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Olesk J, Donahue D, Ross J, Sheehan C, Bennett Z, Armknecht K, Kudary C, Hopf J, Ploplis VA, Castellino FJ, Lee SW, Nallathamby PD. Antimicrobial peptide-conjugated phage-mimicking nanoparticles exhibit potent bactericidal action against Streptococcus pyogenes in murine wound infection models. NANOSCALE ADVANCES 2024; 6:1145-1162. [PMID: 38356633 PMCID: PMC10863710 DOI: 10.1039/d3na00620d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
Streptococcus pyogenes is a causative agent for strep throat, impetigo, and more invasive diseases. The main reason for the treatment failure of streptococcal infections is increased antibiotic resistance. In recent years, infectious diseases caused by pyogenic streptococci resistant to multiple antibiotics have been rising with a significant impact on public health and the veterinary industry. The development of antibiotic resistance and the resulting emergence of multidrug-resistant bacteria have become primary threats to the public health system, commonly leading to nosocomial infections. Many researchers have turned their focus to developing alternative classes of antibacterial agent based on various nanomaterials. We have developed an antibiotic-free nanoparticle system inspired by naturally occurring bacteriophages to fight antibiotic-resistant bacteria. Our phage-mimicking nanoparticles (PhaNPs) display structural mimicry of protein-turret distribution on the head structure of bacteriophages. By mimicking phages, we can take advantage of their evolutionary constant shape and high antibacterial activity while avoiding the immune reactions of the human body experienced by biologically derived phages. We describe the synthesis of hierarchically arranged core-shell nanoparticles, with a silica core conjugated with silver-coated gold nanospheres to which we have chemisorbed the synthetic antimicrobial peptide Syn-71 on the PhaNPs surface, and increased the rapidity of the antibacterial activity of the nanoparticles (PhaNP@Syn71). The antibacterial effect of the PhaNP@Syn71 was tested in vitro and in vivo in mouse wound infection models. In vitro, results showed a dose-dependent complete inhibition of bacterial growth (>99.99%). Cytocompatibility testing on HaCaT human skin keratinocytes showed minimal cytotoxicity of PhaNP@Syn71, being comparable to the vehicle cytotoxicity levels even at higher concentrations, thus proving that our design is biocompatible with human cells. There was a minimum cutoff dosage above which there was no evolution of resistance after prolonged exposure to sub-MIC dosages of PhaNP@Syn71. Application of PhaNP@Syn71 to a mouse wound infection model exhibited high biocompatibility in vivo while showing immediate stabilization of the wound size, and infection free wound healing. Our results suggest the robust utility of antimicrobial peptide-conjugated phage-mimicking nanoparticles as a highly effective antibacterial system that can combat bacterial infections consistently while avoiding the emergence of resistant bacterial strains.
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Affiliation(s)
- Johanna Olesk
- Department of Aerospace and Mechanical Engineering, University of Notre Dame Notre Dame Indiana USA +1 574 631 7868
| | - Deborah Donahue
- W. M. Keck Center for Transgene Research, University of Notre Dame Notre Dame Indiana USA
| | - Jessica Ross
- Department of Biological Sciences, University of Notre Dame Notre Dame Indiana USA
| | - Conor Sheehan
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame Indiana USA
| | - Zach Bennett
- Department of Aerospace and Mechanical Engineering, University of Notre Dame Notre Dame Indiana USA +1 574 631 7868
| | - Kevin Armknecht
- Department of Pre-Professional Studies, University of Notre Dame Notre Dame Indiana USA
| | - Carlie Kudary
- Berthiaume Institute for Precision Health, University of Notre Dame Notre Dame Indiana USA
| | - Juliane Hopf
- Berthiaume Institute for Precision Health, University of Notre Dame Notre Dame Indiana USA
| | - Victoria A Ploplis
- W. M. Keck Center for Transgene Research, University of Notre Dame Notre Dame Indiana USA
| | - Francis J Castellino
- W. M. Keck Center for Transgene Research, University of Notre Dame Notre Dame Indiana USA
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame Notre Dame Indiana USA
| | - Prakash D Nallathamby
- Department of Aerospace and Mechanical Engineering, University of Notre Dame Notre Dame Indiana USA +1 574 631 7868
- Berthiaume Institute for Precision Health, University of Notre Dame Notre Dame Indiana USA
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Toorop MMA, Kraakman MEM, Hoogendijk IV, van Prehn J, Claas ECJ, Wessels E, Boers SA. A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters. J Clin Microbiol 2023; 61:e0055823. [PMID: 37815371 PMCID: PMC10662357 DOI: 10.1128/jcm.00558-23] [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: 05/04/2023] [Accepted: 08/07/2023] [Indexed: 10/11/2023] Open
Abstract
