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Evans S, Stimson J, Pople D, White PJ, Wilcox MH, Robotham JV. Impact of interventions to reduce nosocomial transmission of SARS-CoV-2 in English NHS Trusts: a computational modelling study. BMC Infect Dis 2024; 24:475. [PMID: 38714946 PMCID: PMC11075183 DOI: 10.1186/s12879-024-09330-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Prior to September 2021, 55,000-90,000 hospital inpatients in England were identified as having a potentially nosocomial SARS-CoV-2 infection. This includes cases that were likely missed due to pauci- or asymptomatic infection. Further, high numbers of healthcare workers (HCWs) are thought to have been infected, and there is evidence that some of these cases may also have been nosocomially linked, with both HCW to HCW and patient to HCW transmission being reported. From the start of the SARS-CoV-2 pandemic interventions in hospitals such as testing patients on admission and universal mask wearing were introduced to stop spread within and between patient and HCW populations, the effectiveness of which are largely unknown. MATERIALS/METHODS Using an individual-based model of within-hospital transmission, we estimated the contribution of individual interventions (together and in combination) to the effectiveness of the overall package of interventions implemented in English hospitals during the COVID-19 pandemic. A panel of experts in infection prevention and control informed intervention choice and helped ensure the model reflected implementation in practice. Model parameters and associated uncertainty were derived using national and local data, literature review and formal elicitation of expert opinion. We simulated scenarios to explore how many nosocomial infections might have been seen in patients and HCWs if interventions had not been implemented. We simulated the time period from March-2020 to July-2022 encompassing different strains and multiple doses of vaccination. RESULTS Modelling results suggest that in a scenario without inpatient testing, infection prevention and control measures, and reductions in occupancy and visitors, the number of patients developing a nosocomial SARS-CoV-2 infection could have been twice as high over the course of the pandemic, and over 600,000 HCWs could have been infected in the first wave alone. Isolation of symptomatic HCWs and universal masking by HCWs were the most effective interventions for preventing infections in both patient and HCW populations. Model findings suggest that collectively the interventions introduced over the SARS-CoV-2 pandemic in England averted 400,000 (240,000 - 500,000) infections in inpatients and 410,000 (370,000 - 450,000) HCW infections. CONCLUSIONS Interventions to reduce the spread of nosocomial infections have varying impact, but the package of interventions implemented in England significantly reduced nosocomial transmission to both patients and HCWs over the SARS-CoV-2 pandemic.
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Affiliation(s)
- Stephanie Evans
- Fungal, HCAI, AMU & Sepsis Division, UK Health Security Agency, London, AMR, UK.
- Statistics, Modelling and Economics, UK Health Security Agency, London, UK.
| | - James Stimson
- Fungal, HCAI, AMU & Sepsis Division, UK Health Security Agency, London, AMR, UK
- Statistics, Modelling and Economics, UK Health Security Agency, London, UK
| | - Diane Pople
- Fungal, HCAI, AMU & Sepsis Division, UK Health Security Agency, London, AMR, UK
- Statistics, Modelling and Economics, UK Health Security Agency, London, UK
| | - Peter J White
- Statistics, Modelling and Economics, UK Health Security Agency, London, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- NIHR Health Protection Research Unit in Modelling and Health Economics at Imperial College London in partnership with the UK Health Security Agency and London School of Hygiene and Tropical Medicine, London, UK
| | - Mark H Wilcox
- Healthcare-Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, LS1 9JT, UK
- Microbiology, Leeds Teaching Hospitals, Leeds, UK
| | - Julie V Robotham
- Fungal, HCAI, AMU & Sepsis Division, UK Health Security Agency, London, AMR, UK
- Statistics, Modelling and Economics, UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Modelling and Health Economics at Imperial College London in partnership with the UK Health Security Agency and London School of Hygiene and Tropical Medicine, London, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with the, UK Health Security Agency, Oxford, UK
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Ragan SA, Doyle C, Datta N, Abdic H, Wilcox MH, Montgomery R, Crusz SA, Mahida YR, Monaghan TM. Case Series: Efficacy of Polyclonal Intravenous Immunoglobulin for Refractory Clostridioides difficile Infection. Antibodies (Basel) 2024; 13:26. [PMID: 38651406 PMCID: PMC11036217 DOI: 10.3390/antib13020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/16/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Intravenous immunoglobulin (IVIg) for Clostridioides difficile infection (CDI) no longer features in treatment guidelines. However, IVIg is still used by some clinicians for severe or recurrent CDI (rCDI) cases. The main objective of this study was to investigate the efficacy of IVIg and to identify possible predictors of disease resolution post IVIg administration for patients with CDI. METHODS This retrospective observational cohort study of patients ≥2 years old hospitalised with severe, relapsing, or rCDI treated with IVIg therapy was performed in a large UK tertiary hospital between April 2018 and March 2023. Scanned electronic notes from patient admissions and clinical reporting systems were used to collect relevant data. RESULTS In total, 20/978 patients diagnosed with CDI over the 5-year study were treated with IVIg. Twelve (60%) had hospital-onset CDI. Eleven of the twenty patients (55%) responded to treatment, with a mean of 8.6 (SD 10.7) days to disease resolution. Sixteen (80%) patients were treated for severe CDI and four (20%) for rCDI (n = 3) and relapsing CDI (n = 1). There were no statistically significant differences in possible independent predictors of disease resolution post IVIg administration between groups. There was an average of 6.2 (4.9) days to IVIg administration after diagnosis with no difference between responders and non-responders (p = 0.88) and no further significant difference in additional indicators. Four (36%) of the responders were immunosuppressed compared to just one (11%) of the non-responders (p = 0.15). Six of the responders (two with recurrent and four with severe CDI) improved rapidly within 2 days, and three of these were immunosuppressed. CONCLUSION We observed disease resolution post IVIg therapy in over 50% of patients with refractory CDI. Our data also support a potential enhanced effect of IVIg in immunosuppressed individuals. Thus, the role of IVIg for CDI treatment, particularly in the immunosuppressed, warrants future case-control studies coupled to mechanistic investigations to improve care for this ongoing significant healthcare-associated infection.
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Affiliation(s)
- Sophie A. Ragan
- Department of Gastroenterology, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK; (S.A.R.); (H.A.)
| | - Caitlin Doyle
- School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK; (C.D.); (N.D.)
| | - Neha Datta
- School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK; (C.D.); (N.D.)
| | - Heather Abdic
- Department of Gastroenterology, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK; (S.A.R.); (H.A.)
| | - Mark H. Wilcox
- Healthcare Associated Infection Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds LS9 7TF, UK;
- Department of Microbiology, Leeds Teaching Hospitals, Leeds LS1 3EX, UK
| | - Ros Montgomery
- Infection and Prevention Control, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK;
| | - Shanika A. Crusz
- Department of Microbiology, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK;
| | - Yashwant R. Mahida
- NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK;
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham NG7 2UH, UK
- Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK;
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham NG7 2UH, UK
- Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
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Fitzpatrick F, Brennan R, van Prehn J, Skally M, Brady M, Burns K, Rooney C, Wilcox MH. European Practice for CDI Treatment. Adv Exp Med Biol 2024; 1435:57-84. [PMID: 38175471 DOI: 10.1007/978-3-031-42108-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile infection (CDI) remains a significant cause of morbidity and mortality worldwide. Historically, two antibiotics (metronidazole and vancomycin) and a recent third (fidaxomicin) have been used for CDI treatment; convincing data are now available showing that metronidazole is the least efficacious agent. The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) management guidance for CDI were updated in 2021. This guidance document outlines the treatment options for a variety of CDI clinical scenarios and for non-antimicrobial management (e.g., faecal microbiota transplantation, FMT). One of the main changes is that metronidazole is no longer recommended as first-line CDI treatment. Rather, fidaxomicin is preferred on the basis of reduced recurrence rates with vancomycin as an acceptable alternative. Recommended options for recurrent CDI now include bezlotoxumab as well as FMT.A 2017 survey of 20 European countries highlighted variation internationally in CDI management strategies. A variety of restrictions were in place in 65% countries prior to use of new anti-CDI treatments, including committee/infection specialist approval or economic review/restrictions. This survey was repeated in November 2022 to assess the current landscape of CDI management practices in Europe. Of 64 respondents from 17 countries, national CDI guidelines existed in 14 countries, and 11 have already/plan to incorporate the ESCMID 2021 CDI guidance, though implementation has not been surveyed in 6. Vancomycin is the most commonly used first-line agent for the treatment of CDI (n = 42, 66%), followed by fidaxomicin (n = 30, 47%). Six (9%) respondents use metronidazole as first-line agent for CDI treatment, whereas 22 (34%) only in selected low-risk patient groups. Fidaxomicin is more likely to be used in high-risk patient groups. Availability of anti-CDI therapy influenced prescribing in six respondents (9%). Approval pre-prescription was required before vancomycin (n = 3, 5%), fidaxomicin (n = 10, 6%), bezlotoxumab (n = 11, 17%) and FMT (n = 10, 6%). Implementation of CDI guidelines is rarely audited.Novel anti-CDI agents are being evaluated; it is not yet clear what will be the roles of these agents. The treatment of recurrent CDI is particularly troublesome, and several different live biotherapeutics are being developed, in addition to FMT.
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Affiliation(s)
- Fidelma Fitzpatrick
- Department of Clinical Microbiology, The Royal College of Surgeons in Ireland, Dublin, Ireland.
- Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland.
| | - Robert Brennan
- Department of Clinical Microbiology, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mairead Skally
- Department of Clinical Microbiology, The Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
| | - Melissa Brady
- Health Protection Surveillance Centre (HPSC), Dublin, Ireland
| | - Karen Burns
- Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
| | - Christopher Rooney
- Microbiology, Leeds Teaching Hospitals, Leeds, UK
- University of Leeds, Leeds, UK
| | - Mark H Wilcox
- University of Leeds, Leeds, UK.
- Leeds Teaching Hospitals and Leeds Regional Public Health Laboratory, UK Health Security Agency (UKHSA), Leeds, UK.
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Galley NF, Greetham D, Alamán-Zárate MG, Williamson MP, Evans CA, Spittal WD, Buddle JE, Freeman J, Davis GL, Dickman MJ, Wilcox MH, Lovering AL, Fagan RP, Mesnage S. Clostridioides difficile canonical L,D-transpeptidases catalyze a novel type of peptidoglycan cross-links and are not required for beta-lactam resistance. J Biol Chem 2024; 300:105529. [PMID: 38043796 PMCID: PMC10792238 DOI: 10.1016/j.jbc.2023.105529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea worldwide with significant morbidity and mortality. This organism is naturally resistant to several beta-lactam antibiotics that inhibit the polymerization of peptidoglycan, an essential component of the bacteria cell envelope. Previous work has revealed that C. difficile peptidoglycan has an unusual composition. It mostly contains 3-3 cross-links, catalyzed by enzymes called L,D-transpeptidases (Ldts) that are poorly inhibited by beta-lactams. It was therefore hypothesized that peptidoglycan polymerization by these enzymes could underpin antibiotic resistance. Here, we investigated the catalytic activity of the three canonical Ldts encoded by C. difficile (LdtCd1, LdtCd2, and LdtCd3) in vitro and explored their contribution to growth and antibiotic resistance. We show that two of these enzymes catalyze the formation of novel types of peptidoglycan cross-links using meso-diaminopimelic acid both as a donor and an acceptor, also observed in peptidoglycan sacculi. We demonstrate that the simultaneous deletion of these three genes only has a minor impact on both peptidoglycan structure and resistance to beta-lactams. This unexpected result therefore implies that the formation of 3-3 peptidoglycan cross-links in C. difficile is catalyzed by as yet unidentified noncanonical Ldt enzymes.
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Affiliation(s)
- Nicola F Galley
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Darren Greetham
- School of Biosciences, University of Sheffield, Sheffield, UK
| | | | | | - Caroline A Evans
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - William D Spittal
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Healthcare Associated Infections Research Group, Leeds Institute of Medical Research University of Leeds, Leeds, UK
| | | | - Jane Freeman
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Healthcare Associated Infections Research Group, Leeds Institute of Medical Research University of Leeds, Leeds, UK
| | - Georgina L Davis
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Healthcare Associated Infections Research Group, Leeds Institute of Medical Research University of Leeds, Leeds, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Healthcare Associated Infections Research Group, Leeds Institute of Medical Research University of Leeds, Leeds, UK
| | | | - Robert P Fagan
- School of Biosciences, University of Sheffield, Sheffield, UK
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Evans S, Stimson J, Pople D, Wilcox MH, Hope R, Robotham JV. Evaluating the impact of testing strategies for the detection of nosocomial COVID-19 in English hospitals through data-driven modeling. Front Med (Lausanne) 2023; 10:1166074. [PMID: 37928455 PMCID: PMC10622791 DOI: 10.3389/fmed.2023.1166074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction During the first wave of the COVID-19 pandemic 293,204 inpatients in England tested positive for SARS-CoV-2. It is estimated that 1% of these cases were hospital-associated using European centre for disease prevention and control (ECDC) and Public Health England (PHE) definitions. Guidelines for preventing the spread of SARS-CoV-2 in hospitals have developed over time but the effectiveness and efficiency of testing strategies for preventing nosocomial transmission has not been explored. Methods Using an individual-based model, parameterised using multiple datasets, we simulated the transmission of SARS-CoV-2 to patients and healthcare workers between March and August 2020 and evaluated the efficacy of different testing strategies. These strategies were: 0) Testing only symptomatic patients on admission; 1) Testing all patients on admission; 2) Testing all patients on admission and again between days 5 and 7, and 3) Testing all patients on admission, and again at days 3, and 5-7. In addition to admissions testing, patients that develop a symptomatic infection while in hospital were tested under all strategies. We evaluated the impact of testing strategy, test characteristics and hospital-related factors on the number of nosocomial patient infections. Results Modelling suggests that 84.6% (95% CI: 84.3, 84.7) of community-acquired and 40.8% (40.3, 41.3) of hospital-associated SARS-CoV-2 infections are detectable before a patient is discharged from hospital. Testing all patients on admission and retesting after 3 or 5 days increases the proportion of nosocomial cases detected by 9.2%. Adding discharge testing increases detection by a further 1.5% (relative increase). Increasing occupancy rates, number of beds per bay, or the proportion of admissions wrongly suspected of having COVID-19 on admission and therefore incorrectly cohorted with COVID-19 patients, increases the rate of nosocomial transmission. Over 30,000 patients in England could have been discharged while incubating a non-detected SARS-CoV-2 infection during the first wave of the COVID-19 pandemic, of which 3.3% could have been identified by discharge screening. There was no significant difference in the rates of nosocomial transmission between testing strategies or when the turnaround time of the test was increased. Discussion This study provides insight into the efficacy of testing strategies in a period unbiased by vaccines and variants. The findings are relevant as testing programs for SARS-CoV-2 are scaled back, and possibly if a new vaccine escaping variant emerges.
