Factors affecting reported Clostridioides difficile infection rates; the more you look the more you find, but should you believe what you see?

Reported rates of C. difficile infection (CDI) have increased in many settings; however, these can be affected by factors including testing density (test-density) and diagnostic methods. We aimed to describe the impact of multiple factors on CDI rates. Hospitals (n = 182) across five countries (France, Germany, Italy, Spain, and UK) provided data on; size and type of institution, CDI testing methodology, number of tests/month and patient-bed-days (pbds)/month over one year. Incidence rates were compared between countries, different sized institutions, types of institutions and testing method. After univariate analyses, the highest CDI rates were observed in Italy (average 11.8/10,000pbds/hospital/month), acute/primary hospitals (12.3/10,000pbds/hospital/month), small hospitals (16.7/10,000pbds/hospital/month), and hospitals using methods that do not detect toxin (NO-TOXIN) (e.g. GDH/NAAT or standalone NAAT) (10.7/10,000pbds/hospital/month). After adjusting for test-density, highest incidence rates were still in Italy, acute/primary hospitals and those using NO-TOXIN. The relative rate in long-term healthcare facilities (LTHCFs) increased, but size of institution no longer influenced the CDI rate. Test-density appears to have the largest effect on reported CDI rates. NO-TOXIN testing still influences CDI rates, even after adjusting for test-density, which is consistent with tests that 'overcall' true CDI. Low test-density can mask the true burden of CDI, e.g. in LTHCFs, highlighting the importance of good quality surveillance.

Outcomes of Clostridium difficile-suspected diarrhea in a French university hospital.

Clostridium difficile infection (CDI) produces a variety of clinical presentations ranging from mild diarrhea to severe infection with fulminant colitis, septic shock, and death. CDI puts a heavy burden on healthcare systems due to increased morbidity and mortality, and higher costs. We evaluated the clinical impact of CDI in terms of complications and mortality in a French university hospital compared with patients with diarrhea unrelated to CDI. A 3-year prospective, observational, cohort study was conducted in a French university hospital. Inpatients aged 18 years or older with CDI-suspected diarrhea were eligible to participate in the study and were followed for up to 60 days after CDI testing. Among the 945 patients with diarrhea included, 233 had confirmed CDI. Overall, 106 patients (11.2%) developed at least one of the following complications: colectomy, colitis, ileitis/rectitis, ileus, intestinal perforation, megacolon, multiorgan failure, pancolitis, peritonitis, pseudomembranous colitis, renal failure, and sepsis/septic shock. The complication rate was significantly higher in patients with diarrhea related to C. difficile than in non-CDI patients (26.6% vs 6.2%, P < 0.001). At day 60, 137 (14.5%) patients had died, with 37 deaths among the CDI group (15.9%). Death was attributable to CDI in 15 patients (6.4%). Complications are more frequent among CDI cases than in patients with diarrhea not related to C. difficile. Assessment of CDI is necessary to ensure allocation of sufficient resources to CDI prevention.

Evaluation of a novel molecular assay to diagnose toxigenic strains of Clostridium difficile.

The objective of this study was to evaluate the Amplidiag C. difficile+027® assay, a new molecular method that detects toxin B gene in stool samples and identifies the hypervirulent 027 strain, to diagnose Clostridium difficile infections. The assay was compared to the reference method i.e. toxigenic culture. Amplidiag C. difficile+027® assay was prospectively evaluated from 309 diarrheal stool specimens of patients suspected of C. difficile infection. Forty-five (14.6%) stools were positive by toxigenic culture and 11 (3.6%) stools gave discordant results with the molecular method. PR027 was not recovered during the study. After resolving the discrepant results, the sensitivity, specificity, positive and negative predictive values of Amplidiag C. difficile+027® assay were 91.1% [CI 95% 77.9-97.1], 99.6% [CI 95% 97.6-100], 97.6% [CI 95% 85.9-99.9] and 98.5% [CI 95% 96-99.5], respectively compared to toxigenic culture. This assay is sensitive compared to the toxigenic culture.

