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Zhang Z, Sauerwald N, Cappuccio A, Ramos I, Nair VD, Nudelman G, Zaslavsky E, Ge Y, Gaitas A, Ren H, Brockman J, Geis J, Ramalingam N, King D, McClain MT, Woods CW, Henao R, Burke TW, Tsalik EL, Goforth CW, Lizewski RA, Lizewski SE, Weir DL, Letizia AG, Sealfon SC, Troyanskaya OG. Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease. Cell Rep Methods 2023; 3:100395. [PMID: 36936082 PMCID: PMC10014279 DOI: 10.1016/j.crmeth.2023.100395] [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] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/31/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stability advantages over gene expression for diagnosis. Here, we present a computational framework for developing AS diagnostic biomarkers. Leveraging a large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whole-blood RNA sequencing (RNA-seq) data, we identify a major functional AS program switch upon viral infection. Using an independent cohort, we demonstrate the improved accuracy of AS biomarkers for SARS-CoV-2 diagnosis compared with six reported transcriptome signatures. We then optimize a subset of AS-based biomarkers to develop microfluidic PCR diagnostic assays. This assay achieves nearly perfect test accuracy (61/62 = 98.4%) using a naive principal component classifier, significantly more accurate than a gene expression PCR assay in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host-response diagnosis of infection.
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Affiliation(s)
- Zijun Zhang
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Division of Artificial Intelligence in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angelo Gaitas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hui Ren
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Joel Brockman
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Jennifer Geis
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | | | - David King
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | | | - Dawn L. Weir
- Naval Medical Research Center, Silver Spring, MD, USA
| | | | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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2
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Valdivia HO, Anderson K, Smith D, Pasay C, Salas CJ, Braga G, Lucas CM, Lizewski SE, Joya CA, Kooken JM, Sanchez JF, Cheng Q. Spatiotemporal dynamics of Plasmodium falciparum histidine-rich protein 2 and 3 deletions in Peru. Sci Rep 2022; 12:19845. [PMID: 36400806 PMCID: PMC9674673 DOI: 10.1038/s41598-022-23881-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Peru was the first country where pfhrp2 and pfhrp3 gene deletions were detected despite the fact that rapid diagnostics tests are not commonly used for confirmatory malaria diagnosis. This context provides a unique scenario to study the dynamics of pfhrp2 and pfhrp3 gene deletions without apparent RDTs selection pressure. In this study we characterized the presence of pfhrp2 and pfhrp3 genes on 325 P. falciparum samples collected in Iquitos and surrounding communities between 2011 and 2018 in order to understand the dynamics of gene deletion prevalence, potential associations with clinical symptomatology and parasite genetic background. P. falciparum presence was confirmed by microscopy and PCR of 18 s rRNA, pfmsp1 and pfmsp2. Gene deletions were assessed by amplification of exon1 and exon2 of pfhrp2 and pfhrp3 using gene specific PCRs. Confirmation of absence of HRP2 expression was assessed by ELISA of HRP2 and pLDH. Genotyping of 254 samples were performed using a panel of seven neutral microsatellite markers. Overall, pfhrp2 and pfhrp3 dual gene deletions were detected in 67% (217/324) parasite samples. Concordance between pfhrp2 deletion and negligible HRP2 protein levels was observed (Cohen's Kappa = 0.842). Prevalence of gene deletions was heterogeneous across study sites (adjusted p < 0.005) but there is an overall tendency towards increase through time in the prevalence of dual pfhrp2/3-deleted parasites between 2011 (14.3%) and 2016 (88.39%) stabilizing around 65% in 2018. Dual deletions increase was associated with dominance of a single new parasite haplotype (H8) which rapidly spread to all study sites during the 8 study years. Interestingly, participants infected with dual pfhrp2/3-deleted parasites had a significantly lower parasitemias than those without gene deletions in this cohort. Our study showed the increase of pfhrp2/3 deletions in the absence of RDTs pressure and a clonal replacement of circulating lines in the Peruvian Amazon basin. These results suggest that other factors linked to the pfhrp2/3 deletion provide a selective advantage over non-deleted strains and highlight the need for additional studies and continuing surveillance.
