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Manrique P, Montero I, Fernandez-Gosende M, Martinez N, Cantabrana CH, Rios-Covian D. Past, present, and future of microbiome-based therapies. MICROBIOME RESEARCH REPORTS 2024; 3:23. [PMID: 38841413 PMCID: PMC11149097 DOI: 10.20517/mrr.2023.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 06/07/2024]
Abstract
Technological advances in studying the human microbiome in depth have enabled the identification of microbial signatures associated with health and disease. This confirms the crucial role of microbiota in maintaining homeostasis and the host health status. Nowadays, there are several ways to modulate the microbiota composition to effectively improve host health; therefore, the development of therapeutic treatments based on the gut microbiota is experiencing rapid growth. In this review, we summarize the influence of the gut microbiota on the development of infectious disease and cancer, which are two of the main targets of microbiome-based therapies currently being developed. We analyze the two-way interaction between the gut microbiota and traditional drugs in order to emphasize the influence of gut microbial composition on drug effectivity and treatment response. We explore the different strategies currently available for modulating this ecosystem to our benefit, ranging from 1st generation intervention strategies to more complex 2nd generation microbiome-based therapies and their regulatory framework. Lastly, we finish with a quick overview of what we believe is the future of these strategies, that is 3rd generation microbiome-based therapies developed with the use of artificial intelligence (AI) algorithms.
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Martinez E, Crevecoeur S, Thirion C, Grandjean J, Fall PA, Hayette MP, Michel M, Taminiau B, Louis E, Daube G. Gut Microbiota Associated with Clostridioides difficile Carriage in Three Clinical Groups (Inflammatory Bowel Disease, C. difficile Infection and Healthcare Workers) in Hospital Field. Microorganisms 2023; 11:2527. [PMID: 37894185 PMCID: PMC10609531 DOI: 10.3390/microorganisms11102527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Clostridioides difficile is an anaerobic spore-forming Gram-positive bacterium. C. difficile carriage and 16S rDNA profiling were studied in three clinical groups at three different sampling times: inflammatory bowel disease (IBD) patients, C. difficile infection (CDI) patients and healthcare workers (HCWs). Diversity analysis was realized in the three clinical groups, the positive and negative C. difficile carriage groups and the three analysis periods. Concerning the three clinical groups, β-diversity tests showed significant differences between them, especially between the HCW group and IBD group and between IBD patients and CDI patients. The Simpson index (evenness) showed a significant difference between two clinical groups (HCWs and IBD). Several genera were significantly different in the IBD patient group (Sutterella, Agathobacter) and in the CDI patient group (Enterococcus, Clostridioides). Concerning the positive and negative C. difficile carriage groups, β-diversity tests showed significant differences. Shannon, Simpson and InvSimpson indexes showed significant differences between the two groups. Several genera had significantly different relative prevalences in the negative group (Agathobacter, Sutterella, Anaerostipes, Oscillospira) and the positive group (Enterococcus, Enterobacteriaceae_ge and Enterobacterales_ge). A microbiota footprint was detected in C. difficile-positive carriers. More experiments are needed to test this microbiota footprint to see its impact on C. difficile infection.
