1
|
Alam MT, Stern SR, Frison D, Taylor K, Tagliamonte MS, Nazmus SS, Paisie T, Hilliard NB, Jones RG, Iovine NM, Cherabuddi K, Mavian C, Myers P, Salemi M, Ali A, Morris JG. Seafood-Associated Outbreak of ctx-Negative Vibrio mimicus Causing Cholera-Like Illness, Florida, USA. Emerg Infect Dis 2023; 29:2141-2144. [PMID: 37735754 PMCID: PMC10521627 DOI: 10.3201/eid2910.230486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Vibrio mimicus caused a seafood-associated outbreak in Florida, USA, in which 4 of 6 case-patients were hospitalized; 1 required intensive care for severe diarrhea. Strains were ctx-negative but carried genes for other virulence determinants (hemolysin, proteases, and types I-IV and VI secretion systems). Cholera toxin-negative bacterial strains can cause cholera-like disease.
Collapse
Affiliation(s)
| | | | - Devin Frison
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Katie Taylor
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Massimiliano S. Tagliamonte
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - S. Sakib Nazmus
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Taylor Paisie
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Nicole B. Hilliard
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Riley G. Jones
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Nicole M. Iovine
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Kartik Cherabuddi
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Carla Mavian
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Paul Myers
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Marco Salemi
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | | | | |
Collapse
|
2
|
Couto-Rodriguez M, Danko DC, Jirau Serrano XO, Paisie T, Papciak JC, Szollosi E, Mason CE, Otto C, O’Hara NB, Nagy-Szakal D. 322. Clinical-Grade Metagenomics in Urinary Tract Infections: Improving Performance of Next-Generation Sequencing Assays Using Internal Controls and Machine Learning. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
Shotgun sequencing-based metagenomics is a useful approach to profiling microbiomes in environmental and patient samples. In a clinical setting, metagenomic techniques have the advantage of identifying organisms, which cannot be readily cultured or confirmed by other techniques. We have developed a clinical-grade, streamlined metagenomics-based pipeline that includes regulatory compliant method considerations, such as an internal control followed by a machine-based learning (ML) process to identify pathogens in urine samples.
Methods
We built an optimized novel end-to-end NGS assay pipeline that harnesses pathogen-specific genome data to detect bacterial species. We processed de-identified clinical urine specimens, collected from patients symptomatic for urinary tract infection (UTI). This workflow includes an IPC, QIACube-MDx extraction, library preparation and Illumina NextSeq 550 sequencing and a novel interpretable ML based analytic approach, Biotia-DX. Clinical culture results and qPCR were used as a baseline for the assay to train the ML model and to establish accuracy relative to the clinical standard of care.
Results
We clinically validated over 40 key uropathogens and conducted clinical studies of specificity, intra/inter reproducibility, accuracy in urine specimens (n=300), and limit of detection in E. coli, K. pneumoniae, P. mirabilis, S. aureus, E. faecalis and Candida. Additionally, the implementation of an internal control coupled with our Biotia-DX software provides an accurate (F1 score 94.3%) and highly sensitive clinical grade diagnostic tool.
Conclusion
Urine has historically presented a challenge for diagnostics via culturing, with a high rate of culture-negative results (∼30% on average). We improved the clinical utility of an NGS urine assay by leveraging an IPC and ML software. This decreased the rate of false positive species called in a sample relative to other NGS techniques and allows for greater sensitivity and taxonomic specificity. This assay may be especially useful for low colony-count or negative-culture samples to diagnose and guide patient treatment.
Disclosures
Mara Couto-Rodriguez, MS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company David C. Danko, PhD, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company Xavier O. Jirau Serrano, MS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company Taylor Paisie, MS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company John C. Papciak, BS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company Eszter Szollosi, BS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company Christopher E. Mason, PhD, Biotia Inc.: Advisor/Consultant|Biotia Inc.: Board Member|Biotia Inc.: Ownership Interest Caitlin Otto, PhD, D(ABMM), Biotia Inc.: Advisor/Consultant Niamh B. O'Hara, PhD, Biotia Inc.: Board Member|Biotia Inc.: Ownership Interest Dorottya Nagy-Szakal, MD PhD, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company|Biotia Inc.: Stocks/Bonds.
