More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes

A mutation associated with resistance to synthetic pyrethroids is widespread in US populations of the tropical lineage of Rhipicephalus sanguineus s.l

The brown dog tick, Rhipicephalus sanguineus sensu lato (s.l.), is an important vector for Rickettsia rickettsii, causative agent of Rocky Mountain spotted fever. Current public health prevention and control efforts to protect people involve preventing tick infestations on domestic animals and in and around houses. Primary prevention tools rely on acaricides, often synthetic pyrethroids (SPs); resistance to this chemical class is widespread in ticks and other arthropods. Rhipicephalus sanguineus s.l. is a complex that likely contains multiple unique species and although the distribution of this complex is global, there are differences in morphology, ecology, and perhaps vector competence among these major lineages. Two major lineages within Rh. sanguineus s.l., commonly referred to as temperate and tropical, have been documented from multiple locations in North America, but are thought to occupy different ecological niches. To evaluate potential acaricide resistance and better define the distributions of the tropical and temperate lineages throughout the US and in northern Mexico, we employed a highly multiplexed amplicon sequencing approach to characterize sequence diversity at: 1) three loci within the voltage-gated sodium channel (VGSC) gene, which contains numerous genetic mutations associated with resistance to SPs; 2) a region of the gamma-aminobutyric acid-gated chloride channel gene (GABA-Cl) containing several mutations associated with dieldrin/fipronil resistance in other species; and 3) three mitochondrial genes (COI, 12S, and 16S). We utilized a geographically diverse set of Rh sanguineus s.l. collected from domestic pets in the US in 2013 and a smaller set of ticks collected from canines in Baja California, Mexico in 2021. We determined that a single nucleotide polymorphism (T2134C) in domain III segment 6 of the VGSC, which has previously been associated with SP resistance in Rh. sanguineus s.l., was widespread and abundant in tropical lineage ticks (>50 %) but absent from the temperate lineage, suggesting that resistance to SPs may be common in the tropical lineage. We found evidence of multiple copies of GABA-Cl in ticks from both lineages, with some copies containing mutations associated with fipronil resistance in other species, but the effects of these patterns on fipronil resistance in Rh. sanguineus s.l. are currently unknown. The tropical lineage was abundant and geographically widespread, accounting for 79 % of analyzed ticks and present at 13/14 collection sites. The temperate and tropical lineages co-occurred in four US states, and as far north as New York. None of the ticks we examined were positive for Rickettsia rickettsii or Rickettsia massiliae.

Microbial assessment of commercial pet foods marketed in the United Arab Emirates

Examining the microbiological characteristics of pet food is imperative to safeguard the health and well-being of companion animals, pet owners, and the surrounding environment. Domestic animals, known for carrying harmful microorganisms, pose a significant health risk, especially in close proximity to people and children. Notably, no studies have previously investigated pet food quality in the Gulf Cooperation Council countries, in particular, the United Arab Emirates (UAE). This study examined the microbiological quality of all stock keeping units (SKUs) of pet foods marketed in UAE (n = 118). Parameters assessed include Total Aerobic Microbial Count (TAMC), Enterobacteriaceae, Total Yeast and Mold Count (TYMC), Salmonella, Listeria monocytogenes, and Clostridium species. Among the 118 samples, 33 (28%) exceeded the acceptable TAMC limit of 106 CFU/g, highlighting significant variations based on manufacturers and ingredients. Eight samples (7%) surpassed the maximum Enterobacteriaceae limit of 3 × 102 CFU/g. TYMC levels exhibited variation, with 33 (28%) exceeding the limit of 104 CFU/g. L. monocytogenes was identified in 44 (37%) of the samples, while Salmonella was not detected. Clostridium contamination was observed in 28 (24%) of the samples. Statistical analyses revealed associations between pet food characteristics and microbial quality, underscoring the imperative for international standards to ensure the safety of pet food. These findings carry significant implications for pet owners, regulatory bodies, and the pet food industry, emphasizing the need for ongoing efforts to enhance the overall quality and safety of pet food products.

Culture-independent detection of low-abundant Clostridioides difficile in environmental DNA via PCR

Clostridioides difficile represents a major burden to public health. As a well-known nosocomial pathogen whose occurrence is highly associated with antibiotic treatment, most examined C. difficile strains originated from clinical specimen and were isolated under selective conditions employing antibiotics. This suggests a significant bias among analyzed C. difficile strains, which impedes a holistic view on this pathogen. In order to support extensive isolation of C. difficile strains from environmental samples, we designed a detection PCR that targets the hpdBCA-operon and thereby identifies low abundances of C. difficile in environmental samples. This operon encodes the 4-hydroxyphenylacetate decarboxylase, which catalyzes the production of the antimicrobial compound para-cresol. Amplicon-based analyses of diverse environmental samples demonstrated that the designed PCR is highly specific for C. difficile and successfully detected C. difficile despite its absence in general 16S rRNA gene-based detection strategies. Further analyses revealed the potential of the hpdBCA detection PCR sequence for initial phylogenetic classification, which allows assessment of C. difficile diversity in environmental samples via amplicon sequencing. Our findings furthermore showed that C. difficile strains isolated under antibiotic treatment from environmental samples were originally dominated by other strains according to PCR amplicon results. This provided evidence for selective cultivation of under-represented but antibiotic-resistant isolates. Thereby, we revealed a substantial bias in C. difficile isolation and research.IMPORTANCEClostridioides difficile is a main cause of diarrheic infections after antibiotic treatment with serious morbidity and mortality worldwide. Research on this pathogen and its virulence has focused on bacterial isolation from clinical specimens under antibiotic treatment, which implies a substantial bias in isolated strains. Comprehensive studies, however, require an unbiased strain collection, which is accomplished by isolation of C. difficile from diverse environmental samples and avoidance of antibiotic-based enrichment strategies. Thus, isolation can significantly benefit from our C. difficile-specific detection PCR, which rapidly verifies C. difficile presence in environmental samples and further allows estimation of the C. difficile diversity by using next-generation sequencing.

Prevalence of Clostridioides difficile in dogs (Canis familiaris) with gastrointestinal disorders in Rio de Janeiro

Clostridioides difficile infections (CDI) have a high morbidity and mortality rate and have always been considered a nosocomial disease. Nonetheless, the number of cases of community-acquired CDI is increasing, and new evidence suggests additional C. difficile reservoirs exist. Pathogenic C. difficile strains have been found in livestock, domestic animals, and meat, so a zoonotic transmission has been proposed.

OBJECTIVE

The goal of this study was to isolate C. difficile strains in dogs at a veterinary clinic in Rio de Janeiro, Brazil, and characterize clinical and pathological findings associated with lower gastrointestinal tract disorders.

METHODS

Fifty stool samples and biopsy fragments from dogs were obtained and cultured in the CDBA selective medium. All suggestive C. difficile colonies were confirmed by MALDI-TOF MS and PCR (tpi gene). Vancomycin, metronidazole, moxifloxacin, erythromycin, and rifampicin were tested for antibiotic susceptibility. Biofilm, motility assays, and a PCR for the toxins (tcdA, tcdB, and cdtB), as well as ribotyping, were also performed.

RESULTS

Blood samples and colonic biopsy fragments were examined in C. difficile positive dogs. Ten animals (20%) tested positive for C. difficile by using stool samples, but not from biopsy fragments. Most C. difficile strains were toxigenic: six were A+B+ belonging to RT106; two were A+B+ belonging to RT014/020; and two were A-B- belonging to RT010. All strains were biofilm producers. In the motility test, 40% of strains were as motile as the positive control, CD630 (RT012). In the disc diffusion test, two strains (RT010) were resistant to erythromycin and metronidazole; and another to metronidazole (RT014/020). In terms of C. difficile clinicopathological correlations, no statistically significant morphological changes, such as pseudomembranous and "volcano" lesions, were observed. Regarding hematological data, dogs positive for C. difficile had leucopenia (p = 0.02) and lymphopenia (p = 0.03). There was a significant correlation between senility and the presence of C. difficile in the dogs studied (p = 0,02).

CONCLUSIONS

Although C. difficile has not been linked to canine diarrheal disorders, it appears to be more common in dogs with intestinal dysfunctions. The isolation of ribotypes frequently involved in human CDI outbreaks around the world supports the theory of C. difficile zoonotic transmission.

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.