The recently observed increase in invasive Streptococcus pyogenes infections causes concern in Europe. However, conventional molecular typing methods lack discriminatory power to aid investigations of outbreaks caused by S. pyogenes. Therefore, there is an urgent need for high-resolution molecular typing methods to assess genetic relatedness between S. pyogenes isolates. In the current study, we aimed to develop a novel high-resolution core-genome multilocus sequence typing (cgMLST) scheme for S. pyogenes and compared its discriminatory power to conventional molecular typing methods. The cgMLST scheme was designed with the commercial Ridom SeqSphere+ software package. To define a cluster threshold, the scheme was evaluated using publicly available data from nine defined S. pyogenes outbreaks in the United Kingdom. The cgMLST scheme was then applied to 23 isolates from a suspected S. pyogenes outbreak and 117 S. pyogenes surveillance isolates both from the Netherlands. MLST and emm-typing results were used for comparison to cgMLST results. The allelic differences between isolates from defined outbreaks ranged between 6 and 31 for isolates with the same emm-type, resulting in a proposed cluster threshold of <5 allelic differences out of 1,095 target loci. Seven out of twenty-three (30%) isolates from the suspected outbreak had an allelic difference of <2, thereby identifying a potential cluster that could not be linked to other isolates. The proposed cgMLST scheme shows a higher discriminatory ability when compared to conventional typing methods. The rapid and simple analysis workflow allows for extended detection of clusters of potential outbreak isolates and surveillance and may facilitate the sharing of sequencing results between (inter)national laboratories.
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Affiliation(s)
- Myrthe M. A. Toorop
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Margriet E. M. Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Irene V. Hoogendijk
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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Brouwer S, Rivera-Hernandez T, Curren BF, Harbison-Price N, De Oliveira DMP, Jespersen MG, Davies MR, Walker MJ. Pathogenesis, epidemiology and control of Group A Streptococcus infection. Nat Rev Microbiol 2023; 21:431-447. [PMID: 36894668 PMCID: PMC9998027 DOI: 10.1038/s41579-023-00865-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2023] [Indexed: 03/11/2023]
Abstract
Streptococcus pyogenes (Group A Streptococcus; GAS) is exquisitely adapted to the human host, resulting in asymptomatic infection, pharyngitis, pyoderma, scarlet fever or invasive diseases, with potential for triggering post-infection immune sequelae. GAS deploys a range of virulence determinants to allow colonization, dissemination within the host and transmission, disrupting both innate and adaptive immune responses to infection. Fluctuating global GAS epidemiology is characterized by the emergence of new GAS clones, often associated with the acquisition of new virulence or antimicrobial determinants that are better adapted to the infection niche or averting host immunity. The recent identification of clinical GAS isolates with reduced penicillin sensitivity and increasing macrolide resistance threatens both frontline and penicillin-adjunctive antibiotic treatment. The World Health Organization (WHO) has developed a GAS research and technology road map and has outlined preferred vaccine characteristics, stimulating renewed interest in the development of safe and effective GAS vaccines.
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Affiliation(s)
- Stephan Brouwer
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Bodie F Curren
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nichaela Harbison-Price
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - David M P De Oliveira
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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Khan F, Bai Z, Kelly S, Skidmore B, Dickson C, Nunn A, Rutledge-Taylor K, Wells G. Effectiveness and Safety of Antibiotic Prophylaxis for Persons Exposed to Cases of Invasive Group A Streptococcal Disease: A Systematic Review. Open Forum Infect Dis 2022; 9:ofac244. [PMID: 36046698 PMCID: PMC9424867 DOI: 10.1093/ofid/ofac244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
Among close contacts of patients with invasive group A streptococcal (iGAS) infection, the benefits and harms of chemoprophylaxis are uncertain. We conducted a systematic review of studies that reported on persons who, after being exposed to a case of laboratory-confirmed or probable iGAS, received any antibiotic prophylaxis for the prevention of GAS infection or carriage. Thirty-seven studies including 26 outbreak investigations and 11 case series or reports were included with predominantly descriptive information that suggested that antibiotic prophylaxis may be effective in preventing GAS infection or GAS carriage, with very few serious adverse events. However, current available evidence is scant (with limited information on contacts of iGAS cases) and largely based on studies with weak design and small sample size. Therefore, definitive conclusions on effectiveness of antibiotic prophylaxis cannot be drawn. Well designed prospective studies are required to establish the benefit-harm profile of antibiotic prophylaxis for secondary prevention of GAS disease among close contacts of iGAS cases.
