Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia.

Clostridioides difficile infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of C. difficile ribotypes (RTs) 014/020 (n=169), 002 (n=77) and 056 (n=36), the three most prominent C. difficile strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLSB agents in vitro, but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, n=36) to 115.6 (RT002, ST8, n=77) and 315.9 (RT014/020, STs 2, 13, 14, 49, n=169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, n=14; RT002, n=3; RT056, n=2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse C. difficile strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.

Identifying Contact Time Required for Secondary Transmission of Clostridioides difficile Infections by Using Real-Time Locating System.

Considering patient room shortages and prevalence of other communicable diseases, reassessing the isolation of patients with Clostridioides difficile infection (CDI) is imperative. We conducted a retrospective study to investigate the secondary CDI transmission rate in a hospital in South Korea, where patients with CDI were not isolated. Using data from a real-time locating system and electronic medical records, we investigated patients who had both direct and indirect contact with CDI index patients. The primary outcome was secondary CDI transmission, identified by whole-genome sequencing. Among 909 direct and 2,711 indirect contact cases, 2 instances of secondary transmission were observed (2 [0.05%] of 3,620 cases), 1 transmission via direct contact and 1 via environmental sources. A low level of direct contact (113 minutes) was required for secondary CDI transmission. Our findings support the adoption of exhaustive standard preventive measures, including environmental decontamination, rather than contact isolation of CDI patients in nonoutbreak settings.

Whole-Genome Sequencing Reveals the High Nosocomial Transmission and Antimicrobial Resistance of Clostridioides difficile in a Single Center in China, a Four-Year Retrospective Study.

Clostridioides difficile, which causes life-threatening diarrheal disease, presents an urgent threat to health care systems. In this study, we present a retrospective genomic and epidemiological analysis of C. difficile in a large teaching hospital. First, we collected 894 nonduplicate fecal samples from patients during a whole year to elucidate the C. difficile molecular epidemiology. We then presented a detailed description of the population structure of C. difficile based on 270 isolates separated between 2015 and 2020 and clarified the genetic and phenotypic features by MIC and whole-genome sequencing. We observed a high carriage rate (19.4%, 173/894) of C. difficile among patients in this hospital. The population structure of C. difficile was diverse with a total of 36 distinct STs assigned. In total, 64.8% (175/270) of the isolates were toxigenic, including four CDT-positive (C. difficile transferase) isolates, and 50.4% (135/268) of the isolates were multidrug-resistant. Statistically, the rates of resistance to erythromycin, moxifloxacin, and rifaximin were higher for nontoxigenic isolates. Although no vancomycin-resistant isolates were detected, the MIC for vancomycin was higher for toxigenic isolates (P < 0.01). The in-hospital transmission was observed, with 43.8% (110/251) of isolates being genetically linked to a prior case. However, no strong correlation was detected between the genetic linkage and epidemiological linkage. Asymptomatic colonized patients play the same role in nosocomial transmission as infected patients, raising the issue of routine screening of C. difficile on admission. This work provides an in-depth description of C. difficile in a hospital setting and paves the way for better surveillance and effective prevention of related diseases in China. IMPORTANCE Clostridioides difficile infections (CDI) are the leading cause of healthcare-associated diarrhea and are known to be resistant to multiple antibiotics. In the past decade, C. difficile has emerged rapidly and has spread globally, causing great concern among American and European countries. However, research on CDI remains limited in China. Here, we characterized the comprehensive spectrum of C. difficile by whole-genome sequencing (WGS) in a Chinese hospital, showing a high detection rate among patients, diverse genome characteristics, a high level of antibiotic resistance, and an unknown nosocomial transmission risk of C. difficile. During the study period, two C. difficile transferase (CDT)-positive isolates belonging to a new multilocus sequence type (ST820) were detected, which have caused serious clinical symptoms. This work describes C. difficile integrally and provides new insight into C. difficile surveillance based on WGS in China.

Genomic Analysis of Clostridioides difficile in 2 Regions of the United States Reveals a Diversity of Strains and Limited Transmission.

