Diagnosis and Treatment of Clostridium difficile Infection (CDI)

Gut Microbiota-Gut Metabolites and Clostridioides difficile Infection: Approaching Sustainable Solutions for Therapy

Clostridioides difficile (C. difficile) infection (CDI) is the most common hospital-acquired infection. With the combination of a high rate of antibiotic resistance and recurrence, it has proven to be a debilitating public health threat. Current treatments for CDI include antibiotics and fecal microbiota transplantation, which contribute to recurrent CDIs and potential risks. Therefore, there is an ongoing need to develop new preventative treatment strategies for CDI. Notably, gut microbiota dysbiosis is the primary risk factor for CDI and provides a promising target for developing novel CDI therapy approaches. Along with gut microbiota dysbiosis, a reduction in important gut metabolites like secondary bile acids and short-chain fatty acids (SCFAs) were also seen in patients suffering from CDI. In this review study, we investigated the roles and mechanisms of gut microbiota and gut microbiota-derived gut metabolites, especially secondary bile acids and SCFAs in CDI pathogenesis. Moreover, specific signatures of gut microbiota and gut metabolites, as well as different factors that can modulate the gut microbiota, were also discussed, indicating that gut microbiota modulators like probiotics and prebiotics can be a potential therapeutic strategy for CDI as they can help restore gut microbiota and produce gut metabolites necessary for a healthy gut. The understanding of the associations between gut microbiota-gut metabolites and CDI will allow for developing precise and sustainable approaches, distinct from antibiotics and fecal transplant, for mitigating CDI and other gut microbiota dysbiosis-related diseases.

Gut microbiota and microbiota-based therapies for Clostridioides difficile infection

Clostridioides difficile infection poses significant clinical challenges due to its recurrent nature. Current antibiotic management does not address the underlying issue, that of a disturbed gastrointestinal microbiome, called dysbiosis. This provides a supportive environment for the germination of C. difficile spores which lead to infection and toxin production as well as an array of other health conditions. The use of microbiome restoration therapies such as live biotherapeutics can reverse dysbiosis and lead to good clinical outcomes. Several such therapies are under clinical investigation.

Rapid-format recombinant antibody-based methods for the diagnosis of Clostridioides difficile infection: Recent advances and perspectives

Clostridioides difficile, the most common cause of nosocomial diarrhea, has been continuously reported as a worldwide problem in healthcare settings. Additionally, the emergence of hypervirulent strains of C. difficile has always been a critical concern and led to continuous efforts to develop more accurate diagnostic methods for detection of this recalcitrant pathogen. Currently, the diagnosis of C. difficile infection (CDI) is based on clinical manifestations and laboratory tests for detecting the bacterium and/or its toxins, which exhibit varied sensitivity and specificity. In this regard, development of rapid diagnostic techniques based on antibodies has demonstrated promising results in both research and clinical environments. Recently, application of recombinant antibody (rAb) technologies like phage display has provided a faster and more cost-effective approach for antibody production. The application of rAbs for developing ultrasensitive diagnostic tools ranging from immunoassays to immunosensors, has allowed the researchers to introduce new platforms with high sensitivity and specificity. Additionally, DNA encoding antibodies are directly accessible in these approaches, which enables the application of antibody engineering to increase their sensitivity and specificity. Here, we review the latest studies about the antibody-based ultrasensitive diagnostic platforms for detection of C. difficile bacteria, with an emphasis on rAb technologies.

Antibiotic Resistances and Molecular Characteristics of Clostridioides difficile in ICUs in a Teaching Hospital From Central South China

