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Flynn E, Papanicolas LE, Anagnostou N, Warner MS, Rogers GB. Carbapenemase-producing Enterobacterales: a profound threat to Australian public health. Med J Aust 2023; 219:290-292. [PMID: 37660307 DOI: 10.5694/mja2.52077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023]
Affiliation(s)
- Erin Flynn
- South Australian Health and Medical Research Institute, Adelaide, SA
- Australian National University, Canberra, ACT
| | - Lito E Papanicolas
- Flinders University, Adelaide, SA
- SA Pathology, Royal Adelaide Hospital, Adelaide, SA
| | - Nicholas Anagnostou
- Flinders University, Adelaide, SA
- Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, SA
| | - Morgyn S Warner
- SA Pathology, Royal Adelaide Hospital, Adelaide, SA
- University of Adelaide, Adelaide, SA
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA
- Flinders University, Adelaide, SA
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2
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Taylor SL, Papanicolas LE, Flynn E, Boyd MA, Wesselingh SL, Rogers GB. Preventing empirical antibiotic treatment failure in migrant populations: screening by infection risk, not ethnic background. Int J Infect Dis 2023; 134:168-171. [PMID: 37343782 DOI: 10.1016/j.ijid.2023.06.014] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/14/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Abstract
Multidrug-resistant organisms (MDROs) are a major international health threat. In many low and middle-income countries poorly regulated antibiotic use, limited surveillance, and inadequate sanitation give rise to high rates of antibiotic resistance. A resulting reliance on last-line antibiotic options further contributes to the emergence of MDROs. The potential for these pathogens to spread across international borders is a matter of considerable concern. However, this problem is commonly framed as primarily a threat to the health security of countries where resistance is not yet endemic. In fact, it is little acknowledged that those at greatest risk from antibiotic treatment failure are individuals who move from regions of high MDRO prevalence to settings where standard empirical treatment options remain largely effective. In this perspective, we highlight the poor treatment outcomes for disseminated bacterial infections in individuals who have moved from settings in which MDROs are common to those where MDROs are currently less common. We discuss MDRO screening strategies that could avoid stigmatizing vulnerable populations by focusing on future risk of disseminated infection, rather than past risk of acquisition. In practical terms, this means screening individuals before childbirth, immunosuppressive treatments, major surgery, or other events associated with disseminated infection risk, rather than prioritizing screening for individuals from regions with high carriage rates. We argue that such measures would reduce antibiotic treatment failure and improve outcomes while protecting migrant populations from the divisive consequences of targeted screening programs.
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Affiliation(s)
- Steven L Taylor
- South Australian Health and Medical Research Institute, Adelaide, Australia; College of Medicine and Public Health, Flinders University, Adelaide, Australia.
| | - Lito E Papanicolas
- South Australian Health and Medical Research Institute, Adelaide, Australia; College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Erin Flynn
- South Australian Health and Medical Research Institute, Adelaide, Australia; National Centre for Epidemiology & Population Health, The Australian National University, Canberra, Australia
| | - Mark A Boyd
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Steve L Wesselingh
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, Australia; College of Medicine and Public Health, Flinders University, Adelaide, Australia
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3
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Carpenter L, Shoubridge AP, Flynn E, Lang C, Taylor SL, Papanicolas LE, Collins J, Gordon D, Lynn DJ, Crotty M, Whitehead C, Leong LEX, Wesselingh SL, Ivey K, Inacio MC, Rogers GB. Cohort profile: GRACE - a residential aged care cohort examining factors influencing antimicrobial resistance carriage. BMC Geriatr 2023; 23:521. [PMID: 37641010 PMCID: PMC10464000 DOI: 10.1186/s12877-023-04215-3] [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: 11/17/2022] [Accepted: 08/03/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND The emergence of antimicrobial-resistant bacteria represents a considerable threat to human health, particularly for vulnerable populations such as those living in residential aged care. However, antimicrobial resistance carriage and modes of transmission remain incompletely understood. The Generating evidence on antimicrobial Resistance in the Aged Care Environment (GRACE) study was established to determine principal risk factors of antimicrobial resistance carriage and transmission in residential aged care facilities (RACFs). This article describes the cohort characteristics, national representation, and planned analyses for this study. METHODS Between March 2019 and March 2020, 279 participants were recruited from five South Australian RACFs. The median age was 88.6 years, the median period in residence was 681 days, and 71.7% were female. A dementia diagnosis was recorded in 54.5% and more than two thirds had moderate to severe cognitive impairment (68.8%). 61% had received at least one course of antibiotics in the 12 months prior to enrolment. RESULTS To investigate the representation of the GRACE cohort to Australians in residential aged care, its characteristics were compared to a subset of the historical cohort of the Registry of Senior Australians (ROSA). This included 142,923 individuals who were permanent residents of RACFs on June 30th, 2017. GRACE and ROSA cohorts were similar in age, sex, and duration of residential care, prevalence of health conditions, and recorded dementia diagnoses. Differences were observed in care requirements and antibiotic exposure (both higher for GRACE participants). GRACE participants had fewer hospital visits compared to the ROSA cohort, and a smaller proportion were prescribed psycholeptic medications. CONCLUSIONS We have assembled a cohort of aged care residents that is representative of the Australian aged care population, and which provides a basis for future analyses. Metagenomic data isolated from participants and built environments will be used to determine microbiome and resistome characteristics of an individual and the facility. Individual and facility risk exposures will be aligned with metagenomic data to identify principal determinants for antimicrobial resistance carriage. Ultimately, this analysis will inform measures aimed at reducing the emergence and spread of antimicrobial resistant pathogens in this high-risk population.
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Affiliation(s)
- Lucy Carpenter
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Andrew P Shoubridge
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia.
