in the last 365 days after controlling for previous admissions and length of stay. Cumulative patient-day exposure to previously CDI-positive occupied rooms within both 90 and 365 days were also found to be independently significant, with a 4.5% (OR 1.045; 95% CI = 1.03-1.06) and 4.2% (OR 1.042; 95% CI = 1.03-1.06) increase in odds of CDI with each day of exposure respectively.

DISCUSSION/CONCLUSIONS

This study adds further evidence that hospital environment in patient rooms may contribute to risk for CDI.

Prevalence and antimicrobial resistance pattern of Clostridium difficile among hospitalized diarrheal patients: A systematic review and meta-analysis

Background

Clostridium difficile is the leading cause of infectious diarrhea that develops in patients after hospitalization during antibiotic administration. It has also become a big issue in community-acquired diarrhea. The emergence of hypervirulent strains of C. difficile poses a major problem in hospital-associated diarrhea outbreaks and it is difficult to treat. The antimicrobial resistance in C. difficile has worsened due to the inappropriate use of broad-spectrum antibiotics including cephalosporins, clindamycin, tetracycline, and fluoroquinolones together with the emergence of hypervirulent strains.

Objective

To estimate the pooled prevalence and antimicrobial resistance pattern of C. difficile derived from hospitalized diarrheal patients, a systematic review and meta-analysis was performed.

Methods

Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed to review published studies conducted. We searched bibliographic databases from PubMed, Scopus, Google Scholar, and Cochrane Library for studies on the prevalence and antimicrobial susceptibility testing on C. difficile. The weighted pooled prevalence and resistance for each antimicrobial agent was calculated using a random-effects model. A funnel plot and Egger’s regression test were used to see publication bias.

Results

A total of 15 studies were included. Ten articles for prevalence study and 5 additional studies for antimicrobial susceptibility testing of C. difficile were included. A total of 1967/7852 (25%) C. difficile were isolated from 10 included studies for prevalence study. The overall weighted pooled proportion (WPP) of C. difficile was 30% (95% CI: 10.0–49.0; p<0.001). The analysis showed substantial heterogeneity among studies (Cochran’s test = 7038.73, I2 = 99.87%; p<0.001). The weighed pooled antimicrobial resistance (WPR) were: vancomycin 3%(95% CI: 1.0–4.0, p<0.001); metronidazole 5%(95% CI: 3.0–7.0, p<0.001); clindamycin 61%(95% CI: 52.0–69.0, p<0.001); moxifloxacin 42%(95% CI: 29–54, p<0.001); tetracycline 35%(95% CI: 22–49, p<0.001); erythromycin 61%(95% CI: 48–75, p<0.001) and ciprofloxacin 64%(95% CI: 48–80; p< 0.001) using the random effect model.

Conclusions

A higher weighted pooled prevalence of C. difficile was observed. It needs a great deal of attention to decrease the prevailing prevalence. The resistance of C. difficile to metronidazole and vancomycin was low compared to other drugs used to treat C. difficile infection. Periodic antimicrobial resistance monitoring is vital for appropriate therapy of C. difficile infection.

Cleaning and disinfecting surfaces in hospitals and long-term care facilities for reducing hospital and facility-acquired bacterial and viral infections: A systematic review

BACKGROUND

Multiply drug-resistant organisms (MDROs) in hospitals and long-term care facilities (LTCFs) of particular concern include meticillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococcus, multidrug-resistant Acinetobacter species and extended spectrum beta-lactamase producing organisms. Respiratory viruses include influenza and SARS-CoV-2.

AIM

To assess effectiveness of cleaning and disinfecting surfaces in hospitals and LTCFs.

METHODS

CINAHL, Cochrane CENTRAL Register of Controlled Trials, EMBASE, Medline, and Scopus searched inception to 28 June 2021, no language restrictions, for randomized controlled trials, cleaning, disinfection, hospitals, LTCFs. Abstracts and titles were assessed and data abstracted independently by two authors.

FINDINGS

Of fourteen c-RCTs in hospitals and LTCFs, interventions in ten were focused on reducing patient infections of four MDROs and/or healthcare-associated infections (HAIs). In four c-RCTs patient MDRO and/or HAI rates were significantly reduced with cleaning and disinfection strategies including bleach, quaternary ammonium detergents, ultraviolet irradiation, hydrogen peroxide vapour and copper-treated surfaces or fabrics. Of three c-RCTs focused on reducing MRSA rates, one had significant results and one on Clostridioides difficile had no significant results. Heterogeneity of populations, methods, outcomes and data reporting precluded meta-analysis. Overall risk of bias assessment was low but high for allocation concealment, and GRADE assessment was low risk. No study assessed biofilms.

CONCLUSIONS

Ten c-RCTs focused on reducing multiple MDROs and/or HAIs and four had significant reductions. Three c-RCTs reported only patient MRSA colonization rates (one significant reductions), and one focused on Clostridioides difficile (no significant differences). Standardised primary and secondary outcomes are required for future c-RCTs including detailed biofilm cleaning/disinfection interventions.

The future of Clostridioides difficile diagnostics

PURPOSE OF REVIEW

Although the epidemiology of Clostridioides difficile has changed, this organism continues to cause significant morbidity and mortality. This review addresses current and future approaches to the diagnosis of C. difficile disease.

RECENT FINDINGS

Over the last several years, large prospective studies have confirmed that there is no single optimal test for the diagnosis of C. difficile disease. The pendulum has swung from a focus on rapid molecular diagnosis during the years of the ribotype 027 epidemic, to a call for use of algorithmic approaches that include a test for toxin detection. In addition, diagnostic stewardship has been shown to improve test utilization, especially with molecular methods. Advances in testing include development of ultrasensitive toxin tests and an expansion of biomarkers that may be more C. difficile specific. Microbiome research may be leveraged to inform novel diagnostic approaches based on measurements of volatile and nonvolatile organic compounds in stool.