Clostridioides (C.) difficile is a major healthcare-associated pathogen inducing infectious diarrhea. Approximately 25–33% of patients with antibiotic-associated diarrhea (AAD) and 90% of patients with pseudomembranous enteritis are caused by C. difficile infection (CDI). Stool samples were collected from hospitalized adults with presumptive AAD in four nonneonatal intensive care units (ICUs). Diagnosis of CDI was based on both clinical symptoms and laboratory results. The stool specimens were transferred onto CDIF (C. difficile agar), and C. difficile was finally confirmed by the latex agglutination test. Toxin-producing genes tcdA (A), tcdB (B), and cdt (CDT) were detected by PCR, and all isolates were performed multilocus sequence typing analysis. The antibiotic susceptibility of C. difficile isolates was assessed by the agar dilution method. A total of 184 C. difficile were isolated from 857 specimens in our study, the isolation rate of C. difficile was 21.5% (184/857). The 184 C. difficile were isolated from 179 patients, among these 115 patients were toxin-positive, giving the incidence of CDI being 58.0/10,000 patient days in the four ICUs. Among these 115 toxin-positive C. difficile isolates, 100 (87.0%) isolates produced two toxins (A+B+CDT-), three (2.6%) isolates were A+B+ with binary toxin-producing (A+B+CDT+), and 12 (10.4%) isolates only produced one toxin (A-B+CDT-). A total of 27 sequencing types (STs) were obtained. The most prevalent was ST3 (34 isolates), followed by ST39 (27 isolates), ST54 (19 isolates), ST26 (16 isolates), ST35 (15 isolates), and ST2 (13 isolates). All the ST26 isolates were nontoxigenic. Meanwhile, five STs were newly discovered. Although multidrug resistance was present in ≥50% of these C. difficile isolates, all of them were susceptible to tigecycline, fidaxomicin, metronidazole, and vancomycin. In conclusion, C. difficile isolates producing two toxins (A+B+CDT-) were dominant in our hospital. The most prevalent was ST3, and all ST26 isolates were NTCD. Although multidrug resistance was present in ≥50% of the C. difficile isolates, metronidazole, tigecycline, fidaxomicin, and vancomycin were still effective treatments for CDI in our hospital.

Decreasing ICU-associated Clostridioides difficile infection through fluoroquinolone restriction, the FIRST trial: a study protocol

INTRODUCTION

Clostridioides difficile infection (CDI) is one of the most common healthcare-associated infections in the USA, having high incidence in intensive care units (ICU). Antibiotic use increases risk of CDI, with fluoroquinolones (FQs) particularly implicated. In healthcare settings, antibiotic stewardship (AS) and infection control interventions are effective in CDI control, but there is little evidence regarding the most effective AS interventions. Preprescription authorisation (PPA) restricting FQs is a potentially promising AS intervention to reduce CDI. The FQ Restriction for the Prevention of CDI (FIRST) trial will evaluate the effectiveness of an FQ PPA intervention in reducing CDI rates in adult ICUs compared with preintervention care, and evaluate implementation effectiveness using a human-factors and systems engineering model.

METHODS AND ANALYSIS

This is a multisite, stepped-wedge, cluster, effectiveness-implementation clinical trial. The trial will take place in 12 adult medical-surgical ICUs with ≥10 beds, using Epic as electronic health record (EHR) and pre-existing AS programmes. Sites will receive facilitated implementation support over the 15-month trial period, succeeded by 9 months of follow-up. The intervention comprises a clinical decision support system for FQ PPA, integrated into the site EHRs. Each ICU will be considered a single site and all ICU admissions included in the analysis. Clinical data will be extracted from EHRs throughout the trial and compared with the corresponding pretrial period, which will constitute the baseline for statistical analysis. Outcomes will include ICU-onset CDI rates, FQ days of therapy (DOT), alternative antibiotic DOT, average length of stay and hospital mortality. The study team will also collect implementation data to assess implementation effectiveness using the Systems Engineering Initiative for Patient Safety model.

ETHICS AND DISSEMINATION

The trial was approved by the Institutional Review Board at the University of Wisconsin-Madison (2018-0852-CP015). Results will be made available to participating sites, funders, infectious disease societies, critical care societies and other researchers.

TRIAL REGISTRATION NUMBER

NCT03848689.

Laboratory markers predictive of fulminant Clostridioides difficile infection refractory to fluid resuscitation

Background

Old age, leucocytosis, hypoalbuminemia, and elevated creatinine have been identified as risk factors for fulminant Clostridioides difficile infection (CDI). High ATLAS scores have also been linked to fatal disease. The affiliated studies, however, involved patients prescribed metronidazole - a regimen no longer standard of care. The variables were thus reassessed in patients prescribed optimal therapy.

Methods

Adults hospitalized with CDI at University of Kentucky Medical Center were retrospectively reviewed. Enrolled subjects were separated according to disease classification i.e. non-severe/severe versus fulminant CDI. Fulminant patients were further subdivided into hypotensive persons responsive to fluid resuscitation, and those with sequent shock, ileus, or megacolon. Following partition, the cohorts underwent correlation analysis.

