Prevalence and molecular types of Clostridium difficile isolates from faecal specimens of patients in a tertiary care centre

Insights into the Evolving Epidemiology of Clostridioides difficile Infection and Treatment: A Global Perspective

Clostridioides difficile remains an important public health threat, globally. Since the emergence of the hypervirulent strain, ribotype 027, new strains have been reported to cause C. difficile infection (CDI) with poor health outcomes, including ribotypes 014/020, 017, 056, 106, and 078/126. These strains differ in their geographic distribution, genetic makeup, virulence factors, and antimicrobial susceptibility profiles, which can affect their ability to cause disease and respond to treatment. As such, understanding C. difficile epidemiology is increasingly important to allow for effective prevention measures. Despite the heightened epidemiological surveillance of C. difficile over the past two decades, it remains challenging to accurately estimate the burden and international epidemiological trends given the lack of concerted global effort for surveillance, especially in low- and middle-income countries. This review summarizes the changing epidemiology of C. difficile based on available data within the last decade, highlights the pertinent ribotypes from a global perspective, and discusses evolving treatments for CDI.

Clostridioides difficile Diarrhea: An Emerging Problem in a South Indian Tertiary Care Hospital

Context Clostridioides difficile infection (CDI) is one of the most common infectious causes of hospital-acquired diarrhea. The actual burden of the disease is underestimated in India due to inadequate diagnostic methods and limited studies conducted.

Aims The aim of this study was to determine the burden and risk factors of CDI among patients with hospital-acquired diarrhea.

Methods and Materials Stool specimen of patients (age > 1 year) with hospital-acquired diarrhea were screened for glutamate dehydrogenase antigen and toxin using an enzyme immunoassay. If both antigen and toxin were present, it was reported as positive for toxigenic CDI. Samples positive for antigen and negative for toxin were further tested with Cepheid GeneXpert assay for detecting the toxin producing gene.

Results Of 75 patients (mean age 36.07 ± 20.79, 64% males), 14 (18.67%) patients were positive for toxigenic Clostridioides difficile (C. difficile) and 3 (4%) patients were nontoxigenic C. difficile. Addition of GeneXpert to the testing algorithm increased the yield of toxin detection in 5/14 patients who were negative by toxin assay. On analysis of risk factors, prolonged hospital stay was found to have significant association (p-value = 0.022). Patients with factors like intensive care unit stay, presence of diabetes mellitus as a comorbidity, and exposure to antibiotics like carbapenems and glycopeptides have been found to have a higher prevalence of CDI.

Conclusions The prevalence of CDI in our population was 18.67% and the major risk factor associated was prolonged hospital stay. The addition of GeneXpert for the detection of toxin gene increased the yield from 12 to 18.68%.

Systematic Literature Review on Burden of Clostridioides difficile Infection in India

BACKGROUND

Owing to limited diagnostic facilities and surveillance protocols, there is a paucity on the prevalence data of Clostridioides difficile infections (CDIs) in developing countries such as India.

OBJECTIVE

The aims of these studies are (1) to determine the prevalence of CDI in India, (2) to understand the risk factors of CDI, and (3) to determine the impact of different diagnostic methods on reported CDI rates.

METHOD

A systematic literature search was conducted using PubMed and Google Scholar database to identify Indian studies reporting the prevalence of CDI. A total of 31 studies, published between 1990 and 2020 were included in the final analysis. A chi-square test was used to determine statistically significant association between prevalence rates, accuracy of different diagnosis methods, and antibiotic usage rates of CDI.

RESULTS

The prevalence of CDI was in the range of 3.4% to 18%, and the difference between regional prevalence of CDI was statistically significant (P < .001). The use of antibiotics, hospital stay, comorbidities, recent surgery, and the use of proton-pump inhibitors was considered as risk factors for the development of CDI. Compared to other regions, the rate of antibiotic usage was significantly higher in North India (P < .001). Among different diagnostic methods, C. difficile detection was significantly higher with enzyme-linked immunosorbent assay (18.02%) versus other multiple testing methods used (P < .001).

CONCLUSION

There is a significant burden of CDI across the country. Further surveillance studies are required to monitor changes in prevalence of CDI, risk factors, and accuracy of diagnosis methods for a better understanding of the disease burden in India.

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

BACKGROUND

The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants.

RESULTS

We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3^rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism.

CONCLUSIONS

We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.