SUMMARY

As rates of C. difficile infection decline, emphasis is now on improving test utilization and a quest for improved diagnostic approaches. These approaches may involve implementation of technologies that improve toxin testing, predict patients likely to have disease and/or a severe outcome, and harnessing research on changes in the microbiome to advance metabolomics.

Risk for Clostridioides difficile Infection Among Hospitalized Patients Associated With Multiple Healthcare Exposures Prior to Admission

BACKGROUND

Clostridioides difficile infection (CDI) is a common healthcare-associated infection and is often used as an indicator of hospital safety or quality. However, healthcare exposures occurring prior to hospitalization may increase risk for CDI. We conducted a case-control study comparing hospitalized patients with and without CDI to determine if healthcare exposures prior to hospitalization (ie, clinic visits, antibiotics, family members with CDI) were associated with increased risk for hospital-onset CDI, and how risk varied with time between exposure and hospitalization.

METHODS

Records were collected from a large insurance-claims database from 2001 to 2017 for hospitalized adult patients. Prior healthcare exposures were identified using inpatient, outpatient, emergency department, and prescription drug claims; results were compared between various CDI case definitions.

RESULTS

Hospitalized patients with CDI had significantly more frequent healthcare exposures prior to admission. Healthcare visits, antibiotic use, and family exposures were associated with greater likelihood of CDI during hospitalization. The degree of association diminished with time between exposure and hospitalization. Results were consistent across CDI case definitions.

CONCLUSIONS

Many different prior healthcare exposures appear to increase risk for CDI presenting during hospitalization. Moreover, patients with CDI typically have multiple exposures prior to admission, confounding the ability to attribute cases to a particular stay.

A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains

Clostridioides difficile is the leading cause of healthcare-associated infectious diarrhoea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare environments, and that the primary sites of C. difficile transmission may be strain-dependent. We conducted a multisite genomic epidemiology study to assess differential genomic evidence of healthcare vs community spread for two of the most common C. difficile strains in the USA: sequence type (ST) 1 (associated with ribotype 027) and ST2 (associated with ribotype 014/020). We performed whole-genome sequencing and phylogenetic analyses on 382 ST1 and ST2 C. difficile isolates recovered from stool specimens collected during standard clinical care at 3 geographically distinct US medical centres between 2010 and 2017. ST1 and ST2 isolates both displayed some evidence of phylogenetic clustering by study site, but clustering was stronger and more apparent in ST1, consistent with our healthcare-based study more comprehensively sampling local transmission of ST1 compared to ST2 strains. Analyses of pairwise single-nucleotide variant (SNV) distance distributions were also consistent with more evidence of healthcare transmission of ST1 compared to ST2, with 44 % of ST1 isolates being within two SNVs of another isolate from the same geographical collection site compared to 5.5 % of ST2 isolates (P-value=<0.001). Conversely, ST2 isolates were more likely to have close genetic neighbours across disparate geographical sites compared to ST1 isolates, further supporting non-healthcare routes of spread for ST2 and highlighting the potential for misattributing genomic similarity among ST2 isolates to recent healthcare transmission. Finally, we estimated a lower evolutionary rate for the ST2 lineage compared to the ST1 lineage using Bayesian timed phylogenomic analyses, and hypothesize that this may contribute to observed differences in geographical concordance among closely related isolates. Together, these findings suggest that ST1 and ST2, while both common causes of C. difficile infection in hospitals, show differential reliance on community and hospital spread. This conclusion supports the need for strain-specific criteria for interpreting genomic linkages and emphasizes the importance of considering differences in the epidemiology of circulating strains when devising interventions to reduce the burden of C. difficile infections.

Space-time modeling of child mortality at the Admin-2 level in a low and middle income countries context

The Sustainable Development Goals call for a total reduction of preventable child mortality before 2030. Further, the goals state the desirability to have subnational mortality estimates. Estimates at this level are required for health interventions at the subnational level. In a low and middle income countries context, the data on mortality typically consist of household surveys, which are carried out with a stratified, cluster design, and census microsamples. Most household surveys collect full birth history (FBH) data on birth and death dates of a mother's children, but censuses collect summary birth history (SBH) data which consist only of the number of children born and the number that died. In previous work, direct (survey-weighted) estimates with associated variances were derived from FBH data and smoothed in space and time. Unfortunately, the FBH data from household surveys are usually not sufficiently abundant to obtain yearly estimates at the Admin-2 level (at which interventions are often made). In this paper we describe four extensions to previous work: (i) combining SBH data with FBH data, (ii) modeling on a yearly scale, to combine data on a yearly scale with data at coarser time scales, (iii) adjusting direct estimates in Admin-2 areas where we do not observe any deaths due to small sample sizes, (iv) acknowledge differences in data sources by modeling potential bias arising from the various data sources. The methods are illustrated using household survey and census data from Kenya and Malawi, to produce mortality estimates from 1980 to the time of the most recent survey, and predictions to 2020.

Advances and required improvements in methods to diagnosing Clostridioides difficile infections in the healthcare setting

INTRODUCTION

Clostrididioides difficile is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs.Areas Covered: We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review addresses the evolving epidemiology of Clostridioides difficile infection (CDI) and discusses novel methods/approaches for improving the diagnosis of this important disease.

EXPERT OPINION

No single diagnostic test to date has demonstrated optimum sensitivity and specificity for detection of CDI. Many institutions have developed multi-step algorithms consistent with guidelines established by various professional societies. Some institutions have successfully tried to improve the pretest probability of molecular assays by implementing appropriate sample rejection criteria and establishing best practice alerts at the time of electronic order entry. Others have established PCR cycle threshold cutoffs to attempt to differentiate symptomatic patients from asymptomatic carriers or to make predictions about severity of disease with variable success. As research advances our understanding of C. difficile pathogenesis and pathophysiology, more information on CDI specific biomarkers is emerging. Finally, assessments of the microbiome and metabolome may expand the diagnostic armamentarium with advances in mass spectrometry and sequencing technologies.

Evaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of Clostridioides difficile

Multilocus sequence typing (MLST) is a low-resolution but rapid genotyping method for Clostridioides difficile Whole-genome sequencing (WGS) has emerged as the new gold standard for C. difficile typing, but cost and lack of standardization still limit broad utilization. In this study, we evaluated the potential to combine the portability of MLST with the increased resolution of WGS for a cost-saving approach to routine C. difficile typing. C. difficile strains from two New York City hospitals (hospital A and hospital B) were selected. WGS single-nucleotide polymorphism (wgSNP) was performed using established methods. Sequence types (ST) were determined using PubMLST, while wgSNP analysis was performed using the Bionumerics software. An additional analysis of a subset of data (hospital A) was made comparing the Bionumerics software to the CosmosID pipeline. Cost and turnaround time to results were compared for the algorithmic approach of MLST followed by wgSNP versus direct wgSNP. Among the 202 C. difficile isolates typed, 91% (n = 185/203) clustered within the representative ST, showing a high agreement between MLST and wgSNP. While clustering was similar between the Bionumerics and CosmosID pipelines, large differences in the overall number of SNPs were noted. A two-step algorithm for routine typing results in significantly lower cost than routine use of WGS. Our results suggest that using MLST as a first step in routine typing of C. difficile followed by WGS for MLST concordant strains is a less technically demanding, cost-saving approach for performing C. difficile typing than WGS alone without loss of discriminatory power.

Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission

Fitting stochastic transmission models to electronic patient data can offer detailed insights into the transmission of healthcare-associated infections and improve infection control. Pathogen whole-genome sequencing may improve the precision of model inferences, but computational constraints have limited modelling applications predominantly to small datasets and specific outbreaks, whereas large-scale sequencing studies have mostly relied on simple rules for identifying/excluding plausible transmission. We present a novel approach for integrating detailed epidemiological data on patient contact networks in hospitals with large-scale pathogen sequencing data. We apply our approach to study Clostridioides difficile transmission using a dataset of 1223 infections in Oxfordshire, UK, 2007-2011. 262 (21% [95% credibility interval 20-22%]) infections were estimated to have been acquired from another known case. There was heterogeneity by sequence type (ST) in the proportion of cases acquired from another case with the highest rates in ST1 (ribotype-027), ST42 (ribotype-106) and ST3 (ribotype-001). These same STs also had higher rates of transmission mediated via environmental contamination/spores persisting after patient discharge/recovery; for ST1 these persisted longer than for most other STs except ST3 and ST42. We also identified variation in transmission between hospitals, medical specialties and over time; by 2011 nearly all transmission from known cases had ceased in our hospitals. Our findings support previous work suggesting only a minority of C. difficile infections are acquired from known cases but highlight a greater role for environmental contamination than previously thought. Our approach is applicable to other healthcare-associated infections. Our findings have important implications for effective control of C. difficile.

Clostridium difficile Infection in the Plastic Surgery Population: Lessons from the ACS NSQIP Database

Background:

Clostridium difficile–associated infections (CDI) have a significant impact on morbidity and mortality of hospitalized medical and surgical patients. There is a paucity of data regarding the incidence, impact, and modifiable risk factors in the plastic surgery population.

Methods:

The ACS NSQIP database was retrospectively queried for all cases performed by plastic surgeons during 2016. All plastic surgery cases, combined cases, demographics, and baseline clinical characteristics were extracted from the database. The study population was divided into 2 groups based on the development of CDI. Independent variables for development of CDI were identified.

Results:

During the study period, a total of 29,256 patients underwent a procedure by plastic surgery, with the most commonly performed procedures involving the breast (58%) and trunk (14%). Only 44 patients developed post-operative CDI (0.1%). Factors independently associated with development of CDI were wound classification at the end of the surgery, COPD, procedures involving the trunk, and surgery for reconstruction of pressure ulcers. Outpatient surgery was associated with decreased odds of developing CDI [AOR (95% CI):0.2 (0.1, 0.4), adj P < 0.001]. Staying overnight did not increase the odds of developing CDI; however, staying for >1 day in the hospital was associated with an increased risk of CDI development [AOR (95% CI): 1.03 (1.01, 1.13), adj P = 0.001]. Combined cases, ASA, body mass index, diabetes, and active smoking were not associated with CDI.

Conclusions:

CDI are rare in the plastic surgery population and are most associated with trunk/decubitus ulcer reconstructions, inpatient hospital stay, and contaminated wounds. The patients that usually fit in these categories have acutely or chronically infected wounds, which are often treated with systemic antibiotics. For patient with decubitus ulcers and other trunk reconstruction, the guidelines for pre and post-operative systemic antibiotic usage is not well defined. For patients who have had trunk reconstruction, development of evidence-based antibiotic stewardship guidelines may help these patients by limiting antibiotic usage and thereby reducing the incidence of CDI.

Comparing intervention strategies for reducing Clostridioides difficile transmission in acute healthcare settings: an agent-based modeling study

Background

Clostridioides difficile infection (CDI) is one of the most common healthcare infections. Common strategies aiming at controlling CDI include antibiotic stewardship, environmental decontamination, and improved hand hygiene and contact precautions. Mathematical models provide a framework to evaluate control strategies. Our objective is to evaluate the effectiveness of control strategies in decreasing C. difficile colonization and infection using an agent-based model in an acute healthcare setting.

Methods

We developed an agent-based model that simulates the transmission of C. difficile in medical wards. This model explicitly incorporates healthcare workers (HCWs) as vectors of transmission, tracks individual patient antibiotic histories, incorporates varying risk levels of antibiotics with respect to CDI susceptibility, and tracks contamination levels of ward rooms by C. difficile. Interventions include two forms of antimicrobial stewardship, increased environmental decontamination through room cleaning, improved HCW compliance, and a preliminary assessment of vaccination.

Results

Increased HCW compliance with CDI patients was ranked as the most effective intervention in decreasing colonizations, with reductions up to 56%. Antibiotic stewardship practices were highly ranked after contact precaution compliance. Vaccination and reduction of high-risk antibiotics were the most effective intervention in decreasing CDI. Vaccination reduced CDI cases to up to 90%, and the reduction of high-risk antibiotics decreased CDI cases up to 23%.

