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Kozajda A, Miśkiewicz E, Jeżak K. Zoonotic bacteria in the vicinity of animal farms as a factor disturbing the human microbiome: a review. Int J Occup Med Environ Health 2024; 37:138-152. [PMID: 38577723 PMCID: PMC11142397 DOI: 10.13075/ijomeh.1896.02003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/17/2024] [Indexed: 04/06/2024] Open
Abstract
This review is aimed at summarizing the current state of knowledge about the relationship between environmental exposure to the bioaerosol emitted by intensive livestock farming and changes in the microbiome of people living in livestock farm vicinity. The PubMed, Scopus and Web of Science databases were searched by crossing keywords from the following 3 groups: a) "livestock," "animal farms," "animal breeding"; b) "microbiome," "resistome"; c) "livestock vicinity," "farm vicinity," "neighborhoods and health" in 2010-2022. Literature screening did not reveal any paper related to the full microbiome composition in the population studied. In the study, the authors included 7 papers (5 from the Netherlands, 1 from the USA, and 1 from China). The studies confirmed the carriage of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), livestockassociated MRSA (LA-MRSA MC398) and multidrug-resistant S. aureus (MDRSA) in the nasal microbiome of adults and children living within 500-2000 m from a livestock farm. Clostridium difficile, including LA-ribotype RT078 carriage, was detected in the intestinal microbiome of adults living within 500-1000 m. Extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae were confirmed in the intestinal microbiome of adults living within 500-6200 m. Knowledge on the composition of the microflora of people living in livestock farm vicinity is insufficient to conclude about changes in the microbiome caused by the environmental emission of bioaerosol. The carriage prevalence of the LA-bacteria, including both strains with antimicrobial resistance and antimicrobial resistance genes, confirms the presence of zoonotic bacteria in the human microflora in populations without occupational contact with animals. It cannot be ruled out that zoonotic bacteria, as a component of the microbiome, have a negative impact on people's health. Int J Occup Med Environ Health. 2024;37(2):138-52.
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Affiliation(s)
- Anna Kozajda
- Nofer Institute of Occupational Medicine, Department of Chemical Safety, Biological Safety Unit, Łódź, Poland
| | - Emilia Miśkiewicz
- Nofer Institute of Occupational Medicine, Department of Chemical Safety, Biological Safety Unit, Łódź, Poland
| | - Karolina Jeżak
- Nofer Institute of Occupational Medicine, Department of Chemical Safety, Nofer Institute of Occupational Medicine, Łódź, Poland
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Gilboa M, Baharav N, Melzer E, Regev-Yochay G, Yahav D. Screening for Asymptomatic Clostridioides difficile Carriage Among Hospitalized Patients: A Narrative Review. Infect Dis Ther 2023; 12:2223-2240. [PMID: 37704801 PMCID: PMC10581986 DOI: 10.1007/s40121-023-00856-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 09/15/2023] Open
Abstract
Clostridioides difficile infection (CDI) has become the most common healthcare-associated infection in the United States, with considerable morbidity, mortality, and healthcare costs. Assessing new preventive strategies is vital. We present a literature review of studies evaluating a strategy of screening and isolation of asymptomatic carriers in hospital settings. Asymptomatic detection of C. difficile is reported in ~ 10-20% of admitted patients. Risk factors for carriage include recent hospitalization, previous antibiotics, older age, lower functional capacity, immunosuppression, and others. Asymptomatic C. difficile carriers of toxigenic strains are at higher risk for progression to CDI. They are also shedders of C. difficile spores and may contribute to the persistence and transmission of this bacterium. Screening for asymptomatic carriers at hospital admission can theoretically reduce CDI by isolating carriers to reduce transmission, and implementing antibiotic stewardship measures targeting carriers to prevent progression to clinical illness. Several observational studies, summarized in this review, have reported implementing screening and isolation strategies, and found a reduction in CDI rates. Nevertheless, the data are still limited to a few observational studies, and this strategy is not commonly practiced. Studies supporting screening were performed in North America, coinciding with the period of dominance of the 027/BI/NAP1 strain. Additional studies evaluating screening, followed by infection control and antibiotic stewardship measures, are needed.
