Persistence of wastewater antibiotic resistant bacteria and their genes in human fecal material

Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.info:eu-repo/semantics/submittedVersio

Evaluation of possible risks of antibiotic resistance transmission to humans by wastewater-irrigated crops

A reutilização de águas residuais tratadas tem sido incentivada em todo o mundo, em particular para irrigação agrícola, porque pode ser uma fonte de água confiável e importante, principalmente em países sob estresse hídrico. Ainda se sabe pouco sobre os riscos associados à utilização de águas residuais tratadas, designadamente no que se refere à disseminação de bactérias resistentes a antibióticos (ARB) e genes de resistência a antibióticos (ARGs). Uma das principais consequências da disseminação através da irrigação agrícola utilizando águas residuais tratadas é a contaminação da cadeia alimentar humana. Atualmente, o conhecimento sobre a transmissão de ARB e ARGs para seres humanos a partir de fontes ambientais é escasso. No entanto, a reutilização de águas residuais surge como uma fonte potencial de transmissão direta ou indireta, principalmente através da cadeia alimentar humana. Esta tese explorou estas questões com base em pesquisa bibliográfica e em abordagens experimentais. O estudo foi planeado com o objetivo de inferir se as bactérias que sobrevivem nas águas residuais serão capazes de colonizar as plantas e se ARB isoladas de águas residuais e os respectivos ARGs poderiam persistir na presença da microbiota fecal autóctone de um indivíduo saudável. As hipóteses propostas para este trabalho foram as de que: 1) ARB e ARGs isoladas de águas residuais tratadas podem colonizar plantas e, eventualmente, estabelecer-se como endófitos; 2) ARGs de ARB isoladas de água residual tratada podem persistir na presença da microbiota fecal de um humano saudável. O argumento que suporta esta duas hipóteses é o de que, se ingeridas através de vegetais, as ARB e ARGs poderiam persistir no intestino humano. Utilizaram-se três abordagens principais para testar as hipóteses referidas: a) foi realizada pesquisa bibliográfica com termos de busca relacionados com bactérias endófitas, filtrada para variedades agrícolas edíveis e normalmente consumidas cruas, e que pertencessem a grupos bacterianos também reportados em águas residuais e no microbioma humano; b) analisou-se a presença de ARB e ARGs em isolados bacterianos em vegetais edíveis (agrião e morango prontos para consumo); e c) foi avaliada a persistência de ARGs transportados por ARB isoladas de efluentes na presença de microbiota fecal de uma criança saudável. A investigação baseada na literatura teve como objetivo explorar a diversidade de bactérias endofíticas associadas a diferentes habitats (plantas, águas residuais e microbioma Resumo x humano) e inferir a probabilidade de que as ARB e ARGs possam ser transferidos das águas residuais para as plantas e depois para os seres humanos (Capítulo 3). Este estudo bibliográfico permitiu compilar uma lista de bactérias endofíticas distribuídas por mais de 20 filos reportadas em mais de 45 variedades de vegetais. Como o estudo procurava explorar as possíveis vias de transmissão para humanos, a lista de espécies agrícolas encontradas na literatura foi reduzida apenas a plantas que podem ser consumidas cruas, como sejam alface, cenoura, rabanete, pepino e tomate. Com o objetivo de avaliar a probabilidade dessas plantas captarem bactérias que podem atuar como vetores de resistência a antibióticos, a presença dos grupos bacterianos identificados como endófitos foi também investigada em comunidades microbianas de águas residuais e em microbiomas humanos. Para grupos bacterianos, cuja ocorrência foi relatada nos três tipos de ambiente, endófitos de plantas edíveis/cruas, águas residuais e microbioma humano, foi realizada uma análise exploratória com base em literatura e bases de dados públicas, de genes de resistência a antibióticos e de virulência. Este estudo sugere que bactérias relacionadas com géneros como Enterobacter, Acinetobacter, Pseudomonas e Staphylococcus, cuja relação taxonómica com agentes patogénicos oportunistas e portadores de resistência a antibióticos, é conhecida, podem ser encontrados como endófitos em variedades agrícolas comestíveis, sugerindo que podem ser veiculados por águas residuais e ser transmitidos para o microbioma humano. Esses resultados sustentam a hipótese de que as bactérias transportadas pelas águas residuais, com propriedades fisiológicas e ecológicas semelhantes a bactérias endófitas, podem ser captadas por variedades agrícolas edíveis e, assim, se ingeridas, podem eventualmente colonizar o corpo humano. Deste modo, sugere-se que a irrigação com águas residuais pode aumentar os riscos de transmissão de bactérias clinicamente relevantes do meio ambiente para os seres humanos, através da cadeia alimentar. Com recurso a métodos