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Karunakaran S, Pless LL, Ayres AM, Ciccone C, Penzelik J, Sundermann AJ, Martin EM, Griffith MP, Waggle K, Hodges JC, Harrison LH, Snyder GM. Impact of discontinuation of contact precautions on surveillance- and whole genome sequencing-defined methicillin-resistant Staphylococcus aureus healthcare-associated infections. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e97. [PMID: 38836046 PMCID: PMC11149034 DOI: 10.1017/ash.2024.89] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 06/06/2024]
Abstract
Objective Prior studies evaluating the impact of discontinuation of contact precautions (DcCP) on methicillin-resistant Staphylococcus aureus (MRSA) outcomes have characterized all healthcare-associated infections (HAIs) rather than those likely preventable by contact precautions. We aimed to analyze the impact of DcCP on the rate of MRSA HAI including transmission events identified through whole genome sequencing (WGS) surveillance. Design Quasi experimental interrupted time series. Setting Acute care medical center. Participants Inpatients. Methods The effect of DcCP (use of gowns and gloves) for encounters among patients with MRSA carriage was evaluated using time series analysis of MRSA HAI rates from January 2019 through December 2022, compared to WGS-defined attributable transmission events before and after DcCP in December 2020. Results The MRSA HAI rate was 4.22/10,000 patient days before and 2.98/10,000 patient days after DcCP (incidence rate ratio [IRR] 0.71 [95% confidence interval 0.56-0.89]) with a significant immediate decrease (P = .001). There were 7 WGS-defined attributable transmission events before and 11 events after DcCP (incident rate ratio 0.90 [95% confidence interval 0.30-2.55]). Conclusions DcCP did not result in an increase in MRSA HAI or, in WGS-defined attributable transmission events. Comprehensive analyses of the effect of transmission prevention measures should include outcomes specifically measuring transmission-associated HAI.
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Affiliation(s)
- Sharon Karunakaran
- Division of Pediatric Infectious Diseases, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Lora Lee Pless
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ashley M Ayres
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Carl Ciccone
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Joseph Penzelik
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Alexander J Sundermann
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elise M Martin
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Veterans' Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Marissa P Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kady Waggle
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Lee H Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Graham M Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
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2
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Sundermann AJ, Rangachar Srinivasa V, Mills EG, Griffith MP, Evans E, Chen J, Waggle KD, Snyder GM, Pless LL, Harrison LH, Van Tyne D. Genomic sequencing surveillance of patients colonized with vancomycin-resistant Enterococcus (VRE) improves detection of hospital-associated transmission. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306710. [PMID: 38746387 PMCID: PMC11092704 DOI: 10.1101/2024.05.01.24306710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Vancomycin-resistant enterococcal (VRE) infections pose significant challenges in healthcare. Transmission dynamics of VRE are complex, often involving patient colonization and subsequent transmission through various healthcare-associated vectors. We utilized a whole genome sequencing (WGS) surveillance program at our institution to better understand the contribution of clinical and colonizing isolates to VRE transmission. Methods We performed whole genome sequencing on 352 VRE clinical isolates collected over 34 months and 891 rectal screening isolates collected over a 9-month nested period, and used single nucleotide polymorphisms to assess relatedness. We then performed a geo-temporal transmission analysis considering both clinical and rectal screening isolates compared with clinical isolates alone, and calculated 30-day outcomes of patients. Results VRE rectal carriage constituted 87.3% of VRE acquisition, with an average monthly acquisition rate of 7.6 per 1000 patient days. We identified 185 genetically related clusters containing 2-42 isolates and encompassing 69.6% of all isolates in the dataset. The inclusion of rectal swab isolates increased the detection of clinical isolate clusters (from 53% to 67%, P<0.01). Geo-temporal analysis identified hotspot locations of VRE transmission. Patients with clinical VRE isolates that were closely related to previously sampled rectal swab isolates experienced 30-day ICU admission (17.5%), hospital readmission (9.2%), and death (13.3%). Conclusions Our findings describe the high burden of VRE transmission at our hospital and shed light on the importance of using WGS surveillance of both clinical and rectal screening isolates to better understand the transmission of this pathogen. This study highlights the potential utility of incorporating WGS surveillance of VRE into routine hospital practice for improving infection prevention and patient safety.
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3
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Raabe NJ, Valek AL, Griffith MP, Mills E, Waggle K, Srinivasa VR, Ayres AM, Bradford C, Creager HM, Pless LL, Sundermann AJ, Van Tyne D, Snyder GM, Harrison LH. Real-time genomic epidemiologic investigation of a multispecies plasmid-associated hospital outbreak of NDM-5-producing Enterobacterales infections. Int J Infect Dis 2024; 142:106971. [PMID: 38373647 PMCID: PMC11055495 DOI: 10.1016/j.ijid.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/05/2024] [Accepted: 02/14/2024] [Indexed: 02/21/2024] Open
Abstract
OBJECTIVES New Delhi metallo-β-lactamase (NDM) is an emergent mechanism of carbapenem resistance associated with high mortality and limited treatment options. Because the blaNDM resistance gene is often carried on plasmids, traditional infection prevention and control (IP&C) surveillance methods and reactive whole genome sequencing (WGS) may not detect plasmid transfer in multispecies outbreaks. METHODS Initial outbreak detection of NDM-producing Enterobacterales identified at an acute care hospital occurred via traditional IP&C methods and was supplemented by real-time WGS surveillance performed weekly. To resolve NDM-encoding plasmids, we performed long-read sequencing and constructed hybrid assemblies. WGS data for suspected outbreaks was shared with the IP&C team for assessment and intervention. RESULTS We observed a multispecies outbreak of NDM-5-producing Enterobacterales isolated from 15 patients between February 2021 and February 2023. The 19 clinical and surveillance isolates sequenced included 7 bacterial species encoding the same NDM-5 plasmid. WGS surveillance and epidemiologic investigation characterized 10 horizontal plasmid transfer events and 6 bacterial transmission events between patients in varying hospital units. CONCLUSIONS Our investigation revealed a complex, multispecies outbreak of NDM involving multiple plasmid transfer and bacterial transmission events. We highlight the utility of combining traditional IP&C and prospective genomic methods in identifying and containing plasmid-associated outbreaks.
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Affiliation(s)
- Nathan J Raabe
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Abby L Valek
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, PA, USA
| | - Marissa P Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Emma Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kady Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vatsala Rangachar Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ashley M Ayres
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, PA, USA
| | - Claire Bradford
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, PA, USA
| | - Hannah M Creager
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lora L Pless
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alexander J Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Graham M Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, PA, USA
| | - Lee H Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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4
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Zaatry R, Herren R, Gefen T, Geva-Zatorsky N. Microbiome and infectious disease: diagnostics to therapeutics. Microbes Infect 2024:105345. [PMID: 38670215 DOI: 10.1016/j.micinf.2024.105345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Over 300 years of research on the microbial world has revealed their importance in human health and disease. This review explores the impact and potential of microbial-based detection methods and therapeutic interventions, integrating research of early microbiologists, current findings, and future perspectives.
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Affiliation(s)
- Rawan Zaatry
- Rappaport Faculty of Medicine, Rappaport Technion Integrated Cancer Center, Technion, Haifa, Israel
| | - Rachel Herren
- Rappaport Faculty of Medicine, Rappaport Technion Integrated Cancer Center, Technion, Haifa, Israel
| | - Tal Gefen
- Rappaport Faculty of Medicine, Rappaport Technion Integrated Cancer Center, Technion, Haifa, Israel
| | - Naama Geva-Zatorsky
- Rappaport Faculty of Medicine, Rappaport Technion Integrated Cancer Center, Technion, Haifa, Israel; CIFAR, Humans & the Microbiome, Toronto, Canada.