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.
| | - Erin Flynn
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, ACT, Australia
| | - Catherine Lang
- Registry of Senior Australians, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Steven L Taylor
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Lito E Papanicolas
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- SA Pathology, Adelaide, SA, Australia
| | - Josephine Collins
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia
| | - David Gordon
- SA Pathology, Adelaide, SA, Australia
- Department of Microbiology and Infectious Diseases, Flinders Medical Centre, Adelaide, SA, Australia
| | - David J Lynn
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- Computational & Systems Biology Programme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Maria Crotty
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- Southern Adelaide Local Health Network, SA Health, Adelaide, SA, Australia
| | - Craig Whitehead
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- Southern Adelaide Local Health Network, SA Health, Adelaide, SA, Australia
| | | | - Steve L Wesselingh
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Kerry Ivey
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Maria C Inacio
- Registry of Senior Australians, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Allied Health and Human Performance, University of South Australia, Adelaide, SA, Australia
| | - Geraint B Rogers
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, 5D332, Flinders Medical Centre, Flinders Drive, Bedford Park, Adelaide, SA, 5042, Australia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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Brass A, Shoubridge AP, Larby N, Elms L, Sims SK, Flynn E, Miller C, Crotty M, Papanicolas LE, Wesselingh SL, Morawska L, Bell SC, Taylor SL, Rogers GB. Targeted reduction of airborne viral transmission risk in long-term residential aged care. Age Ageing 2022; 51:6964928. [PMID: 36580555 DOI: 10.1093/ageing/afac316] [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: 09/12/2022] [Indexed: 12/31/2022] Open
Abstract
COVID-19 has demonstrated the devastating consequences of the rapid spread of an airborne virus in residential aged care. We report the use of CO2-based ventilation assessment to empirically identify potential 'super-spreader' zones within an aged care facility, and determine the efficacy of rapidly implemented, inexpensive, risk reduction measures.
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Affiliation(s)
- Amanda Brass
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Andrew P Shoubridge
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Nicolas Larby
- Aged Care Property Services Management, Adelaide, SA, Australia
| | - Levi Elms
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Sarah K Sims
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Erin Flynn
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,National Centre for Epidemiology & Population Health, The Australian National University, Canberra, ACT, Australia
| | - Caroline Miller
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,School of Public Health, University of Adelaide, Adelaide, SA, Australia
| | - Maria Crotty
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Southern Adelaide Local Health Network, SA Health, Adelaide, SA, Australia
| | - Lito E Papanicolas
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.,SA Pathology, SA Health, Adelaide, SA, Australia
| | - Steve L Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Lidia Morawska
- International Laboratory for Air Quality and Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Scott C Bell
- The Prince Charles Hospital, Brisbane, QLD, Australia.,Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Steven L Taylor
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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Wang Y, Taylor SL, Choo JM, Papanicolas LE, Keating R, Hindmarsh K, Thomson RM, Morgan L, Rogers GB, Burr LD. Carriage and Transmission of Macrolide Resistance Genes in Patients With Chronic Respiratory Conditions and Their Close Contacts. Chest 2022; 162:56-65. [DOI: 10.1016/j.chest.2022.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 11/16/2022] Open
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Taylor SL, Papanicolas LE, Richards A, Ababor F, Kang WX, Choo JM, Woods C, Wesselingh SL, Ooi EH, MacFarlane P, Rogers GB. Ear microbiota and middle ear disease: a longitudinal pilot study of Aboriginal children in a remote south Australian setting. BMC Microbiol 2022; 22:24. [PMID: 35026986 PMCID: PMC8756658 DOI: 10.1186/s12866-022-02436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/29/2021] [Indexed: 12/03/2022] Open
Abstract
Background Otitis media (OM) is a major disease burden in Australian Aboriginal children, contributing to serious long-term health outcomes. We report a pilot analysis of OM in children attending an outreach ear and hearing clinic in a remote south Australian community over a two-year period. Our study focuses on longitudinal relationships between ear canal microbiota characteristics with nasopharyngeal microbiota, and clinical and treatment variables. Results Middle ear health status were assessed in 19 children (aged 3 months to 8 years) presenting in remote western South Australia and medical interventions were recorded. Over the two-year study period, chronic suppurative OM was diagnosed at least once in 7 children (37%), acute OM with perforation in 4 children (21%), OM with effusion in 11 children (58%), while only 1 child had no ear disease. Microbiota analysis of 19 children (51 sets of left and right ear canal swabs and nasopharyngeal swabs) revealed a core group of bacterial taxa that included Corynebacterium, Alloiococcus, Staphylococcus, Haemophilus, Turicella, Streptococcus, and Pseudomonas. Within-subject microbiota similarity (between ears) was significantly greater than inter-subject similarity, regardless of differences in ear disease (p = 0.0006). Longitudinal analysis revealed changes in diagnosis to be associated with more pronounced changes in microbiota characteristics, irrespective of time interval. Ear microbiota characteristics differed significantly according to diagnosis (P (perm) = 0.0001). Diagnoses featuring inflammation with tympanic membrane perforation clustering separately to those in which the tympanic membrane was intact, and characterised by increased Proteobacteria, particularly Haemophilus influenzae, Moraxella catarrhalis, and Oligella. While nasopharyngeal microbiota differed significantly in composition to ear microbiota (P (perm) = 0.0001), inter-site similarity was significantly greater in subjects with perforated tympanic membranes, a relationship that was associated with the relative abundance of H. influenzae in ear samples (rs = − 0.71, p = 0.0003). Longitudinal changes in ear microbiology reflected changes in clinical signs and treatment. Conclusions Children attending the ear and hearing clinic in a remote Aboriginal community present with a broad spectrum of OM conditions and severities, consistent with other remote Aboriginal communities. Ear microbiota characteristics align with OM diagnosis and change with disease course. Nasopharyngeal microbiota characteristics are consistent with the contribution of acute upper respiratory infection to OM aetiology. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02436-x.
