Prevalence and molecular characterization of Clostridium difficile isolates from a pig slaughterhouse, pork, and humans in Taiwan

Update on Commonly Used Molecular Typing Methods for Clostridioides difficile

This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.

Global prevalence of Clostridioides difficile in 17,148 food samples from 2009 to 2019: a systematic review and meta-analysis

BACKGROUND

Clostridioides (Clostridium) difficile is an important infectious pathogen, which causes mild-to-severe gastrointestinal infections by creating resistant spores and producing toxins. Spores contaminated foods might be one of the most significant transmission ways of C. difficile-associated infections. This systematic review and meta-analysis study were conducted to investigate the prevalence of C. difficile in food.

METHODS

Articles that published the prevalence of C. difficile in food in PubMed, Web of Science, and Scopus databases were retrieved using selected keywords between January 2009 and December 2019. Finally, 17,148 food samples from 60 studies from 20 countries were evaluated.

RESULTS

The overall prevalence of C. difficile in various foods was 6.3%. The highest and lowest levels of C. difficile contamination were detected to seafood (10.3%) and side dishes (0.8%), respectively. The prevalence of C. difficile was 4% in cooked food, 6.2% in cooked chicken and 10% in cooked seafood.

CONCLUSIONS

There is still little known concerning the food-borne impact of C. difficile, but the reported contamination might pose a public health risk. Therefore, to improve the food safety and prevent contamination with C. difficile spores, it is necessary to observe hygienic issues during foods preparation, cooking and transfer.

Clostridioides difficile in food and food products of animal origin in Assam, India

OBJECTIVE

Considering the paucity of information about food-associated Clostridioides difficile from India, a study was undertaken to establish the prevalence of C. difficile in a variety of foods of animal origin, together with molecular strain characterization and antimicrobial resistance.

METHODS

A total of 235 samples comprising raw meat and meat products, fish products, and milk and milk products were screened for C. difficile. Toxin genes and other parts of PaLoc were amplified in isolated strains. The resistance pattern towards commonly used antimicrobial agents was studied by the Epsilometric test.

RESULTS

C. difficile was isolated from 17(7.23%) different food samples of animal origin, including toxigenic (6) and non-toxigenic (11) isolates. In four toxigenic strains, the tcdA gene could not be detected under used conditions (tcdA-tcdB+). However, all strains had binary toxin-associated genes (cdtA and cdtB). The antimicrobial resistance was highest in non-toxigenic C. difficile isolates in food of animal origin.

CONCLUSION

Meat, meat products and dry fish, but not milk and milk products were contaminated with C. difficile. Contamination rates were low with diverse toxin profiles and antibiotic resistance patterns among the C. difficile strains.

The Environment, Farm Animals and Foods as Sources of Clostridioides difficile Infection in Humans

The recent discovery of the same Clostridioides difficile ribotypes associated with human infection in a broad range of environments, animals and foods, coupled with an ever-increasing rate of community-acquired infections, suggests this pathogen may be foodborne. The objective of this review was to examine the evidence supporting this hypothesis. A review of the literature found that forty-three different ribotypes, including six hypervirulent strains, have been detected in meat and vegetable food products, all of which carry the genes encoding pathogenesis. Of these, nine ribotypes (002, 003, 012, 014, 027, 029, 070, 078 and 126) have been isolated from patients with confirmed community-associated C. difficile infection (CDI). A meta-analysis of this data suggested there is a higher risk of exposure to all ribotypes when consuming shellfish or pork, with the latter being the main foodborne route for ribotypes 027 and 078, the hypervirulent strains that cause most human illnesses. Managing the risk of foodborne CDI is difficult as there are multiple routes of transmission from the farming and processing environment to humans. Moreover, the endospores are resistant to most physical and chemical treatments. The most effective current strategy is, therefore, to limit the use of broad-spectrum antibiotics while advising potentially vulnerable patients to avoid high-risk foods such as shellfish and pork.

Clostridioides difficile in Foods with Animal Origins; Prevalence, Toxigenic Genes, Ribotyping Profile, and Antimicrobial Resistance