A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment

Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. difficile infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled C. difficile from clinical, environmental, and canine reservoirs in Flagstaff, Arizona, USA, to understand the distribution and transmission of the pathogen in a One Health framework; Flagstaff is a medium-sized, geographically isolated city with a single hospital system, making it an ideal site to characterize genomic overlap between sequenced C. difficile isolates across reservoirs. An analysis of 562 genomes from Flagstaff isolates identified 65 sequence types (STs), with eight STs being found across all three reservoirs and another nine found across two reservoirs. A screen of toxin genes in the pathogenicity locus identified nine STs where all isolates lost the toxin genes needed for CDI manifestation (tcdB, tcdA), demonstrating the widespread distribution of non-toxigenic C. difficile (NTCD) isolates in all three reservoirs; 15 NTCD genomes were sequenced from symptomatic, clinical samples, including two from mixed infections that contained both tcdB+ and tcdB- isolates. A comparative single nucleotide polymorphism (SNP) analysis of clinically derived isolates identified 78 genomes falling within clusters separated by ≤2 SNPs, indicating that ~19 % of clinical isolates are associated with potential healthcare-associated transmission clusters; only symptomatic cases were sampled in this study, and we did not sample asymptomatic transmission. Using this same SNP threshold, we identified genomic overlap between canine and soil isolates, as well as putative transmission between environmental and human reservoirs. The core genome of isolates sequenced in this study plus a representative set of public C. difficile genomes (n=136), was 2690 coding region sequences, which constitutes ~70 % of an individual C. difficile genome; this number is significantly higher than has been published in some other studies, suggesting that genome data quality is important in understanding the minimal number of genes needed by C. difficile. This study demonstrates the close genomic overlap among isolates sampled across reservoirs, which was facilitated by maximizing the genomic search space used for comprehensive identification of potential transmission events. Understanding the distribution of toxigenic and non-toxigenic C. difficile across reservoirs has implications for surveillance sampling strategies, characterizing routes of infections, and implementing mitigation measures to limit human infection.

Infrequent intrahousehold transmission of Clostridioides difficile between pet owners and their pets

Companion animals have been shown to carry Clostridioides difficile strains that are similar or identical to strains found in people, and a small number of studies have shown that pets carry genetically identical C. difficile isolates as their owners, suggesting inter-species transmission. However, the directionality of transmission is ultimately unknown, and the frequency with which animals acquire C. difficile following their owners' infection is unclear. The goal of this study was to assess how often pets belonging to people with C. difficile infection carry genetically related C. difficile isolates. We enrolled pet owners from two medical institutions (University of Pennsylvania Health System (UPHS) and The Ohio State University Wexner Medical Center (OSUWMC)) who had diarrhoea with or without positive C. difficile assays and tested their faeces and their pets' faeces for C. difficile using both anaerobic culture and PCR assays. When microorganisms were obtained from both the owner and pet and had the same toxin profile or ribotype, isolates underwent genomic sequencing. Faecal samples were obtained from a total of 59 humans, 72 dogs and 9 cats, representing 47 complete households (i.e. where a sample was available from the owner and at least one pet). Of these, C. difficile was detected in 30 humans, 10 dogs and 0 cats. There were only two households where C. difficile was detected in both the owner and pet. In one of these households, the C. difficile isolates were of different toxin profiles/ribotypes (A+/B+ / RT 499 from the owner, A-/B- / RT PR22386 from the dog). In the other household, the isolates were genetically identical (one SNP difference). Interestingly, the dog from this household had recently received a course of antibiotics (cefpodoxime and metronidazole). Our findings suggest that inter-species transmission of C. difficile occurs infrequently in households with human C. difficile infections.

Molecular epidemiology of Clostridioides difficile in companion animals: Genetic overlap with human strains and public health concerns

Introduction

The changing epidemiology of Clostridioides difficile reflects a well-established and intricate community transmission network. With rising numbers of reported community-acquired infections, recent studies tried to identify the role played by non-human reservoirs in the pathogen's transmission chain. This study aimed at describing the C. difficile strains circulating in canine and feline populations, and to evaluate their genetic overlap with human strains to assess the possibility of interspecies transmission.

Methods

Fecal samples from dogs (n = 335) and cats (n = 140) were collected from two populations (group A and group B) in Portugal. C. difficile isolates were characterized for toxigenic profile and PCR-ribotyping. The presence of genetic determinants of antimicrobial resistance was assessed in all phenotypically resistant isolates. To evaluate the genetic overlap between companion animals and human isolates from Portugal, RT106 (n = 42) and RT014/020 (n = 41) strains from both sources were subjected to whole genome sequencing and integrated with previously sequenced RT106 (n = 43) and RT014/020 (n = 142) genomes from different countries. The genetic overlap was assessed based on core-single nucleotide polymorphism (SNP) using a threshold of 2 SNP.

Results

The overall positivity rate for C. difficile was 26% (76/292) in group A and 18.6% (34/183) in group B. Toxigenic strains accounted for 50% (38/76) and 52.9% (18/34) of animal carriage rates, respectively. The most prevalent ribotypes (RT) were the toxigenic RT106 and RT014/020, and the non-toxigenic RT010 and RT009. Antimicrobial resistance was found for clindamycin (27.9%), metronidazole (17.1%) and moxifloxacin (12.4%), associated with the presence of the ermB gene, the pCD-METRO plasmid and point mutations in the gyrA gene, respectively. Both RT106 and RT014/020 genetic analysis revealed several clusters integrating isolates from animal and human sources, supporting the possibility of clonal interspecies transmission or a shared environmental contamination source.

Discussion

This study shows that companion animals may constitute a source of infection of toxigenic and antimicrobial resistant human associated C. difficile isolates. Additionally, it contributes with important data on the genetic proximity between C. difficile isolates from both sources, adding new information to guide future work on the role of animal reservoirs in the establishment of community associated transmission networks and alerting for potential public health risk.

LupiQuant: A real-time PCR based assay for determining host-to-parasite DNA ratios of Onchocerca lupi and host Canis lupus from onchocercosis samples

Onchocerca lupi is a filarial nematode that causes ocular onchocercosis in canines globally including North America and areas of Europe, North Africa, and the Middle East. Reported incidence of this parasite in canines has continued to steadily escalate since the early 21st century and was more recently documented in humans. Whole genome sequencing (WGS) of this parasite can provide insight into gene content, provide novel surveillance targets, and elucidate the origin and range expansion. However, past attempts of whole genome sequencing of other Onchocerca species reported a substantial portion of their data unusable due to the variable over-abundance of host DNA in samples. Here, we have developed a method to determine the host-to-parasite DNA ratio using a quantitative PCR (qPCR) approach that relies on two standard plasmids each of which contains a single copy gene specific to the parasite genus Onchocerca (major body wall myosin gene, myosin) or a single copy gene specific to the canine host (polycystin-1 precursor, pkd1). These plasmid standards were used to determine the copy number of the myosin and pkd1 genes within a sample to calculate the ratio of parasite and host DNA. Furthermore, whole genome sequence (WGS) data for three O. lupi isolates were consistent with our host-to-parasite DNA ratio results. Our study demonstrates, despite unified DNA extraction methods, variable quantities of host DNA within any one sample which will likely affect downstream WGS applications. Our quantification assay of host-to-parasite genome copy number provides a robust and accurate method of assessing canine host DNA load in an O. lupi specimen that will allow informed sample selection for WGS. This study has also provided the first whole genome draft sequence for this species. This approach is also useful for future focused WGS studies of other parasites.

Dogs as carriers of virulent and resistant genotypes of Clostridioides difficile

While previous research on zoonotic transmission of community-acquired Clostridioides difficile infection (CA-CDI) focused on food-producing animals, the present study aimed to investigate whether dogs are carriers of resistant and/or virulent C. difficile strains. Rectal swabs were collected from 323 dogs and 38 C. difficile isolates (11.8%) were obtained. Isolates were characterized by antimicrobial susceptibility testing, whole-genome sequencing (WGS) and a DNA hybridization assay. Multilocus sequence typing (MLST), core genome MLST (cgMLST) and screening for virulence and antimicrobial resistance genes were performed based on WGS. Minimum inhibitory concentrations for erythromycin, clindamycin, tetracycline, vancomycin and metronidazole were determined by E-test. Out of 38 C. difficile isolates, 28 (73.7%) carried genes for toxins. The majority of isolates belonged to MLST sequence types (STs) of clade I and one to clade V. Several isolates belonged to STs previously associated with human CA-CDI. However, cgMLST showed low genetic relatedness between the isolates of this study and C. difficile strains isolated from humans in Austria for which genome sequences were publicly available. Four isolates (10.5%) displayed resistance to three of the tested antimicrobial agents. Isolates exhibited resistance to erythromycin, clindamycin, tetracycline and metronidazole. These phenotypic resistances were supported by the presence of the resistance genes erm(B), cfr(C) and tet(M). All isolates were susceptible to vancomycin. Our results indicate that dogs may carry virulent and antimicrobial-resistant C. difficile strains.