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Affiliation(s)
- Elisa Martinez
- Food Microbiology Lab, Fundamental and Applied Research for Animals and Health (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, 4000 Liège, Belgium
| | - Sebastien Crevecoeur
- Food Microbiology Lab, Fundamental and Applied Research for Animals and Health (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, 4000 Liège, Belgium
| | - Carine Thirion
- Department of Clinical Sciences, Immunopathology—Infectious Diseases and General Internal Medicine, University Hospital CHU of Liege, 4000 Liège, Belgium
| | - Jessica Grandjean
- Department of Gastroenterology, University Hospital CHU of Liege, 4000 Liège, Belgium
| | | | - Marie-Pierre Hayette
- Department of Biomedical and Preclinical Sciences, Faculty of Medicine, University of Liege, 4000 Liège, Belgium
| | - Moutschen Michel
- Department of Clinical Sciences, Immunopathology—Infectious Diseases and General Internal Medicine, University Hospital CHU of Liege, 4000 Liège, Belgium
| | - Bernard Taminiau
- Food Microbiology Lab, Fundamental and Applied Research for Animals and Health (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, 4000 Liège, Belgium
| | - Edouard Louis
- Department of Gastroenterology, University Hospital CHU of Liege, 4000 Liège, Belgium
| | - Georges Daube
- Food Microbiology Lab, Fundamental and Applied Research for Animals and Health (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, 4000 Liège, Belgium
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Lopez-Santamarina A, Mondragon ADC, Cardelle-Cobas A, Santos EM, Porto-Arias JJ, Cepeda A, Miranda JM. Effects of Unconventional Work and Shift Work on the Human Gut Microbiota and the Potential of Probiotics to Restore Dysbiosis. Nutrients 2023; 15:3070. [PMID: 37447396 DOI: 10.3390/nu15133070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
The work environment is a factor that can significantly influence the composition and functionality of the gut microbiota of workers, in many cases leading to gut dysbiosis that will result in serious health problems. The aim of this paper was to provide a compilation of the different studies that have examined the influence of jobs with unconventional work schedules and environments on the gut microbiota of workers performing such work. As a possible solution, probiotic supplements, via modulation of the gut microbiota, can moderate the effects of sleep disturbance on the immune system, as well as restore the dysbiosis produced. Rotating shift work has been found to be associated with an increase in the risk of various metabolic diseases, such as obesity, metabolic syndrome, and type 2 diabetes. Sleep disturbance or lack of sleep due to night work is also associated with metabolic diseases. In addition, sleep disturbance induces a stress response, both physiologically and psychologically, and disrupts the healthy functioning of the gut microbiota, thus triggering an inflammatory state. Other workers, including military, healthcare, or metallurgy workers, as well as livestock farmers or long-travel seamen, work in environments and schedules that can significantly affect their gut microbiota.
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Affiliation(s)
- Aroa Lopez-Santamarina
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alicia Del Carmen Mondragon
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alejandra Cardelle-Cobas
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Eva Maria Santos
- Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo km. 4.5, Pachuca 42076, Hidalgo, Mexico
| | - Jose Julio Porto-Arias
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alberto Cepeda
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Jose Manuel Miranda
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
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Lim SC, Collins DA, Imwattana K, Knight DR, Perumalsamy S, Hain-Saunders NMR, Putsathit P, Speers D, Riley TV. Whole-genome sequencing links Clostridium (Clostridioides) difficile in a single hospital to diverse environmental sources in the community. J Appl Microbiol 2021; 133:1156-1168. [PMID: 34894035 DOI: 10.1111/jam.15408] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/21/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022]
Abstract
AIMS To investigate if Clostridium (Clostridioides) difficile infection (CDI), traditionally thought of as hospital-acquired, can be genomically linked to hospital or community environmental sources, and to define possible importation routes from the community to the hospital. METHODS AND RESULTS In 2019, C. difficile was isolated from 89/300 (29.7%) floor and 96/300 (32.0%) shoe sole samples at a tertiary hospital in Western Australia. Non-toxigenic C. difficile ribotype (RT) 010 predominated among floor (96.6%) and shoe sole (73.2%) isolates, while toxigenic RT 014/020 was most prevalent among contemporaneous clinical cases (33.0%) at the hospital. Whole-genome sequencing and high-resolution core genome single nucleotide polymorphism (cgSNP) analysis on C. difficile strains from hospital and community sources showed no clinical C. difficile RT 014/020 strains were genetically related, and evidence of frequent long-distance, multi-directional spread between humans, animals and the environment. In addition, cgSNP analysis of environmental RT 010 strains suggested transportation of C. difficile via shoe soles. CONCLUSIONS While C. difficile RT 014/020 appears to spread via routes outside the healthcare system, RT 010 displayed a pattern of possible importation from the community into the hospital. SIGNIFICANCE AND IMPACT OF STUDY These findings suggest developing community-based infection prevention and control strategies could significantly lower rates of CDI in the hospital setting.