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Affiliation(s)
- Faizan Khan
- Cardiovascular Research Methods Centre, University of Ottawa Heart Institute, Ottawa, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Zemin Bai
- Cardiovascular Research Methods Centre, University of Ottawa Heart Institute, Ottawa, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Shannon Kelly
- Cardiovascular Research Methods Centre, University of Ottawa Heart Institute, Ottawa, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Becky Skidmore
- Ottawa Hospital Research Institute, Ottawa, Canada; Ottawa, Ontario, Canada
| | - Catherine Dickson
- Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, Canada
| | - Alexandra Nunn
- Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, Canada
| | - Katie Rutledge-Taylor
- Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, Canada
| | - George Wells
- Cardiovascular Research Methods Centre, University of Ottawa Heart Institute, Ottawa, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
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Späth GF, Bussotti G. GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells. Nucleic Acids Res 2022; 50:e36. [PMID: 34928370 PMCID: PMC8989552 DOI: 10.1093/nar/gkab1237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/01/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022] Open
Abstract
Genome instability has been recognized as a key driver for microbial and cancer adaptation and thus plays a central role in many diseases. Genome instability encompasses different types of genomic alterations, yet most available genome analysis software are limited to just one type of mutation. To overcome this limitation and better understand the role of genetic changes in enhancing pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis. Here, we show its application to whole genome sequencing datasets of Leishmania, Plasmodium, Candida and cancer. Applying GIP on available data sets validated our pipeline and demonstrated the power of our tool to drive biological discovery. Applied to Plasmodium vivax genomes, our pipeline uncovered the convergent amplification of erythrocyte binding proteins and identified a nullisomic strain. Re-analyzing genomes of drug adapted Candida albicans strains revealed correlated copy number variations of functionally related genes, strongly supporting a mechanism of epistatic adaptation through interacting gene-dosage changes. Our results illustrate how GIP can be used for the identification of aneuploidy, gene copy number variations, changes in nucleic acid sequences, and chromosomal rearrangements. Altogether, GIP can shed light on the genetic bases of cell adaptation and drive disease biomarker discovery.
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Affiliation(s)
- Gerald F Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
| | - Giovanni Bussotti
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
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Franklin SM, Crist MB, Perkins KM, Perz JF. Outbreak Response Capacity Assessments and Improvements Among Public Health Department Health Care-Associated Infection Programs-United States, 2015-2017. JOURNAL OF PUBLIC HEALTH MANAGEMENT AND PRACTICE 2022; 28:116-125. [PMID: 32332484 PMCID: PMC10887420 DOI: 10.1097/phh.0000000000001148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
CONTEXT The Centers for Disease Control and Prevention awarded $85 million to health care-associated infection and antibiotic resistance (HAI/AR) programs in March 2015 as part of Infection Control Assessment and Response (ICAR) activities in the Epidemiology and Laboratory Capacity cooperative agreement Domestic Ebola Supplement. PROGRAM One goal of this funding was to assess and improve program capacity to respond to potential health care outbreaks (eg, HAI clusters). All 55 funded programs (in 49 state and 6 local health departments) participated. IMPLEMENTATION The Centers for Disease Control and Prevention developed guidance and tools for HAI/AR programs to document relevant response capacities, assess policies, and measure progress. HAI/AR programs completed an interim assessment in 2016 and a final progress report in 2017. EVALUATION During the project period, 78% (n = 43) of the programs developed new investigation tools, 85% (n = 47) trained staff on outbreak response, and 96% (n = 53) of the programs reported hiring staff to assist with outbreak response activities. Staffing and expertise to support HAI outbreak response increased substantially among awardees reporting staffing limitations on the interim assessment, including in domains such as on-site infection control assessment (n = 20; 83%), laboratory capacity (n = 20; 91%), and data management/analytics (n = 14; 67%). By 2017, reporting requirements in 100% of the programs addressed possible HAI/AR outbreaks; 93% (n = 51) also addressed sentinel events such as identification of novel AR threats. More than 90% (n = 50) of programs enhanced capacities for tracking response activities; in 2016, these systems captured 6665 events (range, 3-1379; median = 46). Health departments also reported wide-ranging efforts to engage regulatory, public health, and health care partners to improve HAI/AR outbreak reporting and investigation. DISCUSSION Broad capacity for responding to HAI/AR outbreaks was enhanced using Ebola ICAR supplemental funding. As response activities expand, health department programs will be challenged to continue building expertise, reporting infrastructure, investigation resources, and effective relations with health care partners.