BACKGROUND: The distribution of Clostridioides difficile strains and transmission dynamics in the United States are not well defined. Whole-genome sequencing across 2 Centers for Disease Control and Prevention Emerging Infections Program C. difficile infection (CDI) surveillance regions (Minnesota and New York) was performed to identify predominant multilocus sequence types (MLSTs) in community-associated (CA) and healthcare-associated (HCA) disease and assess transmission. METHODS: Whole-genome sequencing was performed on C. difficile isolates from patients with CDI over 3 months between 2016 and 2017. Patients were residents of the catchment area without a positive C. difficile test in the preceding 8 weeks. CDI cases were epidemiologically classified as HCA or CA. RESULTS: Of 422 isolates, 212 (50.2%) were HCA and 203 (48.1%) were CA. Predominant MLSTs were sequence type (ST) 42 (9.3%), ST8 (7.8%), and ST2 (8.1%). MLSTs associated with HCA-CDI included ST1 (76%), ST53 (83.3%), and ST43 (80.0%), while those associated with CA-CDI included ST3 (76.9%) and ST41 (77.8%). ST1 was more frequent in New York than in Minnesota (10.8% vs 3.1%). Thirty-three pairs were closely related genomically, 14 of which had potential patient-to-patient transmission supported by record review. CONCLUSIONS: The genomic epidemiology of C. difficile across 2 regions of the United States indicates the presence of a diverse strain profile and limited direct transmission.

Mathematically modeling the effect of touch frequency on the environmental transmission of Clostridioides difficile in healthcare settings.

Clostridioides difficile, formerly Clostridium difficile, is the leading cause of infectious diarrhea and one of the most common healthcare acquired infections in United States hospitals. C. difficile persists well in healthcare environments because it forms spores that can survive for long periods of time and can be transmitted to susceptible patients through contact with contaminated hands and fomites, objects or surfaces that can harbor infectious agents. Fomites can be classified as high-touch or low-touch based on the frequency they are contacted. The mathematical model in this study investigates the relative contribution of high-touch and low-touch fomites on new cases of C. difficile colonization among patients of a hospital ward. The dynamics of transmission are described by a system of ordinary differential equations representing four patient population classes and two pathogen environmental reservoirs. Parameters that have a significant effect on incidence, as determined by a global sensitivity analysis, are varied in stochastic simulations of the system to identify feasible strategies to prevent disease transmission. Results indicate that on average, under one-quarter of asymptomatically colonized patients are exposed to C. difficile via low-touch fomites. In comparison, over three-quarters of colonized patients are colonized through high-touch fomites, despite additional cleaning of high-touch fomites. Increased contacts with high-touch fomites increases the contribution of these fomites to the incidence of colonized individuals and decreasing the duration of a hospital visit reduces the amount of pathogen in the environment. Thus, enhanced efficacy of disinfection upon discharge and extra cleaning of high-touch fomites, reduced contact with high-touch fomites, and higher discharge rates, among other control measures, could lead to a decrease in the incidence of colonized individuals.

A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains.