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Brass A, Shoubridge AP, Crotty M, Morawska L, Bell SC, Qiao M, Woodman RJ, Whitehead C, Inacio MC, Miller C, Corlis M, Larby N, Elms L, Sims SK, Taylor SL, Flynn E, Papanicolas LE, Rogers GB. Prevention of SARS-CoV-2 (COVID-19) transmission in residential aged care using ultraviolet light (PETRA): a two-arm crossover randomised controlled trial protocol. BMC Infect Dis 2021; 21:967. [PMID: 34535091 PMCID: PMC8446719 DOI: 10.1186/s12879-021-06659-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/06/2021] [Indexed: 01/24/2023] Open
Abstract
Background SARS-CoV-2 poses a considerable threat to those living in residential aged care facilities (RACF). RACF COVID-19 outbreaks have been characterised by the rapid spread of infection and high rates of severe disease and associated mortality. Despite a growing body of evidence supporting airborne transmission of SARS-CoV-2, current infection control measures in RACF including hand hygiene, social distancing, and sterilisation of surfaces, focus on contact and droplet transmission. Germicidal ultraviolet (GUV) light has been used widely to prevent airborne pathogen transmission. Our aim is to investigate the efficacy of GUV technology in reducing the risk of SARS-CoV-2 infection in RACF. Methods A multicentre, two-arm double-crossover, randomised controlled trial will be conducted to determine the efficacy of GUV devices to reduce respiratory viral transmission in RACF, as an adjunct to existing infection control measures. The study will be conducted in partnership with three aged care providers in metropolitan and regional South Australia. RACF will be separated into paired within-site zones, then randomised to intervention order (GUV or control). The initial 6-week period will be followed by a 2-week washout before crossover to the second 6-week period. After accounting for estimated within-zone and within-facility correlations of infection, and baseline infection rates (10 per 100 person-days), a sample size of n = 8 zones (n = 40 residents/zone) will provide 89% power to detect a 50% reduction in symptomatic infection rate. The primary outcome will be the incidence rate ratio of combined symptomatic respiratory infections for intervention versus control. Secondary outcomes include incidence rates of hospitalisation for complications associated with respiratory infection; respiratory virus detection in facility air and fomite samples; rates of laboratory confirmed respiratory illnesses and genomic characteristics. Discussion Measures that can be deployed rapidly into RACF, that avoid the requirement for changes in resident and staff behaviour, and that are effective in reducing the risk of airborne SARS-CoV-2 transmission, would provide considerable benefit in safeguarding a highly vulnerable population. In addition, such measures might substantially reduce rates of other respiratory viruses, which contribute considerably to resident morbidity and mortality. Trial registration Australian and New Zealand Clinical Trials Registry ACTRN12621000567820 (registered on 14th May, 2021).
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Affiliation(s)
- Amanda Brass
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,The Microbiome and Host Health Programme, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Andrew P Shoubridge
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia. .,The Microbiome and Host Health Programme, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.
| | - Maria Crotty
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.,Southern Adelaide Local Health Network, SA Health, Adelaide, SA, Australia
| | - Lidia Morawska
- International Laboratory for Air Quality and Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Scott C Bell
- The Prince Charles Hospital, Brisbane, QLD, Australia.,Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Ming Qiao
- SA Pathology, SA Health, Adelaide, SA, Australia
| | - Richard J Woodman
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Flinders Centre for Epidemiology and Biostatistics, Flinders University, Adelaide, SA, Australia
| | - Craig Whitehead
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.,Southern Adelaide Local Health Network, SA Health, Adelaide, SA, Australia
| | - Maria C Inacio
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Registy of Senior Australians, SAHMRI, Adelaide, SA, Australia
| | - Caroline Miller
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,School of Public Health, University of Adelaide, Adelaide, SA, Australia
| | - Megan Corlis
- Australian Nursing & Midwifery Federation, Adelaide, SA, Australia.,UniSA Allied Health & Human Performance, University of South Australia, Adelaide, SA, Australia
| | - Nicolas Larby
- Aged Care Property Services Management, Adelaide, SA, Australia
| | - Levi Elms
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,The Microbiome and Host Health Programme, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Sarah K Sims
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,The Microbiome and Host Health Programme, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Steven L Taylor
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,The Microbiome and Host Health Programme, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Erin Flynn
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,The Microbiome and Host Health Programme, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,National Centre for Epidemiology & Population Health, The Australian National University, Canberra, ACT, Australia
| | - Lito E Papanicolas
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,The Microbiome and Host Health Programme, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,SA Pathology, SA Health, Adelaide, SA, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,The Microbiome and Host Health Programme, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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Sluggett JK, Moldovan M, Lang C, Lynn DJ, Papanicolas LE, Crotty M, Whitehead C, Rogers GB, Wesselingh SL, Inacio MC. Contribution of facility level factors to variation in antibiotic use in long-term care facilities: a national cohort study. J Antimicrob Chemother 2021; 76:1339-1348. [PMID: 33580681 DOI: 10.1093/jac/dkab007] [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: 08/26/2020] [Accepted: 12/29/2020] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVES To examine national variation in systemic antibiotic use in long-term care facilities (LTCFs) and identify facility characteristics associated with antibiotic utilization. METHODS This retrospective cohort study included 312 375 residents of 2536 Australian LTCFs between 2011 and 2016. LTCFs were categorized as low, medium or high antibiotic use facilities according to tertiles of DDDs of systemic antibiotics dispensed per 1000 resident-days. Multivariable logistic regression estimated the associations between facility characteristics (ownership, size, location, medication quality indicator performance, prevalence of after-hours medical practitioner services) and antibiotic use (low versus high). RESULTS LTCFs in the lowest and highest antibiotic use categories received a median of 54.3 (IQR 46.5-60.5) and 106.1 (IQR 95.9-122.3) DDDs/1000 resident-days, respectively. Compared with not-for-profit LTCFs in major cities, government-owned non-metropolitan LTCFs were less likely to experience high antibiotic use [adjusted OR (aOR) 0.47, 95% CI 0.24-0.91]. LTCFs with 69-99 residents were less likely to experience high antibiotic use (aOR 0.69, 95% CI 0.49-0.97) than those with 25-47 residents annually. Greater prevalence of medical practitioner services accessed after-hours was associated with high antibiotic use [aOR 1.10 (per 10% increase in after-hours services), 95% CI 1.01-1.21]. South Australian LTCFs (aOR 2.17, 95% CI 1.38-3.39) were more likely, while Queensland (0.43, 95% CI 0.30-0.62) and Western Australian (aOR 0.34, 95% CI 0.21-0.57) LTCFs were less likely to experience high antibiotic use than New South Wales LTCFs. CONCLUSIONS Considerable facility level variation in systemic antibiotic use was observed across Australian LTCFs. Identification of facility characteristics associated with antibiotic use provides a basis for targeted stewardship initiatives.