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5
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Blane B, Raven KE, Brown NM, Harrison EM, Coll F, Thaxter R, Enoch DA, Gouliouris T, Leek D, Girgis ST, Akram A, Matuszewska M, Rhodes P, Parkhill J, Peacock SJ. Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions. Microb Genom 2024; 10. [PMID: 38630616 DOI: 10.1099/mgen.0.001235] [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] [Indexed: 04/19/2024] Open
Abstract
Genomic epidemiology enhances the ability to detect and refute methicillin-resistant Staphylococcus aureus (MRSA) outbreaks in healthcare settings, but its routine introduction requires further evidence of benefits for patients and resource utilization. We performed a 12 month prospective study at Cambridge University Hospitals NHS Foundation Trust in the UK to capture its impact on hospital infection prevention and control (IPC) decisions. MRSA-positive samples were identified via the hospital microbiology laboratory between November 2018 and November 2019. We included samples from in-patients, clinic out-patients, people reviewed in the Emergency Department and healthcare workers screened by Occupational Health. We sequenced the first MRSA isolate from 823 consecutive individuals, defined their pairwise genetic relatedness, and sought epidemiological links in the hospital and community. Genomic analysis of 823 MRSA isolates identified 72 genetic clusters of two or more isolates containing 339/823 (41 %) of the cases. Epidemiological links were identified between two or more cases for 190 (23 %) individuals in 34/72 clusters. Weekly genomic epidemiology updates were shared with the IPC team, culminating in 49 face-to-face meetings and 21 written communications. Seventeen clusters were identified that were consistent with hospital MRSA transmission, discussion of which led to additional IPC actions in 14 of these. Two outbreaks were also identified where transmission had occurred in the community prior to hospital presentation; these were escalated to relevant IPC teams. We identified 38 instances where two or more in-patients shared a ward location on overlapping dates but carried unrelated MRSA isolates (pseudo-outbreaks); research data led to de-escalation of investigations in six of these. Our findings provide further support for the routine use of genomic epidemiology to enhance and target IPC resources.
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Affiliation(s)
- Beth Blane
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Nicholas M Brown
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Francesc Coll
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Rachel Thaxter
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - David A Enoch
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Danielle Leek
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Sophia T Girgis
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Asha Akram
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Marta Matuszewska
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Paul Rhodes
- Next Gen Diagnostics, LLC, (NGD) Mountain View, CA, USA
- Broers Building, 21 JJ Thomson Ave., Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, UK
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6
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Langford BJ, Branch-Elliman W, Nori P, Marra AR, Bearman G. Confronting the Disruption of the Infectious Diseases Workforce by Artificial Intelligence: What This Means for Us and What We Can Do About It. Open Forum Infect Dis 2024; 11:ofae053. [PMID: 38434616 PMCID: PMC10906702 DOI: 10.1093/ofid/ofae053] [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: 10/07/2023] [Accepted: 01/26/2024] [Indexed: 03/05/2024] Open
Abstract
With the rapid advancement of artificial intelligence (AI), the field of infectious diseases (ID) faces both innovation and disruption. AI and its subfields including machine learning, deep learning, and large language models can support ID clinicians' decision making and streamline their workflow. AI models may help ensure earlier detection of disease, more personalized empiric treatment recommendations, and allocation of human resources to support higher-yield antimicrobial stewardship and infection prevention strategies. AI is unlikely to replace the role of ID experts, but could instead augment it. However, its limitations will need to be carefully addressed and mitigated to ensure safe and effective implementation. ID experts can be engaged in AI implementation by participating in training and education, identifying use cases for AI to help improve patient care, designing, validating and evaluating algorithms, and continuing to advocate for their vital role in patient care.
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Affiliation(s)
- Bradley J Langford
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Hotel Dieu Shaver Health and Rehabilitation Centre, Department of Pharmacy, St Catharines, Ontario, Canada
| | - Westyn Branch-Elliman
- Department of Medicine, Section of Infectious Diseases, Veterans Affairs Boston Healthcare System, Boston, Massachusetts, USA
- National Artificial Intelligence Institute, Department of Veterans Affairs, Washington, District of Columbia, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Priya Nori
- Division of Infectious Diseases, Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alexandre R Marra
- Instituto Israelita de Ensino e Pesquisa Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, Brazil
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Gonzalo Bearman
- Division of Infectious Diseases, Virginia Commonwealth University Health, Virginia Commonwealth University, Richmond, Virginia, USA
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7
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Nordstrom HR, Griffith MP, Rangachar Srinivasa V, Wallace NR, Li A, Cooper VS, Shields RK, Van Tyne D. Harnessing the Diversity of Burkholderia spp. Prophages for Therapeutic Potential. Cells 2024; 13:428. [PMID: 38474392 PMCID: PMC10931425 DOI: 10.3390/cells13050428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Burkholderia spp. are often resistant to antibiotics, and infections with these organisms are difficult to treat. A potential alternative treatment for Burkholderia spp. infections is bacteriophage (phage) therapy; however, it can be difficult to locate phages that target these bacteria. Prophages incorporated into the bacterial genome have been identified within Burkholderia spp. and may represent a source of useful phages for therapy. Here, we investigate whether prophages within Burkholderia spp. clinical isolates can kill conspecific and heterospecific isolates. Thirty-two Burkholderia spp. isolates were induced for prophage release, and harvested phages were tested for lytic activity against the same 32 isolates. Temperate phages were passaged and their host ranges were determined, resulting in four unique phages of prophage origin that showed different ranges of lytic activity. We also analyzed the prophage content of 35 Burkholderia spp. clinical isolate genomes and identified several prophages present in the genomes of multiple isolates of the same species. Finally, we observed that Burkholdera cenocepacia isolates were more phage-susceptible than Burkholderia multivorans isolates. Overall, our findings suggest that prophages present within Burkholderia spp. genomes are a potentially useful starting point for the isolation and development of novel phages for use in phage therapy.
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Affiliation(s)
- Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | | | - Nathan R. Wallace
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anna Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ryan K. Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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8
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Crisan CV, Duncan RP, Van Tyne D, Goldberg JB. Complete genome sequence of Stenotrophomonas maltophilia complex strain STEN00241. Microbiol Resour Announc 2024; 13:e0105323. [PMID: 38132567 PMCID: PMC10868206 DOI: 10.1128/mra.01053-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
We report here the complete, closed genome sequence of Stenotrophomonas maltophilia complex strain STEN00241, which was isolated from patient sputum. The genome is a single contig with a total length of 4,751,329 nucleotides and a GC content of 66.5%.
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Affiliation(s)
- Cristian V. Crisan
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Rebecca P. Duncan
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joanna B. Goldberg
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
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9
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Sundermann AJ, Rangachar Srinivasa V, Mills EG, Griffith MP, Waggle KD, Ayres AM, Pless L, Snyder GM, Harrison LH, Van Tyne D. Two Artificial Tears Outbreak-Associated Cases of Extensively Drug-Resistant Pseudomonas aeruginosa Detected Through Whole Genome Sequencing-Based Surveillance. J Infect Dis 2024; 229:517-521. [PMID: 37700467 PMCID: PMC10873170 DOI: 10.1093/infdis/jiad318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/03/2023] [Indexed: 09/14/2023] Open
Abstract
We describe 2 cases of extensively drug-resistant Pseudomonas aeruginosa infection caused by a strain of public health concern, as it was recently associated with a nationwide outbreak of contaminated artificial tears. Both cases were detected through database review of genomes in the Enhanced Detection System for Hospital-Associated Transmission (EDS-HAT), a routine genome sequencing-based surveillance program. We generated a high-quality reference genome for the outbreak strain from an isolate from our center and examined the mobile elements encoding blaVIM-80 and bla-GES-9 carbapenemases. We used publicly available Pseudomonas aeruginosa genomes to explore the genetic relatedness and antimicrobial resistance genes of the outbreak strain.