dependentes da cultura, avaliou-se a diversidade de bactérias cultiváveis e resistentes a antibióticos que podem ser encontradas em associação com variedades edíveis, especificamente o agrião e morangos prontos para o consumo (capítulo 4). Os agriões prontos para consumo foram adquiridos em supermercados locais, enquanto as amostras de morangos foram colhidas ao longo de uma cadeia de processamento de frutas de uma empresa que produz preparados de frutas para a indústria alimentar. Estudou-se a fração microbiana das folhas de agrião e as bactérias associadas ao morango (comunidade epífita e endofítica). Os isolados de agrião (n = 68) e morango (n = 52) foram caracterizados fenotipicamente de acordo com seu perfil de resistência a antibióticos. Destes, selecionou-se uma coleção de isolados que exibia fenótipo de resistência a pelo menos três classes de Resumo xi antibióticos, para identificação com base na análise da sequência do gene 16S rRNA e caracterização por reação em cadeia da polimerase (PCR) convencional, quanto à presença do gene da integrase de intregrões de classe 1, intl1, os ARGs sul1, blaTEM, blaCTX-M, blaOXA-A e blaSHV, e os grupos de incompatibilidade de plasmídeos com base nos tipos de origem de replicação FIA, FIB, FIC, HI1, HI2, I1-Iγ, L/M, N, P, W, T, A/C, K, B/O, X, Y, F, e FIIA. Além disso, testou-se se as bactérias isoladas de morango e agrião poderiam adquirir ARGs por transformação. Observou-se que o agrião pronto a consumir apresentava contagens de heterotróficos totais na ordem de 3,5 x 107 ± 4,9 x 107 CFU/mL e 5,4 x 105 ± 6,2 x 104 CFU/mL de solução de lavagem de agrião para os supermercados A e B, respectivamente, enquanto o morango processado apresentava contagens de bactérias cultiváveis na ordem de 9,1 x 105 ± 1,8 x 105 CFU/g de peso seco de morango, com alguns dos isolados a apresentarem fenótipos de resistência a antibióticos. Algumas destas bactérias foram identificadas como membros dos géneros Pseudomonas, Stenotrophomonas, Erwinia, Rahnella, Methylobacterium e Chryseobacterium. Alguns destes grupos bacterianos foram anteriormente identificados com endófitos e géneros como Pseudomonas e Stenotrophomonas estão proximamente relacionados com patogénicos oportunistas que podem ser transportadores de ARGs adquiridos. A pesquisa de ARGs, intI1 e grupos de incomatibilidade de plasmídeos revelou que estes elementos genéticos foram encontrados numa pequena fração das bactérias analisadas (2 isolados). Além disso, resultados preliminares sugeriram que os isolados de agrião e morango podem ser suscetíveis a adquirir resistência a antibióticos e, assim, estar envolvidos na disseminação da resistência a antibióticos. O terceiro estudo baseou-se no argumento de que bactérias de águas residuais ou os seus ARGs poderiam ser rapidamente eliminados em presença da complexa comunidade da microbiota fecal. Este estudo foi realizado em ensaios de microcosmo com material fecal (FMAs) inoculado com bactérias isoladas de água residual, portadoras de genes de resistência a antibióticos conhecidos (Capítulo 5). Os isolados de águas residuais inoculados foram Escherichia coli (estirpe A2FCC14) e Enterococcus faecium (estirpe H1EV10), portadores dos ARGs blaTEM, blaCTX, blaOXA-A e vanA, respectivamente. O efeito de condições como a presença ou ausência de oxigénio ou os antibióticos cefotaxima ou vancomicina, na composição da comunidade microbiana do material fecal e na persistência dos ARGs exógenos foram investigados. Os FMAs foram monitorizados nos tempos 0, 1, 3 e 7 dias de incubação, com recurso a métodos de cultivo, PCR quantitativo (qPCR) e análises da comunidade bacteriana com base Resumo xii na sequência nucleotídica de amplicões do gene para o rRNA 16S. Na comunidade bacteriana do material fecal predominavam membros dos filos Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria e Verrucomicrobia. Esta comunidade sofreu aumento na abundância relativa de Proteobacteria, quando os FMA foram incubados na presença de oxigénio. A presença de doses sub-inibitórias de antibióticos não esteve associada a variações relevantes na composição da comunidade microbiana. Os ARGs das ARB inoculadas persistiram durante o período de 7 dias em todos os ensaios e, ao fim de 30 dias, podiam ainda ser quantificados, tanto em condições de aerobiose como de anaerobiose. A adição de doses sub-inibitórias de antibióticos não se correlacionou com variações significativas na persistência das ARB ou ARGs testados, quando comparados os respetivos controlos em antibióticos. Este estudo sugeriu que ARB que vivem em águas residuais podem persistir pelo menos por uma semana na presença de microbiota fecal complexa e, mesmo quando essas ARB estão abaixo do limite de detecção cultivável, os seus ARGs eram quantificáveis por qPCR. Esses resultados apoiam a hipótese de que, se as bactérias das águas residuais, por acaso, atingirem o intestino humano, poderá