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Affiliation(s)
- Su-Chen Lim
- School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Deirdre A Collins
- School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Korakrit Imwattana
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Daniel R Knight
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Biosecurity and One Health Research Centre, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Sicilia Perumalsamy
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Natasza M R Hain-Saunders
- School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia.,Biosecurity and One Health Research Centre, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Papanin Putsathit
- School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - David Speers
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Thomas V Riley
- School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia.,School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Biosecurity and One Health Research Centre, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
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Clostridioides difficile colonization and infection in a cohort of Australian adults with cystic fibrosis. J Hosp Infect 2021; 113:44-51. [PMID: 33775742 DOI: 10.1016/j.jhin.2021.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Little is known about Clostridioides difficile infection (CDI) in patients with cystic fibrosis (CF). The aim of this study was to investigate the prevalence, molecular epidemiology and risk factors for CDI in asymptomatic and symptomatic adults with CF in Western Australia. METHODS Faecal samples from symptomatic and asymptomatic patients were prospectively collected and tested for the presence of C. difficile by toxigenic culture. Ribotyping was performed by established protocols. Logistic regression analysis was performed to analyse the risk factors for C. difficile colonization and infection. Extensive environmental sampling was performed within the CF clinic in Perth. RESULTS The prevalence rates of asymptomatic toxigenic and non-toxigenic C. difficile colonization were 30% (14/46 patients) and 24% (11/46 patients), respectively. Fifteen ribotypes (RTs) of C. difficile were identified, of which non-toxigenic RT 039 was the most common. Among the symptomatic patients, the prevalence of toxigenic CDI was 33% (11/33 patients). Impaired glucose tolerance/diabetes mellitus and duration of intravenous antibiotic use in the past 12 months were significantly associated with increased risk of asymptomatic toxigenic C. difficile carriage and CDI. A trend towards higher CF transmembrane conductance regulator modulator treatment was observed in the CDI group. Extensive environmental sampling showed no evidence of toxigenic C. difficile contamination within the CF clinic. CONCLUSIONS A high prevalence of asymptomatic carriage of toxigenic C. difficile was observed in adults with CF, comparable with that observed in the symptomatic CF population. There was no evidence of direct person-to-person transmission.
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Zheng N, Li SH, Dong B, Sun W, Li HR, Zhang YL, Li P, Fang ZW, Chen CM, Han XY, Li B, Zhang SY, Xu M, Zhang GX, Xin Y, Ma YF, Wan XY, Yan QL. Comparison of the gut microbiota of short-term and long-term medical workers and non-medical controls: a cross-sectional analysis. Clin Microbiol Infect 2020; 27:1285-1292. [PMID: 33160036 DOI: 10.1016/j.cmi.2020.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 07/13/2020] [Accepted: 10/27/2020] [Indexed: 01/03/2023]
Abstract
OBJECTIVES The hospital environment has been implicated in the enrichment and exchange of pathogens and antibiotic resistance, but its potential in shaping the symbiotic microbial community of hospital staff is unclear. This study was designed to evaluate the alteration of the gut microbiome in medical workers compared to non-medical controls. METHODS A prospective cross-sectional cohort study was conducted in the intensive care unit (ICU) and other departments of a centre in north-eastern China. Faecal samples of 175 healthy medical workers-short-term (1-3 months) workers (n = 80) and long-term (>1 year) workers (n = 95)-and 80 healthy non-medical controls were analysed using 16S rRNA amplicon sequencing. The hospital environmental samples (n = 9) were also analysed. RESULTS The gut microbiomes of medical workers exhibited marked deviations in diversity and alteration in microbial composition and function. Short-term workers showed significantly higher abundances of taxa such as Lactobacillus, Butyrivibrio, Clostridiaceae, Clostridium, Ruminococcus, Dialister, Bifidobacterium, Odoribacter, and Desulfovibrio and lower abundances of Bacteroides and Blautia than the controls. Long-term workers showed higher abundances of taxa such as Dialister, Veillonella, Clostridiaceae, Clostridium, Bilophila, Desulfovibrio, Pseudomonas, and Akkermansia and lower abundances of Bacteroides and Coprococcus than the controls. The medical workers' department (ICU versus non-ICU) and position (resident doctor versus nursing staff) also impacted their gut microbiome. Compared with the non-ICU workers, workers in the ICU showed a significant increase in the abundances of Dialister, Enterobacteriaceae, Phascolarctobacterium, Pseudomonas, Veillonella, and Streptococcus and a marked depletion of Faecalibacterium, Blautia, and Coprococcus. In contrast with the nursing staff, the resident doctors showed a significant increase in Erysipelotrichaceae and Clostridium and a decrease in Bacteroides, Blautia, and Ruminococcus in the gut microbiome. Moreover, we found that the microbiota of hospital environments potentially correlated with the workers' gut microbiota. CONCLUSIONS Our findings demonstrated structural changes in the gut microbial community of medical workers.
