Epidemiological and microbiome associations of Clostridioides difficile carriage in infancy and early childhood

Clostridioides (Clostridium) difficile in hospitalised children in Cambodia

BACKGROUND

Children may play an important role in disseminating Clostridioides (Clostridium) difficile within hospital and community settings. In many parts of the world, there has been a recent increase in interest in C. difficile infection (CDI) in paediatric populations.

OBJECTIVES

This study aimed to investigate the prevalence of, risk factors for, and molecular types of C. difficile in hospitalised children in Cambodia.

METHODS

Stool samples were collected from children at the National Paediatric Hospital in Phnom Penh, Cambodia, between June 2022 and March 2023, for C. difficile culture. Toxin gene PCR and PCR ribotyping were performed on all isolates.

RESULTS

Of 122 hospitalised children recruited, C. difficile was identified in 47 (38.5%). Toxigenic strains accounted for 25.5% (12/47), with ribotype (RT) 012 the most predominant (7/12), followed by RTs 014/020 (3/12) and 017 (1/12). Non-toxigenic strains were dominated by RTs QX011, QX675 and 009/QX107. Novel strains represented 70% (33/47) of isolates. Significant risk factors included antimicrobial use in the week before detection (OR = 5.15; 95%CI: 1.125-21.21) and current use of other medications (OR = 13.02, 95%CI: 1.32-128.67). Diarrhoea and abdominal pain were negatively associated with the presence of C. difficile.

CONCLUSIONS

A high prevalence of C. difficile was found in hospitalised children, with a high proportion of non-toxigenic and novel strains. Larger studies are required with whole genome sequencing necessary for characterising novel strains and advancing molecular epidemiological research in Asia.

Clostridioides difficile concentration-dependant alterations in gut microbiota of asymptomatic infants

BACKGROUND

Asymptomatic carriage of Clostridioides difficile is highly prevalent in early infancy, affecting approximately 40% of infants. This phenomenon offers a unique opportunity to study its impact on the gut microbiota without the confounding effects of disease. In this study, we analysed C. difficile-associated gut microbiome alterations in 76 asymptomatic infants, one year after receiving antibiotic treatment during early infancy. The presence and concentration of C. difficile were assessed in relation to gut microbiota structure and an extensive set of metadata.

RESULTS

Bacterial gut community structure was characterized using 16 S rRNA amplicon sequencing, while C. difficile concentration and the presence of the tcdB gene were quantified via digital PCR. C. difficile was detected in 36.8% of infants, with 10.5% testing positive for the tcdB gene. Significant alterations in gut microbiota were observed in relation to C. difficile concentration. Specifically, higher C. difficile loads were associated with reduced microbial diversity, greater deviations from average community structure, and co-occurrence with the genus Escherichia. Conversely, C. difficile colonization alone or the presence of the tcdB gene did not result in significant gut microbiota alterations. Additionally, no host-specific factors were significantly linked to C. difficile prevalence or concentration.

CONCLUSIONS

Asymptomatic carriage of C. difficile in neonates is not associated with significant gut microbiota alterations unless pathogen concentration is considered. Our findings suggest that elevated C. difficile proliferation occurs in dysbiotic infant gut microbiota, characterized by reduced alpha diversity and an increase in Escherichia.

[Advances in the treatment of Clostridium difficile infection in children]

Clostridium difficile infection (CDI) is a major cause of hospital-acquired gastrointestinal infections in children. Current treatment for pediatric CDI primarily involves antibiotics; however, some children experience recurrence after antibiotic treatment, and those with initial recurrence remain at risk for further recurrences following subsequent antibiotic therapy. In such cases, careful consideration of treatment options is necessary. Fecal microbiota transplantation has been shown to be effective for recurrent CDI and has a high safety profile. This article reviews the latest research on the pathogenesis, risk factors, diagnosis, and treatment of pediatric CDI domestically and internationally, with a particular focus on fecal microbiota transplantation therapy.

Understanding the influence of the microbiome on childhood infections

INTRODUCTION

The microbiome is known to have a substantial impact on human health and disease. However, the impacts of the microbiome on immune system development, susceptibility to infectious diseases, and vaccine-elicited immune responses are emerging areas of interest.

AREAS COVERED

In this review, we provide an overview of development of the microbiome during childhood. We highlight available data suggesting that the microbiome is critical to maturation of the immune system and modifies susceptibility to a variety of infections during childhood and adolescence, including respiratory tract infections, Clostridioides difficile infection, and sexually transmitted infections. We discuss currently available and investigational therapeutics that have the potential to modify the microbiome to prevent or treat infections among children. Finally, we review the accumulating evidence that the gut microbiome influences vaccine-elicited immune responses among children.