haver uma colonização bem-sucedida, um tema que merece mais investigação. No geral, a investigação realizada nesta tese sugere que as águas residuais tratadas usadas para irrigação podem conter bactérias com relevância clínica que, por essa via, podem estabelecer associação estável com culturas edíveis, como endófitos. Se, como consequência desse fato, essas bactérias atingirem o intestino humano, há indícios de que terão capacidade para ali persistir. Embora os presentes estudos evidenciem a complexidade desta questão, a tese apresentada sustenta que as águas residuais, as variedades agrícolas edíveis e os humanos podem estar interligados na cadeia de transmissão de ARB e ARGs. Assim, esta tese abre também caminhos para novas investigações neste domínio.The reuse of treated wastewater has been encouraged worldwide, in particular for agricultural irrigation, because it can be a reliable and important water source, mainly in countries under water stress. The recycling of wastewater poses still not evaluated risks concerning, among other, the dissemination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) across distinct One-Health compartments. One of the main concerns associated with such dissemination is the contamination of the human food-chain through crops irrigation with treated wastewater. Currently, the knowledge about the transmission of ARB and ARGs to humans through environmental sources is sparse. However, wastewater reuse emerges as a potential source for direct or indirect transmission, mainly through the human food-chain. This project addressed these issues, through literature- and experiment-based investigation about potential risks of antibiotic resistance transmission to humans emerging from treated wastewater reuse. The study was planned aiming to infer if bacteria surviving in wastewater would be able to colonize plants and if wastewater ARB and the respective ARGs would be able to persist in the presence of the autochthonous fecal microbiota of a healthy human. The research hypotheses of this work were: 1) ARB and ARGs present in treated wastewater are capable of colonizing plants, and establish as endophytes; 2) ARB and ARGs are able to persist in the presence of the autochthonous human gut microbiota. The rationale behind these two hypotheses was that if ingested through vegetables, ARB and ARGs could be able to persist in the human gut. To test the study hypotheses were used three major approaches: a) it was made a literature search seeking to investigate the diversity of endophytic bacteria that belong to groups that can also be found in wastewater and in the human microbiota as well as in edible crops, normally consumed raw - this approach offered a predictor of the likelihood of a crop behave as a possible mode of transmission of ARB to humans; b) it was analysed the presence of potential ARB and ARGs in isolates from ready-to-eat watercress and strawberry; and c) it was assessed the persistence of ARGs harboured by wastewater ARB in the presence of fecal microbiota of a healthy child. The literature-based investigation aimed to explore the diversity of endophytic bacteria associated with different habitats (plant, wastewater, and human microbiota), and infer the probability that ARB and ARGs might be transferred from wastewater to plants and then to humans (Chapter 3). This literature survey permitted to shortlist of more than 20 phyla of Abstract ii endophytic bacteria distributed over more than 45 crop varieties. Because the major focus was on potential links of transmission to humans, the array of crops found in the literature was narrowed to plants that can be consumed raw, such as lettuce, carrot, radish, cucumber and tomato. In order to assess the likelihood that these plants uptake bacteria that might be antibiotic resistance vectors, the bacterial groups identified as endophytes were also investigated as potential wastewater and human microbiome member communities. Finally, for bacterial groups, whose occurrence was reported in the three types of environments, the previous description of antibiotic resistance and virulence genes was surveyed from public databases and literature. The search revealed that members of genera such as Enterobacter, Acinetobacter, Pseudomonas, and Staphylococcus, with known taxonomic proximity to human opportunistic pathogens and harbour of acquired antibiotic resistance may be found as endophytes in edible crops as well as in wastewater or the human microbiota. These results support the hypothesis that bacteria transported by wastewater, with physiological and ecological properties similar to endophytes, may be uptake by edible crops and being ingested may eventually colonize the human body. It is suggested that wastewater irrigation may raise the risks of transmission of clinically relevant bacteria from the environment to humans, via the food-chain. Plant associated bacteria