Clostridioides difficile is an important nosocomial pathogen and is considered as a reason of diarrhea and gastrointestinal infections. As a majority of community-originated C. difficile cases are not related to antibiotic prescription and hospitalization, the food portion as a vector of infection transmission has been raised. An existing survey was aimed evaluating the prevalence, antimicrobial resistance, profile of toxigenic genes, and ribotypes of C. difficile isolated from raw meat and carcass surface swab samples. In total, 485 raw meat and carcass surface swab samples were collected. C. difficile was isolated via culture and a diverse biochemical examination. The assessment of minimum inhibitory concentration (MIC) was addressed to evaluate the antibiotic resistance of isolates. Toxin genes detection and ribotyping were used for isolates characterization. The prevalence of C. difficile contamination in all examined samples was 3.71%. The bacterium was detected in 2.91% of raw meat and 4.48% of carcass surface swab samples. Raw sheep meat (5%) and sheep carcass swab (7.50%) samples harbored the highest C. difficile prevalence. The highest rate of antibiotic resistance was observed toward clindamycin (38.88%), ciprofloxacin (38.88%), metronidazole (44.44%), erythromycin (72.22%), and tetracycline (77.77%). C. difficile bacteria showed the minimum rate of resistance meropenem (16.66%) and chloramphenicol (16.66%). TcdA, tcdB, cdtA, and cdtB toxigenic genes were detected in 22.22%, 44.44%, and 16.66% of isolates, respectively. TcdB + tcdA (27.77%) were the most prevalent combined toxigenic gene profile. Both 027 and 078 ribotypes were identified in C. difficile isolates. The role of raw meat and carcass surface swab samples as toxigenic and antibiotic-resistant C. difficile strains vectors was signified. This study authorizes that food animals, particularly sheep and cattle, are C. difficile carriers at slaughter stages and ribotypes are equal in human cases. Subsequently, contamination of carcasses occurs inside the slaughterhouse.

The emergence of Clostridioides difficile PCR ribotype 127 at a hospital in northeastern Taiwan

BACKGROUND

Several studies have highlighted the incidence of Clostridioides difficile infections (CDIs) in Taiwan and certain ribotypes have been related to severe clinical diseases. A study was conducted to investigate the polymerase chain reaction (PCR) ribotypes and genetic relatedness of clinical C. difficile strains collected from January 2009 to December 2015 at a hospital in northeastern Taiwan.

MATERIAL AND METHODS

A modified two-step typing algorithm for C. difficile was used by combining a modified 8-plex and 3'-truncated tcdA screening PCR. In addition, MLVA typing was adopted for investigation of bacterial clonality and transmission.

RESULTS

Among a total of 86 strains, 24 (28%) were nontoxigenic and 62 (72%) had both tcdA and tcdB (A + B+). No tcdA-negative and tcdB-positive (A^-B⁺) strains were identified. Binary toxin (CDT)-producing (cdtA+/cdtB+) strains were started to be identified in 2013. The 21 (34%) A⁺B⁺ clinical strains with binary toxin and tcdC deletion were identified as RT127 strains, which contained both RT078-lineage markers and fluoroquinolone (FQ)-resistant mutations (Thr82Ile in gyrA). Multiple loci variable-number tandem repeat analysis (MLVA) for phylogenetic relatedness of RT127 strains indicated that 20 of 21 strains belonged to a clonal complex that was identical to a clinical strain collected from southern Taiwan in 2011, suggestive of a clonal expansion in Taiwan.

CONCLUSION

A two-step typing method could rapidly confirm species identification and define the toxin gene profile of C. difficile isolates. The clonal expansion of RT127 strains in Taiwan indicates monitoring and surveillance of toxigenic C. difficile isolates from human, animal, and environment are critical to develop One Health prevention strategies.

Clostridioides difficile in Food-Producing Animals in Romania: First Study on the Prevalence and Antimicrobial Resistance

At present, the epidemiology of the gastrointestinal disease caused by Clostridioides difficile (C. difficile) is starting to be slowly elucidated internationally, although information about the bacteria in the food supply chain is insufficient and, in many countries, even absent. The study was conducted in order to investigate the prevalence of C. difficile isolated from animal feces, as well as to determine the antimicrobial susceptibility of such isolates. The presence of antibiotic resistance determinants has also been evaluated. Overall, a total of 24 (12.5%) C. difficile isolates were recovered (out of the 192 samples collected), the highest percentage of positive isolates being detected in the fecal samples collected from piglets (25%). The majority of the isolates recovered in the current study proved to be toxigenic. Moreover, all C. difficile isolates were susceptible to vancomycin, although a large proportion of the porcine isolates (50%) were resistant to levofloxacin. The tetW and erm(B) genes have also been identified in the porcine isolates. In conclusion, this is the first analysis of the prevalence of C. difficile in food-producing animals in Romania, and it adds further evidence about the possible role of animals as a source of resistant C. difficile strains and a reservoir of antimicrobial resistance determinants.

Clostridioides difficile epidemiology in the Middle and the Far East

OBJECTIVES

Clostridioides difficile is an important pathogen of healthcare-associated gastrointestinal infections. Recently, an increased number of C. difficile infection (CDI) surveillance data has been reported from Asia. The aim of this review is to summarize the data on the prevalence, distribution and molecular epidemiology of CDI in the Middle and the Far East.

METHODS

Literature was drawn from a search of PubMed up to September 30, 2021.