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Affiliation(s)
- Stephanie Evans
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
- Statistics, Modelling and Economics, UK Health Security Agency, London, United Kingdom
- NIHR Health Protection Research Unit in Modelling and Health Economics at Imperial College London in Partnership With UKHSA and the London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - James Stimson
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
- Statistics, Modelling and Economics, UK Health Security Agency, London, United Kingdom
| | - Diane Pople
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
- Statistics, Modelling and Economics, UK Health Security Agency, London, United Kingdom
| | - Mark H Wilcox
- Healthcare-Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
- Microbiology, Leeds Teaching Hospitals, Leeds, United Kingdom
- NIHR Health Protection Research Unit in Healthcare-Associated Infections and Antimicrobial Resistance at University of Oxford in Partnership with UKHSA, Oxford, United Kingdom
| | - Russell Hope
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
| | - Julie V Robotham
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
- NIHR Health Protection Research Unit in Modelling and Health Economics at Imperial College London in Partnership With UKHSA and the London School of Hygiene and Tropical Medicine, London, United Kingdom
- NIHR Health Protection Research Unit in Healthcare-Associated Infections and Antimicrobial Resistance at University of Oxford in Partnership with UKHSA, Oxford, United Kingdom
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Swart N, Sinha AM, Bentley A, Smethurst H, Spencer G, Ceder S, Wilcox MH. A cost-utility analysis of two Clostridioides difficile infection guideline treatment pathways. Clin Microbiol Infect 2023; 29:1291-1297. [PMID: 37356620 DOI: 10.1016/j.cmi.2023.06.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023]
Abstract
OBJECTIVES Treatment guidelines are key drivers of prescribing practice in the management of Clostridioides difficile infection (CDI), but recommendations on best practice can vary. We conducted a cost-utility analysis to compare the treatment pathway recommended by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) guideline with the pathway proposed by the National Institute for Health and Care Excellence (NICE) guideline, from the perspective of the UK National Health Service. METHODS A decision tree modelling approach was adopted to reflect the treatment pathway for CDI as outlined in ESCMID and NICE guidelines. Patients experiencing a CDI infection received up to three treatments per infection to achieve a response and could subsequently experience up to two recurrences. Data on patient demographics, treatment response, recurrence, utilities, CDI-related mortality, and costs were taken from published literature. RESULTS The ESCMID treatment pathway was cost-effective versus the NICE treatment pathway at a threshold of £20 000 per quality-adjusted life year gained, with an incremental cost-effectiveness ratio of £4931. Cost-effectiveness was driven by differences in index infection recommendations (ESCMID recommends fidaxomicin as first-line treatment whereas NICE recommends vancomycin). The model results were robust to variations in inputs investigated in scenarios and sensitivity analyses, and probabilistic sensitivity analysis demonstrated that the ESCMID guideline treatment strategy had a 100% likelihood of being cost-effective versus the NICE treatment strategy. DISCUSSION Compared with the NICE guideline, the ESCMID guideline recommendations for treating an index CDI represent the most cost-effective use of healthcare resources from the perspective of the UK National Health Service.
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Affiliation(s)
| | | | | | | | | | | | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom.
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Olaitan AO, Dureja C, Youngblom MA, Topf MA, Shen WJ, Gonzales-Luna AJ, Deshpande A, Hevener KE, Freeman J, Wilcox MH, Palmer KL, Garey KW, Pepperell CS, Hurdle JG. Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile. Nat Commun 2023; 14:4130. [PMID: 37438331 DOI: 10.1038/s41467-023-39429-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/13/2023] [Indexed: 07/14/2023] Open
Abstract
Severe outbreaks and deaths have been linked to the emergence and global spread of fluoroquinolone-resistant Clostridioides difficile over the past two decades. At the same time, metronidazole, a nitro-containing antibiotic, has shown decreasing clinical efficacy in treating C. difficile infection (CDI). Most metronidazole-resistant C. difficile exhibit an unusual resistance phenotype that can only be detected in susceptibility tests using molecularly intact heme. Here, we describe the mechanism underlying this trait. We find that most metronidazole-resistant C. difficile strains carry a T-to-G mutation (which we term PnimBG) in the promoter of gene nimB, resulting in constitutive transcription. Silencing or deleting nimB eliminates metronidazole resistance. NimB is related to Nim proteins that are known to confer resistance to nitroimidazoles. We show that NimB is a heme-dependent flavin enzyme that degrades nitroimidazoles to amines lacking antimicrobial activity. Furthermore, occurrence of the PnimBG mutation is associated with a Thr82Ile substitution in DNA gyrase that confers fluoroquinolone resistance in epidemic strains. Our findings suggest that the pandemic of fluoroquinolone-resistant C. difficile occurring over the past few decades has also been characterized by widespread resistance to metronidazole.
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Affiliation(s)
- Abiola O Olaitan
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Madison A Youngblom
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Madeline A Topf
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Wan-Jou Shen
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Aditi Deshpande
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jane Freeman
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA.
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA.
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Gonzales-Luna AJ, Skinner AM, Alonso CD, Bouza E, Cornely OA, de Meij TGJ, Drew RJ, Garey KW, Gerding DN, Johnson S, Kahn SA, Kato H, Kelly CP, Kelly CR, Kociolek LK, Kuijper EJ, Louie T, Riley TV, Sandora TJ, Vehreschild MJGT, Wilcox MH, Dubberke ER. Redefining Clostridioides difficile infection antibiotic response and clinical outcomes. Lancet Infect Dis 2023; 23:e259-e265. [PMID: 37062301 DOI: 10.1016/s1473-3099(23)00047-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 04/18/2023]
Abstract
With the approval and development of narrow-spectrum antibiotics for the treatment of Clostridioides difficile infection (CDI), the primary endpoint for treatment success of CDI antibiotic treatment trials has shifted from treatment response at end of therapy to sustained response 30 days after completed therapy. The current definition of a successful response to treatment (three or fewer unformed bowel movements [UBMs] per day for 1-2 days) has not been validated, does not reflect CDI management, and could impair assessments for successful treatment at 30 days. We propose new definitions to optimise trial design to assess sustained response. Primarily, we suggest that the initial response at the end of treatment be defined as (1) three or fewer UBMs per day, (2) a reduction in UBMs of more than 50% per day, (3) a decrease in stool volume of more than 75% for those with ostomy, or (4) attainment of bowel movements of Bristol Stool Form Scale types 1-4, on average, by day 2 after completion of primary CDI therapy (ie, assessed on day 11 and day 12 of a 10-day treatment course) and following an investigator determination that CDI treatment can be ceased.
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Affiliation(s)
- Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Andrew M Skinner
- Department of Medicine, Loyola University Medical Center, Maywood, IL, USA; Department of Medicine and Department of Research, Edward Hines Jr Veterans Administration Hospital, Hines, IL, USA
| | - Carolyn D Alonso
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emilio Bouza
- Department of Microbiology and Infectious Diseases, Universidad Complutense, Madrid, Spain
| | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease, Translational Research, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf and Excellence Center for Medical Mycology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Clinical Trials Centre Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Tim G J de Meij
- Department of Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Richard J Drew
- Clinical Innovation Unit, Rotunda Hospital and Children's Health Ireland, Dublin, Ireland; Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland at Temple Street, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Dale N Gerding
- Department of Medicine and Department of Research, Edward Hines Jr Veterans Administration Hospital, Hines, IL, USA
| | - Stuart Johnson
- Department of Medicine and Department of Research, Edward Hines Jr Veterans Administration Hospital, Hines, IL, USA
| | - Stacy A Kahn
- Division of Gastroenterology, Hepatology & Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Haru Kato
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ciaran P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Colleen R Kelly
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Larry K Kociolek
- Division of Pediatric Infectious Diseases, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands
| | - Thomas Louie
- Infectious Diseases, Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Thomas J Sandora
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Maria J G T Vehreschild
- Infectious Diseases, Department of Internal Medicine, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mark H Wilcox
- Microbiology, Old Medical School, Leeds General Infirmary, Leeds, UK
| | - Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA.
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9
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Wilcox MH. Molecular testing in suspected infectious diarrhoea-the value of negative results. Lancet Infect Dis 2023:S1473-3099(23)00135-4. [PMID: 37116528 DOI: 10.1016/s1473-3099(23)00135-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 04/30/2023]
Affiliation(s)
- Mark H Wilcox
- Leeds Teaching Hospitals & University of Leeds, Microbiology, Leeds General Infirmary, Leeds LS1 3EX, UK.
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10
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Davis Birch WA, Moura IB, Ewin DJ, Wilcox MH, Buckley AM, Culmer PR, Kapur N. MiGut: A scalable in vitro platform for simulating the human gut microbiome-Development, validation and simulation of antibiotic-induced dysbiosis. Microb Biotechnol 2023; 16:1312-1324. [PMID: 37035991 DOI: 10.1111/1751-7915.14259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/22/2023] [Indexed: 04/11/2023] Open
Abstract
In vitro models of the human colon have been used extensively in understanding the human gut microbiome (GM) and evaluating how internal and external factors affect the residing bacterial populations. Such models have been shown to be highly predictive of in vivo outcomes and have a number of advantages over animal models. The complexity required by in vitro models to closely mimic the physiology of the colon poses practical limits on their scalability. The scalable Mini Gut (MiGut) platform presented in this paper allows considerable expansion of model replicates and enables complex study design, without compromising on in vivo reflectiveness as is often the case with other model systems. MiGut has been benchmarked against a validated gut model in a demanding 9-week study. MiGut showed excellent repeatability between model replicates and results were consistent with those of the benchmark system. The novel technology presented in this paper makes it conceivable that tens of models could be run simultaneously, allowing complex microbiome-xenobiotic interactions to be explored in far greater detail, with minimal added resources or complexity. This platform expands the capacity to generate clinically relevant data to support our understanding of the cause-effect relationships that govern the GM.
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Affiliation(s)
- William A Davis Birch
- School of Mechanical Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Ines B Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - Duncan J Ewin
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - Mark H Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
- Microbiology, Leeds Teaching Hospitals NHS Trust, Old Medical School, Leeds General Infirmary, Leeds, LS1 3EX, UK
| | - Anthony M Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
- Microbiome and Nutritional Science Group, Faculty of Food Science and Nutrition, School of Food Science, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter R Culmer
- School of Mechanical Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Nikil Kapur
- School of Mechanical Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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11
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Dingle KE, Freeman J, Didelot X, Quan TP, Eyre DW, Swann J, Spittal WD, Clark EV, Jolley KA, Walker AS, Wilcox MH, Crook DW. Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile. mBio 2023; 14:e0024323. [PMID: 37017518 PMCID: PMC10128037 DOI: 10.1128/mbio.00243-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Clostridioides difficile remains a key cause of healthcare-associated infection, with multidrug-resistant (MDR) lineages causing high-mortality (≥20%) outbreaks. Cephalosporin treatment is a long-established risk factor, and antimicrobial stewardship is a key control. A mechanism underlying raised cephalosporin MICs has not been identified in C. difficile, but among other species, this is often acquired via amino acid substitutions in cell wall transpeptidases (penicillin binding proteins [PBPs]). Here, we investigated five C. difficile transpeptidases (PBP1 to PBP5) for recent substitutions, associated cephalosporin MICs, and co-occurrence with fluoroquinolone resistance. Previously published genome assemblies (n = 7,096) were obtained, representing 16 geographically widespread lineages, including healthcare-associated ST1(027). Recent amino acid substitutions were found within PBP1 (n = 50) and PBP3 (n = 48), ranging from 1 to 10 substitutions per genome. β-Lactam MICs were measured for closely related pairs of wild-type and PBP-substituted isolates separated by 20 to 273 single nucleotide polymorphisms (SNPs). Recombination-corrected phylogenies were constructed to date substitution acquisition. Key substitutions such as PBP3 V497L and PBP1 T674I/N/V emerged independently across multiple lineages. They were associated with extremely high cephalosporin MICs; 1 to 4 doubling dilutions >wild-type, up to 1,506 μg/mL. Substitution patterns varied by lineage and clade, showed geographic structure, and occurred post-1990, coincident with the gyrA and/or gyrB substitutions conferring fluoroquinolone resistance. In conclusion, recent PBP1 and PBP3 substitutions are associated with raised cephalosporin MICs in C. difficile. Their co-occurrence with fluoroquinolone resistance hinders attempts to understand the relative importance of these drugs in the dissemination of epidemic lineages. Further controlled studies of cephalosporin and fluoroquinolone stewardship are needed to determine their relative effectiveness in outbreak control. IMPORTANCE Fluoroquinolone and cephalosporin use in healthcare settings has triggered outbreaks of high-mortality, multidrug-resistant C. difficile infection. Here, we identify a mechanism associated with raised cephalosporin MICs in C. difficile comprising amino acid substitutions in two cell wall transpeptidase enzymes (penicillin binding proteins). The higher the number of substitutions, the greater the impact on phenotype. Dated phylogenies revealed that substitutions associated with raised cephalosporin and fluoroquinolone MICs were co-acquired immediately before clinically important outbreak strains emerged. PBP substitutions were geographically structured within genetic lineages, suggesting adaptation to local antimicrobial prescribing. Antimicrobial stewardship of cephalosporins and fluoroquinolones is an effective means of C. difficile outbreak control. Genetic changes associated with raised MIC may impart a "fitness cost" after antibiotic withdrawal. Our study therefore identifies a mechanism that may explain the contribution of cephalosporin stewardship to resolving outbreak conditions. However, due to the co-occurrence of raised cephalosporin MICs and fluoroquinolone resistance, further work is needed to determine the relative importance of each.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jane Freeman
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
- Healthcare Associated Infections Research Group, The Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- Big Data Institute, Nuffield Department of Population Health, Oxford University of Oxford, Oxford, United Kingdom
| | - Jeremy Swann
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - William D Spittal
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
- Healthcare Associated Infections Research Group, The Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Emma V Clark
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
- Healthcare Associated Infections Research Group, The Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Keith A Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
- Healthcare Associated Infections Research Group, The Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
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12
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Etifa P, Rodríguez C, Harmanus C, Sanders IMJG, Sidorov IA, Mohammed OA, Savage E, Timms AR, Freeman J, Smits WK, Wilcox MH, Baines SD. Non-Toxigenic Clostridioides difficile Strain E4 (NTCD-E4) Prevents Establishment of Primary C. difficile Infection by Epidemic PCR Ribotype 027 in an In Vitro Human Gut Model. Antibiotics (Basel) 2023; 12:antibiotics12030435. [PMID: 36978302 PMCID: PMC10044524 DOI: 10.3390/antibiotics12030435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
Clostridioides difficile infection (CDI) remains a significant healthcare burden. Non-toxigenic C. difficile (NTCD) strains have shown a benefit in preventing porcine enteritis and in human recurrent CDI. In this study, we evaluated the efficacy of metronidazole-resistant NTCD-E4 in preventing CDI facilitated by a range of antimicrobials in an in vitro human gut model. NTCD-E4 spores (at a dose of 107) were instilled 7 days before a clinical ribotype (RT) 027 (at the same dose) strain (210). In separate experiments, four different antimicrobials were used to perturb gut microbiotas; bacterial populations and cytotoxin production were determined using viable counting and Vero cell cytotoxicity, respectively. RT027 and NTCD-E4 proliferated in the in vitro model when inoculated singly, with RT027 demonstrating high-level cytotoxin (3-5-log10-relative units) production. In experiments where the gut model was pre-inoculated with NTCD-E4, RT027 was remained quiescent and failed to produce cytotoxins. NTCD-E4 showed mutations in hsmA and a gene homologous to CD196-1331, previously linked to medium-dependent metronidazole resistance, but lacked other metronidazole resistance determinants. This study showed that RT027 was unable to elicit simulated infection in the presence of NTCD-E4 following stimulation by four different antimicrobials. These data complement animal and clinical studies in suggesting NTCD offer prophylactic potential in the management of human CDI.