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Affiliation(s)
- Janet K Sluggett
- University of South Australia, UniSA Allied Health and Human Performance, Adelaide, South Australia, Australia.,Registry of Senior Australians (ROSA), Healthy Ageing Research Consortium, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,Centre for Medicine Use and Safety, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Max Moldovan
- Registry of Senior Australians (ROSA), Healthy Ageing Research Consortium, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Catherine Lang
- Registry of Senior Australians (ROSA), Healthy Ageing Research Consortium, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - David J Lynn
- Precision Medicine Theme, South Australian Medical and Health Research Institute, Adelaide, South Australia, Australia.,College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Lito E Papanicolas
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia.,Department of Infectious Diseases, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Maria Crotty
- Department of Rehabilitation, Aged and Palliative Care, Flinders Medical Centre, Flinders University, Bedford Park, South Australia, Australia
| | - Craig Whitehead
- Department of Rehabilitation, Aged and Palliative Care, Flinders Medical Centre, Flinders University, Bedford Park, South Australia, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia
| | - Steve L Wesselingh
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia
| | - Maria C Inacio
- University of South Australia, UniSA Allied Health and Human Performance, Adelaide, South Australia, Australia.,Registry of Senior Australians (ROSA), Healthy Ageing Research Consortium, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
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Sluggett JK, Moldovan M, Lynn DJ, Papanicolas LE, Crotty M, Whitehead C, Wesselingh SL, Rogers GB, Inacio MC. National Trends in Antibiotic Use in Australian Residential Aged Care Facilities, 2005-2016. Clin Infect Dis 2021; 72:2167-2174. [PMID: 32460321 DOI: 10.1093/cid/ciaa436] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 02/03/2020] [Accepted: 04/14/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Understanding current patterns of antibiotic use in residential aged care facilities (RACFs) is essential to inform stewardship activities, but limited utilization data exist. This study examined changes in prevalence and consumption of antibiotics in Australian RACFs between 2005-2006 and 2015-2016. METHODS This population-based, repeated cross-sectional analysis included all long-term permanent residents of Australian RACFs between July 2005 and June 2016 who were aged ≥ 65 years. The yearly prevalence rate of antibiotic use and number of defined daily doses (DDDs) of systemic antibiotics per 1000 resident-days were determined annually from linked pharmaceutical claims data. Trends were assessed using ordinary least squares regression. RESULTS This study included 502 752 residents from 3218 RACFs, with 424.9 million resident-days analyzed. Antibiotics were dispensed on 5 608 126 occasions during the study period, of which 88% were for oral use. Cefalexin, amoxicillin-clavulanic acid, and trimethoprim were the most commonly dispensed antibiotics. The annual prevalence of antibiotic use increased from 63.8% (95% confidence interval [CI], 63.3%-64.4%) to 70.3% (95% CI, 69.9%-70.7%) between 2005-2006 and 2015-2016 (0.8% average annual increase, P < .001). There was a 39% relative increase in total consumption of systemic antibiotics, with utilization increasing from 67.6 to 93.8 DDDs/1000 resident-days during the study period (average annual increase of 2.8 DDDs/1000 resident-days, P < .001). CONCLUSIONS This nationwide study showed substantial increases in both prevalence of use and total consumption of antibiotics in Australian RACFs between 2005 and 2016. The increasingly widespread use of antibiotics in Australian RACFs is concerning and points to a need for enhanced efforts to optimize antibiotic use in this setting.
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Affiliation(s)
- Janet K Sluggett
- Registry of Senior Australians, Health Ageing Research Consortium, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,Centre for Medicine Use and Safety, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.,University of South Australia, Allied Health and Human Performance, Adelaide, South Australia, Australia
| | - Max Moldovan
- Registry of Senior Australians, Health Ageing Research Consortium, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - David J Lynn
- Precision Medicine Theme, South Australian Medical and Health Research Institute, Adelaide, South Australia, Australia.,College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Lito E Papanicolas
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia.,Department of Infectious Diseases, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Maria Crotty
- Department of Rehabilitation, Aged and Extended Care, Flinders Medical Centre, Flinders University, Bedford Park, South Australia, Australia
| | - Craig Whitehead
- Department of Rehabilitation, Aged and Extended Care, Flinders Medical Centre, Flinders University, Bedford Park, South Australia, Australia
| | - Steve L Wesselingh
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia
| | - Maria C Inacio
- Registry of Senior Australians, Health Ageing Research Consortium, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,University of South Australia, Allied Health and Human Performance, Adelaide, South Australia, Australia
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Papanicolas LE, Sims SK, Taylor SL, Miller SJ, Karapetis CS, Wesselingh SL, Gordon DL, Rogers GB. Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome. BMC Cancer 2021; 21:591. [PMID: 34022842 PMCID: PMC8141218 DOI: 10.1186/s12885-021-08296-4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/05/2021] [Indexed: 01/04/2023] Open
Abstract
Background The gut microbiota influences many aspects of host physiology, including immune regulation, and is predictive of outcomes in cancer patients. However, whether conventional myelosuppressive chemotherapy affects the gut microbiota in humans with non-haematological malignancy, independent of antibiotic exposure, is unknown. Methods Faecal samples from 19 participants with non-haematological malignancy, who were receiving conventional chemotherapy regimens but not antibiotics, were examined prior to chemotherapy, 7–12 days after chemotherapy, and at the end of the first cycle of treatment. Gut microbiota diversity and composition was determined by 16S rRNA gene amplicon sequencing. Results Compared to pre-chemotherapy samples, samples collected 7–12 days following chemotherapy exhibited increased richness (mean 120 observed species ± SD 38 vs 134 ± 40; p = 0.007) and diversity (Shannon diversity: mean 6.4 ± 0.43 vs 6.6 ± 0.41; p = 0.02). Composition was significantly altered, with a significant decrease in the relative abundance of gram-positive bacteria in the phylum Firmicutes (pre-chemotherapy median relative abundance [IQR] 0.78 [0.11] vs 0.75 [0.11]; p = 0.003), and an increase in the relative abundance of gram-negative bacteria (Bacteroidetes: median [IQR] 0.16 [0.13] vs 0.21 [0.13]; p = 0.01 and Proteobacteria: 0.015 [0.018] vs 0.03 [0.03]; p = 0.02). Differences in microbiota characteristics from baseline were no longer significant at the end of the chemotherapy cycle. Conclusions Conventional chemotherapy results in significant changes in gut microbiota characteristics during the period of predicted myelosuppression post-chemotherapy. Further study is indicated to link microbiome changes during chemotherapy to clinical outcomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08296-4.