Collapse
|
3
|
Alexiev I, Mavian C, Paisie T, Ciccozzi M, Dimitrova R, Gancheva A, Kostadinova A, Seguin-Devaux C, Salemi M. Analysis of the Origin and Dissemination of HIV-1 Subtype C in Bulgaria. Viruses 2022; 14:v14020263. [PMID: 35215855 PMCID: PMC8875591 DOI: 10.3390/v14020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-1 subtype C is the most abundant strain of HIV-1 infections worldwide and was found in the first known patients diagnosed with HIV/AIDS in Bulgaria in 1986. However, there is limited information on the molecular-epidemiological characteristics of this strain in the epidemic of the country. In this study, we analyze the evolutionary history of the introduction and dissemination of HIV-1 subtype C in Bulgaria using global phylogenetic analysis, Bayesian coalescent-based approach, and molecular clock methods. All available samples with HIV-1 subtype C from individuals diagnosed with HIV/AIDS between 1986 and 2017 were analyzed. Men and women were equally represented, and 24.3% of patients reported being infected abroad. The global phylogenetic analysis indicated multiple introductions of HIV-1 subtype C from various countries of the world. The reconstruction of a Bayesian time-scaled phylogenies showed that several Bulgarian strains segregated together in clusters, while others were intermixed in larger clades containing strains isolated from both European and non-European countries. The time-scale of HIV-1 subtype C introductions in Bulgaria demonstrates the early introduction of these viruses in the country. Our in-depth phylogenetic and phylogeographic analyses are compatible with a scenario of multiple early introductions in the country followed by limited local distribution in the subsequent years. HIV-1 subtype C was introduced in the early years of the epidemic, originating from different countries of the world. Due to the comprehensive measures for prevention and control in the early years of the epidemic in Bulgaria, HIV-1 subtype C was not widely disseminated among the general population of the country.
Collapse
Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
- Correspondence: ; Tel.: +359-2-9318071
| | - Carla Mavian
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Taylor Paisie
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico, 00128 Rome, Italy;
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Luxembourg, Luxembourg;
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| |
Collapse
|
4
|
White SK, Mavian C, Elbadry MA, Beau De Rochars VM, Paisie T, Telisma T, Salemi M, Lednicky JA, Morris JG. Detection and phylogenetic characterization of arbovirus dual-infections among persons during a chikungunya fever outbreak, Haiti 2014. PLoS Negl Trop Dis 2018; 12:e0006505. [PMID: 29851952 PMCID: PMC5997359 DOI: 10.1371/journal.pntd.0006505] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/12/2018] [Accepted: 05/07/2018] [Indexed: 01/01/2023] Open
Abstract
In the context of recent arbovirus epidemics, questions about the frequency of simultaneous infection of patients with different arbovirus species have been raised. In 2014, a major Chikungunya virus (CHIKV) epidemic impacted the Caribbean and South America. As part of ongoing screening of schoolchildren presenting with acute undifferentiated febrile illness in rural Haiti, we used RT-PCR to identify CHIKV infections in 82 of 100 children with this diagnosis during May-August 2014. Among these, eight were infected with a second arbovirus: six with Zika virus (ZIKV), one with Dengue virus serotype 2, and one with Mayaro virus (MAYV). These dual infections were only detected following culture of the specimen, suggesting low viral loads of the co-infecting species. Phylogenetic analyses indicated that the ZIKV and MAYV strains differ from those detected later in 2014 and 2015, respectively. Moreover, CHIKV and ZIKV strains from co-infected patients clustered monophyletically in their respective phylogeny, and clock calibration traced back the common ancestor of each clade to an overlapping timeframe of introduction of these arboviruses onto the island.