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Affiliation(s)
- Mayan Gilboa
- Infection Prevention Unit, Sheba Medical Center, Ramat-Gan, Israel.
- Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Tel-Aviv, Israel.
| | - Nadav Baharav
- Infectious Diseases Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Eyal Melzer
- Infection Prevention Unit, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Tel-Aviv, Israel
| | - Gili Regev-Yochay
- Infection Prevention Unit, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Tel-Aviv, Israel
| | - Dafna Yahav
- Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Tel-Aviv, Israel
- Infectious Diseases Unit, Sheba Medical Center, Ramat-Gan, Israel
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Skjøt-Arkil H, Rune Nanthan K, Chen M, Rosenvinge FS. Carrier prevalence of Clostridioides difficile in emergency departments and the association of prior antibiotic consumption: a combined cross-sectional and nested case-control study. J Antimicrob Chemother 2023:dkad213. [PMID: 37409612 DOI: 10.1093/jac/dkad213] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
INTRODUCTION Clostridioides difficile infection is an urgent public health threat, and the incidence has been increasing over the last decades. Knowledge of the prevalence of C. difficile in acutely admitted patients and risk factors for colonization with C. difficile assists emergency departments (EDs) in prioritizing preventive initiatives. This national study aimed to describe prevalence and risk factors for C. difficile carriers acutely admitted to EDs, focusing on the impact of earlier antibiotic prescription. METHODS We conducted a nationwide analytic cross-sectional study with prospective data collection combined with a nested case-control study with retrospective data collection. All adults visiting one of eight Danish EDs were interviewed and examined for C. difficile. Using a national register, we collected the antibiotic history within the 2 years prior to enrolment. The primary outcome was the prevalence of C. difficile colonization, and secondary outcomes were related to risk factors and prior antibiotic prescription. Multivariate analyses examined the association between earlier antibiotic prescription and C. difficile colonization. RESULTS Of 5019 participants, 89 were colonized with C. difficile (prevalence of 1.8%). A significant and exposure-dependent association was found for penicillins [DDD/person-year(PY) > 20; OR 4.93 (95% CI 2.22-10.97)] and fluoroquinolones [DDD/PY > 20; OR 8.81 (95% CI 2.54-30.55)], but not macrolides. Timing of the prescription did not affect the association. CONCLUSIONS One out of 55 patients visiting a Danish ED were colonized with C. difficile. Risk factors for colonization included high age, comorbidity and prior prescription of fluoroquinolones and penicillins.
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Affiliation(s)
- Helene Skjøt-Arkil
- Department of Regional Health Research at University of Southern Denmark, Aabenraa, Denmark
- Emergency Department at University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Kumanan Rune Nanthan
- Emergency Department at University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Ming Chen
- Department of Microbiology at University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Flemming S Rosenvinge
- Department of Clinical Microbiology at Odense University Hospital, and Research Unit of Clinical Microbiology at University of Southern Denmark, Odense, Denmark
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Bocchetti M, Ferraro MG, Melisi F, Grisolia P, Scrima M, Cossu AM, Yau TO. Overview of current detection methods and microRNA potential in Clostridioides difficile infection screening. World J Gastroenterol 2023; 29:3385-3399. [PMID: 37389232 PMCID: PMC10303512 DOI: 10.3748/wjg.v29.i22.3385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/23/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2023] Open
Abstract
Clostridioides difficile (formerly called Clostridium difficile, C. difficile) infection (CDI) is listed as an urgent threat on the 2019 antibiotic resistance threats report in the United States by the Centers for Disease Control and Prevention. Early detection and appropriate disease management appear to be essential. Meanwhile, although the majority of cases are hospital-acquired CDI, community-acquired CDI cases are also on the rise, and this vulnerability is not limited to immunocompromised patients. Gastrointestinal treatments and/or gastrointestinal tract surgeries may be required for patients diagnosed with digestive diseases. Such treatments could suppress or interfere with the patient’s immune system and disrupt gut flora homeostasis, creating a suitable microecosystem for C. difficile overgrowth. Currently, stool-based non-invasive screening is the first-line approach to CDI diagnosis, but the accuracy is varied due to different clinical microbiology detection methods; therefore, improving reliability is clearly required. In this review, we briefly summarised the life cycle and toxicity of C. difficile, and we examined existing diagnostic approaches with an emphasis on novel biomarkers such as microRNAs. These biomarkers can be easily detected through non-invasive liquid biopsy and can yield crucial information about ongoing pathological phenomena, particularly in CDI.