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Affiliation(s)
- Lito E Papanicolas
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia. .,South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, 5042, Australia.
| | - Sarah K Sims
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Steven L Taylor
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - Sophie J Miller
- South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - Christos S Karapetis
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, South Australia, Australia.,Department of Medical Oncology, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Steve L Wesselingh
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - David L Gordon
- Microbiology and Infectious Diseases, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, 5042, Australia
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11
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Taylor SL, Leong LEX, Sims SK, Keating RL, Papanicolas LE, Richard A, Mobegi FM, Wesselingh S, Burr LD, Rogers GB. The cystic fibrosis gut as a potential source of multidrug resistant pathogens. J Cyst Fibros 2020; 20:413-420. [PMID: 33250435 DOI: 10.1016/j.jcf.2020.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 07/11/2020] [Revised: 11/05/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND The emergence of multidrug resistant (MDR) pathogens represents a profound threat to global health. Individuals with CF have amongst the highest cumulative antibiotic exposure of any patient group, including to critically-important last-line agents. While there is little evidence that antibiotic resistance in airway pathogens results in worse clinical outcomes for CF patients, the potential emergence of MDR pathogens in non-respiratory systems, as a consequence of CF care, represents a potential health threat to the wider population, including family and carers. METHODS Stool from 19 adults with CF and 16 healthy adult controls was subjected to metagenomic sequencing, to assess faecal resistome, and culture-based analysis. Resistant isolates were identified phenotypically, and genetic determinants of resistance characterised by whole genome sequencing. RESULTS CF and control faecal resistomes differed significantly (P = 0.0003). The proportion of reads that mapped to mobile genetic elements was significantly higher in CF (P = 0.014) and the composition was significantly different (P = 0.0001). Notably, CF patients displayed higher carriage of plasmid-mediated aminoglycoside-modifying genes ant(6)-Ib, aac(6')-Ip, and aph(3')-IIIa (P < 0.01). Culture-based analysis supported higher aminoglycoside resistance, with a higher proportion of aminoglycoside-resistant, Gram-negative bacteria (P < 0.0001). Isolated extended spectrum beta lactamase (ESBL)-positive Escherichia coli from CF stool exhibited phenotypic resistance to tobramycin and gentamicin. Genomic analysis showed co-localisation of both aminoglycoside resistance and ESBL genes, consistent with MDR emergence through horizontal gene transfer. CONCLUSIONS The carriage of potentially transmissible resistance within the adult CF gut microbiome is considerably greater than in healthy individuals and could contribute to the emergence and dissemination of MDR pathogens.
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Affiliation(s)
- Steven L Taylor
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.
| | - Lex E X Leong
- Microbiology and Infectious Diseases, SA Pathology, South Australia, Australia
| | - Sarah K Sims
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia
| | - Rebecca L Keating
- Department of Respiratory Medicine, Mater Health Services, South Brisbane, QLD, Australia
| | - Lito E Papanicolas
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia
| | - Alyson Richard
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia
| | - Fredrick M Mobegi
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia
| | - Steve Wesselingh
- Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia
| | - Lucy D Burr
- Department of Respiratory Medicine, Mater Health Services, South Brisbane, QLD, Australia; Mater Research - University of Queensland, Aubigny Place, South Brisbane, QLD, Australia
| | - Geraint B Rogers
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia
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12
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Haifer C, Kelly CR, Paramsothy S, Andresen D, Papanicolas LE, McKew GL, Borody TJ, Kamm M, Costello SP, Andrews JM, Begun J, Chan HT, Connor S, Ghaly S, Johnson PD, Lemberg DA, Paramsothy R, Redmond A, Sheorey H, van der Poorten D, Leong RW. Australian consensus statements for the regulation, production and use of faecal microbiota transplantation in clinical practice. Gut 2020; 69:801-810. [PMID: 32047093 DOI: 10.1136/gutjnl-2019-320260] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/17/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Faecal microbiota transplantation (FMT) has proved to be an extremely effective treatment for recurrent Clostridioides difficile infection, and there is interest in its potential application in other gastrointestinal and systemic diseases. However, the recent death and episode of septicaemia following FMT highlights the need for further appraisal and guidelines on donor evaluation, production standards, treatment facilities and acceptable clinical indications. DESIGN For these consensus statements, a 24-member multidisciplinary working group voted online and then convened in-person, using a modified Delphi approach to formulate and refine a series of recommendations based on best evidence and expert opinion. Invitations to participate were directed to Australian experts, with an international delegate assisting the development. The following issues regarding the use of FMT in clinical practice were addressed: donor selection and screening, clinical indications, requirements of FMT centres and future directions. Evidence was rated using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) system. RESULTS Consensus was reached on 27 statements to provide guidance on best practice in FMT. These include: (1) minimum standards for donor screening with recommended clinical selection criteria, blood and stool testing; (2) accepted routes of administration; (3) clinical indications; (4) minimum standards for FMT production and requirements for treatment facilities acknowledging distinction between single-site centres (eg, hospital-based) and stool banks; and (5) recommendations on future research and product development. CONCLUSIONS These FMT consensus statements provide comprehensive recommendations around the production and use of FMT in clinical practice with relevance to clinicians, researchers and policy makers.