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Affiliation(s)
- Steven M Franklin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia (Mr Franklin and Drs Crist, Perkins, and Perz); and Northrop Grumman, Atlanta, Georgia (Mr Franklin)
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Li Y, Dominguez S, Nanduri SA, Rivers J, Mathis S, Li Z, McGee L, Chochua S, Metcalf BJ, Van Beneden CA, Beall B, Miller L. Genomic Characterization of Group A Streptococci Causing Pharyngitis and Invasive Disease in Colorado, USA, June 2016 - April 2017. J Infect Dis 2021; 225:1841-1851. [PMID: 34788828 PMCID: PMC9125432 DOI: 10.1093/infdis/jiab565] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/08/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The genomic features and transmission link of circulating Group A streptococcus (GAS) strains causing different disease types, such as pharyngitis and invasive disease, are not well understood. METHODS We used whole-genome sequencing (WGS) to characterize GAS isolates recovered from persons with pharyngitis and invasive disease in the Denver metropolitan area from June 2016 to April 2017. RESULTS GAS isolates were cultured from 236 invasive and 417 pharyngitis infections. WGS identified 34 emm types. Compared to pharyngitis isolates, invasive isolates were more likely to carry the erm family genes (23% vs. 7.4%, p<0.001), which confer resistance to erythromycin and clindamycin (including inducible resistance), and covS gene inactivation (7% vs. 0.5%, p<0.001). WGS identified 97 genomic clusters (433 isolates; 2-65 isolates per cluster) that consisted of genomically closely related isolates (median SNP (IQR) = 3 (1-4) within cluster). Thirty genomic clusters (200 isolates; 31% of all isolates) contained both pharyngitis and invasive isolates and were found in 11 emm types. CONCLUSIONS In the Denver metropolitan population, mixed disease types were commonly seen in clusters of closely related isolates, indicative of overlapping transmission networks. Antibiotic-resistance and covS inactivation was disproportionally associated with invasive disease.
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Affiliation(s)
- Yuan Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Samuel Dominguez
- University of Colorado School of Medicine Aurora, CO, USA; Children's Hospital Colorado Aurora, CO, USA
| | - Srinivas A Nanduri
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joy Rivers
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Saundra Mathis
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Zhongya Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chris A Van Beneden
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernard Beall
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa Miller
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Critical evaluation of CNA estimators for DNA data using matching confidence masks and WGS technology. Biomed Signal Process Control 2021. [DOI: 10.1016/j.bspc.2021.103004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Castro SA, Dorfmueller HC. A brief review on Group A Streptococcus pathogenesis and vaccine development. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201991. [PMID: 33959354 PMCID: PMC8074923 DOI: 10.1098/rsos.201991] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Streptococcus pyogenes, also known as Group A Streptococcus (GAS), is a Gram-positive human-exclusive pathogen, responsible for more than 500 000 deaths annually worldwide. Upon infection, GAS commonly triggers mild symptoms such as pharyngitis, pyoderma and fever. However, recurrent infections or prolonged exposure to GAS might lead to life-threatening conditions. Necrotizing fasciitis, streptococcal toxic shock syndrome and post-immune mediated diseases, such as poststreptococcal glomerulonephritis, acute rheumatic fever and rheumatic heart disease, contribute to very high mortality rates in non-industrialized countries. Though an initial reduction in GAS infections was observed in high-income countries, global outbreaks of GAS, causing rheumatic fever and acute poststreptococcal glomerulonephritis, have been reported over the last decade. At the same time, our understanding of GAS pathogenesis and transmission has vastly increased, with detailed insight into the various stages of infection, beginning with adhesion, colonization and evasion of the host immune system. Despite deeper knowledge of the impact of GAS on the human body, the development of a successful vaccine for prophylaxis of GAS remains outstanding. In this review, we discuss the challenges involved in identifying a universal GAS vaccine and describe several potential vaccine candidates that we believe warrant pursuit.