Diverse lineages of pathogenic Leptospira species are widespread in the environment in Puerto Rico, USA

Background

Leptospirosis, caused by Leptospira bacteria, is a common zoonosis worldwide, especially in the tropics. Reservoir species and risk factors have been identified but surveys for environmental sources are rare. Furthermore, understanding of environmental Leptospira containing virulence associated genes and possibly capable of causing disease is incomplete, which may convolute leptospirosis diagnosis, prevention, and epidemiology.

Methodology/Principal findings

We collected environmental samples from 22 sites in Puerto Rico during three sampling periods over 14-months (Dec 2018-Feb 2020); 10 water and 10 soil samples were collected at each site. Samples were screened for DNA from potentially pathogenic Leptospira using the lipL32 PCR assay and positive samples were sequenced to assess genetic diversity. One urban site in San Juan was sampled three times over 14 months to assess persistence in soil; live leptospires were obtained during the last sampling period. Isolates were whole genome sequenced and LipL32 expression was assessed in vitro.

We detected pathogenic Leptospira DNA at 15/22 sites; both soil and water were positive at 5/15 sites. We recovered lipL32 sequences from 83/86 positive samples (15/15 positive sites) and secY sequences from 32/86 (10/15 sites); multiple genotypes were identified at 12 sites. These sequences revealed significant diversity across samples, including four novel lipL32 phylogenetic clades within the pathogenic P1 group. Most samples from the serially sampled site were lipL32 positive at each time point. We sequenced the genomes of six saprophytic and two pathogenic Leptospira isolates; the latter represent a novel pathogenic Leptospira species likely belonging to a new serogroup.

Conclusions/Significance

Diverse and novel pathogenic Leptospira are widespread in the environment in Puerto Rico. The disease potential of these lineages is unknown but several were consistently detected for >1 year in soil, which could contaminate water. This work increases understanding of environmental Leptospira diversity and should improve leptospirosis surveillance and diagnostics.

Laboratory diagnosis of Clostridioides (Clostridium) difficile infection in domestic animals: A short review

Despite the known importance of Clostridioides (Clostridium) difficile infection (CDI) in animals, there are no published guidelines for the diagnosis of CDI. The performance of the available commercial methods, all standardized for human stool samples, can vary according to the animal species. Thus, the aim of the present study was to review the literature on the detection of C. difficile in pigs, horses, and dogs. The detection of toxins A and B using enzyme immunoassays seems to have low performance in piglet and dog samples, while it shows high sensitivity for the diagnosis of CDI in foals. On the other hand, tests for the detection of glutamate dehydrogenase (GDH) have a high sensitivity towards detection of C. difficile in animal samples, suggesting that it can be an adequate screening method. A few studies have evaluated real-time PCR or nucleic acid amplification tests in animal samples and, so far, these methods have also shown a low performance for the detection of C. difficile in animals. Although the intestinal lesions caused by CDI can vary among animal species, histopathology can be a useful auxiliary tool for postmortem diagnosis in animals.

Global evolutionary dynamics and resistome analysis of Clostridioides difficile ribotype 017

Clostridioides difficile PCR ribotype (RT) 017 ranks among the most successful strains of C. difficile in the world. In the past three decades, it has caused outbreaks on four continents, more than other ‘epidemic’ strains, but our understanding of the genomic epidemiology underpinning the spread of C. difficile RT 017 is limited. Here, we performed high-resolution phylogenomic and Bayesian evolutionary analyses on an updated and more representative dataset of 282 non-clonal C. difficile RT 017 isolates collected worldwide between 1981 and 2019. These analyses place an estimated time of global dissemination between 1953 and 1983 and identified the acquisition of the ermB-positive transposon Tn6194 as a key factor behind global emergence. This coincided with the introduction of clindamycin, a key inciter of C. difficile infection, into clinical practice in the 1960s. Based on the genomic data alone, the origin of C. difficile RT 017 could not be determined; however, geographical data and records of population movement suggest that C. difficile RT 017 had been moving between Asia and Europe since the Middle Ages and was later transported to North America around 1860 (95 % confidence interval: 1622–1954). A focused epidemiological study of 45 clinical C. difficile RT 017 genomes from a cluster in a tertiary hospital in Thailand revealed that the population consisted of two groups of multidrug-resistant (MDR) C. difficile RT 017 and a group of early, non-MDR C. difficile RT 017. The significant genomic diversity within each MDR group suggests that although they were all isolated from hospitalized patients, there was probably a reservoir of C. difficile RT 017 in the community that contributed to the spread of this pathogen.

Genetic and phenotypic characteristics of Clostridium (Clostridioides) difficile from canine, bovine, and pediatric populations

Objectives:

Carriage of Clostridioides difficile by different species of animals has led to speculation that animals could represent a reservoir of this pathogen for human infections. The objective of this study was to compare C. difficile isolates from humans, dogs, and cattle from a restricted geographic area.

Methods:

C. difficile isolates from 36 dogs and 15 dairy calves underwent whole genome sequencing, and phenotypic assays assessing growth and virulence were performed. Genomes of animal-derived isolates were compared to 29 genomes of isolates from a pediatric population as well as 44 reference genomes.

Results:

Growth rates and relative cytotoxicity of isolates were significantly higher and lower, respectively, in bovine-derived isolates compared to pediatric- and canine-derived isolates. Analysis of core genes showed clustering by host species, though in a few cases, human strains co-clustered with canine or bovine strains, suggesting possible interspecies transmission. Geographic differences (e.g., farm, litter) were small compared to differences between species. In an analysis of accessory genes, the total number of genes in each genome varied between host species, with 6.7% of functional orthologs differentially present/absent between host species and bovine-derived strains having the lowest number of genes. Canine-derived isolates were most likely to be non-toxigenic and more likely to carry phages. A targeted study of episomes identified in local pediatric strains showed sharing of a methicillin-resistance plasmid with dogs, and historic sharing of a wide range of episomes across hosts. Bovine-derived isolates harbored the widest variety of antibiotic-resistance genes, followed by canine

Conclusions:

While C. difficile isolates mostly clustered by host species, occasional co-clustering of canine and pediatric-derived isolates suggests the possibility of interspecies transmission. The presence of a pool of resistance genes in animal-derived isolates with the potential to appear in humans given sufficient pressure from antibiotic use warrants concern.

Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations

Clostridioides difficile is a pathogen often associated with hospital-acquired infection or antimicrobial-induced disease; however, increasing evidence indicates infections can result from community or environmental sources. Most genomic sequencing of C. difficile has focused on clinical strains, although evidence is growing that C. difficile spores are widespread in soil and water in the environment. In this study, we sequenced 38 genomes collected from soil and water isolates in Flagstaff (AZ, USA) and Slovenia in an effort targeted towards environmental surveillance of C. difficile. At the average nucleotide identity (ANI) level, the genomes were divergent to C. difficile at a threshold consistent with different species. A phylogenetic analysis of these divergent genomes together with Clostridioides genomes available in public repositories confirmed the presence of three previously described, cryptic Clostridioides species and added two additional clades. One of the cryptic species (C-III) was almost entirely composed of Arizona and Slovenia genomes, and contained distinct sub-groups from each region (evidenced by SNP and gene-content differences). A comparative genomics analysis identified multiple unique coding sequences per clade, which can serve as markers for subsequent environmental surveys of these cryptic species. Homologues to the C. difficile toxin genes, tcdA and tcdB, were found in cryptic species genomes, although they were not part of the typical pathogenicity locus observed in C. difficile, and in silico PCR suggested that some would not amplify with widely used PCR diagnostic tests. We also identified gene homologues in the binary toxin cluster, including some present on phage and, for what is believed to be the first time, on a plasmid. All isolates were obtained from environmental samples, so the function and disease potential of these toxin homologues is currently unknown. Enzymatic profiles of a subset of cryptic isolates (n=5) demonstrated differences, suggesting that these isolates contain substantial metabolic diversity. Antimicrobial resistance (AMR) was observed across a subset of isolates (n=4), suggesting that AMR mechanisms are intrinsic to the genus, perhaps originating from a shared environmental origin. This study greatly expands our understanding of the genomic diversity of Clostridioides. These results have implications for C. difficile One Health research, for more sensitive C. difficile diagnostics, as well as for understanding the evolutionary history of C. difficile and the development of pathogenesis.