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Affiliation(s)
- Hugo O. Valdivia
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Karen Anderson
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.1049.c0000 0001 2294 1395QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - David Smith
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.1049.c0000 0001 2294 1395QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - Cielo Pasay
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.1049.c0000 0001 2294 1395QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - Carola J. Salas
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Greys Braga
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Carmen M. Lucas
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Stephen E. Lizewski
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Christie A. Joya
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Jennifer M. Kooken
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.507680.c0000 0001 2230 3166Walter Reed Army Institute for Research, Silver Spring, USA
| | - Juan F. Sanchez
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Qin Cheng
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.1049.c0000 0001 2294 1395QIMR-Berghofer Medical Research Institute, Brisbane, Australia
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3
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Sauerwald N, Zhang Z, Ramos I, Nair VD, Soares-Schanoski A, Ge Y, Mao W, Alshammary H, Gonzalez-Reiche AS, van de Guchte A, Goforth CW, Lizewski RA, Lizewski SE, Amper MAS, Vasoya M, Seenarine N, Guevara K, Marjanovic N, Miller CM, Nudelman G, Schilling MA, Sealfon RSG, Termini MS, Vangeti S, Weir DL, Zaslavsky E, Chikina M, Wu YN, Van Bakel H, Letizia AG, Sealfon SC, Troyanskaya OG. Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection. Cell Syst 2022; 13:924-931.e4. [PMID: 36323307 PMCID: PMC9623453 DOI: 10.1016/j.cels.2022.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/11/2022] [Revised: 07/21/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
Male sex is a major risk factor for SARS-CoV-2 infection severity. To understand the basis for this sex difference, we studied SARS-CoV-2 infection in a young adult cohort of United States Marine recruits. Among 2,641 male and 244 female unvaccinated and seronegative recruits studied longitudinally, SARS-CoV-2 infections occurred in 1,033 males and 137 females. We identified sex differences in symptoms, viral load, blood transcriptome, RNA splicing, and proteomic signatures. Females had higher pre-infection expression of antiviral interferon-stimulated gene (ISG) programs. Causal mediation analysis implicated ISG differences in number of symptoms, levels of ISGs, and differential splicing of CD45 lymphocyte phosphatase during infection. Our results indicate that the antiviral innate immunity set point causally contributes to sex differences in response to SARS-CoV-2 infection. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Zijun Zhang
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiguang Mao
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carl W Goforth
- Naval Medical Research Center, Silver Spring, MD 20910, USA
| | | | | | - Mary Anne S Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mital Vasoya
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nitish Seenarine
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristy Guevara
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nada Marjanovic
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Clare M Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Rachel S G Sealfon
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Michael S Termini
- Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC 29902, USA
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dawn L Weir
- Naval Medical Research Center, Silver Spring, MD 20910, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ying Nian Wu
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Harm Van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Department of Computer Science, Princeton University, Princeton, NJ 08540, USA.
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4
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Lizewski RA, Sealfon RSG, Park SW, Smith GR, Porter CK, Gonzalez-Reiche AS, Ge Y, Miller CM, Goforth CW, Pincas H, Termini MS, Ramos I, Nair VD, Lizewski SE, Alshammary H, Cer RZ, Chen HW, George MC, Arnold CE, Glang LA, Long KA, Malagon F, Marayag JJ, Nunez E, Rice GK, Santa Ana E, Schilling MA, Smith DR, Sugiharto VA, Sun P, van de Guchte A, Khan Z, Dutta J, Vangeti S, Voegtly LJ, Weir DL, Metcalf CJE, Troyanskaya OG, Bishop-Lilly KA, Grenfell BT, van Bakel H, Letizia AG, Sealfon SC. SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures. Epidemiology 2022; 33:797-807. [PMID: 35944149 PMCID: PMC9531985 DOI: 10.1097/ede.0000000000001523] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/20/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Marine recruits training at Parris Island experienced an unexpectedly high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, despite preventive measures including a supervised, 2-week, pre-entry quarantine. We characterize SARS-CoV-2 transmission in this cohort. METHODS Between May and November 2020, we monitored 2,469 unvaccinated, mostly male, Marine recruits prospectively during basic training. If participants tested negative for SARS-CoV-2 by quantitative polymerase chain reaction (qPCR) at the end of quarantine, they were transferred to the training site in segregated companies and underwent biweekly testing for 6 weeks. We assessed the effects of coronavirus disease 2019 (COVID-19) prevention measures on other respiratory infections with passive surveillance data, performed phylogenetic analysis, and modeled transmission dynamics and testing regimens. RESULTS Preventive measures were associated with drastically lower rates of other respiratory illnesses. However, among the trainees, 1,107 (44.8%) tested SARS-CoV-2-positive, with either mild or no symptoms. Phylogenetic analysis of viral genomes from 580 participants revealed that all cases but one were linked to five independent introductions, each characterized by accumulation of mutations across and within companies, and similar viral isolates in individuals from the same company. Variation in company transmission rates (mean reproduction number R 0 ; 5.5 [95% confidence interval [CI], 5.0, 6.1]) could be accounted for by multiple initial cases within a company and superspreader events. Simulations indicate that frequent rapid-report testing with case isolation may minimize outbreaks. CONCLUSIONS Transmission of wild-type SARS-CoV-2 among Marine recruits was approximately twice that seen in the community. Insights from SARS-CoV-2 outbreak dynamics and mutations spread in a remote, congregate setting may inform effective mitigation strategies.