RESULTS

The meta-analysis of data from 111 studies revealed the pooled CDI prevalence rate in the Middle and the Far East of 12.4% (95% CI 11.4-13.3); 48 studies used PCR for CDI laboratory diagnoses. The predominant types (RT)/sequence type (ST) differ between individual countries (24 studies, 14 countries). Frequently found RTs were 001, 002, 012, 017, 018 and 126; RT017 was predominant in the Far East. The epidemic RT027 was detected in 8 countries (22 studies), but its predominance was reported only in three studies (Israel and Iran). The contamination of vegetable and meat or meat products and/or intestinal carriage of C. difficile in food and companion animals have been reported; the C. difficile RTs/STs identified overlapped with those identified in humans.

CONCLUSIONS

A large number of studies on CDI prevalence in humans from the Middle and the Far East have been published; countries with no available data were identified. The number of studies on C. difficile from non-human sources is limited. Comparative genomic studies of isolates from different sources are needed.

Survivability of Clostridioides difficile spores in fermented pork summer sausage during refrigerated storage

Background and Aim:

Clostridioides difficile is a spore-forming pathogen that causes serious enteric disease in humans. Strains have been isolated from food animals and meat, including pork, which suggest a potential for foodborne transmission. Pork summer sausage is a popular fermented meat product, which is consumed cooked or cooked to a lower internal temperature due to acidification of the product. The effect of acidity and cooking on the viability of C. difficile spores in a fermented meat product has not been determined. Therefore, the aim was to study the survivability of C. difficile spores in fermented pork summer sausage.

Materials and Methods:

Fermented pork sausages were prepared according to a commercial recipe with or without starter culture and C. difficile spores followed by fermentation at 37°C for ~12 h under 85% relative humidity until pH 5.0 was reached and further processed as cooked (>57°C) or uncooked (≤57°C) and stored at 4°C. C. difficile spores in sausages were enumerated at 1 h following inoculation and on days 0, 1, 7, 14, 21, 30, 60, and 90 of storage.

Results:

It was observed that C. difficile spore viability in control unfermented treatment was significantly different on day 0 from the fermented, fermented cooked, and control unfermented cooked treatments (p<0.05); however, there was no significant difference among the latter three treatment groups throughout 90 days of storage (p>0.05). On day 90 of storage, the unfermented control sausages yielded ~4.0 log colony-forming unit (CFU)/g of C. difficile spores compared to ~3.5 log CFU/g recovered from fermented samples and the unfermented cooked control samples identifying spore viability in all treatment groups.

Conclusion:

C. difficile spores were found to survive the acidity and cooking of fermented pork summer sausage and storage at 4°C for 3 months, thereby highlighting the need for effective intervention strategies to reduce the risk of C. difficile contamination in pork products.

Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China

Clostridioides difficile is the most common pathogen causing antibiotic-associated diarrhea. Previous studies showed that diverse sources, aside from C. difficile infection (CDI) patients, played a major role in C. difficile hospital transmission. This study aimed to investigate relationships and transmission potential of C. difficile strains from different sources. A prospective study was conducted both in the intensive care unit (ICU) and six livestock farms in China in 2018–2019. Ninety-eight strains from CDI patients (10 isolates), asymptomatic hospitalized carriers (55), the ICU environment (12), animals (14), soil (4), and farmers (3) were collected. Sequence type (ST) 3/ribotype (RT) 001, ST35/RT046, and ST48/RT596 were dominant types, distributed widely in multiple sources. Core-genome single-nucleotide polymorphism (cgSNP) analysis showed that hospital and farm strains shared several common clonal groups (CGs, strains separated by ≤ 2 cgSNPs) (CG4/ST3/RT001, CG7/ST35/RT046, CG11/ST48/RT596). CDI patients, asymptomatic carriers, and the ICU environment strains also shared several common CGs. The number of virulence genes was not statistically different between strains from different sources. Multi-source strains in the same CG carried identical virulence gene sequences, including pathogenicity genes at the pathogenicity locus and adhesion-related genes at S-layer cassette. Resistance genes (ermB, tetM, etc.) were widespread in multiple sources, and multi-source strains in the same CG had similar resistance phenotypes and carried consistent transposons and plasmid types. The study indicated that interspecies and cross-regional transmission of C. difficile occurs between animals, the environment, and humans. Community-associated strains from both farms and asymptomatic hospitalized carriers were important reservoirs of CDI in hospitals.