Evaluation of an immunochromatographic test for the detection of glutamate dehydrogenase for the diagnosis of Clostridioides (Clostridium) difficile infection in dogs

This study aimed to evaluate an immunochromatographic test used to detect glutamate dehydrogenase (GDH) for the diagnosis of Clostridium difficile infection (CDI) in dogs. Fecal samples of 119 diarrheic dogs were subjected to toxigenic culture as the "gold standard" method and to GDH detection (Ecodiagnostica, Brazil). Samples positive for toxigenic C. difficile strains and those positive in the GDH test were also subjected to A/B toxin detection using an enzyme immunoassay kit (C. difficile Tox A/B II, Techlab Inc., USA). Sensitivity, specificity, and positive and negative predictive values (PPV and NPV, respectively) were measured for GDH detection and compared with the toxigenic culture results. A total of 19 (15.9%) dogs were positive for toxigenic C. difficile. Of these, 10 (52.6%) dogs were positive for A/B toxins using the enzyme immunoassay kit and 18 (15.2%) were positive in the GDH test, leading to a sensitivity and NPV of 89.4% and 97.9%, respectively. Three animals, two of which were colonized with non-toxigenic strains, were positive for GDH, though not confirmed with CDI, resulting in a high specificity (97%) and PPV (85%). The results suggest that the lateral flow test for GDH detection could be a useful method for diagnosing CDI in dogs, similar to that previously described for humans and other animal species.

Performance of commercial PCR assays to detect toxigenic Clostridioides difficile in the feces of puppies

Clostridioides difficile is an important enteric pathogen that causes significant morbidity and mortality in humans. With community‐acquired infections on the rise, it is important to identify reservoirs of the pathogen. Companion animals can be asymptomatic carriers of C. difficile and may therefore represent a reservoir, but epidemiological studies of C. difficile within the pet‐owner unit are needed, along with validated methods to detect C. difficile in both people and animals. The goal of this study was to assess the performance of commercial qPCR assays and a multiplex PCR for C. difficile compared to toxigenic culture. These assays were tested on up to 103 fecal samples from puppies, a population in which the prevalence of C. difficile is the highest. The sensitivities, specificities, positive predictive values and negative predictive values were respectively 84.2%, 87.7%, 61.5%, and 95.9% for the Cepheid GeneXpert; 66.7%, 66.7%, 29.6%, and 90.9% for the DiaSorin Simplexa; and 94.4%, 85.0%, 65.4%, and 98.1%, for the multiplex qPCR. The agreement was highest between the GeneXpert and the multiplex PCR (90.1% agreement, with a kappa statistic of 0.77). For diagnostic purposes, the positive predictive values of the assays were low. However, the high sensitivities of the assays could render them useful for epidemiologic purposes.

Companion animals might be a reservoir of Clostridioides difficile. Diagnostic assays that are validated in both people and pets are needed to conduct epidemiological investigations within the pet‐owner unit. We found that at least one commercial PCR assay to detect C. difficile in people is also highly sensitive in dogs and could therefore be used for epidemiological purposes within the pet‐owner unit.

Complete Genome Sequence of Peptacetobacter (Clostridium) hiranonis Strain DGF055142, Isolated from Dog Feces from Flagstaff, Arizona, USA, 2019

A single-chromosome closed genome of Peptacetobacter (Clostridium) hiranonis strain DGF055142 was generated using Illumina MiSeq short reads paired with Oxford Nanopore MinION long reads. This isolate was obtained from a canine in Flagstaff, Arizona, in 2019. Peptacetobacter (C.) hiranonis was hypothesized to contribute to canine Clostridium difficile infection resistance.

A single-chromosome closed genome of Peptacetobacter (Clostridium) hiranonis strain DGF055142 was generated using Illumina MiSeq short reads paired with Oxford Nanopore MinION long reads. This isolate was obtained from a canine in Flagstaff, Arizona, in 2019. Peptacetobacter (C.) hiranonis was hypothesized to contribute to canine Clostridium difficile infection resistance.

Dogs are carriers of Clostridioides difficile lineages associated with human community-acquired infections

There is an increasing concern about the role of animals as reservoirs of Clostridioides difficile. In this study, we investigated prevalence, antimicrobial resistance and zoonotic potential of C. difficile in dogs. Two-hundred and twenty-five dog faecal deposits were collected from trashcans in nine public gardens. C. difficile was isolated using selective plating and enrichment culture, identified by MALDI-TOF, tested for susceptibility to seven antibiotics by E-test, and sequenced on an Illumina NextSeq platform. Genome sequences were analysed to determine multilocus sequence types and resistance and toxin gene profiles. Zoonotic potential was assessed by measuring genetic variations of core genome (cg)MLST types between canine isolates and 216 temporally and spatially related human clinical isolates from a national database. C. difficile was isolated from 11 samples (4.9%). Seven isolates were toxigenic (tcdA+, tcdB+, cdtA/B-) and belonged to the sequence types ST2, ST6, ST10 and ST42. The four non-toxigenic isolates were assigned to ST15, ST26 and one novel ST. ST2, corresponding to PCR ribotype RT014/020, was the dominating lineage (n = 4) and, together with ST26 and ST42 isolates, showed close resemblance to human isolates, i.e. 2-5 allelic differences among the 1999 genes analysed by cgMLST. Three non-toxigenic isolates displayed resistance to clindamycin, erythromycin and tetracycline mediated by erm(B) and tet(M). Resistance to metronidazole, moxifloxacine, rifampicin or vancomycin was not detected. In conclusion, a small proportion of faecal deposits contained toxigenic C. difficile such as ST2 (RT014/020), which is a major cause of community-acquired infections. Our finding suggests that pathogenic strains can be exchanged between dogs and humans.

Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota

The relationship between the gut microbiota and Clostridioides difficile, and its role in the severity of C. difficile infection in humans is an area of active research. Intestinal carriage of toxigenic and non-toxigenic C. difficile strains, with and without clinical signs, is reported in animals, however few studies have looked at the risk factors associated with C. difficile carriage and the role of the host gut microbiota. Here, we isolated and characterized C. difficile strains from different animal species (predominantly canines (dogs), felines (cats), and equines (horses)) that were brought in for tertiary care at North Carolina State University Veterinary Hospital. C. difficile strains were characterized by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16S rRNA gene sequencing was done on animal feces to investigate the relationship between the presence of C. difficile and the gut microbiota in different hosts. Here, we show that C. difficile was recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes including ones known to cause CDI in humans. The presence of C. difficile results in a shift in the fecal microbial community structure in both canines and equines. Commensal Clostridium hiranonis was negatively associated with C. difficile in canines. Further experimentation showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts.

Prevalence, Colonization, Epidemiology, and Public Health Significance of Clostridioides difficile in Companion Animals

Clostridioides difficile, previously Clostrdium difficile, is a major cause of antibiotic-associated enteric disease in humans in hospital settings. Increased incidence of C. difficile infection (CDI) in community settings raises concerns over an alternative source of CDI for humans. The detection of genetically similar and toxigenic C. difficile isolates in companion animals, including asymptomatic pets, suggests the potential role of household pets as a source of community-associated CDI. The close association between companion animals and humans, in addition to the use of similar antibiotics in both species, could provide a selective advantage for the emergence of new C. difficile strains and thus increase the incidental transmission of CDI to humans. Therefore, screening household pets for C. difficile is becoming increasingly important from a public health standpoint and may become a part of routine testing in the future, for the benefit of susceptible or infected individuals within a household. In this review, we analyze available information on prevalence, pathophysiology, epidemiology, and molecular genetics of C. difficile infection, focusing on companion animals and evaluate the risk of pet-borne transmission of CDI as an emerging public health concern. Molecular epidemiological characterization of companion animal C. difficile strains could provide further insights into the interspecies transmission of CDI. The mosaic nature of C. difficile genomes and their susceptibility to horizontal gene transfer may facilitate the inter-mixing of genetic material, which could increase the possibility of the emergence of new community-associated CDI strains. However, detailed genome-wide characterization and comparative genome analysis are warranted to confirm this hypothesis.