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Affiliation(s)
- Ning Zheng
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China; Intensive Care Unit, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Sheng-Hui Li
- Shenzhen Puensum Genetech Institute, Shenzhen, China
| | - Bo Dong
- Shenzhen Puensum Genetech Institute, Shenzhen, China
| | - Wen Sun
- Yang-sheng (Health Nurturing) Institute, Beijing University of Chinese Medicine, Beijing, China
| | - Huai-Rui Li
- Department of Anesthesiology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yong-Li Zhang
- Intensive Care Unit, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Peng Li
- Shenzhen Puensum Genetech Institute, Shenzhen, China
| | - Zhi-Wei Fang
- Shenzhen Puensum Genetech Institute, Shenzhen, China
| | - Chang-Ming Chen
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xiu-Yan Han
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Bo Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Si-Yi Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Miao Xu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Gui-Xin Zhang
- General Surgery Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yi Xin
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yu-Fang Ma
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xian-Yao Wan
- Intensive Care Unit, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Qiu-Long Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.
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Aguirre-García GM, Garza-González E, Morfin-Otero R, Camacho-Ortiz A. Clostridioides difficile infections among healthcare workers. Am J Infect Control 2020; 48:1270-1272. [PMID: 32122672 DOI: 10.1016/j.ajic.2020.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/06/2020] [Accepted: 01/09/2020] [Indexed: 11/16/2022]
Abstract
Health care workers (HCWs) are constantly exposed to patients with Clostridiodes difficile infection (CDI) although their risk developing infection is unknown. We designed a retrospective comparative study including HCWs with CDI and 2 comparator groups with a 1:2 ratio: HCWs without CDI and admitted patients with CDI. Antibiotics were the strongest risk factor for developing CDI in HCWs whether or not there was clinical exposure to patients with this infection.
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Affiliation(s)
- Gloria M Aguirre-García
- Department of Infectious Diseases, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Elvira Garza-González
- Department of Infectious Diseases, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Rayo Morfin-Otero
- Department of Infectious Diseases, Hospital Civil de Guadalajara 'Fray Antonio Alcalde', e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Adrián Camacho-Ortiz
- Department of Infectious Diseases, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México.
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Reducing C. difficile in children: An agent-based modeling approach to evaluate intervention effectiveness. Infect Control Hosp Epidemiol 2020; 41:522-530. [PMID: 32052722 DOI: 10.1017/ice.2020.14] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Clostridioides difficile infection (CDI) is rapidly increasing in children's hospitals nationwide. Thus, we aimed to compare the effectiveness of 9 infection prevention interventions and 6 multiple-intervention bundles at reducing hospital-onset CDI and asymptomatic C. difficile colonization. DESIGN Agent-based simulation model of C. difficile transmission. SETTING Computer-simulated, 80-bed freestanding, tertiary-care pediatric hospital, including 8 identical wards with 10 single-bed patient rooms each. PARTICIPANTS The model includes 5 distinct agent types: patients, visitors, caregivers, nurses, and physicians. INTERVENTIONS Daily and terminal environmental disinfection, screening at admission, reduced intrahospital patient transfers, healthcare worker (HCW), visitor, and patient hand hygiene, and HCW and visitor contact precautions. RESULTS The model predicted that daily environmental disinfection with sporicidal product, combined with screening for asymptomatic C. difficile at admission, was the most effective 2-pronged infection prevention bundle, reducing hospital-onset CDI by 62.0% and asymptomatic colonization by 88.4%. Single-intervention strategies, including daily disinfection, terminal disinfection, asymptomatic screening at admission, HCW hand hygiene, and patient hand hygiene, as well as decreasing intrahospital patient transfers, all also reduced both hospital-onset CDI and asymptomatic colonization in the model. Visitor hand hygiene and visitor and HCW contact precautions were not effective at reducing either measure. CONCLUSIONS Hospitals can achieve substantial reduction in hospital-onset CDIs by implementing a small number of highly effective interventions.
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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei. Nat Commun 2020; 11:466. [PMID: 31980604 PMCID: PMC6981164 DOI: 10.1038/s41467-019-14139-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of blaIMP-4 carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the blaIMP-4 gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak. Antibiotic-resistant bacteria are an urgent threat to human health. Here, Roberts et al. characterise and monitor an ongoing hospital outbreak of carbapenemase-producing Enterobacter hormaechei by integrating several technologies for whole-genome sequencing and shotgun metagenomics.