Findings

Forty-five subjects had non-severe/severe disease. Thirteen fulminant CDI patients responded to fluid resuscitation. Seventeen fulminant CDI patients developed shock, ileus, or megacolon. Median WBC counts, albumin values, and ATLAS scores varied among the cohorts. Although WBC counts were similar among the fulminant subsets, declining albumin values and increasing ATLAS scores mirrored disease worsening. Logistic regression revealed albumin values < 20 g/L (odds ratio [OR] 3.91) and ATLAS scores ≥ 6 (OR 5.03) to predict critical illness in hypotensive persons.

Conclusion

Median WBC counts, albumin values, and ATLAS scores differed in patients separated by CDI severity. A notable variance in albumin values and ATLAS scores between fluid responsive fulminant disease and critical illness was moreover seen. The finding suggests hypoalbuminemia and high ATLAS scores in hypotensive CDI patients may herald shock, ileus, or megacolon.

Severe Clostridium difficile infection with extremely high leucocytosis complicated by a concomitant bloodstream infection caused by Klebsiella pneumoniae after osteomyelitis surgery: A case report

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Exposure to antibiotics after surgery increase risk of Cl. difficile infection.

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Sudden high leucocytosis may be sign of poor outcome in Cl. difficile case.

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Oral Vancomycin could be responsible for the growth of bloodstream Kl. pneumonia.

Introduction

Clostridium difficile is one of the most common healthcare-associated infections. Pseudomembranous colitis is a serious complication of Clostridium difficile infection (CDI) after septic surgery and antibacterial therapy. A sudden white blood cell (WBC) count increase and extremely high leucocytosis may be a predictor of a poor outcome.

Presentation of case

A 77 years old male was hospitalised because of lower leg osteomyelitis and was operated. He received antibacterial treatment with Cefazolin for three days and then developed a high WBC count. The course of the disease was fulminant, with a rapid increase in the WBC count up to 132,000/mm³ and a septic shock, and required cardiovascular and ventilatory support. The patient was started on intravenous Metronidazole (500 mg every eight hours) and oral Vancomycin (500 mg every six hours). The patient’s condition gradually improved over a period of six days. Then a hyperthermia above 39 degrees Celsius, hypotension and painful abdominal bloating developed, and the WBC count peaked to 186,000/mm³. The blood cultures were positive for Klebsiella pneumoniae. The patient died.

Discussion

In our case, we describe a community-onset, healthcare-facility-associated, severe CDI complicated by a blood stream infection. The administration of oral Vancomycin, which is highly active against the intestinal flora, could have been responsible for the persistence and overgrowth of Klebsiella pneumoniae.

Conclusions

Severe CDIs after orthopaedic surgery and antibacterial treatment complicated by the development of nosocomial infection significantly worsen the prognosis of the disease. Careful consideration of antibacterial therapy and early symptom recognition may help prevent catastrophic events.

GABAergic but not Antidepressant Medications Increase Risk for Clostridioides difficile Infection in a National Cohort of Veterans

Background

Clostridioides difficile infection (CDI) is primarily mediated by alterations in the host gut ecosystem. While antibiotic use is the primary risk factor for CDI, other medications that modulate the gut ecosystem, particularly those targeting the gut-brain axis, could impact CDI risk. This study aimed to investigate the association between recent antidepressant and gamma-aminobutyric acid (GABA)-ergic medication use with CDI risk in a national cohort of United States veterans.

Methods

This was a retrospective case-control study of patients seen in Veterans Health Administration facilities from October 2002 to September 2014. CDI and non-CDI control patients were propensity score matched 1:1 using a maximum caliper of 0.0001. Antidepressant and GABAergic medication use 90 days before cohort inclusion were analyzed for CDI association using bivariable and multivariable logistic regression models.

Results

A total of 85 831 patients were included, and 9287 CDI and 9287 control patients were propensity score matched. Antidepressant use overall was not significantly associated with CDI risk (odds ratio [OR], 1.05; 95% CI, 0.98-1.12), although GABAergic medication use was associated with increased risk (OR, 1.81; 95% CI, 1.70-1.92). In multivariable models of individual medications/classes, benzodiazepines had the strongest CDI association (OR, 1.91; 95% CI, 1.77-2.07). SSRIs (OR, 0.88; 95% CI, 0.81-0.95) and bupropion (OR, 0.67; 95% CI, 0.57-0.78) were negatively associated with CDI.

Conclusions

In this national study of veterans, GABAergic medication use was a positive predictor of CDI risk, though antidepressant use was not. Further research is needed to understand biological mechanisms, and confirmatory studies are needed to validate these findings.

