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Elsheikh R, Makram AM. Multidrug-Resistant Organisms: The Silent Plight of Burn Patients. J Burn Care Res 2024; 45:877-886. [PMID: 38695094 PMCID: PMC11303128 DOI: 10.1093/jbcr/irae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Indexed: 07/20/2024]
Abstract
The global increasing spread of multidrug-resistant organisms (MDROs) is threatening the control of various infections in vulnerable populations and patient groups. One of the most affected groups is patients with burns, who are prone to hyperinfection as they suffer from a hypermetabolic state and weaken immune barriers. Those patients also share the infection risk of patients hospitalized for a long time, including ventilator-associated pneumonia and urinary tract infections. While some preventative and therapeutic management styles are still controversial, we discuss consensuses here. In this review, we aim to present the current knowledge on multidrug resistance with a special focus on patients with burns, discuss various causative organisms and their treatment options, and highlight the importance of antibiotic stewardship and teamwork in responding to an outbreak of MDROs.
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Affiliation(s)
- Randa Elsheikh
- Deanery of Biomedical Sciences at Edinburgh Medical School, University of Edinburgh, Edinburgh EH8 9YL, UK
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2
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Kunishima H, Ichiki K, Ohge H, Sakamoto F, Sato Y, Suzuki H, Nakamura A, Fujimura S, Matsumoto K, Mikamo H, Mizutani T, Morinaga Y, Mori M, Yamagishi Y, Yoshizawa S. Japanese Society for infection prevention and control guide to Clostridioides difficile infection prevention and control. J Infect Chemother 2024; 30:673-715. [PMID: 38714273 DOI: 10.1016/j.jiac.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 05/09/2024]
Affiliation(s)
- Hiroyuki Kunishima
- Department of Infectious Diseases. St. Marianna University School of Medicine, Japan.
| | - Kaoru Ichiki
- Department of Infection Control and Prevention, Hyogo Medical University Hospital, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
| | - Fumie Sakamoto
- Quality Improvement and Safety Center, Itabashi Chuo Medical Center, Japan
| | - Yuka Sato
- Department of Infection Control and Nursing, Graduate School of Nursing, Aichi Medical University, Japan
| | - Hiromichi Suzuki
- Department of Infectious Diseases, University of Tsukuba School of Medicine and Health Sciences, Japan
| | - Atsushi Nakamura
- Department of Infection Prevention and Control, Graduate School of Medical Sciences, Nagoya City University, Japan
| | - Shigeru Fujimura
- Division of Clinical Infectious Diseases and Chemotherapy, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Japan
| | - Kazuaki Matsumoto
- Division of Pharmacodynamics, Faculty of Pharmacy, Keio University, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, Japan
| | | | - Yoshitomo Morinaga
- Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
| | - Minako Mori
- Department of Infection Control, Hiroshima University Hospital, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Kochi Medical School, Kochi University, Japan
| | - Sadako Yoshizawa
- Department of Laboratory Medicine/Department of Microbiology and Infectious Diseases, Faculty of Medicine, Toho University, Japan
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3
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Acosta N, Bautista MA, Waddell BJ, Du K, McCalder J, Pradhan P, Sedaghat N, Papparis C, Beaudet AB, Chen J, Van Doorn J, Xiang K, Chan L, Vivas L, Low K, Lu X, Lee J, Westlund P, Chekouo T, Dai X, Cabaj J, Bhatnagar S, Ruecker N, Achari G, Clark RG, Pearce C, Harrison JJ, Meddings J, Leal J, Ellison J, Missaghi B, Kanji JN, Larios O, Rennert‐May E, Kim J, Hrudey SE, Lee BE, Pang X, Frankowski K, Conly J, Hubert CRJ, Parkins MD. Surveillance for SARS-CoV-2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks. J Med Virol 2023; 95:e28442. [PMID: 36579780 PMCID: PMC9880705 DOI: 10.1002/jmv.28442] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022]
Abstract
Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR. Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Barbara J. Waddell
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Kristine Du
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Navid Sedaghat
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Jianwei Chen
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Kevin Xiang
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Leslie Chan
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Laura Vivas
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Kashtin Low
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Xuewen Lu
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jangwoo Lee
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Thierry Chekouo
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
- Division of Biostatistics, School of Public HealthUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Xiaotian Dai
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jason Cabaj
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Provincial Population & Public HealthAlberta Health ServicesCalgaryCanada
- O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
| | - Srijak Bhatnagar
- Faculty of Science and TechnologyAthabasca UniversityAthabascaAlbertaCanada
| | | | - Gopal Achari
- Department of Civil EngineeringUniversity of CalgaryCalgaryCanada
| | - Rhonda G. Clark
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Craig Pearce
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Joe J. Harrison
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jon Meddings
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jenine Leal
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada
- O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jennifer Ellison
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Bayan Missaghi
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jamil N. Kanji