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Affiliation(s)
- Craig Haifer
- The University of Sydney, Sydney, New South Wales, Australia
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Colleen R Kelly
- Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Sudarshan Paramsothy
- The University of Sydney, Sydney, New South Wales, Australia
- Concord Repatriation General Hospital, Sydney, New South Wales, Australia
| | - David Andresen
- The University of Sydney, Sydney, New South Wales, Australia
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Lito E Papanicolas
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Genevieve L McKew
- The University of Sydney, Sydney, New South Wales, Australia
- Concord Repatriation General Hospital, Sydney, New South Wales, Australia
| | - Thomas J Borody
- Centre for Digestive Diseases, Sydney, New South Wales, Australia
| | - Michael Kamm
- St Vincent's Hospital, Melbourne, Victoria, Australia
- The University of Melbourne, Melbourne, Victoria, Australia
| | - Samuel P Costello
- The Queen Elizabeth Hospital, Woodville, South Australia, Australia
- BiomeBank, Adelaide, South Australia, Australia
| | - Jane M Andrews
- Royal Adelaide Hospital, Adelaide, South Australia, Australia
- The University of Adelaide, Adelaide, South Australia, Australia
| | - Jakob Begun
- The University of Queensland, Brisbane, Queensland, Australia
- Mater Hospital Brisbane, Brisbane, Queensland, Australia
| | | | - Susan Connor
- Liverpool Hospital, Sydney, New South Wales, Australia
- University of New South Wales, Sydney, New South Wales, Australia
| | - Simon Ghaly
- St Vincent's Hospital, Sydney, New South Wales, Australia
- University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Dr Johnson
- The University of Melbourne, Melbourne, Victoria, Australia
- Austin Hospital, Melbourne, Victoria, Australia
| | - Daniel A Lemberg
- University of New South Wales, Sydney, New South Wales, Australia
- Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | | | - Andrew Redmond
- The University of Queensland, Brisbane, Queensland, Australia
- Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | | | - David van der Poorten
- The University of Sydney, Sydney, New South Wales, Australia
- Westmead Hospital, Sydney, New South Wales, Australia
| | - Rupert W Leong
- The University of Sydney, Sydney, New South Wales, Australia
- Concord Repatriation General Hospital, Sydney, New South Wales, Australia
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13
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Papanicolas LE, Warner M, Wesselingh SL, Rogers GB. Protect commensal gut bacteria to improve antimicrobial stewardship. Clin Microbiol Infect 2020; 26:814-815. [PMID: 32234452 DOI: 10.1016/j.cmi.2020.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/18/2020] [Accepted: 03/21/2020] [Indexed: 01/12/2023]
Affiliation(s)
- L E Papanicolas
- Microbiome & Host Health Programme, The South Australian Health and Medical Research Institute, Adelaide, SA, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, SA, Australia
| | - M Warner
- Central Adelaide Local Health Network, Adelaide, SA, Australia
| | - S L Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - G B Rogers
- Microbiome & Host Health Programme, The South Australian Health and Medical Research Institute, Adelaide, SA, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, SA, Australia.
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14
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Papanicolas LE, Gordon DL, Wesselingh SL, Rogers GB. Improving Risk-Benefit in Faecal Transplantation through Microbiome Screening. Trends Microbiol 2020; 28:331-339. [PMID: 31952909 DOI: 10.1016/j.tim.2019.12.009] [Citation(s) in RCA: 17] [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: 08/27/2019] [Revised: 11/21/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Faecal microbiota transplantation (FMT) has been shown to be effective in the treatment of a growing number of conditions, and its clinical use continues to rise. However, recent cases of antibiotic-resistant pathogen transmission through FMT, resulting in at least one case of fatal sepsis, highlight the need to reevaluate current donor screening practices. Commensal gut microbes profoundly influence infection risk but are not routinely assessed in donor stool. Extending the assessment of donor material beyond pathogen populations to include the composition and structure of the wider faecal microbiota has the potential to reduce infectious complications in FMT recipients.
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Affiliation(s)
- Lito E Papanicolas
- Microbiome and Host Health Programme, the South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, Flinders University, Adelaide, South Australia, Australia
| | | | - Geraint B Rogers
- Microbiome and Host Health Programme, the South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.
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15
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Douglas CA, Ivey KL, Papanicolas LE, Best KP, Muhlhausler BS, Rogers GB. DNA extraction approaches substantially influence the assessment of the human breast milk microbiome. Sci Rep 2020; 10:123. [PMID: 31924794 PMCID: PMC6954186 DOI: 10.1038/s41598-019-55568-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 08/14/2019] [Accepted: 11/20/2019] [Indexed: 01/21/2023] Open
Abstract
In addition to providing nutritional and bioactive factors necessary for infant development, human breast milk contains bacteria that contribute to the establishment of commensal microbiota in the infant. However, the composition of this bacterial community differs considerably between studies. We hypothesised that bacterial DNA extraction methodology from breast milk samples are a substantial contributor to these inter-study differences. We tested this hypothesis by applying five widely employed methodologies to a mock breast milk sample and four individual human breast milk samples. Significant differences in DNA yield and purity were observed between methods (P < 0.05). Microbiota composition, assessed by 16S rRNA gene amplicon sequencing, also differed significantly with extraction methodology (P < 0.05), including in the contribution of contaminant signal. Concerningly, many of the bacterial taxa identified here as contaminants have been reported as components of the breast milk microbiome in other studies. These findings highlight the importance of using stringent, well-validated, DNA extraction methodologies for analysis of the breast milk microbiome, and exercising caution interpreting microbiota data from low-biomass contexts.