Clostridioides difficile is the leading cause of healthcare-associated infectious diarrhoea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare environments, and that the primary sites of C. difficile transmission may be strain-dependent. We conducted a multisite genomic epidemiology study to assess differential genomic evidence of healthcare vs community spread for two of the most common C. difficile strains in the USA: sequence type (ST) 1 (associated with ribotype 027) and ST2 (associated with ribotype 014/020). We performed whole-genome sequencing and phylogenetic analyses on 382 ST1 and ST2 C. difficile isolates recovered from stool specimens collected during standard clinical care at 3 geographically distinct US medical centres between 2010 and 2017. ST1 and ST2 isolates both displayed some evidence of phylogenetic clustering by study site, but clustering was stronger and more apparent in ST1, consistent with our healthcare-based study more comprehensively sampling local transmission of ST1 compared to ST2 strains. Analyses of pairwise single-nucleotide variant (SNV) distance distributions were also consistent with more evidence of healthcare transmission of ST1 compared to ST2, with 44 % of ST1 isolates being within two SNVs of another isolate from the same geographical collection site compared to 5.5 % of ST2 isolates (P-value=<0.001). Conversely, ST2 isolates were more likely to have close genetic neighbours across disparate geographical sites compared to ST1 isolates, further supporting non-healthcare routes of spread for ST2 and highlighting the potential for misattributing genomic similarity among ST2 isolates to recent healthcare transmission. Finally, we estimated a lower evolutionary rate for the ST2 lineage compared to the ST1 lineage using Bayesian timed phylogenomic analyses, and hypothesize that this may contribute to observed differences in geographical concordance among closely related isolates. Together, these findings suggest that ST1 and ST2, while both common causes of C. difficile infection in hospitals, show differential reliance on community and hospital spread. This conclusion supports the need for strain-specific criteria for interpreting genomic linkages and emphasizes the importance of considering differences in the epidemiology of circulating strains when devising interventions to reduce the burden of C. difficile infections.

Genomic evolution and virulence association of Clostridioides difficile sequence type 37 (ribotype 017) in China.

Clostridioides difficile sequence type (ST) 37 (ribotype 017) is one of the most prevalent genotypes circulating in China. However, its genomic evolution and virulence determinants were rarely explored. Whole-genome sequencing, phylogeographic and phylogenetic analyses were conducted for C. difficile ST37 isolates. The 325 ST37 genomes from six continents, including North America (n = 66), South America (n = 4), Oceania (n = 7), Africa (n = 9), Europe (n = 138) and Asia (n = 101), were clustered into six major lineages, with region-dependent distributions, harbouring an array of antibiotic-resistance genes. The ST37 strains from China were divided into four distinct sublineages, showing five importation times and international sources. Isolates associated with severe infections exhibited significantly higher toxin productions, tcdB mRNA levels, and sporulation capacities (P < 0.001). Kyoto Encyclopedia of Genes and Genomes analysis showed 10 metabolic pathways were significantly enriched in the mutations among isolates associated with severe CDI (P < 0.05). Gene mutations in glycometabolism, amino acid metabolism and biosynthesis virtually causing instability in protein activity were correlated positively to the transcription of tcdR and negatively to the expression of toxin repressor genes, ccpA and codY. In summary, our study firstly presented genomic insights into genetic characteristics and virulence association of C. difficile ST37 in China. Gene mutations in certain important metabolic pathways are associated with severe symptoms and correlated with higher virulence in C. difficile ST37 isolates.

Densitometric analysis of rep-PCR data: Insight into genetic variability and transmission of Clostridium perfringens typed with an improved multiplex PCR.

An epidemiological study was conducted in North-East India (part of Indo-Burma biodiversity hotspot) to better understand the distribution, diversity, and transmission of Clostridium perfringens among livestock, pets, wild animals (captive), and humans. A total of 160 C. perfringens isolates were recovered from 642 diarrhoeic faecal samples with an isolation rate of 24.92%. Isolation rate was the highest among captive wild animals (37.5%) followed by dog (34.6%), human (33.8%), pig (32.7%), cattle (20.8%), goat (18.3%) and poultry (9.3%). Isolates were toxin typed using a seven gene multiplex PCR designed for simultaneous detection of cpa, cpb, cpb2, etx, iap, cpe and netB. The majority of isolates, 128 (80%) were of type A, followed by 17 (10.62%), 5 (3.12%), 4 (2.5%), 3 (1.87%), 2 (1.25%) and 1 (0.63%) isolates of type C, D, E, G, F and B, respectively. Beta 2 toxin gene was present in 65 (50%) of type A isolates, followed by 7 (41.2%), 4 (80%), 1(25%), and 1 (100%) of type C, D, G and B isolates, respectively. Beta 2 toxin has a high prevalence among dogs (28.6%), cattle (27.3%), and pig (20.8%) compared to humans, goat, wild animals, and poultry (1.2-14.3%). The prevalence of CPE and NetB toxin-positive strains was low, with only 3 (1.8%) and 5 (3.1%) isolates, respectively. Association of C. perfringens with diarrhoea in Civet Cat, Golden Langur, and Gray Langur has been reported for the first time. The genetic diversity and transmission of isolates were investigated using automated rep-PCR (Diversilab®, bioMérieux) using two densitometry-based matrices: modified Kullback-Leibler (KL) and Pearson's correlation (PC). The PC and modified KL matrices formed three distinct clusters with 59% and 27.2% similarity, respectively. C. perfringens diversity and transmission were best studied using modified KL matrix that placed more emphasis on the presence of bands rather than intensity. However, the PC method was found to be more suitable for differentiating strains within a toxin type, with slightly higher D-values.

