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Eguiluz M, Qquellon J, Vargas SK, Reyes-Diaz M, Konda KA, Caceres CF, Klausner JD. Molecular Characterization of Genital and Extragenital Lesions With the PlexPCR VHS Assay in Patients Diagnosed With Syphilis. Open Forum Infect Dis 2023; 10:ofad483. [PMID: 37869408 PMCID: PMC10588620 DOI: 10.1093/ofid/ofad483] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
Background Syphilis diagnosis relies on immunologic markers and clinical protocols. However, syphilitic lesions can be confused with other genital ulcer diseases. Methods Using a PlexPCR VHS assay, we analyzed lesion DNA samples from 87 individuals who were clinically diagnosed with early syphilis infection and had at least 1 positive serologic test result. DNA was detected by the PlexPCR VHS multiplex assay and β-globin genes. Results Among the participants, 99% (86/87) had a positive rapid treponemal test result. DNA was successfully detected in 91% (79/87) of the lesion samples. PlexPCR VHS identified 5 herpes simplex virus (HSV)/Treponema pallidum coinfections (2 HSV-1 and 3 HSV-2), only T pallidum DNA in 62% (49/79), and only HSV-2 in 12.7% (10/79). While 19% (15/79) were negative for all pathogens, none were varicella zoster virus positive. The PlexPCR VHS had 68.4% agreement with the clinical diagnosis. Conclusions Since the PlexPCR VHS detects multiple organisms simultaneously, it can help to confirm actual syphilis and identify other pathogen coinfections or the pathogen causing the ulcer.
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Affiliation(s)
- Maria Eguiluz
- Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jazmin Qquellon
- Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Silver K Vargas
- Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru
- School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Michael Reyes-Diaz
- Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kelika A Konda
- Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Carlos F Caceres
- Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jeffrey D Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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Qquellon J, Vargas SK, Eguiluz M, Vasquez F, Durand D, Allan-Blitz LT, Konda KA, Ochoa TJ, Caceres CF, Klausner JD. Extra-genital Neisseria gonorrhoeae infections with genetic mutations conferring ciprofloxacin resistance among men who have sex with men and transgender women in Lima, Peru. Int J STD AIDS 2023; 34:245-250. [PMID: 36637128 PMCID: PMC9950594 DOI: 10.1177/09564624221147326] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/07/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND The increasing prevalence of drug-resistant Neisseria gonorrhoeae (NG) infections has caused great concern. Ciprofloxacin remains the empiric antimicrobial recommended to treat NG infections in Peru disregarding the susceptibility profile of circulating NG strains. We report the prevalence of individuals infected with NG strains presenting mutations in the gyrA gene that confers ciprofloxacin resistance. METHODS We conducted a descriptive study assessing extragenital swab samples collected from a cohort of men who have sex with men and transgender women in Lima, Peru. Anal and pharyngeal NG positive swabs for Aptima Combo 2 assay (Hologic Inc., USA) were used for DNA extraction. We performed TaqMan real time PCR assays to detect a point mutation at codon Ser91 of the gyrase A (gyrA) gene. RESULTS From 156 individuals who had at least one positive sample for NG reported by the Aptima assay, 80 individuals had at least one amplified DNA for the gyrA gene. We found that 67 of them (84.0%) were infected with a gyrA-mutated NG strain at the Ser91 codon. CONCLUSIONS We report a high prevalence of gyrA mutation conferring ciprofloxacin resistance among individuals with extragenital NG infection. Empirical treatment of NG needs to be urgently updated in Peru in concordance with international guidelines.
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Affiliation(s)
- Jazmin Qquellon
- Center for Interdisciplinary
Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano
Heredia, Lima, Peru
| | - Silver K Vargas
- Center for Interdisciplinary
Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano
Heredia, Lima, Peru
- School of Public Health and
Administration, Universidad Peruana Cayetano
Heredia, Lima, Peru
| | - Maria Eguiluz
- Center for Interdisciplinary
Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano
Heredia, Lima, Peru
| | - Francesca Vasquez
- Center for Interdisciplinary
Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano
Heredia, Lima, Peru
| | - David Durand
- Instituto de Medicina Tropical
“Alexander Von Humboldt”, Universidad Peruana Cayetano
Heredia, Lima, Peru
| | - Lao-Tzu Allan-Blitz
- Division of Global Health Equity,
Department of Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
| | - Kelika A Konda
- Center for Interdisciplinary
Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano
Heredia, Lima, Peru
- Division of Infectious Diseases,
David Geffen School of Medicine, University of
California, Los Angeles, CA, USA
| | - Theresa J Ochoa
- Instituto de Medicina Tropical
“Alexander Von Humboldt”, Universidad Peruana Cayetano
Heredia, Lima, Peru
| | - Carlos F Caceres
- Center for Interdisciplinary
Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano
Heredia, Lima, Peru
| | - Jeffrey D Klausner
- Department of Population and Public
Health Sciences, Keck School of Medicine, University of Southern
California, Los Angeles, CA, USA
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Lieberman NAP, Armstrong TD, Chung B, Pfalmer D, Hennelly CM, Haynes A, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Conte ID, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitja O, Rompalo A, Mulcahy F, Hook EW, Hoffman IF, Matoga MM, Zheng H, Yang B, Lopez-Medina E, Ramirez LG, Radolf JD, Hawley KL, Salazar JC, Lukehart SA, Seña AC, Parr JB, Giacani L, Greninger AL. High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny. Front Microbiol 2022; 13:1007056. [PMID: 36204625 PMCID: PMC9531955 DOI: 10.3389/fmicb.2022.1007056] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Sequencing of most Treponema pallidum genomes excludes repeat regions in tp0470 and the tp0433 gene, encoding the acidic repeat protein (arp). As a first step to understanding the evolution and function of these genes and the proteins they encode, we developed a protocol to nanopore sequence tp0470 and arp genes from 212 clinical samples collected from ten countries on six continents. Both tp0470 and arp repeat structures recapitulate the whole genome phylogeny, with subclade-specific patterns emerging. The number of tp0470 repeats is on average appears to be higher in Nichols-like clade strains than in SS14-like clade strains. Consistent with previous studies, we found that 14-repeat arp sequences predominate across both major clades, but the combination and order of repeat type varies among subclades, with many arp sequence variants limited to a single subclade. Although strains that were closely related by whole genome sequencing frequently had the same arp repeat length, this was not always the case. Structural modeling of TP0470 suggested that the eight residue repeats form an extended α-helix, predicted to be periplasmic. Modeling of the ARP revealed a C-terminal sporulation-related repeat (SPOR) domain, predicted to bind denuded peptidoglycan, with repeat regions possibly incorporated into a highly charged β-sheet. Outside of the repeats, all TP0470 and ARP amino acid sequences were identical. Together, our data, along with functional considerations, suggests that both TP0470 and ARP proteins may be involved in T. pallidum cell envelope remodeling and homeostasis, with their highly plastic repeat regions playing as-yet-undetermined roles.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Thaddeus D. Armstrong