Spatio-temporal variability of the epidemic 027 Clostridium difficile strains in France based on MLVA typing.

MLVA analysis of 103 PCR ribotype 027 strains showed a regional specificity and the persistence of the same clone within a hospital several years apart. Capillary electrophoresis PCR ribotyping led to the identification of seven 027 variant strains and five 176 strains, four of them being implicated in an outbreak.

Factors predictive of severe Clostridium difficile infection depend on the definition used.

CONTEXT: Clostridium difficile infection (CDI) produces a variety of clinical presentations ranging from mild diarrhea to severe infection with fulminant colitis, septic shock, and death. Over the past decade, the emergence of the BI/NAP1/027 strain has been linked to higher prevalence and severity of CDI. The guidelines to treat patients with CDI are currently based on severity factors identified in the literature and on expert opinion and have not been systematically evaluated. OBJECTIVE: The objective of this study was to identify factors associated with severe CDI defined according to four different severity definitions (Def): the 2010 SHEA/IDSA guidelines (Def1), the 2014 ESCMID guidelines (Def2), complicated CDI at the end of diarrhea (Def3), and our hospital-specific guidelines (white blood cell (WBC) count ≥15 × 10(9)/L, serum creatinine concentration >50% above baseline, pseudomembranous colitis, megacolon, intestinal perforation, or septic shock requiring intensive care unit admission. METHODS: A three-year cohort study was conducted in a university hospital in Lyon, France. All hospitalized (≥48 h) patients ≥18 years old, suffering from CDI, and agreeing to participate were included. Patients were followed-up for 60 days after CDI diagnosis. After bivariate regression analyses, factors associated with severe CDI during the course of disease were identified by a multivariate logistic regression. Statistical significance was reached with a two-sided p-value <0.05. RESULTS: 233 CDI patients diagnosed between 2011 and 2014 were included for a mean incidence rate of 2.15 cases/1000 hospitalized patients or 3.16 cases/10,000 patient days. Mean age was 65.3 years and 52.5% were men. Death occurred in 37 patients (15.9%) within 60 days of diagnosis. Death was related to CDI in 15 patients (40.5%). Frequency of severe CDI ranges from 11.6% to 59.2% depending on the case-definition. Factors independently associated with severe CDI were: age ≥68 years, male gender, renal disease, and serum albumin <30 g/L according to Def1 (n = 106, 45.5%); exposure to antivirals in the previous 4 weeks, renal disease, and blood neutrophils >7,5 × 10(9)/L in patients with Def2 (n = 138, 59.2%); abdominal pain, serum albumin <30 g/L, and WBC >10 × 10(9)/L according to Def3 (n = 27, 11.6%); age ≥68 years, renal disease, serum albumin <30 g/L, serum lactate dehydrogenase >248 IU/L, and blood neutrophils >7,5 × 10(9)/L were associated with severe CDI in patients with Def4 (n = 113, 48.5%). CONCLUSIONS: Our results indicate that appropriate case definition is needed for characterizing patients at risk of developing severe CDI. Our study suggest that serum albumin and the presence of renal disease, associated with severe CDI in three definitions, may be useful for identifying patients at risk of a poor outcome.

Clostridium difficile associated reactive arthritis: Case report and literature review.

INTRODUCTION: Extra-gastro-intestinal tract manifestations associated with Clostridium difficile infection (CDI), including reactive arthritis (ReA), are uncommon. METHOD: We report a case of ReA associated with a relapse of CDI in a 46-year-old woman. A toxigenic C. difficile strain was isolated from stools and characterized as PCR-ribotype 014/020/077. We conducted a comprehensive literature review of ReA associated with CDI (ReA-CDI). Diagnostic criteria for ReA-CDI were: (i) evidence of aseptic synovitis (confirmed by culture) developing during or immediately after colitis, (ii) presence of a toxigenic C. difficile strain in stool samples, and (iii) absence of other causes of colitis and arthritis. RESULTS: Forty-nine cases of ReA-CDI (excluding the present report) have already been described since 1976. Of these reports, Mean age of patients was 38 years (SD: 18.5), 46% were male, and 68% had HLA B27 genotype. Sixty-nine percent of patients received a ß-lactamin treatment before CDI. ReA-CDI occurred a median 10 days (range 0-55 days) after CDI. Outcome was favorable in 90% of patients and oral non anti-inflammatory drugs were required for 55%. CONCLUSION: ReA-CDI remains uncommon. Compared to the general population, it is more likely observed in younger patients with HLA B27-positive genotype.