Association of Visitor Contact Precautions With Estimated Hospital-Onset Clostridioides difficile Infection Rates in Acute Care Hospitals.

Importance: Visitor contact precautions (VCPs) are commonly used to reduce the transmission of Clostridioides difficile at health care institutions. Implementing VCPs requires considerable personnel and personal protective equipment resources. However, it is unknown whether VCPs are associated with reduced hospital-onset C difficile infection (HO-CDI) rates. Objective: To estimate the association between VCPs and HO-CDI rates using simulation modeling. Design, Setting, and Participants: This simulation study, conducted between July 27, 2020, and August 11, 2020, used an established agent-based simulation model of C difficile transmission in a 200-bed acute care adult hospital to estimate the association between VCPs and HO-CDI while varying assumptions about factors such as patient susceptibility, behavior, and C difficile transmission. The model simulated hospital activity for 1 year among a homogeneous, simulated adult population. Interventions: No VCP use vs ideal use of VCPs under different hospital configurations. Main Outcomes and Measures: The rate of HO-CDI per 10 000 patient-days according to the Centers for Disease Control and Prevention's definition of HO-CDI. Results: With use of the simulation model, the baseline rate of HO-CDI was 7.94 10 000 patient-days (95% CI, 7.91-7.98 per 10 000 patient-days) with no VCP use compared with 7.97 per 10 000 patient-days (95% CI, 7.93-8.01 per 10 000 patient-days) with ideal VCP use. Visitor contact precautions were not associated with a reduction of more than 1% in HO-CDI rates in any of the tested scenarios and hospital settings. Independently increasing the hand-hygiene compliance of the average health care worker and environmental cleaning compliance by no more than 2% each was associated with greater HO-CDI reduction compared with all other scenarios, including VCPs. Conclusions and Relevance: In this simulation study, the association between VCPs and HO-CDI was minimal, but improvements in health care worker hand hygiene and environmental cleaning were associated with greater reductions in estimated HO-CDI. Hospitals may achieve a higher rate of reduction for HO-CDI by focusing on making small improvements in compliance with interventions other than VCP.

Clostridioides difficile on dairy farms and potential risk to dairy farm workers.

Clostridioides difficile causes severe colitis in people and is a significant enteric pathogen in many species of animals, including swine, horses, and potentially cattle. C. difficile is shed in feces, and transmission occurs horizontally via the fecal-oral route. Livestock has been suggested as a potential reservoir for C. difficile, and while studies have shown that swine and farm workers can be colonized with identical clones of C. difficile, the zoonotic transmission of C. difficile from livestock to people has not been definitively demonstrated. The goal of this study was to determine whether dairy calves and dairy farm workers harbored genetically similar isolates of C. difficile. First, we validated a glove juice protocol for detecting C. difficile on farm workers' hands. We then visited 23 farms and collected 1) fecal samples from 92 dairy calves, 2) hand rinsates from 38 dairy farm workers, and 3) fecal samples from five of the dairy farm workers who were willing to submit them. All samples underwent anaerobic culture and qPCR to detect C. difficile. C. difficile was detected on 15 of the farms (65.2%, 95% confidence interval (CI) 42.7%-83.6%) and in 28 calves (30.4%, 95% CI 21.2-40.9%) but in none of the hand rinsates or human fecal samples. Thus, the zoonotic transmission of C. difficile on dairy farms could not be demonstrated, and dairy farmers did not appear to be at increased risk of acquiring C. difficile via the fecal-oral route.

Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission.

Fitting stochastic transmission models to electronic patient data can offer detailed insights into the transmission of healthcare-associated infections and improve infection control. Pathogen whole-genome sequencing may improve the precision of model inferences, but computational constraints have limited modelling applications predominantly to small datasets and specific outbreaks, whereas large-scale sequencing studies have mostly relied on simple rules for identifying/excluding plausible transmission. We present a novel approach for integrating detailed epidemiological data on patient contact networks in hospitals with large-scale pathogen sequencing data. We apply our approach to study Clostridioides difficile transmission using a dataset of 1223 infections in Oxfordshire, UK, 2007-2011. 262 (21% [95% credibility interval 20-22%]) infections were estimated to have been acquired from another known case. There was heterogeneity by sequence type (ST) in the proportion of cases acquired from another case with the highest rates in ST1 (ribotype-027), ST42 (ribotype-106) and ST3 (ribotype-001). These same STs also had higher rates of transmission mediated via environmental contamination/spores persisting after patient discharge/recovery; for ST1 these persisted longer than for most other STs except ST3 and ST42. We also identified variation in transmission between hospitals, medical specialties and over time; by 2011 nearly all transmission from known cases had ceased in our hospitals. Our findings support previous work suggesting only a minority of C. difficile infections are acquired from known cases but highlight a greater role for environmental contamination than previously thought. Our approach is applicable to other healthcare-associated infections. Our findings have important implications for effective control of C. difficile.

Prevention of Clostridioides difficile in hospitals: A position paper of the International Society for Infectious Diseases.

Clostridioides difficile infection is an increasing presence worldwide. Prevention is multipronged, reflecting a complex and evolving epidemiology. Multiple guidelines exist regarding the prevention of C. difficile infection in healthcare settings; however, existing guidelines do not address C. difficile in low- and middle-income countries (LMIC). Nevertheless, the prevalence of C. difficile in LMIC likely parallels, if not exceeds, that of high-income countries, and LMIC may experience additional challenges in C. difficile diagnosis and control. A panel of experts was convened by the International Society for Infectious Diseases (ISID) to review the current state of C. difficile infections globally and make evidence-based recommendations for infection prevention that are broadly applicable.

Whole genome sequencing of Clostridioides difficile PCR ribotype 046 suggests transmission between pigs and humans.

BACKGROUND: A zoonotic association has been suggested for several PCR ribotypes (RTs) of Clostridioides difficile. In central parts of Sweden, RT046 was found dominant in neonatal pigs at the same time as a RT046 hospital C. difficile infection (CDI) outbreak occurred in the southern parts of the country. OBJECTIVE: To detect possible transmission of RT046 between pig farms and human CDI cases in Sweden and investigate the diversity of RT046 in the pig population using whole genome sequencing (WGS). METHODS: WGS was performed on 47 C. difficile isolates from pigs (n = 22), the farm environment (n = 7) and human cases of CDI (n = 18). Two different core genome multilocus sequencing typing (cgMLST) schemes were used together with a single nucleotide polymorphisms (SNP) analysis and the results were related to time and location of isolation of the isolates. RESULTS: The pig isolates were closely related (≤6 cgMLST alleles differing in both cgMLST schemes) and conserved over time and were clearly separated from isolates from the human hospital outbreak (≥76 and ≥90 cgMLST alleles differing in the two cgMLST schemes). However, two human isolates were closely related to the pig isolates, suggesting possible transmission. The SNP analysis was not more discriminate than cgMLST. CONCLUSION: No general pattern suggesting zoonotic transmission was apparent between pigs and humans, although contrasting results from two isolates still make transmission possible. Our results support the need for high resolution WGS typing when investigating hospital and environmental transmission of C. difficile.

Comparing intervention strategies for reducing Clostridioides difficile transmission in acute healthcare settings: an agent-based modeling study.