Association of Household Exposure to Primary Clostridioides difficile Infection With Secondary Infection in Family Members

Importance

Clostridioides difficile infection (CDI) is a common hospital-acquired infection. Whether family members are more likely to experience a CDI following CDI in another separate family member remains to be studied.

Objective

To determine the incidence of potential family transmission of CDI.

Design, Setting, and Participants

In this case-control study comparing the incidence of CDI among individuals with prior exposure to a family member with CDI to those without prior family exposure, individuals were binned into monthly enrollment strata based on exposure status (eg, family exposure) and confounding factors (eg, age, prior antibiotic use). Data were derived from population-based, longitudinal commercial insurance claims from the Truven Marketscan Commercial Claims and Encounters and Medicare Supplemental databases from 2001 to 2017. Households with at least 2 family members continuously enrolled for at least 1 month were eligible. CDI incidence was computed within each stratum. A regression model was used to compare incidence of CDI while controlling for possible confounding characteristics.

Exposures

Index CDI cases were identified using inpatient and outpatient diagnosis codes. Exposure risks 60 days prior to infection included CDI diagnosed in another family member, prior hospitalization, and antibiotic use.

Main Outcomes and Measures

The primary outcome was the incidence of CDI in a given monthly enrollment stratum. Separate analyses were considered for CDI diagnosed in outpatient or hospital settings.

Results

A total of 224 818 cases of CDI, representing 194 424 enrollees (55.9% female; mean [SD] age, 52.8 [22.2] years) occurred in families with at least 2 enrollees. Of these, 1074 CDI events (4.8%) occurred following CDI diagnosis in a separate family member. Prior family exposure was significantly associated with increased incidence of CDI, with an incidence rate ratio (IRR) of 12.47 (95% CI, 8.86-16.97); this prior family exposure represented the factor with the second highest IRR behind hospital exposure (IRR, 16.18 [95% CI, 15.31-17.10]). For community-onset CDI cases without prior hospitalization, the IRR for family exposure was 21.74 (95% CI, 15.12-30.01). Age (IRR, 9.90 [95% CI, 8.92-10.98] for ages ≥65 years compared with ages 0-17 years), antibiotic use (IRR, 3.73 [95% CI, 3.41-4.08] for low-risk and 14.26 [95% CI, 13.27-15.31] for high-risk antibiotics compared with no antibiotics), and female sex (IRR, 1.44 [95% CI, 1.36-1.53]) were also positively associated with incidence.

Conclusions and Relevance

This study found that individuals with family exposure may be at significantly greater risk for acquiring CDI, which highlights the importance of the shared environment in the transmission and acquisition of C difficile.

Fecal shedding of Salmonella spp., Clostridium perfringens, and Clostridioides difficile in dogs fed raw meat-based diets in Brazil and their owners' motivation

The present study aimed to explore the motivations of Brazilian dog owners and their knowledge about the risks related to raw meat-based diets (RMBD) as well as to evaluate important enteropathogens such as Salmonella spp., C. perfringens, and C. difficile, in feces of dogs fed different diets. The majority of the pet owners (69.3%) reported to have chosen this diet for their dogs, considering it to be more “natural”. A large number of owners declared that RMBD do not pose health risks for their animals (87.9%) or humans (98.8%), even though almost one third of the respondents (34.8%) declared having at least one individual at high risk of infection in contact with RMBD-fed dogs. Stool samples from 46 RMBD-fed dogs and 192 dogs fed commercial dry feed were collected. The present study revealed that dogs fed raw meat diets were almost 30 times more likely to be positive for Salmonella spp. than dogs on a conventional diet. Some of the serovars detected were commonly associated with human salmonellosis, such as S. Typhimurium and S. Saintpaul, and were multidrug resistant. RMBD-fed dogs were more likely to be positive for C. perfringens type A (p = 0.008) and one C. perfringens type F was isolated from these animals. Two toxigenic strains (4.3%) of C. difficile were isolated only from raw meat-fed dogs, all of which were under antibiotic therapy. These toxigenic C. difficile isolates were classified as RT106/ST54 and RT600/ST149, previously associated with infection in dogs and humans. The present work revealed that the owners have a tendency to ignore or are unaware of the risks associated with raw meat diets for dogs. Also, the higher fecal shedding of important enteropathogens in dogs fed RMBD suggests that this diet poses a risk for the animals and the people in contact with them.

Isolation of Clostridium perfringens and Clostridioides difficile in diarrheic and nondiarrheic cats

The occurrence and characteristics of Clostridioides (previously Clostridium) difficile and Clostridium perfringens in the feces of diarrheic and non-diarrheic cats was investigated. Apparently healthy animals were more likely to be positive for C. perfringens type A (p = 0.009). Two isolates (0.7%), one each from a diarrheic and an apparently healthy cat, were positive for the enterotoxin-encoding gene but negative for the NetF-encoding gene. Six toxigenic C. difficile isolates were isolated, all RT106 and ST42, which is commonly reported in humans with C. difficile infection.

Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability

Background

Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data commonly do not account for errors potentially introduced by contamination, which could lead to the wrong assessment of allele frequency both in basic and clinical research.

Results

We used a taxonomic filter to remove contaminant reads from more than 4000 bacterial samples from 20 different studies and performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS. We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling. We used both real and simulated data to evaluate and implement reliable, contamination-aware analysis pipelines.

Conclusion

As sequencing technologies consolidate as precision tools that are increasingly adopted in the research and clinical context, our results urge for the implementation of contamination-aware analysis pipelines. Taxonomic classifiers are a powerful tool to implement such pipelines.

Clostridioides difficile Spores: Bile Acid Sensors and Trojan Horses of Transmission

The Gram-positive, spore-forming bacterium, Clostridioides difficile is the leading cause of healthcare-associated infections in the United States, although it also causes a significant number of community-acquired infections. C. difficile infections, which range in severity from mild diarrhea to toxic megacolon, cost more to treat than matched infections, with an annual treatment cost of approximately $6 billion for almost half-a-million infections. These high-treatment costs are due to the high rates of C. difficile disease recurrence (>20%) and necessity for special disinfection measures. These complications arise in part because C. difficile makes metabolically dormant spores, which are the major infectious particle of this obligate anaerobe. These seemingly inanimate life forms are inert to antibiotics, resistant to commonly used disinfectants, readily disseminated, and capable of surviving in the environment for a long period of time. However, upon sensing specific bile salts in the vertebrate gut, C. difficile spores transform back into the vegetative cells that are responsible for causing disease. This review discusses how spores are ideal vectors for disease transmission and how antibiotics modulate this process. We also describe the resistance properties of spores and how they create challenges eradicating spores, as well as promote their spread. Lastly, environmental reservoirs of C. difficile spores and strategies for destroying them particularly in health care environments will be discussed.

Clostridium (Clostridioides) difficile in animals

Clostridium (Clostridioides) difficile is a gram-positive, spore-forming bacterium that is an important cause of disease in people, a variably important cause of disease in some animal species, and an apparently harmless commensal in others. Regardless of whether it is a known pathogen in a particular species, it can also be found in healthy individuals, sometimes at high prevalences and typically with higher rates of carriage in young individuals. As it is investigated in more animal species, it is apparent that this bacterium is widely disseminated in a diverse range of domestic and wild animal species. Although it can be found in most species in which investigations have been performed, there are pronounced intra- and inter-species differences in prevalence and clinical relevance. A wide range of strains can be identified, some that appear to be animal associated and others that are found in humans and animals. A large percentage of strains that cause disease in people can at least sporadically be found in animals. It is a potentially important zoonotic pathogen, but there is limited direct evidence of animal-human transmission. Although C. difficile has been studied extensively over the past few decades, it remains an enigmatic organism in many ways.

Association Between Environmental Factors and Toxigenic Clostridioides difficile Carriage at Hospital Admission

IMPORTANCE

Clostridioides difficile infection is the most frequent health care-associated infection in the United States. However, exposure to this organism might occur outside the health care setting.

OBJECTIVE

To examine whether exposure to environmental factors, such as livestock farms, is associated with a higher probability of being colonized with C difficile at hospital admission.

DESIGN, SETTING, AND PARTICIPANTS

This retrospective cohort study was conducted from May 1, 2017, to June 30, 2018, at a teaching-affiliated hospital in Milwaukee, Wisconsin. All consecutive patients underwent C difficile screening using a nucleic acid amplification test at hospital admission. Data analyses were performed from July 2018 to October 2019.