[Clostridium difficile colitis]. / Colites à clostridium difficile.

C. difficile is a spore-forming anaerobic enteropathogen responsible for a wide range of clinical features ranging from mild uncomplicated diarrhoea to severe debilitating disease, toxic megacolon, or even perforation and sometimes death. Risk factors for C. difficile infection (CDI) include age > 65 years, previous hospitalization and recent antibiotic therapy. Main virulence factors of C. difficile are toxins A (TcdA) and B (TcdB). Since 2005, a new hypervirulent strain has emerged. This epidemic strain named 027/NAP/BI has been responsible for outbreaks worldwide, with increased mortality and severity. Antibiotic treatment of CDI is based on severity of the disease and relies on the use of oral metronidazole, vancomycin or fidaxomicin. Control of CDI needs an antimicrobial stewardship policy and the implementation of contact precautions for the infected patients.

Molecular test based on isothermal helicase-dependent amplification for detection of the Clostridium difficile toxin A gene.

The AmpliVue Clostridium difficile assay and a glutamate dehydrogenase (GDH)-illumigene algorithm were evaluated using 308 diarrheal stool specimens of patients suspected of having C. difficile infection. Compared to the enriched toxigenic culture method, the sensitivities, specificities, and positive and negative predictive values of the AmpliVue C. difficile assay and the GDH-illumigene-based algorithm were 91.7% (95% confidence interval [CI], 76.4 to 97.8), 100% (95% CI, 98.3 to 100), 100% (95% CI, 87 to 100), and 98.9% (95% CI, 96.6 to 99.7), respectively.

Contribution of MALDI-TOF mass spectrometry and machine learning including deep learning techniques for the detection of virulence factors of Clostridioides difficile strains.

Clostridioides difficile (CD) infections are defined by toxins A (TcdA) and B (TcdB) along with the binary toxin (CDT). The emergence of the 'hypervirulent' (Hv) strain PR 027, along with PR 176 and 181, two decades ago, reshaped CD infection epidemiology in Europe. This study assessed MALDI-TOF mass spectrometry (MALDI-TOF MS) combined with machine learning (ML) and Deep Learning (DL) to identify toxigenic strains (producing TcdA, TcdB with or without CDT) and Hv strains. In total, 201 CD strains were analysed, comprising 151 toxigenic (24 ToxA+B+CDT+, 22 ToxA+B+CDT+ Hv+ and 105 ToxA+B+CDT-) and 50 non-toxigenic (ToxA-B-) strains. The DL-based classifier exhibited a 0.95 negative predictive value for excluding ToxA-B- strains, showcasing accuracy in identifying this strain category. Sensitivity in correctly identifying ToxA+B+CDT- strains ranged from 0.68 to 0.91. Additionally, all classifiers consistently demonstrated high specificity (>0.96) in detecting ToxA+B+CDT+ strains. The classifiers' performances for Hv strain detection were linked to high specificity (≥0.96). This study highlights MALDI-TOF MS enhanced by ML techniques as a rapid and cost-effective tool for identifying CD strain virulence factors. Our results brought a proof-of-concept concerning the ability of MALDI-TOF MS coupled with ML techniques to detect virulence factor and potentially improve the outbreak's management.

Evaluation of the chromogenic agar chromID C. difficile.