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Gagnière C, Bourrier A, Seksik P, Gornet JM, DeWit O, Nancey S, Altwegg R, Abitbol V, Laharie D, Reenaers C, Buisson A, Pariente B, Viennot S, Vuitton L, Stefanescu C, Marteau P, Bouguen G, Cosnes J, Amiot A. Risk of serious infection in healthcare workers with inflammatory bowel disease: a case-control study of the Groupe d'Etude Thérapeutique des Affections Inflammatoires du tube Digestif (GETAID). Aliment Pharmacol Ther 2018; 48:713-722. [PMID: 30069921 DOI: 10.1111/apt.14926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/10/2018] [Accepted: 07/07/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Whether healthcare workers with inflammatory bowel disease (IBD) are at increased risk of severe infection due to daily pathogen exposure is controversial. AIM To assess the risk of severe infection in healthcare workers with IBD in a large multicentre case-control study. METHODS The study population comprised 482 healthcare workers with IBD from 17 centres who were matched for gender, age, disease subtype and year of diagnosis to 482 controls (non-healthcare workers with IBD). The study period was between the date of diagnosis of IBD and June 2016. Severe infection was defined as any community-acquired infection that required hospitalisation. RESULTS With a median follow-up of 9.3 years, 139 severe infections were recorded among cases and controls, including 30 Clostridium difficile infections, 33 severe viral infections, nine tuberculosis infections, 21 community-acquired pneumonia and 46 others. No difference was observed between healthcare workers and controls regarding the overall incidence rates of severe infection. An increased risk of tuberculosis was noted in healthcare workers. In multivariate analysis in the entire study population, severe infection was associated with current exposure to corticosteroids (OR = 3.05, 95% CI [2.06-4.52], P < 0.001), immunosuppressants (OR = 1.98, 95% CI [1.38-2.84], P < 0.001) and anti-TNF agents (OR = 2.93, 95% CI [2.02-4.27], P < 0.001) and reduced with Crohn's disease (OR = 0.63, 95% CI [0.43-0.91], P = 0.01). CONCLUSIONS Healthcare workers with IBD do not have an increased risk of severe infection compared with other patients with IBD, except for tuberculosis. Screening for tuberculosis exposure should be assessed in this high-risk population when treated with anti-TNF agents.
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Barker AK, Alagoz O, Safdar N. Interventions to Reduce the Incidence of Hospital-Onset Clostridium difficile Infection: An Agent-Based Modeling Approach to Evaluate Clinical Effectiveness in Adult Acute Care Hospitals. Clin Infect Dis 2018; 66:1192-1203. [PMID: 29112710 PMCID: PMC5888988 DOI: 10.1093/cid/cix962] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/31/2017] [Indexed: 12/18/2022] Open
Abstract
Background Despite intensified efforts to reduce hospital-onset Clostridium difficile infection (HO-CDI), its clinical and economic impacts continue to worsen. Many institutions have adopted bundled interventions that vary considerably in composition, strength of evidence, and effectiveness. Considerable gaps remain in our knowledge of intervention effectiveness and disease transmission, which hinders HO-CDI prevention. Methods We developed an agent-based model of C. difficile transmission in a 200-bed adult hospital using studies from the literature, supplemented with primary data collection. The model includes an environmental component and 4 distinct agent types: patients, visitors, nurses, and physicians. We used the model to evaluate the comparative clinical effectiveness of 9 single interventions and 8 multiple-intervention bundles at reducing HO-CDI and asymptomatic C. difficile colonization. Results Daily cleaning with sporicidal disinfectant and C. difficile screening at admission were the most effective single-intervention strategies, reducing HO-CDI by 68.9% and 35.7%, respectively (both P < .001). Combining these interventions into a 2-intervention bundle reduced HO-CDI by 82.3% and asymptomatic hospital-onset colonization by 90.6% (both, P < .001). Adding patient hand hygiene to healthcare worker hand hygiene reduced HO-CDI rates an additional 7.9%. Visitor hand hygiene and contact precaution interventions did not reduce HO-CDI, compared with baseline. Excluding those strategies, healthcare worker contact precautions were the least effective intervention at reducing hospital-onset colonization and infection. Conclusions Identifying and managing the vast hospital reservoir of asymptomatic C. difficile by screening and daily cleaning with sporicidal disinfectant are high-yield strategies. These findings provide much-needed data regarding which interventions to prioritize for optimal C. difficile control.