BACKGROUND: Clostridioides difficile infection (CDI) is one of the most common healthcare infections. Common strategies aiming at controlling CDI include antibiotic stewardship, environmental decontamination, and improved hand hygiene and contact precautions. Mathematical models provide a framework to evaluate control strategies. Our objective is to evaluate the effectiveness of control strategies in decreasing C. difficile colonization and infection using an agent-based model in an acute healthcare setting. METHODS: We developed an agent-based model that simulates the transmission of C. difficile in medical wards. This model explicitly incorporates healthcare workers (HCWs) as vectors of transmission, tracks individual patient antibiotic histories, incorporates varying risk levels of antibiotics with respect to CDI susceptibility, and tracks contamination levels of ward rooms by C. difficile. Interventions include two forms of antimicrobial stewardship, increased environmental decontamination through room cleaning, improved HCW compliance, and a preliminary assessment of vaccination. RESULTS: Increased HCW compliance with CDI patients was ranked as the most effective intervention in decreasing colonizations, with reductions up to 56%. Antibiotic stewardship practices were highly ranked after contact precaution compliance. Vaccination and reduction of high-risk antibiotics were the most effective intervention in decreasing CDI. Vaccination reduced CDI cases to up to 90%, and the reduction of high-risk antibiotics decreased CDI cases up to 23%. CONCLUSIONS: Overall, interventions that decrease patient susceptibility to colonization by C. difficile, such as antibiotic stewardship, were the most effective interventions in reducing both colonizations and CDI cases.

Evaluation of the Cost-effectiveness of Infection Control Strategies to Reduce Hospital-Onset Clostridioides difficile Infection.

Importance: Clostridioides difficile infection is the most common hospital-acquired infection in the United States, yet few studies have evaluated the cost-effectiveness of infection control initiatives targeting C difficile. Objective: To compare the cost-effectiveness of 9 C difficile single intervention strategies and 8 multi-intervention bundles. Design, Setting, and Participants: This economic evaluation was conducted in a simulated 200-bed tertiary, acute care, adult hospital. The study relied on clinical outcomes from a published agent-based simulation model of C difficile transmission. The model included 4 agent types (ie, patients, nurses, physicians, and visitors). Cost and utility estimates were derived from the literature. Interventions: Daily sporicidal cleaning, terminal sporicidal cleaning, health care worker hand hygiene, patient hand hygiene, visitor hand hygiene, health care worker contact precautions, visitor contact precautions, C difficile screening at admission, and reduced intrahospital patient transfers. Main Outcomes and Measures: Cost-effectiveness was evaluated from the hospital perspective and defined by 2 measures: cost per hospital-onset C difficile infection averted and cost per quality-adjusted life-year (QALY). Results: In this agent-based model of a simulated 200-bed tertiary, acute care, adult hospital, 5 of 9 single intervention strategies were dominant, reducing cost, increasing QALYs, and averting hospital-onset C difficile infection compared with baseline standard hospital practices. They were daily cleaning (most cost-effective, saving $358 268 and 36.8 QALYs annually), health care worker hand hygiene, patient hand hygiene, terminal cleaning, and reducing intrahospital patient transfers. Screening at admission cost $1283/QALY, while health care worker contact precautions and visitor hand hygiene interventions cost $123 264/QALY and $5 730 987/QALY, respectively. Visitor contact precautions was dominated, with increased cost and decreased QALYs. Adding screening, health care worker hand hygiene, and patient hand hygiene sequentially to the daily cleaning intervention formed 2-pronged, 3-pronged, and 4-pronged multi-intervention bundles that cost an additional $29 616/QALY, $50 196/QALY, and $146 792/QALY, respectively. Conclusions and Relevance: The findings of this study suggest that institutions should seek to streamline their infection control initiatives and prioritize a smaller number of highly cost-effective interventions. Daily sporicidal cleaning was among several cost-saving strategies that could be prioritized over minimally effective, costly strategies, such as visitor contact precautions.