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Affiliation(s)
- Perezimor Etifa
- Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, Reading RG6 6DZ, UK
| | - César Rodríguez
- Facultad de Microbiología & CIET, Universidad de Costa Rica, San Pedro 11501-2060, Costa Rica
| | - Céline Harmanus
- Leiden University Medical Center, Department of Medical Microbiology, Albinusdreef, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Ingrid M. J. G. Sanders
- Leiden University Medical Center, Department of Medical Microbiology, Albinusdreef, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Igor A. Sidorov
- Leiden University Medical Center, Department of Medical Microbiology, Albinusdreef, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Olufunmilayo A. Mohammed
- Department of Clinical, Pharmaceutical and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Emily Savage
- Department of Clinical, Pharmaceutical and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Andrew R. Timms
- Department of Clinical, Pharmaceutical and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Jane Freeman
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds LS1 3EX, UK
| | - Wiep Klaas Smits
- Leiden University Medical Center, Department of Medical Microbiology, Albinusdreef, P.O. Box 9600, 2300 RC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Mark H. Wilcox
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds LS1 3EX, UK
| | - Simon D. Baines
- Department of Clinical, Pharmaceutical and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
- Correspondence:
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13
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Agnew E, Davies KA, Viprey VF, Evans S, Davis GL, Hope R, Wilcox MH, Wingen-Heimann SM, Robotham JV. Impact of testing on Clostridioides difficile infection in hospitals across Europe: a mathematical model. Clin Microbiol Infect 2023:S1198-743X(23)00057-5. [PMID: 36773769 DOI: 10.1016/j.cmi.2023.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/18/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
OBJECTIVES The prevalence of Clostridioides difficile infection (CDI) has been shown to vary markedly between European countries, both in hospitals and in the community. Determining the true prevalence has proven challenging. Without systematic testing in hospitals, the unchecked transmission of CDI can lead to large outbreaks in more susceptible cohorts. We investigate the success of CDI surveillance and control measures across Europe, by examining the dynamics of disease spread from the community into a hospital setting. We focus on national differences, such as variability in testing and sampling, disease prevalence in communities and hospitals, and antimicrobial usage. METHODS We developed a stochastic, compartmental, dynamic mathematical model parameterized using sampling and testing rate data from COMBACTE-CDI, a multicountry study in which all diarrhoeal stool samples (N = 3163) from European laboratories were tested for CDI, and data for antimicrobial usage and incidence of hospital cases sourced from the European Centre for Disease Prevention and Control. RESULTS The framework estimates the prevalence of CDI among hospital patients across European countries and explores how national differences impact the dynamics, transmission, and relative incidence of CDI within the hospital setting. The model illustrates the mechanisms influencing these national differences, namely, antimicrobial usage rates, national sampling and testing rates, and community prevalence of CDI. DISCUSSION Differential costs for testing and practicalities of scaling up testing mean every country needs to consider balancing CDI testing costs against the costs of treatment and care of patients with CDI.
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Affiliation(s)
- Emily Agnew
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK.
| | - Kerrie A Davies
- COMBACTE-CDI European Coordinator Laboratory, Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; European Society of Clinical Microbiology and Infectious Diseases Study Group for Clostridioides difficile, UK
| | - Virginie F Viprey
- COMBACTE-CDI European Coordinator Laboratory, Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Stephanie Evans
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - Georgina L Davis
- COMBACTE-CDI European Coordinator Laboratory, Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Russell Hope
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - Mark H Wilcox
- COMBACTE-CDI European Coordinator Laboratory, Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; European Society of Clinical Microbiology and Infectious Diseases Study Group for Clostridioides difficile, UK
| | - Sebastian M Wingen-Heimann
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; FOM University of Applied Sciences, Cologne, Germany
| | - Julie V Robotham
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
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14
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Garey KW, Rose W, Gunter K, Serio AW, Wilcox MH. Omadacycline and Clostridioides difficile: A Systematic Review of Preclinical and Clinical Evidence. Ann Pharmacother 2023; 57:184-192. [PMID: 35656828 PMCID: PMC9874691 DOI: 10.1177/10600280221089007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVE The objective of this systematic review is to summarize in vitro, preclinical, and human data related to omadacycline and Clostridioides difficile infection (CDI). DATA SOURCES PubMed and Google Scholar were searched for "omadacycline" AND ("Clostridium difficile" OR "C difficile" OR "Clostridioides difficile") for any studies published before February 15, 2022. The US Food and Drug Administration (FDA) Adverse Events Reporting System (AERS) was searched for omadacycline (for reports including "C. difficile" or "CDI" or "gastrointestinal infection"). The publications list publicly available at Paratek Pharmaceuticals, Inc. Web site was reviewed. STUDY SELECTION AND DATA EXTRACTION Publications presenting primary data on omadacycline and C. difficile published in English were included. DATA SYNTHESIS Preclinical and clinical evidence was extracted from 14 studies. No case reports in indexed literature and no reports on FDA AERS were found. Omadacycline has potent in vitro activity against many C. difficile clinical strains and diverse ribotypes. In phase 3 studies, there were no reports of CDI in patients who received omadacycline for either community-acquired bacterial pneumonia or acute bacterial skin and skin structure infection. RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE Omadacycline should be considered a low-risk antibiotic regarding its propensity to cause CDI. CONCLUSIONS Reducing the burden of CDI on patients and the health care system should be a priority. Patients with appropriate indications who are at heightened risk of CDI may be suitable candidates for omadacycline therapy. In these patients, omadacycline may be preferable to antibiotics with a high CDI risk.
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Affiliation(s)
- Kevin W. Garey
- University of Houston College of
Pharmacy, Houston, TX, USA
| | - Warren Rose
- School of Pharmacy, University of
Wisconsin–Madison, Madison, WI, USA
| | - Kyle Gunter
- Paratek Pharmaceuticals, Inc., King of
Prussia, PA, USA,Kyle Gunter, Director of Medical Science,
Paratek Pharmaceuticals, Inc., 1000 First Avenue, Suite 200, King of Prussia, PA
19406, USA.
| | | | - Mark H. Wilcox
- University of Leeds & Leeds
Teaching Hospitals, Leeds, UK
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15
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Viprey VF, Granata G, Vendrik KEW, Davis GL, Petrosillo N, Kuijper EJ, Vilken T, Lammens C, Schotsman JJ, Benson AD, Cataldo MA, van der Kooi TII, Wilcox MH, Davies KA, Davies KA, Wilcox MH, Kuijper E, Rupnik M, Wingen-Heimann S, Tacconelli E, Vilken T, Petrosillo N, Bonten M, Cleuziat P, Webber C, Rupnik M, Wilcox M. European survey on the current surveillance practices, management guidelines, treatment pathways and heterogeneity of testing of Clostridioides difficile, 2018-2019: results from The Combatting Bacterial Resistance in Europe CDI (COMBACTE-CDI). J Hosp Infect 2023; 131:213-220. [PMID: 36462673 DOI: 10.1016/j.jhin.2022.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Awareness and compliance with international guidelines for diagnosis and clinical management of Clostridioides difficile infection (CDI) are unknown. AIM To compare the awareness and compliance with the recommended strategies for diagnosis and clinical management of CDI across Europe in 2018-2019. METHODS Hospital sites and their associated community practices across 12 European countries completed an online survey in 2018-2019, to report on their practices in terms of surveillance, prevention, diagnosis, and treatment of CDI. Responses were collected from 105 hospitals and 39 community general practitioners (GPs). FINDINGS Hospital sites of 11 countries reported participation in national surveillance schemes compared with six countries for international schemes. The European Society of Clinical Microbiology and Infectious Diseases (ESCMID)-recommended CDI testing methodologies were used by 82% (86/105) of hospitals, however countries reporting the highest incidence of CDI used non-recommended tests. Over 75% (80/105) of hospitals were aware of the most recent European CDI treatment guidelines at the time of this survey compared with only 26% (10/39) of surveyed GPs. However, up to 15% (16/105) of hospitals reported using the non-recommended metronidazole for recurrent CDI cases, sites in countries with lower awareness of CDI treatment guidelines. Only 37% (39/105) of hospitals adopted contact isolation precautions in case of suspected CDI. CONCLUSION Good awareness of guidelines for the management of CDI was observed across the surveyed European hospital sites. However, low compliance with diagnostic testing guidelines, infection control measures for suspected CDI, and insufficient awareness of treatment guidelines continued to be reported in some countries.
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Affiliation(s)
- V F Viprey
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
| | - G Granata
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - K E W Vendrik
- Leiden University Medical Center, Leiden, the Netherlands; National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - G L Davis
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - N Petrosillo
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - E J Kuijper
- Leiden University Medical Center, Leiden, the Netherlands; National Institute for Public Health and the Environment, Bilthoven, the Netherlands; European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides Difficile (ESGCD)
| | - T Vilken
- Laboratory of Medical Microbiology, University of Antwerp, Antwerp, Belgium
| | - C Lammens
- Laboratory of Medical Microbiology, University of Antwerp, Antwerp, Belgium
| | - J J Schotsman
- University Medical Centre Utrecht, Utrecht, the Netherlands
| | - A D Benson
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - M A Cataldo
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - T I I van der Kooi
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - M H Wilcox
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides Difficile (ESGCD); Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - K A Davies
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides Difficile (ESGCD); Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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16
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Wingen-Heimann SM, Davies K, Viprey VF, Davis G, Wilcox MH, Vehreschild MJGT, Lurienne L, Bandinelli PA, Cornely OA, Vilken T, Hopff SM, Vehreschild JJ, Webber C, Rupnik M, Wilcox M. Clostridioides difficile infection (CDI): A pan-European multi-center cost and resource utilization study, results from the Combatting Bacterial Resistance in Europe CDI (COMBACTE-CDI). Clin Microbiol Infect 2022; 29:651.e1-651.e8. [PMID: 36586512 DOI: 10.1016/j.cmi.2022.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Clostridioides difficile infection (CDI) is one of the leading nosocomial infections worldwide, resulting in a significantly increasing burden on the healthcare systems. However, Pan-European data about cost and resource utilization of CDI treatment do not exist. METHODS A retrospective analysis within the Combatting Bacterial Resistance in Europe CDI project was conducted based on resource costs for inpatient treatment and productivity costs. Country-specific cost values were converted to EURO referred to 1 January, 2019 values. Differences in price levels for healthcare services among the participating countries were adjusted by using an international approach of the Organisation for Economic Co-operation and Development. As the study focused on patients with recurrent CDI, the observed study population was categorized into (a) patients with CDI but without CDI recurrence (case group), (b) patients with CDI recurrence (recurrence group), and (c) patients without CDI (control group). RESULTS Overall, 430 hospitalized patients from 12 European countries were included into the analysis between July 2018 and November 2018. Distribution of mean hospital length of stay and mean overall costs per patient between the case group, recurrence group, and control group were as follows: 22 days (95% CI 17-27 days) vs. 55 days (95% CI 17-94 days) vs. 26 days (95% CI 22-31 days; p 0.008) and € 15 242 (95% CI 10 593-19 891) vs. € 52 024 (95% CI 715-103 334) vs. € 21 759 (95% CI 16 484-27 035; p 0.010), respectively. The CDI recurrence rate during the observational period was 18%. Change escalation in CDI medication (OR 3.735) and treatment in an intensive care unit (OR 5.454) were found to be the most important variables associated with increased overall costs of patients with CDI. CONCLUSIONS Treatment of patients with recurrent CDI results in a significant burden. Prevention of CDI recurrences should be in focus of daily patient care to identify the most cost-effective treatment strategy.
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Affiliation(s)
- Sebastian M Wingen-Heimann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; University of Applied Sciences for Economics and Management (FOM), Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn-Cologne Duesseldorf, Cologne, Germany.