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Affiliation(s)
- Sowmya Ajay Castro
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Helge C. Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
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Avire NJ, Whiley H, Ross K. A Review of Streptococcus pyogenes: Public Health Risk Factors, Prevention and Control. Pathogens 2021; 10:248. [PMID: 33671684 PMCID: PMC7926438 DOI: 10.3390/pathogens10020248] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 01/10/2023] Open
Abstract
Streptococcus pyogenes, (colloquially named "group A streptococcus" (GAS)), is a pathogen of public health significance, infecting 18.1 million people worldwide and resulting in 500,000 deaths each year. This review identified published articles on the risk factors and public health prevention and control strategies for mitigating GAS diseases. The pathogen causing GAS diseases is commonly transmitted via respiratory droplets, touching skin sores caused by GAS or through contact with contaminated material or equipment. Foodborne transmission is also possible, although there is need for further research to quantify this route of infection. It was found that GAS diseases are highly prevalent in developing countries, and among indigenous populations and low socioeconomic areas in developed countries. Children, the immunocompromised and the elderly are at the greatest risk of S. pyogenes infections and the associated sequelae, with transmission rates being higher in schools, kindergartens, hospitals and residential care homes. This was attributed to overcrowding and the higher level of social contact in these settings. Prevention and control measures should target the improvement of living conditions, and personal and hand hygiene. Adherence to infection prevention and control practices should be emphasized in high-risk settings. Resource distribution by governments, especially in developed countries, should also be considered.
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Affiliation(s)
| | | | - Kirstin Ross
- Environmental Health, College of Science and Engineering, Flinders University, Adelaide 5001, Australia; (N.J.A.); (H.W.)
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Sequential Quadriplex Real-Time PCR for Identifying 20 Common emm Types of Group A Streptococcus. J Clin Microbiol 2020; 59:JCM.01764-20. [PMID: 33087429 PMCID: PMC7771451 DOI: 10.1128/jcm.01764-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/11/2020] [Indexed: 11/20/2022] Open
Abstract
We developed a sequential quadriplex real-time PCR-based method for rapid identification of 20 emm types commonly found in invasive group A Streptococcus (iGAS) strains recovered through the Centers for Disease Control and Prevention’s Active Bacterial Core surveillance. Each emm real-time PCR assay showed high specificity and accurately identified the respective target emm type, including emm subtypes in the United States. We developed a sequential quadriplex real-time PCR-based method for rapid identification of 20 emm types commonly found in invasive group A Streptococcus (iGAS) strains recovered through the Centers for Disease Control and Prevention’s Active Bacterial Core surveillance. Each emm real-time PCR assay showed high specificity and accurately identified the respective target emm type, including emm subtypes in the United States. Furthermore, this method is useful for rapid typing of GAS isolates and culture-negative specimens during outbreak investigations.
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Jespersen MG, Lacey JA, Tong SYC, Davies MR. Global genomic epidemiology of Streptococcus pyogenes. INFECTION GENETICS AND EVOLUTION 2020; 86:104609. [PMID: 33147506 DOI: 10.1016/j.meegid.2020.104609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 02/04/2023]
Abstract
Streptococcus pyogenes is one of the Top 10 human infectious disease killers worldwide causing a range of clinical manifestations in humans. Colonizing a range of ecological niches within its sole host, the human, is key to the ability of this opportunistic pathogen to cause direct and post-infectious manifestations. The expansion of genome sequencing capabilities and data availability over the last decade has led to an improved understanding of the evolutionary dynamics of this pathogen within a global framework where epidemiological relationships and evolutionary mechanisms may not be universal. This review uses the recent publication by Davies et al., 2019 as an updated global framework to address S. pyogenes population genomics, highlighting how genomics is being used to gain new insights into evolutionary processes, transmission pathways, and vaccine design.