Clostridium difficile-associated Diarrhea in Developing Countries: A Systematic Review and Meta-Analysis

Introduction

The prevalence of Clostridium difficile infection is rapidly increasing worldwide, but prevalence is difficult to estimate in developing countries where awareness, diagnostic resources, and surveillance protocols are limited. As diarrhea is the hallmark symptom, we conducted a systematic review and meta-analysis to determine the prevalence and incidence of C. difficile infection in patients in these regions who presented with diarrhea.

Methods

We conducted a systematic literature search of MEDLINE/PubMed, Scopus, and Latin-American and Caribbean Health Sciences Literature databases to identify and analyze data from recent studies providing prevalence or incidence rates of C. difficile-associated diarrhea in developing countries within four regions: Africa–Middle East, developing Asia, Latin America, and China. Our objectives were to determine the current prevalence and incidence density rates of first episodes of C. difficile-associated diarrhea in developing countries.

Results

Within the regions included in our analysis, prevalence of C. difficile infection in patients with diarrhea was 15% (95% CI 13–17%) (including community and hospitalized patients), with no significant difference across regions. The incidence of C. difficile infection in 17 studies including this information was 8.5 per 10,000 patient-days (95% CI 5.83–12.46). Prevalence was significantly higher in hospitalized patients versus community patients (p  = 0.0227).

Conclusion

Our prevalence estimate of 15% is concerning; however, low awareness and inconsistent diagnostic and surveillance protocols suggest this is markedly underestimated. Enhanced awareness and management of C. difficile infection in patients with diarrhea, along with improvements in infection control and surveillance practices, should be implemented to reduce prevalence of C. difficile-associated diarrhea in developing countries.

Funding

Pfizer Inc.

Electronic supplementary material

The online version of this article (10.1007/s40121-019-0231-8) contains supplementary material, which is available to authorized users.

Toxigenic Clostridium difficile isolates from clinically significant diarrhoea in patients from a tertiary care centre

Background & objectives:

Clostridium difficile is the primary cause of hospital-acquired colitis in patients receiving antibiotics. The pathogenicity of the organism is mainly due to the production of toxins. This study was conducted to investigate the presence of toxigenic C. difficile in the faecal samples of hospitalized patients suspected to have C. difficile infection (CDI) and corroborating the findings with their clinical and demographic data.

Methods:

Diarrhoeic samples obtained from 1110 hospitalized patients were cultured for C. difficile and the isolates confirmed by phenotypic and molecular methods. Toxigenicity of the isolates was determined using enzyme-linked immunosorbent assay for toxins A and B. Details of patients included in the study were noted and analyzed.

Results:

Of the 1110 patients (mean age 39±19.6 yr), 63.9 per cent were males and 36.1 per cent were females. The major antibiotics received by the patients were nitazoxanide (23.9%), penicillins/penicillin combinations (19.0%), quinolones including fluoroquinolones (13.1%), carbapenems (11.5%), glycopeptides (11.0%) and cephalosporins (8.4%). The clinical symptoms predominantly present were watery diarrhoea (56.4%), fever (40.0%) and abdominal pain (35.3%). The underlying diseases were gastrointestinal disorders (52.6%), followed by cancers (13.2%), surgical conditions (8.3%), and hepatic disorders (8.0%). Of the 174 C. difficile isolates, 54.6 per cent were toxigenic. Toxigenic C. difficile was present in all patients with surgical conditions, 65.2 per cent with cancers and 57.1 per cent with gastrointestinal disorders.

Interpretation & conclusions:

C. difficile was found to be an important cause of gastrointestinal infections in hospitalized patients with underlying diseases and on antibiotics. Clinical conditions of the patients correlating with toxigenic culture can be an important tool for establishing CDI diagnosis.

Assessing the Burden of Clostridium difficile Infection in Low- and Middle-Income Countries

In contrast to the significant resources invested in the diagnosis and prevention of Clostridium difficile infection (CDI) in resource-rich settings, in resource-limited settings patients with community- and hospital-acquired diarrhea may not routinely be tested for CDI. Is CDI actually less frequent or severe in resource-limited settings, or might we be missing an important opportunity to prevent CDI-related morbidity and mortality (and to promote antibiotic stewardship) in these settings? Here, we review the literature to assess the overall burden of CDI in low- and middle-income countries.

The emergence of Clostridium difficile infection in Asia: A systematic review and meta-analysis of incidence and impact

Background

Clostridium difficile infection (CDI) is the most common healthcare associated infection and is highly prevalent in Europe and North America. Limited data is available on the prevalence of CDI in Asia. However, secular increases in prevalence of risk factors for CDI suggest that it may be emerging as a major cause of morbidity, highlighting the urgent need for a systematic study of the prevalence of CDI in Asia.

