18. Global Surveillance of Clostridioides difficile Demonstrates High Prevalence in Non-Healthcare Settings

Background Clostridioides difficile is a Gram-positive, spore-forming, toxin-producing organism that is the leading cause of healthcare-associated infections. However, past studies have isolated C. difficile spores from the community, suggesting an environmental reservoir that may play a role in transmission. This study aimed to examine the prevalence and strain types of C. difficile isolated from the United States (US) and internationally. Methods From 2014 to 2017, environmental swabs were collected from public areas, healthcare settings, and shoe soles. Samples were considered positive for C. difficile following growth on CCFA plates and confirmatory PCR testing for toxin genes and fluorescent PCR ribotyping (RT). The rate of C. difficile positivity and associated RT distribution were compared between settings, including shoe soles which were investigated for their potential role in environmental transmission. Results A total of 11,986 unique isolates were obtained primarily from the US (n=11,002; 92%) in addition to 11 other countries including Taiwan (n=200) and India (n=187). Samples were categorized as being from outdoor environments (n=2,992), private residences (n=2,772), shoe soles (n=1,420), public buildings (n=1,104) or acute care settings (n=3,698). Worldwide C. difficile sample positivity was 26% and was similar between US and non-US sampling sites. In the US, private residences (26.2%) and outdoor environments (24.1%) had the highest positivity rate compared to public buildings (17.2%). In a Texas sub-analysis (n=8,571), positivity rates were highest from outdoor samples (27%) and were similar between private residences (24%) and healthcare buildings (24%). The most prevalent RTs overall were F014-020 (16.4%), F106 (14.9%), and FP310 (11%). Shoe soles had the highest positivity rate (45%) with similar RT distribution between shoe soles and environmental samples. Conclusion Using a worldwide sample, 26% of environmental samples tested positive for toxigenic C. difficile strains from healthcare and non-healthcare sites. Community stewardship efforts will be needed to reduce the risk of CDI in vulnerable patients. Shoe sole sampling may be an ideal surveillance tool to test for emerging epidemic strains. Disclosures Kevin W. Garey, Pharm.D., M.S., FASHP, Summit Therapeutics (Research Grant or Support)

Soils, Biofortification, and Human Health Under COVID-19: Challenges and Opportunities

Soil is an important source of resources required for human health and well-being. Soil is also a major environmental reservoir of pathogenic organisms. This may include viruses like the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which through 2020 and 2021 created dramatic catastrophes worldwide as the causative agent of the coronavirus disease of 2019 (COVID-19). So, soil has both positive and negative impacts on human health. One of the major positive impacts is the transfer of nutrients from soil to plants, and from there to humans through their diet. Biofortification is able to enhance the levels of nutrients essential to human health in the crops we consume and represents a sustainable solution to address malnutrition, which in turn may strengthen the human immune system against COVID-19. This nutrient transfer works better when we have healthy soils. Therefore, soils and biofortification have important roles to play in combatting the COVID-19 pandemic. However, several questions still remain, such as what are the expected environmental impacts of COVID-19 on soil? Can SARS-CoV-2 be transmitted through soil, and under what conditions? Which soil processes and properties influence SARS-CoV-2 survival rates and times, as well as transmission? What are the specific links between soil health and COVID-19? What are the projected soil management scenarios in response to COVID-19? Questions such as these deserve more attention as the world seeks to recover from its most recent pandemic.

Amoebae as Targets for Toxins or Effectors Secreted by Mammalian Pathogens

Numerous microorganisms, pathogenic for mammals, come from the environment where they encounter predators such as free-living amoebae (FLA). The selective pressure due to this interaction could have generated virulence traits that are deleterious for amoebae and represents a weapon against mammals. Toxins are one of these powerful tools that are essential for bacteria or fungi to survive. Which amoebae are used as a model to study the effects of toxins? What amoeba functions have been reported to be disrupted by toxins and bacterial secreted factors? Do bacteria and fungi effectors affect eukaryotic cells similarly? Here, we review some studies allowing to answer these questions, highlighting the necessity to extend investigations of microbial pathogenicity, from mammals to the environmental reservoir that are amoebae.

Pandemic Vibrio cholerae Acquired Competitive Traits from an Environmental Vibrio Species

Background: Vibrio cholerae, the causative agent of cholera, is a human pathogen that thrives in estuarine environments. V. cholerae competes with neighboring microbes by the contact-dependent translocation of toxic effectors with the type VI secretion system (T6SS). Effector types are highly variable across V. cholerae strains, but all pandemic isolates encode the same set of distinct effectors. It is possible that acquisition of these effectors via horizontal gene transfer played a role in the development of pandemic V. cholerae. Results: We assessed the distribution of V. cholerae T6SS loci across multiple Vibrio species. We showed that the fish-pathogen V. anguillarum encodes all three V. cholerae core loci as well as two of the four additional auxiliary clusters. We further demonstrated that V. anguillarum shares T6SS effectors with V. cholerae, including every pandemic-associated V. cholerae effector. We identified a novel T6SS cluster (Accessory Aux1) that is widespread in V. anguillarum and encodes the pandemic V. cholerae effector TseL. We highlighted potential gene transfer events of Accessory Aux1 from V. anguillarum to V. cholerae. Finally, we showed that TseL from V. cholerae can be neutralized by the V. anguillarum Accessory Aux1 immunity protein and vice versa, indicating V. anguillarum as the donor of tseL to the V. cholerae species. Conclusions: V. anguillarum constitutes an environmental reservoir of pandemic-associated V. cholerae T6SS effectors. V. anguillarum and V. cholerae likely share an environmental niche, compete, and exchange T6SS effectors. Further, our findings highlight the fish as a potential reservoir of pandemic V. cholerae.