were also searched on ready-to-eat watercress and strawberry, based on culture-dependent methods (Chapter 4). Ready-to-eat watercress were purchased at local supermarkets and strawberries samples were collected along a fruit processing chain of a company that produces fruits preparations for the food industry. Bacteria adsorbed onto watercress leaves as well as strawberry-associated bacteria (epiphytic and endophytic community) were isolated and analysed. The antibiotic resistance phenotype of watercress (n=68) and strawberry (n=52) isolates was characterized. Isolates exhibiting resistance to at least three antibiotics classes were selected for identification based on the 16S rRNA gene sequence analysis, and the presence of class 1 integron integrase gene intl1, the ARGs sul1, blaTEM, blaCTX-M, blaOXA-A and blaSHV and the plasmid incompatibility groups FIA, FIB, FIC, HI1, HI2, I1-Iγ, L/M, N, P, W, T, A/C, K, B/O, X, Y, F, and FIIA by conventional Polymerase Chain Reaction (PCR) were screened. Some isolates were also tested for the capacity to acquire ARGs by transformation assay. Ready-to-eat watercress presented counts of total heterotrophs in the order of 3.5 x 107 ± 4.9 x 107 and 5.4 x 105 ± 6.2 x 104 CFU/mL of watercress washing solution for supermarket A and B, respectively, whilst processed strawberry presented counts of total heterotrophs in the order of 9.1 x 105 ± 1.8 x 105 CFU/g of strawberry dry weight, with some isolates exhibiting antibiotic resistance phenotypes. The Abstract iii bacteria identified belong to the genera Pseudomonas, Stenotrophomonas, Erwinia, Rahnella, Methylobacterium, and Chryseobacterium. These bacterial taxa were previously identified as endophytes and some, such as members of the genera Pseudomonas and Stenotrophomonas are closely related to human opportunistic pathogens that can harbor acquired ARGs. The screening of ARGs, int1 and plasmid incompatibility groups revealed that these genetic elements were present within a minority group (2 isolates) of the examined plant-associated bacterial isolates. Additionally, preliminary results suggested that watercress and strawberry isolates could be susceptible to acquire antibiotic resistance and thus be involved in the dissemination of antibiotic resistance. The third study was designed based on the arguments that wastewater bacteria as well as their harboured ARGs would be rapidly lost in the complex community of fecal microbiota. This study was performed using fecal microcosm assays (FMAs) inoculated with wastewater ARB isolates harbouring known ARGs (Chapter 5). The inoculated wastewater isolates were Escherichia coli (strain A2FCC14) and Enterococcus faecium (strain H1EV10), harbouring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The effect of variables such as the presence or absence of oxygen or sub-inhibitory dose of the antibiotic cefotaxime or vancomycin on the feces microbial community composition and on the persistence of the exogenous ARGs were investigated. FMAs were monitored at time 0, 1, 3 and 7 days of incubation based on cultivation methods, quantitative PCR (qPCR) and 16S rRNA gene sequence amplicon community analyses. The fecal bacterial community was characterized by the predominance of members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia. The presence of oxygen was associated with an increase in the relative abundance of Proteobacteria, while antibiotics did not lead to consistent microbial community composition variations. The ARGs harboured by the inoculated ARB persisted over the 7 days incubation period in all the assays and could still be quantified at least for one month, under both aerobic and anaerobic conditions. Sub-inhibitory concentrations of antibiotics were not correlated with significant variations on the persistence of the tested ARB or ARGs, when compared with antibiotic-free microcosms. This microcosm-based investigation suggested that wastewater ARB can persist at least for a week in the complex fecal microbiota and, even when these ARB are below the culture detection limit, their ARGs were quantifiable by qPCR. These results support the hypothesis that, if wastewater bacteria by chance can reach the human Abstract iv gut, a successful colonization cannot be disregarded, a topic that deserves further investigation. Overall, the investigation conducted in this thesis suggests that bacteria with potential clinical relevance that may occur in treated wastewater used for irrigation, may establish stable association with edible crops, as endophytes. If, as consequence of this fact, these bacteria reach the human gut, they may be capable of persisting there. Although this investigation put in evidence the complexity of this issue, showing that further studies are required, the thesis presented is that the wastewater, edible crops and humans may be part of the same transmission link chain of ARB and ARGs