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Affiliation(s)
- Anna K Barker
- Department of Population Health Sciences, School of Medicine and Public Health, Madison, Wisconsin
| | - Oguzhan Alagoz
- Department of Population Health Sciences, School of Medicine and Public Health, Madison, Wisconsin
- Department of Industrial and Systems Engineering, College of Engineering, Madison, Wisconsin
| | - Nasia Safdar
- Division of Infectious Diseases, Department of Medicine, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, Wisconsin
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin
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Abstract
Clostridium difficile is the main causative agent of antibiotic-associated and health care-associated infective diarrhea. Recently, there has been growing interest in alternative sources of C. difficile other than patients with Clostridium difficile infection (CDI) and the hospital environment. Notably, the role of C. difficile-colonized patients as a possible source of transmission has received attention. In this review, we present a comprehensive overview of the current understanding of C. difficile colonization. Findings from gut microbiota studies yield more insights into determinants that are important for acquiring or resisting colonization and progression to CDI. In discussions on the prevalence of C. difficile colonization among populations and its associated risk factors, colonized patients at hospital admission merit more attention, as findings from the literature have pointed to their role in both health care-associated transmission of C. difficile and a higher risk of progression to CDI once admitted. C. difficile colonization among patients at admission may have clinical implications, although further research is needed to identify if interventions are beneficial for preventing transmission or overcoming progression to CDI.
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Shallis RM, Terry CM, Lim SH. Changes in intestinal microbiota and their effects on allogeneic stem cell transplantation. Am J Hematol 2018; 93:122-128. [PMID: 28842931 DOI: 10.1002/ajh.24896] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/31/2017] [Accepted: 08/22/2017] [Indexed: 12/30/2022]
Abstract
The human intestinal microbiota is essential for microbial homeostasis, regulation of metabolism, and intestinal immune tolerance. Rapidly evolving understanding of the importance of the microbiota implicates changes in the composition and function of intestinal microbial communities in an assortment of systemic conditions. Complications following allogeneic stem cell transplant now join the ever-expanding list of pathologic states regulated by intestinal microbiota. Dysbiosis, or disruption of the normal ecology of this microbiome, has been directly implicated in the pathogenesis of entities such as Clostridium difficile infections, graft-versus-host disease (GVHD), and most recently disease relapse, all of which are major causes of morbidity and mortality in patients undergoing allogeneic stem cell transplant. In this review, we elucidate the key origins of microbiotic alterations and discuss how dysbiosis influences complications following allogeneic stem cell transplant. Our emerging understanding of the importance of a balanced and diverse intestinal microbiota is prompting investigation into the appropriate treatment of dysbiosis, reliable and early detection of such, and ultimately its prevention in patients to improve the outcome following allogeneic hematopoietic stem cell transplant.
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Affiliation(s)
- Rory M. Shallis
- Division of Hematology and Oncology; Rhode Island Hospital/Brown University Warren Alpert School of Medicine; Providence Rhode Island
| | - Christopher M. Terry
- Division of Hematology and Oncology; Rhode Island Hospital/Brown University Warren Alpert School of Medicine; Providence Rhode Island
| | - Seah H. Lim
- Division of Hematology and Oncology; Rhode Island Hospital/Brown University Warren Alpert School of Medicine; Providence Rhode Island
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14
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Clostridium difficile infection: epidemiology, diagnosis and understanding transmission. Nat Rev Gastroenterol Hepatol 2016; 13:206-16. [PMID: 26956066 DOI: 10.1038/nrgastro.2016.25] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Clostridium difficile infection (CDI) continues to affect patients in hospitals and communities worldwide. The spectrum of clinical disease ranges from mild diarrhoea to toxic megacolon, colonic perforation and death. However, this bacterium might also be carried asymptomatically in the gut, potentially leading to 'silent' onward transmission. Modern technologies, such as whole-genome sequencing and multi-locus variable-number tandem-repeat analysis, are helping to track C. difficile transmission across health-care facilities, countries and continents, offering the potential to illuminate previously under-recognized sources of infection. These typing strategies have also demonstrated heterogeneity in terms of CDI incidence and strain types reflecting different stages of epidemic spread. However, comparison of CDI epidemiology, particularly between countries, is challenging due to wide-ranging approaches to sampling and testing. Diagnostic strategies for C. difficile are complicated both by the wide range of bacterial targets and tests available and the need to differentiate between toxin-producing and non-toxigenic strains. Multistep diagnostic algorithms have been recommended to improve sensitivity and specificity. In this Review, we describe the latest advances in the understanding of C. difficile epidemiology, transmission and diagnosis, and discuss the effect of these developments on the clinical management of CDI.