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Affiliation(s)
- Chloe A Douglas
- South Australian Health and Medical Research Institute, Healthy Mothers, Babies and Children Theme, Women's and Children's Hospital, King William Road, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Microbiome & Host Health Programme, Adelaide, South Australia, Australia
- Faculty of Health Science, Discipline of Medicine - Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kerry L Ivey
- South Australian Health and Medical Research Institute, Microbiome & Host Health Programme, Adelaide, South Australia, Australia
- Harvard T.H. Chan School of Public Health, Department of Nutrition, Boston, Massachusetts, USA
| | - Lito E Papanicolas
- South Australian Health and Medical Research Institute, Microbiome & Host Health Programme, Adelaide, South Australia, Australia
| | - Karen P Best
- South Australian Health and Medical Research Institute, Healthy Mothers, Babies and Children Theme, Women's and Children's Hospital, King William Road, Adelaide, South Australia, Australia
| | - Beverly S Muhlhausler
- South Australian Health and Medical Research Institute, Healthy Mothers, Babies and Children Theme, Women's and Children's Hospital, King William Road, Adelaide, South Australia, Australia
- Nutrition & Health Program, Health and Biosecurity, CSIRO, Adelaide, South Australia, Australia
- Department of Food and Wine Science, School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Microbiome & Host Health Programme, Adelaide, South Australia, Australia.
- College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia.
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16
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Papanicolas LE, Wesselingh SL, Rogers GB. Do we really understand how faecal microbiota transplantation works? Authors' reply. EBioMedicine 2019; 42:40. [PMID: 30898649 PMCID: PMC6491388 DOI: 10.1016/j.ebiom.2019.03.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 12/26/2022] Open
Affiliation(s)
- Lito E Papanicolas
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia; Department of Infectious Diseases, Royal Adelaide Hospital, Adelaide, South Australia, Australia.
| | - Steve L Wesselingh
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia.
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Bedford Park, South Australia, Australia.
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17
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Ashokan A, Papanicolas LE, Leong LEX, Theodossi M, Daniel S, Wesselingh SL, Rogers GB, Gordon DL. Case report: Identification of intra-laboratory blood culture contamination with Staphylococcus aureus by whole genome sequencing. Diagn Microbiol Infect Dis 2019; 94:331-333. [PMID: 30885397 DOI: 10.1016/j.diagmicrobio.2019.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/16/2019] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
Staphylococcus aureus in blood cultures is rarely considered a contaminant. We report a case of intra-laboratory contamination between blood culture bottles which was confirmed by whole genome sequencing, highlighting the importance of molecular analysis in the clinical laboratory setting.
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Affiliation(s)
- Anushia Ashokan
- Infection and Immunity Theme, South Australia Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, 5000, Australia; SAHMRI Microbiome Research Laboratory, Flinders University School of Medicine, Bedford Park, South Australia, 5042, Australia; University of Adelaide, Adelaide, South Australia, 5000, Australia.
| | - Lito E Papanicolas
- Infection and Immunity Theme, South Australia Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, 5000, Australia; SAHMRI Microbiome Research Laboratory, Flinders University School of Medicine, Bedford Park, South Australia, 5042, Australia
| | - Lex E X Leong
- Infection and Immunity Theme, South Australia Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, 5000, Australia; SAHMRI Microbiome Research Laboratory, Flinders University School of Medicine, Bedford Park, South Australia, 5042, Australia
| | - Maria Theodossi
- South Australia(SA) Pathology, Flinders Medical Centre, Bedford Park, South Australia, 5042, Australia
| | - Santhosh Daniel
- Department of Microbiology and Infectious Diseases, Flinders Medical Centre, Bedford Park, South Australia, 5042, Australia
| | - Steve L Wesselingh
- Infection and Immunity Theme, South Australia Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, 5000, Australia; SAHMRI Microbiome Research Laboratory, Flinders University School of Medicine, Bedford Park, South Australia, 5042, Australia
| | - Geraint B Rogers
- Infection and Immunity Theme, South Australia Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, 5000, Australia; SAHMRI Microbiome Research Laboratory, Flinders University School of Medicine, Bedford Park, South Australia, 5042, Australia
| | - David L Gordon
- South Australia(SA) Pathology, Flinders Medical Centre, Bedford Park, South Australia, 5042, Australia; Department of Microbiology and Infectious Diseases, Flinders Medical Centre, Bedford Park, South Australia, 5042, Australia
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18
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Papanicolas LE, Wang Y, Choo JM, Gordon DL, Wesselingh SL, Rogers GB. Optimisation of a propidium monoazide based method to determine the viability of microbes in faecal slurries for transplantation. J Microbiol Methods 2018; 156:40-45. [PMID: 30529117 DOI: 10.1016/j.mimet.2018.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 06/04/2018] [Revised: 12/01/2018] [Accepted: 12/03/2018] [Indexed: 02/02/2023]
Abstract
The efficacy of faecal microbiota transplantation (FMT) as a therapeutic intervention may depend on the viability of the microorganisms in faecal slurries (FS) prepared from donor stool. However, determining the viability of these organisms is challenging. Most microorganisms in stool are refractory to culture using standard techniques, and culture-independent PCR-based methods derive signal from both viable and non-viable cells. Propidium monoazide (PMA) treatment has been shown to be effective in preventing PCR amplification of DNA from non-viable bacteria in a range of contexts. However, this methodology can be sensitive to factors such as bacterial load and sample turbidity. We describe the optimisation of a PMA treatment methodology for FS that restricts quantitative PCR-based bacterial enumeration to viable cells. When applied to concentrated FS (10-25% stool content), PMA treatment at 100 μM concentration was ineffective in preventing DNA amplification from heat-killed cells. Efficacy was not significantly improved by doubling the PMA concentration. However, PMA treatment efficacy was improved markedly following 10-fold sample dilution, and was found to be optimal at 100-fold dilution. Substantial reductions in viable bacterial load could be observed following both freeze-thaw and heat-treatment of FS. This method successfully prevented DNA amplification of heat-killed Pseudomonas and Staphylococcus spiked into stool and could reliably determine the proportion of live bacteria and viable E. coli counts present in fresh and heat-treated stool. With appropriate sample dilution, PMA treatment excluded >97% of non-viable cells from amplification in all assays, without significantly affecting the amplification of DNA from viable cells. This method can be applied to optimise sample processing of FMT donor material, and to characterise bacterial viability within faecal samples more widely.
