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Sanchez-Vicente S, Tokarz R. Tick-Borne Co-Infections: Challenges in Molecular and Serologic Diagnoses. Pathogens 2023; 12:1371. [PMID: 38003835 PMCID: PMC10674443 DOI: 10.3390/pathogens12111371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/14/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
Co-infections are a poorly understood aspect of tick-borne diseases. In the United States alone, nineteen different tick-borne pathogens have been identified. The majority of these agents are transmitted by only two tick species, Ixodes scapularis and Amblyomma americanum. Surveillance studies have demonstrated the presence of multiple pathogens in individual ticks suggesting a risk of polymicrobial transmission to humans. However, relatively few studies have explored this relationship and its impact on human disease. One of the key factors for this deficiency are the intrinsic limitations associated with molecular and serologic assays employed for the diagnosis of tick-borne diseases. Limitations in the sensitivity, specificity and most importantly, the capacity for inclusion of multiple agents within a single assay represent the primary challenges for the accurate detection of polymicrobial tick-borne infections. This review will focus on outlining these limitations and discuss potential solutions for the enhanced diagnosis of tick-borne co-infections.
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Affiliation(s)
- Santiago Sanchez-Vicente
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA;
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA;
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
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Briese T, Tokarz R, Bateman L, Che X, Guo C, Jain K, Kapoor V, Levine S, Hornig M, Oleynik A, Quan PL, Wong WH, Williams BL, Vernon SD, Klimas NG, Peterson DL, Montoya JG, Ian Lipkin W. A multicenter virome analysis of blood, feces, and saliva in myalgic encephalomyelitis/chronic fatigue syndrome. J Med Virol 2023; 95:e28993. [PMID: 37526404 DOI: 10.1002/jmv.28993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is estimated to affect 0.4%-2.5% of the global population. Most cases are unexplained; however, some patients describe an antecedent viral infection or response to antiviral medications. We report here a multicenter study for the presence of viral nucleic acid in blood, feces, and saliva of patients with ME/CFS using polymerase chain reaction and high-throughput sequencing. We found no consistent group-specific differences other than a lower prevalence of anelloviruses in cases compared to healthy controls. Our findings suggest that future investigations into viral infections in ME/CFS should focus on adaptive immune responses rather than surveillance for viral gene products.
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Affiliation(s)
- Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Alexandra Oleynik
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Wai H Wong
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | | | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, USA
- Bruce W. Carter Miami Veterans Affairs Medical Center, Geriatric Research Education and Research Center, Miami, Florida, USA
| | | | - Jose G Montoya
- Jack S. Remington Laboratory for Specialty Diagnostics of Toxoplasmosis, Palo Alto Medical Foundation, Palo Alto, USA
| | - Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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3
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Cummings MJ, Bakamutumaho B, Jain K, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Nayiga I, Kyebambe S, Che X, Sameroff S, Tokarz R, Wong W, Postler TS, Larsen MH, Lipkin WI, Lutwama JJ, O’Donnell MR. Brief Report: Detection of Urine Lipoarabinomannan Is Associated With Proinflammatory Innate Immune Activation, Impaired Host Defense, and Organ Dysfunction in Adults With Severe HIV-Associated Tuberculosis in Uganda. J Acquir Immune Defic Syndr 2023; 93:79-85. [PMID: 36701194 PMCID: PMC10079575 DOI: 10.1097/qai.0000000000003159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND The immunopathology of disseminated HIV-associated tuberculosis (HIV/TB), a leading cause of critical illness and death among persons living with HIV in sub-Saharan Africa, is incompletely understood. Reflective of hematogenously disseminated TB, detection of lipoarabinomannan (LAM) in urine is associated with greater bacillary burden and poor outcomes in adults with HIV/TB. METHODS We determined the relationship between detection of urine TB-LAM, organ dysfunction, and host immune responses in a prospective cohort of adults hospitalized with severe HIV/TB in Uganda. Generalized additive models were used to analyze the association between urine TB-LAM grade and concentrations of 14 soluble immune mediators. Whole-blood RNA-sequencing data were used to compare transcriptional profiles between patients with high- vs. low-grade TB-LAM results. RESULTS Among 157 hospitalized persons living with HIV, 40 (25.5%) had positive urine TB-LAM testing. Higher TB-LAM grade was associated with more severe physiologic derangement, organ dysfunction, and shock. Adjusted generalized additive models showed that higher TB-LAM grade was significantly associated with higher concentrations of mediators reflecting proinflammatory innate and T-cell activation and chemotaxis (IL-8, MIF, MIP-1β/CCL4, and sIL-2Ra/sCD25). Transcriptionally, patients with higher TB-LAM grades demonstrated multifaceted impairment of antibacterial defense including reduced expression of genes encoding cytotoxic and autophagy-related proteins and impaired cross-talk between innate and cell-mediated immune effectors. CONCLUSIONS Our findings add to emerging data suggesting pathobiological relationships between LAM, TB dissemination, innate cell activation, and evasion of host immunity in severe HIV/TB. Further translational studies are needed to elucidate the role for immunomodulatory therapies, in addition to optimized anti-TB treatment, in this often critically ill population.
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Affiliation(s)
- Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Immunizable Diseases Unit, Uganda Virus Research Institute, Entebbe, Uganda
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joyce Namulondo
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Moses Muwanga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | | | - Irene Nayiga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Stephen Kyebambe
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Wai Wong
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S. Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michelle H. Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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Grassmann AA, Tokarz R, Golino C, McLain MA, Groshong AM, Radolf JD, Caimano MJ. BosR and PlzA reciprocally regulate RpoS function to sustain Borrelia burgdorferi in ticks and mammals. J Clin Invest 2023; 133:e166710. [PMID: 36649080 PMCID: PMC9974103 DOI: 10.1172/jci166710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
The RNA polymerase alternative σ factor RpoS in Borrelia burgdorferi (Bb), the Lyme disease pathogen, is responsible for programmatic-positive and -negative gene regulation essential for the spirochete's dual-host enzootic cycle. RpoS is expressed during tick-to-mammal transmission and throughout mammalian infection. Although the mammalian-phase RpoS regulon is well described, its counterpart during the transmission blood meal is unknown. Here, we used Bb-specific transcript enrichment by tick-borne disease capture sequencing (TBDCapSeq) to compare the transcriptomes of WT and ΔrpoS Bb in engorged nymphs and following mammalian host-adaptation within dialysis membrane chambers. TBDCapSeq revealed dramatic changes in the contours of the RpoS regulon within ticks and mammals and further confirmed that RpoS-mediated repression is specific to the mammalian-phase of Bb's enzootic cycle. We also provide evidence that RpoS-dependent gene regulation, including repression of tick-phase genes, is required for persistence in mice. Comparative transcriptomics of engineered Bb strains revealed that the Borrelia oxidative stress response regulator (BosR), a noncanonical Fur family member, and the cyclic diguanosine monophosphate (c-di-GMP) effector PlzA reciprocally regulate the function of RNA polymerase complexed with RpoS. BosR is required for RpoS-mediated transcription activation and repression in addition to its well-defined role promoting transcription of rpoS by the RNA polymerase alternative σ factor RpoN. During transmission, ligand-bound PlzA antagonizes RpoS-mediated repression, presumably acting through BosR.
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Affiliation(s)
| | - Rafal Tokarz
- Center for Infection and Immunity and
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Caroline Golino
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | | | - Ashley M. Groshong
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
- Department of Molecular Biology and Biophysics
- Department of Genetics and Genome Sciences, and
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Melissa J. Caimano
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
- Department of Molecular Biology and Biophysics
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Cummings MJ, Bakamutumaho B, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Jain K, Postler TS, Muwanga M, Nsereko C, Nayiga I, Kyebambe S, Che X, Sameroff S, Tokarz R, Shah SS, Larsen MH, Lipkin WI, Lutwama JJ, O’Donnell MR. HIV infection drives pro-inflammatory immunothrombotic pathway activation and organ dysfunction among adults with sepsis in Uganda. AIDS 2023; 37:233-245. [PMID: 36355913 PMCID: PMC9780191 DOI: 10.1097/qad.0000000000003410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND The global burden of sepsis is concentrated in high HIV-burden settings in sub-Saharan Africa (SSA). Despite this, little is known about the immunopathology of sepsis in persons with HIV (PWH) in the region. We sought to determine the influence of HIV on host immune responses and organ dysfunction among adults hospitalized with suspected sepsis in Uganda. DESIGN Prospective cohort study. METHODS We compared organ dysfunction and 30-day outcome profiles of PWH and those without HIV. We quantified 14 soluble immune mediators, reflective of key domains of sepsis immunopathology, and performed whole-blood RNA-sequencing on samples from a subset of patients. We used propensity score methods to match PWH and those without HIV by demographics, illness duration, and clinical severity, and compared immune mediator concentrations and gene expression profiles across propensity score-matched groups. RESULTS Among 299 patients, 157 (52.5%) were PWH (clinical stage 3 or 4 in 80.3%, 67.7% with known HIV on antiretroviral therapy). PWH presented with more severe physiologic derangement and shock, and had higher 30-day mortality (34.5% vs. 10.2%; P < 0.001). Across propensity score-matched groups, PWH exhibited greater pro-inflammatory immune activation, including upregulation of interleukin (IL)-6, IL-8, IL-15, IL-17 and HMGB1 signaling, with concomitant T-cell exhaustion, prothrombotic pathway activation, and angiopoeitin-2-related endothelial dysfunction. CONCLUSIONS Sepsis-related organ dysfunction and mortality in Uganda disproportionately affect PWH, who demonstrate exaggerated activation of multiple immunothrombotic and metabolic pathways implicated in sepsis pathogenesis. Further investigations are needed to refine understanding of sepsis immunopathology in PWH, particularly mechanisms amenable to therapeutic manipulation.
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Affiliation(s)
- Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Immunizable Diseases Unit, Uganda Virus Research Institute, Entebbe, Uganda
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joyce Namulondo
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S. Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Moses Muwanga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | | | - Irene Nayiga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Stephen Kyebambe
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Shivang S. Shah
- Division of Infectious Diseases, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michelle H. Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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Bajwa WI, Tsynman L, Egizi AM, Tokarz R, Maestas LP, Fonseca DM. The Gulf Coast Tick, Amblyomma maculatum (Ixodida: Ixodidae), and Spotted Fever Group Rickettsia in the Highly Urbanized Northeastern United States. J Med Entomol 2022; 59:1434-1442. [PMID: 35639921 DOI: 10.1093/jme/tjac053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 06/15/2023]
Abstract
We report the multi-year collection of the Gulf Coast tick, Amblyomma maculatum Koch (Acaridae: Ixodida: Ixodidae) in Staten Island, New York City (NYC) as well as their detection in Brooklyn, NYC, and in Atlantic and Cumberland counties in southern New Jersey, USA. The first and most common detections were of adults, however in Freshkills Park on Staten Island larvae were also collected in a following year. The presence of larvae indicates that adults are successfully finding hosts in Staten Island. While it is still unknown how A. americanum reached Staten Island, immatures of this species often parasitize migratory birds, which are now often seen in Freshkills Park. We describe the landscape features of the area in Staten Island where populations were highest and larvae were detected, which could have facilitated the establishment of A. maculatum. Notably, we also report the presence of human pathogens Rickettsia parkeri in 5/10 (50%) of adults tested and R. felis in 1/24 (4.17%) of larvae tested. In addition to established populations in Staten Island we found evidence of A. maculatum in NJ and other NYC boroughs, suggesting current or future establishment is possible. The failure thus far to detect established populations in these areas may be due to inherent difficulties in detecting low density, spatially heterogeneous incipient populations, which could require targeted surveillance efforts for this species. We discuss the consequences to public health of the establishment of A. maculatum and detection of two additional rickettsial pathogens in the densely populated northeastern United States.