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom; The European Study Group for C. difficile, European Society of Clinical Microbiology and Infectious Disease
| | - Virginie F Viprey
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Georgina Davis
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | | | - Oliver A Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn-Cologne Duesseldorf, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Clinical Trials Centre Cologne (ZKS Köln), Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, Cologne, Germany
| | - Tuba Vilken
- University of Antwerp, Vaccine & Infectious Disease Institute, Laboratory of Medical Microbiology, Antwerp, Belgium
| | - Sina M Hopff
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn-Cologne Duesseldorf, Cologne, Germany
| | - Jörg Janne Vehreschild
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany; Department II of Internal Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt am Main, Germany
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Gonzales-Luna AJ, Skinner AM, Alonso CD, Cornely OA, Garey KW, Gerding DN, Johnson S, Kahn SA, Kelly CP, Kelly CR, Kociolek LK, Kuijper EJ, Kuijper EJ, Louie TJ, Riley TV, Sandora TJ, Vehreschild M, Wilcox MH, Dubberke ER. 221. Assessment and Proposed Revision of Clinical Trial Clostridioides difficile Infection Clinical Response and Outcomes Definitions. Open Forum Infect Dis 2022. [PMCID: PMC9751887 DOI: 10.1093/ofid/ofac492.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Clostridioides difficile infection (CDI) research is limited by a lack of standardized definitions for clinical response and disease outcomes, which impacts clinical drug development and results comparison between studies. We aimed to assess outcome definitions in CDI therapeutic trials to propose new versions that are clinically relevant, discrete and objective. Methods A multidisciplinary group of CDI experts met monthly to review response endpoints from published clinical trials of antibiotic therapy for CDI. Previously published phase III or IV trials were assessed for outcome definitions. Discussions were held to reach a consensus on new clinical trial endpoints for adults and children to improve the accuracy and clinical relevance of measures of treatment success. Results Significant heterogeneity was noted amongst the primary endpoints in phase III and IV CDI antibiotic treatment trials. Initial clinical cure (ICC), strictly defined as < 3 unformed bowel movements/24 hour, and sustained clinical cure (SCC) were primary outcome measures for recent clinical trials. The strict ICC definition incompletely measures treatment success as assessed in clinical practice and, since ICC is necessary to achieve SCC, may lead to type II error for SCC. A set of proposed alternative outcome definitions was developed using the terms initial response (IR) and sustained response (SR) (Figure 1). IR allows for investigator assessment of overall improvement in CDI response more analogous to clinical practice and will lead to more patients eligible to meet SR. Achievement of SR requires both IR and no need for retreatment of CDI by day 30 after antibiotic completion and is the more relevant endpoint for CDI therapeutic development. The use of a less restrictive IR definition will more accurately capture early responses to treatment and importantly increase the validity of SR. The shortening of follow-up period by 30 days is also anticipated to reduce costs and efforts associated with conducting trials. Timeline of CDI outcome assessments for clinical trials
![]() Conclusion The set of definitions proposed here will more accurately capture clinical success and standardize the approach to outcome assessment in trials of CDI therapeutics. Disclosures Carolyn D. Alonso, MD, Cidara Therapeutics: Advisor/Consultant|Merck: Advisor/Consultant Oliver A. Cornely, Prof. Dr., Abbott: Honoraria|Abbvie: Advisor/Consultant|Actelion: Board Member|Al-Jazeera Pharmaceuticals: Honoraria|Allecra Therapeutics: Board Member|Amplyx: Advisor/Consultant|Amplyx: Grant/Research Support|Astellas: Honoraria|Basilea: Advisor/Consultant|Basilea: Grant/Research Support|Biocon: Advisor/Consultant|Biosys: Advisor/Consultant|BMBF: Grant/Research Support|Cidara: Advisor/Consultant|Cidara: Board Member|Cidara: Expert Testimony|Cidara: Grant/Research Support|CoRe Consulting: Stocks/Bonds|Da Volterra: Advisor/Consultant|DLR: Grant/Research Support|DZIF: Grant/Research Support|Entasis: Board Member|EU Directorate-General for Resarch and Innovation: Grant/Research Support|F2G: Grant/Research Support|German Patent and Trade Mark Office: German patent (DE 10 2021 113 007.7)|Gilead: Advisor/Consultant|Gilead: Grant/Research Support|Grupo Biotoscana/United Medical/Knight: Honoraria|Hikma: Honoraria|IQVIA: Board Member|Janssen: Board Member|Matinas: Advisor/Consultant|Matinas: Grant/Research Support|MedPace: Advisor/Consultant|MedPace: Grant/Research Support|MedScape: Honoraria|MedUpdate: Honoraria|Menarini: Advisor/Consultant|Merck/MSD: Grant/Research Support|Merck/MSD: Honoraria|Molecular Partners: Advisor/Consultant|MSG-ERC: Advisor/Consultant|Mundipharma: Grant/Research Support|Mylan: Honoraria|Noxxon: Advisor/Consultant|Octapharma: Advisor/Consultant|Octapharma: Grant/Research Support|Paratek: Board Member|Pardes: Advisor/Consultant|Pfizer: Grant/Research Support|Pfizer: Honoraria|Projektträger Jülich: Grant/Research Support|PSI: Advisor/Consultant|PSI: Board Member|Pulmocide: Board Member|Scynexis: Advisor/Consultant|Scynexis: Grant/Research Support|Seres: Advisor/Consultant|Shionogi: Board Member|Wiley (Blackwell): Editor-in-Chief, Mycoses Kevin W. Garey, PharmD, MS, Acurx Pharmaceuticals: Grant/Research Support|Paratek Pharmaceuticals: Grant/Research Support|Seres Therapeutics: Grant/Research Support|Summit Pharmaceuticals: Grant/Research Support Dale N. Gerding, MD, Destiny Pharma plc.: Advisor/Consultant Stuart Johnson, M.D., Ferring Pharmaceuticals: Membership on Ferring Publication Steering Committee|Ferring Pharmaceuticals: Employee|Summit Plc: Advisor/Consultant Stacy A. Kahn, MD, Lilly: Stocks/Bonds Ciaran P. Kelly, n/a, Artugen: Advisor/Consultant|Facile Therapeutics: Advisor/Consultant|Ferring Pharma: Advisor/Consultant|Finch: Advisor/Consultant|Finch: Advisor/Consultant|First Light Biosciences: Advisor/Consultant|First Light Biosciences: Ownership Interest|Milky Way Biosciences: Advisor/Consultant|Milky Way Biosciences: Grant/Research Support|Pfizer: Advisor/Consultant|Seres Therapeutics: Advisor/Consultant|Summit Therapeutics: Advisor/Consultant Larry K. Kociolek, MD, MSCI, Merck: Grant/Research Support Thomas J. Louie, MD, Artugen: Advisor/Consultant|Artugen: Grant/Research Support|Crestone: Advisor/Consultant|Crestone: Grant/Research Support|Finch Therapeutics: Advisor/Consultant|Finch Therapeutics: Grant/Research Support|Rebiotix: Advisor/Consultant|Rebiotix: Grant/Research Support|Seres Therapeutics: Advisor/Consultant|Seres Therapeutics: Grant/Research Support|summit plc: Advisor/Consultant|summit plc: Grant/Research Support|Vedanta Biosciences: Advisor/Consultant|Vedanta Biosciences: Grant/Research Support Maria Vehreschild, Prof. Dr., 3M: speaker fee|Astellas: Advisor/Consultant|Astellas: speaker fee|biologische heilmittel heel gmbh: Grant/Research Support|BioNtech: Grant/Research Support|EUMEDICA: Advisor/Consultant|Farmak International Holding: Advisor/Consultant|Ferring: Advisor/Consultant|Ferring: Speaker fee|Gilead Sciences: Advisor/Consultant|Immunic AG: Advisor/Consultant|MaaT: Advisor/Consultant|Merck: Advisor/Consultant|Merck: speaker fee|MSD: Advisor/Consultant|MSD: Grant/Research Support|MSD: speaker fees|Pfizer: speaker fee|Roche Molecular Systems: Grant/Research Support|Roche Molecular Systems: speaker fees|SocraRTec R&D GmbH: Advisor/Consultant|Takeda California: Grant/Research Support Professor Mark H. Wilcox, MD, FRCPath, GSK: Advisor/Consultant|GSK: Board Member|GSK: Grant/Research Support|Pfizer: Advisor/Consultant|Phico Therapeutics: Board Member|Seres: Advisor/Consultant|Seres: Board Member|Seres: Grant/Research Support|Summit: Advisor/Consultant|Summit: Grant/Research Support Erik R. Dubberke, MD, MSPH, Abbott: Advisor/Consultant|Ferring: Advisor/Consultant|Ferring: Grant/Research Support|Merck: Advisor/Consultant|Pfizer: Advisor/Consultant|Pfizer: Grant/Research Support|Seres: Advisor/Consultant|Summit: Advisor/Consultant|Synthetic Biologics: Grant/Research Support.
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Affiliation(s)
| | - Andrew M Skinner
- Loyola University Chicago Stritch School of Medicine, Maywood, Illinois
| | | | - Oliver A Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Kevin W Garey
- University of Houston College of Pharmacy, Houston, Texas
| | - Dale N Gerding
- Edward Hines, Jr. Veterans Affairs Hospital, Hines, Illinois
| | - Stuart Johnson
- Hines VA Hospital and Loyola University Medical Center, Hines, Illinois
| | - Stacy A Kahn
- Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ciaran P Kelly
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Colleen R Kelly
- Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Larry K Kociolek
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Ed J Kuijper
- Leiden University Medical Center and RIVM, Leiden, Zuid-Holland, Netherlands
| | - Ed J Kuijper
- Leiden University Medical Center and RIVM, Leiden, Zuid-Holland, Netherlands
| | | | - Thomas V Riley
- The University of Western Australia, Nedlands, Western Australia, Australia
| | | | - Maria Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany, Frankfurt, Hessen, Germany
| | - Mark H Wilcox
- University of Leeds; Leeds Teaching Hospitals NHS Trust, Leeds, England, United Kingdom
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18
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Moura IB, Bentley K, Wilcox MH. Assessment of potential for viral contamination of user and environment via aerosols generated during hand drying: A pilot study. Front Public Health 2022; 10:1010802. [PMID: 36388368 PMCID: PMC9641239 DOI: 10.3389/fpubh.2022.1010802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/10/2022] [Indexed: 01/27/2023] Open
Abstract
Background Hand drying is an essential step of hand hygiene, helping remove microbes remaining on hands following handwashing. However, it is unclear whether particles dispersed or aerosolized during hand drying can also have an impact on microbe dissemination and so pose an infection risk. Methods We used a PR772 bacteriophage to investigate whether microorganisms remaining on hands can disperse in the washroom environment and contaminate facemasks of others sharing the same space, as a surrogate for virus inhalation risk. Hand drying using either a jet air dryer or paper towels were performed, and mask contamination by splattering and droplet deposition was investigated, up to 15 min following each procedure. Results Facemask contamination by splattering was 10-fold higher when a jet air dryer was used, compared with hand drying by paper towels, for both the person performing the hand drying and for standby users stationed at 1 and 2 m distance. Facemask contamination by droplet/aerosols deposition was higher in the first 5 min following hand drying, for both methods; however, virus load was significantly higher when a jet air dryer was used. In the jet air dryer assays, facemask contamination increased at 15 min post-hand drying, suggesting aerosolization of small particles that remain airborne for longer. Conclusion When using a jet air dryer, virus contamination dispersed further and for a longer period of time (up to 15 min post hand-drying). The method chosen for hand drying can potentially impact the airborne dissemination of microbial pathogens, including respiratory virus, and so potentially increase the risk of exposure and infection for other washroom users.
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Affiliation(s)
- Ines B. Moura
- Faculty of Medicine and Health, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Karen Bentley
- Faculty of Medicine and Health, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Mark H. Wilcox
- Faculty of Medicine and Health, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom,Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, United Kingdom,*Correspondence: Mark H. Wilcox
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19
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Moura IB, Grada A, Spittal W, Clark E, Ewin D, Altringham J, Fumero E, Wilcox MH, Buckley AM. Profiling the Effects of Systemic Antibiotics for Acne, Including the Narrow-Spectrum Antibiotic Sarecycline, on the Human Gut Microbiota. Front Microbiol 2022; 13:901911. [PMID: 35711781 PMCID: PMC9194605 DOI: 10.3389/fmicb.2022.901911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Treatment for moderate-to-severe acne vulgaris relies on prolonged use of oral tetracycline-class antibiotics; however, these broad-spectrum antibiotics are often associated with off-target effects and negative gastrointestinal sequelae. Sarecycline is a narrow-spectrum antibiotic treatment option. Here, we investigated the effect of prolonged sarecycline exposure, compared with broad-spectrum tetracyclines (doxycycline and minocycline) upon the colonic microbiota. Three in vitro models of the human colon were instilled with either minocycline, doxycycline or sarecycline, and we measured microbiota abundance and diversity changes during and after antibiotic exposure. Significant reductions in microbial diversity were observed following minocycline and doxycycline exposure, which failed to recover post antibiotic withdrawal. Specifically, minocycline caused a ~10% decline in Lactobacillaceae and Bifidobacteriaceae abundances, while doxycycline caused a ~7% decline in Lactobacillaceae and Bacteroidaceae abundances. Both minocycline and doxycycline were associated with a large expansion (>10%) of Enterobacteriaceae. Sarecycline caused a slight decline in bacterial diversity at the start of treatment, but abundances of most families remained stable during treatment. Ruminococcaceae and Desulfovibrionaceae decreased 9% and 4%, respectively, and a transient increased in Enterobacteriaceae abundance was observed during sarecycline administration. All populations recovered to pre-antibiotic levels after sarecycline exposure. Overall, sarecycline had minimal and transient impact on the gut microbiota composition and diversity, when compared to minocycline and doxycycline.
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Affiliation(s)
- Ines B Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom
| | | | - William Spittal
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom
| | - Emma Clark
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom
| | - Duncan Ewin
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom
| | - James Altringham
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom
| | | | - Mark H Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom.,Department of Microbiology, Leeds Teaching Hospital NHS Trust, Old Medical School, Leeds General Infirmary, Leeds, United Kingdom
| | - Anthony M Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom.,Microbiome and Nutritional Science Group, School of Food Science, Faculty of Food Science and Nutrition, University of Leeds, Leeds, United Kingdom
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20
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Viprey VF, Davis GL, Benson AD, Ewin D, Spittal W, Vernon JJ, Rupnik M, Banz A, Allantaz F, Cleuziat P, Wilcox MH, Davies KA. A point-prevalence study on community and inpatient Clostridioides difficile infections (CDI): results from Combatting Bacterial Resistance in Europe CDI (COMBACTE-CDI), July to November 2018. Euro Surveill 2022; 27:2100704. [PMID: 35775426 PMCID: PMC9248264 DOI: 10.2807/1560-7917.es.2022.27.26.2100704] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/05/2022] [Indexed: 11/20/2022] Open
Abstract
BackgroundThere is a paucity of data on community-based Clostridioides difficile infection (CDI) and how these compare with inpatient CDI.AimTo compare data on the populations with CDI in hospitals vs the community across 12 European countries.MethodsFor this point-prevalence study (July-November 2018), testing sites sent residual diagnostic material on sampling days to a coordinating laboratory for CDI testing and PCR ribotyping (n = 3,163). Information on whether CDI testing was requested at the original site was used to identify undiagnosed CDI. We used medical records to identify differences between healthcare settings in patient demographics and risk factors for detection of C. difficile with or without free toxin.ResultsThe CDI positivity rate was 4.4% (country range: 0-16.2) in hospital samples, and 1.3% (country range: 0-2.2%) in community samples. The highest prevalence of toxinotype IIIb (027, 181 and 176) was seen in eastern European countries (56%; 43/77), the region with the lowest testing rate (58%; 164/281). Different predisposing risk factors were observed (use of broad-spectrum penicillins in the community (OR: 8.09 (1.9-35.6), p = 0.01); fluoroquinolones/cephalosporins in hospitals (OR: 2.2 (1.2-4.3), p = 0.01; OR: 2.0 (1.1-3.7), p = 0.02)). Half of community CDI cases were undetected because of absence of clinical suspicion, accounting for three times more undiagnosed adults in the community compared with hospitals (ca 111,000 vs 37,000 cases/year in Europe).ConclusionThese findings support recommendations for improving diagnosis in patients presenting with diarrhoea in the community, to guide good practice to limit the spread of CDI.
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Affiliation(s)
- Virginie F Viprey
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Georgina L Davis
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Anthony D Benson
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Duncan Ewin
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - William Spittal
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Jon J Vernon
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides difficile (ESGCD)
| | | | | | | | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides difficile (ESGCD)
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Kerrie A Davies
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides difficile (ESGCD)
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
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21
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Moore MP, Wilcox MH, Walker AS, Eyre DW. K-mer based prediction of Clostridioides difficile relatedness and ribotypes. Microb Genom 2022; 8. [PMID: 35384833 PMCID: PMC9453075 DOI: 10.1099/mgen.0.000804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Comparative analysis of Clostridioides difficile whole-genome sequencing (WGS) data enables fine scaled investigation of transmission and is increasingly becoming part of routine surveillance. However, these analyses are constrained by the computational requirements of the large volumes of data involved. By decomposing WGS reads or assemblies into k-mers and using the dimensionality reduction technique MinHash, it is possible to rapidly approximate genomic distances without alignment. Here we assessed the performance of MinHash, as implemented by sourmash, in predicting single nucleotide differences between genomes (SNPs) and C. difficile ribotypes (RTs). For a set of 1905 diverse C. difficile genomes (differing by 0–168 519 SNPs), using sourmash to screen for closely related genomes, at a sensitivity of 100 % for pairs ≤10 SNPs, sourmash reduced the number of pairs from 1 813 560 overall to 161 934, i.e. by 91 %, with a positive predictive value of 32 % to correctly identify pairs ≤10 SNPs (maximum SNP distance 4144). At a sensitivity of 95 %, pairs were reduced by 94 % to 108 266 and PPV increased to 45 % (maximum SNP distance 1009). Increasing the MinHash sketch size above 2000 produced minimal performance improvement. We also explored a MinHash similarity-based ribotype prediction method. Genomes with known ribotypes (n=3937) were split into a training set (2937) and test set (1000) randomly. The training set was used to construct a sourmash index against which genomes from the test set were compared. If the closest five genomes in the index had the same ribotype this was taken to predict the searched genome’s ribotype. Using our MinHash ribotype index, predicted ribotypes were correct in 780/1000 (78 %) genomes, incorrect in 20 (2 %), and indeterminant in 200 (20 %). Relaxing the classifier to 4/5 closest matches with the same RT improved the correct predictions to 87 %. Using MinHash it is possible to subsample C. difficile genome k-mer hashes and use them to approximate small genomic differences within minutes, significantly reducing the search space for further analysis.