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Affiliation(s)
- Magnus G Jespersen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jake A Lacey
- Doherty Department, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Doherty Department, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, VIC, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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Vijayakumar K, Manigandan V, Jeyapragash D, Bharathidasan V, Anandharaj B, Sathya M. Eucalyptol inhibits biofilm formation of Streptococcus pyogenes and its mediated virulence factors. J Med Microbiol 2020; 69:1308-1318. [PMID: 32930658 DOI: 10.1099/jmm.0.001253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Introduction. Streptococcus pyogenes is a diverse virulent synthesis pathogen responsible for invasive systemic infections. Establishment of antibiotic resistance in the pathogen has produced a need for new antibiofilm agents to control the biofilm formation and reduce biofilm-associated resistance development.Aim. The present study investigates the in vitro antibiofilm activity of eucalyptol against S. pyogenes.Methodology. The antibiofilm potential of eucalyptol was assessed using a microdilution method and their biofilm inhibition efficacy was visualized by microscopic analysis. The biochemical assays were performed to assess the influence of eucalyptol on virulence productions. Real-time PCR analysis was performed to evaluate the expression profile of the virulence genes.Results. Eucalyptol showed significant antibiofilm potential in a dose-dependent manner without affecting bacterial growth. Eucalyptol at 300 µg ml-1 (biofilm inhibitory concentration) significantly inhibited the initial stage of biofilm formation in S. pyogenes. However, eucalyptol failed to diminish the mature biofilms of S. pyogenes at biofilm inhibitory concentration and it effectively reduced the biofilm formation on stainless steel, titanium, and silicone surfaces. The biochemical assay results revealed that eucalyptol greatly affects the cell-surface hydrophobicity, auto-aggregation, extracellular protease, haemolysis and hyaluronic acid synthesis. Further, the gene-expression analysis results showed significant downregulation of virulence gene expression upon eucalyptol treatment.Conclusion. The present study suggests that eucalyptol applies its antibiofilm assets by intruding the initial biofilm formation of S. pyogenes. Supplementary studies are needed to understand the mode of action involved in biofilm inhibition.
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Affiliation(s)
- Karuppiah Vijayakumar
- Centre of advanced study in Marine Biology, Annamalai University, Parangipettai - 608 502, Tamil Nadu, India
| | - Vajravelu Manigandan
- Centre of advanced study in Marine Biology, Annamalai University, Parangipettai - 608 502, Tamil Nadu, India
| | - Danaraj Jeyapragash
- Department of Biotechnology, Karpagam academy of higher education, Eachanari, Coimbatore-641 021, Tamil Nadu, India
| | - Veeraiyan Bharathidasan
- Centre of advanced study in Marine Biology, Annamalai University, Parangipettai - 608 502, Tamil Nadu, India
| | - Balaiyan Anandharaj
- Department of Botany, Annamalai University, Annamalai Nagar, Chidambaram - 608 002, Tamil Nadu, India
| | - Madhavan Sathya
- Department of Botany, Annamalai University, Annamalai Nagar, Chidambaram - 608 002, Tamil Nadu, India
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14
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Li Y, Rivers J, Mathis S, Li Z, Velusamy S, Nanduri SA, Van Beneden CA, Snippes-Vagnone P, Lynfield R, McGee L, Chochua S, Metcalf BJ, Beall B. Genomic Surveillance of Streptococcus pyogenes Strains Causing Invasive Disease, United States, 2016-2017. Front Microbiol 2020; 11:1547. [PMID: 32849323 PMCID: PMC7396493 DOI: 10.3389/fmicb.2020.01547] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Streptococcus pyogenes is a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common. Understanding the current prevalence and dynamics of S. pyogenes lineages could inform vaccine development and disease control strategies. METHODS We used whole-genome sequencing (WGS) to characterize all invasive S. pyogenes isolates obtained through the United States Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) in 2016 and 2017. We determined the distribution of strain features, including emm type, antibiotic resistance determinants, and selected virulence factors. Changes in strain feature distribution between years 2016 and 2017 were evaluated. Phylogenetic analysis was used to identify expanding lineages within emm type. RESULTS Seventy-one emm types were identified from 3873 isolates characterized. The emm types targeted by a 30-valent M protein-based vaccine accounted for 3230 (89%) isolates. The relative frequencies of emm types collected during the 2 years were similar. While all isolates were penicillin-susceptible, erythromycin-resistant isolates increased from 273 (16% of 2016 isolates) to 432 (23% of 2017 isolates), mainly driven by increase of the erm-positive emm types 92 and 83. The prevalence of 24 virulence factors, including 11 streptococcal pyrogenic toxins, ranged from 6 to 90%. In each of three emm types (emm 49, 82, and 92), a subgroup of isolates significantly expanded between 2016 and 2017 compared to isolates outside of the subgroup (P-values < 0.0001). Specific genomic sequence changes were associated with these expanded lineages. CONCLUSIONS While the overall population structure of invasive S. pyogenes isolates in the United States remained stable, some lineages, including several that were antibiotic-resistant, increased between 2016 and 2017. Continued genomic surveillance can help monitor and characterize bacterial features associated with emerging strains from invasive infections.