Update in Infectious Diseases 2019

The IX Course of Antimicrobials and Infectious Diseases update included a review of the main issues in clinical microbiology, epidemiology and clinical aspects for a current approach of infectious pathology. The present introduction summarizes about the most important meetings related to infectious diseases during 2018 (ECCMID, IAS, ASM and ID Week). In addition, the course provides a practical information to focus on nosocomial infection models, with immunosuppressed patients or complex multidrug-resistant pathogens. The closing lecture of this year reviewed the infection during donation process.

Laboratory-developed test for detection of acute Clostridium difficile infections with the capacity for quantitative sample normalization

We describe a laboratory-developed test intended for the detection of acute Clostridium difficile infections (CDI) with the capacity for quantitative sample normalization. The test is based on the detection of the tcdB gene. However, this biomarker is also present among people without symptoms, implying that individuals with diarrhea, not caused by C. difficile may nonetheless test positive. Therefore, clinical diagnosis based on this format of testing can be challenging. In order to improve diagnostic assays capability, tcdB-based quantification methods were suggested as a potential solution, however they did not increase clinical specificity. We report methodology for a dual biomarker monitoring (total bacterial load and tcdB assay), allowing for the calculation of the relative presence of tcdB in the total bacterial population in the tested samples. We believe that this approach is clinically relevant to current assays and can improve CDI testing algorithms.

Emerging drugs for the treatment of clostridium difficile

INTRODUCTION

Clostridium difficile or Clostridioides difficile (C. difficile) infection represents the most common cause of healthcare-associated infection. Over the last decades, the incidence and severity of C. difficile infection is rapidly increasing, with a significant impact on morbidity and mortality, and burden on health care system. Orally administered vancomycin and fidaxomicin are the therapeutic options of choice for initial C. difficile infection and fecal microbiota transplant for the recurrence infection. Furthermore, in recent years several new antibiotics with narrow-spectrum activity and low intestinal resorption have been developed, including surotomycin, cadazolid, and ridinilazol, and novel toxoid vaccines are expected to be efficacious in the prevention of C. difficile infection. Areas covered: Literature review was performed to select publications about current guidelines and phase-II/III trials on emerging drugs. These include novel antibiotics, monoclonal antibodies, vaccines, and fecal microbiota transplantation. Expert opinion: We have today a wide spectrum of promising therapeutic possibilities against infection. Pivotal future clinical trials may be crucial in developing effective strategies to optimize outcomes, mainly in high-risk population.

Doctor, my patient has CDI and should continue to receive antibiotics. The (unresolved) risk of recurrent CDI

Recurrence rate ranges from 12% to 40% of all cases of Clostridium difficile infection (CDI) and proposes an exceptional clinical challenge. Conventionally, treatment options of CDI have been limited to regimes of established antibiotics (eg, pulsed/tapered vancomycin) or "improvised" alternative antibiotics (eg. teicoplanin, tigecycline, nitazoxanide or rifaximin) occasionally even in combination, but faecal microbiota transplantation is emerging as a useful and quite safe alternative. In recent years, promising new strategies have emerged for effective prevention of recurrent CDI (rCDI) including new an-timicrobials (eg, fidaxomicin) and monoclonal antibodies (eg, bezlotoxumab). Despite promising progress in this area, difficulties remain for making the best use of these resources due to uncertainty over patient selection. This positioning review describes the current epidemiology of rCDI, its clinical impact and risk factors, some of the measures used for treating and preventing rCDI, and some of the emerging treatment options. It then describes some of the barriers that need to be overcome.

Clostridium difficile Infections: A Global Overview of Drug Sensitivity and Resistance Mechanisms

Clostridium difficile (C. difficile) is the most prevalent causative pathogen of healthcare-associated diarrhea. Notably, over the past 10 years, the number of Clostridium difficile outbreaks has increased with the rate of morbidity and mortality. The occurrence and spread of C. difficile strains that are resistant to multiple antimicrobial drugs complicate prevention as well as potential treatment options. Most C. difficile isolates are still susceptible to metronidazole and vancomycin. Incidences of C. difficile resistance to other antimicrobial drugs have also been reported. Most of the antibiotics correlated with C. difficile infection (CDI), such as ampicillin, amoxicillin, cephalosporins, clindamycin, and fluoroquinolones, continue to be associated with the highest risk for CDI. Still, the detailed mechanism of resistance to metronidazole or vancomycin is not clear. Alternation in the target sites of the antibiotics is the main mechanism of erythromycin, fluoroquinolone, and rifamycin resistance in C. difficile. In this review, different antimicrobial agents are discussed and C. difficile resistance patterns and their mechanism of survival are summarized.