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Affiliation(s)
| | - Rachel S. G. Sealfon
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY
| | - Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Gregory R. Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hanna Pincas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Regina Z. Cer
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
| | - Hua Wei Chen
- Naval Medical Research Center, Silver Spring, MD
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD
| | | | - Catherine E. Arnold
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Defense Threat Reduction Agency, Fort Belvoir, VA
| | - Lindsay A. Glang
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | - Kyle A. Long
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | - Francisco Malagon
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | | | - Edgar Nunez
- Naval Medical Research Center, Silver Spring, MD
| | - Gregory K. Rice
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | | | | | - Darci R. Smith
- Immunodiagnostics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
| | - Victor A. Sugiharto
- Naval Medical Research Center, Silver Spring, MD
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD
| | - Peifang Sun
- Naval Medical Research Center, Silver Spring, MD
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jayeeta Dutta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Logan J. Voegtly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | - Dawn L. Weir
- Naval Medical Research Center, Silver Spring, MD
| | | | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY
- Department of Computer Science, Princeton University, Princeton, NJ
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Kimberly A. Bishop-Lilly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
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5
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Villena FE, Sanchez JF, Nolasco O, Braga G, Ricopa L, Barazorda K, Salas CJ, Lucas C, Lizewski SE, Joya CA, Gamboa D, Delgado-Ratto C, Valdivia HO. Drug resistance and population structure of Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon. Sci Rep 2022; 12:16474. [PMID: 36182962 PMCID: PMC9526214 DOI: 10.1038/s41598-022-21028-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/21/2022] [Indexed: 11/22/2022] Open
Abstract
Malaria is a major health problem in Peru despite substantial progress achieved by the ongoing malaria elimination program. This study explored the population genetics of 63 Plasmodium falciparum and 170 P. vivax cases collected in the Peruvian Amazon Basin between 2015 and 2019. Microscopy and PCR were used for malaria detection and positive samples were genotyped at neutral and drug resistance-associated regions. The P. falciparum population exhibited a low nucleotide diversity (π = 0.02) whereas the P. vivax population presented a higher genetic diversity (π = 0.34). All P. falciparum samples (n = 63) carried chloroquine (CQ) resistant mutations on Pfcrt. Most P. falciparum samples (53 out of 54) carried sulfadoxine (SD) resistant mutations on Pfdhfr and Pfdhps. No evidence was found of artemisinin resistance mutations on kelch13. Population structure showed that a single cluster accounted for 93.4% of the P. falciparum samples whereas three clusters were found for P. vivax. Our study shows a low genetic diversity for both species with significant differences in genetic sub-structuring. The high prevalence of CQ-resistance mutations could be a result of indirect selection pressures driven by the P. vivax treatment scheme. These results could be useful for public health authorities to safeguard the progress that Peru has achieved towards malaria elimination.
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Affiliation(s)
| | - Juan F Sanchez
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Oscar Nolasco
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Greys Braga
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | | | | | - Carola J Salas
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Carmen Lucas
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Stephen E Lizewski
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Christie A Joya
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru.,Malaria Research Group (MaRCH), Global Health Institute, University of Antwerp, 2610, Antwerp, Belgium
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru.