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Affiliation(s)
- Alexander J Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
| | - Vatsala Rangachar Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
- Department of Epidemiology, School of Public Health, University of Pittsburgh
| | - Emma G Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
| | - Marissa P Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
- Department of Epidemiology, School of Public Health, University of Pittsburgh
| | - Kady D Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
- Department of Epidemiology, School of Public Health, University of Pittsburgh
| | - Ashley M Ayres
- Department of Infection Control and Hospital Epidemiology, University of Pittsburgh Medical Center–Presbyterian Hospital, Pittsburgh, Pennsylvania
| | - Lora Pless
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
| | - Graham M Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
- Department of Infection Control and Hospital Epidemiology, University of Pittsburgh Medical Center–Presbyterian Hospital, Pittsburgh, Pennsylvania
| | - Lee H Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
- Department of Epidemiology, School of Public Health, University of Pittsburgh
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine
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10
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Selvaraj Anand S, Wu CT, Bremer J, Bhatti M, Treangen TJ, Kalia A, Shelburne SA, Shropshire WC. Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA. Microb Genom 2024; 10:001201. [PMID: 38407244 PMCID: PMC10926705 DOI: 10.1099/mgen.0.001201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 02/27/2024] Open
Abstract
Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in the USA remains limited. We performed whole-genome sequencing of 3GC-R K. pneumoniae bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R K. pneumoniae population. Of the 178 3GC-R K. pneumoniae bacteraemias that occurred during our study time frame, we were able to analyse 153 (86 %) bacteraemia isolates, 126 initial and 27 recurrent isolates. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant CG, 307, accounted for 37 (29 %) index isolates and displayed a significant correlation (Pearson correlation test P value=0.03) with the annual frequency of 3GC-R K. pneumoniae bacteraemia. Interestingly, only 11 % (4/37) of CG307 isolates belonged to the commonly detected 'Texas-specific' clade that has been observed in previous Texas-based K. pneumoniae antimicrobial-resistance surveillance studies. We identified nearly half of our CG307 isolates (n=18) belonged to a novel, monophyletic CG307 sub-clade characterized by the chromosomally encoded bla SHV-205 and unique accessory genome content. This CG307 sub-clade was detected in various regions of the USA, with genome sequences from 24 additional strains becoming recently available in the National Center for Biotechnology Information (NCBI) SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R K. pneumoniae bacteraemia among cancer patients seen in Houston, TX, and has recently been isolated throughout the USA.
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Affiliation(s)
- Selvalakshmi Selvaraj Anand
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Chin-Ting Wu
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Jordan Bremer
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Micah Bhatti
- Department of Laboratory Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - William C. Shropshire
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
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11
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Sundermann AJ, Javaid W. Whole-genome sequencing surveillance: Growing evidence for a future potential practice standard of infection prevention. Infect Control Hosp Epidemiol 2024; 45:135-136. [PMID: 38073562 DOI: 10.1017/ice.2023.261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Affiliation(s)
- Alexander J Sundermann
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Waleed Javaid
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York
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12
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Simon SJ, Sater M, Herriott I, Huntley M, Briars E, Hollenbeck BL. Staphylococcus epidermidis joint isolates: Whole-genome sequencing demonstrates evidence of hospital transmission and common antimicrobial resistance. Infect Control Hosp Epidemiol 2024; 45:150-156. [PMID: 38099465 DOI: 10.1017/ice.2023.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
OBJECTIVE We investigated genetic, epidemiologic, and environmental factors contributing to positive Staphylococcus epidermidis joint cultures. DESIGN Retrospective cohort study with whole-genome sequencing (WGS). PATIENTS We identified S. epidermidis isolates from hip or knee cultures in patients with 1 or more prior corresponding intra-articular procedure at our hospital. METHODS WGS and single-nucleotide polymorphism-based clonality analyses were performed, including species identification, in silico multilocus sequence typing (MLST), phylogenomic analysis, and genotypic assessment of the prevalence of specific antibiotic resistance and virulence genes. Epidemiologic review was performed to compare cluster and noncluster cases. RESULTS In total, 60 phenotypically distinct S. epidermidis isolates were identified. After removal of duplicates and impure samples, 48 isolates were used for the phylogenomic analysis, and 45 (93.7%) isolates were included in the clonality analysis. Notably, 5 S. epidermidis strains (10.4%) showed phenotypic susceptibility to oxacillin yet harbored mecA, and 3 (6.2%) strains showed phenotypic resistance despite not having mecA. Smr was found in all isolates, and mupA positivity was not observed. We also identified 6 clonal clusters from the clonality analysis, which accounted for 14 (31.1%) of the 45 S. epidermidis isolates. Our epidemiologic investigation revealed ties to common aspirations or operative procedures, although no specific common source was identified. CONCLUSIONS Most S. epidermidis isolates from clinical joint samples are diverse in origin, but we identified an important subset of 31.1% that belonged to subclinical healthcare-associated clusters. Clusters appeared to resolve spontaneously over time, suggesting the benefit of routine hospital infection control and disinfection practices.
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Affiliation(s)
- Samantha J Simon
- Research Department, New England Baptist Hospital, Boston, Massachusetts
| | | | | | | | | | - Brian L Hollenbeck
- Research Department, New England Baptist Hospital, Boston, Massachusetts
- Infectious Diseases, New England Baptist Hospital, Boston, Massachusetts
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13
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Sundermann AJ, Griffith MP, Srinivasa VR, Waggle K, Snyder GM, Van Tyne D, Pless L, Harrison LH. Prolonged bacterial carriage and hospital transmission detected by whole genome sequencing surveillance. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e11. [PMID: 38415095 PMCID: PMC10897709 DOI: 10.1017/ash.2024.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 02/29/2024]
Affiliation(s)
- Alexander J. Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marissa P. Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vatsala Rangachar Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kady Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lora Pless
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
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14
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Nordstrom HR, Griffith MP, Srinivasa VR, Wallace NR, Li A, Cooper VS, Shields RK, Van Tyne D. Harnessing the diversity of Burkholderia spp. prophages for therapeutic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577087. [PMID: 38328162 PMCID: PMC10849711 DOI: 10.1101/2024.01.24.577087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Burkholderia spp. are often resistant to antibiotics, and infections with these organisms are difficult to treat. A potential alternative treatment for Burkholderia spp. infections is bacteriophage (phage) therapy; however, it can be difficult to locate phages that target these bacteria. Prophages incorporated into the bacterial genome have been identified within Burkholderia spp. and may represent a source of useful phages for therapy. Here we investigate whether prophages within Burkholderia spp. clinical isolates can kill conspecific and heterospecific isolates. Thirty-two Burkholderia spp. isolates were induced for prophage release, and harvested prophages were tested for lytic activity against the same 32 isolates. Lytic phages were passaged and their host ranges were determined, resulting in four unique phages of prophage origin that showed different ranges of lytic activity. We also analyzed the prophage content of 35 Burkholderia spp. clinical isolate genomes, and identified several prophages present in the genomes of multiple isolates of the same species. Finally, we observed that B. cenocepacia isolates were more phage-susceptible than Burkholderia multivorans isolates. Overall, our findings suggest that prophages present within Burkholderia spp. genomes are a potentially useful starting point for the isolation and development of novel phages for use in phage therapy.
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Affiliation(s)
- Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | | | - Nathan R. Wallace
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anna Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ryan K. Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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15
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Smith AB, Specker JT, Hewlett KK, Scoggins TR, Knight M, Lustig AM, Li Y, Evans KM, Guo Y, She Q, Christopher MW, Garrett TJ, Moustafa AM, Van Tyne D, Prentice BM, Zackular JP. Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection. mBio 2024; 15:e0165623. [PMID: 38078767 PMCID: PMC10790701 DOI: 10.1128/mbio.01656-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/23/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.