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Affiliation(s)
- Waheed I Bajwa
- New York City Department of Health and Mental Hygiene, 125 Worth Street, New York, NY 10013, USA
| | - Leonid Tsynman
- New York City Department of Health and Mental Hygiene, 125 Worth Street, New York, NY 10013, USA
| | - Andrea M Egizi
- Tick-Borne Disease Program, Monmouth County Mosquito Control Division, 1901 Wayside Road, Tinton Falls, NJ 07724, USA
- Center for Vector Biology, Rutgers University, 180 Jones Avenue, New Brunswick, NJ 08901, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - Lauren P Maestas
- Delaware Division of Fish and Wildlife, Mosquito Control Section, 2430 Old County Road, Newark, DE 19702, USA
| | - Dina M Fonseca
- Center for Vector Biology, Rutgers University, 180 Jones Avenue, New Brunswick, NJ 08901, USA
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Tagliafierro T, Joshi S, Sameroff S, Marques A, Dumler JS, Mishra N, Sanchez-Vicente S, Wormser GP, Marcos LA, Lipkin WI, Tokarz R. Detection of antibodies to Anaplasma phagocytophilum and Babesia microti using linear peptides. Ticks Tick Borne Dis 2022; 13:101999. [DOI: 10.1016/j.ttbdis.2022.101999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/03/2022] [Accepted: 06/25/2022] [Indexed: 11/30/2022]
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8
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Sanchez-Vicente S, Jain K, Tagliafierro T, Gokden A, Kapoor V, Guo C, Horn EJ, Lipkin WI, Tokarz R. Capture Sequencing Enables Sensitive Detection of Tick-Borne Agents in Human Blood. Front Microbiol 2022; 13:837621. [PMID: 35330765 PMCID: PMC8940530 DOI: 10.3389/fmicb.2022.837621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Assay sensitivity can be a limiting factor in the use of PCR as a tool for the detection of tick-borne pathogens in blood. We evaluated the performance of Tick-borne disease Capture Sequencing Assay (TBDCapSeq), a capture sequencing assay targeting tick-borne agents, to test 158 whole blood specimens obtained from the Lyme Disease Biobank. These included samples from 98 individuals with signs and symptoms of acute Lyme disease, 25 healthy individuals residing in Lyme disease endemic areas, and 35 samples collected from patients admitted to the Massachusetts General Hospital or referred to the infectious disease clinic. Compared to PCR, TBDCapSeq had better sensitivity and could identify infections with a wider range of tick-borne agents. TBDCapSeq identified a higher rate of samples positive for Borrelia burgdorferi (8 vs. 1 by PCR) and Babesia microti (26 vs. 15 by PCR). TBDCapSeq also identified previously unknown infections with Borrelia miyamotoi, Ehrlichia, and Rickettsia species. Overall, TBDCapSeq identified a pathogen in 43 samples vs. 23 using PCR, with four co-infections detected versus zero by PCR. We conclude that capture sequencing enables superior detection of tick-borne agents relative to PCR.
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Affiliation(s)
- Santiago Sanchez-Vicente
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Alper Gokden
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | | | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York City, NY, United States
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9
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Cummings MJ, Bakamutumaho B, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Sameroff S, Tokarz R, Wong W, Shah SS, Larsen MH, Lipkin WI, Lutwama JJ, O’Donnell MR. Multidimensional analysis of the host response reveals prognostic and pathogen-driven immune subtypes among adults with sepsis in Uganda. Crit Care 2022; 26:36. [PMID: 35130948 PMCID: PMC8822787 DOI: 10.1186/s13054-022-03907-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022] Open
Abstract
Background The global burden of sepsis is concentrated in sub-Saharan Africa, where severe infections disproportionately affect young, HIV-infected adults and high-burden pathogens are unique. In this context, poor understanding of sepsis immunopathology represents a crucial barrier to development of locally-effective treatment strategies. We sought to determine inter-individual immunologic heterogeneity among adults hospitalized with sepsis in a sub-Saharan African setting, and characterize associations between immune subtypes, infecting pathogens, and clinical outcomes. Methods Among a prospective observational cohort of 288 adults hospitalized with suspected sepsis in Uganda, we applied machine learning methods to 14 soluble host immune mediators, reflective of key domains of sepsis immunopathology (innate and adaptive immune activation, endothelial dysfunction, fibrinolysis), to identify immune subtypes in randomly-split discovery (N = 201) and internal validation (N = 87) sub-cohorts. In parallel, we applied similar methods to whole-blood RNA-sequencing data from a consecutive subset of patients (N = 128) to identify transcriptional subtypes, which we characterized using biological pathway and immune cell-type deconvolution analyses. Results Unsupervised clustering consistently identified two immune subtypes defined by differential activation of pro-inflammatory innate and adaptive immune pathways, with transcriptional evidence of concomitant CD56(-)/CD16( +) NK-cell expansion, T-cell exhaustion, and oxidative-stress and hypoxia-induced metabolic and cell-cycle reprogramming in the hyperinflammatory subtype. Immune subtypes defined by greater pro-inflammatory immune activation, T-cell exhaustion, and metabolic reprogramming were consistently associated with a high-prevalence of severe and often disseminated HIV-associated tuberculosis, as well as more extensive organ dysfunction, worse functional outcomes, and higher 30-day mortality. Conclusions Our results highlight unique host- and pathogen-driven features of sepsis immunopathology in sub-Saharan Africa, including the importance of severe HIV-associated tuberculosis, and reinforce the need to develop more biologically-informed treatment strategies in the region, particularly those incorporating immunomodulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13054-022-03907-3.
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10
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McGill F, Tokarz R, Thomson EC, Filipe A, Sameroff S, Jain K, Bhuva N, Ashraf S, Lipkin WI, Corless C, Pattabiraman C, Gibney B, Griffiths MJ, Geretti AM, Michael BD, Beeching NJ, McKee D, Hart IJ, Mutton K, Jung A, Miller A, Solomon T. Viral capture sequencing detects unexpected viruses in the cerebrospinal fluid of adults with meningitis. J Infect 2022; 84:499-510. [PMID: 34990710 DOI: 10.1016/j.jinf.2021.12.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Many patients with meningitis have no aetiology identified leading to unnecessary antimicrobials and prolonged hospitalisation. We used viral capture sequencing to identify possible pathogenic viruses in adults with community-acquired meningitis. METHODS Cerebrospinal fluid (CSF) from 73 patients was tested by VirCapSeq-VERT, a probe set designed to capture viral targets using high throughput sequencing. Patients were categorised as suspected viral meningitis - CSF pleocytosis, no pathogen identified (n = 38), proven viral meningitis - CSF pleocytosis with a pathogen identified (n = 15) or not meningitis - no CSF pleocytosis (n = 20). RESULTS VirCapSeq-VERT detected virus in the CSF of 16/38 (42%) of those with suspected viral meningitis, including twelve individual viruses. A potentially clinically relevant virus was detected in 9/16 (56%). Unexpectedly Toscana virus, rotavirus and Saffold virus were detected and assessed to be potential causative agents. CONCLUSION VirCapSeq-VERT increases the probability of detecting a virus. Using this agnostic approach we identified Toscana virus and, for the first time in adults, rotavirus and Saffold virus, as potential causative agents in adult meningitis. Further work is needed to determine the prevalence of atypical viral candidates as well as the clinical impact of using sequencing methods in real time. This knowledge can help to reduce antimicrobial use and hospitalisations leading to both patient and health system benefits.
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Affiliation(s)
- Fiona McGill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Leeds Teaching Hospitals NHS Trust, Leeds, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Emma C Thomson
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - Ana Filipe
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Nishit Bhuva
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Shirin Ashraf
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Caroline Corless
- Liverpool Specialist virology centre, Department of Infection and Immunity, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Chitra Pattabiraman
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; National Institute for Mental Health and Neurosciences, Bangalore, India
| | - Barry Gibney
- UK Health Security Agency (previously Public Health England), UK
| | - Michael J Griffiths
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Alder Hey Children's NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Anna Maria Geretti
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Faculty of Medicine, University of Rome Tor Vergata
| | - Benedict D Michael
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Nicholas J Beeching
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Liverpool School of Tropical Medicine, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - David McKee
- Central Manchester Foundation Trust, Manchester, UK
| | - Ian J Hart
- Liverpool Specialist virology centre, Department of Infection and Immunity, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Ken Mutton
- University of Manchester, Manchester, UK
| | - Agam Jung
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Alastair Miller
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tom Solomon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
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Abstract
Within the past 30 yr molecular assays have largely supplanted classical methods for detection of tick-borne agents. Enhancements provided by molecular assays, including speed, throughput, sensitivity, and specificity, have resulted in a rapid increase in the number of newly characterized tick-borne agents. The use of unbiased high throughput sequencing has enabled the prompt identification of new pathogens and the examination of tick microbiomes. These efforts have led to the identification of hundreds of new tick-borne agents in the last decade alone. However, little is currently known about the majority of these agents beyond their phylogenetic classification. Our article outlines the primary methods involved in tick-borne agent discovery and the current status of our understanding of tick-borne agent diversity.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
- Corresponding author, e-mail:
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY
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12
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Sameroff S, Tokarz R, Jain K, Oleynik A, Carrington CVF, Lipkin WI, Oura CAL. Novel quaranjavirus and other viral sequences identified from ticks parasitizing hunted wildlife in Trinidad and Tobago. Ticks Tick Borne Dis 2021; 12:101730. [PMID: 33957484 DOI: 10.1016/j.ttbdis.2021.101730] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023]
Abstract
Hunters are at a higher risk for exposure to zoonotic pathogens due to their close interactions with wildlife and arthropod vectors. In this study, high throughput sequencing was used to explore the viromes of two tick species, Amblyomma dissimile and Haemaphysalis juxtakochi, removed from hunted wildlife in Trinidad and Tobago. We identified sequences from 3 new viral species, from the viral families Orthomyxoviridae, Chuviridae and Tetraviridae in A. dissimile.
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Affiliation(s)
- Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, United States; School of Veterinary Medicine, The University of the West Indies, St. Augustine, Trinidad and Tobago.
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, United States; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, United States
| | - Alexandra Oleynik
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, United States
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, United States
| | - Christopher A L Oura
- School of Veterinary Medicine, The University of the West Indies, St. Augustine, Trinidad and Tobago
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13
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Tufts DM, Sameroff S, Tagliafierro T, Jain K, Oleynik A, VanAcker MC, Diuk-Wasser MA, Lipkin WI, Tokarz R. A metagenomic examination of the pathobiome of the invasive tick species, Haemaphysalis longicornis, collected from a New York City borough, USA. Ticks Tick Borne Dis 2020; 11:101516. [PMID: 32993936 DOI: 10.1016/j.ttbdis.2020.101516] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/09/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022]
Abstract
Haemaphysalis longicornis, the Asian longhorned tick, is an invasive tick species that has spread rapidly across the northeastern and southeastern regions of the United States in recent years. This invasive pest species, known to transmit several tick-borne pathogens in its native range, is a potential threat to wildlife, livestock, domestic animals, and humans. Questing larval (n = 25), nymph (n = 10), and adult (n = 123), along with host-derived adult (n = 25) H. longicornis ticks were collected from various locations on Staten Island, NY. The pathobiome of each specimen was examined using two different high throughput sequencing approaches, virus enrichment and shotgun metagenomics. An average of 45,828,061 total reads per sample were recovered from the virus enriched samples and an average of 11,381,144 total reads per sample were obtained using shotgun metagenomics. Aside from endogenous viral sequences, no viruses were identified through either approach. Through shotgun metagenomics, Coxiella-like bacteria, Legionella, Sphingomonas, and other bacterial species were recovered. The Coxiella-like agent was ubiquitous and present at high abundances in all samples, suggesting it may be an endosymbiont. The other bacterial agents are not known to be transmitted by ticks. From these analyses, H. longicornis do not appear to host any endemic human tick-borne pathogens in the New York City region.