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Affiliation(s)
- Matthew Phillip Moore
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Mark H Wilcox
- Healthcare Associated Infection Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
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22
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Vehreschild MJGT, Ducher A, Louie T, Cornely OA, Feger C, Dane A, Varastet M, Vitry F, de Gunzburg J, Andremont A, Mentré F, Wilcox MH. An open randomized multicentre Phase 2 trial to assess the safety of DAV132 and its efficacy to protect gut microbiota diversity in hospitalized patients treated with fluoroquinolones. J Antimicrob Chemother 2022; 77:1155-1165. [PMID: 35016205 PMCID: PMC8969469 DOI: 10.1093/jac/dkab474] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/19/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DAV132 (colon-targeted adsorbent) has prevented antibiotic-induced effects on microbiota in healthy volunteers. OBJECTIVES To assess DAV132 safety and biological efficacy in patients. PATIENTS AND METHODS An open-label, randomized [stratification: fluoroquinolone (FQ) indication] multicentre trial comparing DAV132 (7.5 g, 3 times a day, orally) with No-DAV132 in hospitalized patients requiring 5-21 day treatment with FQs and at risk of Clostridioides difficile infection (CDI). FQ and DAV132 were started simultaneously, DAV132 was administered for 48 h more, and patients were followed up for 51 days. The primary endpoint was the rate of adverse events (AEs) independently adjudicated as related to DAV132 and/or FQ. The planned sample size of 260 patients would provide a 95% CI of ±11.4%, assuming a 33% treatment-related AE rate. Plasma and faecal FQ concentrations, intestinal microbiota diversity, intestinal colonization with C. difficile, MDR bacteria and yeasts, and ex vivo resistance to C. difficile faecal colonization were assessed. RESULTS Two hundred and forty-three patients (median age 71 years; 96% with chronic comorbidity) were included (No-DAV132, n = 120; DAV132, n = 123). DAV132- and/or FQ-related AEs did not differ significantly: 18 (14.8%) versus 13 (10.8%) in DAV132 versus No-DAV132 patients (difference 3.9%; 95% CI: -4.7 to 12.6). Day 4 FQ plasma levels were unaffected. DAV132 was associated with a >98% reduction in faecal FQ levels (Day 4 to end of treatment; P < 0.001), less impaired microbiota diversity (Shannon index; P = 0.003), increased ex vivo resistance to C. difficile colonization (P = 0.0003) and less frequent FQ-induced VRE acquisition (P = 0.01). CONCLUSIONS In FQ-treated hospitalized patients, DAV132 was well tolerated, and FQ plasma concentrations unaffected. DAV132 preserved intestinal microbiota diversity and C. difficile colonization resistance.
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Affiliation(s)
- Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Thomas Louie
- Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Oliver A Cornely
- Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Chair Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Celine Feger
- Da Volterra, Paris, France.,EMIBiotech, Paris, France
| | | | | | | | | | - Antoine Andremont
- Da Volterra, Paris, France.,Université de Paris, IAME, INSERM U1137, Paris, France
| | - France Mentré
- Université de Paris, IAME, INSERM U1137, Paris, France
| | - Mark H Wilcox
- Leeds Institute of Medical Research, University of Leeds and Leeds Teaching Hospitals, Leeds, UK
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23
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Abstract
PURPOSE OF REVIEW There is a paradox when treating Clostridium difficile infection (CDI); treatment antibiotics reduce C. difficile colonization but cause further microbiota disruption and can lead to recurrent disease. The success of faecal microbiota transplants (FMT) in treating CDI has become a new research area in microbiome restorative therapies but are they a viable long-term treatment option? RECENT FINDINGS C. difficile displays metabolic flexibility to use different nutritional sources during CDI. Using microbiome therapies for the efficient restoration of bile homeostasis and to reduce the bioavailability of preferential nutrients will target the germination ability of C. difficile spores and the growth rate of vegetative cells. Several biotechnology companies have developed microbiome therapeutics for treating CDI, which are undergoing clinical trials. SUMMARY There is confidence in using restorative microbiome therapies for treating CDI after the demonstrated efficacy of FMT, where several biotechnology companies are aiming to supply what would be a 'first in class' treatment option. Efficient removal of C. difficile from the different intestinal biogeographies should be considered in future microbiome therapies. With the gut microbiota implicated in different diseases, more work is needed to assess the long-term consequences of microbiome therapies.
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Affiliation(s)
- Anthony M Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health
- Microbiome and Nutritional Science Group, School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds
| | - Ines B Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health
| | - Mark H Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health
- Microbiology, Leeds Teaching Hospital NHS Trust, Old Medical School, Leeds General Infirmary, Leeds, UK
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Abstract
PURPOSE OF REVIEW COVID-19 patients can present gastrointestinal symptoms, being diarrhoea one of the most frequent, suggesting intestinal health can be impacted by COVID-19. Here, we will discuss whether there is a correlation between the presence of SARS-CoV-2 RNA in faeces and diarrhoea, the relevance of gastrointestinal symptoms in disease diagnosis and transmission, and how COVID-19 can impact the gut microbial balance. RECENT FINDINGS SARS-CoV-2 RNA has been reported in faeces or rectal swabs of COVID-19 patients with and without diarrhoea, suggesting faecal shedding can occur independently of gastrointestinal symptoms. However, the presence of the virus in the intestine can persist beyond its presence in the respiratory tract, with some reports suggesting that SARS-CoV-2 in the faeces can be infectious.COVID-19 can impact the gut microbiota causing an enhancement of biosynthesis pathways that favour the expansion of bacterial pathogens in the inflamed gut, and causing a decline in commensals involved in the human immune response. SUMMARY Gastrointestinal symptoms may be the first indication of COVID-19. SARS-CoV-2 in faeces can potentiate routes of disease transmission, particularly as the high viral loads reported in patients with severe illness suggest virus replication in the intestine may be possible.
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Affiliation(s)
- Ines B. Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
| | - Anthony M. Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
| | - Mark H. Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
- Microbiology, Leeds Teaching Hospital NHS Trust, Old Medical School, Leeds General Infirmary, Leeds, UK
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van Prehn J, Reigadas E, Vogelzang EH, Bouza E, Hristea A, Guery B, Krutova M, Norén T, Allerberger F, Coia JE, Goorhuis A, van Rossen TM, Ooijevaar RE, Burns K, Scharvik Olesen BR, Tschudin-Sutter S, Wilcox MH, Vehreschild MJGT, Fitzpatrick F, Kuijper EJ. European Society of Clinical Microbiology and Infectious Diseases: 2021 update on the treatment guidance document for Clostridioides difficile infection in adults. Clin Microbiol Infect 2021; 27 Suppl 2:S1-S21. [PMID: 34678515 DOI: 10.1016/j.cmi.2021.09.038] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/23/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022]
Abstract
SCOPE In 2009, the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) published the first treatment guidance document for Clostridioides difficile infection (CDI). This document was updated in 2014. The growing literature on CDI antimicrobial treatment and novel treatment approaches, such as faecal microbiota transplantation (FMT) and toxin-binding monoclonal antibodies, prompted the ESCMID study group on C. difficile (ESGCD) to update the 2014 treatment guidance document for CDI in adults. METHODS AND QUESTIONS Key questions on CDI treatment were formulated by the guideline committee and included: What is the best treatment for initial, severe, severe-complicated, refractory, recurrent and multiple recurrent CDI? What is the best treatment when no oral therapy is possible? Can prognostic factors identify patients at risk for severe and recurrent CDI and is there a place for CDI prophylaxis? Outcome measures for treatment strategy were: clinical cure, recurrence and sustained cure. For studies on surgical interventions and severe-complicated CDI the outcome was mortality. Appraisal of available literature and drafting of recommendations was performed by the guideline drafting group. The total body of evidence for the recommendations on CDI treatment consists of the literature described in the previous guidelines, supplemented with a systematic literature search on randomized clinical trials and observational studies from 2012 and onwards. The Grades of Recommendation Assessment, Development and Evaluation (GRADE) system was used to grade the strength of our recommendations and the quality of the evidence. The guideline committee was invited to comment on the recommendations. The guideline draft was sent to external experts and a patients' representative for review. Full ESCMID endorsement was obtained after a public consultation procedure. RECOMMENDATIONS Important changes compared with previous guideline include but are not limited to: metronidazole is no longer recommended for treatment of CDI when fidaxomicin or vancomycin are available, fidaxomicin is the preferred agent for treatment of initial CDI and the first recurrence of CDI when available and feasible, FMT or bezlotoxumab in addition to standard of care antibiotics (SoC) are preferred for treatment of a second or further recurrence of CDI, bezlotoxumab in addition to SoC is recommended for the first recurrence of CDI when fidaxomicin was used to manage the initial CDI episode, and bezlotoxumab is considered as an ancillary treatment to vancomycin for a CDI episode with high risk of recurrence when fidaxomicin is not available. Contrary to the previous guideline, in the current guideline emphasis is placed on risk for recurrence as a factor that determines treatment strategy for the individual patient, rather than the disease severity.
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Affiliation(s)
- Joffrey van Prehn
- Department of Medical Microbiology, Centre for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Elena Reigadas
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Erik H Vogelzang
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
| | - Emilio Bouza
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Adriana Hristea
- University of Medicine and Pharmacy Carol Davila, National Institute for Infectious Diseases Prof Dr Matei Bals, Romania
| | - Benoit Guery
- Infectious Diseases Specialist, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Torbjorn Norén
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden
| | | | - John E Coia
- Department of Clinical Microbiology, Hospital South West Jutland and Department of Regional Health Research IRS, University of Southern Denmark, Esbjerg, Denmark
| | - Abraham Goorhuis
- Department of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, the Netherlands
| | - Tessel M van Rossen
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
| | - Rogier E Ooijevaar
- Department of Gastroenterology, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
| | - Karen Burns
- Departments of Clinical Microbiology, Beaumont Hospital & Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Sarah Tschudin-Sutter
- Department of Infectious Diseases and Infection Control, University Hospital Basel, University Basel, Universitatsspital, Basel, Switzerland
| | - Mark H Wilcox
- Department of Microbiology, Old Medical, School Leeds General Infirmary, Leeds Teaching Hospitals & University of Leeds, Leeds, United Kingdom
| | - Maria J G T Vehreschild
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany; Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Fidelma Fitzpatrick
- Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland; Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ed J Kuijper
- Department of Medical Microbiology, Centre for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands; National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
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Wilcox MH, Dryden M. Update on the epidemiology of healthcare-acquired bacterial infections: focus on complicated skin and skin structure infections. J Antimicrob Chemother 2021; 76:iv2-iv8. [PMID: 34849996 PMCID: PMC8632754 DOI: 10.1093/jac/dkab350] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Healthcare-associated infections (HCAIs) are a threat to patient safety and cause substantial medical and economic burden in acute care and long-term care facilities. Risk factors for HCAIs include patient characteristics, the type of care and the setting. Local surveillance data and microbiological characterization are crucial tools for guiding antimicrobial treatment and informing efforts to reduce the incidence of HCAI. Skin and soft tissue infections, including superficial and deep incisional surgical site infections, are among the most frequent HCAIs. Other skin and soft tissue infections associated with healthcare settings include vascular access site infections, infected burns and traumas, and decubitus ulcer infections.
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Affiliation(s)
- Mark H Wilcox
- Department of Medical Microbiology, Leeds Teaching Hospitals & University of Leeds, Leeds, UK
| | - Matthew Dryden
- Hampshire Hospitals NHS Foundation Trust, Winchester, UK
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Wilson JD, Wallace HE, Loftus-Keeling M, Ward H, Davies B, Vargas-Palacios A, Hulme C, Wilcox MH. Swab-yourself Trial With Economic Monitoring and Testing for Infections Collectively (SYSTEMATIC): Part 1. A Diagnostic Accuracy and Cost-effectiveness Study Comparing Clinician-taken vs Self-taken Rectal and Pharyngeal Samples for the Diagnosis of Gonorrhea and Chlamydia. Clin Infect Dis 2021; 73:e3172-e3180. [PMID: 32877521 DOI: 10.1093/cid/ciaa1266] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Urogenital testing misses extragenital Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT). Extragenital self-sampling is frequently undertaken despite no robust randomized, controlled trial evidence of efficacy. We compared clinician-taken rectal and pharyngeal samples with self-taken samples for diagnostic accuracy and cost in men who have sex with men (MSM) and in females. METHODS This was a prospective convenience sample from a UK sexual health clinic. We randomized the order of clinician- and self-taken samples from the pharynx and rectum, plus first catch urine (MSM) and vulvovaginal swabs (females), for NG/CT detection. RESULTS Of 1793 participants (1284 females, 509 MSM), 116 had NG detected (75 urogenital, 83 rectum, 72 pharynx); 9.4% infected females and 67.3% MSM were urogenital-negative. A total of 276 had CT detected (217 urogenital, 249 rectum, 63 pharynx); 13.1% infected females and 71.8% MSM were urogenital-negative. Sexual history did not identify those with rectal infections. There was no difference in diagnostic accuracy between clinician- and self-taken samples from the rectum or pharynx. Clinicians took swabs more quickly than participants, so costs were lower. However, in asymptomatic people, nonqualified clinicians would oversee self-swabbing making these costs lower. CONCLUSIONS There was no difference in the diagnostic accuracy of clinician-taken compared with self-taken extragenital samples. Sexual history did not identify those with rectal infections, so individuals should have extragenital clinician- or self-taken samples. Clinician-taken swabs cost less than self-taken swabs; however, in asymptomatic people or those who perform home testing, the costs would be lower than for clinician-taken swabs. CLINICAL TRIALS REGISTRATION NCT02371109.