Advances in the diagnosis and treatment of Clostridium difficile infections

Clostridium difficile is a leading cause of antibiotic-associated diarrhea worldwide. The diagnosis of C. difficile infection (CDI) requires both clinical manifestations and a positive laboratory test for C. difficile and/or its toxins. While antibiotic therapy is the treatment of choice for CDI, there are relatively few classes of effective antibiotics currently available. Therefore, the development of novel antibiotics and/or alternative treatment strategies for CDI has received a great deal of attention in recent years. A number of emerging agents such as cadazolid, surotomycin, ridinilazole, and bezlotoxumab have demonstrated activity against C. difficile; some of these have been approved for limited clinical use and some are in clinical trials. In addition, other approaches such as early and accurate diagnosis of CDI as well as disease prevention are important for clinical management. While the toxigenic culture and the cell cytotoxicity neutralization assay are still recognized as the gold standard for the diagnosis of CDI, new diagnostic approaches such as nucleic acid amplification methods have become available. In this review, we will discuss both current and emerging diagnostic and therapeutic modalities for CDI.

Antibiotic Resistance and Toxin Production of Clostridium difficile Isolates from the Hospitalized Patients in a Large Hospital in Florida

Clostridium difficile is an important cause of nosocomial acquired antibiotic-associated diarrhea causing an estimated 453,000 cases with 29,000 deaths yearly in the U.S. Both antibiotic resistance and toxin expression of C. difficile correlate with the severity of C. difficile infection (CDI). In this report, a total of 139 C. difficile isolates from patients diagnosed with CDI in Tampa General Hospital (Florida) in 2016 were studied for antibiotic resistance profiles of 12 types of antibiotics and toxin production. Antibiotic resistance determined by broth microdilution method showed that strains resistant to multi-antibiotics are common. Six strains (4.32%) showed resistance to six types of antibiotics. Twenty strains (14.39%) showed resistance to five types of antibiotics. Seventeen strains (12.24%) showed resistance to four types of antibiotics. Thirty-nine strains (28.06%) showed resistance to three types of antibiotic. Thirty-four strains (24.46%) showed resistance to two types of antibiotics. While, all isolates were susceptible to metronidazole, and rifaximin, we found that one isolate (0.72%) displayed resistance to vancomycin (MIC ≥ 8 μg/ml), and another one was resistant to fidaxomicin (MIC >1 μg/ml). The percentage of isolates resistant to cefoxitin, ceftriaxone, chloramphenicol, ampicillin, clindamycin, erythromycin, gatifloxacin, and moxifloxacin was 75.54, 10.79, 5.76, 67.63, 82.70, 45.32, 28.06, and 28.78%, respectively. Toxin profiling by PCR showed the isolates include 101 (72.66%) A+B+CDT-strains, 23 (16.55%) A+B+CDT+ strains, 3 (2.16%) A-B+CDT+ strains, 1 (0.72%) A-B+CDT-strains, and 11 (7.91%) A-B-CDT-strains. Toxin production determined by ELISA using supernatants of bacterial culture harvested at 12, 24, 48, and 72 h of post inoculation (hpi) showed that the toxins were mainly produced between 48 and 72 hpi, and toxin B (TcdB) was produced faster than toxin A (TcdA) during the experimental time (72 hpi). In addition, the binary-positive strains were likely to yield more toxins compared to the binary-negative strains. This work contributes to the current understanding of the antibiotic resistance and virulence of C. difficile clinical strains.

Evaluation of Copan FecalSwab as Specimen Type for Use in Xpert C. difficile Assay

Liquid-based microbiology (LBM) devices incorporating flocked swabs and preservation medium ease transport of specimens and improve specimen yield compared to traditional fiber wound swabs; however, the performance of LBM collection devices has not been evaluated in many molecular assays. It is unclear how the differences in matrix and specimen loading with an LBM device will affect test performance compared to traditional collection devices. The purpose of this study was to evaluate the performance of specimens collected in FecalSwab transport medium (Copan Diagnostics, Murrieta, CA) compared to unpreserved stool using the Cepheid Xpert C. difficile assay (Cepheid, Sunnyvale, CA). Results equivalent to unpreserved stool samples were obtained when 400 μl of FecalSwab-preserved stool was employed in the Xpert assay. The positive and negative percent agreement of specimens inoculated with FecalSwab medium (n = 281) was 97.0% (95% confidence interval [CI], 90.9 to 96.4%) and 99.4% (95% CI, 96.4 to 99.9%), respectively, compared to reference results obtained using unpreserved stool. Throughout this study, only four discrepant results occurred when comparing preserved specimens to unpreserved stool specimens in the Xpert C. difficile PCR assay. Post discrepant analysis, using the BD MAX Cdiff assay, the specificity and sensitivity both increased to 100%. The high positive and negative percent agreements observed in this study suggest that stool preserved in FecalSwab media yields equivalent results to using unpreserved stool when tested on the Xpert C. difficile assay, allowing laboratories to adopt this liquid-based microbiology collection device.