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Affiliation(s)
- Danielle M Tufts
- Columbia University, Ecology, Evolution, and Environmental Biology Department, 1200 Amsterdam Ave, New York, NY 10027, United States.
| | - Stephen Sameroff
- Columbia University, Center for Infection and Immunity, Mailman School of Public Health, 722 West 168th Street, New York, NY 10032, United States
| | - Teresa Tagliafierro
- Columbia University, Center for Infection and Immunity, Mailman School of Public Health, 722 West 168th Street, New York, NY 10032, United States
| | - Komal Jain
- Columbia University, Center for Infection and Immunity, Mailman School of Public Health, 722 West 168th Street, New York, NY 10032, United States
| | - Alexandra Oleynik
- Columbia University, Center for Infection and Immunity, Mailman School of Public Health, 722 West 168th Street, New York, NY 10032, United States
| | - Meredith C VanAcker
- Columbia University, Ecology, Evolution, and Environmental Biology Department, 1200 Amsterdam Ave, New York, NY 10027, United States
| | - Maria A Diuk-Wasser
- Columbia University, Ecology, Evolution, and Environmental Biology Department, 1200 Amsterdam Ave, New York, NY 10027, United States
| | - W Ian Lipkin
- Columbia University, Center for Infection and Immunity, Mailman School of Public Health, 722 West 168th Street, New York, NY 10032, United States; Columbia University, Department of Epidemiology, Mailman School of Public Health, 722 West 168th Street, New York, NY 10032, United States
| | - Rafal Tokarz
- Columbia University, Center for Infection and Immunity, Mailman School of Public Health, 722 West 168th Street, New York, NY 10032, United States; Columbia University, Department of Epidemiology, Mailman School of Public Health, 722 West 168th Street, New York, NY 10032, United States
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14
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Tokarz R, Tagliafierro T, Ian Lipkin W, Marques AR. Characterization of a Monanema nematode in Ixodes scapularis. Parasit Vectors 2020; 13:371. [PMID: 32709241 PMCID: PMC7379800 DOI: 10.1186/s13071-020-04228-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 04/23/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022] Open
Abstract
Background Metagenomic studies have revealed the presence of a filarial nematode in Ixodes scapularis. The phylogeny of this agent, and its potential for human infection, are unknown. Methods We used existing metagenomic data from I. scapularis to determine the phylogeny of this tick-associated nematode and employed quantitative PCR to determine if the presence of this agent had an effect on the burden of Borrelia burgdorferi. We also developed a Luciferase Immunoprecipitation System assay using the Av33 antigen as a target to investigate the presence of antibodies against this nematode in 128 serum specimens from patients with Lyme disease and babesiosis. To demonstrate assay utility, we used 15 sera from patients with onchocerciasis as controls. Results We show that this agent is a new species in the genus Monanema and its presence in vector ticks does not impact the burden of B. burgdorferi. We did not detect IgG antibodies to this agent in 127 of 128 sera from patients with Lyme disease or babesiosis. One sample had reactivity above the threshold, but at the low-level equivalent to the least reactive onchocerciasis sera. This low positive signal could be a result of cross-reacting antibodies, antibodies from a previous infection with a filarial nematode, or, less likely, a exposure to the Ixodes scapularis-associated nematode. Conclusions We found no evidence that this nematode contributes to the spectrum of human tick-borne infections.![]()
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Adriana R Marques
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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15
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Cummings MJ, Tokarz R, Bakamutumaho B, Kayiwa J, Byaruhanga T, Owor N, Namagambo B, Wolf A, Mathema B, Lutwama JJ, Schluger NW, Lipkin WI, O'Donnell MR. Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda. Clin Infect Dis 2020; 68:1118-1125. [PMID: 30099510 PMCID: PMC6424078 DOI: 10.1093/cid/ciy656] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 08/06/2018] [Indexed: 12/16/2022] Open
Abstract
Background Precision public health is a novel set of methods to target disease prevention and mitigation interventions to high-risk subpopulations. We applied a precision public health strategy to syndromic surveillance for severe acute respiratory infection (SARI) in Uganda by combining spatiotemporal analytics with genomic sequencing to detect and characterize viral respiratory pathogens with epidemic potential. Methods Using a national surveillance network we identified patients with unexplained, influenza-negative SARI from 2010 to 2015. Spatiotemporal analyses were performed retrospectively to identify clusters of unexplained SARI. Within clusters, respiratory viruses were detected and characterized in naso- and oropharyngeal swab samples using a novel oligonucleotide probe capture (VirCapSeq-VERT) and high-throughput sequencing platform. Linkage to conventional epidemiologic strategies further characterized transmission dynamics of identified pathogens. Results Among 2901 unexplained SARI cases, 9 clusters were detected, accounting for 301 (10.4%) cases. Clusters were more likely to occur in urban areas and during biannual rainy seasons. Within detected clusters, we identified an unrecognized outbreak of measles-associated SARI; sequence analysis implicated cocirculation of endemic genotype B3 and genotype D4 likely imported from England. We also detected a likely nosocomial SARI cluster associated with a novel picobirnavirus most closely related to swine and dromedary viruses. Conclusions Using a precision approach to public health surveillance, we detected and characterized the genomics of vaccine-preventable and zoonotic respiratory viruses associated with clusters of severe respiratory infections in Uganda. Future studies are needed to assess the feasibility, scalability, and impact of applying similar approaches during real-time public health surveillance in low-income settings.
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Affiliation(s)
- Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York
| | - Rafal Tokarz
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York
| | | | - John Kayiwa
- National Influenza Center, Uganda Virus Research Institute, Entebbe
| | | | - Nicholas Owor
- National Influenza Center, Uganda Virus Research Institute, Entebbe
| | | | - Allison Wolf
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York
| | - Julius J Lutwama
- National Influenza Center, Uganda Virus Research Institute, Entebbe
| | - Neil W Schluger
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York.,Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York
| | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York
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16
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Carrión D, Kaali S, Kinney PL, Owusu-Agyei S, Chillrud S, Yawson AK, Quinn A, Wylie B, Ae-Ngibise K, Lee AG, Tokarz R, Iddrisu L, Jack DW, Asante KP. Examining the relationship between household air pollution and infant microbial nasal carriage in a Ghanaian cohort. Environ Int 2019; 133:105150. [PMID: 31518936 PMCID: PMC6868532 DOI: 10.1016/j.envint.2019.105150] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/19/2019] [Accepted: 09/02/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Pneumonia, a leading cause of childhood mortality, is associated with household air pollution (HAP) exposure. Mechanisms between HAP and pneumonia are poorly understood, but studies suggest that HAP may increase the likelihood of bacterial, instead of viral, pneumonia. We assessed the relationship between HAP and infant microbial nasal carriage among 260 infants participating in the Ghana Randomized Air Pollution and Health Study (GRAPHS). METHODS Data are from GRAPHS, a cluster-randomized controlled trial of cookstove interventions (improved biomass or LPG) versus the 3-stone (baseline) cookstove. Infants were surveyed for pneumonia during the first year of life and had routine personal exposure assessments. Nasopharyngeal swabs collected from pneumonia cases (n = 130) and healthy controls (n = 130) were analyzed for presence of 22 common respiratory microbes by MassTag polymerase chain reaction. Data analyses included intention-to-treat (ITT) comparisons of microbial species presence by study arm, and exposure-response relationships. RESULTS In ITT analyses, 3-stone arm participants had a higher mean number of microbial species than the LPG (LPG: 2.71, 3-stone: 3.34, p < 0.0001, n = 260). This difference was driven by increased bacterial (p < 0.0001) rather than viral species presence (non-significant). Results were pronounced in pneumonia cases and attenuated in healthy controls. Higher prevalence bacterial species were Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis. Exposure-response relationships did not yield significant associations between measured CO and nasal microbial carriage. CONCLUSIONS Our intention-to-treat findings are consistent with a link between HAP and bacterial nasal carriage. No relationships were found for viral carriage. Given the null results in exposure-response analysis, it is likely that a pollutant besides CO is driving these differences.
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Affiliation(s)
| | - Seyram Kaali
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Patrick L Kinney
- Department of Environmental Health, Boston University, Boston, USA
| | | | - Steven Chillrud
- Lamont-Doherty Earth Observatory, Columbia University, New York, USA
| | | | - Ashlinn Quinn
- Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Blair Wylie
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, USA
| | | | - Alison G Lee
- Icahn School of Medicine at Mount Sinai, New York, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Columbia University, New York, USA
| | | | - Darby W Jack
- Department of Environmental Health Sciences, Columbia University, New York, USA.
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17
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Tokarz R, Tagliafierro T, Caciula A, Mishra N, Thakkar R, Chauhan LV, Sameroff S, Delaney S, Wormser GP, Marques A, Lipkin WI. Identification of immunoreactive linear epitopes of Borrelia miyamotoi. Ticks Tick Borne Dis 2019; 11:101314. [PMID: 31636001 DOI: 10.1016/j.ttbdis.2019.101314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/30/2019] [Accepted: 10/13/2019] [Indexed: 11/19/2022]
Abstract
Borrelia miyamotoi is an emerging tick-borne spirochete transmitted by ixodid ticks. Current serologic assays for B. miyamotoi are impacted by genetic similarities to other Borrelia and limited understanding of optimal antigenic targets. In this study, we employed the TBD-Serochip, a peptide array platform, to identify new linear targets for serologic detection of B. miyamotoi. We examined a wide range of suspected B. miyamotoi antigens and identified 352 IgM and 91 IgG reactive peptides, with the majority mapping to variable membrane proteins. These included peptides within conserved fragments of variable membrane proteins that may have greater potential for differential diagnosis. We also identified reactive regions on FlaB, and demonstrate crossreactivity of B. burgdorferi s.l. C6 with a B. miyamotoi C6-like peptide. The panel of linear peptides identified in this study can be used to enhance serodiagnosis of B. miyamotoi.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States.
| | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Adrian Caciula
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Lokendra V Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shannon Delaney
- Department of Psychiatry, Columbia University, New York, NY, United States
| | - Gary P Wormser
- Division of Infectious Diseases, New York Medical College, Valhalla, NY, United States
| | - Adriana Marques
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
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18
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Tokarz R, Hyams JS, Mack DR, Boyle B, Griffiths AM, LeLeiko NS, Sauer CG, Shah S, Markowitz J, Baker SS, Rosh J, Baldassano RN, Kugathasan S, Walters T, Tagliafierro T, Sameroff S, Lee B, Che X, Oleynik A, Denson LA, Lipkin WI. Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis. Inflamm Bowel Dis 2019; 25:1656-1662. [PMID: 31112614 PMCID: PMC7108593 DOI: 10.1093/ibd/izz099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Viral infections have been suggested as possible triggers for the onset of ulcerative colitis (UC). METHODS We employed VirCapSeq-Vert, a high-throughput sequencing virus capture platform, to examine the stool virome of children with newly diagnosed moderate to severe UC. We surveyed fecal samples collected at presentation, after symptom remission, and from a control group diagnosed with irritable bowel syndrome. RESULTS Seventy subjects with UC (mean age 13 years, 45 had moderate symptoms, 25 had severe, 69 of 70 had a Mayo endoscopy subscore 2/3) were studied. We detected a wide range of animal viruses that were taxonomically classified into 12 viral families. A virus was present in 50% of fecal samples collected at presentation, 41% of samples collected after remission, and 40% of samples in our control group. The most frequently identified viruses were diet-based gyroviruses. The UC cohort had a significantly higher prevalence of anelloviruses compared with the control cohort. However, we did not identify a single virus that can be implicated in the onset of UC and did not find an association between UC disease severity and viral presence. CONCLUSION Presence of virus in stool was not associated with the onset of pediatric UC.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA,Address correspondence to: Rafal Tokarz, Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, New York, NY 10032, USA. E-mail:
| | | | - David R Mack
- Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | - Sapana Shah
- Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - James Markowitz
- Cohen Children’s Medical Center of New York, New Hyde Park, NY, USA
| | - Susan S Baker
- Women & Children’s Hospital of Buffalo WCHOB, Buffalo, NY, USA
| | - Joel Rosh
- Goryeb Children’s Hospital, Atlantic Health, Morristown, NJ, USA
| | | | | | | | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Bohyun Lee
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Alexandra Oleynik
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | | | - W Ian Lipkin
- Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
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19
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Mishra N, Ng J, Rakeman JL, Perry MJ, Centurioni DA, Dean AB, Price A, Thakkar R, Angus AG, Williamson P, Delwart E, Carrington C, Sahadeo N, Che X, Briese T, Tokarz R, Lipkin WI. One-step pentaplex real-time polymerase chain reaction assay for detection of zika, dengue, chikungunya, West nile viruses and a human housekeeping gene. J Clin Virol 2019; 120:44-50. [PMID: 31557664 DOI: 10.1016/j.jcv.2019.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/14/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Recent emergence of Zika virus (ZIKV), and the global spread of dengue (DENV), chikungunya (CHIKV) and West Nile viruses (WNV) raised urgent need of accurate and affordable molecular diagnosis of these clinically indistinguishable arboviral infections. OBJECTIVES We established a pentaplex real-time reverse transcription PCR (rRT-PCR) assay (CII-ArboViroPlex rRT-PCR) for specific and sensitive detection of the African and American genotypes of ZIKV, all four serotypes of DENV, CHIKV, WNV and a housekeeping gene as internal control in single reaction. STUDY DESIGN Specific primers and probe sets were designed for ZIKV, DENV, CHIKV, WNV and RNase P (housekeeping gene) and tested for in-vitro transcribed RNA standards, virus cultures, clinical samples positive for ZIKV, DENV, CHIKV and WNV and limit of detection (LOD) were determined for each. Results Using ten-fold serially diluted in-vitro transcribed RNA, CII- ArboViroPlex rRT-PCR assay has LOD of 100 RNA copies/reaction (Rn) for ZIKV in serum or urine, 100 RNA copies/Rn for DENV in serum, and 10 RNA copies/Rn for CHIKV and WNV in serum. LODs from sera spiked with quantitated viral stocks were 2.6 × 102 GEQ/Rn for ZIKV, 2.2 × 101 GEQ/Rn for DENV-1, 9.4 × 100 GEQ/Rn for DENV-2, 2.3 × 102 GEQ/Rn for DENV-3, 1.4 × 103 GEQ/Rn for DENV-4, 2.7 × 102 GEQ/Rn for CHIKV, and 1.05 × 101 GEQ/Rn for WNV. CONCLUSIONS The CII-ArboViroPlex rRT-PCR assay is a quantitative one-step pentaplex rRT-PCR assay for the molecular detection and differential diagnosis of ZIKV, DENV, CHIKV, WNV and a human housekeeping gene control in a single- PCR reaction.