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Affiliation(s)
- Janet D Wilson
- Leeds Sexual Health, Leeds Teaching Hospitals National Health Service Trust, Leeds, United Kingdom
| | - Harriet E Wallace
- Leeds Sexual Health, Leeds Teaching Hospitals National Health Service Trust, Leeds, United Kingdom
| | - Michelle Loftus-Keeling
- Leeds Sexual Health, Leeds Teaching Hospitals National Health Service Trust, Leeds, United Kingdom
| | - Helen Ward
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Bethan Davies
- Department of Epidemiology and Biostatistics, Imperial College, London, United Kingdom
| | | | - Claire Hulme
- Academic Unit of Health Economics, University of Leeds, Leeds, United Kingdom
| | - Mark H Wilcox
- Department of Clinical Microbiology, Leeds Teaching Hospitals National Health Service Trust, Leeds, United Kingdom
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Wilson JD, Wallace HE, Loftus-Keeling M, Ward H, Davies B, Vargas-Palacios A, Hulme C, Wilcox MH. Swab-Yourself Trial With Economic Monitoring and Testing for Infections Collectively (SYSTEMATIC): Part 2. A Diagnostic Accuracy and Cost-effectiveness Study Comparing Rectal, Pharyngeal, and Urogenital Samples Analyzed Individually, Versus as a Pooled Specimen, for the Diagnosis of Gonorrhea and Chlamydia. Clin Infect Dis 2021; 73:e3183-e3193. [PMID: 33044490 DOI: 10.1093/cid/ciaa1546] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Sexual history does not accurately identify those with extragenital Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT), so universal extragenital sampling is recommended. Nucleic acid amplification tests (NAATs) are expensive. If urogenital, plus rectal and pharyngeal, samples are analyzed, the diagnostic cost is trebled. Pooling samples into 1 NAAT container would cost the same as urogenital samples alone. We compared clinician triple samples analyzed individually with self-taken pooled samples for diagnostic accuracy, and cost, in men who have sex with men (MSM) and females. METHODS This was a prospective, convenience sample in United Kingdom sexual health clinic. Randomized order of clinician and self-samples from pharynx, rectum, plus first-catch urine (FCU) in MSM and vulvovaginal swabs (VVS) in females, for NG and CT detection. RESULTS Of 1793 participants (1284 females, 509 MSM), 116 had NG detected (75 urogenital, 83 rectum, 72 pharynx); 276 had CT detected (217 urogenital, 249 rectum, 63 pharynx). There was no difference in sensitivities between clinician triple samples and self-pooled specimens for NG (99.1% and 98.3%), but clinician samples analyzed individually identified 3% more chlamydia infections than pooled (99.3% and 96.0%; P = .027). However, pooled specimens identified more infections than VVS/FCU alone. Pooled specimens missed 2 NG and 11 CT infections, whereas VVS/FCU missed 41 NG and 58 CT infections. Self-taken pooled specimens were the most cost-effective. CONCLUSIONS FCU/VVS testing alone missed many infections. Self-taken pooled samples were as sensitive as clinician triple samples for identifying NG, but clinician samples analyzed individually identified 3% more CT infections than pooled. The extragenital sampling was achievable at no additional diagnostic cost to the FCU/VVS. CLINICAL TRIALS REGISTRATION NCT02371109.
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Affiliation(s)
- Janet D Wilson
- Leeds Sexual Health, Leeds Teaching Hospitals National Health Services Trust, Leeds, United Kingdom
| | - Harriet E Wallace
- Leeds Sexual Health, Leeds Teaching Hospitals National Health Services Trust, Leeds, United Kingdom
| | - Michelle Loftus-Keeling
- Leeds Sexual Health, Leeds Teaching Hospitals National Health Services Trust, Leeds, United Kingdom
| | - Helen Ward
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Bethan Davies
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | | | - Claire Hulme
- Academic Unit of Health Economics, University of Leeds, Leeds, United Kingdom
| | - Mark H Wilcox
- Department of Clinical Microbiology, Leeds Teaching Hospitals National Health Services Trust, Leeds, United Kingdom
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Elfassy A, Kalina WV, French R, Nguyen H, Tan C, Sebastian S, Wilcox MH, Davies K, Kutzler MA, Jansen KU, Anderson A, Pride MW. Development and clinical validation of an automated cell cytotoxicity neutralization assay for detecting Clostridioides difficile toxins in clinically relevant stools samples. Anaerobe 2021; 71:102415. [PMID: 34298152 DOI: 10.1016/j.anaerobe.2021.102415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVES To improve the diagnostic accuracy of Clostridioides difficile infection, current U.S. and E.U. guidelines recommend multistep testing that detects the presence of C. difficile and toxin in clinically relevant stool samples to confirm active disease. An accepted gold standard to detect C. difficile toxins is the cell cytotoxicity neutralization assay (CCNA). Although highly sensitive, the traditional CCNA has limitations. One such limitation is the subjective interpretation of an analyst to recognize cytopathic effects in cultured cells exposed to a fecal sample containing toxin. To overcome this limitation, an automated CCNA was developed that replaces most human pipetting steps with robotics and incorporates CellTiterGlo® for a semi-quantitative, non-subjective measure of cell viability instead of microscopy. METHODS To determine sample positivity and control for non-specific cytopathic effects, two thresholds were defined and validated by evaluating the sample with/without antitoxin antisera (sample-antitoxin/sample + antitoxin): 1) a >70% cell viability threshold was validated with samples containing anti-toxin, and 2) a >1.2-fold difference cut-off where sample results above the cut-off are considered positive. RESULTS Assay validation demonstrated excellent accuracy, precision, and sample linearity with an LOD of 126.9 pg/mL toxin-B in stool. The positivity cut-offs were clinically validated by comparing 322 diarrheal stool sample results with those run in a predicate, microscopic readout-based CCNA. The automated CCNA demonstrated 96% sensitivity and 100% specificity compared with the predicate CCNA. CONCLUSIONS Overall, the automated CCNA provides a specific, sensitive, and reproducible tool to support determination of CDI epidemiology or the efficacy of interventions such as vaccines.
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Affiliation(s)
- Arik Elfassy
- Pfizer Vaccines Research and Development, Pearl River, NY, USA; Current Affiliation: Elusys Therapeutics, Parsippany, NJ, USA
| | - Warren V Kalina
- Pfizer Vaccines Research and Development, Pearl River, NY, USA
| | - Roger French
- Pfizer Vaccines Research and Development, Pearl River, NY, USA
| | - Ha Nguyen
- Pfizer Vaccines Research and Development, Pearl River, NY, USA
| | - Charles Tan
- Pfizer Vaccines Research and Development, Pearl River, NY, USA
| | - Shite Sebastian
- Pfizer Vaccines Research and Development, Pearl River, NY, USA; Current Affiliation: Affinivax, Lexington, MA, USA
| | - Mark H Wilcox
- Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | | | | | | | - Michael W Pride
- Pfizer Vaccines Research and Development, Pearl River, NY, USA.
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Kong LY, Wilson JD, Moura IB, Fawley W, Kelly L, Walker AS, Eyre DW, Wilcox MH. Utility of Whole Genome Sequencing in Assessing and Enhancing Partner Notification of Neisseria gonorrhoeae Infection. Sex Transm Dis 2021; 48:773-780. [PMID: 34110743 DOI: 10.1097/olq.0000000000001419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Gonorrhea is a sexually transmitted infection of global concern. We investigated whole-genome sequencing (WGS) as a tool to measure and enhance partner notification (PN) in gonorrhea management. METHODS Between May and November 2018, all N. gonorrhoeae isolated from patients attending Leeds Sexual Health, United Kingdom, underwent WGS. Reports listing sequences within 20 single-nucleotide polymorphisms (SNPs) of study isolates within a database containing select isolates from April 1, 2016, to November 15, 2018, were issued to clinicians. The proportion of cases with a potential transmission partner identified by PN was determined from patient and PN data. The WGS reports were reviewed to identify additional cases within 6 SNPs or less and verified for PN concordance. RESULTS Three hundred eighty isolates from 377 cases were successfully sequenced; 292 had traceable/contactable partners and 69 (18%) had a potential transmission partner identified by PN. Concordant PN and WGS links were identified in 47 partner pairs. Of 308 cases with no transmission partner by PN, 185 (60%) had a case within 6 SNPs or less; examination of these cases' PN data identified 7 partner pairs with previously unrecognized PN link, giving a total of 54 pairs; all had 4 or less SNP differences. The WGS clusters confirmed gaps in partner finding, at individual and group levels. Despite the clinic providing sexual health services to the whole city, 35 cases with multiple partners had no genetically related case, suggesting multiple undiagnosed infections. CONCLUSIONS Whole-genome sequencing could improve gonorrhea PN and control by identifying new links and clusters with significant gaps in partner finding.
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Affiliation(s)
| | | | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds
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Buckley AM, Moura IB, Altringham J, Ewin D, Clark E, Bentley K, Wilkinson V, Spittal W, Davis G, Wilcox MH. The use of first-generation cephalosporin antibiotics, cefalexin and cefradine, is not associated with induction of simulated Clostridioides difficile infection. J Antimicrob Chemother 2021; 77:148-154. [PMID: 34561709 PMCID: PMC8730689 DOI: 10.1093/jac/dkab349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/23/2021] [Indexed: 02/04/2023] Open
Abstract
Objectives The use of broad-spectrum cephalosporins is associated with induction of Clostridioides difficile infection (CDI). Recent knowledge on the importance of the healthy microbiota in preventing pathogen colonization/outgrowth highlights the caution needed when prescribing broad-spectrum antibiotics. The use of historical narrow-spectrum antibiotics, such as first-generation cephalosporins, is gaining increased attention once more as they have a reduced impact on the microbiota whilst treating infections. Here, the effects of two first-generation cephalosporins, compared with a third-generation cephalosporin, on the human microbiota were investigated and their propensity to induce simulated CDI. Methods Three in vitro chemostat models, which simulate the physiochemical conditions of the human colon, were seeded with a human faecal slurry and instilled with either narrow-spectrum cephalosporins, cefalexin and cefradine, or a broad-spectrum cephalosporin, ceftriaxone, at concentrations reflective of colonic levels. Results Instillation of cefalexin was associated with reduced recoveries of Bifidobacterium and Enterobacteriaceae; however, Clostridium spp. recoveries remained unaffected. Cefradine exposure was associated with decreased recoveries of Bifidobacterium spp., Bacteroides spp. and Enterobacteriaceae. These changes were not associated with induction of CDI, as we observed a lack of C. difficile spore germination/proliferation, thus no toxin was detected. This is in contrast to a model exposed to ceftriaxone, where CDI was observed. Conclusions These model data suggest that the minimal impact of first-generation cephalosporins, namely cefalexin and cefradine, on the intestinal microbiota results in a low propensity to induce CDI.
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Affiliation(s)
- Anthony M Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Ines B Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - James Altringham
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Duncan Ewin
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Emma Clark
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Karen Bentley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Vikki Wilkinson
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - William Spittal
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Georgina Davis
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Mark H Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK.,Microbiology, Leeds Teaching Hospitals NHS Trust, Old Medical School, Leeds General Infirmary, Leeds, LS1 3EX, UK
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Johnson S, Lavergne V, Skinner AM, Gonzales-Luna AJ, Garey KW, Kelly CP, Wilcox MH. Clinical Practice Guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 Focused Update Guidelines on Management of Clostridioides difficile Infection in Adults. Clin Infect Dis 2021; 73:755-757. [PMID: 34492699 DOI: 10.1093/cid/ciab718] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
This clinical practice guideline is a focused update on management of Clostridioides difficile infection (CDI) in adults specifically addressing the use of fidaxomicin and bezlotoxumab for the treatment of CDI. This guideline was developed by a multidisciplinary panel representing the Infectious Diseases Society of America (IDSA) and the Society for Healthcare Epidemiology of America (SHEA). This guideline is intended for use by healthcare professionals who care for adults with CDI, including specialists in infectious diseases, gastroenterologists, hospitalists, pharmacists, and any clinicians and healthcare providers caring for these patients. The panel's recommendations for the management CDI are based upon evidence derived from topic-specific systematic literature reviews. Summarized below are the recommendations for the management of CDI in adults. The panel followed a systematic process which included a standardized methodology for rating the certainty of the evidence and strength of recommendation using the GRADE approach (Grading of Recommendations Assessment, Development, and Evaluation). A detailed description of background, methods, evidence summary and rationale that support each recommendation, and knowledge gaps can be found online in the full text.
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Affiliation(s)
- Stuart Johnson
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA.,Loyola University Medical Center, Maywood, Illinois, USA
| | - Valéry Lavergne
- Department of Medical Microbiology and Infection Control, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Andrew M Skinner
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA.,Loyola University Medical Center, Maywood, Illinois, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Ciaran P Kelly
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, and Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
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Rooney CM, Mankia K, Mitra S, Moura IB, Emery P, Wilcox MH. Perturbations of the gut microbiome in anti-CCP positive individuals at risk of developing rheumatoid arthritis. Rheumatology (Oxford) 2021; 60:3380-3387. [PMID: 33313854 DOI: 10.1093/rheumatology/keaa792] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/15/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Individuals with newly diagnosed RA have a distinct microbiome when compared with healthy controls. However, little is known as to when these microbiome perturbations begin. Using a prospective at-risk cohort of individuals positive for anti-citrullinated protein (anti-CCP) antibody with new onset musculoskeletal symptoms, but without clinical arthritis, we investigated for the presence of a gut dysbiosis before the onset of RA. METHODS The gut microbiota of 25 anti-CCP positive individuals without clinical synovitis were sequenced targeting the V4 region of the 16S rRNA gene. Using a publicly available database, a control population of 44 individuals, approximately matched in age, gender, diet and ethnicity was selected for comparison, using the same sequencing methodology. Median interval between sample collection and progression to RA was 188 days. Taxonomic analysis was performed using QIIME and MEGAN, and statistical analysis using R software. RESULTS There were significant differences (P =0.01) at family level in gut microbiomes of anti-CCP positive individuals vs controls. The anti-CCP positive population had an overabundance of Lachnospiraceae, Helicobacteraceae, Ruminococcaceae, Erysipelotrichaceae and Bifidobacteriaceae, among others. Five individuals progressed to RA between sample collection and analysis. Clustering of the progressor population was observed on a phylogenetic network created using a probabilistic similarity index (Goodall's index). CONCLUSIONS Anti-CCP positive at-risk individuals without clinical synovitis appear to have a distinct gut microbiome compared with healthy controls. Phylogenetic clustering was observed in individuals who progressed to RA, suggesting that distinct taxa are associated with the development of RA many months before its onset.