Conclusions

Overall, interventions that decrease patient susceptibility to colonization by C. difficile, such as antibiotic stewardship, were the most effective interventions in reducing both colonizations and CDI cases.

Molecular epidemiology of antimicrobial resistant microorganisms in the 21th century: a review of the literature

Healthcare-associated infections (HAIs) are the most frequent and severe complication acquired in healthcare settings with high impact in terms of morbidity, mortality and costs. Many bacteria could be implicated in these infections, but, expecially multidrug resistance bacteria could play an important role. Many microbial typing technologies have been developed until to the the bacterial whole-genome sequencing and the choice of a molecular typing method therefore will depend on the skill level and resources of the laboratory and the aim and scale of the investigation. In several studies the molecular investigation of pathogens involved in HAIs was performed with many microorganisms identified as causative agents such as Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Clostridium difficile, Acinetobacter spp., Enterobacter spp., Enterococcus spp., Staphylococcus aureus and several more minor species. Here, we will describe the most and least frequently reported clonal complex, sequence types and ribotypes with their worldwide geographic distribution for the most important species involved in HAIs.

Some simple rules for estimating reproduction numbers in the presence of reservoir exposure or imported cases

For many diseases, the basic reproduction number (R0) is a threshold parameter for disease extinction or survival in isolated populations. However no human population is fully isolated from other human or animal populations. We use compartmental models to derive simple rules for the basic reproduction number in populations where an endemic disease is sustained by a combination of local transmission within the population and exposure from some other source: either a reservoir exposure or imported cases. We introduce the idea of a reservoir-driven or importation-driven disease: diseases that would become extinct in the population of interest without reservoir exposure or imported cases (since R0<1), but nevertheless may be sufficiently transmissible that many or most infections are acquired from humans in that population. We show that in the simplest case, R0<1 if and only if the proportion of infections acquired from the external source exceeds the disease prevalence and explore how population heterogeneity and the interactions of multiple strains affect this rule. We apply these rules in two case studies of Clostridium difficile infection and colonisation: C. difficile in the hospital setting accounting for imported cases, and C. difficile in the general human population accounting for exposure to animal reservoirs. We demonstrate that even the hospital-adapted, highly-transmissible NAP1/RT027 strain of C. difficile had a reproduction number <1 in a landmark study of hospitalised patients and therefore was sustained by colonised and infected admissions to the study hospital. We argue that C. difficile should be considered reservoir-driven if as little as 13.0% of transmission can be attributed to animal reservoirs.

Global and Historical Distribution of Clostridioides difficile in the Human Diet (1981-2019): Systematic Review and Meta-Analysis of 21886 Samples Reveal Sources of Heterogeneity, High-Risk Foods, and Unexpected Higher Prevalence Toward the Tropic

Clostridioides difficile (CD) is a spore-forming bacterium that causes life-threatening intestinal infections in humans. Although formerly regarded as exclusively nosocomial, there is increasing genomic evidence that person-to-person transmission accounts for only <25% of cases, supporting the culture-based hypothesis that foods may be routine sources of CD-spore ingestion in humans. To synthesize the evidence on the risk of CD exposure via foods, we conducted a systematic review and meta-analysis of studies reporting the culture prevalence of CD in foods between January 1981 and November 2019. Meta-analyses, risk-ratio estimates, and meta-regression were used to estimate weighed-prevalence across studies and food types to identify laboratory and geographical sources of heterogeneity. In total, 21886 food samples were tested for CD between 1981 and 2019 (96.4%, n = 21084, 2007–2019; 232 food-sample-sets; 79 studies; 25 countries). Culture methodology, sample size and type, region, and latitude were sources of heterogeneity (p < 0.05). Although non-strictly-anaerobic methods were reported in some studies, and we confirmed experimentally that improper anaerobiosis of media/sample-handling affects CD recovery in agar (Fisher, p < 0.01), most studies (>72%) employed the same (one-of-six) culture strategy. Because the prevalence was also meta-analytically similar across six culture strategies reported, all studies were integrated using three meta-analytical methods. At the study level (n = 79), the four-decade global cumulative-prevalence of CD in the human diet was 4.1% (95%CI = −3.71, 11.91). At the food-set level (n = 232, mean 12.9 g/sample, similar across regions p > 0.2; 95%CI = 9.7–16.2), the weighted prevalence ranged between 4.5% (95%CI = 3–6%; all studies) and 8% (95%CI = 7–8%; only CD-positive-studies). Risk-ratio ranking and meta-regression showed that milk was the least likely source of CD, while seafood, leafy green vegetables, pork, and poultry carried higher risks (p < 0.05). Across regions, the risk of CD in foods for foodborne exposure reproducibly decreased with Earth latitude (p < 0.001). In conclusion, CD in the human diet is a global non-random-source of foodborne exposure that occurs independently of laboratory culture methods, across regions, and at a variable level depending on food type and latitude. The latitudinal trend (high CD-food-prevalence toward tropic) is unexpectedly inverse to the epidemiological observations of CD-infections in humans (frequent in temperate regions). Findings suggest the plausible hypothesis that ecologically-richer microbiomes in the tropic might protect against intestinal CD colonization/infections despite CD ingestion.