Prevalence, Molecular Characterization and Antimicrobial Susceptibility of Clostridioides difficile Isolated from Pig Carcasses and Pork Products in Central Italy

In the last decade, the incidence and severity of Clostridioides difficile infections (CDIs) in humans have been increasing and community-associated infections have been described. For these reasons, the interest in C. difficile in food and in food animals has increased, suggesting other possible sources of C. difficile acquisition. This study evaluated the presence of C. difficile on pig carcasses at the slaughterhouse and in pork products in Central Italy. The contamination rate on pig carcasses was 4/179 (2.3%). Regarding food samples, a total of 216 pork products were tested (74 raw meat preparations and 142 ready-to-eat food samples made by cured raw meat). The real-time PCR screening was positive for 1/74 raw meat preparation (1.35%) and for 1/142 ready-to-eat food samples (0.7%) C. difficile was isolated only from the raw meat preparation (pork sausage). All the isolated strains were toxigenic and susceptible to all the tested antibiotics. Strains isolated from carcass samples displayed A+B+CDTa+CDTb+ profile, were toxinotype IV and belonged to the same ribotype arbitrary named TV93, while the one isolated from food samples displayed A+B+CDTa-CDTb- profile and it was not possible to determine ribotype and toxinotype, because it was lost after freeze storage. It was concluded that the prevalence of C. difficile in the pork supply chain is very low.

Raw Animal Meats as Potential Sources of Clostridium difficile in Al-Jouf, Saudi Arabia

Clostridium difficile present in feces of food animals may contaminate their meats and act as a potential source of C. difficile infection (CDI) to humans. C. difficile resistance to antibiotics, its production of toxins and spores play major roles in the pathogenesis of CDI. This is the first study to evaluate C. difficile prevalence in retail raw animal meats, its antibiotics susceptibilities and toxigenic activities in Al-Jouf, Saudi Arabia. Totally, 240 meat samples were tested. C. difficile was identified by standard microbiological and biochemical methods. Vitek-2 compact system confirmed C. difficile isolates were 15/240 (6.3%). Toxins A/B were not detected by Xpect C. difficile toxin A/B tests. Although all isolates were susceptible to vancomycin and metronidazole, variable degrees of reduced susceptibilities to moxifloxacin, clindamycin or tetracycline antibiotics were detected by Epsilon tests. C. difficile strains with reduced susceptibility to antibiotics should be investigated. Variability between the worldwide reported C. difficile contamination levels could be due to absence of a gold standard procedure for its isolation. Establishment of a unified testing algorithm for C. difficile detection in food products is definitely essential to evaluate the inter-regional variation in its prevalence on national and international levels. Proper use of antimicrobials during animal husbandry is crucial to control the selective drug pressure on C. difficile strains associated with food animals. Investigating the protective or pathogenic potential of non-toxigenic C. difficile strains and the possibility of gene transfer from certain toxigenic/ antibiotics-resistant to non-toxigenic/antibiotics-sensitive strains, respectively, should be worthy of attention.

Clostridioides difficile infection: an emerging zoonosis?

INTRODUCTION

Clostridioides difficile (C. difficile) infection (CDI) is the most common cause of antibiotic-associated diarrhea and one of the common infections in healthcare facilities. In recent decades, there has been an emerging threat of community-acquired CDI (CA-CDI). Environmental transmission of C. difficile in the community setting has become a major concern, and animals are an important reservoir for C. difficile causing human diseases.

AREAS COVERED

In this article, the molecular epidemiology of C. difficile in animals and recent evidences of zoonotic transfer to humans are reviewed based on an electronic search in the databases of PubMed and Google Scholar.

EXPERT OPINION

C. difficile can be found in stool from diarrheal dogs and cats; therefore, household pets could be a potential source. C. difficile will threaten human health because hypervirulent C. difficile ribotype 078 strains have been found in retail chickens, pig farms, and slaughterhouses. Risk factors for fecal C. difficile carriage in animals include young age, dietary changes, and antibiotic abuse in domestic animals. With the advent of whole genome sequencing techniques, there will be more solid evidence indicating zoonotic transfer of C. difficile from animals to humans.

Clostridioides difficile in Non-hospital Sources (Animals, Food, and Environment) in Asian Countries: A Literature Review

Context: Clostridioides difficile (C. difficile) is an agent responsible for severe infection with a high mortality rate in healthcare facilities. With the discovery of C. difficile in the community, it was assumed that this bacterium might be transmitted to humans through non-hospital sources. Evidence Acquisition: This study examined different aspects of the epidemiology of C. difficile in Asian countries with a review of the literature using search engines such as Web of Science, Scopus, and PubMed. Results: Based on the literature pertaining to Asia, the highest rate of C. difficile is found in samples collected from farm animals, red meat, and meat-based products. Two ribotypes 027 and 078, as hypervirulent factors, were found in different non-hospital sources. Resistance to the most frequently used antibiotics in healthcare setting was observed in C. difficile. Conclusions: Due to the heterogeneity of the examination of C. difficile, understanding the actual condition of C. difficile is difficult. However, the presence of two hypervirulent ribotypes of C. difficile in non-hospital sources is alarming. It seems that it is necessary to perform further studies on C. difficile in non-hospital sources. Defining a focal point for such research could be helpful to explore the situation of C. difficile in clinical settings and communities of Asian countries.