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Affiliation(s)
- Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jennifer L Rakeman
- Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Michael J Perry
- Biodefense Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Dominick A Centurioni
- Biodefense Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Amy B Dean
- Virology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Andreina Garcia Angus
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - Eric Delwart
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Christine Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
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20
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Abstract
Tick-borne diseases have doubled in the last 12 years, and their geographic distribution has spread as well. The clinical spectrum of tick-borne diseases can range from asymptomatic to fatal infections, with a disproportionate incidence in children and the elderly. In the last few years, new agents have been discovered, and genetic changes have helped in the spread of pathogens and ticks. Polymicrobial infections, mostly in Ixodes scapularis, can complicate diagnostics and augment disease severity. Amblyomma americanum ticks have expanded their range, resulting in a dynamic and complex situation, possibly fueled by climate change. To document these changes, using molecular biology strategies for pathogen detection, an assessment of 12 microbes (9 pathogens and 3 symbionts) in three species of ticks was done in Suffolk County, New York. At least one agent was detected in 63% of I. scapularis ticksBorrelia burgdorferi was the most prevalent pathogen (57% in adults; 27% in nymphs), followed by Babesia microti (14% in adults; 15% in nymphs), Anaplasma phagocytophilum (14% in adults; 2% in nymphs), Borrelia miyamotoi (3% in adults), and Powassan virus (2% in adults). Polymicrobial infections were detected in 22% of I. scapularis ticks, with coinfections of B. burgdorferi and B. microti (9%) and of B. burgdorferi and A. phagocytophilum (7%). Three Ehrlichia species were detected in 4% of A. americanum ticks. The rickettsiae constituted the largest prokaryotic biomass of all the ticks tested and included Rickettsia amblyommatis, Rickettsia buchneri, and Rickettsia montanensis The high rates of polymicrobial infection in ticks present an opportunity to study the biological interrelationships of pathogens and their vectors.IMPORTANCE Tick-borne diseases have increased in prevalence in the United States and abroad. The reasons for these increases are multifactorial, but climate change is likely to be a major factor. One of the main features of the increase is the geographic expansion of tick vectors, notably Amblyomma americanum, which has brought new pathogens to new areas. The clinical spectrum of tick-borne diseases can range from asymptomatic to fatal infections, with a disproportionate incidence in children and the elderly. In addition, new pathogens that are cotransmitted by Ixodes scapularis have been discovered and have led to difficult diagnoses and to disease severity. Of these, Borrelia burgdorferi, the agent of Lyme disease, continues to be the most frequently transmitted pathogen. However, Babesia microti, Borrelia miyamotoi (another spirochete), Anaplasma phagocytophilum, and Powassan virus are frequent cotransmitted agents. Polymicrobial infection has important consequences for the diagnosis and management of tick-borne diseases.
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Affiliation(s)
- Santiago Sanchez-Vicente
- Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, USA
| | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - James L Coleman
- Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, USA
| | - Jorge L Benach
- Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
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21
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Mishra N, Ng TFF, Marine RL, Jain K, Ng J, Thakkar R, Caciula A, Price A, Garcia JA, Burns JC, Thakur KT, Hetzler KL, Routh JA, Konopka-Anstadt JL, Nix WA, Tokarz R, Briese T, Oberste MS, Lipkin WI. Antibodies to Enteroviruses in Cerebrospinal Fluid of Patients with Acute Flaccid Myelitis. mBio 2019; 10:e01903-19. [PMID: 31409689 PMCID: PMC6692520 DOI: 10.1128/mbio.01903-19] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023] Open
Abstract
Acute flaccid myelitis (AFM) has caused motor paralysis in >560 children in the United States since 2014. The temporal association of enterovirus (EV) outbreaks with increases in AFM cases and reports of fever, respiratory, or gastrointestinal illness prior to AFM in >90% of cases suggest a role for infectious agents. Cerebrospinal fluid (CSF) from 14 AFM and 5 non-AFM patients with central nervous system (CNS) diseases in 2018 were investigated by viral-capture high-throughput sequencing (VirCapSeq-VERT system). These CSF and serum samples, as well as multiple controls, were tested for antibodies to human EVs using peptide microarrays. EV RNA was confirmed in CSF from only 1 adult AFM case and 1 non-AFM case. In contrast, antibodies to EV peptides were present in CSF of 11 of 14 AFM patients (79%), significantly higher than controls, including non-AFM patients (1/5 [20%]), children with Kawasaki disease (0/10), and adults with non-AFM CNS diseases (2/11 [18%]) (P = 0.023, 0.0001, and 0.0028, respectively). Six of 14 CSF samples (43%) and 8 of 11 sera (73%) from AFM patients were immunoreactive to an EV-D68-specific peptide, whereas the three control groups were not immunoreactive in either CSF (0/5, 0/10, and 0/11; P = 0.008, 0.0003, and 0.035, respectively) or sera (0/2, 0/8, and 0/5; P = 0.139, 0.002, and 0.009, respectively).IMPORTANCE The presence in cerebrospinal fluid of antibodies to EV peptides at higher levels than non-AFM controls supports the plausibility of a link between EV infection and AFM that warrants further investigation and has the potential to lead to strategies for diagnosis and prevention of disease.
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MESH Headings
- Adolescent
- Adult
- Antibodies, Viral/blood
- Antibodies, Viral/cerebrospinal fluid
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- Central Nervous System Viral Diseases/blood
- Central Nervous System Viral Diseases/cerebrospinal fluid
- Child
- Enterovirus D, Human/genetics
- Enterovirus D, Human/immunology
- Enterovirus D, Human/isolation & purification
- Enterovirus Infections/blood
- Enterovirus Infections/cerebrospinal fluid
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Male
- Middle Aged
- Myelitis/blood
- Myelitis/cerebrospinal fluid
- Neuromuscular Diseases/blood
- Neuromuscular Diseases/cerebrospinal fluid
- Protein Array Analysis
- RNA, Viral/blood
- RNA, Viral/cerebrospinal fluid
- RNA, Viral/genetics
- Young Adult
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Affiliation(s)
- Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Terry Fei Fan Ng
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rachel L Marine
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Adrian Caciula
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Joel A Garcia
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Jane C Burns
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA
| | - Kiran T Thakur
- Division of Critical Care and Hospitalist Neurology, Department of Neurology, Columbia Irving University Medical Center, New York, New York, USA
| | - Kimbell L Hetzler
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Janell A Routh
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - W Allan Nix
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
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22
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Sameroff S, Tokarz R, Charles RA, Jain K, Oleynik A, Che X, Georges K, Carrington CV, Lipkin WI, Oura C. Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago. Sci Rep 2019; 9:10421. [PMID: 31320705 PMCID: PMC6639388 DOI: 10.1038/s41598-019-46914-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/04/2019] [Indexed: 11/09/2022] Open
Abstract
Ticks are vectors of a wide variety of pathogens that are implicated in mild to severe disease in humans and other animals. Nonetheless, the full range of tick-borne pathogens is unknown. Viruses, in particular, have been neglected in discovery efforts targeting tick-borne agents. High throughput sequencing was used to characterize the virome of 638 ticks, including Rhipicephalus microplus (n = 320), Rhipicephalus sanguineus (n = 300), and Amblyomma ovale (n = 18) collected throughout Trinidad and Tobago in 2017 and 2018. Sequences representing nine viruses were identified, including five novel species within Tymovirales, Bunyavirales, Chuviridae, Rhabdoviridae, and Flaviviridae. Thereafter the frequency of detection of viral sequences in individual tick species was investigated.
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Affiliation(s)
- Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA. .,School of Veterinary Medicine, The University of the West Indies, St. Augustine, Trinidad and Tobago.
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA
| | - Roxanne Albertha Charles
- School of Veterinary Medicine, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA
| | - Alexandra Oleynik
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA
| | - Karla Georges
- School of Veterinary Medicine, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Christine V Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA
| | - Chris Oura
- School of Veterinary Medicine, The University of the West Indies, St. Augustine, Trinidad and Tobago
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23
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Shi T, McAllister DA, O'Brien KL, Simoes EAF, Madhi SA, Gessner BD, Polack FP, Balsells E, Acacio S, Aguayo C, Alassani I, Ali A, Antonio M, Awasthi S, Awori JO, Azziz-Baumgartner E, Baggett HC, Baillie VL, Balmaseda A, Barahona A, Basnet S, Bassat Q, Basualdo W, Bigogo G, Bont L, Breiman RF, Brooks WA, Broor S, Bruce N, Bruden D, Buchy P, Campbell S, Carosone-Link P, Chadha M, Chipeta J, Chou M, Clara W, Cohen C, de Cuellar E, Dang DA, Dash-Yandag B, Deloria-Knoll M, Dherani M, Eap T, Ebruke BE, Echavarria M, de Freitas Lázaro Emediato CC, Fasce RA, Feikin DR, Feng L, Gentile A, Gordon A, Goswami D, Goyet S, Groome M, Halasa N, Hirve S, Homaira N, Howie SRC, Jara J, Jroundi I, Kartasasmita CB, Khuri-Bulos N, Kotloff KL, Krishnan A, Libster R, Lopez O, Lucero MG, Lucion F, Lupisan SP, Marcone DN, McCracken JP, Mejia M, Moisi JC, Montgomery JM, Moore DP, Moraleda C, Moyes J, Munywoki P, Mutyara K, Nicol MP, Nokes DJ, Nymadawa P, da Costa Oliveira MT, Oshitani H, Pandey N, Paranhos-Baccalà G, Phillips LN, Picot VS, Rahman M, Rakoto-Andrianarivelo M, Rasmussen ZA, Rath BA, Robinson A, Romero C, Russomando G, Salimi V, Sawatwong P, Scheltema N, Schweiger B, Scott JAG, Seidenberg P, Shen K, Singleton R, Sotomayor V, Strand TA, Sutanto A, Sylla M, Tapia MD, Thamthitiwat S, Thomas ED, Tokarz R, Turner C, Venter M, Waicharoen S, Wang J, Watthanaworawit W, Yoshida LM, Yu H, Zar HJ, Campbell H, Nair H. Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: a systematic review and modelling study. Lancet 2017; 390:946-958. [PMID: 28689664 PMCID: PMC5592248 DOI: 10.1016/s0140-6736(17)30938-8] [Citation(s) in RCA: 1430] [Impact Index Per Article: 204.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/07/2017] [Accepted: 03/30/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND We have previously estimated that respiratory syncytial virus (RSV) was associated with 22% of all episodes of (severe) acute lower respiratory infection (ALRI) resulting in 55 000 to 199 000 deaths in children younger than 5 years in 2005. In the past 5 years, major research activity on RSV has yielded substantial new data from developing countries. With a considerably expanded dataset from a large international collaboration, we aimed to estimate the global incidence, hospital admission rate, and mortality from RSV-ALRI episodes in young children in 2015. METHODS We estimated the incidence and hospital admission rate of RSV-associated ALRI (RSV-ALRI) in children younger than 5 years stratified by age and World Bank income regions from a systematic review of studies published between Jan 1, 1995, and Dec 31, 2016, and unpublished data from 76 high quality population-based studies. We estimated the RSV-ALRI incidence for 132 developing countries using a risk factor-based model and 2015 population estimates. We estimated the in-hospital RSV-ALRI mortality by combining in-hospital case fatality ratios with hospital admission estimates from hospital-based (published and unpublished) studies. We also estimated overall RSV-ALRI mortality by identifying studies reporting monthly data for ALRI mortality in the community and RSV activity. FINDINGS We estimated that globally in 2015, 33·1 million (uncertainty range [UR] 21·6-50·3) episodes of RSV-ALRI, resulted in about 3·2 million (2·7-3·8) hospital admissions, and 59 600 (48 000-74 500) in-hospital deaths in children younger than 5 years. In children younger than 6 months, 1·4 million (UR 1·2-1·7) hospital admissions, and 27 300 (UR 20 700-36 200) in-hospital deaths were due to RSV-ALRI. We also estimated that the overall RSV-ALRI mortality could be as high as 118 200 (UR 94 600-149 400). Incidence and mortality varied substantially from year to year in any given population. INTERPRETATION Globally, RSV is a common cause of childhood ALRI and a major cause of hospital admissions in young children, resulting in a substantial burden on health-care services. About 45% of hospital admissions and in-hospital deaths due to RSV-ALRI occur in children younger than 6 months. An effective maternal RSV vaccine or monoclonal antibody could have a substantial effect on disease burden in this age group. FUNDING The Bill & Melinda Gates Foundation.