Effectiveness and cost-effectiveness of a Clostridium difficile vaccine candidate in a hospital setting

Toxoid vaccines against Clostridium difficile infections (CDI) appear promising in reducing the risk of developing toxin-mediated symptoms. We sought to evaluate the effectiveness and cost-effectiveness of a vaccine candidate in a hospital setting. We developed an agent-based simulation model of nosocomial CDI in a 300-bed hospital. Targeting high-risk patients for vaccination, we estimated the reduction of symptomatic CDI. Using the net reduction of CDI-associated isolation days, we evaluated the vaccine's cost-effectiveness from a healthcare provider perspective over a 2-year period with an average monthly incidence of 5 cases per 10,000 patient-days pre-vaccination. Assuming a vaccine efficacy in the range 60-90%, vaccinating 40% of high-risk patients pre-admission reduced symptomatic CDI by 16.6% (95% CI: 15.2, 17.9). When the vaccine coverage increased to 80%, the reduction of symptomatic CDI was 34.6% (95% CI: 33.7, 35.9). For a willingness to pay (WTP) of CDN$1000 (corresponding to the average costs of case isolation per day), vaccine was cost-effective for vaccination costs per individual (VCPI) up to CDN$111 in the scenario of 40% vaccine coverage. With the same WTP, vaccine was cost-effective for VCPI up to CDN$121 when the vaccine coverage increased to 80%. A significant portion (~80%) of hospital colonization is caused by environmental transmission of C. difficile, which markedly reduced the effectiveness of vaccine below its assumed efficacy. However, due to the number of CDI-associated isolation days averted, vaccination of high-risk patients can be cost-effective depending on the WTP and the VCPI.

Clostridium difficile: Investigating Transmission Patterns Between Infected and Colonized Patients Using Whole Genome Sequencing

Background

Whole genome sequencing (WGS) studies can enhance our understanding of the role of patients with asymptomatic Clostridium difficile colonization in transmission.

Methods

Isolates obtained from patients with Clostridium difficile infection (CDI) and colonization identified in a study conducted during 2006-2007 at 6 Canadian hospitals underwent typing by pulsed-field gel electrophoresis, multilocus sequence typing, and WGS. Isolates from incident CDI cases not in the initial study were also sequenced where possible. Ward movement and typing data were combined to identify plausible donors for each CDI case, as defined by shared time and space within predefined limits. Proportions of plausible donors for CDI cases that were colonized, infected, or both were examined.

Results

Five hundred fifty-four isolates were sequenced successfully, 353 from colonized patients and 201 from CDI cases. The NAP1/027/ST1 strain was the most common strain, found in 124 (62%) of infected and 92 (26%) of colonized patients. A donor with a plausible ward link was found for 81 CDI cases (40%) using WGS with a threshold of ≤2 single nucleotide polymorphisms to determine relatedness. Sixty-five (32%) CDI cases could be linked to both infected and colonized donors. Exclusive linkages to infected and colonized donors were found for 28 (14%) and 12 (6%) CDI cases, respectively.

Conclusions

Colonized patients contribute to transmission, but CDI cases are more likely linked to other infected patients than colonized patients in this cohort with high rates of the NAP1/027/ST1 strain, highlighting the importance of local prevalence of virulent strains in determining transmission dynamics.

Environmental shedding of toxigenic Clostridioides difficile by asymptomatic carriers: A prospective observational study

OBJECTIVES

The aim was to compare the burden of environmental shedding of toxigenic Clostridioides difficile among asymptomatic carriers, C. difficile-infected (CDI) patients and non-carriers in an inpatient non-epidemic setting.

METHODS

C. difficile carriage was determined by positive toxin-B PCR from rectal swabs of asymptomatic patients. Active CDI was defined as a positive two-step enzyme immunoassay/polymerase chain reaction (EIA/PCR) test in patients with more than three unformed stools/24 hr. C. difficile environmental contamination was assessed by obtaining specimens from ten sites in the patients' rooms. Toxigenic strains were identified by PCR. We created a contamination scale to define the overall level of room contamination that ranged from clean to heavy contamination.

RESULTS

One hundred and seventeen rooms were screened: 70 rooms inhabited by C. difficile carriers, 30 rooms by active CDI patients and 17 rooms by non C. difficile -carriers (control). In the carrier rooms 29 (41%) had more than residual contamination, from which 17 (24%) were heavily contaminated. In the CDI rooms 12 (40%) had more than residual contamination from which three (10%) were heavily contaminated, while in the control rooms, one room (6%) had more than residual contamination and none were heavily contaminated. In a multivariate analysis, the contamination score of rooms inhabited by carriers did not differ from rooms of CDI patients, yet both were significantly more contaminated than those of non-carriers odd ratio 12.23 and 11.16 (95% confidence interval 1.5-99.96 p 0.0195, and 1.19-104.49 p 0.035), respectively.

DISCUSSION

Here we show that the rooms of C. difficile carriers are as contaminated as those of patients with active CDI and significantly more than those of non-carriers.

Patient and Strain Characteristics Associated With Clostridium difficile Transmission and Adverse Outcomes

Background

No study has used whole-genome sequencing (WGS) to investigate risk factors for Clostridium difficile (CD) transmission between cases, or assessed the impact of recent acquisition on patient outcome.

Methods

This 20 month retrospective cohort study included consecutive cytotoxin-positive diarrheal samples, which underwent culture, ribotyping, and WGS (Illumina). Sequenced isolates were compared using single nucleotide variants (SNVs). Independent predictors of acquisition from another case, onward transmission, 120-day recurrence, and 30-day mortality were identified using logistic regression with backwards elimination.

Results

Of 660 CD cases, 640 (97%) were sequenced, of which 567 (89%) shared a ribotype with a prior case, but only 227 (35%) were ≤2 SNVs from a prior case, supporting recent acquisition. Plausible (<2 SNVs) recent ward-based acquisition from a symptomatic case was more frequent in certain ribotypes; 64% (67/105) for ribotype-027 cases, compared with 11% (6/57) for ribotype-078. Independent risk factors (adjusted P < .05) for CD acquisition included older age, longer inpatient duration, and ribotype; these factors, and male sex, increased onward transmission. Patients with a plausible donor had a greater risk of recurrence (adjusted P = .001) and trended towards greater 30-day mortality (adjusted P = .06). Ribotype had no additional mortality or recurrence impact after adjusting for acquisition (P > .1).

Conclusions

Greater transmission of certain lineages suggests CD may have different reservoirs and modes of transmission. Acquiring CD from a recent case is associated with poorer clinical outcomes. Clinical characteristics associated with increased healthcare-associated CD transmission could be used to target preventative interventions.

Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA)

A panel of experts was convened by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA) to update the 2010 clinical practice guideline on Clostridium difficile infection (CDI) in adults. The update, which has incorporated recommendations for children (following the adult recommendations for epidemiology, diagnosis, and treatment), includes significant changes in the management of this infection and reflects the evolving controversy over best methods for diagnosis. Clostridium difficile remains the most important cause of healthcare-associated diarrhea and has become the most commonly identified cause of healthcare-associated infection in adults in the United States. Moreover, C. difficile has established itself as an important community pathogen. Although the prevalence of the epidemic and virulent ribotype 027 strain has declined markedly along with overall CDI rates in parts of Europe, it remains one of the most commonly identified strains in the United States where it causes a sizable minority of CDIs, especially healthcare-associated CDIs. This guideline updates recommendations regarding epidemiology, diagnosis, treatment, infection prevention, and environmental management.

Pediatric oncology and stem cell transplant patients with healthcare-associated Clostridium difficile infection were already colonized on admission

Clostridium difficile is the leading cause of healthcare-associated infections worldwide. The diagnosis of C. difficile infection (CDI) in pediatric oncology patients is complex as diarrhea is common, and there is a high rate of colonization in infants and young children. This study was conducted to assess the accuracy of the surveillance definitions of healthcare-associated CDI (HA-CDI) and to determine the prevalence of toxigenic C. difficile colonization among pediatric oncology and stem cell transplant patients.

METHODS

A prospective cohort study was conducted over a three-year period in an inpatient pediatric oncology and stem cell transplant setting. Baseline stool samples were collected within three days of admission and were genotypically compared with clinically indicated samples submitted after three days of admission.

RESULTS

A total of 175 patients were recruited with a total of 536 admissions. The adjusted prevalence of baseline toxigenic C. difficile colonization among admissions was 32.8%. Seventy-eight percent of positive admissions did not have history of CDI. Colonization with a toxigenic strain on admission was predictive of CDI (OR = 28.6; 95% CI, 6.58-124.39; P < 0.001). Nearly all clinical isolates (8/9) shared identical pulsed-field gel electrophoresis patterns with baseline isolates or were closely related (1/9). Only one of the 11 cases that were considered HA-CDI was potentially nosocomially acquired.

CONCLUSION

The prevalence of colonization with toxigenic C. difficile in our cohort is high. Unfortunately, the current CDI surveillance definitions overestimate the incidence of HA-CDI in pediatric oncology and stem cell transplantation settings.

Seasonality and community interventions in a mathematical model of Clostridium difficile transmission

BACKGROUND

Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated diarrhoea with peak incidence in late winter or early autumn. Although CDI is commonly associated with hospitals, community transmission is important.

AIM

To explore potential drivers of CDI seasonality and the effect of community-based interventions to reduce transmission.

METHODS

A mechanistic compartmental model of C. difficile transmission in a hospital and surrounding community was used to determine the effect of reducing transmission or antibiotic prescriptions in these settings. The model was extended to allow for seasonal antibiotic prescriptions and seasonal transmission.

FINDINGS

Modelling antibiotic seasonality reproduced the seasonality of CDI, including approximate magnitude (13.9-15.1% above annual mean) and timing of peaks (0.7-1.0 months after peak antibiotics). Halving seasonal excess prescriptions reduced the incidence of CDI by 6-18%. Seasonal transmission produced larger seasonal peaks in the prevalence of community colonization (14.8-22.1% above mean) than seasonal antibiotic prescriptions (0.2-1.7% above mean). Reducing transmission from symptomatic or hospitalized patients had little effect on community-acquired CDI, but reducing transmission in the community by ≥7% or transmission from infants by ≥30% eliminated the pathogen. Reducing antibiotic prescription rates led to approximately proportional reductions in infections, but limited reductions in the prevalence of colonization.

CONCLUSION

Seasonal variation in antibiotic prescription rates can account for the observed magnitude and timing of C. difficile seasonality. Even complete prevention of transmission from hospitalized patients or symptomatic patients cannot eliminate the pathogen, but interventions to reduce transmission from community residents or infants could have a large impact on both hospital- and community-acquired infections.

2019 update of the WSES guidelines for management of Clostridioides (Clostridium) difficile infection in surgical patients

In the last three decades, Clostridium difficile infection (CDI) has increased in incidence and severity in many countries worldwide. The increase in CDI incidence has been particularly apparent among surgical patients. Therefore, prevention of CDI and optimization of management in the surgical patient are paramount. An international multidisciplinary panel of experts from the World Society of Emergency Surgery (WSES) updated its guidelines for management of CDI in surgical patients according to the most recent available literature. The update includes recent changes introduced in the management of this infection.

The impact of corticosteroid use on inpatients with inflammatory bowel disease and positive polymerase chain reaction for Clostridium difficile

Background/Aims

Optimal management of inflammatory bowel disease (IBD) with concomitant Clostridium difficile infection (CDI) is controversial, especially when CDI diagnosis is made by polymerase chain reaction (PCR) testing, which may reflect colonization without infection.

Methods

We performed a multicenter review of all inpatients with IBD and PCR diagnosed CDI. Outcomes included length of stay, 30- and 90-day readmission, colectomy during admission and within 3 months, intensive care unit (ICU) admission, CDI relapse and death for patients who received corticosteroid (CS) after CDI diagnosis versus those that did not. Propensity-adjusted regression analysis of outcomes based on CS usage was performed.

Results

We identified 177 IBD patients with CDI, 112 ulcerative colitis and 65 Crohn’s disease. For IBD overall, CS after CDI diagnosis was associated with prolonged hospitalization (5.5 days: 95% confidence interval [CI], 1.5–9.6 days; P=0.008), higher colectomy rate within 3 months (odds ratio [OR], 5.5; 95% CI, 1.1–28.2; P=0.042) and more frequent ICU admissions (OR, 7.8; 95% CI, 1.5–41.6; P=0.017) versus no CS. CS use post-CDI diagnosis in UC patients was associated with prolonged hospitalization (6.2 days: 95% CI, 0.4– 12.0 days; P=0.036) and more frequent ICU admissions (OR, 7.4; 95% CI, 1.1–48.7; P=0.036).