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Affiliation(s)
- Lito E Papanicolas
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.
| | - Yanan Wang
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Jocelyn M Choo
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, Flinders University, Adelaide, South Australia, Australia
| | - Steve L Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
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19
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Papanicolas LE, Gordon DL, Wesselingh SL, Rogers GB. Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? Trends Microbiol 2017; 26:393-400. [PMID: 29146383 DOI: 10.1016/j.tim.2017.10.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 07/18/2017] [Revised: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 01/04/2023]
Abstract
The global spread of antibiotic-resistant pathogens threatens to increase the mortality of cancer patients significantly. We propose that chemotherapy contributes to the emergence of antibiotic-resistant bacteria within the gut and, in combination with antibiotics, drives pathogen overgrowth and translocation into the bloodstream. In our model, these processes are mediated by the effects of chemotherapy on bacterial mutagenesis and horizontal gene transfer, the disruption of commensal gut microbiology, and alterations to host physiology. Clinically, this model manifests as a cycle of recurrent sepsis, with each episode involving ever more resistant organisms and requiring increasingly broad-spectrum antimicrobial therapy. Therapies that restore the gut microbiota following chemotherapy or antibiotics could provide a means to break this cycle of infection and treatment failure.
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Affiliation(s)
- Lito E Papanicolas
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, Flinders University, Adelaide, South Australia, Australia
| | - Steve L Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.
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Papanicolas LE, Nelson R, Warner MS. Influence of antimicrobial susceptibility reporting on junior doctors' decision to prescribe antimicrobials inappropriately. J Antimicrob Chemother 2017; 72:1202-1205. [PMID: 27999044 DOI: 10.1093/jac/dkw525] [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: 05/30/2016] [Accepted: 11/07/2016] [Indexed: 11/14/2022] Open
Abstract
Objectives Inappropriate antimicrobial use drives antimicrobial resistance and is a global public health problem. This study examined whether withholding antimicrobial susceptibilities in combination with interpretive comments on microbiological reports influenced the decision to inappropriately prescribe antibiotics in a controlled survey. Methods Seventy junior doctors attending educational sessions were given one of two surveys describing four clinical case vignettes (scenarios) in which antimicrobial treatment was not indicated. They were asked to select their preferred treatment from multiple choices. In the scenarios labelled 'A', the laboratory report did not report antibiotic susceptibilities, but included comments from the microbiologist. In the scenarios labelled 'B', the laboratory report included full organism identification and susceptibility results without additional comments. Results For scenarios 1, 2 and 3 there was a significantly higher probability ( P < 0.01) that the doctor selected an answer involving antibiotic treatment if he/she received the 'B' version of the scenario where reports included antimicrobial susceptibilities, but no interpretive comments. This was significant in both interns and more senior doctors. In scenario 4, of which there were two versions, there was no difference seen in the answers between the groups given scenario A or B. Conclusions The results of this survey suggest that withholding antimicrobial susceptibility results in combination with interpretive comments on microbiology reports significantly influences the decision of junior doctors to prescribe antibiotics in low-acuity outpatient setting scenarios (represented in scenarios 1-3), but not in inpatient scenarios (represented in scenario 4).
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Affiliation(s)
- Lito E Papanicolas
- Department of Infectious Diseases, The Queen Elizabeth Hospital, Level 2C, 28 Woodville Road, Woodville, South Australia 5011, Australia
| | - Renjy Nelson
- Department of Infectious Diseases, The Queen Elizabeth Hospital, Level 2C, 28 Woodville Road, Woodville, South Australia 5011, Australia
| | - Morgyn S Warner
- Department of Infectious Diseases, The Queen Elizabeth Hospital, Level 2C, 28 Woodville Road, Woodville, South Australia 5011, Australia.,Microbiology and Infectious Diseases Directorate, SA Pathology, Frome Road, Adelaide, South Australia 5000, Australia.,School of Medicine, University of Adelaide, 30 Frome Road, Adelaide, South Australia 5000, Australia
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Papanicolas LE, Bell JM, Weldhagen GF, Bastian I. Ceftriaxone treatment failure in cephalosporin-susceptible Escherichia coli bacteraemia. Int J Antimicrob Agents 2013; 41:298-9. [PMID: 23312600 DOI: 10.1016/j.ijantimicag.2012.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 11/13/2012] [Indexed: 11/16/2022]
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Papanicolas LE, Holds JM, Bak N. Meningitis and pneumonitis caused by pet rodents. Med J Aust 2012. [DOI: 10.5694/j.1326-5377.2012.tb04211.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Papanicolas LE, Holds JM, Bak N. Lessons from practice ‐ Meningitis and pneumonitis caused by pet rodents. Med J Aust 2012; 196:202-3. [DOI: 10.5694/mja11.10841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 11/02/2011] [Indexed: 11/17/2022]
Affiliation(s)
| | | | - Narin Bak
- Royal Adelaide Hospital, Adelaide, SA
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Towle CA, Wright M, Hecht AC, Kuong SJ, Papanicolas LE, Totkovic R, Mankin HJ, Treadwell BV. A matrix metalloproteinase proenzyme activator produced by articular cartilage. Biochem Biophys Res Commun 1998; 247:324-31. [PMID: 9642125 DOI: 10.1006/bbrc.1998.8781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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: 11/22/2022]
Abstract
Matrix metalloproteinases (MMPs) are involved in connective tissue turnover under physiological and pathological conditions. MMP activity is regulated by the requirement for zymogen activation. This report describes a proMMP-3 activator produced by articular cartilage. The activator initiates a step-wise processing of proMMP-3 to generate an array of active species. Sequencing of activation intermediates demonstrated cleavage on the NH2-terminal side of certain basic residues in the MMP-3 propeptide. Metal ion chelators inhibited activator-dependent proteolysis, and activity was restored by low levels of ZnCl2. These catalytic properties suggest similarity to members of the insulinase superfamily of metalloendopeptidases with in vitro specificity for single arginine or paired basic processing sites in a variety of prohormones. Dibasic sites also exist in the propeptides of several MMPs including proMMP-3. This is the first report that cartilage produces a potent MMP proenzyme activator, opening the possibility of a novel intrinsic activation pathway for catabolic processes in this avascular tissue.
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Affiliation(s)
- C A Towle
- Orthopaedic Research Laboratories, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
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