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Affiliation(s)
- Alexander B. Smith
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Katharine K. Hewlett
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Troy R. Scoggins
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Montana Knight
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Abigail M. Lustig
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yanhong Li
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Tsinghua University School of Medicine, Beijing, China
| | - Kirsten M. Evans
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yingchan Guo
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Qianxuan She
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Timothy J. Garrett
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Ahmed M. Moustafa
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Boone M. Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Joseph P. Zackular
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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16
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Arzilli G, De Vita E, Pasquale M, Carloni LM, Pellegrini M, Di Giacomo M, Esposito E, Porretta AD, Rizzo C. Innovative Techniques for Infection Control and Surveillance in Hospital Settings and Long-Term Care Facilities: A Scoping Review. Antibiotics (Basel) 2024; 13:77. [PMID: 38247635 PMCID: PMC10812752 DOI: 10.3390/antibiotics13010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Healthcare-associated infections (HAIs) pose significant challenges in healthcare systems, with preventable surveillance playing a crucial role. Traditional surveillance, although effective, is resource-intensive. The development of new technologies, such as artificial intelligence (AI), can support traditional surveillance in analysing an increasing amount of health data or meeting patient needs. We conducted a scoping review, following the PRISMA-ScR guideline, searching for studies of new digital technologies applied to the surveillance, control, and prevention of HAIs in hospitals and LTCFs published from 2018 to 4 November 2023. The literature search yielded 1292 articles. After title/abstract screening and full-text screening, 43 articles were included. The mean study duration was 43.7 months. Surgical site infections (SSIs) were the most-investigated HAI and machine learning was the most-applied technology. Three main themes emerged from the thematic analysis: patient empowerment, workload reduction and cost reduction, and improved sensitivity and personalization. Comparative analysis between new technologies and traditional methods showed different population types, with machine learning methods examining larger populations for AI algorithm training. While digital tools show promise in HAI surveillance, especially for SSIs, challenges persist in resource distribution and interdisciplinary integration in healthcare settings, highlighting the need for ongoing development and implementation strategies.
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Affiliation(s)
- Guglielmo Arzilli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
| | - Erica De Vita
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
| | - Milena Pasquale
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
| | - Luca Marcello Carloni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
| | - Marzia Pellegrini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
| | - Martina Di Giacomo
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
| | - Enrica Esposito
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
| | - Andrea Davide Porretta
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
- University Hospital of Pisa, 56124, Pisa, Italy
| | - Caterina Rizzo
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (G.A.); (M.P.); (L.M.C.); (M.P.); (M.D.G.); (E.E.); (A.D.P.); (C.R.)
- University Hospital of Pisa, 56124, Pisa, Italy
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17
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Shankarnarayan SA, Charlebois DA. Machine learning to identify clinically relevant Candida yeast species. Med Mycol 2024; 62:myad134. [PMID: 38130236 DOI: 10.1093/mmy/myad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
Fungal infections, especially due to Candida species, are on the rise. Multi-drug resistant organisms such as Candida auris are difficult and time consuming to identify accurately. Machine learning is increasingly being used in health care, especially in medical imaging. In this study, we evaluated the effectiveness of six convolutional neural networks (CNNs) to identify four clinically important Candida species. Wet-mounted images were captured using bright field live-cell microscopy followed by separating single-cells, budding-cells, and cell-group images which were then subjected to different machine learning algorithms (custom CNN, VGG16, ResNet50, InceptionV3, EfficientNetB0, and EfficientNetB7) to learn and predict Candida species. Among the six algorithms tested, the InceptionV3 model performed best in predicting Candida species from microscopy images. All models performed poorly on raw images obtained directly from the microscope. The performance of all models increased when trained on single and budding cell images. The InceptionV3 model identified budding cells of C. albicans, C. auris, C. glabrata (Nakaseomyces glabrata), and C. haemulonii in 97.0%, 74.0%, 68.0%, and 66.0% cases, respectively. For single cells of C. albicans, C. auris, C. glabrata, and C. haemulonii InceptionV3 identified 97.0%, 73.0%, 69.0%, and 73.0% cases, respectively. The sensitivity and specificity of InceptionV3 were 77.1% and 92.4%, respectively. Overall, this study provides proof of the concept that microscopy images from wet-mounted slides can be used to identify Candida yeast species using machine learning quickly and accurately.
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Affiliation(s)
| | - Daniel A Charlebois
- Department of Physics, University of Alberta, Edmonton, Alberta, T6G-2E1, Canada
- Department of Physics, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G-2E9, Canada
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18
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Crisan CV, Van Tyne D, Goldberg JB. The type VI secretion system of the emerging pathogen Stenotrophomonas maltophilia complex has antibacterial properties. mSphere 2023; 8:e0058423. [PMID: 37975665 PMCID: PMC10732056 DOI: 10.1128/msphere.00584-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Infections with the opportunistic pathogen Stenotrophomonas maltophilia complex can be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the type VI secretion system (T6SS) allows S. maltophilia complex to eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal of S. maltophilia complex. The T6SS may confer survival advantages to S. maltophilia complex isolates in polymicrobial communities in both environmental settings and during infections.
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Affiliation(s)
- Cristian V. Crisan
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children’s Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joanna B. Goldberg
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children’s Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
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19
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Doyle H, Valek AL, Murillo T, Ayres AM, Slaughter J, Berg ML, Snyder GM. A novel approach to correcting attribution of Clostridioides difficile in a healthcare setting. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e246. [PMID: 38156213 PMCID: PMC10753511 DOI: 10.1017/ash.2023.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 12/30/2023]
Abstract
Objective To describe a novel attribution metric estimating the causal source location of healthcare-associated Clostridioides difficile and compare it with the current US National Healthcare Safety Network (NHSN) surveillance reporting standard. Design Quality improvement study. Setting Two acute care facilities. Methods A novel attribution metric assigned days of attribution to locations where patients were located for 14 days before and the day of their C. difficile diagnosis. We correlated the NHSN-assigned unit attribution with the novel attribution measure and compared the proportion of attribution assigned to inpatient units. Results During a 30-month period, there were 727 NHSN C. difficile healthcare-associated infections (HAIs) and 409 non-HAIs; the novel metric attributed 17,034 days. The correlation coefficients for NHSN and novel attributions among non-ICU units were 0.79 (95% CI, 0.76-0.82) and 0.74 (95% CI, 0.70-0.78) and among ICU units were 0.70 (95% CI, 0.63-0.76) and 0.69 (95% CI, 0.60-0.77) at facilities A and B, respectively. The distribution of difference in percent attribution showed higher inpatient unit attribution using NHSN measure than the novel attribution metric: 38% of ICU units and 15% of non-ICU units in facility A, and 20% of ICU units and 25% of non-ICU units in facility B had a median difference >0; no inpatient units showed a greater attribution using the novel attribution metric. Conclusion The novel attribution metric shifts attribution from inpatient units to other settings and correlates modestly with NHSN methodology of attribution. If validated, the attribution metric may more accurately target C. difficile reduction efforts.
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Affiliation(s)
- Hunter Doyle
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Abby L. Valek
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Theresa Murillo
- Department of Infection Prevention and Control, UPMC Senior Communities, Pittsburgh, PA, USA
| | - Ashley M. Ayres
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Julie Slaughter
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Madeline L. Berg
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Graham M. Snyder
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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20
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Cho ST, Mills EG, Griffith MP, Nordstrom HR, McElheny CL, Harrison LH, Doi Y, Van Tyne D. Evolution of extended-spectrum β-lactamase-producing ST131 Escherichia coli at a single hospital over 15 years. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571174. [PMID: 38168243 PMCID: PMC10760032 DOI: 10.1101/2023.12.11.571174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Escherichia coli belonging to sequence type ST131 constitute a globally distributed pandemic lineage that causes multidrug-resistant extra-intestinal infections. ST131 E. coli frequently produce extended-spectrum β-lactamases (ESBLs), which confer resistance to many β-lactam antibiotics and make infections difficult to treat. We sequenced the genomes of 154 ESBL-producing E. coli clinical isolates belonging to the ST131 lineage from patients at the University of Pittsburgh Medical Center (UPMC) between 2004 and 2018. Isolates belonged to the well described ST131 clades A (8%), B (3%), C1 (33%), and C2 (54%). An additional four isolates belonged to another distinct subclade within clade C and encoded genomic characteristics that have not been previously described. Time-dated phylogenetic analysis estimated that the most recent common ancestor (MRCA) for all clade C isolates from UPMC emerged around 1989, consistent with previous studies. We identified multiple genes potentially under selection in clade C, including the cell wall assembly gene ftsI, the LPS biosynthesis gene arnC, and the yersiniabactin uptake receptor fyuA. Diverse ESBL genes belonging to the blaCTX-M, blaSHV, and blaTEM families were identified; these genes were found at varying numbers of loci and in variable numbers of copies across isolates. Analysis of ESBL flanking regions revealed diverse mobile elements that varied by ESBL type. Overall, our findings show that ST131 subclades C1 and C2 dominated and were stably maintained among patients in the same hospital and uncover possible signals of ongoing adaptation within the clade C ST131 lineage.