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Affiliation(s)
- Christopher M Rooney
- Leeds Institute of Medical Research, University of Leeds, Leeds General Infirmary, Leeds, UK.,Leeds Institute of Rheumatic and Musculoskeletal Medicine, Chapel Allerton Hospital, Leeds, UK
| | - Kulveer Mankia
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, Chapel Allerton Hospital, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital, Leeds, UK
| | - Suparna Mitra
- Leeds Institute of Medical Research, University of Leeds, Leeds General Infirmary, Leeds, UK
| | - Ines B Moura
- Leeds Institute of Medical Research, University of Leeds, Leeds General Infirmary, Leeds, UK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, Chapel Allerton Hospital, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital, Leeds, UK
| | - Mark H Wilcox
- Leeds Institute of Medical Research, University of Leeds, Leeds General Infirmary, Leeds, UK
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García-Fiñana M, Hughes DM, Cheyne CP, Burnside G, Stockbridge M, Fowler TA, Fowler VL, Wilcox MH, Semple MG, Buchan I. Performance of the Innova SARS-CoV-2 antigen rapid lateral flow test in the Liverpool asymptomatic testing pilot: population based cohort study. BMJ 2021; 374:n1637. [PMID: 34230058 PMCID: PMC8259455 DOI: 10.1136/bmj.n1637] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To assess the performance of the SARS-CoV-2 antigen rapid lateral flow test (LFT) versus polymerase chain reaction testing in the asymptomatic general population attending testing centres. DESIGN Observational cohort study. SETTING Community LFT pilot at covid-19 testing sites in Liverpool, UK. PARTICIPANTS 5869 asymptomatic adults (≥18 years) voluntarily attending one of 48 testing sites during 6-29 November 2020. INTERVENTIONS Participants were tested using both an Innova LFT and a quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) test based on supervised self-administered swabbing at testing sites. MAIN OUTCOME MEASURES Sensitivity, specificity, and predictive values of LFT compared with RT-qPCR in an epidemic steady state of covid-19 among adults with no classic symptoms of the disease. RESULTS Of 5869 test results, 22 (0.4%) LFT results and 343 (5.8%) RT-qPCR results were void (that is, when the control line fails to appear within 30 minutes). Excluding the void results, the LFT versus RT-qPCR showed a sensitivity of 40.0% (95% confidence interval 28.5% to 52.4%; 28/70), specificity of 99.9% (99.8% to 99.99%; 5431/5434), positive predictive value of 90.3% (74.2% to 98.0%; 28/31), and negative predictive value of 99.2% (99.0% to 99.4%; 5431/5473). When the void samples were assumed to be negative, a sensitivity was observed for LFT of 37.8% (26.8% to 49.9%; 28/74), specificity of 99.6% (99.4% to 99.8%; 5431/5452), positive predictive value of 84.8% (68.1% to 94.9%; 28/33), and negative predictive value of 93.4% (92.7% to 94.0%; 5431/5814). The sensitivity in participants with an RT-qPCR cycle threshold (Ct) of <18.3 (approximate viral loads >106 RNA copies/mL) was 90.9% (58.7% to 99.8%; 10/11), a Ct of <24.4 (>104 RNA copies/mL) was 69.4% (51.9% to 83.7%; 25/36), and a Ct of >24.4 (<104 RNA copies/mL) was 9.7% (1.9% to 23.7%; 3/34). LFT is likely to detect at least three fifths and at most 998 in every 1000 people with a positive RT-qPCR test result with high viral load. CONCLUSIONS The Innova LFT can be useful for identifying infections among adults who report no symptoms of covid-19, particularly those with high viral load who are more likely to infect others. The number of asymptomatic adults with lower Ct (indicating higher viral load) missed by LFT, although small, should be considered when using single LFT in high consequence settings. Clear and accurate communication with the public about how to interpret test results is important, given the chance of missing some cases, even at high viral loads. Further research is needed to understand how infectiousness is reflected in the viral antigen shedding detected by LFT versus the viral loads approximated by RT-qPCR.
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Affiliation(s)
- Marta García-Fiñana
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | - David M Hughes
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | - Christopher P Cheyne
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | - Girvan Burnside
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | | | - Tom A Fowler
- Department of Health and Social Care, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Mark H Wilcox
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Iain Buchan
- Institute of Population Health Sciences, University of Liverpool, Liverpool, UK
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35
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Buckley AM, Moura IB, Arai N, Spittal W, Clark E, Nishida Y, Harris HC, Bentley K, Davis G, Wang D, Mitra S, Higashiyama T, Wilcox MH. Trehalose-Induced Remodelling of the Human Microbiota Affects Clostridioides difficile Infection Outcome in an In Vitro Colonic Model: A Pilot Study. Front Cell Infect Microbiol 2021; 11:670935. [PMID: 34277467 PMCID: PMC8284250 DOI: 10.3389/fcimb.2021.670935] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/02/2021] [Indexed: 12/19/2022] Open
Abstract
Within the human intestinal tract, dietary, microbial- and host-derived compounds are used as signals by many pathogenic organisms, including Clostridioides difficile. Trehalose has been reported to enhance virulence of certain C. difficile ribotypes; however, such variants are widespread and not correlated with clinical outcomes for patients suffering from C. difficile infection (CDI). Here, we make preliminary observations on how trehalose supplementation affects the microbiota in an in vitro model and show that trehalose-induced changes can reduce the outgrowth of C. difficile, preventing simulated CDI. Three clinically reflective human gut models simulated the effects of sugar (trehalose or glucose) or saline ingestion on the microbiota. Models were instilled with sugar or saline and further exposed to C. difficile spores. The recovery of the microbiota following antibiotic treatment and CDI induction was monitored in each model. The human microbiota remodelled to utilise the bioavailable trehalose. Clindamycin induction caused simulated CDI in models supplemented with either glucose or saline; however, trehalose supplementation did not result in CDI, although limited spore germination did occur. The absence of CDI in trehalose model was associated with enhanced abundances of Finegoldia, Faecalibacterium and Oscillospira, and reduced abundances of Klebsiella and Clostridium spp., compared with the other models. Functional analysis of the microbiota in the trehalose model revealed differences in the metabolic pathways, such as amino acid metabolism, which could be attributed to prevention of CDI. Our data show that trehalose supplementation remodelled the microbiota, which prevented simulated CDI, potentially due to enhanced recovery of nutritionally competitive microbiota against C. difficile.
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Affiliation(s)
- Anthony M. Buckley
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Ines B. Moura
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Norie Arai
- R&D Division, Hayashibara Co. Ltd./NAGASE Group, Okayama, Japan
| | - William Spittal
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Emma Clark
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | | | - Hannah C. Harris
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Karen Bentley
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Georgina Davis
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Dapeng Wang
- LeedsOmics, University of Leeds, Leeds, United Kingdom
| | - Suparna Mitra
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | | | - Mark H. Wilcox
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
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Guery B, Georgopali A, Karas A, Kazeem G, Michon I, Wilcox MH, Cornely OA. Pharmacokinetic analysis of an extended-pulsed fidaxomicin regimen for the treatment of Clostridioides (Clostridium) difficile infection in patients aged 60 years and older in the EXTEND randomized controlled trial. J Antimicrob Chemother 2021; 75:1014-1018. [PMID: 31960058 DOI: 10.1093/jac/dkz549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Fidaxomicin is a recommended treatment for Clostridioides difficile infection (CDI) and reduces CDI recurrence incidence versus vancomycin. An extended-pulsed fidaxomicin (EPFX) regimen further reduces recurrence frequency. However, the pharmacokinetic profile of fidaxomicin in an EPFX regimen is unknown. OBJECTIVES To evaluate plasma and stool concentrations of fidaxomicin and its metabolite, OP-1118, after EPFX administration for CDI. METHODS In the Phase 3b/4 EXTEND trial, patients aged ≥60 years with toxin-confirmed CDI were randomized to receive EPFX (oral fidaxomicin twice daily, Days 1-5; once daily on alternate days, Days 7-25). Fidaxomicin and OP-1118 concentrations were determined using post-dose plasma samples obtained on Days 5 ± 1, 12 ± 1 and 25/26, and post-dose stool samples obtained on Days 5 ± 1, 12 ± 1 and 26 ± 1. RESULTS Plasma samples from 14 patients were included in the pharmacokinetic analysis; 12 of these patients provided stool samples. Median (range) plasma concentrations of fidaxomicin on Day 5 ± 1 and Day 25/26 were 0.0252 (0.0038-0.1220) mg/L and 0.0069 (0-0.0887) mg/L, respectively, and those of OP-1118 were 0.0648 (0.0142-0.3250) mg/L and 0.0206 (0-0.3720) mg/L, respectively. Median (range) stool concentrations of fidaxomicin and OP-1118 on Day 26 ± 1 were 272.5 (0-524) mg/kg and 280.5 (0-1120) mg/kg, respectively. CONCLUSIONS EPFX treatment maintained fidaxomicin stool concentrations above the C. difficile MIC90 until Day 26 ± 1. Systemic exposure to fidaxomicin and OP-1118 was low throughout and there was no evidence of accumulation in plasma or stool during treatment.
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Affiliation(s)
- Benoit Guery
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | | | | | | | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals & University of Leeds, Leeds, UK.,Healthcare Associated Infections Research Group, Section of Molecular Gastroenterology, Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Oliver A Cornely
- Department I of Internal Medicine, University Hospital of Cologne and German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, Cologne, Germany
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37
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Johnson S, Lavergne V, Skinner AM, Gonzales-Luna AJ, Garey KW, Kelly CP, Wilcox MH. Clinical Practice Guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 Focused Update Guidelines on Management of Clostridioides difficile Infection in Adults. Clin Infect Dis 2021; 73:e1029-e1044. [PMID: 34164674 DOI: 10.1093/cid/ciab549] [Citation(s) in RCA: 198] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Indexed: 12/19/2022] Open
Abstract
This clinical practice guideline is a focused update on management of Clostridioides difficile infection (CDI) in adults specifically addressing the use of fidaxomicin and bezlotoxumab for the treatment of CDI. This guideline was developed by a multidisciplinary panel representing the Infectious Diseases Society of America (IDSA) and the Society for Healthcare Epidemiology of America (SHEA). This guideline is intended for use by healthcare professionals who care for adults with CDI, including specialists in infectious diseases, gastroenterologists, hospitalists, pharmacists, and any clinicians and healthcare providers caring for these patients. The panel's recommendations for the management CDI are based upon evidence derived from topic-specific systematic literature reviews.Summarized below are the recommendations for the management of CDI in adults. The panel followed a systematic process which included a standardized methodology for rating the certainty of the evidence and strength of recommendation using the GRADE approach (Grading of Recommendations Assessment, Development and Evaluation) (see Figure 1). A detailed description of background, methods, evidence summary and rationale that support each recommendation, and knowledge gaps can be found online in the full text.
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Affiliation(s)
- Stuart Johnson
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, and Loyola University Medical Center, Maywood, Illinois, Loyola University Medical Center, Maywood, Illinois
| | - Valéry Lavergne
- Department of Medical Microbiology and Infection Control, Vancouver General Hospital, Vancouver, British Columbia, Canada; Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Andrew M Skinner
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, and Loyola University Medical Center, Maywood, Illinois, Loyola University Medical Center, Maywood, Illinois
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas
| | - Ciaran P Kelly
- Dept of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, and Leeds Institute of Medical Research, University of Leeds, Leeds, UK
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Rooney CM, McIntyre J, Ritchie L, Wilcox MH. Evidence review of physical distancing and partition screens to reduce healthcare acquired SARS-CoV-2. Infect Prev Pract 2021; 3:100144. [PMID: 34316581 PMCID: PMC8081747 DOI: 10.1016/j.infpip.2021.100144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/21/2021] [Indexed: 12/21/2022] Open
Abstract
We review the evidence base for two newly introduced Infection prevention and control strategies within UK hospitals. The new standard infection control precaution of 2 metres physical distancing and the use of partition screens as a means of source control of infection for SARS-CoV-2. Following review of Ovid-MEDLINE and governmental SAGE outputs there is limited evidence to support the use of 2 metres physical distancing and partition screens within healthcare.
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Affiliation(s)
- C M Rooney
- Leeds Teaching Hospitals Trust, UK.,Leeds Institute of Medical Research, University of Leeds, UK
| | - J McIntyre
- Infection Prevention and Control, NHS England and NHS Improvement, UK
| | - L Ritchie
- Infection Prevention and Control, NHS England and NHS Improvement, UK
| | - M H Wilcox
- Leeds Teaching Hospitals Trust, UK.,Leeds Institute of Medical Research, University of Leeds, UK
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Harris HC, Buckley AM, Spittal W, Ewin D, Clark E, Altringham J, Bentley K, Moura IB, Wilcox MH, Woodford N, Davies K, Chilton CH. The effect of intestinal microbiota dysbiosis on growth and detection of carbapenemase-producing Enterobacterales within an in vitro gut model. J Hosp Infect 2021; 113:1-9. [PMID: 33932556 DOI: 10.1016/j.jhin.2021.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/18/2021] [Accepted: 04/14/2021] [Indexed: 01/07/2023]
Abstract
BACKGROUND Carbapenemase-producing Enterobacterales (CPE) can colonize the gut and are of major clinical concern. Identification of CPE colonization is problematic; there is no gold-standard detection method, and the effects of antibiotic exposure and microbiota dysbiosis on detection are unknown. AIM Based on a national survey we selected four CPE screening assays in common use. We used a clinically reflective in vitro model of human gut microbiota to investigate the performance of each test to detect three different CPE strains under different, clinically relevant antibiotic exposures. METHODS Twelve gut models were seeded with a pooled faecal slurry and exposed to CPE either before, after, concomitant with, or in the absence of piperacillin-tazobactam (358 mg/L, 3 × daily, seven days). Total Enterobacterales and CPE populations were enumerated daily. Regular screening for CPE was performed using Cepheid Xpert® Carba-R molecular test, and with Brilliance™ CRE, Colorex™ mSuperCARBA and CHROMID® CARBA SMART agars. FINDINGS Detection of CPE when the microbiota are intact is problematic. Antibiotic exposure disrupts microbiota populations and allows CPE proliferation, increasing detection. The performances of assays varied, particularly with respect to different CPE strains. The Cepheid assay performed better than the three agar methods for detecting a low level of CPE within an intact microbiota, although performance of all screening methods was comparable when CPE populations increased in a disrupted microbiota. CONCLUSION CPE strains differed in their dynamics of colonization in an in vitro gut model and in their subsequent response to antibiotic exposure. This affected detection by molecular and screening methods, which has implications for the sensitivity of CPE screening in healthcare settings.
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Affiliation(s)
- H C Harris
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - A M Buckley
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - W Spittal
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - D Ewin
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - E Clark
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - J Altringham
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - K Bentley
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - I B Moura
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - M H Wilcox
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK; Department of Microbiology, Leeds Teaching Hospitals NHS Trust, The General Infirmary, Leeds, UK
| | - N Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI), Reference Unit, Microbiology Services - Colindale, Public Health England, UK
| | - K Davies
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK; Department of Microbiology, Leeds Teaching Hospitals NHS Trust, The General Infirmary, Leeds, UK
| | - C H Chilton
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK.
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Goldstein EJC, Citron DM, Gerding DN, Wilcox MH, Gabryelski L, Pedley A, Zeng Z, Dorr MB. Bezlotoxumab for the Prevention of Recurrent Clostridioides difficile Infection: 12-Month Observational Data From the Randomized Phase III Trial, MODIFY II. Clin Infect Dis 2021; 71:1102-1105. [PMID: 31883370 DOI: 10.1093/cid/ciz1151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/18/2019] [Indexed: 11/13/2022] Open
Abstract
From Monoclonal Antibodies for C. difficile Therapy II, no participants (n = 0/69) with a sustained clinical cure through 12 weeks following bezlotoxumab infusion experienced recurrent Clostridioides difficile infection (rCDI) after 9 months (versus actoxumab + bezlotoxumab, n = 2/65; versus placebo, n = 1/34). Bezlotoxumab's efficacy appears to be due to prevention rather than delayed onset of rCDI. Clinical Trials Registration. NCT01513239.