Three selective media (chromID C. difficile agar, taurocholate cycloserine cefoxitin agar [TCCA; homemade], and CLO medium) were compared from 406 stool samples of patients suspected of having Clostridium difficile infection. The sensitivities of chromID C. difficile agar at 24 h and 48 h, CLO medium, and TCCA were 74.1%, 87%, 85.2%, and 70.4%, respectively.

Decolonization of asymptomatic carriage of multi-drug resistant bacteria by bacteriophages?

Antimicrobial resistance is a major threat to human and animal health and accounted for up to 4.5 million deaths worldwide in 2019. Asymptomatic colonization of the digestive tract by multidrug resistant (multi-resistant) bacteria such as extended-spectrum beta-lactamase-, or carbapenemase- producing Enterobacterales is (i) a risk factor for infection by these multi-resistant bacteria, (ii) a risk factor of dissemination of these multi-resistant bacteria among patients and in the community, and (iii) allows the exchange of resistance genes between bacteria. Hence, decolonization or reduction of the gastrointestinal tract colonization of these multi-resistant bacteria needs to be urgently explored. Developing new non-antibiotic strategies to limit or eradicate multi-resistant bacteria carriage without globally disrupting the microbiota is considered a priority to fight against antibiotic resistance. Probiotics or Fecal Microbiota Transplantation are alternative strategies to antibiotics that have been considered to decolonize intestinal tract from MDR bacteria but there is currently no evidence demonstrating their efficacy. Lytic bacteriophages are viruses that kill bacteria and therefore could be considered as a promising strategy to combat antibiotic resistance. Successful decolonization by bacteriophages has already been observed clinically. Here, we discuss the current alternative strategies considered to decolonize the digestive tract of multidrug resistant bacteria, briefly describing probiotics and fecal microbiota transplantation approaches, and then detail the in vivo and in vitro studies using bacteriophages, while discussing their limits regarding the animal models used, the characteristics of phages used and their activity in regards of the gut anatomy.

Accuracy of ICD-10 codes for surveillance of Clostridium difficile infections, France.

The sensitivity and specificity of surveillance for Clostridium difficile infections according to International Classification of Diseases, 10th revision, codes were compared with laboratory results as standard. Sensitivity was 35.6%; specificity was 99.9%. Concordance between the 2 methods was moderate. Surveillance based on ICD-10 codes underestimated the rate based on laboratory results.

[Clostridioides difficile: updated recommendations]. / Clostridioides difficile : des recommandations actualisées.

CLOSTRIDIOIDES DIFFICILE: UPDATED RECOMMENDATIONS Clostridioides difficile is a spore-forming anaerobic enteropathogen responsible for a wide spectrum of clinical features ranging from mild uncomplicated diarrhoea to severe debilitating disease, toxic megacolon, or even perforation and sometimes death. Risk factors for CDI include age >65 years, previous hospitalization and recent antibiotic therapy. Main virulence factors of C. difficile are toxins A (TcdA) and B (TcdB). The emergence and dissemination of a new hypervirulent strain (027/NAP/BI) in 2005 has stimulated clinical and basic research on C. difficile. Major advances have been made regarding the CDI epidemiology (better recognition of community acquired CDI), diagnosis (molecular tests) and therapy (new drugs such as fidaxomicin, bezlotoxumab, and fecal microbiota transplantation) aspects. These advances have allowed the updating of management recommendations, under the aegis of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Antibiotic treatment of CDI depends on both the severity of the infection, and the risk/number of recurrences. Prevention of CDI requires an antimicrobial stewardship policy and the implementation of contact precautions for the infected patients.

