Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations.

Clostridioides difficile is a pathogen often associated with hospital-acquired infection or antimicrobial-induced disease; however, increasing evidence indicates infections can result from community or environmental sources. Most genomic sequencing of C. difficile has focused on clinical strains, although evidence is growing that C. difficile spores are widespread in soil and water in the environment. In this study, we sequenced 38 genomes collected from soil and water isolates in Flagstaff (AZ, USA) and Slovenia in an effort targeted towards environmental surveillance of C. difficile. At the average nucleotide identity (ANI) level, the genomes were divergent to C. difficile at a threshold consistent with different species. A phylogenetic analysis of these divergent genomes together with Clostridioides genomes available in public repositories confirmed the presence of three previously described, cryptic Clostridioides species and added two additional clades. One of the cryptic species (C-III) was almost entirely composed of Arizona and Slovenia genomes, and contained distinct sub-groups from each region (evidenced by SNP and gene-content differences). A comparative genomics analysis identified multiple unique coding sequences per clade, which can serve as markers for subsequent environmental surveys of these cryptic species. Homologues to the C. difficile toxin genes, tcdA and tcdB, were found in cryptic species genomes, although they were not part of the typical pathogenicity locus observed in C. difficile, and in silico PCR suggested that some would not amplify with widely used PCR diagnostic tests. We also identified gene homologues in the binary toxin cluster, including some present on phage and, for what is believed to be the first time, on a plasmid. All isolates were obtained from environmental samples, so the function and disease potential of these toxin homologues is currently unknown. Enzymatic profiles of a subset of cryptic isolates (n=5) demonstrated differences, suggesting that these isolates contain substantial metabolic diversity. Antimicrobial resistance (AMR) was observed across a subset of isolates (n=4), suggesting that AMR mechanisms are intrinsic to the genus, perhaps originating from a shared environmental origin. This study greatly expands our understanding of the genomic diversity of Clostridioides. These results have implications for C. difficile One Health research, for more sensitive C. difficile diagnostics, as well as for understanding the evolutionary history of C. difficile and the development of pathogenesis.

Clinical Significance of Toxigenic Clostridioides difficile Growth in Stool Cultures during the Era of Nonculture Methods for the Diagnosis of C. difficile Infection.

The importance of the detection of relevant toxins or toxin genes to diagnose Clostridioides difficile infection (CDI) or the prediction of clinical outcomes of CDI has been emphasized in recent years. Although stool culture of C. difficile is not routinely recommended in the era of nonculture methods as the preferred tools for CDI diagnosis, the clinical significance of toxigenic C. difficile growth (tCdG) in stool cultures was analyzed. A clinical study was conducted in medical wards of Tainan Hospital, Ministry of Health and Welfare, in southern Taiwan. Diarrheal adults with fecal glutamate dehydrogenase and C. difficile toxin between January 2013 and April 2020 were included. Of the 209 patients with CDI, 158 (75.6%) had tCdG found in stool cultures, and the rest (51, 24.4%) had no tCdG in stool. Only prior ceftazidime or ceftriaxone therapy was independently associated with no tCdG in stool (odds ratio [OR] 2.17, P = 0.02). Compared to the patients with tCDG in stool, those without tCdG in stool experienced treatment success more often (97.1% versus 67.0%, P < 0.001) if treated with metronidazole or vancomycin but had a similar in-hospital mortality or recurrence rate. In the multivariate analysis among 114 patients with CDI treated with metronidazole or vancomycin, treatment success was independently associated with no tCdG in stool (OR 12.7, P = 0.02). Despite the limited utility of stool cultures in CDI diagnoses, no tCdG in stool culture heralds a favorable therapeutic outcome among adults with CDI treated with metronidazole or vancomycin. IMPORTANCE The importance of detecting toxins or toxin genes when diagnosing Clostridioides difficile infections (CDIs) or predicting the severity and outcomes of CDI has been emphasized in recent years. Although the yielding of C. difficile from stool cultures might implicate higher bacterial loads in fecal samples, in an era of nonculture methods for the standard diagnosis of CDIs, clinical significance of positive stool cultures of toxigenic C. difficile was analyzed in this study. Despite the limited ability of stool cultures in CDI diagnoses, no yielding of C. difficile growth might predict the successful CDI therapy.

What's a SNP between friends: The lineage of Clostridioides difficile R20291 can effect research outcomes.

Clostridioides difficile R20291 is the most studied PCR-Ribotype 027 isolate. The two predominant lineages of this hypervirulent strain, however, exhibit substantive phenotypic differences and possess genomes that differ by a small number of nucleotide changes. It is important that the source of R20291 is taken into account in research outcomes.

Development and validation of a simple and robust model to predict 30-day mortality in patients with Clostridioides difficile-associated enterocolitis.

OBJECTIVE: Clostridioides difficile infection (CDI) is a common healthcare-associated infection and associated with high morbidity and mortality. As current guidelines recommend treatment stratified for disease severity, this study aimed to identify predictors of 30-day mortality in order to develop a robust prediction model. DESIGN: This was a retrospective analysis of 207 inpatients with CDI who were treated at the Jena University Hospital between September 2011 and December 2015. In a training cohort (n=127), predictors of 30-day mortality were identified by receiver operating characteristics analysis and logistic regression. The derived model was validated in an independent cohort of 80 inpatients with CDI. RESULTS: Within 30 days, 35 (28%) patients in the training cohort died from any cause. C-reactive protein (CRP) of ≥121 mg/L (OR 3.80; 95% CI 1.64 to 7.80; p=0.003) and lower systolic blood pressure of ≤104 mm Hg (OR 3.73; 95% CI 1.63 to 8.53; p=0.002) at diagnosis as well as development of renal impairment (serum creatinine >1.5×baseline; OR 5.61; 95% CI 1.94 to 16.26; p=0.035) within the first 6 days were associated with 30-day mortality in univariate analysis. The use of these parameters enabled correct mortality prediction in 73% of cases on the day of diagnosis and in 76% at day 6. In the validation cohort, 30-day mortality was 18/80 (23%). Our model enabled a 73.7% correct prediction concerning 30-day mortality on day 6 after diagnosis of CDI. CONCLUSION: Hypotension and CRP elevation on the day of diagnosis as well as occurrence of kidney dysfunction during the first 6 days are suitable parameters to predict 30-day mortality in patients with CDI who need to be treated in the hospital.