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6
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Sedegah M, Porter C, Hollingdale MR, Ganeshan H, Huang J, Goforth CW, Belmonte M, Belmonte A, Weir DL, Lizewski RA, Lizewski SE, Sealfon SC, Jani V, Cheng Y, Inoue S, Velasco R, Villasante E, Sun P, Letizia AG. CHARM: COVID-19 Health Action Response for Marines-Association of antigen-specific interferon-gamma and IL2 responses with asymptomatic and symptomatic infections after a positive qPCR SARS-CoV-2 test. PLoS One 2022; 17:e0266691. [PMID: 35390102 PMCID: PMC8989306 DOI: 10.1371/journal.pone.0266691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/30/2021] [Accepted: 03/24/2022] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2 T cell responses are associated with COVID-19 recovery, and Class I- and Class II-restricted epitopes have been identified in the spike (S), nucleocapsid (N) and membrane (M) proteins and others. This prospective COVID-19 Health Action Response for Marines (CHARM) study enabled assessment of T cell responses against S, N and M proteins in symptomatic and asymptomatic SARS-CoV-2 infected participants. At enrollment all participants were negative by qPCR; follow-up occurred biweekly and bimonthly for the next 6 weeks. Study participants who tested positive by qPCR SARS-CoV-2 test were enrolled in an immune response sub-study. FluoroSpot interferon-gamma (IFN-γ) and IL2 responses following qPCR-confirmed infection at enrollment (day 0), day 7 and 14 and more than 28 days later were measured using pools of 17mer peptides covering S, N, and M proteins, or CD4+CD8 peptide pools containing predicted epitopes from multiple SARS-CoV-2 antigens. Among 124 asymptomatic and 105 symptomatic participants, SARS-CoV-2 infection generated IFN-γ responses to the S, N and M proteins that persisted longer in asymptomatic cases. IFN-γ responses were significantly (p = 0.001) more frequent to the N pool (51.4%) than the M pool (18.9%) among asymptomatic but not symptomatic subjects. Asymptomatic IFN-γ responders to the CD4+CD8 pool responded more frequently to the S pool (55.6%) and N pool (57.1%), than the M pool (7.1%), but not symptomatic participants. The frequencies of IFN-γ responses to the S and N+M pools peaked 7 days after the positive qPCR test among asymptomatic (S pool: 22.2%; N+M pool: 28.7%) and symptomatic (S pool: 15.3%; N+M pool 21.9%) participants and dropped by >28 days. Magnitudes of post-infection IFN-γ and IL2 responses to the N+M pool were significantly correlated with IFN-γ and IL2 responses to the N and M pools. These data further support the central role of Th1-biased cell mediated immunity IFN-γ and IL2 responses, particularly to the N protein, in controlling COVID-19 symptoms, and justify T cell-based COVID-19 vaccines that include the N and S proteins.
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Affiliation(s)
- Martha Sedegah
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Chad Porter
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Michael R. Hollingdale
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Harini Ganeshan
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Jun Huang
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Carl W. Goforth
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Maria Belmonte
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Arnel Belmonte
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- GDIT, MD, United States of America
| | - Dawn L. Weir
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | | | | | - Stuart C. Sealfon
- Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Vihasi Jani
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Ying Cheng
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Leidos, Reston, VA, United States of America
| | - Sandra Inoue
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- GDIT, MD, United States of America
| | - Rachael Velasco
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Eileen Villasante
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Peifang Sun
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Andrew G. Letizia
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
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7
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Barazorda KA, Salas CJ, Braga G, Ricopa L, Ampuero JS, Siles C, Sanchez JF, Montano S, Lizewski SE, Joya CA, Bishop DK, Valdivia HO. Validation study of Boil & Spin Malachite Green Loop Mediated Isothermal Amplification (B&S MG-LAMP) versus microscopy for malaria detection in the Peruvian Amazon. PLoS One 2021; 16:e0258722. [PMID: 34695122 PMCID: PMC8544869 DOI: 10.1371/journal.pone.0258722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
Malaria elimination efforts in Peru have dramatically reduced the incidence of cases in the Amazon Basin. To achieve the elimination, the detection of asymptomatic and submicroscopic carriers becomes a priority. Therefore, efforts should focus on tests sensitive enough to detect low-density parasitemia, deployable to resource-limited areas and affordable for large screening purposes. In this study, we assessed the performance of the Malachite–Green LAMP (MG-LAMP) using heat-treated DNA extraction (Boil & Spin; B&S MG-LAMP) on 283 whole blood samples collected from 9 different sites in Loreto, Peru and compared its performance to expert and field microscopy. A real-time PCR assay was used to quantify the parasite density. In addition, we explored a modified version of the B&S MG-LAMP for detection of submicroscopic infection in 500 samples and compared the turnaround time and cost of the MG-LAMP with microscopy. Compared to expert microscopy, the genus B&S MG-LAMP had a sensitivity of 99.4% (95%CI: 96.9%– 100%) and specificity of 97.1% (95%CI: 91.9%– 99.4%). The P. vivax specific B&S MG-LAMP had a sensitivity of 99.4% (96.6%– 100%) and specificity of 99.2% (95.5%– 100%) and the P. falciparum assay had a sensitivity of 100% (95%CI: 78.2%– 100%) and specificity of 99.3% (95%CI: 97.3%– 99.8%). The modified genus B&S MG-LAMP assay detected eight submicroscopic malaria cases (1.6%) which the species-specific assays did not identify. The turnaround time of B&S MG-LAMP was faster than expert microscopy with as many as 60 samples being processed per day by field technicians with limited training and utilizing a simple heat-block. The modified B&S MG-LAMP offers a simple and sensitive molecular test of choice for the detection of submicroscopic infections that can be used for mass screening in resources limited facilities in endemic settings nearing elimination and where a deployable test is required.