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Affiliation(s)
- Yuan Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Joy Rivers
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Saundra Mathis
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Zhongya Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Srinivasan Velusamy
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Srinivas A. Nanduri
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Chris A. Van Beneden
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | | | - Ruth Lynfield
- Minnesota Department of Health, St Paul, MN, United States
| | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Sopio Chochua
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Benjamin J. Metcalf
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Bernard Beall
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
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15
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Munanga A. Critical Infection Control Adaptations to Survive COVID-19 in Retirement Communities. J Gerontol Nurs 2020; 46:3-5. [DOI: 10.3928/00989134-20200511-03] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Albert Munanga
- Regional Director of Health and Wellness Era Living, Affiliate Faculty, Department of Biobehavioral Nursing and Health Informatics, University of Washington Seattle, Washington
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16
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Worthing KA, Werno A, Pink R, McIntyre L, Carter GP, Williamson DA, Davies MR. Biphasic Outbreak of Invasive Group A Streptococcus Disease in Eldercare Facility, New Zealand. Emerg Infect Dis 2020; 26:841-848. [PMID: 32308193 PMCID: PMC7181915 DOI: 10.3201/eid2605.190131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A 3-month outbreak of invasive group A Streptococcus disease at an eldercare facility, in which 5 persons died, was biphasic. Although targeted chemoprophylaxis contained the initial outbreak, a second phase of the outbreak occurred after infection control processes ended. To retrospectively investigate the genomic epidemiology of the biphasic outbreak, we used whole-genome sequencing and multiple bioinformatics approaches. Analysis of isolates from the outbreak and isolates prospectively collected during the outbreak response indicated a single S. pyogenes emm81 clone among residents and staff members. Outbreak isolates differed from nonoutbreak emm81 isolates by harboring an integrative conjugative genomic element that contained the macrolide resistance determinant erm(TR). This study shows how retrospective high-resolution genomic investigations identified rapid spread of a closed-facilty clonal outbreak that was controlled, but not readily cleared, by infection control management procedures.
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Affiliation(s)
- Kate A. Worthing
- The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia (K.A. Worthing, L. McIntyre, G.P. Carter, D.A. Williamson, M.R. Davies)
- Canterbury Health Laboratories, South Island, New Zealand (A. Werno)
- Canterbury District Health Board, South Island (R. Pink)
| | - Anja Werno
- The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia (K.A. Worthing, L. McIntyre, G.P. Carter, D.A. Williamson, M.R. Davies)
- Canterbury Health Laboratories, South Island, New Zealand (A. Werno)
- Canterbury District Health Board, South Island (R. Pink)
| | - Ramon Pink
- The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia (K.A. Worthing, L. McIntyre, G.P. Carter, D.A. Williamson, M.R. Davies)
- Canterbury Health Laboratories, South Island, New Zealand (A. Werno)
- Canterbury District Health Board, South Island (R. Pink)
| | - Liam McIntyre
- The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia (K.A. Worthing, L. McIntyre, G.P. Carter, D.A. Williamson, M.R. Davies)
- Canterbury Health Laboratories, South Island, New Zealand (A. Werno)
- Canterbury District Health Board, South Island (R. Pink)
| | - Glen P. Carter
- The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia (K.A. Worthing, L. McIntyre, G.P. Carter, D.A. Williamson, M.R. Davies)
- Canterbury Health Laboratories, South Island, New Zealand (A. Werno)
- Canterbury District Health Board, South Island (R. Pink)
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17
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Lee MH, Lee GA, Lee SH, Park YH. A systematic review on the causes of the transmission and control measures of outbreaks in long-term care facilities: Back to basics of infection control. PLoS One 2020; 15:e0229911. [PMID: 32155208 PMCID: PMC7064182 DOI: 10.1371/journal.pone.0229911] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The unique characteristics of long-term care facilities (LTCFs) including host factors and living conditions contribute to the spread of contagious pathogens. Control measures are essential to interrupt the transmission and to manage outbreaks effectively. AIM The aim of this systematic review was to verify the causes and problems contributing to transmission and to identify control measures during outbreaks in LTCFs. METHODS Four electronic databases were searched for articles published from 2007 to 2018. Articles written in English reporting outbreaks in LTCFs were included. The quality of the studies was assessed using the risk-of-bias assessment tool for nonrandomized studies. FINDINGS A total of 37 studies were included in the qualitative synthesis. The most commonly reported single pathogen was influenza virus, followed by group A streptococcus (GAS). Of the studies that identified the cause, about half of them noted outbreaks transmitted via person-to-person. Suboptimal infection control practice including inadequate decontamination and poor hand hygiene was the most frequently raised issue propagating transmission. Especially, lapses in specific care procedures were linked with outbreaks of GAS and hepatitis B and C viruses. About 60% of the included studies reported affected cases among staff, but only a few studies implemented work restriction during outbreaks. CONCLUSIONS This review indicates that the violation of basic infection control practice could be a major role in introducing and facilitating the spread of contagious diseases in LTCFs. It shows the need to promote compliance with basic practices of infection control to prevent outbreaks in LTCFs.