MALDI-TOF MS: An alternative approach for ribotyping Clostridioides difficile isolates in Brazil

Clostridioides difficile is an important organism causing healthcare-associated infections. It has been documented that specific strains caused multiple outbreaks globally, and patients infected with those strains are more likely to develop severe C. difficile infection (CDI). With the appearance of a variant strain, BI/NAP1 ribotype 027, responsible for several outbreaks and high mortality rates worldwide, the epidemiology of the CDI changed drastically in the United States, Europe, and some Latin American countries. Although the epidemic strain 027 was not yet detected in Brazil, there are ribotypes exclusively found in the country, such as, 131, 132, 133, 135, 142 and 143, which are responsible for outbreaks in Brazilian hospitals and nursing homes. Although PCR-ribotyping is the most used method in epidemiology studies of C. difficile, it is not available in Brazil. This study aimed to develop and validate an in-house database for detecting C. difficile ribotypes, usually involved in CDI in Brazilian hospitals, by using MALDI-TOF MS. A database with 19 different ribotypes, 13 with worldwide circulation and 6 Brazilian-restricted, was created based on 27 spectra readings of each ribotype. After BioNumerics analysis, neighbor-joining trees revealed that spectra were distributed in clusters according to ribotypes, showing that MALDI-TOF MS could discriminate all 19 ribotypes. Moreover, each ribotype showed a different profile with 42 biomarkers detected in total. Based on their intensity and occurrence, 13 biomarkers were chosen to compose ribotype-specific profiles, and in silico analysis showed that most of these biomarkers were uncharacterized proteins or well-conserved peptides, such as ribosomal proteins. A double-blind assessment using the 13 biomarkers correctly assigned the ribotype in 73% of the spectra analyzed, with 94%-100% of correct hits for 027 and for Brazilian ribotypes. Although further analyses are required, our results show that MALDI-TOF MS might be a reliable, fast and feasible alternative for epidemiological surveillance of C. difficile in Brazil.

Detection and pathogenic potential of Clostridium difficile in commercial meat and meat products in Brazil

The aims of this study were to evaluate the occurrence of Clostridium difficile in commercial raw meat and meat products commercialized in Brazil, and to determine the pathogenic potential and antimicrobial susceptibility of the isolates. After selective enrichment, the isolation of C. difficile involved plating with and without an alcohol shock treatment onto C. difficile moxalactam agar (CDMNA). The toxigenic profile was determined through PCR for detection of tcdA, tcdB, cdtA and cdtB genes and an enzyme-linked immunosorbent assay for toxin A/B. C. difficile was isolated from 8.9% (17 out of 192) of analyzed samples. Plating without alcohol treatment (sensitivity of 88.23%) was more efficient than with alcohol treatment (sensitivity of 29.41%) in C. difficile isolation. The profile A + B+CDT- was observed in 35.0% (28/80) of the isolates. The A/B toxin was tested in 44 isolates and 15.9% of them were positive. Resistance to clindamycin, ceftizoxime tetracycline, metronidazole, vancomycin, and ceftriaxone were observed among isolates. Multi-drug resistance was detected in 36.4% (8/22) of the isolates evaluated.

High contamination rates of shoes of veterinarians, veterinary support staff and veterinary students with Clostridioides difficile spores

Clostridioides difficile is often found in animals and their environment. However, not much has been reported on veterinary clinics environment in terms of the spore load, prevalence and PCR ribotype diversity. The aim of this study was to assess the prevalence of C. difficile on shoe soles of veterinarians, veterinary support staff and veterinary students at the Veterinary Faculty campus. Altogether, 50 shoe sole swabs were collected, and the positivity rates ranged from 86.7% in swabs from veterinarians to 100% in swabs from support staff and students. Non‐toxigenic and toxigenic strains representing toxinotypes 0, IV and XIX were isolated and distributed into 17 different PCR ribotypes, most common being 010, 014/020, SLO002 and 009. PCR ribotype 010 was the most prevalent and isolated from shoe soles sampled in 6/7 areas. Students' shoes had highest ribotype diversity (15/17 PCR ribotypes) but showed a low overlap with ribotype isolated from vets and support staff shoes. Veterinary students are likely the main vectors of C. difficile spores transmissions among veterinary teaching clinics and the hospital.