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Affiliation(s)
| | - Carola J. Salas
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Greys Braga
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Leonila Ricopa
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Julia S. Ampuero
- Department of Virology and Emerging infections, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Crystyan Siles
- Department of Virology and Emerging infections, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Juan F. Sanchez
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Silvia Montano
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Stephen E. Lizewski
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Christie A. Joya
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Danett K. Bishop
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Hugo O. Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
- * E-mail:
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8
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Letizia AG, Smith DR, Ge Y, Ramos I, Sealfon RSG, Goforth C, Gonzalez-Reiche AS, Vangeti S, Weir DL, Alshammary H, Chen HW, George MC, Soares-Schanoski A, Lizewski RA, Lizewski SE, Marayag J, Miller CM, Nunez E, Porter CK, Ana ES, Schilling M, Sugiharto VA, Sun P, Termini M, van de Guchte A, Troyanskaya OG, van Bakel H, Sealfon SC. Viable virus shedding during SARS-CoV-2 reinfection. Lancet Respir Med 2021; 9:e56-e57. [PMID: 33964243 PMCID: PMC8099311 DOI: 10.1016/s2213-2600(21)00219-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/27/2021] [Indexed: 11/03/2022]
Affiliation(s)
| | - Darci R Smith
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Carl Goforth
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Ana S Gonzalez-Reiche
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dawn L Weir
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Hala Alshammary
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hua Wei Chen
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Mary-Catherine George
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | - Jan Marayag
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Clare M Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edgar Nunez
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Chad K Porter
- Naval Medical Research Center, Silver Spring, MD, USA
| | | | | | | | - Peifang Sun
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Michael Termini
- Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC, USA
| | - Adriana van de Guchte
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Harm van Bakel
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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9
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Letizia AG, Ge Y, Vangeti S, Goforth C, Weir DL, Kuzmina NA, Balinsky CA, Chen HW, Ewing D, Soares-Schanoski A, George MC, Graham WD, Jones F, Bharaj P, Lizewski RA, Lizewski SE, Marayag J, Marjanovic N, Miller CM, Mofsowitz S, Nair VD, Nunez E, Parent DM, Porter CK, Santa Ana E, Schilling M, Stadlbauer D, Sugiharto VA, Termini M, Sun P, Tracy RP, Krammer F, Bukreyev A, Ramos I, Sealfon SC. SARS-CoV-2 seropositivity and subsequent infection risk in healthy young adults: a prospective cohort study. Lancet Respir Med 2021; 9:712-720. [PMID: 33865504 PMCID: PMC8049591 DOI: 10.1016/s2213-2600(21)00158-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 01/23/2023]
Abstract
Background Whether young adults who are infected with SARS-CoV-2 are at risk of subsequent infection is uncertain. We investigated the risk of subsequent SARS-CoV-2 infection among young adults seropositive for a previous infection. Methods This analysis was performed as part of the prospective COVID-19 Health Action Response for Marines study (CHARM). CHARM included predominantly male US Marine recruits, aged 18–20 years, following a 2-week unsupervised quarantine at home. After the home quarantine period, upon arrival at a Marine-supervised 2-week quarantine facility (college campus or hotel), participants were enrolled and were assessed for baseline SARS-CoV-2 IgG seropositivity, defined as a dilution of 1:150 or more on receptor-binding domain and full-length spike protein ELISA. Participants also completed a questionnaire consisting of demographic information, risk factors, reporting of 14 specific COVID-19-related symptoms or any other unspecified symptom, and brief medical history. SARS-CoV-2 infection was assessed by PCR at weeks 0, 1, and 2 of quarantine and participants completed a follow-up questionnaire, which included questions about the same COVID-19-related symptoms since the last study visit. Participants were excluded at this stage if they had a positive PCR test during quarantine. Participants who had three negative swab PCR results during quarantine and a baseline serum serology test at the beginning of the supervised quarantine that identified them as seronegative or seropositive for SARS-CoV-2 then went on to basic training at Marine Corps Recruit Depot—Parris Island. Three PCR tests were done at weeks 2, 4, and 6 in both seropositive and seronegative groups, along with the follow-up symptom questionnaire and baseline neutralising antibody titres on all subsequently infected seropositive and selected seropositive uninfected participants (prospective study period). Findings Between May 11, 2020, and Nov 2, 2020, we enrolled 3249 participants, of whom 3168 (98%) continued into the 2-week quarantine period. 