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Affiliation(s)
- Min Hye Lee
- The Research Institute of Nursing Science, College of Nursing, Seoul National University, Seoul, South Korea
| | - Gyeoung Ah Lee
- College of Nursing, Seoul National University, Seoul, South Korea
| | - Seong Hyeon Lee
- College of Nursing, Seoul National University, Seoul, South Korea
| | - Yeon-Hwan Park
- The Research Institute of Nursing Science, College of Nursing, Seoul National University, Seoul, South Korea
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18
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Konrad P, Hufnagel M, Berner R, Toepfner N. Long-term, single-center surveillance of non-invasive group A streptococcal (GAS) infections, emm types and emm clusters. Eur J Clin Microbiol Infect Dis 2019; 39:273-280. [PMID: 31758439 DOI: 10.1007/s10096-019-03719-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Group A streptococci (GAS) are among the most frequent pathogens in children. Many epidemiological studies focus on specific GAS infections (such as tonsillopharyngitis or invasive disease), on GAS carriers or on post-streptococcal sequelae. By comparison, reports on regional GAS characteristics, particularly circulating non-invasive GAS in Europe, are rare. In a monocentric study, all GAS isolated from pediatric patients at a tertiary care hospital over a 6-year period (2006-2012) were characterized. GAS emm types and clusters were determined. Associated patient data were analyzed. Five hundred sixty-six GAS strains were collected. GAS tonsillopharyngitis was most common (71.6%), followed by pyoderma (6.0%), otitis media (3.7%), perineal dermatitis (3.4%), and invasive infections (1.4%). Colonizing strains represented 13.6% of GAS. GAS emm12 was most prevalent among invasive and non-invasive isolates. Emm1, emm4, emm28, and emm89 were the most frequent non-invasive GAS strains. The emm E4 cluster was most common, followed by the A-C4, A-C3, and E1. Among the GAS infections, different emm types and clusters were identified, e.g., emm4 was more common among patients with scarlet fever. Three new emm subtypes were characterized: emm29.13, emm36.7, and emm75.5. This comprehensive review of a large, local GAS cohort points to the differences between and similarities among GAS genotypes and disease manifestations, while minimizing regional variations. Considerable deviation from previous epidemiological findings is described, especially regarding the frequent detection of emm1 and emm89 in non-invasive GAS infections. Periodic updates on molecular and epidemiological GAS characteristics are needed to track the multifaceted pathogenic potential of GAS.
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Affiliation(s)
- Peter Konrad
- Department of Pediatrics, Carl Gustav Carus University Hospital, Technical University Dresden, Dresden, Germany
| | - Markus Hufnagel
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Reinhard Berner
- Department of Pediatrics, Carl Gustav Carus University Hospital, Technical University Dresden, Dresden, Germany
| | - Nicole Toepfner
- Department of Pediatrics, Carl Gustav Carus University Hospital, Technical University Dresden, Dresden, Germany.
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19
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Balloux F, Brønstad Brynildsrud O, van Dorp L, Shaw LP, Chen H, Harris KA, Wang H, Eldholm V. From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. Trends Microbiol 2018; 26:1035-1048. [PMID: 30193960 PMCID: PMC6249990 DOI: 10.1016/j.tim.2018.08.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions.
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Affiliation(s)
- Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions.
| | - Ola Brønstad Brynildsrud
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway; These authors made equal contributions
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions
| | - Liam P Shaw
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Hongbin Chen
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Kathryn A Harris
- Great Ormond Street Hospital NHS Foundation Trust, Department of Microbiology, Virology & Infection Prevention & Control, London WC1N 3JH, UK
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Vegard Eldholm
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway
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