Collapse
Affiliation(s)
- Sarah K. White
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Maha A. Elbadry
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
| | - Valery Madsen Beau De Rochars
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Health Services Research, Management and Policy, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
| | - Taylor Paisie
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Taina Telisma
- Christianville Foundation School Clinic, Gressier, Haiti
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - John A. Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
| | - J. Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| |
Collapse
|
5
|
Blohm GM, Lednicky JA, Márquez M, White SK, Loeb JC, Pacheco CA, Nolan DJ, Paisie T, Salemi M, Rodríguez-Morales AJ, Glenn Morris J, Pulliam JRC, Paniz-Mondolfi AE. Evidence for Mother-to-Child Transmission of Zika Virus Through Breast Milk. Clin Infect Dis 2018; 66:1120-1121. [PMID: 29300859 PMCID: PMC6019007 DOI: 10.1093/cid/cix968] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/30/2017] [Indexed: 11/13/2022] Open
Abstract
Zikavirus (ZIKV) is an emerging viral pathogen that continues to spread throughout different regions of the world. Herein we report a case that provides further evidence that ZIKV transmission can occur through breastfeeding by providing a detailed clinical, genomic, and virological case-based description.
Collapse
Affiliation(s)
- Gabriela M Blohm
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
- Emerging Pathogens Institute, University of Florida, Gainesville
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Universidad Centroccidental Lisandro Alvarado, Lara, Venezuela
| | - John A Lednicky
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
- Emerging Pathogens Institute, University of Florida, Gainesville
| | - Marilianna Márquez
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Universidad Centroccidental Lisandro Alvarado, Lara, Venezuela
- Health Sciences Department, College of Medicine, Universidad Centroccidental Lisandro Alvarado, Lara, Venezuela
| | - Sarah K White
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
- Emerging Pathogens Institute, University of Florida, Gainesville
| | - Julia C Loeb
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
- Emerging Pathogens Institute, University of Florida, Gainesville
| | | | - David J Nolan
- Emerging Pathogens Institute, University of Florida, Gainesville
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville
- Bioinfoexperts LLC, Thibodaux, Louisiana
| | - Taylor Paisie
- Emerging Pathogens Institute, University of Florida, Gainesville
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville
| | - Alfonso J Rodríguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Colombia
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville
- Department of Internal Medicine, Division of Infectious Diseases and Global Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville
| | - Juliet R C Pulliam
- Emerging Pathogens Institute, University of Florida, Gainesville
- DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch, South Africa
| | - Alberto E Paniz-Mondolfi
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Universidad Centroccidental Lisandro Alvarado, Lara, Venezuela
- Department of Infectious Diseases and Tropical Medicine, Instituto Diagnóstico Barquisimeto, IDB Biomedical Research Institute, Lara, Barquisimeto, Venezuela
| |
Collapse
|
6
|
Bonny TS, Driver JP, Paisie T, Salemi M, Morris JG, Shender LA, Smith L, Enloe C, Oxenrider K, Gore JA, Loeb JC, Wu CY, Lednicky JA. Detection of Alphacoronavirus vRNA in the Feces of Brazilian Free-Tailed Bats (Tadarida brasiliensis) from a Colony in Florida, USA. Diseases 2017; 5:diseases5010007. [PMID: 28933360 PMCID: PMC5456339 DOI: 10.3390/diseases5010007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/18/2017] [Accepted: 02/23/2017] [Indexed: 12/23/2022] Open
Abstract
Bats are natural reservoirs of coronaviruses and other viruses with zoonotic potential. Florida has indigenous non-migratory populations of Brazilian free-tailed bats (Tadarida brasiliensis) that mostly roost in colonies in artificial structures. Unlike their counterparts in Brazil and Mexico, the viruses harbored by the Florida bats have been underexplored. We report the detection of an alphacoronavirus RNA-dependent RNA polymerase (RdRp) gene sequence in the feces of two of 19 different T. brasiliensis that were capture/release bats that had been evaluated for overall health. The RdRp sequence is similar but not identical to previously detected sequences in the feces of two different species of bats (T. brasiliensis and Molossus molossus) in Brazil. In common with the experience of others doing similar work, attempts to isolate the virus in cell cultures were unsuccessful. We surmise that this and highly related alphacoronavirus are carried by Brazilian free-tailed bats living in a wide eco-spatial region. As various coronaviruses (CoVs) that affect humans emerged from bats, our study raises the question whether CoVs such as the one detected in our work are yet-to-be-detected pathogens of humans and animals other than bats.