Global and Historical Distribution of Clostridioides difficile in the Human Diet (1981-2019): Systematic Review and Meta-Analysis of 21886 Samples Reveal Sources of Heterogeneity, High-Risk Foods, and Unexpected Higher Prevalence Toward the Tropic

Clostridioides difficile (CD) is a spore-forming bacterium that causes life-threatening intestinal infections in humans. Although formerly regarded as exclusively nosocomial, there is increasing genomic evidence that person-to-person transmission accounts for only <25% of cases, supporting the culture-based hypothesis that foods may be routine sources of CD-spore ingestion in humans. To synthesize the evidence on the risk of CD exposure via foods, we conducted a systematic review and meta-analysis of studies reporting the culture prevalence of CD in foods between January 1981 and November 2019. Meta-analyses, risk-ratio estimates, and meta-regression were used to estimate weighed-prevalence across studies and food types to identify laboratory and geographical sources of heterogeneity. In total, 21886 food samples were tested for CD between 1981 and 2019 (96.4%, n = 21084, 2007–2019; 232 food-sample-sets; 79 studies; 25 countries). Culture methodology, sample size and type, region, and latitude were sources of heterogeneity (p < 0.05). Although non-strictly-anaerobic methods were reported in some studies, and we confirmed experimentally that improper anaerobiosis of media/sample-handling affects CD recovery in agar (Fisher, p < 0.01), most studies (>72%) employed the same (one-of-six) culture strategy. Because the prevalence was also meta-analytically similar across six culture strategies reported, all studies were integrated using three meta-analytical methods. At the study level (n = 79), the four-decade global cumulative-prevalence of CD in the human diet was 4.1% (95%CI = −3.71, 11.91). At the food-set level (n = 232, mean 12.9 g/sample, similar across regions p > 0.2; 95%CI = 9.7–16.2), the weighted prevalence ranged between 4.5% (95%CI = 3–6%; all studies) and 8% (95%CI = 7–8%; only CD-positive-studies). Risk-ratio ranking and meta-regression showed that milk was the least likely source of CD, while seafood, leafy green vegetables, pork, and poultry carried higher risks (p < 0.05). Across regions, the risk of CD in foods for foodborne exposure reproducibly decreased with Earth latitude (p < 0.001). In conclusion, CD in the human diet is a global non-random-source of foodborne exposure that occurs independently of laboratory culture methods, across regions, and at a variable level depending on food type and latitude. The latitudinal trend (high CD-food-prevalence toward tropic) is unexpectedly inverse to the epidemiological observations of CD-infections in humans (frequent in temperate regions). Findings suggest the plausible hypothesis that ecologically-richer microbiomes in the tropic might protect against intestinal CD colonization/infections despite CD ingestion.

Clostridium difficile ribotype 017 - characterization, evolution and epidemiology of the dominant strain in Asia

Clostridium difficile ribotype (RT) 017 is an important toxigenic C. difficile RT which, due to a deletion in the repetitive region of the tcdA gene, only produces functional toxin B. Strains belonging to this RT were initially dismissed as nonpathogenic and circulated largely undetected for almost two decades until they rose to prominence following a series of outbreaks in the early 2000s. Despite lacking a functional toxin A, C. difficile RT 017 strains have been shown subsequently to be capable of causing disease as severe as that caused by strains producing both toxins A and B. While C. difficile RT 017 strains can be found in almost every continent today, epidemiological studies suggest that the RT is endemic in Asia and that the global spread of this MLST clade 4 lineage member is a relatively recent event. C. difficile RT 017 transmission appears to be mostly from human to human with only a handful of reports of isolations from animals. An important feature of C. difficile RT 017 strains is their resistance to several antimicrobials and this has been documented as a possible factor driving multiple outbreaks in different parts of the world. This review summarizes what is currently known regarding the emergence and evolution of strains belonging to C. difficile RT 017 as well as features that have allowed it to become an RT of global importance.