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Morgan DJ, Leekha S, Croft L, Burnham CAD, Johnson JK, Pineles L, Harris AD, Dubberke ER. The Importance of Colonization with Clostridium difficile on Infection and Transmission. Curr Infect Dis Rep 2015; 17:499. [DOI: 10.1007/s11908-015-0499-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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16
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Spina A, Kerr KG, Cormican M, Barbut F, Eigentler A, Zerva L, Tassios P, Popescu GA, Rafila A, Eerola E, Batista J, Maass M, Aschbacher R, Olsen KEP, Allerberger F. Spectrum of enteropathogens detected by the FilmArray GI Panel in a multicentre study of community-acquired gastroenteritis. Clin Microbiol Infect 2015; 21:719-28. [PMID: 25908431 DOI: 10.1016/j.cmi.2015.04.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 03/05/2015] [Accepted: 04/09/2015] [Indexed: 11/18/2022]
Abstract
The European, multicentre, quarterly point-prevalence study of community-acquired diarrhoea (EUCODI) analysed stool samples received at ten participating clinical microbiology laboratories (Austria, Finland, France, Germany, Greece, Ireland, Italy, Portugal, Romania, and the UK) in 2014. On four specified days, each local laboratory submitted samples from ≤20 consecutive patients to the Austrian Study Centre for further testing with the FilmArray GI Panel (BioFire Diagnostics, Salt Lake City, UT, USA). Of the 709 samples from as many patients received, 325 (45.8%) tested negative, 268 (37.8%) yielded only one organism, and 116 (16.4%) yielded multiple organisms. Positivity rates ranged from 41% (30 of 73 samples) in France to 74% (59 of 80 samples) in Romania. With the exception of Entamoeba histolytica and Vibrio cholerae, all of the 22 targeted pathogens were detected at least once. Enteropathogenic Escherichia coli, Campylobacter species, toxigenic Clostridium difficile, enteroaggregative E. coli, norovirus and enterotoxigenic E. coli were the six most commonly detected pathogens. When tested according to local protocols, seven of 128 positive samples (5.5%) yielded multiple organisms. Overall, the FilmArray GI Panel detected at least one organism in 54.2% (384/709) of the samples, as compared with 18.1% (128/709) when testing was performed with conventional techniques locally. This underlines the considerable potential of multiplex PCR to improve routine stool diagnostics in community-acquired diarrhoea. Classic culture methods directed at the isolation of specific pathogens are increasingly becoming second-line tools, being deployed when rapid molecular tests give positive results. This optimizes the yield from stool examinations and dramatically improves the timeliness of diagnosis.
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Affiliation(s)
- A Spina
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - K G Kerr
- Harrogate & District NHS Foundation Trust, Harrogate, UK
| | - M Cormican
- National University of Ireland, Galway, Ireland
| | - F Barbut
- Hôpital Saint-Antoine, Paris, France
| | | | - L Zerva
- Attikon University Hospital, Athens-Chaidari, Greece
| | - P Tassios
- Attikon University Hospital, Athens-Chaidari, Greece
| | - G A Popescu
- National Institute for Infectious Diseases and Carol Davila University, Bucharest, Romania
| | - A Rafila
- National Institute for Infectious Diseases and Carol Davila University, Bucharest, Romania
| | - E Eerola
- Turku University, Turku, Finland
| | - J Batista
- Occidental Hospital Centre, Lisbon, Portugal
| | - M Maass
- Labor Dr Heidrich & Kollegen MVZ, Hamburg, Germany
| | - R Aschbacher
- Laboratorio Aziendale di Microbiologia e Virologia, Bolzano, Italy
| | | | - F Allerberger
- Austrian Agency for Health and Food Safety, Vienna, Austria.