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Affiliation(s)
- Ting Shi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK
| | | | - Katherine L O'Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MS, USA
| | | | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Evelyn Balsells
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK
| | - Sozinho Acacio
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | | | | | - Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Pakistan
| | - Martin Antonio
- Medical Research Council Unit The Gambia, Basse, The Gambia
| | - Shally Awasthi
- Department of Pediatrics, King George's Medical University, Lucknow (UP), India
| | - Juliet O Awori
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Eduardo Azziz-Baumgartner
- International Centre for Diarrhoeal Disease Research, Bangladesh; Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand; Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vicky L Baillie
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Alfredo Barahona
- Hospital Materno Infantil Jose Domingo de Obaldia, Ciudad De David, Chiriqui, Panama
| | - Sudha Basnet
- Center for International Health, University of Bergen, Norway; Department of Child Health, Tribhuvan University Institute of Medicine, Nepal
| | - Quique Bassat
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; ISGlobal, Barcelona Ctr Int Health Res (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
| | - Wilma Basualdo
- Hospital General Pediátrico Niños de Acosta Ñu, Ministerio de Salud Pública y Bienestar Social, San Lorenzo, Paraguay
| | - Godfrey Bigogo
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Louis Bont
- Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands
| | | | - W Abdullah Brooks
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MS, USA; International Centre for Diarrhoeal Disease Research, Bangladesh
| | - Shobha Broor
- All India Institute of Medical Sciences, New Delhi, India
| | - Nigel Bruce
- Department of Public Health and Policy, University of Liverpool, Liverpool, UK
| | - Dana Bruden
- Arctic Investigations Program, National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centres for Disease Control and Prevention, Anchorage, AK, USA
| | - Philippe Buchy
- Institute Pasteur Cambodia, Children's Hospital Colorado, Aurora, CO, USA; GSK Vaccines Singapore, Children's Hospital Colorado, Aurora, CO, USA
| | - Stuart Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK
| | - Phyllis Carosone-Link
- Department of Pediatric Infectious Diseases, Children's Hospital Colorado, Aurora, CO, USA
| | | | | | - Monidarin Chou
- Rodolphe Merieux Laboratory, Faculty of Pharmacy, University of Health Sciences, Phnom Penh, Cambodia
| | - Wilfrido Clara
- Centers for Disease Control and Prevention, Central American Region, Guatemala City, Guatemala
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Duc-Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Maria Deloria-Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MS, USA
| | - Mukesh Dherani
- Department of Public Health and Policy, University of Liverpool, Liverpool, UK
| | - Tekchheng Eap
- Department of Pneumology, National Pediatric Hospital, Phnom Penh, Cambodia
| | | | | | | | | | - Daniel R Feikin
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Luzhao Feng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Angela Gentile
- Epidemiology Department, Austral University and Ricardo Gutiérrez Children Hospital, Argentina
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Doli Goswami
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MS, USA; International Centre for Diarrhoeal Disease Research, Bangladesh
| | - Sophie Goyet
- Institute Pasteur Cambodia, Children's Hospital Colorado, Aurora, CO, USA
| | - Michelle Groome
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Nusrat Homaira
- International Centre for Diarrhoeal Disease Research, Bangladesh; School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, NSW, Australia
| | - Stephen R C Howie
- Medical Research Council Unit The Gambia, Basse, The Gambia; Department of Paediatrics, University of Auckland, Auckland, New Zealand; Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Jorge Jara
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala
| | - Imane Jroundi
- ISGlobal, Barcelona Ctr Int Health Res (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Unit of Training and Research in Public Health, School of Medicine and Pharmacy of Rabat, University Mohamed V, Rabat, Morocco
| | | | | | - Karen L Kotloff
- Department of Pediatrics and Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anand Krishnan
- All India Institute of Medical Sciences, New Delhi, India
| | - Romina Libster
- Fundacion INFANT, Buenos Aires, Argentina; Vanderbilt University, Nashville, TN, USA; National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Olga Lopez
- Hospital Dr Ernesto Torres Galdames, Iquique, Chile
| | - Marilla G Lucero
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Florencia Lucion
- Epidemiology Department, Austral University and Ricardo Gutiérrez Children Hospital, Argentina
| | - Socorro P Lupisan
- Research Institute for Tropical Medicine-Department of Health, Philippines
| | - Debora N Marcone
- Centro de Educación Médica envestigaciones Clínicas "CEMIC", Argentina
| | - John P McCracken
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala
| | - Mario Mejia
- Ministry of Public Health and Social Welfare, Guatemala
| | | | - Joel M Montgomery
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - David P Moore
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Cinta Moraleda
- ISGlobal, Barcelona Ctr Int Health Res (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick Munywoki
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya; Pwani University, Kilifi, Kenya
| | | | - Mark P Nicol
- Division of Medical Microbiology, University of Cape Town and National Health Laboratory Services, South Africa
| | - D James Nokes
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya; School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | - Histoshi Oshitani
- Tohoku University Graduate School of Medicine, Department of Virology, Miyagi Prefecture, Japan
| | - Nitin Pandey
- Department of Pediatrics, King George's Medical University, Lucknow (UP), India
| | - Gláucia Paranhos-Baccalà
- Emerging Pathofens Laboratory, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Lia N Phillips
- Emory University, Rollins School of Public Health, AT, USA
| | - Valentina Sanchez Picot
- Emerging Pathofens Laboratory, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | | | | | - Zeba A Rasmussen
- Fogarty International Center Division of International Epidemiology and Population Studies, NIH, Bethesda, MD, USA
| | - Barbara A Rath
- Department of Pediatrics, Charité University Medical Center, Berlin, Germany
| | | | - Candice Romero
- United States Naval Medical Research Unit No. 6, Callao, Peru
| | - Graciela Russomando
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asuncion, Paraguay
| | - Vahid Salimi
- School of Public Health, Virology Department, Tehran University of Medical Sciences, Iran
| | - Pongpun Sawatwong
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Nienke Scheltema
- Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands
| | | | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya; London School of Hygiene & Tropical Medicine, London, UK
| | - Phil Seidenberg
- Department of Emergency Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Kunling Shen
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Beijing, China
| | - Rosalyn Singleton
- Arctic Investigations Program, National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centres for Disease Control and Prevention, Anchorage, AK, USA; Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | | | - Tor A Strand
- Center for International Health, University of Bergen, Norway; Department of Research, Innlandet Hospital Trust, Lillehammer, Norway
| | | | | | - Milagritos D Tapia
- Department of Pediatrics and Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Somsak Thamthitiwat
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Elizabeth D Thomas
- Fogarty International Center Division of International Epidemiology and Population Studies, NIH, Bethesda, MD, USA
| | - Rafal Tokarz
- Centre for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Marietjie Venter
- Centre for Viral Zoonosis, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Sunthareeya Waicharoen
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, China
| | - Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Lay-Myint Yoshida
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hongjie Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Heather J Zar
- Department of Paediatrics and Child Heath, Red Cross War Memorial Children's Hospital and MRC Unit on Child & Adolescent Health, University of Cape Town, South Africa
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK
| | - Harish Nair
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK; Public Health Foundation of India, New Delhi, India.
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Fullerton HJ, Luna JM, Wintermark M, Hills NK, Tokarz R, Li Y, Glaser C, DeVeber GA, Lipkin WI, Elkind MSV. Parvovirus B19 Infection in Children With Arterial Ischemic Stroke. Stroke 2017; 48:2875-2877. [PMID: 28864597 DOI: 10.1161/strokeaha.117.018272] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/07/2017] [Accepted: 08/01/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE Case-control studies suggest that acute infection transiently increases the risk of childhood arterial ischemic stroke. We hypothesized that an unbiased pathogen discovery approach utilizing MassTag-polymerase chain reaction would identify pathogens in the blood of childhood arterial ischemic stroke cases. METHODS The multicenter international VIPS study (Vascular Effects of Infection in Pediatric Stroke) enrolled arterial ischemic stroke cases, and stroke-free controls, aged 29 days through 18 years. Parental interview included questions on recent infections. In this pilot study, we used MassTag-polymerase chain reaction to test the plasma of the first 161 cases and 34 controls enrolled for a panel of 28 common bacterial and viral pathogens. RESULTS Pathogen DNA was detected in no controls and 14 cases (8.7%): parvovirus B19 (n=10), herpesvirus 6 (n=2), adenovirus (n=1), and rhinovirus 6C (n=1). Parvovirus B19 infection was confirmed by serologies in all 10; infection was subclinical in 8. Four cases with parvovirus B19 had underlying congenital heart disease, whereas another 5 had a distinct arteriopathy involving a long-segment stenosis of the distal internal carotid and proximal middle cerebral arteries. CONCLUSIONS Using MassTag-polymerase chain reaction, we detected parvovirus B19-a virus known to infect erythrocytes and endothelial cells-in some cases of childhood arterial ischemic stroke. This approach can generate new, testable hypotheses about childhood stroke pathogenesis.
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Affiliation(s)
- Heather J Fullerton
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - Jorge M Luna
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - Max Wintermark
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - Nancy K Hills
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - Rafal Tokarz
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - Ying Li
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - Carol Glaser
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - Gabrielle A DeVeber
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - W Ian Lipkin
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.)
| | - Mitchell S V Elkind
- From the Department of Neurology (H.J.F.), Department of Pediatrics (H.J.F.), and Department of Biostatistics and Epidemiology (N.K.H.), University of California, San Francisco; Department of Epidemiology (J.M.L., R.T., W.I.L., M.S.V.E.) and Department of Neurology (M.S.V.E.), Columbia University College of Physicians and Surgeons, New York, NY; Department of Radiology, Stanford University, Palo Alto, CA (M.W., Y.L.); Department of Pediatrics (Infectious Disease), Kaiser Permanente, Oakland, CA (C.G.); and Department of Neurology, Hospital for Sick Children, Toronto, Canada (G.A.D.).
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Alonso-Guallart P, Zitsman J, Sondermeijer H, Chaudhry S, Weiner J, Griesemer A, Tokarz R, Pereira M, Hammer S, Sykes M, Duran-Struuck R. Treatment Approaches and Clinical Parameters Predictive of CMV Disease and Resolution in Immunodeficient Cynomolgus Macaques – a Clinically Relevant Large Animal Model. Biol Blood Marrow Transplant 2016. [DOI: 10.1016/j.bbmt.2015.11.765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Tadin A, Tokarz R, Markotić A, Margaletić J, Turk N, Habuš J, Svoboda P, Vucelja M, Desai A, Jain K, Lipkin WI. Molecular Survey of Zoonotic Agents in Rodents and Other Small Mammals in Croatia. Am J Trop Med Hyg 2015; 94:466-73. [PMID: 26711522 DOI: 10.4269/ajtmh.15-0517] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/02/2015] [Indexed: 11/07/2022] Open
Abstract
Croatia is a focus for many rodent-borne zoonosis. Here, we report a survey of 242 rodents and small mammals, including 43 Myodes glareolus, 131 Apodemus flavicollis, 53 Apodemus agrarius, three Apodemus sylvaticus, six Sorex araneus, four Microtus arvalis, one Microtus agrestis, and one Muscardinus avellanarius, collected at eight sites in Croatia over an 8-year period. Multiplex MassTag polymerase chain reaction (PCR) was used for detection of Borrelia, Rickettsia, Bartonella, Babesia, Ehrlichia, Anaplasma, Francisella tularensis, and Coxiella burnetii. Individual PCR assays were used for detection of Leptospira, lymphocytic choriomeningitis virus, orthopoxviruses, flaviviruses, hantaviruses, and Toxoplasma gondii. Of the rodents, 52 (21.5%) were infected with Leptospira, 9 (3.7%) with Borrelia miyamotoi, 5 (2%) with Borrelia afzelii, 29 (12.0%) with Bartonella, 8 (3.3%) with Babesia microti, 2 (0.8%) with Ehrlichia, 4 (1.7%) with Anaplasma, 2 (0.8%) with F. tularensis, 43 (17.8%) with hantaviruses, and 1 (0.4%) with an orthopoxvirus. Other agents were not detected. Multiple infections were found in 32 rodents (13.2%): dual infections in 26 rodents (10.7%), triple infections in four rodents (2.9%), and quadruple infections in two rodents (0.8%). Our findings indicate that rodents in Croatia harbor a wide range of bacteria and viruses that are pathogenic to humans.