Experimental inoculation and nose-to-nose transmission of Clostridioides difficile between weaned piglets.

In piglets, Clostridioides (C.) difficile infection presents mostly subclinical manifestation. As this agent became important in veterinary medicine due to a hypothesis of zoonosis, the objective of this study was to evaluate the transmission of C. difficile by nose-to-nose contact in young piglets. Six 20-day-old piglets were separated into three groups (infected, sentinel and control), and distributed in different isolation cabinets which allowed nose-to-nose contact only between infected and sentinel groups. The challenged group received an inoculum 106 CFU/mL of C. difficile 096 by oropharyngeal route. Rectal swab samples were daily collected for microbiological and molecular analysis. Euthanasia of all piglets was performed 18 days after challenge to evaluate anatomical, histological and microbiological lesions of the organs of these animals. The challenged and sentinel groups showed clinical signs of infection and genes encoding TcdB were detected by conventional PCR in both groups, confirming the transmission of the pathogen from the challenged to the sentinel piglets. At necropsy, tonsil, liver, spleen, mesenteric lymph nodes, ileocolic lymph nodes, jejunum, ileum, proximal colon, distal colon and cecum were collected for microbiological analysis; lesions were observed varying in degree and intensity. This study demonstrated a novel route of transmission of C. difficile between young piglets, which was proven to occur by nose-to-nose contact.

A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics.

Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled C. difficile genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of C. difficile at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals (P<10-4) or single wards (P=0.01) within hospitals, indicating they represented local transmission clusters. We also detected several HC2 clusters spanning more than one hospital that by retrospective epidemiological analysis were confirmed to be associated with inter-hospital patient transfers. In contrast, clustering at level HC150 correlated with k-mer-based classification and was largely compatible with PCR ribotyping, thus enabling comparisons to earlier surveillance data. EnteroBase enables contextual interpretation of a growing collection of assembled, quality-controlled C. difficile genome sequences and their associated metadata. Hierarchical clustering rapidly identifies database entries that are related at multiple levels of genetic distance, facilitating communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile.

Zinc Level and Its Role in Recurrent Clostridium difficile Infection: A Case Report and Literature Review.

Clostridium difficile infection is a common nosocomial infection in US hospitals, accounting for approximately 12 800 deaths annually in the United States. These infections are often associated with the use of antibiotics, which can alter the gut microbiome and thus render patients susceptible to C difficile infection. C difficile is often spread via fecal oral transmission. Multiple medications have been developed, but recurrence rates reach 60% after treatment. Recent data have shown that zinc supplementation decreases the recurrence of C difficile infection. In this article, we present a case of recurrent C difficile infection with zinc deficiency in which zinc supplementation improved the symptoms and reduced the incidence of recurrence.

Applying a mixed methods design to test saturation for qualitative data in health outcomes research.

Saturation, a core concept in qualitative research, suggests when data collection might end. It is reached when no new relevant information emerges with additional interviews. The aim of this research was to explore whether a mixed methods design could contribute to the demonstration of saturation. Firstly, saturation was conceptualized mathematically using set theory. Secondly, a conversion mixed design was conducted: a set of codes derived from qualitative interviews were quantitized and analyzed using partial least squares (PLS) regression to document whether saturation was reached. A qualitative study conducted by other researchers prior to this work (i.e. none of the present authors was involved in this study) was used to test saturation using PLS regression. This illustrative qualitative study aimed to investigate the impact of Clostridium difficile infection (CDI) on nurses' work in the hospital and the results were published elsewhere (Guillemin et al. 2015). Semi-structured interviews were conducted with 12 nurses. Saturation was characterized by the cumulative percentage of variability accounted for by PLS factors. After 12 interviews, this percentage was 51% which suggests that saturation was achieved at least on main themes. Two main themes identifying similarities in the experience of nurses caring for patients with CDI were identified: Organization/Coordination of the working day and Time-consuming work. Although dependent on the coding of qualitative data, PLS regression of quantitized data from qualitative interviews generated useful information for the determination of saturation.