CLOSTRIDIOIDES DIFFICILE: DES RECOMMANDATIONS ACTUALISÉES Clostridioides difficile est un bacille à Gram positif anaérobie sporulé responsable d'un large spectre d'infections digestives : de la diarrhée simple spontanément résolutive à la colite pseudomembraneuse qui peut se compliquer de mégacôlon toxique, de perforation et entraîner le décès du patient. Les principaux facteurs de risque d'infections à C. difficile (ICD) sont l'âge supérieur à 65 ans, l'administration d'antibiotiques et les antécédents d'hospitalisation. La virulence des souches est liée à la production de deux toxines, TcdA et TcdB. L'émergence et la dissémination rapide d'un clone dit « hypervirulent ¼ (027/ NAP/BI) en 2005 a stimulé la recherche clinique et fondamentale. Des avancées majeures ont été réalisées tant sur le plan épidémiologique (meilleure reconnaissance des formes communautaires d'ICD), diagnostique (nouveaux tests moléculaires) que thérapeutique (nouveaux traitements comme la fidaxomicine, le bezlotoxumab, ou la transplantation de microbiote fécal) ; ces progrès ont permis la mise à jour des recommandations de prise à charge, sous l'égide de la Société européenne de microbiologie clinique et des maladies infectieuses (ESCMID). Le traitement antibiotique des ICD dépend à la fois de la sévérité de l'infection, du risque et du nombre de récidives. Le contrôle de l'infection requiert, d'une part, la maîtrise de la consommation d'antibiotiques et, d'autre part, la mise en œuvre de précautions « contact ¼ vis-à-vis des patients infectés.

Evaluation of a loop-mediated isothermal amplification assay for diagnosis of Clostridium difficile infections.

A new assay (illumigene C. difficile; Meridian Bioscience), based on the original loop-mediated isothermal amplification (LAMP) assay, was evaluated with 472 unformed stools from patients suspected of Clostridium difficile infection. Compared to the toxigenic culture, the sensitivity, specificity, and positive and negative predictive values were 91.8, 99.1, 91.8, and 99.1% for the illumigene C. difficile assay and 69.4, 100, 100, and 96.6% for the cytotoxicity assay, respectively.

Epidemiology and control of Clostridium difficile infections in healthcare settings: an update.

PURPOSE OF REVIEW: The epidemiology of Clostridium difficile infections (CDIs) has dramatically changed over the last decade in both North America and Europe. The objectives of this review are to highlight the recent epidemiological data and to provide an overview of the current knowledge of infection control measures. RECENT FINDINGS: Since 2003, many countries have reported increased incidence of CDI and outbreaks of severe cases of CDI. This trend is assumed to be due, in part, to the emergence and rapid spread of a 'hypervirulent' strain, known as 027/BI/NAP1. This strain has become endemic in many hospitals in North America and Europe. CDI rates have also increased in the community and new genotypes (e.g. PCR ribotype 078) are emerging in both humans and animals. To prevent cross-contamination and to reduce the incidence of CDI, infection control guidelines, based primarily on experience of hospitals during outbreaks, have been recently updated in Europe and the United States. CDI prevention relies on a bundle of measures including antimicrobial stewardship, prompt diagnosis, and the implementation of contact precautions. Currently, most of these measures have appeared effective in controlling outbreaks, but the best methods to reduce CDI incidence in settings of endemicity are still unknown. SUMMARY: The recent changes in CDI epidemiology have pushed infection control healthcare workers and scientific societies to revisit and update their guidelines for infection control.

Revisiting Species Identification within the Enterobacter cloacae Complex by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify pathogens, despite some limitations of the technique. The Enterobacter cloacae complex (ECC) taxonomy has recently been expanded, leading to uncertain identification of some species within the ECC when commercial MALDI-TOF MS is used. This technique is especially unsuited in the case of E. hormaechei, the main species responsible for infections and one of the most prone, within the ECC, to acquire antibiotic resistance. Hence, rapid and reliable identification at the species level could improve patient management. Here, we evaluated the performance of the Bruker Microflex MALDI-TOF MS instrument to identify ECC isolates using two databases and algorithms in comparison to the hsp60 gene sequencing reference method: the Bruker database included in the MALDI Biotyper software and an extensive online database coupled to an original Mass Spectrometric Identification (MSI) algorithm. Among a panel of 94 ECC isolates tested in triplicate, the online database coupled to MSI software allowed the highest rate of identification at the species level (92%) compared to the MALDI Biotyper database (25%), especially for the species E. hormaechei (97% versus 20%). We show that by creating a database of MALDI-TOF reference spectral profiles with a high number of representatives associated with the performant MSI software, we were able to substantially improve the identification of the E. cloacae complex members, with only 8% of isolates misidentified at the species level. This online database is available through a free online MSI application (https://msi.happy-dev.fr/). IMPORTANCE Creation of a database of MALDI-TOF reference spectral profiles with a high number of representatives associated with the performant MSI software enables substantial improvement in identification of E. cloacae complex members. Moreover, this online database is available through a free online MSI application (https://msi.happy-dev.fr/).