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Affiliation(s)
- Shu-Ting Cho
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Emma G. Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lee H. Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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21
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Sundermann AJ, Griffith M, Rangachar Srinivasa V, Ereifej D, Waggle K, Van Tyne D, Snyder GM, Pasculle AW, Bartholow T, Pless L, Harrison LH. Environmental contamination of postmortem blood cultures detected by whole-genome sequencing surveillance. Infect Control Hosp Epidemiol 2023; 44:2103-2105. [PMID: 37615108 PMCID: PMC10755148 DOI: 10.1017/ice.2023.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/09/2023] [Accepted: 07/22/2023] [Indexed: 08/25/2023]
Affiliation(s)
- Alexander J. Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Marissa Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Vatsala Rangachar Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Deena Ereifej
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kady Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - A. William Pasculle
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Clinical Microbiology Laboratory, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - Tanner Bartholow
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lora Pless
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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22
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Rose R, Feehan A, Lain BN, Ashcraft D, Nolan DJ, Velez-Climent L, Huston C, LaFleur T, Rosenthal S, Fogel GB, Miele L, Pankey G, Garcia-Diaz J, Lamers SL. Whole-genome sequencing of carbapenem-resistant Enterobacterales isolates in southeast Louisiana reveals persistent genetic clusters spanning multiple locations. J Infect Public Health 2023; 16:1911-1917. [PMID: 37866269 DOI: 10.1016/j.jiph.2023.10.013] [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: 05/01/2023] [Revised: 10/02/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions in the Ochsner Health network in southeast Louisiana. METHODS Short genomic reads were generated using Illumina sequencing and assembled for each isolate. Isolates were classified as Enterobacter spp. (n = 20), Klebsiella spp. (n = 30), and Escherichia coli (n = 1) and grouped into 19 different multi-locus sequence types (MLST). Species and patient-specific core genomes were constructed representing ∼50% of the chromosomal genome. RESULTS We identified two sets of patients with genetically related infections; in both cases, the related isolates were collected > 6 months apart, and in one case, the isolates were collected in different locations. On the other hand, we identified four sets of patients with isolates of the same species collected within 21 days from the same location; however, none had genetically related infections. Genes associated with resistance to carbapenem drugs (blaKPC and/or blaCTX-M-15) were found in 76% of the isolates. We found three blaKPC variants (blaKPC-2, blaKPC-3, and blaKPC-4) associated with four different Enterobacter MLST variants, and two blaKPC variants (blaKPC-2, blaKPC-3) associated with seven different Klebsiella MLST variants. CONCLUSIONS Molecular surveillance is increasingly becoming a powerful tool to understand bacterial spread in both community and clinical settings. This study provides evidence that genetically related infections in clinical settings do not necessarily reflect temporal associations, and vice versa. Our results also highlight the regional genomic and resistance diversity within related bacterial lineages.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA.
| | - Amy Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | | | | | | | | | - Lucio Miele
- Translational Science and Genetics at LSU Health Science Center, New Orleans, LA, USA
| | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA
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23
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Krishnan J, Woods CW, Holodniy M, Nicholson BP, Marconi VC, Ammons MCB, Jinadatha C, Pyarajan S, Wang-Rodriguez J, Garcia AP, Battles JK. Nationwide Genomic Surveillance and Response to COVID-19: The VA SeqFORCE and SeqCURE Consortiums. Fed Pract 2023; 40:S44-S47. [PMID: 38577303 PMCID: PMC10988620 DOI: 10.12788/fp.0417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Background The US Department of Veterans Affairs (VA) has dedicated significant resources toward countering the COVID-19 pandemic. Sequencing for Research Clinical and Epidemiology (SeqFORCE) and Sequencing Collaborations United for Research and Epidemiology (SeqCURE) were developed as clinical and research consortiums, respectively, focused on the genetic COVID-19 surveillance. Observations Through genetic sequencing, VA SeqFORCE and SeqCURE collaborations contributed to the COVID-19 pandemic response and scientific understanding. Future directions for each program include the assessment of the unique impact of COVID-19 on the veteran population, as well as the adaptation of these programs to future infectious disease threats. We foresee the use of these established platforms beyond infectious diseases. Conclusions VA SeqFORCE and SeqCURE were established as clinical and research programs dedicated to sequencing COVID-19 as part of ongoing clinical and surveillance efforts. In the future, we anticipate that having these programs embedded within the largest integrated health care system in the US will enable the study of pathogens and pandemics beyond COVID-19 and at an unprecedented scale. The investment in these programs will form an integral part of our nation's response to emerging infectious diseases, with future applications to precision medicine and beyond.
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Affiliation(s)
- Jay Krishnan
- Duke University School of Medicine, Durham, North Carolina
- Durham Veterans Affairs Medical Center, North Carolina
| | - Christopher W. Woods
- Duke University School of Medicine, Durham, North Carolina
- Durham Veterans Affairs Medical Center, North Carolina
| | - Mark Holodniy
- Public Health National Program Office, Department of Veterans Affairs, Washington, DC
- Stanford University, California
| | - Bradly P. Nicholson
- Durham Veterans Affairs Medical Center, North Carolina
- Institute for Medical Research, Durham Veterans Affairs Medical Center, North Carolina
| | - Vincent C. Marconi
- Atlanta Veterans Affairs Medical Center, Decatur, Georgia
- Emory University School of Medicine and Rollins School of Public Health, Atlanta, Georgia
| | - Mary Cloud B. Ammons
- Idaho Veterans Research and Education Foundation & Boise Veterans Affairs Medical Center
| | - Chetan Jinadatha
- Central Texas Veterans Health Care System, Temple
- Texas A&M University School of Medicine, Bryan
| | - Saiju Pyarajan
- Center for Data and Computational Sciences, Veterans Affairs Boston Healthcare System, Massachusetts
| | - Jessica Wang-Rodriguez
- National Pathology and Laboratory Medicine Service, Department of Veterans Affairs, Washington, DC
| | - Amanda P. Garcia
- Office of Research and Development, Department of Veterans Affairs, Washington, DC
| | - Jane K. Battles
- Office of Research and Development, Department of Veterans Affairs, Washington, DC
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24
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Sundermann AJ, Penzelik J, Ayres A, Snyder GM, Harrison LH. Sensitivity of National Healthcare Safety Network definitions to capture healthcare-associated transmission identified by whole-genome sequencing surveillance. Infect Control Hosp Epidemiol 2023; 44:1663-1665. [PMID: 36974518 PMCID: PMC10533730 DOI: 10.1017/ice.2023.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/29/2023]
Abstract
The National Healthcare Safety Network (NHSN) definitions are critical for standardizing healthcare-associated infection surveillance in US healthcare facilities. However, their use in accurately detecting healthcare-associated transmission (HAT) has not been measured. Using whole-genome sequencing surveillance data, we show that the NHSN has a sensitivity of 44.4% in detecting HAT.