An outbreak of Clostridioides difficile infections due to a 027-like PCR ribotype 181 in a rehabilitation centre: Epidemiological and microbiological characteristics.

Clostridioides difficile is one of the most important healthcare-associated pathogens. Recently, several new 027-like types have been found that all belong to the multilocus sequence typing (MLST) Clade 2. We report a rapidly spreading outbreak of C. difficile infections (CDI) due to a newly identified PCR ribotype (RT) 181 in a Rehabilitation Centre (RC). Genomic analysis revealed the outbreak strain, not previously identified in Greece, belonged to clade 2, sequence type (ST) 1 and had a 18bp deletion in tcdC at position 311 together with a single nucleotide deletion at position 117, similarly to RT 027. The presence of a clonal outbreak was confirmed by whole genome sequencing, yet the source of this ribotype remained unclear. The emergence and rapid spread of new C. difficile ribotypes highlights the need for ongoing C. difficile surveillance and better understanding of overall Clade 2 phylogeny.

Incidence and Risk Factors of Recurrent Clostridioides difficile Infection in Patients With Cirrhosis.

INTRODUCTION: Clostridioides difficile infection (CDI) is common in patients with cirrhosis and is associated with poor outcomes. CDI risk factors in this population have been well characterized; however, risk factors of recurrent CDI (R-CDI) after treatment have not been explored. We sought to estimate the incidence of R-CDI and its associated risk factors in patients with cirrhosis. METHODS: We performed a cohort study of patients with cirrhosis hospitalized with CDI between 2012 and 2016. We collected patient characteristics, including detailed information on the CDI, features of the underlying liver disease, and outcomes including R-CDI, hospital readmission, and mortality. R-CDI was defined as CDI occurring 2-8 weeks after the initial episode. Cox proportional hazards model was used to identify variables independently associated with the outcomes. RESULTS: A total of 257 hospitalized patients with cirrhosis and CDI were included. CDI was community associated in 22.6%. The incidence of R-CDI was 11.9%. R-CDI was not significantly associated with medications at hospital admission or discharge. Independent risk factors of R-CDI included increased Charlson Comorbidity Index (hazard ratio [HR] 1.30; 95% confidence interval [CI]: 1.09-1.55) and use of lactulose (HR 2.58; 95% CI: 1.09-6.09). The 30-day readmission rate was 37%, and readmission was associated with increased Charlson Comorbidity Index (HR 1.12; 95% CI: 1.03-1.23) and Model for End-Stage Liver Disease score (HR 1.04; 95% CI: 1.01-1.07). The 90-day mortality was 22.8%. DISCUSSION: In patients with cirrhosis, R-CDI is associated with comorbidity burden and lactulose use. Attention to these factors might aid clinicians in efforts to prevent R-CDI and improve outcomes in this population.

Reducing Fluoroquinolone Use and Clostridioides difficile Infections in Community Nursing Homes Through Hospital-Nursing Home Collaboration.

OBJECTIVE: Nursing homes (NHs) are an important target for antibiotic stewardship (AS). We describe a collaborative model to reduce Clostridioides difficile infections (CDIs) in NHs through optimization of antibiotic use including a reduction in high-risk antibiotics such as fluoroquinolones. DESIGN: Quasi-experimental, pre- and post-intervention study. SETTING AND PARTICIPANTS: Six NHs in Monroe County, NY. METHODS: A hospital-based AS expert team assisted NHs in identifying targets for improving antibiotic use. Interventions included (1) collaboration with a medical director advisory group to develop NH consensus guidelines for testing and treatment of 2 syndromes (urinary tract infections and pneumonia) for which fluoroquinolone use is common, (2) provision of multifaceted NH staff education on these guidelines and education of residents and family members on the judicious use of antibiotics, and (3) sharing facility-specific and comparative antibiotic and CDI data. We used Poisson regression to estimate antibiotic use per 1000 resident days (RD) and CDIs per 10,000 RD, pre- and post-intervention. Segmented regression analysis was used to estimate changes in fluoroquinolone and total antibiotic rates over time. RESULTS: Postintervention, the monthly rate of fluoroquinolone days of therapy (DOT) per 1000 RD significantly decreased by 39% [rate ratio (RR) 0.61, 95% confidence interval (CI) 0.59-0.62, P < .001] across all NHs and the total antibiotic DOT decreased by 9% (RR 0.91, 95% CI 0.90-0.92, P < .001). Interrupted time series analysis of fluoroquinolone and total DOT rates confirmed these changes. The quarterly CDI rate decreased by 18% (RR 0.82, 95% CI 0.68-0.99, P = .042). CONCLUSIONS AND IMPLICATIONS: A hospital-NH partnership with a medical director advisory group achieved a significant reduction in total antibiotic and fluoroquinolone use and contributed to a reduction in CDI incidence. This approach offers one way for NHs to gain access to AS expertise and resources and to standardize practices within the local community.