3076 (95%) participants, 2825 (92%) of whom were men, were then followed up during the prospective study period after quarantine for 6 weeks. Among 189 seropositive participants, 19 (10%) had at least one positive PCR test for SARS-CoV-2 during the 6-week follow-up (1·1 cases per person-year). In contrast, 1079 (48%) of 2247 seronegative participants tested positive (6·2 cases per person-year). The incidence rate ratio was 0·18 (95% CI 0·11–0·28; p<0·001). Among seropositive recruits, infection was more likely with lower baseline full-length spike protein IgG titres than in those with higher baseline full-length spike protein IgG titres (hazard ratio 0·45 [95% CI 0·32–0·65]; p<0·001). Infected seropositive participants had viral loads that were about 10-times lower than those of infected seronegative participants (ORF1ab gene cycle threshold difference 3·95 [95% CI 1·23–6·67]; p=0·004). Among seropositive participants, baseline neutralising titres were detected in 45 (83%) of 54 uninfected and in six (32%) of 19 infected participants during the 6 weeks of observation (ID50 difference p<0·0001). Interpretation Seropositive young adults had about one-fifth the risk of subsequent infection compared with seronegative individuals. Although antibodies induced by initial infection are largely protective, they do not guarantee effective SARS-CoV-2 neutralisation activity or immunity against subsequent infection. These findings might be relevant for optimisation of mass vaccination strategies. Funding Defense Health Agency and Defense Advanced Research Projects Agency.
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Affiliation(s)
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carl Goforth
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Dawn L Weir
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Natalia A Kuzmina
- Department of Pathology University of Texas Medical Branch and Galveston National Laboratory, Galveston, TX, USA
| | | | - Hua Wei Chen
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Dan Ewing
- Naval Medical Research Center, Silver Spring, MD, USA
| | | | | | | | - Franca Jones
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Preeti Bharaj
- Department of Pathology University of Texas Medical Branch and Galveston National Laboratory, Galveston, TX, USA
| | | | | | - Jan Marayag
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Nada Marjanovic
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clare M Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sagie Mofsowitz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Nunez
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Danielle M Parent
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Chad K Porter
- Naval Medical Research Center, Silver Spring, MD, USA
| | | | | | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Michael Termini
- and Naval Medical Readiness and Training Command Beaufort, Beaufort, SC, USA
| | - Peifang Sun
- Naval Medical Research Center, Silver Spring, MD, USA
| | - Russell P Tracy
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander Bukreyev
- Department of Pathology University of Texas Medical Branch and Galveston National Laboratory, Galveston, TX, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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10
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Leski TA, Bangura U, Jimmy DH, Ansumana R, Lizewski SE, Stenger DA, Taitt CR, Vora GJ. Multidrug-resistant tet(X)-containing hospital isolates in Sierra Leone. Int J Antimicrob Agents 2013; 42:83-6. [PMID: 23688520 DOI: 10.1016/j.ijantimicag.2013.04.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 04/01/2013] [Accepted: 04/09/2013] [Indexed: 11/26/2022]
Abstract
The tet(X) gene encodes a flavin-dependent monooxygenase that confers resistance to all clinically relevant tetracycline antibiotics including tigecycline. It has only previously been identified in environmental and non-human pathogenic bacteria. To investigate levels of multidrug resistance in Bo, Sierra Leone, a molecular epidemiological study was conducted using an antimicrobial resistance determinant microarray (ARDM), PCR and DNA sequencing. The study found that 21% of isolates from Mercy Hospital (Bo, Sierra Leone) were tet(X)-positive, all of which originated from urinary specimens. Use of molecular epidemiological surveillance tools has provided the first evidence of tet(X)-containing multidrug-resistant Gram-negative hospital isolates in a hospital in Sierra Leone.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