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Affiliation(s)
- Alexander J Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joseph Penzelik
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - Ashley Ayres
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - Graham M Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - Lee H Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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25
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Theodosiou AA, Read RC. Artificial intelligence, machine learning and deep learning: Potential resources for the infection clinician. J Infect 2023; 87:287-294. [PMID: 37468046 DOI: 10.1016/j.jinf.2023.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Artificial intelligence (AI), machine learning and deep learning (including generative AI) are increasingly being investigated in the context of research and management of human infection. OBJECTIVES We summarise recent and potential future applications of AI and its relevance to clinical infection practice. METHODS 1617 PubMed results were screened, with priority given to clinical trials, systematic reviews and meta-analyses. This narrative review focusses on studies using prospectively collected real-world data with clinical validation, and on research with translational potential, such as novel drug discovery and microbiome-based interventions. RESULTS There is some evidence of clinical utility of AI applied to laboratory diagnostics (e.g. digital culture plate reading, malaria diagnosis, antimicrobial resistance profiling), clinical imaging analysis (e.g. pulmonary tuberculosis diagnosis), clinical decision support tools (e.g. sepsis prediction, antimicrobial prescribing) and public health outbreak management (e.g. COVID-19). Most studies to date lack any real-world validation or clinical utility metrics. Significant heterogeneity in study design and reporting limits comparability. Many practical and ethical issues exist, including algorithm transparency and risk of bias. CONCLUSIONS Interest in and development of AI-based tools for infection research and management are undoubtedly gaining pace, although the real-world clinical utility to date appears much more modest.
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Affiliation(s)
- Anastasia A Theodosiou
- Clinical and Experimental Sciences and NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom.
| | - Robert C Read
- Clinical and Experimental Sciences and NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom
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26
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Shields RK, Kline EG, Squires KM, Van Tyne D, Doi Y. In vitro activity of cefiderocol against Pseudomonas aeruginosa demonstrating evolved resistance to novel β-lactam/β-lactamase inhibitors. JAC Antimicrob Resist 2023; 5:dlad107. [PMID: 37795425 PMCID: PMC10546814 DOI: 10.1093/jacamr/dlad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023] Open
Abstract
Background Cefiderocol demonstrates excellent activity against MDR Pseudomonas aeruginosa; however, the activity against isolates from patients previously treated with β-lactam agents is unknown. We aimed to determine the activity of cefiderocol against P. aeruginosa collected before and after treatment with traditional β-lactams and new β-lactam/β-lactamase inhibitors. Methods Cefiderocol MICs were determined in triplicate in iron-depleted cation-adjusted Mueller-Hinton broth and compared with β-lactam MICs tested by standard methods. All isolates underwent WGS analysis to identify mutations associated with resistance. Results One hundred and seventy-eight P. aeruginosa isolates were evaluated; 48% (86/178) were non-susceptible to ceftazidime/avibactam, ceftolozane/tazobactam and/or imipenem/relebactam. The cefiderocol MIC50 and MIC90 were 0.12 and 1 mg/L, respectively. Median cefiderocol MICs did not vary against isolates classified as MDR, XDR, or those non-susceptible to ceftazidime/avibactam, ceftolozane/tazobactam and/or imipenem/relebactam when compared with non-MDR isolates. Against isolates collected from patients previously treated with ceftolozane/tazobactam, cefiderocol MICs were increased 4-fold compared with baseline. Cross-resistance to cefiderocol was identified in 21% (3/14) of patients who developed treatment-emergent resistance to ceftolozane/tazobactam. Overall, 6% (11/178) of isolates demonstrated cefiderocol MICs ≥2 mg/L, which were disproportionately collected from patients previously treated with ceftolozane/tazobactam (73%; 8/11). Isolates with reduced cefiderocol susceptibility harboured mutations in ampC, tonB-dependent receptors, the response regulator pirR and ftsI. Conclusions Cefiderocol demonstrates excellent in vitro activity against P. aeruginosa isolates exposed to other novel β-lactam agents; however, some exceptions were identified. Cross-resistance between cefiderocol and ceftolozane/tazobactam was evident, but not with ceftazidime/avibactam or imipenem/relebactam. Reduced cefiderocol susceptibility was mediated by mutations in ampC and tonB-dependent receptors.
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Affiliation(s)
- Ryan K Shields
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Innovative Antimicrobial Therapy, University of Pittsburgh, Pittsburgh, PA, USA
- Antibiotic Management Program, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ellen G Kline
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin M Squires
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daria Van Tyne
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Innovative Antimicrobial Therapy, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yohei Doi
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Innovative Antimicrobial Therapy, University of Pittsburgh, Pittsburgh, PA, USA
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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27
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Boral J, Pınarlık F, Ekinci G, Can F, Ergönül Ö. Does Emerging Carbapenem Resistance in Acinetobacter baumannii Increase the Case Fatality Rate? Systematic Review and Meta-Analysis. Infect Dis Rep 2023; 15:564-575. [PMID: 37888136 PMCID: PMC10606343 DOI: 10.3390/idr15050055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND In the era of rising carbapenem resistance, we aimed to investigate the change in mortality rate and positivity of carbapenemase genes in Acinetobacter baumannii. METHODS Preferred Reporting Items for Systematic Review (PRISMA) guidelines were adopted in this systematic review. Our literature search included the Cochrane Library, Pubmed, Scopus, Web of Science, Medline, Tubitak TR Dizin, and Harman databases for studies dating back from 2003 to 2023 reporting bloodstream A. baumannii infections in Türkiye. A simple linear regression model was used to determine the association between resistance, mortality, and time. RESULTS A total of 1717 studies were identified through a literature search, and 21 articles were selected based on the availability of the data regarding mortality and resistance rate (four articles) or the molecular epidemiology of carbapenem-resistant A. baumannii (17 articles) in Türkiye. From 2007 to 2018, the carbapenem resistance rate increased (p = 0.025). The OXA-23 and OXA-58 positivities were inversely correlated (p = 0.025). CONCLUSIONS Despite the emergence of carbapenem resistance, mortality did not increase in parallel, which may be due to improved medical advancements or the fitness cost of bacteria upon prolonged antimicrobial exposure. Therefore, we suggest further global research with the foresight to assess clonal relatedness that might affect the carbapenem resistance rate.
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Affiliation(s)
- Jale Boral
- Graduate School of Health Sciences, Koç University, Istanbul 34010, Türkiye; (J.B.)
- Koç University İşBank Center for Infectious Diseases, Koç University Hospital (KUISCID), Istanbul 34010, Türkiye;
| | - Fatihan Pınarlık
- Graduate School of Health Sciences, Koç University, Istanbul 34010, Türkiye; (J.B.)
- Koç University İşBank Center for Infectious Diseases, Koç University Hospital (KUISCID), Istanbul 34010, Türkiye;
| | - Güz Ekinci
- Graduate School of Health Sciences, Koç University, Istanbul 34010, Türkiye; (J.B.)
- Koç University İşBank Center for Infectious Diseases, Koç University Hospital (KUISCID), Istanbul 34010, Türkiye;
| | - Füsun Can
- Koç University İşBank Center for Infectious Diseases, Koç University Hospital (KUISCID), Istanbul 34010, Türkiye;
- Department of Medical Microbiology, School of Medicine, Koç University, Istanbul 34010, Türkiye
| | - Önder Ergönül
- Koç University İşBank Center for Infectious Diseases, Koç University Hospital (KUISCID), Istanbul 34010, Türkiye;
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Koç University, Istanbul 34010, Türkiye
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28
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Raabe NJ, Valek AL, Griffith MP, Mills E, Waggle K, Srinivasa VR, Ayres AM, Bradford C, Creager H, Pless LL, Sundermann AJ, Van Tyne D, Snyder GM, Harrison LH. Genomic Epidemiologic Investigation of a Multispecies Hospital Outbreak of NDM-5-Producing Enterobacterales Infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.31.23294545. [PMID: 37693518 PMCID: PMC10491379 DOI: 10.1101/2023.08.31.23294545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background New Delhi metallo-β-lactamase (NDM) represents an emergent mechanism of carbapenem resistance associated with high mortality and limited antimicrobial treatment options. Because the blaNDM resistance gene is often carried on plasmids, traditional infection prevention and control (IP&C) surveillance methods like speciation, antimicrobial resistance testing, and reactive whole genome sequencing (WGS) may not detect plasmid transfer in multispecies outbreaks. Methods Initial outbreak detection of NDM-producing Enterobacterales identified at an acute care hospital occurred via traditional IP&C methods and was supplemented by real-time WGS surveillance, which was performed weekly using the Illumina platform. To resolve NDM-encoding plasmids, we performed long-read Oxford Nanopore sequencing and constructed hybrid assemblies using Illumina and Nanopore sequencing data. Reports of relatedness between NDM-producing organisms and reactive WGS for suspected outbreaks were shared with the IP&C team for assessment and intervention. Findings We observed a multispecies outbreak of NDM-5-producing Enterobacterales isolated from 15 patients between February 2021 and February 2023. The 19 clinical and surveillance isolates sequenced included seven bacterial species and each encoded the same NDM-5 plasmid, which showed high homology to NDM plasmids previously observed in Asia. WGS surveillance and epidemiologic investigation characterized ten horizontal plasmid transfer events and six bacterial transmission events between patients housed in varying hospital units. Transmission prevention focused on enhanced observation and adherence to basic infection prevention measures. Interpretation Our investigation revealed a complex, multispecies outbreak of NDM that involved multiple plasmid transfer and bacterial transmission events, increasing the complexity of outbreak identification and transmission prevention. Our investigation highlights the utility of combining traditional IP&C and prospective genomic methods in identifying and containing plasmid-associated outbreaks. Funding This work was funded in part by the National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH) (R01AI127472) (R21AI1783691).