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Affiliation(s)
- Ante Tadin
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Rafal Tokarz
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Alemka Markotić
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Josip Margaletić
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Nenad Turk
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Josipa Habuš
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Petra Svoboda
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Marko Vucelja
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Aaloki Desai
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Komal Jain
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - W Ian Lipkin
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević," Zagreb, Croatia; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York; Faculty of Forestry, University of Zagreb, Zagreb, Croatia; Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
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Gordon CL, Tokarz R, Briese T, Lipkin WI, Jain K, Whittier S, Shah J, Connolly ES, Yin MT. Evaluation of a multiplex polymerase chain reaction for early diagnosis of ventriculostomy-related infections. J Neurosurg 2015; 123:1586-92. [PMID: 26023998 DOI: 10.3171/2014.11.jns141036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECT Diagnosis of ventriculostomy-related infections (VRIs) is challenging due to the lack of rapid, sensitive assays for pathogen detection. The authors report the development of a multiplex polymerase chain reaction (PCR) assay for differential diagnosis of common VRI pathogens. METHODS MassTag PCR was used to develop a multiplex assay for detection of 11 VRI pathogens. The assay was established and optimized using cloned template standards and spiked samples and was then evaluated on CSF specimens from ventricular drains. Subjects were grouped into definite VRI, possible VRI, or no VRI based on conventional microbiology, CSF evaluation, and clinical parameters. RESULTS CSF specimens were obtained from 45 subjects (median age 49 years, interquartile range 32-63 years; 51% were male). The assay detected 10-100 genome copies. It detected a pathogen in 100% (6 of 6) of definite VRI cases in which a pathogen targeted by the assay was present; these represented 67% of all definite VRIs (6 of 9). Among subjects with a possible VRI, the assay detected a pathogen in 29% (5 of 17). In subjects without overt infection the presence of a pathogen was detected in 32% of subjects (6 of 19), albeit with lower signal compared with the VRI group. CONCLUSIONS MassTag PCR enabled parallel testing of CSF specimens for 11 pathogens of VRI. The high sensitivity of PCR combined with possible device colonization, specimen contamination, and concurrent antibiotic treatments limit the clinical value of the assay, similar to other current diagnostic approaches. With further optimization, multiplex PCR may provide timely identification of multiple possible VRI pathogens and guide management, complementing classic culture approaches.
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Affiliation(s)
- Claire L Gordon
- Division of Infectious Disease, Department of Medicine, and.,Department of Medicine, University of Melbourne, Victoria, Australia
| | | | - Thomas Briese
- Center for Infection and Immunity and.,Department of Epidemiology, Mailman School of Public Health, Columbia University Medical Center
| | | | | | - Susan Whittier
- Clinical Microbiology Service, NewYork-Presbyterian Hospital, New York, New York; and
| | - Jayesh Shah
- Division of Infectious Disease, Department of Medicine, and
| | | | - Michael T Yin
- Division of Infectious Disease, Department of Medicine, and
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Abstract
The family Coronaviridae represents a diverse group of vertebrate RNA viruses, all with genomes greater than 26,000 nt. Here, we report the discovery and genetic characterization of a novel virus present in cattle with respiratory disease. Phylogenetic characterization of this virus revealed that it clusters within the subfamily Torovirinae, in the family Coronaviridae. The complete genome consists of only 20,261 nt and represents the smallest reported coronavirus genome. We identified seven ORFs, including the canonical nidovirus ORF1a and ORF1b. Analysis of polyprotein 1ab revealed that this virus, tentatively named bovine nidovirus (BoNV), shares the highest homology with the recently described python-borne nidoviruses and contains several conserved nidovirus motifs, but does not encode the NendoU or O-MT domains that are present in other viruses within the family Coronaviridae. In concert with its reduced genome, the atypical domain architecture indicates that this virus represents a unique lineage within the order Nidovirales.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY 10032, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY 10032, USA
| | - Richard A Hesse
- Kansas State Veterinary Diagnostic Laboratory and Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, 66508, USA
| | - Ben M Hause
- Kansas State Veterinary Diagnostic Laboratory and Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, 66508, USA
| | - Aaloki Desai
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY 10032, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY 10032, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY 10032, USA
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Ly N, Tokarz R, Mishra N, Sameroff S, Jain K, Rachmat A, An US, Newell S, Harrison DJ, Lipkin WI. Multiplex PCR analysis of clusters of unexplained viral respiratory tract infection in Cambodia. Virol J 2014; 11:224. [PMID: 25514971 PMCID: PMC4280028 DOI: 10.1186/s12985-014-0224-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/05/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Fevers of unknown origin constitute a substantial disease burden in Southeast Asia. In majority of the cases, the cause of acute febrile illness is not identified. METHODS We used MassTag PCR, a multiplex assay platform, to test for the presence of 15 viral respiratory agents from 85 patients with unexplained respiratory illness representing six disease clusters that occurred in Cambodia between 2009 and 2012. RESULTS We detected a virus in 37 (44%) of the cases. Human rhinovirus, the virus detected most frequently, was found in both children and adults. The viruses most frequently detected in children and adults, respectively, were respiratory syncytial virus and enterovirus 68. Sequence analysis indicated that two distinct clades of enterovirus 68 were circulating during this time period. CONCLUSIONS This is the first report of enterovirus 68 in Cambodia and contributes to the appreciation of this virus as an important respiratory pathogen.
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Affiliation(s)
- Nary Ly
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Agus Rachmat
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Ung Sam An
- National Institute of Public Health, Cambodian Ministry of Health, Phnom Penh, Cambodia.
| | - Steven Newell
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Dustin J Harrison
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
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Razuri H, Tokarz R, Ghersi BM, Salmon-Mulanovich G, Guezala MC, Albujar C, Mendoza AP, Tinoco YO, Cruz C, Silva M, Vasquez A, Pacheco V, Ströher U, Guerrero LW, Cannon D, Nichol ST, Hirschberg DL, Lipkin WI, Bausch DG, Montgomery JM. Andes hantavirus variant in rodents, southern Amazon Basin, Peru. Emerg Infect Dis 2014; 20:257-60. [PMID: 24447689 PMCID: PMC3901500 DOI: 10.3201/eid2002.131418] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated hantaviruses in rodents in the southern Amazon Basin of Peru and identified an Andes virus variant from Neacomys spinosus mice. This finding extends the known range of this virus in South America and the range of recognized hantaviruses in Peru. Further studies of the epizoology of hantaviruses in this region are warranted.
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Uccellini L, Ossiboff RJ, de Matos REC, Morrisey JK, Petrosov A, Navarrete-Macias I, Jain K, Hicks AL, Buckles EL, Tokarz R, McAloose D, Lipkin WI. Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius). Virol J 2014; 11:144. [PMID: 25106433 PMCID: PMC4254391 DOI: 10.1186/1743-422x-11-144] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/08/2014] [Indexed: 11/23/2022] Open
Abstract
Background Respiratory infections are important causes of morbidity and mortality in reptiles; however, the causative agents are only infrequently identified. Findings Pneumonia, tracheitis and esophagitis were reported in a collection of ball pythons (Python regius). Eight of 12 snakes had evidence of bacterial pneumonia. High-throughput sequencing of total extracted nucleic acids from lung, esophagus and spleen revealed a novel nidovirus. PCR indicated the presence of viral RNA in lung, trachea, esophagus, liver, and spleen. In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. Conclusions This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA.
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32
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Howie SRC, Morris GAJ, Tokarz R, Ebruke BE, Machuka EM, Ideh RC, Chimah O, Secka O, Townend J, Dione M, Oluwalana C, Njie M, Jallow M, Hill PC, Antonio M, Greenwood B, Briese T, Mulholland K, Corrah T, Lipkin WI, Adegbola RA. Etiology of severe childhood pneumonia in the Gambia, West Africa, determined by conventional and molecular microbiological analyses of lung and pleural aspirate samples. Clin Infect Dis 2014; 59:682-5. [PMID: 24867789 PMCID: PMC4130311 DOI: 10.1093/cid/ciu384] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcuspneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. Multiple pathogens were detected frequently, notably Haemophilus influenzae (mostly nontypeable) together with S. pneumoniae.
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Affiliation(s)
| | | | - Rafal Tokarz
- Center for Infection and Immunity, Columbia University, New York, New York
| | | | | | - Readon C Ideh
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Osaretin Chimah
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Ousman Secka
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - John Townend
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Michel Dione
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | | | - Malick Njie
- Ministry of Health and Social Welfare, Banjul, Republic of The Gambia
| | - Mariatou Jallow
- Ministry of Health and Social Welfare, Banjul, Republic of The Gambia
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Martin Antonio
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Brian Greenwood
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University, New York, New York
| | - Kim Mulholland
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Tumani Corrah
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, New York
| | - Richard A Adegbola
- Medical Research Council Unit, Fajara, Republic of The Gambia GlaxoSmithKline Vaccines, Wavre, Belgium
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Hsu CC, Tokarz R, Briese T, Tsai HC, Quan PL, Lipkin WI. Use of staged molecular analysis to determine causes of unexplained central nervous system infections. Emerg Infect Dis 2014; 19:1470-7. [PMID: 23965845 PMCID: PMC3810931 DOI: 10.3201/eid1909.130474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
No agent is implicated in most central nervous system (CNS) infections. To investigate cerebrospinal fluid samples from patients with CNS infections of unknown cause in 1 hospital in Taiwan, we used a staged molecular approach, incorporating techniques including multiplex MassTag PCR, 16S rRNA PCR, DNA microarray, and high-throughput pyrosequencing. We determined the infectious agent for 31 (24%) of 131 previously negative samples. Candidate pathogens were identified for 25 (27%) of 94 unexplained meningitis cases and 6 (16%) of 37 unexplained encephalitis cases. Epstein-Barr virus (18 infections) accounted for most of the identified agents in unexplained meningitis cases, followed by Escherichia coli (5), enterovirus (2), human herpesvirus 2 (1), and Mycobacterium tuberculosis. Herpesviruses were identified in samples from patients with unexplained encephalitis cases, including varicella-zoster virus (3 infections), human herpesvirus 1 (2), and cytomegalovirus (1). Our study confirms the power of multiplex MassTag PCR as a rapid diagnostic tool for identifying pathogens causing unexplained CNS infections.
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Tokarz R, Sameroff S, Leon MS, Jain K, Lipkin WI. Genome characterization of Long Island tick rhabdovirus, a new virus identified in Amblyomma americanum ticks. Virol J 2014; 11:26. [PMID: 24517260 PMCID: PMC3928085 DOI: 10.1186/1743-422x-11-26] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 02/10/2014] [Indexed: 01/08/2023] Open
Abstract
Background Ticks are implicated as hosts to a wide range of animal and human pathogens. The full range of microbes harbored by ticks has not yet been fully explored. Methods As part of a viral surveillance and discovery project in arthropods, we used unbiased high-throughput sequencing to examine viromes of ticks collected on Long Island, New York in 2013. Results We detected and sequenced the complete genome of a novel rhabdovirus originating from a pool of Amblyomma americanum ticks. This virus, which we provisionally name Long Island tick rhabdovirus, is distantly related to Moussa virus from Africa. Conclusions The Long Island tick rhabdovirus may represent a novel species within family Rhabdoviridae.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, New York, NY 10032, USA.
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35
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Luna JM, Fullerton HJ, Wintermark M, deVeber G, Hills N, Muhammad K, Tokarz R, Lipkin WI, Elkind MS. Abstract 36: Parvovirus B19 DNA Prevalence is Increased in Pediatric Stroke Patients Compared to Controls: Pilot Findings From the Vascular Effects of Infection in Pediatric Stroke (VIPS) Study. Stroke 2014. [DOI: 10.1161/str.45.suppl_1.36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Mechanisms underlying childhood arterial ischemic stroke_and childhood cerebral arteriopathies in particular_remain poorly understood. There is evidence that viral syndromes are associated with stroke onset.
Objective:
We hypothesized that an unbiased pathogen discovery approach utilizing MassTag polymerase chain reaction (PCR), a multiplex assay that permits simultaneous testing, would identify candidate pathogens associated with stroke risk in blood from childhood stroke patients compared to controls.
Methods:
Serum samples from 162 pediatric arterial ischemic stroke cases and 36 stroke-free control children with minor traumatic injuries were collected in the multi-center international VIPS study; parental interview included questions on recent infections. Samples were analyzed by MassTag-PCR for a panel of 28 bacterial and viral pathogens. Presence of arteriopathy was determined by blinded, centralized review of vascular imaging.
Results:
Median (IQR) age of cases was 8.1 (2.8, 16.0) years; 31% were girls; and 34% had a reported infection in the prior 4 weeks. Median (IQR) age of controls was 7.3 (2.5, 14.3) years; and 41% were girls. Viral pathogen DNA was detected in 14 of 163 (9.2%) of cases and 0 of 37 (0%) of controls: parvovirus B19 (n=10), herpesvirus 6 (n=2), adenovirus (n=1), and rhinovirus 6C (n=1). Copy number of parvovirus B19/microliter of plasma varied from 11 to 1.3 x 104. Among 10 patients with parvovirus B19, 8 had other, non-infectious stroke risk factors, and 5 had a distinct arteriopathy involving a long-segment of the internal carotid artery (Table).
Conclusion:
Parvovirus B19, a virus capable of infecting erythrocytes and endothelial cells, may be a multi-factorial contributor to childhood ischemic stroke, potentially triggering events among children with congenital heart disease or trauma. MassTag-PCR enhances the detection of pathogens potentially associated with stroke in pediatric stroke patients.