Genomic Delineation of Zoonotic Origins of Clostridium difficile

Clostridium difficile is toxin-producing antimicrobial resistant (AMR) enteropathogen historically associated with diarrhea and pseudomembranous colitis in hospitalized patients. In recent years, there have been dramatic increases in the incidence and severity of C. difficile infection (CDI), and associated morbidity and mortality, in both healthcare and community settings. C. difficile is an ancient and diverse species that displays a sympatric lifestyle, establishing itself in a range of ecological niches external to the healthcare system. These sources/reservoirs include food, water, soil, and over a dozen animal species, in particular, livestock such as pigs and cattle. In a manner analogous to human infection, excessive antimicrobial exposure, particularly to cephalosporins, is driving the expansion of C. difficile in livestock populations worldwide. Subsequent spore contamination of meat, vegetables grown in soil containing animal feces, agricultural by-products such as compost and manure, and the environment in general (households, lawns, and public spaces) is contributing to a persistent community source/reservoir of C. difficile and the insidious rise of CDI in the community. The whole-genome sequencing era continues to redefine our view of this complex pathogen. The application of high-resolution microbial genomics in a One Health framework (encompassing clinical, veterinary, and environment derived datasets) is the optimal paradigm for advancing our understanding of CDI in humans and animals. This approach has begun to yield critical insights into the genetic diversity, evolution, AMR, and zoonotic potential of C. difficile. In Europe, North America, and Australia, microevolutionary analysis of the C. difficile core genome shows strains common to humans and animals (livestock or companion animals) do not form distinct populations but share a recent evolutionary history. Moreover, for C. difficile sequence type 11 and PCR ribotypes 078 and 014, major lineages of One Health importance, this approach has substantiated inter-species clonal transmission between animals and humans. These findings indicate either a zoonosis or anthroponosis. Moreover, they challenge the existing paradigm and the long-held misconception that CDI is primarily a healthcare-associated infection. In this article, evolutionary, and zoonotic aspects of CDI are discussed, including the anthropomorphic factors that contribute to the spread of C. difficile from the farm to the community.

Evolutionary and Genomic Insights into Clostridioides difficile Sequence Type 11: a Diverse Zoonotic and Antimicrobial-Resistant Lineage of Global One Health Importance

Historically, Clostridioides difficile (Clostridium difficile) has been associated with life-threatening diarrhea in hospitalized patients. Increasing rates of C. difficile infection (CDI) in the community suggest exposure to C. difficile reservoirs outside the hospital, including animals, the environment, or food. C. difficile sequence type 11 (ST11) is known to infect/colonize livestock worldwide and comprises multiple ribotypes, many of which cause disease in humans, suggesting CDI may be a zoonosis. Using high-resolution genomics, we investigated the evolution and zoonotic potential of ST11 and a new closely related ST258 lineage sourced from diverse origins. We found multiple intra- and interspecies clonal transmission events in all ribotype sublineages. Clones were spread across multiple continents, often without any health care association, indicative of zoonotic/anthroponotic long-range dissemination in the community. ST11 possesses a massive pan-genome and numerous clinically important antimicrobial resistance elements and prophages, which likely contribute to the success of this globally disseminated lineage of One Health importance.

Clostridioides difficile (Clostridium difficile) sequence type 11 (ST11) is well established in production animal populations worldwide and contributes considerably to the global burden of C. difficile infection (CDI) in humans. Increasing evidence of shared ancestry and genetic overlap of PCR ribotype 078 (RT078), the most common ST11 sublineage, between human and animal populations suggests that CDI may be a zoonosis. We performed whole-genome sequencing (WGS) on a collection of 207 ST11 and closely related ST258 isolates of human and veterinary/environmental origin, comprising 16 RTs collected from Australia, Asia, Europe, and North America. Core genome single nucleotide variant (SNV) analysis identified multiple intraspecies and interspecies clonal groups (isolates separated by ≤2 core genome SNVs) in all the major RT sublineages: 078, 126, 127, 033, and 288. Clonal groups comprised isolates spread across different states, countries, and continents, indicative of reciprocal long-range dissemination and possible zoonotic/anthroponotic transmission. Antimicrobial resistance genotypes and phenotypes varied across host species, geographic regions, and RTs and included macrolide/lincosamide resistance (Tn6194 [ermB]), tetracycline resistance (Tn6190 [tetM] and Tn6164 [tet44]), and fluoroquinolone resistance (gyrA/B mutations), as well as numerous aminoglycoside resistance cassettes. The population was defined by a large “open” pan-genome (10,378 genes), a remarkably small core genome of 2,058 genes (only 19.8% of the gene pool), and an accessory genome containing a large and diverse collection of important prophages of the Siphoviridae and Myoviridae. This study provides novel insights into strain relatedness and genetic variability of C. difficile ST11, a lineage of global One Health importance.

Detection of Clostridium difficile in the environment in a veterinary teaching hospital

The present study focused on detecting the presence of Clostridium difficile on veterinary hospital surfaces of large and small animal areas at the Universidad Complutense of Madrid. Isolated C. difficile strains were further characterized and investigated for antimicrobial susceptibility testing. Of n = 23 sampling area, 17% were positive for the presence of C. difficile. The isolates belonged to PCR ribotypes 078, 014, 039, and 154, of which RT 078 and 014 are also frequently found as human pathogens. Two isolates had high level resistance to metronidazole. These results suggest that the veterinary hospital environment constitutes a potential reservoir of zoonotical transferable C. difficile.