EXPOSURES

The distances from patient residence to the nearest livestock farms, meat processing plants, raw materials services, and sewage facilities were measured in addition to risk factors previously evaluated in other studies.

MAIN OUTCOMES AND MEASURES

The main outcome was a positive result on C difficile screening tests performed within 72 hours of hospital admission.

RESULTS

A total of 3043 patients admitted to the hospital were included in the final analysis. Of those, 1564 (51.4%) were women and 2074 (68.9%) were white, with a mean (SD) age of 62.0 (15.9) years; 978 patients (32.1%) were admitted to hematology-oncology units. At first admission, 318 patients (10.4%) were detected through testing as C difficile carriers. Multivariable logistic regression analyses were performed on a stratified sample of patients based on hematology-oncology admission status. These analyses indicated that although patients admitted to hematology-oncology units were 35% more likely to be colonized with C difficile, no significant association existed between their sociodemographic and economic characteristics or health care and environmental exposures and the likelihood of a positive C difficile test result. In contrast, among patients admitted to non-hematology-oncology units, comorbidities increased the likelihood for colonization by more than 4 times; women had 60% greater colonization than men, and a history of recent hospitalization (ie, within the preceding 6 months) increased the likelihood of colonization by 70%. Residential proximity to livestock farms were all significantly associated with a higher likelihood of a positive C difficile test result. Residential proximity to livestock farms more than doubled the probability of C difficile colonization in patients admitted to non-hematology-oncology units.

CONCLUSIONS AND RELEVANCE

A shorter distance between residence and livestock farms was associated with C difficile colonization. Knowledge of the epidemiology of C difficile in the community surrounding the hospital is important, as it has potential implications for the incidence of hospital-onset C difficile infection.

Clostridioides (Clostridium) Difficile in Food-Producing Animals, Horses and Household Pets: A Comprehensive Review

Clostridioides (Clostridium) difficile is ubiquitous in the environment and is also considered as a bacterium of great importance in diarrhea-associated disease for humans and different animal species. Food animals and household pets are frequently found positive for toxigenic C. difficile without exposing clinical signs of infection. Humans and animals share common C. difficile ribotypes (RTs) suggesting potential zoonotic transmission. However, the role of animals for the development of human infection due to C. difficile remains unclear. One major public health issue is the existence of asymptomatic animals that carry and shed the bacterium to the environment, and infect individuals or populations, directly or through the food chain. C. difficile ribotype 078 is frequently isolated from food animals and household pets as well as from their environment. Nevertheless, direct evidence for the transmission of this particular ribotype from animals to humans has never been established. This review will summarize the current available data on epidemiology, clinical presentations, risk factors and laboratory diagnosis of C. difficile infection in food animals and household pets, outline potential prevention and control strategies, and also describe the current evidence towards a zoonotic potential of C. difficile infection.

Evaluation of microbial contamination and effects of storage in raw meat-based dog foods purchased online

Feeding raw-meat-based diets to companion animals has become a widespread practice, and many owners are now accustomed to buying frozen ingredients online. The goals of this study were to assess the microbiological quality of raw-meat dog foods obtained from specialized websites and to evaluate the effects of storage at different temperatures for a few days. Twenty-nine raw dog food products were processed for quantitative bacteriology (i.e. total viable count, TVC; Escherichia coli; faecal coliforms, FC) and sulphite-reducing clostridia, and analysed for the presence of Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica and Clostridium difficile. Every sample was examined right after the delivery (T0), after 24 to 48 hr and after 72 hr, both at 2°C and 7°C. At T0, the mean score for the TVC was 5.9 × 10⁶  cfu/g (SD = 4.8 × 10⁷  cfu/g), while those for E. coli and FC were 1.1 × 10⁴  cfu/g (SD = 2.5 × 10⁵  cfu/g) and 3.3 × 10³  cfu/g (SD = 6.5 × 10⁴  cfu/g) respectively. The samples stored at 2°C had a significant increase of all parameters (TVC: p < .01; E. coli: p = .03; FC: p = .04) through time. Noteworthy differences between the analyses performed at 2°C and 7°C were found for TVC (p < .01), being the samples considerably more contaminated at higher temperatures. No sample tested positive for Salmonella spp., while L. monocytogenes was isolated from 19 products, Y. enterocolitica from three products and Clostridium perfringens and C. difficile from four and six products respectively. The microbiological quality of raw-meat dog foods sold online appears to be poor, carrying considerable amounts of potentially zoonotic bacteria and reaching greater levels of bacterial contaminations if not kept at proper refrigeration temperatures and fed soon after defrosting.

Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico

BACKGROUND

Burkholderia pseudomallei is a soil-dwelling bacterium and the causative agent of melioidosis. The global burden and distribution of melioidosis is poorly understood, including in the Caribbean. B. pseudomallei was previously isolated from humans and soil in eastern Puerto Rico but the abundance and distribution of B. pseudomallei in Puerto Rico as a whole has not been thoroughly investigated.

METHODOLOGY/PRINCIPAL FINDINGS

We collected 600 environmental samples (500 soil and 100 water) from 60 sites around Puerto Rico. We identified B. pseudomallei by isolating it via culturing and/or using PCR to detect its DNA within complex DNA extracts. Only three adjacent soil samples from one site were positive for B. pseudomallei with PCR; we obtained 55 isolates from two of these samples. The 55 B. pseudomallei isolates exhibited fine-scale variation in the core genome and contained four novel genomic islands. Phylogenetic analyses grouped Puerto Rico B. pseudomallei isolates into a monophyletic clade containing other Caribbean isolates, which was nested inside a larger clade containing all isolates from Central/South America. Other Burkholderia species were commonly observed in Puerto Rico; we cultured 129 isolates from multiple soil and water samples collected at numerous sites around Puerto Rico, including representatives of B. anthina, B. cenocepacia, B. cepacia, B. contaminans, B. glumae, B. seminalis, B. stagnalis, B. ubonensis, and several unidentified novel Burkholderia spp.

CONCLUSIONS/SIGNIFICANCE

B. pseudomallei was only detected in three soil samples collected at one site in north central Puerto Rico with only two of those samples yielding isolates. All previous human and environmental B. pseudomallei isolates were obtained from eastern Puerto Rico. These findings suggest B. pseudomallei is ecologically established and widely dispersed in the environment in Puerto Rico but rare. Phylogeographic patterns suggest the source of B. pseudomallei populations in Puerto Rico and elsewhere in the Caribbean may have been Central or South America.

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

Clostridioides difficile is a ubiquitous, diarrhoeagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of C. difficile cases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in the C. difficile multilocus sequence typing scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat unrelated infections, which creates conditions ideal for C. difficile colonization and proliferation. In this study, we analysed 27 isolates from a healthcare network in northern Arizona, USA, and 1352 publicly available ST1 genomes to place locally sampled isolates into a global context. Whole genome, single nucleotide polymorphism analysis demonstrated that at least six separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates, which were only identified via whole genome sequence analysis. Antibiotic resistance heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally and in northern Arizona, we compared all high-quality C. difficile genomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all other C. difficile genomes; analyses of other toxigenic C. difficile sequence types demonstrate that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type with C. difficile infection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinical C. difficile isolates provides a high-resolution surveillance strategy for monitoring persistence and transmission of C. difficile and for assessing the performance of infection prevention and control strategies.

Characterization of Clostridioides difficile ribotypes in domestic dogs in Rio de Janeiro, Brazil

Clostridioides difficile is the major etiologic agent of nosocomial bacterial diarrhoea and pseudomembranous colitis. The pathogenesis of C. difficile infection (CDI)involves two cytotoxic enzymes (TcdA, TcdB) that cause colonic epithelial damage, fluid accumulation and enteritis. CDI has been demonstrated in a variety of animal species and some reports have recently raised the importance of wild animals as a reservoir of this pathogen and possible transmission to humans and domestic animals. The aim of this study was to characterize C. difficile isolates obtained from pet dogs in Rio de Janeiro, Brazil. A total of 50 faecal samples were obtained from healthy and diarrheic dogs. Five of fifty samples (10%) grew C. difficile. Of those, three belonged to the PCR ribotype 106 (ST 42) and were toxigenic (A⁺B⁺). The other two strains belonged to the PCR ribotype 010 (ST 15) and were not toxin producers (A^-B^-). None of the isolates tested positive for the binary toxin genes. Considering the antimicrobial resistance patterns of all isolates using EUCAST breakpoints, all strains were sensitive to metronidazole and vancomycin. However, two strains (ribotype 106 and ribotype 010), were resistant to clindamycin (≤256 μg/mL). All strains were strong biofilm producers. Our study provides evidence that dogs can act as reservoirs for C. difficile epidemic ribotypes.