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada
- Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
- Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Oscar Larios
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
- Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
| | - Elissa Rennert‐May
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Joseph Kim
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada
- Department of Analytical and Environmental ToxicologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Bonita E. Lee
- Department of PediatricsUniversity of AlbertaEdmontonAlbertaCanada
- Women & Children's Health Research InstituteEdmontonAlbertaCanada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Xiaoli Pang
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada
- Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin Frankowski
- Advancing Canadian Water AssetsUniversity of CalgaryCalgaryCanada
| | - John Conly
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | | | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
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Adams C, Peterson SR, Hall AJ, Parashar U, Lopman BA. Associations of infection control measures and norovirus outbreak outcomes in healthcare settings: a systematic review and meta-analysis. Expert Rev Anti Infect Ther 2022; 20:279-290. [PMID: 34225537 PMCID: PMC8810727 DOI: 10.1080/14787210.2021.1949985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Although most norovirus outbreaks in high-income countries occur in healthcare facilities, information on associations between control measures and outbreak outcomes in these settings is lacking. METHODS We conducted a systematic review/meta-analysis to assess associations between norovirus outbreak control measures and outcomes in hospitals and long-term care facilities (LTCFs), globally. Using regression analyses stratified by setting (hospital/LTCF), we compared durations, attack rates, and case counts for outbreaks in which control measures were reportedly implemented to those in which they were not. RESULTS We identified 102 papers describing 162 norovirus outbreaks. Control measures were reportedly implemented in 118 (73%) outbreaks and were associated with 0.6 (95% CI: 0.3-1.1) times smaller patient case counts and 0.7 (95% CI: 0.4, 1.0) times shorter durations in hospitals but 1.5 (95% CI: 1.1-2.2), 1.5 (95% CI: 1.0-2.1) and 1.6 (95% CI: 1.0-2.6) times larger overall, resident and staff case counts, respectively, and 1.4 (95% CI: 1.0-2.0) times longer durations in LTCFs. CONCLUSIONS Reported implementation of control measures was associated with smaller/shorter outbreaks in hospitals but larger/longer outbreaks in LTCFs. Control measures were likely implemented in response to larger/longer outbreaks in LTCFs, rather than causing them. Prospective observational or intervention studies are needed to determine effectiveness.
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Affiliation(s)
- Carly Adams
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Rd, Atlanta, GA 30322, USA,Corresponding author
| | - Shenita R Peterson
- Woodruff Health Science Center Library, Emory University, 1462 Clifton Rd, Atlanta, GA 30322, USA
| | - Aron J Hall
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA
| | - Umesh Parashar
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA
| | - Benjamin A Lopman
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Rd, Atlanta, GA 30322, USA
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5
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Ndagi U, Falaki AA, Abdullahi M, Lawal MM, Soliman ME. Antibiotic resistance: bioinformatics-based understanding as a functional strategy for drug design. RSC Adv 2020; 10:18451-18468. [PMID: 35685616 PMCID: PMC9122625 DOI: 10.1039/d0ra01484b] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022] Open
Abstract
The use of antibiotics to manage infectious diseases dates back to ancient civilization, but the lack of a clear distinction between the therapeutic and toxic dose has been a major challenge. This precipitates the notion that antibiotic resistance was from time immemorial, principally because of a lack of adequate knowledge of therapeutic doses and continuous exposure of these bacteria to suboptimal plasma concentration of antibiotics. With the discovery of penicillin by Alexander Fleming in 1924, a milestone in bacterial infections' treatment was achieved. This forms the foundation for the modern era of antibiotic drugs. Antibiotics such as penicillins, cephalosporins, quinolones, tetracycline, macrolides, sulphonamides, aminoglycosides and glycopeptides are the mainstay in managing severe bacterial infections, but resistant strains of bacteria have emerged and hampered the progress of research in this field. Recently, new approaches to research involving bacteria resistance to antibiotics have appeared; these involve combining the molecular understanding of bacteria systems with the knowledge of bioinformatics. Consequently, many molecules have been developed to curb resistance associated with different bacterial infections. However, because of increased emphasis on the clinical relevance of antibiotics, the synergy between in silico study and in vivo study is well cemented and this facilitates the discovery of potent antibiotics. In this review, we seek to give an overview of earlier reviews and molecular and structural understanding of bacteria resistance to antibiotics, while focusing on the recent bioinformatics approach to antibacterial drug discovery. Understanding the evolution of antibiotic resistance at the molecular level as a functional tool for bioinformatic-based drug design.![]()
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Affiliation(s)
- Umar Ndagi
- Centre for Trans-Sahara Disease, Vaccine and Drug Research
- Ibrahim Badamasi Babangida University
- Lapai
- Nigeria
| | - Abubakar A. Falaki
- Department of Microbiology
- School of Agriculture and Applied Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Maryam Abdullahi
- Faculty of Pharmaceutical Sciences