Whole genome sequencing of Escherichia coli isolates from aquatic environments in the context of the COVID-19 pandemic: A multicenter study conducted in Cameroon, Brazil and Madagascar

Introduction: The COVID-19 pandemic has brought attention to antimicrobial resistance (AMR), a major global health concern. The COVID-19 pandemic is increasing antimicrobial misuse and could have an impact on water microbial communities, and the likely interaction between SARS-CoV-2 and the aquatic microbial community has been less studied. In low- and middle-income countries, wastewater treatment plants are not available or do not function, so untreated wastewater is discharged directly into nearby water sources. The consortium Cameroon, Brazil, and Madagascar has set itself the goal of detecting and characterizing Escherichia coli isolates circulating in aquatic environment that have been influenced by the presence of SARV-CoV-2. Methods: Fom January to June 2022, wastewater samples were collected monthly in the cities of Yaounde, Antananarivo and Sao Paulo, in different points and nearby healthcare facilities receiving COVID-19 patients and in one control site and screened for the presence of ESBL and carbapenemase producing Escherichia coli on selective culture media. AMR patterns were determined according to CASFM guidelines, and Next Generation Sequencing (NGS) was performed to screen for (antimicrobial resistance genes) ARGs in the isolates. In addition, the presence of SARV-CoV-2 in water samples was investigated by RT-qPCR Results: A total of 41 strains of Escherichia coli predominantly ESBL phenotype (73,1%) were isolated with 10, 15 and 16 isolates respectively for Cameroon, Brazil and Madagascar, mainly in wastewater from hospitals receiving COVID-19 patients (82,9%). The pattern of multi-resistance to antimicrobials has been confirmed, observed in most isolates with the presence of a wide variety of variants of ARGs for most antimicrobial families and 26.8% of isolates with carbapenem ARGs. NGS showed a large diversity of ST and 04 strains of Madagascar belonged to ST-648 and present both at the hospital site and in surface waters at different months. SARS-CoV-2 RNA was detected in 34,14 % of sites where Escherichia coli was present and had no significant impact on its detection (p>0.05). Discussion: Escherichia coli is an AMR pathogen commonly found in water, and its prevalence in hospital sites may be due to the fact that conditions for AMR emergence are favorable there. The predominance of the ESBL phenotype on carbapenemases may be explained by the fact that carbapenems are considered a treatment option of last resort. The wide variety of ARGs presents a significant risk of therapeutic failure, and of potential acquisition of AMR by the bacterial community, as these genes are plasmid mediated. Conclusion: This study highlights high prevalence of Escherichia coli carrying ESBL and carbapenemases genes circulating in aquatic environments in the study countries, although no direct link could be found between the frequency of SARS-CoV-2. This study provides evidence to stakeholders to reinforce regulations on management of hospital and municipal wastewater