Molecular epidemiology of Clostridioides difficile in domestic dogs and zoo animals

Animals such as domestic dogs and zoo animals reside in close proximity to humans and could contribute to the dissemination of Clostridioides difficile spores which are common in the community environment. The purpose of this study was to assess C. difficile colonization in domestic dogs attending a day boarding facility and zoo animals receiving systemic antibiotics. Stool samples and paw swabs were collected from dogs who attended a day boarding facility. Stool samples were also collected from zoo animals starting systemic antibiotics. Finally, environmental samples were collected from nearby public parks. Stool samples and swabs were incubated anaerobically in enrichment broth for C. difficile growth, PCR was done to confirm presence of toxin genes, and PCR ribotyping was performed for strain characterization. During the study period, 136 dog stool samples were obtained, the paws of 16 dogs were swabbed, and 250 environmental swabs from surrounding public parks were obtained. Twenty-three of 136 dog stool samples (17%) and 9 of 16 dog paws sampled (56%) grew toxigenic C. difficile. One hundred and four stool samples from 49 zoo animals were collected of which 19 (18%) grew toxigenic C. difficile. Rates of toxigenic C. difficile colonization increased significantly during antibiotic therapy (33%) and then returned to baseline during the follow-up (11%) period (p = 0.019). Fifty-five of 250 environmental swabs from public parks (22%) grew toxigenic C. difficile. Ribotypes associated with human disease including 106 and 014-020 were isolated from all sources. This study demonstrated a high rate of toxigenic C. difficile colonization in domestic dogs and zoo animals with ribotypes similar to those causing human disease. These results demonstrate the relationship between humans, animals, and the environment in the dissemination of spores.

Diversity, Virulence, and Antimicrobial Resistance in Isolates From the Newly Emerging Klebsiella pneumoniae ST101 Lineage

The global dissemination of Klebsiella pneumoniae and Klebsiella pneumoniae carbapenemase (KPC) has been largely attributed to a few high-risk sequence types (STs) (ST258, ST11, ST512) associated with human disease. ST101 is an emerging clone that has been identified in different parts of the world with the potential to become a global, persistent public health threat. Recent research suggests the ST101 lineage is associated with an 11% increase in mortality rate in comparison to non-ST101 infections. In this study, we generated a high-quality, near-finished genome assembly of a multidrug-resistant (MDR) isolate from Italy (isolate 4743) that is a single locus variant of ST101 (ST1685). We demonstrate that the 4743 genome contains virulence features such as an integrative conjugative element carrying the yersiniabactin siderophore (ICEKp3), the mannose-resistant Klebsiella-like (type III) fimbriae cluster (mrkABCDFHIJ), the ferric uptake system (kfuABC), the yersiniabactin receptor gene fyuA, a capsular K type K17, and an O antigen type of O1. K. pneumoniae 4743 carries the blaKPC-2 carbapenemase gene along with genes conferring resistance to aminoglycosides, beta-lactams, fluoroquinolones, fosfomycin, macrolides, lincosamides, and streptogramin B. A comparative genomics analysis of 44 ST101 genomes as well as newly sequenced isolate 4743 identified variable antimicrobial resistance (AMR) resistance profiles and incompatibility plasmid types, but similar virulence factor profiles. Using Bayesian methodologies, we estimate the common ancestor for the ST101 lineage emerged in 1990 (95% HPD: 1965 to 2007) and isolates within the lineage acquired bla KPC after the divergence from its parental clonal group and dissemination. The identification of virulence factors and antibiotic resistance genes acquired by this newly emerging clone provides insight into the reported increased mortality rates and highlights its potential success as a persistent nosocomial pathogen. With a combination of both colistin resistance, carbapenem resistance, and several known virulence factors, the ST101 genetic repertoire may be a "perfect storm" allowing for a newly emerging, high-risk, extensively antibiotic resistant clone. This high-risk clone appears adept at acquiring resistance and may perpetuate the dissemination of extensive antimicrobial resistance. Greater focus on the acquisition of virulence factors and antibiotic resistance genes is crucial for understanding the spread of antibiotic resistance.

A single introduction of Yersinia pestis to Brazil during the 3rd plague pandemic

Yersinia pestis was introduced to Brazil during the third plague pandemic and currently exists in several recognized foci. There is currently limited available phylogeographic data regarding Y. pestis in Brazil. We generated whole genome sequences for 411 Y. pestis strains from six Brazilian foci to investigate the phylogeography of Y. pestis in Brazil; these strains were isolated from 1966 to 1997. All 411 strains were assigned to a single monophyletic clade within the 1.ORI population, indicating a single Y. pestis introduction was responsible for the successful establishment of endemic foci in Brazil. There was a moderate level of genomic diversity but little population structure among the 411 Brazilian Y. pestis strains, consistent with a radial expansion wherein Y. pestis spread rapidly from the coast to the interior of Brazil and became ecologically established. Overall, there were no strong spatial or temporal patterns among the Brazilian strains. However, strains from the same focus tended to be more closely related and strains isolated from foci closer to the coast tended to fall in more basal positions in the whole genome phylogeny than strains from more interior foci. Overall, the patterns observed in Brazil are similar to other locations affected during the 3rd plague pandemic such as in North America and Madagascar.

Clostridium difficile colitis and zoonotic origins-a narrative review

Clostridium difficile is a major cause of hospital-associated diarrhoea, and in severe cases leads to pseudomembranous colitis and toxic megacolon. The frequency of C. difficile infection (CDI) has increased in recent decades, with 453 000 cases identified in 2011 in the USA. This is related to antibiotic-selection pressure, disruption of normal host intestinal microbiota and emergence of antibiotic-resistant C. difficile strains. The burden of community-acquired CDI has been increasingly appreciated, with disease identified in patients previously considered low-risk, such as young women or patients with no prior antibiotic exposure. C. difficile has been identified in livestock animals, meat products, seafood and salads. It has been postulated that the pool of C. difficile in the agricultural industry may contribute to human CDI. There is widespread environmental dispersal of C. difficile spores. Domestic households, turf lawns and public spaces are extensively contaminated, providing a potential reservoir for community-acquired CDI. In Australia, this is particularly associated with porcine-derived C. difficile UK PCR ribotype 014/020. In this article, the epidemiological differences between hospital- and community-acquired CDI are discussed, including some emerging evidence for community-acquired CDI being a possible zoonosis.

Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity

Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.

Clostridioides difficile infection in dogs with chronic-recurring diarrhea responsive to dietary changes

Five dogs with chronic-recurring diarrhea were positive for Clostridioides difficile infection (CDI), but were unresponsive to treatment with metronidazole. One of these animals was subjected to a colonoscopy, which revealed eosinophilic infiltration of the colon. All five animals completely recovered after dietary changes. The present work suggests that CDI might occur in dogs with other intestinal alterations. In addition, this report suggests that dysbiosis should be considered in animals that have chronic-recurring diarrhea and test positive for C. difficile.

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C. difficile infection (CDI) in dogs are still largely unknown.

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Five dogs with chronic-recurring diarrhea were positive for CDI.

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All animals completely recovered after dietary changes.

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Dysbiosis should be considered in dogs with chronic-recurring diarrhea and CDI.

Clostridium difficile Exposures, Colonization, and the Microbiome: Implications for Prevention

New studies have been published regarding the epidemiology of Clostridium difficile in topics such as asymptomatic C. difficile colonization, community-associated C. difficile infection, environmental contamination outside healthcare settings, animal colonization, and the interactions between C. difficile and the gut microbiome. In addition to summarizing these findings, this review offers a perspective on the potential impact of high-throughput sequencing and other potential techniques on the prevention of C. difficile.Infect Control Hosp Epidemiol 2018;39:596-602.