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11
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Howard EC, Hamdan LJ, Lizewski SE, Ringeisen BR. High frequency of glucose-utilizing mutants in Shewanella oneidensis MR-1. FEMS Microbiol Lett 2011; 327:9-14. [DOI: 10.1111/j.1574-6968.2011.02450.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/22/2011] [Accepted: 10/26/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Leila J. Hamdan
- Marine Biogeochemistry Section, Code 6114; U.S. Naval Research Laboratory; Washington; DC; USA
| | - Stephen E. Lizewski
- Laboratory for Biosensors & Biomaterials, Code 6910; U.S. Naval Research Laboratory; Washington; DC; USA
| | - Bradley R. Ringeisen
- Bioenergy and Biofabrication Section, Code 6115; U.S. Naval Research Laboratory; Washington; DC; USA
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12
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Biffinger JC, Fitzgerald LA, Ray R, Little BJ, Lizewski SE, Petersen ER, Ringeisen BR, Sanders WC, Sheehan PE, Pietron JJ, Baldwin JW, Nadeau LJ, Johnson GR, Ribbens M, Finkel SE, Nealson KH. The utility of Shewanella japonica for microbial fuel cells. Bioresour Technol 2011; 102:290-297. [PMID: 20663660 DOI: 10.1016/j.biortech.2010.06.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/09/2010] [Accepted: 06/17/2010] [Indexed: 05/29/2023]
Abstract
Shewanella-containing microbial fuel cells (MFCs) typically use the fresh water wild-type strain Shewanella oneidensis MR-1 due to its metabolic diversity and facultative oxidant tolerance. However, S. oneidensis MR-1 is not capable of metabolizing polysaccharides for extracellular electron transfer. The applicability of Shewanella japonica (an agar-lytic Shewanella strain) for power applications was analyzed using a diverse array of carbon sources for current generation from MFCs, cellular physiological responses at an electrode surface, biofilm formation, and the presence of soluble extracellular mediators for electron transfer to carbon electrodes. Critically, air-exposed S. japonica utilizes biosynthesized extracellular mediators for electron transfer to carbon electrodes with sucrose as the sole carbon source.
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Affiliation(s)
- Justin C Biffinger
- Chemistry Division, US Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, DC 20375, USA.
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13
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Carterson AJ, Morici LA, Jackson DW, Frisk A, Lizewski SE, Jupiter R, Simpson K, Kunz DA, Davis SH, Schurr JR, Hassett DJ, Schurr MJ. The transcriptional regulator AlgR controls cyanide production in Pseudomonas aeruginosa. J Bacteriol 2004; 186:6837-44. [PMID: 15466037 PMCID: PMC522194 DOI: 10.1128/jb.186.20.6837-6844.2004] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [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
Pseudomonas aeruginosa is an opportunistic pathogen that causes chronic lung infections in cystic fibrosis (CF) patients. One characteristic of P. aeruginosa CF isolates is the overproduction of the exopolysaccharide alginate, controlled by AlgR. Transcriptional profiling analyses comparing mucoid P. aeruginosa strains to their isogenic algR deletion strains showed that the transcription of cyanide-synthesizing genes (hcnAB) was approximately 3-fold lower in the algR mutants. S1 nuclease protection assays corroborated these findings, indicating that AlgR activates hcnA transcription in mucoid P. aeruginosa. Quantification of hydrogen cyanide (HCN) production from laboratory isolates revealed that mucoid laboratory strains made sevenfold more HCN than their nonmucoid parental strains. In addition, comparison of laboratory and clinically derived nonmucoid strains revealed that HCN was fivefold higher in the nonmucoid CF isolates. Moreover, the average amount of cyanide produced by mucoid clinical isolates was 4.7 +/- 0.85 micromol of HCN/mg of protein versus 2.4 +/- 0.40 micromol of HCN/mg of protein for nonmucoid strains from a survey conducted with 41 P. aeruginosa CF isolates from 24 patients. Our data indicate that (i) mucoid P. aeruginosa regardless of their origin (laboratory or clinically derived) produce more cyanide than their nonmucoid counterparts, (ii) AlgR regulates HCN production in P. aeruginosa, and (iii) P. aeruginosa CF isolates are more hypercyanogenic than nonmucoid laboratory strains. Taken together, cyanide production may be a relevant virulence factor in CF lung disease, the production of which is regulated, in part, by AlgR.