EXPERT OPINION

Recent advances in sequencing technologies have led to an explosion of studies associating the human microbiome with the risk and severity of infectious diseases. As our knowledge of the extent to which the microbiome influences childhood infections continues to grow, microbiome-based diagnostics and therapeutics will increasingly be incorporated into clinical practice to improve the prevention, diagnosis, and treatment of infectious diseases among children.

Clostridioides difficile in calves, cattle and humans from Dutch dairy farms: Predominance of PCR ribotype 695 (clade 5, sequence type 11) in cattle

Background

Clostridioides difficile is a leading cause of infectious diarrhea in both humans and livestock. In particular, C. difficile strains belonging to sequence type (ST) 11 are common enteropathogens. The aim of this study was to determine the presence and genetic relatedness of C. difficile types in dairy cattle and calves.

Method

Dutch dairy farms were visited between February and December 2021. Feces was collected from adult dairy cattle and calves of two age categories (<4 weeks and 4 weeks-4 months). Fecal samples were also requested from dairy farmers, family members and employees. Fecal samples were cultured in an enrichment medium for 10-15 days and subcultured on solid media for capillary PCR ribotyping and whole genome sequencing.

Results

C. difficile was detected on 31 out of 157 (19.8%) dairy farms. The highest prevalence was found in calves <4 weeks (17.5%). None of the 99 human samples collected were positive. Thirty-seven cultured isolates belonged to 11 different PCR ribotypes (RT) of which RT695 (56.8%) and RT078/126 (16.2%) were most abundant. In the database of the Netherlands National Expertise Centre for C. difficile infections (CDI, >10.000 patient isolates), RT695 was found in only two patients with hospital-onset CDI, diagnosed in 2020 and 2021. Sequence analysis of 21C. difficile RT695 from cattle revealed that all isolates belonged to clade 5, ST11 and contained genes encoding toxin A, toxin B and binary toxin. RT695 strains carried antimicrobial resistance genes typically found in clade 5C. difficile. Groups of genetically related RT695 isolates were found between dairy farms, whereas identical strains were only present in individual farms.

Conclusions

C. difficile was found in ∼20% of dairy farms with a predominance of the relatively unknown RT695. Isolates of RT695 belonged to the same clade and sequence type as RT078/126, which is recognized as an important zoonotic type.

Delivery mode impacts gut bacteriophage colonization during infancy

Background

Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory and immune health outcomes. Although gut bacteriophages can alter gut microbiome composition and impact host immune responses, little is known about how delivery mode impacts bacteriophage colonization over time. To begin to address this we examined how delivery mode affected bacteriophage colonization over the first two years of life.

Results

Shotgun metagenomic sequencing was conducted on 272 serial stool samples from 55 infants, collected at 1-2 days of life and 2, 6, 12 and 24 months. 33/55 (60%) infants were born by vaginal delivery. DNA viruses were identified, and by host inference, 94% of the viral sequences were found to be bacteriophages. Alpha diversity of the virome was increased in vaginally delivered infants compared to cesarean section delivered infants at 2 months (Shannon index, p=0.022). Beta diversity significantly differed by delivery mode at 2, 6, and 12 months when stratified by peripartum antibiotic use (Bray-Curtis dissimilarity, all p<0.05). Significant differentially abundant predicted bacteriophage hosts by delivery mode were seen at all time points. Moreover, there were differences in predicted bacteriophage functional gene abundances up to 24 months by delivery mode. Many of the functions considered to play a role in host response were increased in vaginal delivery.

Conclusions

Clear differences in bacteriophage composition and function were seen by delivery mode over the first two years of life. Given that phages are known to affect host immune response, our results suggest that future investigation into how delivery mode may lead to adverse inflammatory outcomes should not only include bacterial microbial colonization but also the potential role of bacteriophages and transkingdom interactions.

Therapeutic Approach Targeting Gut Microbiome in Gastrointestinal Infectious Diseases

While emerging evidence highlights the significance of gut microbiome in gastrointestinal infectious diseases, treatments like Fecal Microbiota Transplantation (FMT) and probiotics are gaining popularity, especially for diarrhea patients. However, the specific role of the gut microbiome in different gastrointestinal infectious diseases remains uncertain. There is no consensus on whether gut modulation therapy is universally effective for all such infections. In this comprehensive review, we examine recent developments of the gut microbiome's involvement in several gastrointestinal infectious diseases, including infection of Helicobacter pylori, Clostridium difficile, Vibrio cholerae, enteric viruses, Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa Staphylococcus aureus, Candida albicans, and Giardia duodenalis. We have also incorporated information about fungi and engineered bacteria in gastrointestinal infectious diseases, aiming for a more comprehensive overview of the role of the gut microbiome. This review will provide insights into the pathogenic mechanisms of the gut microbiome while exploring the microbiome's potential in the prevention, diagnosis, prediction, and treatment of gastrointestinal infections.