[Clostridium-difficile-associated infections]. / Infections à Clostridium difficile.

C. difficile is a spore-forming anaerobic enteropathogen. This bacillus is responsible for virtually all cases of pseudomembranous colitis and for 15 to 25% of cases of antibiotic-associated diarrhoea. Clostridium difficile associated-infections (CDI) have a wide range of clinical features which vary from mild uncomplicated diarrhoea to severe debilitating disease, paralytic ileus, toxic megacolon, or even perforation and sometimes death. Risk factors for CDI include age > 65 years, previous hospitalization and recent antibiotic therapy. Main virulence factors for this pathogen are toxins A and B. A third toxin, the binary toxin, has been found in up to 10% of strains from infected patients. For some years, a new hypervirulent strain has emerged. This epidemic strain belongs to PCR-ribotype 027 and is responsible for outbreaks with increased mortality and severity in North America and Europe. The most effective antibiotics for treatment are oral metronidazole and vancomycin. Control of CDI needs to prevent the emergence of CDI by minimizing the number of patients exposed to antimicrobials and to limit cross transmission.

Contribution of the autolysin AtlA to the bactericidal activity of amoxicillin against Enterococcus faecalis JH2-2.

The bactericidal activity of amoxicillin was investigated against Enterococcus faecalis JH2-2 and against an isogenic mutant deficient in the production of the N-acetylglucosaminidase AtlA. Comparison of the two strains indicated that this autolysin contributes to killing by amoxicillin both in vitro and in a rabbit model of experimental endocarditis.

Carriage and colonization of C. difficile in preterm neonates: A longitudinal prospective study.

BACKGROUND: Premature neonates (PN) present multiple risk factors for high frequencies and high levels of colonization by C. difficile, yet data is missing about this specific pediatric population. Here, we investigated PN C. difficile carriage and colonization dynamics, analyzed the impact of perinatal determinants on colonization, and characterized the isolates. METHODS: A one year longitudinal monocentric prospective cohort study was performed on 121 PN. C. difficile strains isolated from fecal samples on selective medium were identified and characterized by PCR (tpi housekeeping gene; tcdA and tcdB, and binary toxin genes), capillary gel-based electrophoresis PCR-ribotyping, and Multi-Locus Variable-number tandem-repeat Analysis (MLVA). RESULTS: Of the 379 samples analyzed, 199 (52%) were C. difficile culture positive with the mean levels of C. difficile colonization decreasing significantly (P = .027) over time. During hospitalization, C. difficile colonization frequency increased up to 61% with 95% of the strains belonging to both non-toxigenic PCR-ribotypes (RTs) FR082 (35%) and 032 (60%). After hospital discharge, if a higher diversity in RTs was observed, RTs FR082 and 032 remained predominant (respectively 40% and 28%). MLVA showed clonal relationship within each FR082 and 032 RTs. Ten toxigenic strains (5%) were isolated, all tcdA+/tcdB+ except for one tcdA-/tcdB+, and all being acquired after hospitalization. At 1 week, the only factors found to be linked with a higher frequency of C. difficile colonization were a higher gestational age (P = 0.006) and a higher birth weight (P = 0.016). CONCLUSION: The dynamics of C. difficile colonization in PN followed a specific pattern. C. difficile colonization rapidly occurred after birth with a low diversity of non-toxigenic RTs. After hospitalization, non-toxigenic RTs diversity increased. Sporadic carriage of toxigenic strains was observed after hospitalization.