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Affiliation(s)
- Alexander J Carterson
- Department of Microbiology and Immunology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112-2699, USA
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14
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Lizewski SE, Schurr JR, Jackson DW, Frisk A, Carterson AJ, Schurr MJ. Identification of AlgR-regulated genes in Pseudomonas aeruginosa by use of microarray analysis. J Bacteriol 2004; 186:5672-84. [PMID: 15317771 PMCID: PMC516850 DOI: 10.1128/jb.186.17.5672-5684.2004] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [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: 01/27/2023] Open
Abstract
The Pseudomonas aeruginosa transcriptional regulator AlgR controls a variety of different processes, including alginate production, type IV pilus function, and virulence, indicating that AlgR plays a pivotal role in the regulation of gene expression. In order to characterize the AlgR regulon, Pseudomonas Affymetrix GeneChips were used to generate the transcriptional profiles of (i) P. aeruginosa PAO1 versus its algR mutant in mid-logarithmic phase, (ii) P. aeruginosa PAO1 versus its algR mutant in stationary growth phase, and (iii) PAO1 versus PAO1 harboring an algR overexpression plasmid. Expression analysis revealed that, during mid-logarithmic growth, AlgR activated the expression of 58 genes while it repressed the expression of 37 others, while during stationary phase, it activated expression of 45 genes and repression of 14 genes. Confirmatory experiments were performed on two genes found to be AlgR repressed (hcnA and PA1557) and one AlgR-activated operon (fimU-pilVWXY1Y2). An S1 nuclease protection assay demonstrated that AlgR repressed both known hcnA promoters in PAO1. Additionally, direct measurement of hydrogen cyanide (HCN) production showed that P. aeruginosa PAO1 produced threefold-less HCN than did its algR deletion strain. AlgR also repressed transcription of two promoters of the uncharacterized open reading frame PA1557. Further, the twitching motility defect of an algR mutant was complemented by the fimTU-pilVWXY1Y2E operon, thus identifying the AlgR-controlled genes responsible for this defect in an algR mutant. This study identified four new roles for AlgR: (i) AlgR can repress gene transcription, (ii) AlgR activates the fimTU-pilVWXY1Y2E operon, (iii) AlgR regulates HCN production, and (iv) AlgR controls transcription of the putative cbb3-type cytochrome PA1557.
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Affiliation(s)
- Stephen E Lizewski
- Department of Microbiology and Immunology, Program in Molecular Pathogenesis and Immunity, Louisiana Center for Lung Biology and Immunotherapy, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112-2699, USA
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15
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Abstract
Chronic Pseudomonas aeruginosa lung infection is the major cause of morbidity and mortality in cystic fibrosis (CF) patients. One P. aeruginosa virulence factor unique to CF isolates is overproduction of alginate, phenotypically termed mucoidy. Mucoidy is the result of increased transcription from the algD gene and is activated by the transcriptional regulator AlgR. Mutations in algR result in a nonmucoid phenotype and loss of twitching motility. Additionally, AlgR controls transcription of algC, encoding a dual-function enzyme necessary for both lipopolysaccharide (LPS) and alginate production. Therefore, to determine the effect of algR on P. aeruginosa virulence, an algR mutant was examined for sensitivity to reactive oxygen intermediates, killing by phagocytes, systemic virulence, and the ability to maintain a murine lung infection. We found that P. aeruginosa PAO700 (algR::Gm(r)) was less lethal than PAO1, as tested in an acute septicemia infection mouse model, and was cleared more efficiently in a mouse pneumonia model. Additionally, the algR mutant (PAO700) was more sensitive to hypochlorite. However, PAO700 was more resistant to hydrogen peroxide and killed less readily in an acellular myeloperoxidase assay than PAO1. There was little difference in killing between PAO1 and PAO700 with macrophage-like J774 cells and human polymorhonuclear leukocytes. Two-dimensional gel analysis of P. aeruginosa algR mutant and wild-type protein extracts revealed 47 differentially regulated proteins, suggesting that AlgR plays both a positive role and a negative role in gene expression. Together, these results imply that AlgR is necessary for virulence and regulates genes in addition to the genes associated with alginate and LPS production and pilus function.
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Affiliation(s)
- Stephen E Lizewski
- Department of Microbiology and Immunology, Program in Molecular Pathogenesis and Immunity, Tulane University Health Sciences Center, New Orleans, Louisiana 70112-2699, USA
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