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36
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Tokarz R, Haq S, Sameroff S, Howie SRC, Lipkin WI. Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C. J Gen Virol 2013; 94:1995-2004. [PMID: 23761409 DOI: 10.1099/vir.0.053462-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Saddef Haq
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Stephen R C Howie
- Child Survival Theme, Medical Research Council Unit, Banjul, Fajara, Gambia
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
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37
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Tokarz R, Hirschberg DL, Sameroff S, Haq S, Luna G, Bennett AJ, Silva M, Leguia M, Kasper M, Bausch DG, Lipkin WI. Genomic analysis of two novel human enterovirus C genotypes found in respiratory samples from Peru. J Gen Virol 2012; 94:120-127. [PMID: 23034595 DOI: 10.1099/vir.0.046250-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the discovery of two enteroviruses detected in nasopharyngeal samples obtained from subjects with respiratory disease in Peru. Phylogenetic analysis indicated that both viruses belong to a clade within the species Human enterovirus C, which includes the recently characterized human enteroviruses 109 and 104. Members of this clade have undergone significant genomic rearrangement, as indicated by deletions in the hypervariable region of the 5' UTR and the VP1 protein, as well as recombination within the non-structural genes. Our findings and review of published sequences suggests that several novel human enterovirus C serotypes are currently circulating worldwide.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - David L Hirschberg
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Saddef Haq
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - Andrew J Bennett
- US Naval Medical Research Unit 6, Lima, Peru.,Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Maria Silva
- US Naval Medical Research Unit 6, Lima, Peru
| | | | | | | | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
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Tokarz R, Firth C, Madhi SA, Howie SRC, Wu W, Sall AA, Haq S, Briese T, Lipkin WI. Worldwide emergence of multiple clades of enterovirus 68. J Gen Virol 2012; 93:1952-1958. [PMID: 22694903 DOI: 10.1099/vir.0.043935-0] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human enterovirus 68 (EV-D68) is a historically rarely reported virus linked with respiratory disease. In the past 3 years, a large increase in respiratory disease associated with EV-D68 has been reported, with documented outbreaks in North America, Europe and Asia. In several outbreaks, genetic differences were identified among the circulating strains, indicating the presence of multiple clades. In this report, we analyse archived and novel EV-D68 strains from Africa and the USA, obtained from patients with respiratory illness. Phylogenetic analysis of all EV-D68 sequences indicates that, over the past two decades, multiple clades of the virus have emerged and spread rapidly worldwide. All clades appear to be currently circulating and contributing to respiratory disease.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - Cadhla Firth
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.,National Institute of Communicable Diseases, Division of National Health Laboratory Service, Sandringham, Johannesburg, 2131, South Africa
| | - Stephen R C Howie
- Child Survival Theme, Medical Research Council Unit, PO Box 273, Banjul, The Gambia
| | - Winfred Wu
- New York City Department of Health and Mental Hygiene, Gotham Center, 42-09 28th St, New York, NY 11101, USA
| | - Amadou Alpha Sall
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - Saddef Haq
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
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Nair H, Brooks WA, Katz M, Roca A, Berkley JA, Madhi SA, Simmerman JM, Gordon A, Sato M, Howie S, Krishnan A, Ope M, Lindblade KA, Carosone-Link P, Lucero M, Ochieng W, Kamimoto L, Dueger E, Bhat N, Vong S, Theodoratou E, Chittaganpitch M, Chimah O, Balmaseda A, Buchy P, Harris E, Evans V, Katayose M, Gaur B, O'Callaghan-Gordo C, Goswami D, Arvelo W, Venter M, Briese T, Tokarz R, Widdowson MA, Mounts AW, Breiman RF, Feikin DR, Klugman KP, Olsen SJ, Gessner BD, Wright PF, Rudan I, Broor S, Simões EAF, Campbell H. Global burden of respiratory infections due to seasonal influenza in young children: a systematic review and meta-analysis. Lancet 2011; 378:1917-30. [PMID: 22078723 DOI: 10.1016/s0140-6736(11)61051-9] [Citation(s) in RCA: 662] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND The global burden of disease attributable to seasonal influenza virus in children is unknown. We aimed to estimate the global incidence of and mortality from lower respiratory infections associated with influenza in children younger than 5 years. METHODS We estimated the incidence of influenza episodes, influenza-associated acute lower respiratory infections (ALRI), and influenza-associated severe ALRI in children younger than 5 years, stratified by age, with data from a systematic review of studies published between Jan 1, 1995, and Oct 31, 2010, and 16 unpublished population-based studies. We applied these incidence estimates to global population estimates for 2008 to calculate estimates for that year. We estimated possible bounds for influenza-associated ALRI mortality by combining incidence estimates with case fatality ratios from hospital-based reports and identifying studies with population-based data for influenza seasonality and monthly ALRI mortality. FINDINGS We identified 43 suitable studies, with data for around 8 million children. We estimated that, in 2008, 90 million (95% CI 49-162 million) new cases of influenza (data from nine studies), 20 million (13-32 million) cases of influenza-associated ALRI (13% of all cases of paediatric ALRI; data from six studies), and 1 million (1-2 million) cases of influenza-associated severe ALRI (7% of cases of all severe paediatric ALRI; data from 39 studies) occurred worldwide in children younger than 5 years. We estimated there were 28,000-111,500 deaths in children younger than 5 years attributable to influenza-associated ALRI in 2008, with 99% of these deaths occurring in developing countries. Incidence and mortality varied substantially from year to year in any one setting. INTERPRETATION Influenza is a common pathogen identified in children with ALRI and results in a substantial burden on health services worldwide. Sufficient data to precisely estimate the role of influenza in childhood mortality from ALRI are not available. FUNDING WHO; Bill & Melinda Gates Foundation.
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Affiliation(s)
- Harish Nair
- Centre for Population Health Sciences, Global Health Academy, The University of Edinburgh, Edinburgh, UK.
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Tokarz R, Firth C, Street C, Cox-Foster DL, Lipkin WI. Lack of evidence for an association between Iridovirus and colony collapse disorder. PLoS One 2011; 6:e21844. [PMID: 21738798 PMCID: PMC3128115 DOI: 10.1371/journal.pone.0021844] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [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: 03/04/2011] [Accepted: 06/07/2011] [Indexed: 11/18/2022] Open
Abstract
Colony collapse disorder (CCD) is characterized by the unexplained losses of large numbers of adult worker bees (Apis mellifera) from apparently healthy colonies. Although infections, toxins, and other stressors have been associated with the onset of CCD, the pathogenesis of this disorder remains obscure. Recently, a proteomics study implicated a double-stranded DNA virus, invertebrate iridescent virus (Family Iridoviridae) along with a microsporidium (Nosema sp.) as the cause of CCD. We tested the validity of this relationship using two independent methods: (i) we surveyed healthy and CCD colonies from the United States and Israel for the presence of members of the Iridovirus genus and (ii) we reanalyzed metagenomics data previously generated from RNA pools of CCD colonies for the presence of Iridovirus-like sequences. Neither analysis revealed any evidence to suggest the presence of an Iridovirus in healthy or CCD colonies.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Cadhla Firth
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Craig Street
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Diana L. Cox-Foster
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- * E-mail:
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Tokarz R, Kapoor V, Wu W, Lurio J, Jain K, Mostashari F, Briese T, Ian Lipkin W. Longitudinal molecular microbial analysis of influenza-like illness in New York City, May 2009 through May 2010. Virol J 2011; 8:288. [PMID: 21658237 PMCID: PMC3121709 DOI: 10.1186/1743-422x-8-288] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [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: 05/25/2011] [Accepted: 06/09/2011] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND We performed a longitudinal study of viral etiology in samples collected in New York City during May 2009 to May 2010 from outpatients with fever or respiratory disease symptoms in the context of a pilot respiratory virus surveillance system. METHODS Samples were assessed for the presence of 13 viruses, including influenza A virus, by MassTag PCR. RESULTS At least one virus was detected in 52% of 940 samples analyzed, with 3% showing co-infections. The most frequently detected agents were rhinoviruses and influenza A, all representing the 2009 pandemic H1N1 strain. The incidence of influenza H1N1-positive samples was highest in late spring 2009, followed by a decline in summer and early fall, when rhinovirus infections became predominant before H1N1 reemerged in winter. Our study also identified a focal outbreak of enterovirus 68 in the early fall of 2009. CONCLUSION MassTag multiplex PCR affords opportunities to track the epidemiology of infectious diseases and may guide clinicians and public health practitioners in influenza-like illness and outbreak management. Nonetheless, a substantial proportion of influenza-like illness remains unexplained underscoring the need for additional platforms.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, USA
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, USA
| | - Winfred Wu
- The New York City Department of Health and Mental Hygiene, New York, USA
| | - Joseph Lurio
- The Institute for Family Health, New York, New York, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, USA
| | - Farzad Mostashari
- The New York City Department of Health and Mental Hygiene, New York, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, USA
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Abstract
Ixodes scapularis ticks are clinically important hematophagous vectors. A single tick bite can lead to a polymicrobial infection. We determined the prevalence of polymicrobial infection with Borrelia burgdorferi, Anaplasma phagocytophilum, Babesia microti, Borrelia miyamotoi, and Powassan virus in 286 adult ticks from the two counties in New York State where Lyme disease is endemic, utilizing a MassTag multiplex polymerase chain reaction assay. Seventy-one percent of the ticks harbored at least one organism; 30% had a polymicrobial infection. Infections with three microbes were detected in 5% of the ticks. One tick was infected with four organisms. Our results show that coinfection is a frequent occurrence in ticks in the two counties surveyed.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
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43
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Palacios G, Hornig M, Cisterna D, Savji N, Bussetti AV, Kapoor V, Hui J, Tokarz R, Briese T, Baumeister E, Lipkin WI. Streptococcus pneumoniae coinfection is correlated with the severity of H1N1 pandemic influenza. PLoS One 2009; 4:e8540. [PMID: 20046873 PMCID: PMC2795195 DOI: 10.1371/journal.pone.0008540] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 12/09/2009] [Indexed: 11/25/2022] Open
Abstract
Background Initial reports in May 2009 of the novel influenza strain H1N1pdm estimated a case fatality rate (CFR) of 0.6%, similar to that of seasonal influenza. In July 2009, however, Argentina reported 3056 cases with 137 deaths, representing a CFR of 4.5%. Potential explanations for increased CFR included virus reassortment or genetic drift, or infection of a more vulnerable population. Virus genomic sequencing of 26 Argentinian samples representing both severe and mild disease indicated no evidence of reassortment, mutations associated with resistance to antiviral drugs, or genetic drift that might contribute to virulence. Furthermore, no evidence was found for increased frequency of risk factors for H1N1pdm disease. Methods/Principal Findings We examined nasopharyngeal swab samples (NPS) from 199 cases of H1N1pdm infection from Argentina with MassTag PCR, testing for 33 additional microbial agents. The study population consisted of 199 H1N1pdm-infected subjects sampled between 23 June and 4 July 2009. Thirty-nine had severe disease defined as death (n = 20) or hospitalization (n = 19); 160 had mild disease. At least one additional agent of potential pathogenic importance was identified in 152 samples (76%), including Streptococcus pneumoniae (n = 62); Haemophilus influenzae (n = 104); human respiratory syncytial virus A (n = 11) and B (n = 1); human rhinovirus A (n = 1) and B (n = 4); human coronaviruses 229E (n = 1) and OC43 (n = 2); Klebsiella pneumoniae (n = 2); Acinetobacter baumannii (n = 2); Serratia marcescens (n = 1); and Staphylococcus aureus (n = 35) and methicillin-resistant S. aureus (MRSA, n = 6). The presence of S. pneumoniae was strongly correlated with severe disease. S. pneumoniae was present in 56.4% of severe cases versus 25% of mild cases; more than one-third of H1N1pdm NPS with S. pneumoniae were from subjects with severe disease (22 of 62 S. pneumoniae-positive NPS, p = 0.0004). In subjects 6 to 55 years of age, the adjusted odds ratio (OR) of severe disease in the presence of S. pneumoniae was 125.5 (95% confidence interval [CI], 16.95, 928.72; p<0.0001). Conclusions/Significance The association of S. pneumoniae with morbidity and mortality is established in the current and previous influenza pandemics. However, this study is the first to demonstrate the prognostic significance of non-invasive antemortem diagnosis of S. pneumoniae infection and may provide insights into clinical management.