Non-toxigenic strain of Clostridioides difficile Z31 reduces the occurrence of C. difficile infection (CDI) in one-day-old piglets on a commercial pig farm

Neonatal porcine diarrhea (NPD) is a current problem on pig farms and is caused by several enteropathogens. Among them, Clostridioides difficile stands out due to its importance in piglets and zoonotic potential. A non-toxigenic strain of C. difficile (NTCD), named Z31, was previously tested in hamster and piglet experimental models as a strategy to prevent C. difficile infection (CDI). To evaluate the capacity of the strain Z31 to prevent CDI and NPD in one-day-old piglets on a commercial farm, 90 piglets from 16 litters received 1 × 10⁶ spores of Z31 while 84 animals from the same litters served as controls. Animals were clinically evaluated, and fecal samples were collected 24 h after administration and submitted to A/B toxin detection and isolation of C. difficile. Stool samples were also submitted to rotavirus, Escherichia coli, and Clostridium perfringens detection. Administration of Z31 reduced the incidence of CDI in treated animals (7.8%) when compared to the control group (25.0%; P = 0.003). In animals that developed CDI, the intensity of diarrhea was lower in those that received Z31 than in the control group. Neonatal porcine diarrhea was reduced in treated animals when compared to untreated animals (P < 0.001). The present study suggests that Z31 can potentially be used to prevent CDI in piglets on commercial farms.

Prevalence, genotype and antimicrobial resistance of Clostridium difficile isolates from healthy pets in Eastern China

BACKGROUND

Clostridium difficile (C. difficile) is a main cause of antibiotic-associated diarrhoea in humans. Several studies have been performed to reveal the prevalence rate of C. difficile in cats and dogs. However, little is known about the epidemiology of C. difficile in healthy pets in China. This study aimed to assess the burden of C. difficile shedding by healthy dogs and cats in China. Furthermore, the genetic diversity and antimicrobial susceptibility patterns of the recovered isolates were determined.

METHODS

A total of 175 faecal samples were collected from 146 healthy dogs and 29 cats. C. difficile strains were isolated and identified from the feces of these pets. The characterized C. difficile strains were typed by multilocus sequence typing (MLST), and the MICs of the isolates were determined against ampicillin, clindamycin, tetracycline, moxifloxacin, chloramphenicol, cefoxitin, metronidazole and vancomycin by the agar dilution method.

RESULTS

Overall, 3 faecal samples (1.7%) were C. difficile culture positive. One sample (0.7%) from a dog was C. difficile culture positive, while two cats (7.0%) yielded positive cultures. The prevalence rate differed significantly between cats and dogs. These isolates were typed into 3 MLST genotypes and were susceptible to chloramphenicol, tetracycline, metronidazole and moxifloxacin and resistant to ampicillin, clindamycin and cefoxitin. Notably, one strain, D141-1, which was resistant to three kinds of antibiotics and carried toxin genes, was recovered in the faeces of a healthy dog.

CONCLUSION

Our results suggest that common pets may be a source of pathogenic C. difficile, indicating that household transmission of C. difficile from pets to humans can not be excluded.

Multidrug-resistant Clostridium difficile ribotypes 078 and 014/5-FLI01 in piglets from Costa Rica

Though an overlap of Clostridium difficile PCR ribotypes (RT) in humans and animals has been noted -particularly in piglets-information regarding C. difficile isolates from swine is scarce in Latin America. A characterization of 10 C. difficile isolates obtained from this origin in Costa Rica revealed the presence of the RT078 (n = 4) and RT014/5-FLI01 (n = 6) ribotypes. Unlike two previous reports from the region, all isolates were multidrug resistant (MDR). According to a minimum spanning tree (MST) analysis, our RT078 isolates formed a clonal complex with some German RT078 isolates and the already noted overlap of RT078 strains in humans and animals. This unanticipated high level of genetic relatedness confirms the transcontinental spread and geographically unlimited clustering of RT078.

Distribution and tracking of Clostridium difficile and Clostridium perfringens in a free-range pig abattoir and processing plant

The presence and genetic diversity of Clostridium difficile and C. perfringens along the slaughtering process of pigs reared in a free-range system was assessed. A total of 270 samples from trucks, lairage, slaughter line and quartering were analyzed, and recovered isolates were toxinotyped and genotyped. C. difficile and C. perfringens were retrieved from 14.4% and 12.6% of samples, respectively. The highest percentage of positive samples for C. difficile was detected in trucks (80%) whereas C. perfringens was more prevalent in cecal and colonic samples obtained in the slaughter line (85% and 45%, respectively). C. difficile isolates (n = 105) were classified into 17 PCR ribotypes (including 010, 078, and 126) and 95 AFLP genotypes. C. perfringens isolates (n = 85) belonged to toxinotypes A (94.1%) and C (5.9%) and were classified into 80 AFLP genotypes. The same genotypes of C. difficile and C. perfringens were isolated from different pigs and occasionally from environmental samples, suggesting a risk of contaminated meat products.