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Affiliation(s)
- Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Maria Grazia Ferraro
- School of Infection and Immunity, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II,” Naples 80131, Italy
| | - Federica Melisi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Piera Grisolia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Marianna Scrima
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Alessia Maria Cossu
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Tung On Yau
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
- Department of Rural Land Use, Scotland’s Rural College, Aberdeen AB21 9YA, Scotland, United Kingdom
- Department of Health Science, University of the People, Pasadena, CA 9110112, United States
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Cho J, Cunningham S, Pu M, Lennon RJ, Dens Higano J, Jeraldo P, Sampathkumar P, Shannon S, Kashyap PC, Patel R. Clostridioides difficile Whole-genome Sequencing Differentiates Relapse With the Same Strain From Reinfection With a New Strain. Clin Infect Dis 2021; 72:806-813. [PMID: 32064535 DOI: 10.1093/cid/ciaa159] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/14/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Current approaches in tracking Clostridioides difficile infection (CDI) and individualizing patient management are incompletely defined. METHODS We recruited 468 subjects with CDI at Mayo Clinic Rochester between May and December 2016 and performed whole-genome sequencing (WGS) on C. difficile isolates from 397. WGS was also performed on isolates from a subset of the subjects at the time of a recurrence of infection. The sequence data were analyzed by determining core genome multilocus sequence type (cgMLST), with isolates grouped by allelic differences and the predicted ribotype. RESULTS There were no correlations between C. difficile isolates based either on cgMLST or ribotype groupings and CDI outcome. An epidemiologic assessment of hospitalized subjects harboring C. difficile isolates with ≤2 allelic differences, based on standard infection prevention and control assessment, revealed no evidence of person-to-person transmission. Interestingly, community-acquired CDI subjects in 40% of groups with ≤2 allelic differences resided within the same zip code. Among 18 subjects clinically classified as having recurrent CDI, WGS revealed 14 with initial and subsequent isolates differing by ≤2 allelic differences, suggesting a relapse of infection with the same initial strain, and 4 with isolates differing by >50 allelic differences, suggesting reinfection. Among the 5 subjects classified as having a reinfection based on the timing of recurrence, 3 had isolates with ≤2 allelic differences between them, suggesting a relapse, and 2 had isolates differing by >50 allelic differences, suggesting reinfection. CONCLUSIONS Our findings point to potential transmission of C. difficile in the community. WGS better differentiates relapse from reinfection than do definitions based on the timing of recurrence.