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Affiliation(s)
- Nathan J. Raabe
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, Pennsylvania 15261, USA
| | - Abby L. Valek
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, 200 Lothrop Street, Pittsburgh, Pennsylvania 15213, USA
| | - Marissa P. Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
| | - Emma Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
| | - Kady Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, Pennsylvania 15261, USA
| | - Vatsala Rangachar Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
| | - Ashley M. Ayres
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, 200 Lothrop Street, Pittsburgh, Pennsylvania 15213, USA
| | - Claire Bradford
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, 200 Lothrop Street, Pittsburgh, Pennsylvania 15213, USA
| | - Hannah Creager
- Department of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street Pittsburgh, PA 15213
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop St, S-417 BST, Pittsburgh, PA 15261
| | - Lora L. Pless
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
| | - Alexander J. Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, 200 Lothrop Street, Pittsburgh, Pennsylvania 15213, USA
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, Pennsylvania 15261, USA
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Crisan CV, Van Tyne D, Goldberg JB. The Type VI Secretion System of the Emerging Pathogen Stenotrophomonas maltophilia has Antibacterial Properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542968. [PMID: 37398041 PMCID: PMC10312562 DOI: 10.1101/2023.05.30.542968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Antagonistic behaviors between bacterial cells can have profound effects on microbial populations and disease outcomes. Polymicrobial interactions may be mediated by contact-dependent proteins with antibacterial properties. The Type VI Secretion System (T6SS) is a macromolecular weapon used by Gram-negative bacteria to translocate proteins into adjacent cells. The T6SS is used by pathogens to escape immune cells, eliminate commensal bacteria, and facilitate infection. Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that causes a wide range of infections in immunocompromised patients and infects the lungs of patients with cystic fibrosis. Infections with the bacterium can be deadly and are challenging to treat because many isolates are multidrug-resistant. We found that globally dispersed S. maltophilia clinical and environmental strains possess T6SS genes. We demonstrate that the T6SS of an S. maltophilia patient isolate is active and can eliminate other bacteria. Furthermore, we provide evidence that the T6SS contributes to the competitive fitness of S. maltophilia against a co-infecting Pseudomonas aeruginosa isolate, and that the T6SS alters the cellular organization of S. maltophilia and P. aeruginosa co-cultures. This study expands our knowledge of the mechanisms employed by S. maltophilia to secrete antibacterial proteins and compete against other bacteria. IMPORTANCE Infections with the opportunistic pathogen Stenotrophomonas maltophilia can be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the T6SS allows S. maltophilia to eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal of S. maltophilia . The T6SS may confer survival advantages to S. maltophilia isolates in polymicrobial communities in both environmental settings and during infections.
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Avershina E, Khezri A, Ahmad R. Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12040781. [PMID: 37107143 PMCID: PMC10135054 DOI: 10.3390/antibiotics12040781] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Science, UiT The Arctic University of Norway, Hansine Hansens veg, 189019 Tromsø, Norway
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Sundermann AJ, Srinivasa VR, Mills EG, Griffith MP, Waggle KD, Ayres AM, Pless L, Snyder GM, Harrison LH, Van Tyne D. Two artificial tears outbreak-associated cases of XDR Pseudomonas aeruginosa detected through whole genome sequencing-based surveillance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.11.23288417. [PMID: 37131775 PMCID: PMC10153325 DOI: 10.1101/2023.04.11.23288417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We describe two cases of XDR Pseudomonas aeruginosa infection caused by a strain of public health concern recently associated with a nationwide outbreak of contaminated artificial tears. Both cases were detected through database review of genomes in the Enhanced Detection System for Hospital-Associated Transmission (EDS-HAT), a routine genome sequencing-based surveillance program. We generated a high-quality reference genome for the outbreak strain from one of the case isolates from our center and examined the mobile elements encoding bla VIM-80 and bla GES-9 carbapenemases. We then used publicly available P. aeruginosa genomes to explore the genetic relatedness and antimicrobial resistance genes of the outbreak strain.
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Affiliation(s)
- Alexander J. Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vatsala Rangachar Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emma G. Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marissa P. Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kady D. Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ashley M. Ayres
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania, USA
| | - Lora Pless
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania, USA
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Branch-Elliman W, Sundermann AJ, Wiens J, Shenoy ES. The future of automated infection detection: Innovation to transform practice (Part III/III). ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e26. [PMID: 36865708 PMCID: PMC9972533 DOI: 10.1017/ash.2022.333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 06/18/2023]
Abstract
Current methods of emergency-room-based syndromic surveillance were insufficient to detect early community spread of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in the United States, which slowed the infection prevention and control response to the novel pathogen. Emerging technologies and automated infection surveillance have the potential to improve upon current practice standards and to revolutionize the practice of infection detection, prevention and control both inside and outside of healthcare settings. Genomics, natural language processing, and machine learning can be leveraged to improve identification of transmission events and aid and evaluate outbreak response. In the near future, automated infection detection strategies can be used to advance a true "Learning Healthcare System" that will support near-real-time quality improvement efforts and advance the scientific basis for the practice of infection control.
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Affiliation(s)
- Westyn Branch-Elliman
- Section of Infectious Diseases, Department of Medicine, Veterans’ Affairs (VA) Boston Healthcare System, Boston, Massachusetts
- VA Boston Center for Healthcare Organization and Implementation Research (CHOIR), Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Alexander J. Sundermann
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jenna Wiens
- Division of Computer Science and Engineering, University of Michigan, Ann Arbor, Michigan
| | - Erica S. Shenoy
- Harvard Medical School, Boston, Massachusetts
- Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
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Metagenomic Antimicrobial Susceptibility Testing from Simulated Native Patient Samples. Antibiotics (Basel) 2023; 12:antibiotics12020366. [PMID: 36830277 PMCID: PMC9952719 DOI: 10.3390/antibiotics12020366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Genomic antimicrobial susceptibility testing (AST) has been shown to be accurate for many pathogens and antimicrobials. However, these methods have not been systematically evaluated for clinical metagenomic data. We investigate the performance of in-silico AST from clinical metagenomes (MG-AST). Using isolate sequencing data from a multi-center study on antimicrobial resistance (AMR) as well as shotgun-sequenced septic urine samples, we simulate over 2000 complicated urinary tract infection (cUTI) metagenomes with known resistance phenotype to 5 antimicrobials. Applying rule-based and machine learning-based genomic AST classifiers, we explore the impact of sequencing depth and technology, metagenome complexity, and bioinformatics processing approaches on AST accuracy. By using an optimized metagenomics assembly and binning workflow, MG-AST achieved balanced accuracy within 5.1% of isolate-derived genomic AST. For poly-microbial infections, taxonomic sample complexity and relatedness of taxa in the sample is a key factor influencing metagenomic binning and downstream MG-AST accuracy. We show that the reassignment of putative plasmid contigs by their predicted host range and investigation of whole resistome capabilities improved MG-AST performance on poly-microbial samples. We further demonstrate that machine learning-based methods enable MG-AST with superior accuracy compared to rule-based approaches on simulated native patient samples.