Methods

We systematically searched PubMed/Medline and Embase for publications from Asia between 2000–16 examining prevalence of CDI. A random-effects meta-analysis was performed to calculate the pooled prevalence of CDI in Asia and to identify subgroups and regions at high risk.

Results

Our meta-analysis included 51 studies from throughout Asia including 37,663 patients at risk among whom confirmed CDI was found in 4,343 patients. The pooled proportion of confirmed CDI among all patients with diarrhea was 14.8% with a higher prevalence in East Asia (19.5%), compared with South Asia (10.5%) or the Middle East (11.1%). There were an estimated 5.3 episodes of CDI per 10,000 patient days, similar to rates reported from Europe and North America. Infections due to hypervirulent strains were rare. CDI-related mortality was 8.9%.

Conclusions

In a meta-analysis of 51 studies, we observed similar rates of CDI in Asia in comparison to Europe and North America. Increased awareness and improved surveillance of Clostridium difficile is essential to reduce incidence and morbidity.

Toxinotyping and Sequencing of Clostridium difficile Isolates from Patients in a Tertiary Care Hospital of Northern India

BACKGROUND

Clostridium difficile is an important cause of infectious colitis among hospitalized patients across the globe. The pathogenic potential of C. difficile in producing significant morbidity and mortality is mainly due to production of toxins A and B. The outbreaks of C. difficile infection (CDI) are due to changes in the genetic sequences of the organism. There is hardly any molecular study reported on the prevalent types of C. difficile strains in India. Toxinotyping and sequencing of locally circulating C. difficile isolates from patients presenting to our tertiary care center of North India were done.

MATERIALS AND METHODS

C. difficile strains (n = 174) isolated from 1,110 fecal samples from patients with suspected CDI were subjected to toxinotyping and partial sequencing of tcdA and tcdB genes. Comparison of nucleotide sequences with reference C. difficile 630 strain using BLAST was made and translated into corresponding amino acid sequences by ExPASy.

RESULTS AND DISCUSSION

Of 174 C. difficile isolates, 121 were toxigenic, belonging to toxinotype 0 (n = 76) and VIII (n = 45). Partial sequencing of toxin genes using bioinformatics approaches revealed changes in toxin A sequences of five (50%) C. difficile isolates, but the translated nucleotide sequences showed substitution in only three of them. No variation was seen in the toxin B nucleotide sequences. Interstrain variations were found in the clinical C. difficile isolates in our region.

CONCLUSION

PCR amplified toxigenic genes followed by sequencing can help to identify genetic changes and pathogenicity of varied collection of C. difficile isolates.

Prevalence and molecular epidemiology of Clostridium difficile infection in Thailand

Little is known about Clostridium difficile infection (CDI) in Asia generally, and specifically in Thailand. Given the high prevalence of inappropriate antibiotic usage in this region, CDI is likely to be common. This study investigated the prevalence and molecular epidemiology of CDI in Thailand. Stool specimens collected from inpatients with diarrhoea at Siriraj hospital in Bangkok (n = 422) were cultured on ChromID Cdiff agar and any presumptive C. difficile colonies were identified, PCR ribotyped and toxin profiled. As part of the routine C. difficile testing at Siriraj Hospital, 370 specimens also underwent testing with the BD MAX Cdiff assay to detect the presence of tcdB. With direct culture, 105 different isolates of C. difficile were recovered from 23.7% (100/422) of the stool specimens. The prevalence of toxigenic and nontoxigenic isolates was 9.2% (39/422) and 15.6% (66/422), respectively. Of the toxigenic isolates, 69.2% (27/39) and 30.8% (12/39) were tcdA and tcdB positive (A⁺B⁺), and A⁻B⁺, respectively; none contained binary toxin genes. The five most prevalent ribotypes (RTs) were 014/020 group (17/105), 010 (12/105), 017 (12/105), 039 (9/105) and 009 (6/105). Using toxigenic culture as the reference standard, the sensitivity, specificity, positive predictive value and negative predictive value of the BD MAX Cdiff assay were 68.6, 95.1, 63.2 and 96.1%, respectively. The high proportion of A⁻B⁺, RT 017 strains emphasises the need for diagnostic tests that detect either both toxins or just tcdB. Continued surveillance that involves stool culturing will allow molecular tracking and assist in elucidating the epidemiology of CDI in Thailand.