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Affiliation(s)
- Janice Cho
- Division of Gastroenterology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Meng Pu
- Division of Gastroenterology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ryan J Lennon
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Patricio Jeraldo
- Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Priya Sampathkumar
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Samantha Shannon
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Purna C Kashyap
- Division of Gastroenterology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.,Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Khader K, Munoz-Price LS, Hanson R, Stevens V, Keegan LT, Thomas A, Pezzin LE, Nattinger A, Singh S, Samore MH. Transmission Dynamics of Clostridioides difficile in 2 High-Acuity Hospital Units. Clin Infect Dis 2021; 72:S1-S7. [PMID: 33512524 PMCID: PMC7844587 DOI: 10.1093/cid/ciaa1580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/14/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The key epidemiological drivers of Clostridioides difficile transmission are not well understood. We estimated epidemiological parameters to characterize variation in C. difficile transmission, while accounting for the imperfect nature of surveillance tests. METHODS We conducted a retrospective analysis of C. difficile surveillance tests for patients admitted to a bone marrow transplant (BMT) unit or a solid tumor unit (STU) in a 565-bed tertiary hospital. We constructed a transmission model for estimating key parameters, including admission prevalence, transmission rate, and duration of colonization to understand the potential variation in C. difficile dynamics between these 2 units. RESULTS A combined 2425 patients had 5491 admissions into 1 of the 2 units. A total of 3559 surveillance tests were collected from 1394 patients, with 11% of the surveillance tests being positive for C. difficile. We estimate that the transmission rate in the BMT unit was nearly 3-fold higher at 0.29 acquisitions per percentage colonized per 1000 days, compared to our estimate in the STU (0.10). Our model suggests that 20% of individuals admitted into either the STU or BMT unit were colonized with C. difficile at the time of admission. In contrast, the percentage of surveillance tests that were positive within 1 day of admission to either unit for C. difficile was 13.4%, with 15.4% in the STU and 11.6% in the BMT unit. CONCLUSIONS Although prevalence was similar between the units, there were important differences in the rates of transmission and clearance. Influential factors may include antimicrobial exposure or other patient-care factors.
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Affiliation(s)
- Karim Khader
- Informatics, Decision-Enhancement, and Analytic Sciences (IDEAS) Center of Innovation, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | | | - Ryan Hanson
- Collaborative for Healthcare Delivery Science, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Vanessa Stevens
- Informatics, Decision-Enhancement, and Analytic Sciences (IDEAS) Center of Innovation, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Lindsay T Keegan
- Informatics, Decision-Enhancement, and Analytic Sciences (IDEAS) Center of Innovation, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Alun Thomas
- Informatics, Decision-Enhancement, and Analytic Sciences (IDEAS) Center of Innovation, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Liliana E Pezzin
- Collaborative for Healthcare Delivery Science, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Ann Nattinger
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Collaborative for Healthcare Delivery Science, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Siddhartha Singh
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Collaborative for Healthcare Delivery Science, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Matthew H Samore
- Informatics, Decision-Enhancement, and Analytic Sciences (IDEAS) Center of Innovation, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
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Risk factors for Clostridioides difficile colonization among hospitalized adults: A meta-analysis and systematic review. Infect Control Hosp Epidemiol 2020; 42:565-572. [PMID: 33118886 DOI: 10.1017/ice.2020.1236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To identify risk factors for asymptomatic Clostridioides difficile colonization among hospitalized adults utilizing a meta-analysis, which may enable early identification of colonized patients at risk of spreading C. difficile. DESIGN Meta-analysis and systematic review. METHODS We systematically searched MEDLINE, Scopus, Web of Science, and EMBASE from January 1, 1975, to February 15, 2020, for articles related to C. difficile colonization among hospitalized adults. Studies with multivariable analyses evaluating risk factors for asymptomatic colonization were eligible. RESULTS Among 5,506 studies identified in the search, 19 studies met the inclusion criteria. Included studies reported 20,334 adult patients of whom 1,588 were asymptomatically colonized with C. difficile. Factors associated with an increased risk of colonization were hospitalization in the previous 6 months (OR, 2.18; 95% CI, 1.86-2.56; P < .001), use of gastric acid suppression therapy within the previous 8 weeks (OR, 1.42; 95% CI, 1.17-1.73; P < .001), tube feeding (OR, 2.02; 95% CI, 1.06-3.85; P = .03), and corticosteroid use in the previous 8 weeks (OR, 1.58; 95% CI, 1.14-2.17; P = .006). Receipt of antibiotics in the previous 3 months (OR, 1.37; 95% CI, 0.94-2.01; P = .10) was not associated with statistically significant effects on risk of colonization. CONCLUSIONS C. difficile colonization was significantly associated with previous hospitalization, gastric acid suppression, tube feeding, and corticosteroid use. Recognition of these risk factors may assist in identifying asymptomatic carriers of C. difficile and taking appropriate measures to reduce transmission.
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