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Talbot BM, Jacko NF, Petit RA, Pegues DA, Shumaker MJ, Read TD, David MZ. Unsuspected Clonal Spread of Methicillin-Resistant Staphylococcus aureus Causing Bloodstream Infections in Hospitalized Adults Detected Using Whole Genome Sequencing. Clin Infect Dis 2022; 75:2104-2112. [PMID: 35510945 DOI: 10.1093/cid/ciac339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/11/2022] [Accepted: 04/27/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Though detection of transmission clusters of methicillin-resistant Staphylococcus aureus (MRSA) infections is a priority for infection control personnel in hospitals, the transmission dynamics of MRSA among hospitalized patients with bloodstream infections (BSIs) has not been thoroughly studied. Whole genome sequencing (WGS) of MRSA isolates for surveillance is valuable for detecting outbreaks in hospitals, but the bioinformatic approaches used are diverse and difficult to compare. METHODS We combined short-read WGS with genotypic, phenotypic, and epidemiological characteristics of 106 MRSA BSI isolates collected for routine microbiological diagnosis from inpatients in 2 hospitals over 12 months. Clinical data and hospitalization history were abstracted from electronic medical records. We compared 3 genome sequence alignment strategies to assess similarity in cluster ascertainment. We conducted logistic regression to measure the probability of predicting prior hospital overlap between clustered patient isolates by the genetic distance of their isolates. RESULTS While the 3 alignment approaches detected similar results, they showed some variation. A gene family-based alignment pipeline was most consistent across MRSA clonal complexes. We identified 9 unique clusters of closely related BSI isolates. Most BSIs were healthcare associated and community onset. Our logistic model showed that with 13 single-nucleotide polymorphisms, the likelihood that any 2 patients in a cluster had overlapped in a hospital was 50%. CONCLUSIONS Multiple clusters of closely related MRSA isolates can be identified using WGS among strains cultured from BSI in 2 hospitals. Genomic clustering of these infections suggests that transmission resulted from a mix of community spread and healthcare exposures long before BSI diagnosis.
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Affiliation(s)
- Brooke M Talbot
- Graduate School of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
| | - Natasia F Jacko
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert A Petit
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David A Pegues
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Margot J Shumaker
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Timothy D Read
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Michael Z David
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Enterococci enhance Clostridioides difficile pathogenesis. Nature 2022; 611:780-786. [PMID: 36385534 PMCID: PMC9691601 DOI: 10.1038/s41586-022-05438-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/11/2022] [Indexed: 11/17/2022]
Abstract
Enteric pathogens are exposed to a dynamic polymicrobial environment in the gastrointestinal tract1. This microbial community has been shown to be important during infection, but there are few examples illustrating how microbial interactions can influence the virulence of invading pathogens2. Here we show that expansion of a group of antibiotic-resistant, opportunistic pathogens in the gut-the enterococci-enhances the fitness and pathogenesis of Clostridioides difficile. Through a parallel process of nutrient restriction and cross-feeding, enterococci shape the metabolic environment in the gut and reprogramme C. difficile metabolism. Enterococci provide fermentable amino acids, including leucine and ornithine, which increase C. difficile fitness in the antibiotic-perturbed gut. Parallel depletion of arginine by enterococci through arginine catabolism provides a metabolic cue for C. difficile that facilitates increased virulence. We find evidence of microbial interaction between these two pathogenic organisms in multiple mouse models of infection and patients infected with C. difficile. These findings provide mechanistic insights into the role of pathogenic microbiota in the susceptibility to and the severity of C. difficile infection.
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Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance. mSystems 2022; 7:e0138421. [PMID: 35695507 PMCID: PMC9238379 DOI: 10.1128/msystems.01384-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here, we describe the diversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of bacterial isolate genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 groups of related species. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal-component analysis of accessory genes (PCA-A). Core genome genetic distances and rates of evolution varied among species, which has practical implications for defining shared ancestry during outbreaks and for our broader understanding of the origins of bacterial strains and species. Finally, antimicrobial resistance genes and putative mobile genetic elements were frequently observed, and our systematic analysis revealed patterns of occurrence across the different species sampled from our hospital. Overall, this study shows how understanding the population structure of diverse pathogens circulating in a single health care setting can improve the discriminatory power of genomic epidemiology studies and can help define the processes leading to strain and species differentiation. IMPORTANCE Hospitalized patients are at increased risk of becoming infected with antibiotic-resistant organisms. We used whole-genome sequencing to survey and compare over 3,000 clinical bacterial isolates collected from hospitalized patients at a large medical center over a 2-year period. We identified nearly 100 different bacterial species, which we divided into 14 different groups of related species. When we examined how genetic relatedness differed between species, we found that different species were likely evolving at different rates within our hospital. This is significant because the identification of bacterial outbreaks in the hospital currently relies on genetic similarity cutoffs, which are often applied uniformly across organisms. Finally, we found that antibiotic resistance genes and mobile genetic elements were abundant and were shared among the bacterial isolates we sampled. Overall, this study provides an in-depth view of the genomic diversity and evolutionary processes of bacteria sampled from hospitalized patients, as well as genetic similarity estimates that can inform hospital outbreak detection and prevention efforts.
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Brady MB, VonVille HM, White JF, Martin EM, Raabe NJ, Slaughter JM, Snyder GM. Transmission visualizations of healthcare infection clusters: A scoping review. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2022; 2:e92. [PMID: 36483443 PMCID: PMC9726548 DOI: 10.1017/ash.2022.237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 06/17/2023]
Abstract
OBJECTIVE To evaluate infectious pathogen transmission data visualizations in outbreak publications. DESIGN Scoping review. METHODS Medline was searched for outbreak investigations of infectious diseases within healthcare facilities that included ≥1 data visualization of transmission using data observable by an infection preventionist showing temporal and/or spatial relationships. Abstracted data included the nature of the cluster(s) (pathogen, scope of transmission, and individuals involved) and data visualization characteristics including visualization type, transmission elements, and software. RESULTS From 1,957 articles retrieved, we analyzed 30 articles including 37 data visualizations. The median cluster size was 20.5 individuals (range, 7-1,963) and lasted a median of 214 days (range, 12-5,204). Among the data visualization types, 10 (27%) were floor-plan transmission maps, 6 (16%) were timelines, 11 (30%) were transmission networks, 3 (8%) were Gantt charts, 4 (11%) were cluster map, and 4 (11%) were other types. In addition, 26 data visualizations (70%) contained spatial elements, 26 (70%) included person type, and 19 (51%) contained time elements. None of the data visualizations contained contagious periods and only 2 (5%) contained symptom-onset date. CONCLUSIONS The data visualizations of healthcare-associated infectious disease outbreaks in the systematic review were diverse in type and visualization elements, though no data visualization contained all elements important to deriving hypotheses about transmission pathways. These findings aid in understanding the visualizing transmission pathways by describing essential elements of the data visualization and will inform the creation of a standardized mapping tool to aid in earlier initiation of interventions to prevent transmission.
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Affiliation(s)
- Mya B. Brady
- Department of Infection Prevention and Control, UPMC Presbyterian–Shadyside, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Helena M. VonVille
- University of Pittsburgh Health Sciences Library System, Pittsburgh, Pennsylvania
| | - Joseph F. White
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania
| | - Elise M. Martin
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Veterans’ Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | - Nathan J. Raabe
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania
| | - Julie M. Slaughter
- Department of Infection Prevention and Control, UPMC Presbyterian–Shadyside, Pittsburgh, Pennsylvania
| | - Graham M. Snyder
- Department of Infection Prevention and Control, UPMC Presbyterian–Shadyside, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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