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Affiliation(s)
- Gustavo Palacios
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- * E-mail: (GP); (WIL)
| | - Mady Hornig
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Daniel Cisterna
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional de Laboratorios e Institutos de Salud “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Nazir Savji
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Ana Valeria Bussetti
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Jeffrey Hui
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Elsa Baumeister
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional de Laboratorios e Institutos de Salud “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- * E-mail: (GP); (WIL)
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44
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Coleman JL, Katona LI, Kuhlow C, Toledo A, Okan NA, Tokarz R, Benach JL. Evidence that two ATP-dependent (Lon) proteases in Borrelia burgdorferi serve different functions. PLoS Pathog 2009; 5:e1000676. [PMID: 19956677 PMCID: PMC2777506 DOI: 10.1371/journal.ppat.1000676] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [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: 08/14/2009] [Accepted: 10/30/2009] [Indexed: 12/02/2022] Open
Abstract
The canonical ATP-dependent protease Lon participates in an assortment of biological processes in bacteria, including the catalysis of damaged or senescent proteins and short-lived regulatory proteins. Borrelia spirochetes are unusual in that they code for two putative ATP-dependent Lon homologs, Lon-1 and Lon-2. Borrelia burgdorferi, the etiologic agent of Lyme disease, is transmitted through the blood feeding of Ixodes ticks. Previous work in our laboratory reported that B. burgdorferi lon-1 is upregulated transcriptionally by exposure to blood in vitro, while lon-2 is not. Because blood induction of Lon-1 may be of importance in the regulation of virulence factors critical for spirochete transmission, the clarification of functional roles for these two proteases in B. burgdorferi was the object of this study. On the chromosome, lon-2 is immediately downstream of ATP-dependent proteases clpP and clpX, an arrangement identical to that of lon of Escherichia coli. Phylogenetic analysis revealed that Lon-1 and Lon-2 cluster separately due to differences in the NH2-terminal substrate binding domains that may reflect differences in substrate specificity. Recombinant Lon-1 manifested properties of an ATP-dependent chaperone-protease in vitro but did not complement an E. coli Lon mutant, while Lon-2 corrected two characteristic Lon-mutant phenotypes. We conclude that B. burgdorferi Lons -1 and -2 have distinct functional roles. Lon-2 functions in a manner consistent with canonical Lon, engaged in cellular homeostasis. Lon-1, by virtue of its blood induction, and as a unique feature of the Borreliae, may be important in host adaptation from the arthropod to a warm-blooded host. Lyme disease, caused by the spirochete Borrelia burgdorferi, is the most prevalent arthropod-borne disease in North America. In nature, the bacterium oscillates between its tick vector host (Ixodes spp.) and small rodents (Peromyscus spp.). B. burgdorferi is able to persist in these two very different host environments by modulating the expression of surface lipoproteins proteins, or other proteins, in response to host factors or environmental cues such as temperature and pH. Our interest in this process led to the identification of a homolog of the E. coli ATP-dependent lon protease (lon-1) in B. burgdorferi that was upregulated in response to blood. The prototypical Lon of E. coli is a conserved protease important for the destruction of abnormal and short-lived proteins. B. burgdorferi is unusual in that it also codes for a second lon homolog, lon-2, that was not upregulated in response to blood. In this study, we sought to clarify the roles for Lon-1 and Lon-2 in B. burgdorferi. We present evidence that Lon-1 is an ATP- and Mg2+-dependent protease but does not function in a manner consistent with a prototypical Lon. Lon-2, however, functionally complemented Lon in E. coli. Thus, Lon-1 and Lon-2 appear to have distinct roles in B. burgdorferi; Lon-1 by virtue of its blood induction may be important in host adaptation, while Lon-2 is the functional homolog of E. coli Lon.
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Affiliation(s)
- James L Coleman
- State of New York Department of Health, Stony Brook University, Stony Brook, New York, United States of America.
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45
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Tokarz R, Kapoor V, Samuel JE, Bouyer DH, Briese T, Lipkin WI. Detection of tick-borne pathogens by MassTag polymerase chain reaction. Vector Borne Zoonotic Dis 2009; 9:147-52. [PMID: 18800864 DOI: 10.1089/vbz.2008.0088] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MassTag polymerase chain reaction (PCR) is a platform that enables microbe detection using primers labeled through a photocleavable link with tags that vary in molecular weight. After multiplex PCR, tags are released by ultraviolet irradiation and analyzed by mass spectroscopy. The identification of a microbe in a sample is determined by its cognate tags. Here we describe establishment and implementation of a MassTag PCR panel for surveillance of microbes implicated in tick-vectored infectious diseases.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
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46
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Dominguez SR, Briese T, Palacios G, Hui J, Villari J, Kapoor V, Tokarz R, Glodé MP, Anderson MS, Robinson CC, Holmes KV, Lipkin WI. Multiplex MassTag-PCR for respiratory pathogens in pediatric nasopharyngeal washes negative by conventional diagnostic testing shows a high prevalence of viruses belonging to a newly recognized rhinovirus clade. J Clin Virol 2008; 43:219-22. [PMID: 18674964 PMCID: PMC2603178 DOI: 10.1016/j.jcv.2008.06.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 06/03/2008] [Accepted: 06/09/2008] [Indexed: 11/02/2022]
Abstract
BACKGROUND Respiratory infections are the most common infectious diseases in humans worldwide and are a leading cause of death in children less than 5 years of age. OBJECTIVES Identify candidate pathogens in pediatric patients with unexplained respiratory disease. STUDY DESIGN Forty-four nasopharyngeal washes collected during the 2004-2005 winter season from pediatric patients with respiratory illnesses that tested negative for 7 common respiratory pathogens by culture and direct immunofluorescence assays were analyzed by MassTag-PCR. To distinguish human enteroviruses (HEV) and rhinoviruses (HRV), samples positive for picornaviruses were further characterized by sequence analysis. RESULTS Candidate pathogens were detected by MassTag PCR in 27 of the 44 (61%) specimens that previously were rated negative. Sixteen of these 27 specimens (59%) contained picornaviruses; of these 9 (57%) contained RNA of a recently discovered clade of rhinoviruses. Bocaviruses were detected in three patients by RT-PCR. CONCLUSIONS Our study confirms that multiplex MassTag-PCR enhances the detection of pathogens in clinical specimens, and shows that previously unrecognized rhinoviruses, that potentially form a species HRV-C, may cause a significant amount of pediatric respiratory disease.
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Affiliation(s)
- Samuel R Dominguez
- Department of Pediatrics, The Children's Hospital, University of Colorado Denver School of Medicine, Aurora, CO, USA
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Abstract
Borrelia burgdorferi contains a gene that codes for a Fur homologue. The function of this Fur protein is unknown; however, spirochetes grown at 23 or 35 degrees C expressed fur as determined by reverse transcriptase PCR. The fur gene (BB0647) was cloned and overexpressed as a His-Fur fusion protein in Escherichia coli. The fusion protein was purified by zinc-chelate chromatography, and the N-terminal His tag was removed to generate recombinant Fur for use in mobility shift studies. Fur bound DNA containing the E. coli Fur box sequence (GATAATGATAATCATTATC) or Bacillus subtilis Per box sequence (TTATAAT-ATTATAA) with an apparent Kd of approximately 20 nM. Fur also bound the upstream sequences of three Borrelia genes: BB0646 (gene encoding a hydrolase of the alpha/beta-fold family), BB0647 (fur), and BB0690 (napA). Addition of metal ions was not required. Binding activity was greatly decreased by either exposure to oxidizing agents (H2O2, t-butyl hydroperoxide, cumene hydroperoxide, or diamide) or by addition of Zn2+. B. burgdorferi NapA is a homologue of Dps. Dps functions in E. coli to protect DNA against damage during periods of redox stress. Fur may function in B. burgdorferi as a repressor and regulate oxidative stress genes. Additional genes (10 chromosomal and 15 plasmid) that may be Fur regulated were identified by in silico analysis.
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Affiliation(s)
- Laura I Katona
- Department of Molecular Genetics and Microbiology, Center for Infectious Diseases, State University of New York at Stony Brook, Stony Brook, New York 11794-5120, USA.
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Tokarz R, Anderton JM, Katona LI, Benach JL. Combined effects of blood and temperature shift on Borrelia burgdorferi gene expression as determined by whole genome DNA array. Infect Immun 2004; 72:5419-32. [PMID: 15322040 PMCID: PMC517457 DOI: 10.1128/iai.72.9.5419-5432.2004] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Borrelia burgdorferi undergoes differential gene expression during transmission from its tick vector to a vertebrate host. The addition of blood to a spirochete culture at 35 degrees C for 48 h had a dramatic effect on gene expression of this organism. Utilizing B. burgdorferi whole genome DNA arrays, we compared the transcriptomes of the spirochetes following a 2-day temperature shift with blood and without blood. Using combined data from three independent RNA isolations we demonstrated that the addition of blood led to a differential expression of 154 genes. Of these, 75 genes were upregulated, with 49 (65%) of them encoded on plasmids. Blood supplementation of cultures also resulted in the downregulation of 79 genes, where 56 (70%) were plasmid encoded. We verified our results by reverse transcriptase PCR of several genes in both flat and feeding ticks. In the 2-day experiment we observed the effect that exposure to increased temperature and blood combined had on B. burgdorferi gene expression at this crucial time when the spirochetes begin to move from the vector to a new vertebrate host. These changes, among others, coincide with the upregulation of the chemotaxis and sensing regulons, of the lp38-encoded ABC transporter, of proteases capable of remodeling the outer surface of the spirochetes, and of the recombination genes of cp32 as a transient or initial part of the stress response of the phage. These are all functions that could cause or facilitate the changes that spirochetes undergo following a blood meal in the tick.
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Affiliation(s)
- Rafal Tokarz
- Department of Molecular Genetics and Microbiology, Center for Infectious Diseases, Stony Brook University, 248 Centers for Molecular Medicine, Stony Brook, NY 11794-5120, USA
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49
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Anderton JM, Tokarz R, Thill CD, Kuhlow CJ, Brooks CS, Akins DR, Katona LI, Benach JL. Whole-genome DNA array analysis of the response of Borrelia burgdorferi to a bactericidal monoclonal antibody. Infect Immun 2004; 72:2035-44. [PMID: 15039324 PMCID: PMC375205 DOI: 10.1128/iai.72.4.2035-2044.2004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identification and characterization of genes that contribute to infection with Borrelia burgdorferi and, of those, genes that are targets of host responses is important for understanding the pathogenesis of Lyme disease. The complement-independent bactericidal monoclonal antibody (MAb) CB2 recognizes a carboxy-terminal, hydrophilic epitope of the outer surface protein B (OspB). CB2 kills B. burgdorferi by an unknown bactericidal mechanism. Upon binding of CB2 to OspB, differentially expressed gene products may be responsible for, or associated with, the death of the organism. A time course of the response of B. burgdorferi to CB2 was completed to analyze the differential gene expression in the bacteria over a period of visual morphological changes. Bacteria were treated with a sublethal concentration in which spirochetes were visibly distressed by the antibody but not lysed. Preliminary whole-genome DNA arrays at various time points within 1 h of incubation of B. burgdorferi with the antibody showed that most significant changes occurred at 25 min. Circular plasmid 32 (cp32)-encoded genes were active in this period of time, including the blyA homologs, phage holin system genes. DNA array data show that three blyA homologs were upregulated significantly, >/==" BORDER="0">2 standard deviations from the mean of the log ratios, and a P value of </=0.01. Quantitative real-time PCR analysis verified blyA and blyB upregulation over an 18- to 35-min time course. The hypothesis to test is whether the killing mechanism of CB2 is through uncontrolled expression of the blyA and blyB phage holin system.
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Affiliation(s)
- Julie M Anderton
- Center for Infectious Diseases and Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
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50
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Liang J, Lints R, Foehr ML, Tokarz R, Yu L, Emmons SW, Liu J, Savage-Dunn C. TheCaenorhabditis elegans schnurrihomologsma-9mediates stage- and cell type-specific responses to DBL-1 BMP-related signaling. Development 2003; 130:6453-64. [PMID: 14627718 DOI: 10.1242/dev.00863] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Caenorhabditis elegans, the DBL-1 pathway, a BMP/TGFβ-related signaling cascade, regulates body size and male tail development. We have cloned a new gene, sma-9, that encodes the C. elegans homolog of Schnurri, a large zinc finger transcription factor that regulates dpp target genes in Drosophila. Genetic interactions, the sma-9 loss-of-function phenotype, and the expression pattern suggest that sma-9 acts as a downstream component and is required in the DBL-1 signaling pathway, and thus provide the first evidence of a conserved role for Schnurri proteins in BMP signaling. Analysis of sma-9 mutant phenotypes demonstrates that SMA-9 activity is temporally and spatially restricted relative to known DBL-1 pathway components. In contrast with Drosophila schnurri, the presence of multiple alternatively spliced sma-9 transcripts suggests protein isoforms with potentially different cell sublocalization and molecular functions. We propose that SMA-9 isoforms function as transcriptional cofactors that confer specific responses to DBL-1 pathway activation.
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Affiliation(s)
- Jun Liang
- Department of Biology, Queens College, The City University of New York, Flushing, NY 11367, USA
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