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Säll O, Johansson K, Norén T. Low colonization rates of Clostridium difficile among patients and healthcare workers at Örebro University Hospital in Sweden. APMIS 2015; 123:240-4. [PMID: 25627981 DOI: 10.1111/apm.12353] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/09/2014] [Indexed: 11/29/2022]
Abstract
The aim of this study was to investigate the rate of asymptomatic colonization rate of Clostridium difficile among both healthcare workers (HCWs) and patients in a hospital ward in Sweden. In a prospective observational study, asymptomatic HCWs (n = 22) (22/60; 37%) attending patients in an infectious disease ward in Sweden participated and were screened once for C. difficile. At the same time, 58 consecutive patients (58/227; 26%) admitted to the same ward were screened for C. difficile, first at admission and thereafter two times weekly. Fecal samples were obtained by rectal swabs and cultured anaerobically using both cycloserine-cefoxitin-fructose agar and enrichment (Cooked Meat broth). All samples were also tested by loop-mediated isothermal amplification and isolates were tested for the presence of toxin A or B by enzyme immunoassay. None of the analyzed fecal samples from HCWs contained C. difficile. Among the patients during a 2-month observational period, three of the 58 patients (5.2%) were culture positive regarding C. difficile on admission and one additional patient became asymptomatically colonized with C. difficile during the hospital stay. Thus, the colonization rates were 0% (0/22) (95% confidence interval (CI): 0-15.4%) among HCWs and 5.2% (3/58) (95% CI: 1.1-14.4%) among patients at admission. As the HCWs were screened only once, we have not studied transient colonization. In conclusion, with observed low colonization rates, we find no support that HCWs would be an important source for C. difficile transmission.
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Affiliation(s)
- Olof Säll
- Faculty of Medicine and Health, Department of Infectious Diseases, Örebro University, Örebro, Sweden
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18
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Healthcare workers as vectors of infectious diseases. Eur J Clin Microbiol Infect Dis 2014; 33:1477-88. [PMID: 24798250 DOI: 10.1007/s10096-014-2119-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/09/2014] [Indexed: 01/05/2023]
Abstract
Nosocomial infections cause considerable morbidity and mortality. Healthcare workers (HCWs) may serve as vectors of many infectious diseases, many of which are not often primarily considered as healthcare-associated. The probability of pathogen transmission to patients depends on several factors, such as the characteristics of a pathogen, HCW and patient. Pathogens with high transmission potential from HCWs to patients include norovirus, respiratory infections, measles and influenza. In contrast, human immunodeficiency virus (HIV) and viral hepatitis are unlikely to be transferred. The prevention of HCW-associated transmission of pathogens include systematic vaccinations towards preventable diseases, continuous education, hand hygiene surveillance, active feedback and adequate staff resources.
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Luo P, Liu Y, Xia Y, Xu H, Xie G. Aptamer biosensor for sensitive detection of toxin A of Clostridium difficile using gold nanoparticles synthesized by Bacillus stearothermophilus. Biosens Bioelectron 2013; 54:217-21. [PMID: 24287407 DOI: 10.1016/j.bios.2013.11.013] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/20/2013] [Accepted: 11/04/2013] [Indexed: 01/05/2023]
Abstract
A sensitive electrochemical biosensor was developed to detect toxin A (TOA) of Clostridium difficile based on an aptamer selected by the systematic evolution of ligands using exponential enrichment and gold nanoparticles (GNPS) synthesized by Bacillus stearothermophilus. The thiolated single-stranded DNA used as the capture probe (CP) was first self-assembled on a Nafion-thionine-GNPS-modified screen-printed electrode (SPE) through an Au-thiol interaction. The horseradish peroxidase (HRP)-labeled aptamer probe (AP) was then hybridized to the complementary oligonucleotide of CP to form an aptamer-DNA duplex. In the absence of TOA, the aptamer-DNA duplex modified the electrode surface with HRP, so that an amperometric response was induced based on the electrocatalytic properties of thionine. This was mediated by the electrons that were generated in the enzymatic reaction of hydrogen peroxide under HRP catalysis. After the specific recognition of TOA, an aptamer-TOA complex was produced rather than the aptamer-DNA duplex, forcing the HRP-labeled AP to dissociate from the electrode surface, which reduced the catalytic capacity of HRP and reduced the response current. The reduction in the response current correlated linearly with the concentration of TOA in the range of 0-200 ng/mL. The detection limit was shown to be 1 nM for TOA. This biosensor was applied to the analysis of TOA and showed good selectivity, reproducibility, stability, and accuracy.
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Affiliation(s)
- Peng Luo
- Clinical Laboratory, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, PR China.
| | - Yi Liu
- Department of Medical Technique, Chongqing Medical and Pharmaceutical College, Chongqing 400030, PR China
| | - Yun Xia
- Clinical Laboratory, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, PR China
| | - Huajian Xu
- Clinical Laboratory, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, PR China
| | - Guoming Xie
- Key Laboratory of Medical Diagnostics of Ministry of Education, Chongqing Medical University, Chongqing 400016, PR China
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