Understanding Clostridium difficile Colonization

Clostridium difficile is the main causative agent of antibiotic-associated and health care-associated infective diarrhea. Recently, there has been growing interest in alternative sources of C. difficile other than patients with Clostridium difficile infection (CDI) and the hospital environment. Notably, the role of C. difficile-colonized patients as a possible source of transmission has received attention. In this review, we present a comprehensive overview of the current understanding of C. difficile colonization. Findings from gut microbiota studies yield more insights into determinants that are important for acquiring or resisting colonization and progression to CDI. In discussions on the prevalence of C. difficile colonization among populations and its associated risk factors, colonized patients at hospital admission merit more attention, as findings from the literature have pointed to their role in both health care-associated transmission of C. difficile and a higher risk of progression to CDI once admitted. C. difficile colonization among patients at admission may have clinical implications, although further research is needed to identify if interventions are beneficial for preventing transmission or overcoming progression to CDI.

Preliminary studies on isolates of Clostridium difficile from dogs and exotic pets

Background

Clostridium difficile infection (CDI) is recognised as an emerging disease in both humans and some animal species. During the past few years, insights into human CDI epidemiology changed and C. difficile is also considered as an emerging community-acquired pathogen. Certain ribotypes (RT) are possibly associated with zoonotic transmission. The objective of this study was to assess the presence of C. difficile in a population of pets and to characterise the isolates.

Results

Faecal samples from a total of 90 diarrhoeic dogs and 24 from exotic animal species (both diarrhoeic and non-diarrhoeic) were analysed. Clostridium difficile was isolated from 6 (6.7%) dogs and one reptile sample (4.2%). Four (66.7%) of the six dog strains were capable of producing toxins. Four known different RTs were detected in dogs (010, 014, 123 and 358) and a new one was found in a faecal sample of an exotic animal. This new RT isolate was negative for all toxin genes tested and belonged to sequence type 347 which has been proposed as a Clade-III member. Importantly, two dog strains showed a stable resistance to metronidazole (initial MIC values: 128 and 48 μg/ml).

Conclusions

The results obtained in this study suggest the implementation of antimicrobial susceptibility surveillance programs to assess the prevalence of metronidazole resistance in dogs; molecular studies to elucidate C. difficile metronidazole resistance mechanisms are warranted. Based on the similarity between the ribotypes observed in dogs and those described in humans, the zoonotic transmission should be further explored. Furthermore, exotic animals have shown to harbor uncommon C. difficile strains which require further genomic studies.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1402-7) contains supplementary material, which is available to authorized users.

Aliyu S, F. Hadjirin N, A. Holmes M, Török E, M. Brown N, Parkhill J, Peacock S. Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages

There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C. difficile from 65 patients were highly diverse and that most cases were not linked to other active cases in the hospital. In total, 186 C. difficile isolates were isolated from effluent water obtained from 18 municipal treatment plants at the point of release into the environment. Whole genome comparisons of clinical and environmental isolates demonstrated highly related populations, and confirmed extensive release of toxigenic C. difficile into surface waters. An analysis based on multilocus sequence types (STs) identified 19 distinct STs in the clinical collection and 38 STs in the wastewater collection, with 13 of 44 STs common to both clinical and wastewater collections. Furthermore, we identified five pairs of highly similar isolates (≤2 SNPs different in the core genome) in clinical and wastewater collections. Strategies to control community acquisition should consider the need for bacterial control of treated wastewater.

New insights into transmission of Clostridium difficile infection-narrative review

BACKGROUND

Traditionally, Clostridium difficile has been considered a typical healthcare-associated pathogen-that is, one transmitted within healthcare facilities and thus prevented by implementation of standard infection control measures. Recently this concept has been challenged by studies suggesting a relevant role for community acquisition of C. difficile.

AIMS

To discusses the current literature, compiled during the last decade, reporting on sources of acquisition of C. difficile and subsequent transmission.

SOURCES

The databases PubMed, Medline, Embase and the Cochrane Database were searched for articles published from 1 January 2007 to 30 June 2017 reporting on possible transmission pathways of C. difficile and/or suggesting a source of acquisition of C. difficile. All study types reporting on adult populations were considered; case reports and series were excluded. The PRISMA guidelines for the reporting of systematic reviews were followed.

CONTENT

Among 24 original articles included, 63% report on transmission of C. difficile in healthcare settings and 37% investigate sources and transmission of C. difficile in the community. Contact with symptomatic carriers (53.3%), the hospital environment (40.0%) and asymptomatic carriers (20%) were the most commonly reported transmission pathways within healthcare settings. The leading sources for acquisition of C. difficile in the community include direct contact with symptomatic and asymptomatic carriers in the community, including infants (30%) and residents of long-term non-acute care facilities (30%), followed by contact with contaminated environments in outpatient care settings (20%) and exposure to livestock or livestock farms (20%).

IMPLICATIONS

In healthcare settings, future control efforts may need to focus on extending cleaning and disinfection procedures beyond the immediate surroundings of symptomatic carriers. Potential targets to prevent acquisition of C. difficile in the community include household settings, long-term care facilities and outpatient settings, while the role of livestock in entertaining transmission requires further investigation.

The incidence of Clostridioides difficile and Clostridium perfringens netF-positive strains in diarrheic dogs

The aim of this study was to examine the incidence of Clostridioides (previously Clostridium) difficile and Clostridium perfringens in the feces of diarrheic and non-diarrheic dogs. Also, the presence of other common canine enteropathogens was examined. Toxigenic C. difficile and C. perfringens positive for the NetF-encoding gene (netF) were detected in 11 (11.9%) and seven (7.6%) diarrheic dogs, respectively. Three dogs were diagnosed simultaneously with toxigenic C. difficile and netF-positive C. perfringens. Among other enteropathogens, Giardia sp. was the most common agent detected in dogs positive for toxigenic C. difficile or netF-positive C. perfringens. The results suggest that C. difficile and C. perfringens occur more frequently as a primary cause of diarrhea.

Evidence-Based Practice in the Treatment for Antibiotic-Associated Diarrhea in the Intensive Care Unit

Unit nurses provide care to patients with serious health conditions. Often antibiotics are recommended to fight infections. Sometimes patients are on proton pump inhibitors (PPI). Antibiotics and PPIs may lead to diarrhea, causing the patient more discomfort, and possibly leading to a more serious infection. One serious infection is caused by Clostridium difficile, which causes death in some cases. About 75% of patients on antibiotics may not need antibiotics. Several studies showed less diarrhea in patients on probiotics. However, probiotics cause harm to some patients, which needs to be considered. Nurses need to ensure that antibiotic stewardship is followed.

Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay

Diverse members of the genus Clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species of clostridia produce BoNTs, the majority of human botulism cases have been attributed to Clostridium botulinum groups I and II. Recent comparative genomic studies have demonstrated the genomic diversity within these BoNT-producing species. This report introduces a multiplex PCR assay for differentiating members of C. botulinum group I, C. sporogenes, and two major subgroups within C. botulinum group II. Coding region sequences unique to each of the four species/subgroups were identified by in silico analyses of thousands of genome assemblies, and PCR primers were designed to amplify each marker. The resulting multiplex PCR assay correctly assigned 41 tested isolates to the appropriate species or subgroup. A separate PCR assay to determine the presence of the ntnh gene (a gene associated with the botulinum neurotoxin gene cluster) was developed and validated. The ntnh gene PCR assay provides information about the presence or absence of the botulinum neurotoxin gene cluster and the type of gene cluster present (ha positive [ha⁺] or orfX⁺). The increased availability of whole-genome sequence data and comparative genomic tools enabled the design of these assays, which provide valuable information for characterizing BoNT-producing clostridia. The PCR assays are rapid, inexpensive tests that can be applied to a variety of sample types to assign isolates to species/subgroups and to detect clostridia with botulinum neurotoxin gene (bont) clusters.

IMPORTANCE Diverse clostridia produce the botulinum neurotoxin, one of the most potent known neurotoxins. In this study, a multiplex PCR assay was developed to differentiate clostridia that are most commonly isolated in connection with human botulism cases: C. botulinum group I, C. sporogenes, and two major subgroups within C. botulinum group II. Since BoNT-producing and nontoxigenic isolates can be found in each species, a PCR assay to determine the presence of the ntnh gene, which is a universally present component of bont gene clusters, and to provide information about the type (ha⁺ or orfX⁺) of bont gene cluster present in a sample was also developed. The PCR assays provide simple, rapid, and inexpensive tools for screening uncharacterized isolates from clinical or environmental samples. The information provided by these assays can inform epidemiological studies, aid with identifying mixtures of isolates and unknown isolates in culture collections, and confirm the presence of bacteria of interest.