- Ahmadu Bello University Zaria
- Nigeria
| | - Monsurat M. Lawal
- School of Laboratory Medicine and Medical Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahmoud E. Soliman
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu Natal
- Durban 4001
- South Africa
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6
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Lachiewicz AM, Hauck CG, Weber DJ, Cairns BA, van Duin D. Bacterial Infections After Burn Injuries: Impact of Multidrug Resistance. Clin Infect Dis 2018; 65:2130-2136. [PMID: 29194526 DOI: 10.1093/cid/cix682] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/11/2017] [Indexed: 12/14/2022] Open
Abstract
Patients who are admitted to the hospital after sustaining a large burn injury are at high risk for developing hospital-associated infections. If patients survive the initial 72 hours after a burn injury, infections are the most common cause of death. Ventilator-associated pneumonia is the most important infection in this patient population. The risk of infections caused by multidrug-resistant bacterial pathogens increases with hospital length of stay in burn patients. In the first days of the postburn hospitalization, more susceptible, Gram-positive organisms predominate, whereas later more resistant Gram-negative organisms are found. These findings impact the choice of empiric antibiotics in critically ill burn patients. A proactive infection control approach is essential in burn units. Furthermore, a multidisciplinary approach to burn patients with a team that includes an infectious disease specialist and a pharmacist in addition to the burn surgeon is highly recommended.
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Affiliation(s)
- Anne M Lachiewicz
- Division of Infectious Diseases, University of North Carolina at Chapel Hill
| | - Christopher G Hauck
- Division of Infectious Diseases, University of North Carolina at Chapel Hill
| | - David J Weber
- Division of Infectious Diseases, University of North Carolina at Chapel Hill
| | - Bruce A Cairns
- Department of Surgery, University of North Carolina at Chapel Hill.,North Carolina Jaycee Burn Center, Chapel Hill
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina at Chapel Hill
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7
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Caeiro JP, Garzón MI. Controlling infectious disease outbreaks in low-income and middle-income countries. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2018; 10:55-64. [PMID: 32226321 PMCID: PMC7100832 DOI: 10.1007/s40506-018-0154-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
When an infectious disease outbreak is detected or suspected, a healthcare facility's infection control personnel should be notified and an outbreak control team formed that is pertinent to the size and severity of the outbreak and healthcare facility. Management of an infectious disease outbreak in a middle- or low-income country is challenging. Cost-effective recommendations that are easy to carry out and that have been stratified according to the type of infection and prevention and control intervention used are provided in this paper and constitute basic practices.
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Affiliation(s)
- Juan Pablo Caeiro
- Hospital Privado Universitario, Naciones Unidades 346, Córdoba, Argentina
| | - María I. Garzón
- Hospital Privado Universitario, Naciones Unidades 346, Córdoba, Argentina
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8
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Environmental scan of infection prevention and control practices for containment of hospital-acquired infectious disease outbreaks in acute care hospital settings across Canada. Am J Infect Control 2017; 45:1116-1126. [PMID: 28732739 DOI: 10.1016/j.ajic.2017.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 11/23/2022]
Abstract
BACKGROUND Ward closure is a method of controlling hospital-acquired infectious diseases outbreaks and is often coupled with other practices. However, the value and efficacy of ward closures remains uncertain. PURPOSE To understand the current practices and perceptions with respect to ward closure for hospital-acquired infectious disease outbreaks in acute care hospital settings across Canada. METHODS A Web-based environmental scan survey was developed by a team of infection prevention and control (IPC) experts and distributed to 235 IPC professionals at acute care sites across Canada. Data were analyzed using a mixed-methods approach of descriptive statistics and thematic analysis. RESULTS A total of 110 completed responses showed that 70% of sites reported at least 1 outbreak during 2013, 44% of these sites reported the use of ward closure. Ward closure was considered an "appropriate," "sometimes appropriate," or "not appropriate" strategy to control outbreaks by 50%, 45%, and 5% of participants, respectively. System capacity issues and overall risk assessment were main factors influencing the decision to close hospital wards following an outbreak. DISCUSSION Results suggest the use of ward closure for containment of hospital-acquired infectious disease outbreaks in Canadian acute care health settings is mixed, with outbreak control methods varying. The successful implementation of ward closure was dependent on overall support for the IPC team within hospital administration.
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9
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Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev 2017; 30:1015-1063. [PMID: 28855266 PMCID: PMC5608882 DOI: 10.1128/cmr.00016-17] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.
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Affiliation(s)
- Scott Quainoo
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Jordy P M Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sacha A F T van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Heiman F L Wertheim
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
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