Persistence of wastewater antibiotic resistant bacteria and their genes in human fecal material

ABSTRACT Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&amp;ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.</jats:p

The risk of transmitting antibiotic resistance through endophytic bacteria

Antibiotic resistance is a global human health threat distributed across humans, animals, plants, and the environment. Under the One-Health concept (humans, animals, and environment), the contamination of water bodies and soil by antibiotic-resistant bacteria cannot be dissociated from its potential transmission to humans. Edible plants can be colonized by a vast diversity of bacteria, representing an important link between the environment and humans in the One-Health triad. Based on multiple examples of bacterial groups that comprise endophytes reported in edible plants, and that have close phylogenetic proximity with human opportunistic pathogens, we argue that plants exposed to human-derived biological contamination may represent a path of transmission of antibiotic resistance to humans.info:eu-repo/semantics/acceptedVersio

The Glossaryfication Web Service – an automated glossary creation tool to support One Health communication

Efficient communication and collaboration across sectors is an important precondition for true One Health Surveillance (OHS) activities. Despite the overall willingness to embrace the One Health paradigm, it is still challenging to accomplish this in day-to-day practice due to the differences in terminology and interpretation of sector-specific terms. In this sense, simple interventions like the inclusion of integrative glossaries in OHS documents (e.g. reports, research papers and guidelines) would help to reduce misunderstandings and could significantly improve the written communication in OHS. Here, we present the Glossaryfication Web Service that generates a document-specific glossary for any text file provided by the user. The web service automatically adds the available definitions with their corresponding references for the words in the document that match with terms in the user-selected glossaries.The Glossaryfication Web Service was developed to provide added value to the OHEJP Glossary that was developed within the OHEJP project ORION. The OHEJP Glossary improves the communication and collaboration among OH sectors by providing an online resource that lists relevant OH terms and sector-specific definitions. The Glossaryfication Web Service supports the practical use of the curated OHEJP Glossary and can also source information from other glossaries relevant for OH professionals (currently supporting the online CDC, WHO and EFSA glossaries).The Glossaryfication Web Service was created using the open-source software KNIME and the KNIME Text Processing extension (https://www.knime.com/knime-text-processing). The Glossaryfication KNIME workflow is deployed on BfR’s KNIME Server infrastructure providing an easy-to-use web interface where the users can upload their documents (any text-type file e.g. PDF, Word, Excel) and select the desired glossary to compare with. The Glossaryfication KNIME workflow reads in the document provided via the web interface and applies natural language processing (e.g. text cleaning, stemming), transforming (bag-of-words generation) and information retrieval methods to identify the matching terms in the selected glossaries.The Glossaryfication Web Service generates as an output a table containing all the terms that match with the selected glossaries. It also provides the available definitions, corresponding references and additional meta-information, e.g. the term frequency, i.e., how often each term appears in the given text, and the sectoral classification (only for the OHEJP Glossary terms). Furthermore, the workflow generates a tag cloud where the terms are categorized as: (i) exact match when the term in the text matches exactly with the entry of this term in the glossary; (ii) inexact match when the term appears in the text slightly modified (e.g. plural forms or suffixes) and (iii) non-matching that corresponds to all the other words appearing in the text that do not match with any glossary term. Through the user interface, the users can then choose if they want to download the whole list of terms, select only the exact/inexact matching terms, or just choose those terms and definitions that match with the meaning intended for this term in the user-provided document. The resulting table of terms can be downloaded as an Excel file and added to the user’s document as a document-specific glossary.The Glossaryfication Web Service provides an easy-to-adopt solution to enrich documents and reports with more comprehensive and unambiguous glossaries. Furthermore, it improves the referentiality of terms and definitions from different OH sectors. An additional feature provided by the Glossaryfication Web Service is the possibility of extending its use to other glossaries from other national or international institutions allowing the user to customize this glossary creation service.

The Glossaryfication Web Service: an automated glossary creation tool to support the One Health community

In many interdisciplinary research domains, the creation of a shared understanding of relevant terms is considered the foundation for efficient cross-sector communication and interpretation of data and information. This is also true for the domain of One Health (OH) where many One Health Surveillance (OHS) documents rarely contain glossaries with a list of terms for which their specific meaning in the context of the given document is defined Cornelia et al. 2018, Buschhardt et al. 2021. The absence of glossaries within these documents may lead to misinterpretation of surveillance results due to the wrong interpretation of terminology specifically when term definitions differ across OH sectors. Under the One Health EJP project ORION, the OHEJP Glossary was recently created. The OHEJP Glossary is a tool to improve communication and collaboration among OH sectors by providing an easy-to-use online resource that lists relevant OH terms and sector-specific definitions. To improve the accessibility of content from the OHEJP Glossary and support the creation of integrative glossaries in future OHS-related documents, the OHEJP Glossaryfication Web Service was created. This service can support the practical use of the OHEJP Glossary and other relevant online glossaries by OH professionals.The Glossaryfication Web Service (GWS) is an application that automatically identifies terms in any uploaded text-based document and creates a document-specific list of matching definitions in selected online glossaries. This auto-generated document-specific glossary can easily be adjusted by the user, e.g. by selecting the desired definition in case multiple definitions were found for a specific term. The document-specific glossary could then be downloaded, manually adjusted, and finally included into the original document where it supports the correct interpretation of terminology used within the document. Especially in sector-specific reports such as from animal health or public health authorities, this can be beneficial to ensure the correct interpretation by other OH sectors in the future. The GWS developed with the open-source desktop software KNIME Analytics Platform and runs as a web service on a KNIME Web Server infrastructure. The core data processing functionality in the GWS is based on KNIME’s Textprocessing extension. KNIME's JavaScript nodes provided the basis for an interactive user interface where users can easily upload their files and select between different reference glossaries such as the OHEJP Glossary, the CDC Glossary, the WHO Glossary, or the EFSA Glossary. After retrieval of the user input settings, the GWS tags words within the provided document and maps these tagged words with matching entries in the selected glossaries. As the main output, the user receives a downloadable list of matching terms with their corresponding definitions, sectorial assignments, and references, which can then be added by the user to the original document. The GWS is freely accessible via this link as well as the underlying KNIME workflow