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Affiliation(s)
| | - Diane M Citron
- R. M. Alden Research Laboratory, Santa Monica, California, USA
| | | | - Mark H Wilcox
- Leeds Teaching Hospitals and University of Leeds, Leeds, West Yorkshire, United Kingdom
| | | | | | - Zhen Zeng
- Merck & Co., Inc., Kenilworth, New Jersey, USA
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Pai MP, Wilcox MH, Chitra S, McGovern PC. Safety and efficacy of omadacycline by BMI categories and diabetes history in two Phase III randomized studies of patients with acute bacterial skin and skin structure infections. J Antimicrob Chemother 2021; 76:1315-1322. [PMID: 33458763 PMCID: PMC8050767 DOI: 10.1093/jac/dkaa558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/10/2020] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES The objectives of this post-hoc analysis were to examine the safety and efficacy of omadacycline by BMI categories and diabetes history in adults with acute bacterial skin and skin structure infections (ABSSSI) from two pivotal Phase III studies. PATIENTS AND METHODS OASIS-1 (ClinicalTrials.gov identifier NCT02378480): patients were randomized 1:1 to IV omadacycline or linezolid for 7-14 days, with optional transition to oral medication. OASIS-2 (ClinicalTrials.gov identifier NCT02877927): patients received once-daily oral omadacycline or twice-daily oral linezolid for 7-14 days. Early clinical response (ECR) was defined as ≥20% reduction in lesion size 48-72 h after the first dose. Clinical success at post-treatment evaluation (PTE; 7-14 days after the last dose) was defined as symptom resolution such that antibacterial therapy was unnecessary. Safety was assessed by treatment-emergent adverse events and laboratory measures. Between-treatment comparisons were made with regard to WHO BMI categories and diabetes history. RESULTS Patients were evenly distributed among healthy weight, overweight and obese groups. Clinical success for omadacycline-treated patients at ECR and PTE was similar across BMI categories. Outcomes by diabetes status were similar in omadacycline- and linezolid-treated patients: at ECR, clinical success rates were lower for those with diabetes; at PTE, clinical success was similar between treatment groups regardless of diabetes history. The safety of omadacycline and linezolid was largely similar across BMI groups and by diabetes history. CONCLUSIONS Omadacycline efficacy in patients with higher BMI and in patients with diabetes was consistent with results from two pivotal Phase III ABSSSI trials. Fixed-dose omadacycline is an appropriate treatment for ABSSSI in adults regardless of BMI.
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Affiliation(s)
- Manjunath P Pai
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark H Wilcox
- University of Leeds & Leeds Teaching Hospitals, Leeds LS2 9JT, UK
| | - Surya Chitra
- Paratek Pharmaceuticals, Inc., King of Prussia, PA 19406, USA
| | - Paul C McGovern
- Paratek Pharmaceuticals, Inc., King of Prussia, PA 19406, USA
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Abstract
We examine 3 different approaches to protecting the gut microbiome: highly targeted antibiotics, antibiotic destruction, and antibiotic binding. Each approach shows promise to prevent the off-target effects of antibiotics on the gut microbiome.
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Affiliation(s)
- C M Rooney
- Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom.,Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, United Kingdom
| | - S Ahmed
- Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom.,Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, United Kingdom
| | - M H Wilcox
- Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom.,Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, United Kingdom
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43
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Kelly CP, Poxton IR, Shen J, Wilcox MH, Gerding DN, Zhao X, Laterza OF, Railkar R, Guris D, Dorr MB. Effect of Endogenous Clostridioides difficile Toxin Antibodies on Recurrence of C. difficile Infection. Clin Infect Dis 2021; 71:81-86. [PMID: 31628838 DOI: 10.1093/cid/ciz809] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/30/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Endogenous antibodies (eAbs) against Clostridioides (Clostridium) difficile toxins may protect against recurrence of C. difficile infection (rCDI). This hypothesis was tested using placebo group data from MODIFY (Monoclonal Antibodies for C. difficile Therapy) I and II (NCT01241552 and NCT01513239, respectively), global, randomized phase 3 trials that assessed the efficacy and safety of the antitoxin monoclonal antibodies bezlotoxumab and actoxumab in participants receiving antibiotic therapy for CDI. METHODS A placebo infusion (normal saline) was administered on study day 1. Serum samples were collected on day 1, week 4, and week 12, and eAb-A and eAb-B titers were measured by 2 validated electrochemiluminescence immunoassays. Rates of initial clinical cure and rCDI were summarized by eAb titer category (low, medium, high) at each time point. RESULTS Serum eAb titers were available from a total of 773 participants. The proportion of participants with high eAb-A and eAb-B titers increased over time. Rates of initial clinical cure were similar across eAb titer categories. There was no correlation between eAb-A titers and rCDI rate at any time point. However, there was a negative correlation between rCDI and eAb-B titer on day 1 and week 4. rCDI occurred in 22% of participants with high eAb-B titers at baseline compared with 35% with low or medium titers (P = .015). CONCLUSIONS Higher eAb titers against toxin B, but not toxin A, were associated with protection against rCDI. These data are consistent with the observed efficacy of bezlotoxumab, and lack of efficacy of actoxumab, in the MODIFY trials. CLINICAL TRIALS REGISTRATION NCT01241552 and NCT01513239.
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Affiliation(s)
- Ciarán P Kelly
- Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Ian R Poxton
- University of Edinburgh, Edinburgh, United Kingdom
| | | | - Mark H Wilcox
- Leeds Teaching Hospitals and University of Leeds, United Kingdom
| | - Dale N Gerding
- Loyola University Chicago Stritch School of Medicine, Maywood.,Edward Hines Jr Veterans Affairs Hospital, Hines, Illinois
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44
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Normington C, Moura IB, Bryant JA, Ewin DJ, Clark EV, Kettle MJ, Harris HC, Spittal W, Davis G, Henn MR, Ford CB, Wilcox MH, Buckley AM. Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection. NPJ Biofilms Microbiomes 2021; 7:16. [PMID: 33547298 PMCID: PMC7864922 DOI: 10.1038/s41522-021-00184-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022] Open
Abstract
C. difficile infection (CDI) is a worldwide healthcare problem with ~30% of cases failing primary therapy, placing a burden on healthcare systems and increasing patient morbidity. We have little understanding of why these therapies fail. Here, we use a clinically validated in vitro gut model to assess the contribution of biofilms towards recurrent disease and to investigate biofilm microbiota-C. difficile interactions. Initial experiments show that C. difficile cells became associated with the colonic biofilm microbiota and are not depleted by vancomycin or faecal microbiota transplant therapies. We observe that transferring biofilm encased C. difficile cells into a C. difficile naïve but CDI susceptible model induces CDI. Members of the biofilm community can impact C. difficile biofilm formation by acting either antagonistically or synergistically. We highlight the importance of biofilms as a reservoir for C. difficile, which can be a cause for recurrent infections.
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Affiliation(s)
- Charmaine Normington
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Ines B Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Jessica A Bryant
- Microbiome Sciences, Seres Therapeutics Inc., Cambridge, MA, USA
| | - Duncan J Ewin
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Emma V Clark
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Morgan J Kettle
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Hannah C Harris
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - William Spittal
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Georgina Davis
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Matthew R Henn
- Microbiome Sciences, Seres Therapeutics Inc., Cambridge, MA, USA
| | | | - Mark H Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK
| | - Anthony M Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, LS1 9JT, UK.
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45
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Azimirad M, Krutova M, Yadegar A, Shahrokh S, Olfatifar M, Aghdaei HA, Fawley WN, Wilcox MH, Zali MR. Clostridioides difficile ribotypes 001 and 126 were predominant in Tehran healthcare settings from 2004 to 2018: a 14-year-long cross-sectional study. Emerg Microbes Infect 2021; 9:1432-1443. [PMID: 32520657 PMCID: PMC7473134 DOI: 10.1080/22221751.2020.1780949] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile infection (CDI) remains a major healthcare problem worldwide, however, little is known about CDI epidemiology in Iran. Between December 2004 and November 2018, 3649 stool samples were collected from patients in 69 hospitals and medical centres in Tehran and were cultured for the presence of C. difficile; isolates were characterized by PCR ribotyping and toxin genes detection. A total of 582 C. difficile isolates were obtained and the overall CDI prevalence was 15.9%; 290 (49.8%) cases were healthcare-associated (HA) and 292 (50.2%) cases were community-associated (CA). Of these, DNA of 513 isolates submitted for ribotyping. The ribotype and/or WEBRIBO type could be assessed in 366 (62.9%) isolates. The most frequent RTs were 001 (n = 75, 12.9%), 126 (n = 65, 11.2%) and 084 (n = 19, 3.3%); the toxin gene profile tcdA + B + /cdtA + B + (n = 112, 19.2%) was the most common. Fifteen C. difficile isolates (2.6%) did not carry any toxin genes. There was no difference between frequently found RTs in HA-CDI and CA-CDI, except for RT 029 which was more likely to be associated with healthcare origin (12/15, p-value = 0.02). No isolate of RTs 027 or 078 was identified. Importantly, RTs 031, 038, 039, 084, 085 reported previously as RTs with an absence of toxin genes, revealed the presence of toxin genes in our study. Using Simpson's reciprocal index of diversity, we found that RT diversity decreased as the prevalence of the RT 084 increased (R = -0.78, p-value = 0.041). Different patterns in CDI epidemiology underscore the importance of local surveillance and infection control measures in Tehran healthcare settings.
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Affiliation(s)
- Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides Difficile (ESGCD)
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Meysam Olfatifar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Warren N Fawley
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides Difficile (ESGCD).,Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust & University of Leeds, Leeds, UK
| | - Mark H Wilcox
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides Difficile (ESGCD).,Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust & University of Leeds, Leeds, UK
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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46
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Buckley AM, Moura IB, Wilcox MH. Is there a causal relationship between trehalose consumption and Clostridioides difficile infection? Curr Opin Gastroenterol 2021; 37:9-14. [PMID: 33105252 DOI: 10.1097/mog.0000000000000695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Trehalose metabolism appears to play a role in the pathogenicity of some microbes. It has been claimed that trehalose consumption may be a risk factor for Clostridioides difficile infection (CDI), but the evidence for a causal link is contentious. RECENT FINDINGS Epidemic ribotypes of C. difficile harbour mutations or have acquired extra genes that mean these strains can utilize lower concentrations of bioavailable trehalose, providing a competitive metabolic advantage in some CDI animal models. By contrast, evidence has emerged to show that trehalose-induced microbiota changes can help protect/reduce CDI in other models. In addition, C. difficile trehalose metabolic variants are widespread among epidemic and nonepidemic ribotypes alike, and the occurrence of these trehalose variants was not associated with increase disease severity or mortality. SUMMARY Currently, there is no proven causal association between the incidence or severity of human CDI and the presence of trehalose metabolism variants. Furthermore, microbial metabolism reduces trehalose bioavailability, potentially removing this competitive advantage for C. difficile trehalose metabolism variants. Taken together, trehalose consumed as part of a normal diet has no increased risk of CDI.
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Affiliation(s)
- Anthony M Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
| | - Ines B Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
| | - Mark H Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
- Department of Microbiology, Leeds Teaching Hospital NHS Trust, Old Medical School, Leeds General Infirmary, Leeds, UK
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47
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Abstract
PURPOSE OF REVIEW We discuss the potential role of the faecal chain in COVID-19 and highlight recent studies using waste water-based epidemiology (WBE) to track severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RECENT FINDINGS WBE has been suggested as an adjunct to improve disease surveillance and aid early detection of circulating disease. SARS-CoV-2, the aetiological agent of COVID-19, is an enveloped virus, and as such, typically not associated with the waste water environment, given high susceptibility to degradation in aqueous conditions. A review of the current literature supports the ability to detect of SARS-CoV-2 in waste water and suggests methods to predict community prevalence based on viral quantification. SUMMARY The summary of current practices shows that while the isolation of SARS-CoV-2 is possible from waste water, issues remain regarding the efficacy of virial concentration and subsequent quantification and alignment with epidemiological data.
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48
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Buckley AM, Altringham J, Clark E, Bently K, Spittal W, Ewin D, Wilkinson V, Davis G, Moura IB, Wilcox MH. Eravacycline, a novel tetracycline derivative, does not induce Clostridioides difficile infection in an in vitro human gut model. J Antimicrob Chemother 2021; 76:171-178. [PMID: 32929459 DOI: 10.1093/jac/dkaa386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/18/2020] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES The approval of new antibiotics is essential to combat infections caused by antimicrobial-resistant pathogens; however, such agents should be tested to determine their effect on the resident microbiota and propensity to select for opportunistic pathogens, such as Clostridioides difficile. Eravacycline is a new antibiotic for the treatment of complicated intra-abdominal infections. Here, we determined the effects of eravacycline compared with moxifloxacin on the microbiota and if these were conducive to induction of C. difficile infection (CDI). METHODS We seeded in vitro chemostat models, which simulate the physiological conditions of the human colon, with a human faecal slurry and instilled gut-reflective concentrations of either eravacycline or moxifloxacin. RESULTS Eravacycline instillation was associated with decreased Bifidobacterium, Lactobacillus and Clostridium species, which recovered 1 week after exposure. However, Bacteroides spp. levels decreased to below the limit of detection and did not recover prior to the end of the experiment. Post-eravacycline, a bloom of aerobic bacterial species occurred, including Enterobacteriaceae, compared with pre-antibiotic, which remained high for the duration of the experiment. These changes in microbiota were not associated with induction of CDI, as we observed a lack of C. difficile spore germination and thus no toxin was detected. Moxifloxacin exposure sufficiently disrupted the microbiota to induce simulated CDI, where C. difficile spore germination, outgrowth and toxin production were seen. CONCLUSIONS These model data suggest that, despite the initial impact of eravacycline on the intestinal microbiota, similar to clinical trial data, this novel tetracycline has a low propensity to induce CDI.
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Affiliation(s)
- Anthony M Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - James Altringham
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - Emma Clark
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - Karen Bently
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - William Spittal
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - Duncan Ewin
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - Vikki Wilkinson
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - Georgina Davis
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - Ines B Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
| | - Mark H Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 9JT, UK
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49
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Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, Wilcox MH, Farkas K. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. Sci Total Environ 2020; 749:141364. [PMID: 32836117 PMCID: PMC7836549 DOI: 10.1016/j.scitotenv.2020.141364] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 04/14/2023]
Abstract
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
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Affiliation(s)
- David L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus Midlothian, EH25 9RG, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Luke S Hillary
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE, UK
| | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 3EX, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
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50
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Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, Wilcox MH, Farkas K. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. Sci Total Environ 2020; 749:141364. [PMID: 32836117 DOI: 10.20944/preprints202007.0471.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 05/18/2023]
Abstract
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
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Affiliation(s)
- David L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus Midlothian, EH25 9RG, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Luke S Hillary
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE, UK
| | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 3EX, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
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