Conclusions

CS use among IBD inpatients with CDI diagnosed by PCR is associated with poorer outcomes and would seem to reinforce the importance of C. difficile toxin assay to help distinguish colonization from infection. This adverse effect appears more prominent among those with UC.

Evidence of transmission of Clostridium difficile in asymptomatic patients following admission screening in a tertiary care hospital

BACKGROUND

Clostridium difficile (CD) is the leading cause of infectious health-care associated diarrhea. However, little is known regarding CD carriage and transmission amongst asymptomatic colonizers. We evaluated carriage, characterized strains and examined epidemiologic linkages in asymptomatic colonized CD patients.

METHODS

Rectal swabs from asymptomatic patients admitted to the general medicine ward from April 1-June 30 2012 were collected. PCR-confirmed CD colonies were ribotyped and characterized by Modified-Multi Locus Variable Number Tandem Repeat Analysis (MMLVA).

RESULTS

1549-swabs were collected from 474-patients. Overall, 50/474(10.6%) were CD PCR-positive, 24/50 were colonized at admission, while 26/50 were first identified > = 72 hours after admission. Amongst the 50 CD PCR-positive patients, 90% were asymptomatically colonized and 80% of individuals carried toxigenic CD-strains, including ribotype-027 (5/45:11%). MMLVA revealed five-clusters involving 15-patients harboring toxigenic (4/5) and non-toxigenic CD strains (1/5). In two clusters, patients were CD positive on admission while in the other three clusters involving 10 patients, we observed CD transmission from asymptomatically colonized patients to 8 previously CD-negative patients.

CONCLUSIONS

We identified increasing rates of colonization during admission to medical wards. MMLVA typing effectively discriminated between strains and suggests that 20% of patients with CD colonization acquired their strain(s) from asymptomatically colonized individuals in hospital.

Molecular epidemiology of Clostridium difficile infection in Iranian hospitals

Background

Clostridium difficile infection (CDI) is known as one of the most important causes of nosocomial infections. The main objective of this study was to evaluate the presence of Clostridium difficile in the stool of hospitalized patients with diarrhea as well as in their environments.

Methods

C. difficile isolates were characterized according to the presence of toxin genes and antibiotic resistance. Multilocus Sequence Typing Analysis (MLST) was applied for finding the genetic polymorphism and relationship among strain lineages.

Results

A total of 821 samples (574 stools and 247 swabs) were collected between April 2015 and May 2017. The prevalence of C. difficile isolates was 28.6% (164/574) in patients and 19% (47/247) in swabs taken from medical devices, hands of healthcare workers and skin patient sites. Finally, 11.5% (66/574) toxigenic C. difficile strains isolated from stool samples of inpatients and 4.4% (11/247) from hands of healthcare workers and skin patient sites. All the toxigenic isolates were inhibited by a low concentration of vancomycin (MIC < 0.5 μg/ml). About 43% (33/77) and 39% of isolates were resistant to Clindamycin and moxifloxacin respectively. All isolates were susceptible to metronidazole. Toxigenic C. difficile strains were analyzed by MLST and were divided into 4 different STs. The detected types were ST-54 (57.9%), followed by ST-2 (31.6. %), ST-15 (5.3%) and ST-37 (5.3%), while none of the isolates were identified as ST-1 or ST-11. Significant risk factors for CDI appear to be advanced age, undergoing chemotherapy, previous surgery, and residence in the nursing home.

Conclusions

CDI is common in Iran and further studies are recommended to monitor its epidemiological variations. Moreover, greater attempts must be made to encourage antibiotic stewardship by healthcare workers and the public.

2019 update of the WSES guidelines for management of Clostridioides (Clostridium) difficile infection in surgical patients

In the last three decades, Clostridium difficile infection (CDI) has increased in incidence and severity in many countries worldwide. The increase in CDI incidence has been particularly apparent among surgical patients. Therefore, prevention of CDI and optimization of management in the surgical patient are paramount. An international multidisciplinary panel of experts from the World Society of Emergency Surgery (WSES) updated its guidelines for management of CDI in surgical patients according to the most recent available literature. The update includes recent changes introduced in the management of this infection.

Sharing is not always a good thing: Use of a DNA marker to investigate the potential for ward-to-ward dissemination of healthcare-associated pathogens

A DNA marker inoculated onto portable equipment on a medical ward was disseminated to other wards when equipment was shared and to a physician work room and the hospital cafeteria by personnel. These results demonstrate the plausibility of pathogen transmission in healthcare facilities in the absence of shared ward exposure.

Overall bioburden by total colony count does not predict the presence of pathogens with high clinical relevance in hospital and community environments

BACKGROUND

Healthcare-associated infections (HAIs) affect millions of patients, increasing morbidity and mortality. Pathogens of HAIs originate from both the patient's own flora and the environment, including multi-drug-resistant organisms.

AIMS

To determine the bioburden on different types of high-touch surfaces, and to identify cultures to species level and stratify strains into those of low and high clinical relevance.

DESIGN

Association between bioburden and presence of pathogens of high clinical relevance (PHCR) in a tertiary care centre and urban environment.

METHODS

The overall bioburden measured by total colony count (TCC) was assessed using tryptic soy agar contact plates and two selective agars to improve detection of PHCR. Isolates were routinely identified to species level using matrix-assisted laser desorption/ionization - time of flight mass spectrometry (MALDI-TOF). The definition of PHCR was based on listings outlined by the Centers for Disease Control and Prevention.

FINDINGS

In total, 1431 contact plates were processed from 477 surfaces: 153 from hospitals and 324 from publicly accessible institutions or devices. At least one PHCR was identified from cultures from 73 samples. TCC was found to be poorly correlated with the presence of PHCR.

CONCLUSION

TCC poorly predicted the presence of PHCR, rendering the results from environmental sampling difficult to interpret. MALDI-TOF enables the identification of large numbers of isolates from the environment at low cost. Further studies on environmental contamination should use MALDI-TOF to identify all pathogens grown.