Assessing the effect of patient screening and isolation on curtailing Clostridium difficile infection in hospital settings

BACKGROUND

Patient screening at the time of hospital admission is not recommended as a routine practice, but may be an important strategy for containment of Clostridium difficile infection (CDI) in hospital settings. We sought to investigate the effect of patient screening in the presence of asymptomatic carriers and in the context of imperfect patient isolation.

METHODS

We developed and parameterized a stochastic simulation model for the transmission dynamics of CDI in a hospital ward.

RESULTS

We found that the transmission of CDI in the hospital, either through asymptomatic carriers or as a results of ineffective implementation of infection control practices, at the time of hospital admission. The results show that, for a sufficiently high reproduction number of CDI, the disease can persist within a hospital setting in the presence of in-ward transmission, even when there are no asymptomatically colonized patients at the time of hospital admission.

CONCLUSIONS

Our findings have significant public health and clinical implications, especially in light of the emergence and community spread of hypervirulent CDI strains with enhanced transmission rates and toxin production. Rapid detection of colonized patients remains an important component of CDI control, especially in the context of asymptomatic transmission. Screening of in-hospital patients with potential exposure to colonized patients or contaminated environment and equipment can help reduce the rates of silent transmission of CDI through asymptomatic carriers.

Update on Antimicrobial Resistance in Clostridium difficile: Resistance Mechanisms and Antimicrobial Susceptibility Testing

Oral antibiotics such as metronidazole, vancomycin and fidaxomicin are therapies of choice for Clostridium difficile infection. Several important mechanisms for C. difficile antibiotic resistance have been described, including the acquisition of antibiotic resistance genes via the transfer of mobile genetic elements, selective pressure in vivo resulting in gene mutations, altered expression of redox-active proteins, iron metabolism, and DNA repair, as well as via biofilm formation. This update summarizes new information published since 2010 on phenotypic and genotypic resistance mechanisms in C. difficile and addresses susceptibility test methods and other strategies to counter antibiotic resistance of C. difficile.

Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization

BACKGROUND

Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better understanding of this organism and the relationship between its genotype and phenotype is essential to the search for an effective treatment. Genome-scale metabolic models contain all known biochemical reactions of a microorganism and can be used to investigate this relationship.

RESULTS

We present icdf834, an updated metabolic network of C. difficile that builds on iMLTC806cdf and features 1227 reactions, 834 genes, and 807 metabolites. We used this metabolic network to reconstruct the metabolic landscape of this bacterium. The standard metabolic model cannot account for changes in the bacterial metabolism in response to different environmental conditions. To account for this limitation, we also integrated transcriptomic data, which details the gene expression of the bacterium in a wide array of environments. Importantly, to bridge the gap between gene expression levels and protein abundance, we accounted for the synonymous codon usage bias of the bacterium in the model. To our knowledge, this is the first time codon usage has been quantified and integrated into a metabolic model. The metabolic fluxes were defined as a function of protein abundance. To determine potential therapeutic targets using the model, we conducted gene essentiality and metabolic pathway sensitivity analyses and calculated flux control coefficients. We obtained 92.3% accuracy in predicting gene essentiality when compared to experimental data for C. difficile R20291 (ribotype 027) homologs. We validated our context-specific metabolic models using sensitivity and robustness analyses and compared model predictions with literature on C. difficile. The model predicts interesting facets of the bacterium's metabolism, such as changes in the bacterium's growth in response to different environmental conditions.

CONCLUSIONS

After an extensive validation process, we used icdf834 to obtain state-of-the-art predictions of therapeutic targets for C. difficile. We show how context-specific metabolic models augmented with codon usage information can be a beneficial resource for better understanding C. difficile and for identifying novel therapeutic targets. We remark that our approach can be applied to investigate and treat against other pathogens.