Outbreak of OXA-48-producing Enterobacterales in a haematological ward associated with an uncommon environmental reservoir, France, 2016 to 2019

The hospital water environment, including the wastewater drainage system, is increasingly reported as a potential reservoir for carbapenemase-producing Enterobacterales (CPE). We investigated a persistent outbreak of OXA-48 CPE (primarily Citrobacter freundii) in a haematological ward of a French teaching hospital by epidemiological, microbiological and environmental methods. Between January 2016 and June 2019, we detected 37 new OXA-48 CPE-colonised and/or ‑infected patients in the haematological ward. In October 2017, a unit dedicated to CPE-colonised and/or ‑infected patients was created. Eleven additional sporadic acquisitions were identified after this date without any obvious epidemiological link between patients, except in one case. Environmental investigations of the haematological ward (June–August 2018) identified seven of 74 toilets and one of 39 drains positive for OXA-48 CPE (seven C. freundii, one Enterobacter sakazakii, one Escherichia coli). Whole genome comparisons identified a clonal dissemination of OXA-48-producing C. freundii from the hospital environment to patients. In addition to strict routine infection control measures, an intensive cleaning programme was performed (descaling and bleaching) and all toilet bowls and tanks were changed. These additional measures helped to contain the outbreak. This study highlights that toilets can be a possible source of transmission of OXA-48 CPE.

The Important Role of Metal Ions for Survival of Francisella in Water within Amoeba Environment

Francisella tularensis is a gram-negative facultative intracellular bacterium that resists harsh environments. Several outbreaks of tularemia are linked to the consumption and contact with spring water. The number of F. tularensis in some waters is high, while in others, this bacterium does not survive. Except organic compounds, metals could be important for the survival of F. tularensis in water. Some Francisella strains showed the association with amoeba, which may act as the environmental reservoir. This study was aimed at following the role of metal ions and/or amoeba in the existence and replication of F. novicida in spring waters by growth kinetics, acquisition of metals, and ultrastructural analyses of bacteria. The bacteria showed a longer survival in water with higher initial concentrations of Mn and Zn. Although Mn and Zn were necessary for the survival of F. novicida, the results also showed that the bacterium does not grow in water with high levels of Zn. In contrast, high levels of Mn did not have such a negative effect on the survival of this bacterium in water. In addition, while F. novicida benefits presence of amoeba in spring water, the number of amoebae is decreasing in a coculture model with F. novicida.

Population genetics as a tool to elucidate pathogen reservoirs: Lessons from Pseudogymnoascus destructans, the causative agent of white-nose disease in bats

Emerging infectious diseases pose a major threat to human, animal, and plant health. The risk of species-extinctions increases when pathogens can survive in the absence of the host, for example in environmental reservoirs. However, identifying such reservoirs and modes of infection is often highly challenging. In this study, we investigated the presence and nature of an environmental reservoir for the ascomycete fungus Pseudogymnoascus destructans, the causative agent of white-nose disease. We also characterised the modes and timing of transmission of the pathogen; key elements to better understand the disease dynamics. Using 18 microsatellite markers, we determined the genotypic and genic (based on allele frequencies) differentiation between 1,497 P. destructans isolates collected from nine closely situated hibernacula in North-Eastern Germany. One hibernaculum was the focus of intensive sampling in which both the bats and walls of the site were sampled at regular intervals over five consecutive winter seasons (1,062 isolates). We found significant genic differentiation between sites and few multi-locus genotypes shared across hibernacula (genotypic differentiation). This demonstrates that each hibernaculum has an essentially unique population of the fungus. This would be expected if bats purge viable P. destructans over the summer, preventing the mixing and exchange of the pathogen in maternity colonies, where bats from all of the studied hibernacula meet. Results from the intensively sampled site show higher measures of genotypic richness on walls compared to bats, the absence of genic differentiation between bats and walls, and stable relative abundance of multi-locus genotypes over multiple winter seasons. This clearly implicates hibernacula walls as the main environmental reservoir of the pathogen, from which bats become re-infected annually.

Streamlined copper defenses make Bordetella pertussis reliant on custom-made operon

Copper is both essential and toxic to living beings, which tightly controls its intracellular concentration. At the host–pathogen interface, copper is used by phagocytic cells to kill invading microorganisms. We investigated copper homeostasis in Bordetella pertussis, which lives in the human respiratory mucosa and has no environmental reservoir. B. pertussis has considerably streamlined copper homeostasis mechanisms relative to other Gram-negative bacteria. Its single remaining defense line consists of a metallochaperone diverted for copper passivation, CopZ, and two peroxide detoxification enzymes, PrxGrx and GorB, which together fight stresses encountered in phagocytic cells. Those proteins are encoded by an original, composite operon assembled in an environmental ancestor, which is under sensitive control by copper. This system appears to contribute to persistent infection in the nasal cavity of B. pertussis-infected mice. Combining responses to co-occurring stresses in a tailored operon reveals a strategy adopted by a host-restricted pathogen to optimize survival at minimal energy expenditure.