Collapse
Affiliation(s)
- Tania S Bonny
- Department of Environmental and Global Health, University of Florida, Gainesville, FL 32610, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
| | - John P Driver
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611-0910, USA.
| | - Taylor Paisie
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
- Genetics and Genomics, Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA.
| | - John Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
- Department of Medicine, University of Florida, Gainesville, FL 32610-0277, USA.
| | - Lisa A Shender
- Florida Fish and Wildlife Conservation Commission, Gainesville, FL 32601, USA.
| | - Lisa Smith
- Florida Fish and Wildlife Conservation Commission, Gainesville, FL 32601, USA.
| | - Carolyn Enloe
- Florida Fish and Wildlife Conservation Commission, Gainesville, FL 32601, USA.
| | - Kevin Oxenrider
- Florida Fish and Wildlife Conservation Commission, Gainesville, FL 32601, USA.
| | - Jeffery A Gore
- Florida Fish and Wildlife Conservation Commission, Gainesville, FL 32601, USA.
| | - Julia C Loeb
- Department of Environmental and Global Health, University of Florida, Gainesville, FL 32610, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Chang-Yu Wu
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - John A Lednicky
- Department of Environmental and Global Health, University of Florida, Gainesville, FL 32610, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
7
|
Cherabuddi K, Iovine NM, Shah K, White SK, Paisie T, Salemi M, Morris JG, Lednicky JA. Zika and Chikungunya virus co-infection in a traveller returning from Colombia, 2016: virus isolation and genetic analysis. JMM Case Rep 2016; 3:e005072. [PMID: 28348794 PMCID: PMC5343122 DOI: 10.1099/jmmcr.0.005072] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/15/2016] [Indexed: 11/18/2022] Open
Abstract
Introduction: Zikavirus (ZIKV) and Chikungunyavirus (CHIKV) can share the same mosquito vector, and co-infections by these viruses can occur in humans. While infections with these viruses share commonalities, CHIKV is unique in causing arthritis and arthralgias that may persist for a year or more. These infections are commonly diagnosed by RT–PCR-based methods during the acute phase of infection. Even with the high specificity and sensitivity characteristic of PCR, false negatives can occur, highlighting the need for additional diagnostic methods for confirmation. Case presentation: On her return to the USA, a traveller to Colombia, South America developed an illness consistent with Zika, Chikungunya and/or Dengue. RT-PCR of her samples was positive only for ZIKV. However, arthralgias persisted for months, raising concerns about co-infection with CHIKV or Mayaro viruses. Cell cultures inoculated with her original clinical samples demonstrated two types of cytopathic effects, and both ZIKV and CHIKV were identified in the supernatants. On phylogenetic analyses, both viruses were found to be related to strains found in Colombia. Conclusion: These findings highlight the need to consider CHIKV co-infection in patients with prolonged rheumatological symptoms after diagnosis with ZIKV, and the usefulness of cell culture as an amplification step for low-viremia blood and other samples.
Collapse
Affiliation(s)
- Kartikeya Cherabuddi
- Division of Infectious Diseases and Global Health, Department of Medicine, College of Medicine, University of Florida , Gainesville, FL , USA
| | - Nicole M Iovine
- Division of Infectious Diseases and Global Health, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Kairav Shah
- Division of Infectious Diseases and Global Health, Department of Medicine, College of Medicine, University of Florida , Gainesville, FL , USA
| | - Sarah K White
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Taylor Paisie
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - J Glenn Morris
- Division of Infectious Diseases and Global Health, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - John A Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| |
Collapse
|