Primary Prevention of Clostridium difficile-Associated Diarrhea: Current Controversies and Future Tools

PURPOSE OF REVIEW

Clostridium difficile infection (CDI) is a major cause of morbidity and mortality in hospitalized patients and rates in most places have not decreased significantly despite broad efforts by both hospitals and public health entities. This review aims to provide readers with a better understanding of the limitations of current prevention strategies. We also review potential future tools that may be available for the primary prevention of CDI in the next decade.

RECENT FINDINGS

Research over the last decade has expanded our appreciation of the role of asymptomatic shedding in the healthcare setting and in the community. This review demonstrates that poor quality data underlies even well-established guidance from national authorities on basic topics such as contact precautions, avoidance of alcohol-based hand hygiene products, CDI testing, supplemental cleaning modalities, and the use of bleach solutions. Additionally, we review research on novel preventative interventions such as identification of asymptomatic carriers, supplemental environmental cleaning technologies, vaccines, and the manipulation of the intestinal microbiome. While there is preliminary data that supports further research in all of these areas, the research is not yet robust enough on which to base local or national policy recommendations, though late-phase human clinical trials of CDI vaccine trials are ongoing. Over the last decade, researchers have begun to reassess the traditional infection prevention model for CDI. Data suggesting a greater role for asymptomatic shedders has increased our understanding of current vertical prevention techniques and is forcing researchers to look more at new processes and technologies to decrease disease incidence.

Comparison of Control of Clostridium difficile Infection in Six English Hospitals Using Whole-Genome Sequencing

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.

Understanding Clostridium difficile Colonization

Clostridium difficile is the main causative agent of antibiotic-associated and health care-associated infective diarrhea. Recently, there has been growing interest in alternative sources of C. difficile other than patients with Clostridium difficile infection (CDI) and the hospital environment. Notably, the role of C. difficile-colonized patients as a possible source of transmission has received attention. In this review, we present a comprehensive overview of the current understanding of C. difficile colonization. Findings from gut microbiota studies yield more insights into determinants that are important for acquiring or resisting colonization and progression to CDI. In discussions on the prevalence of C. difficile colonization among populations and its associated risk factors, colonized patients at hospital admission merit more attention, as findings from the literature have pointed to their role in both health care-associated transmission of C. difficile and a higher risk of progression to CDI once admitted. C. difficile colonization among patients at admission may have clinical implications, although further research is needed to identify if interventions are beneficial for preventing transmission or overcoming progression to CDI.

When are pathogen genome sequences informative of transmission events?

Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data.

The increasing availability of genetic sequence data has sparked an interest in using pathogen whole genome sequences to reconstruct the history of individual transmission events in an infectious disease outbreak. However, such methodologies rely on pathogen genomes mutating rapidly enough to discriminate between infected individuals, an assumption that remains to be investigated. To determine pathogen outbreaks for which genetic data is expected to be informative of transmission events, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating pathogen genome sequences sampled from transmission pairs. We characterise transmission divergence of ten major outbreak causing pathogens using simulations and find significant variation between diseases, with viral outbreaks generally exhibiting higher transmission divergence than bacterial ones. We reconstruct these outbreaks using the R-packages outbreaker and phybreak and find that genetic sequence data, though useful for rapidly evolving pathogens, provides little to no information about outbreaks with low transmission divergence, such as Streptococcus pneumoniae and Shigella sonnei. Our results demonstrate the need to incorporate other sources of outbreak data, such as contact tracing data and spatial location data, into outbreak reconstruction tools.

Applications of network analysis to routinely collected health care data: a systematic review

Objective

To survey network analyses of datasets collected in the course of routine operations in health care settings and identify driving questions, methods, needs, and potential for future research.

Materials and Methods

A search strategy was designed to find studies that applied network analysis to routinely collected health care datasets and was adapted to 3 bibliographic databases. The results were grouped according to a thematic analysis of their settings, objectives, data, and methods. Each group received a methodological synthesis.

Results

The search found 189 distinct studies reported before August 2016. We manually partitioned the sample into 4 groups, which investigated institutional exchange, physician collaboration, clinical co-occurrence, and workplace interaction networks. Several robust and ongoing research programs were discerned within (and sometimes across) the groups. Little interaction was observed between these programs, despite conceptual and methodological similarities.

Discussion

We use the literature sample to inform a discussion of good practice at this methodological interface, including the concordance of motivations, study design, data, and tools and the validation and standardization of techniques. We then highlight instances of positive feedback between methodological development and knowledge domains and assess the overall cohesion of the sample.

Epidemiology of Clostridium Difficile Infection in a Large Hospital in Northern Italy: Questioning the Ward-Based Transmission

Background:

Clostridium Difficile infection (CDI) is considered a ward-based nosocomial infection, due to contagion among patients. Molecular studies recently questioned ward-based contact for disease spread.

Objective:

To investigate whether it is plausible that CDI spread in San Martino Hospital of Genoa was due to a ward-based contact and patient-to-patient diffusion.

Methods:

We conducted a retrospective cohort study of CDI cases from April 2010 to March 2015. We referred to Hospital data set and Admission Service. Multilevel modelling approach and ecological analysis were used to assess C. difficile infection risk according to wards and time of occurrence. Six representative CD strains were ribotyped to assess a possible equivalence.

Results:

The assessment of 514 CDI cases showed that the risk of disease and rate of incidence in wards were independent, while frequency of cases and number of wards involved exhibited a positive relationship, excluding the typical epidemic pattern of contagious diffusion, i.e., many cases in few wards. The extra-binomial variability due to ward clustering was not significant, indicating homogeneity in the probability of CDI occurrence across all wards. Three hundred sixty-eight patients changed ward, without showing connection between the frequency of cases in new wards and incidence among new subjects. Trigonometric components described a significant contribution of seasonality, with excess of CDI cases during the winter months. Molecular analysis showed different ribotypes of CD strains from the same ward.

Conclusion:

From our results it seems unlikely that in our institution CDI occurrence is due to ward-based contact and inter-human contagion of the organism.