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Benjamin Chung
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Daniel Pfalmer
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Christopher M. Hennelly
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Austin Haynes
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Emily Romeis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Qian-Qiu Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Rui-Li Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cai-Xia Kou
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Giulia Ciccarese
- Section of Dermatology, Department of Health Sciences, San Martino University Hospital, Genoa, Italy
| | - Ivano Dal Conte
- Sexual Health Center, Department of Prevention, ASL Città di Torino, Turin, Italy
| | - Marco Cusini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Drago
- Section of Dermatology, Department of Health Sciences, San Martino University Hospital, Genoa, Italy
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- School of Public Health and Administration “Carlos Vidal Layseca”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Oriol Mitja
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
- Lihir Medical Centre, International SOS, Londolovit, Papua New Guinea
| | - Anne Rompalo
- Department of Infectious Diseases, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Fiona Mulcahy
- Department of Genito Urinary Medicine and Infectious Diseases, St. James’s Hospital, Dublin, Ireland
| | - Edward W. Hook
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Irving F. Hoffman
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Project-Malawi, Lilongwe, Malawi
| | - Mitch M. Matoga
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Project-Malawi, Lilongwe, Malawi
| | - Heping Zheng
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Institute for Global Health and Sexually Transmitted Infections, Guangzhou, China
| | - Bin Yang
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Institute for Global Health and Sexually Transmitted Infections, Guangzhou, China
| | - Eduardo Lopez-Medina
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Centro de Estudios en Infectología Pediátrica (CEIP), Cali, Colombia
| | - Lady G. Ramirez
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Universidad ICESI, Cali, Colombia
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, United States
| | - Kelly L. Hawley
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Juan C. Salazar
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Sheila A. Lukehart
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Arlene C. Seña
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan B. Parr
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lorenzo Giacani
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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Lieberman NAP, Lin MJ, Xie H, Shrestha L, Nguyen T, Huang ML, Haynes AM, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Dal Conte I, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitjà O, Rompalo A, Mulcahy F, Hook EW, Lukehart SA, Casto AM, Roychoudhury P, DiMaio F, Giacani L, Greninger AL. Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar. PLoS Negl Trop Dis 2021; 15:e0010063. [PMID: 34936652 PMCID: PMC8735616 DOI: 10.1371/journal.pntd.0010063] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 09/09/2021] [Revised: 01/06/2022] [Accepted: 12/06/2021] [Indexed: 11/19/2022] Open
Abstract
In spite of its immutable susceptibility to penicillin, Treponema pallidum (T. pallidum) subsp. pallidum continues to cause millions of cases of syphilis each year worldwide, resulting in significant morbidity and mortality and underscoring the urgency of developing an effective vaccine to curtail the spread of the infection. Several technical challenges, including absence of an in vitro culture system until very recently, have hampered efforts to catalog the diversity of strains collected worldwide. Here, we provide near-complete genomes from 196 T. pallidum strains-including 191 T. pallidum subsp. pallidum-sequenced directly from patient samples collected from 8 countries and 6 continents. Maximum likelihood phylogeny revealed that samples from most sites were predominantly SS14 clade. However, 99% (84/85) of the samples from Madagascar formed two of the five distinct Nichols subclades. Although recombination was uncommon in the evolution of modern circulating strains, we found multiple putative recombination events between T. pallidum subsp. pallidum and subsp. endemicum, shaping the genomes of several subclades. Temporal analysis dated the most recent common ancestor of Nichols and SS14 clades to 1717 (95% HPD: 1543-1869), in agreement with other recent studies. Rates of SNP accumulation varied significantly among subclades, particularly among different Nichols subclades, and was associated in the Nichols A subclade with a C394F substitution in TP0380, a ERCC3-like DNA repair helicase. Our data highlight the role played by variation in genes encoding putative surface-exposed outer membrane proteins in defining separate lineages, and provide a critical resource for the design of broadly protective syphilis vaccines targeting surface antigens.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Michelle J. Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Tien Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Austin M. Haynes
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Qian-Qiu Wang
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Rui-Li Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cai-Xia Kou
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Giulia Ciccarese
- Health Sciences Department, Section of Dermatology, San Martino University Hospital, Genoa, Italy
| | - Ivano Dal Conte
- STI Clinic, Infectious Diseases Unit, University of Turin, Turin, Italy
| | - Marco Cusini
- Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Drago
- Health Sciences Department, Section of Dermatology, San Martino University Hospital, Genoa, Italy
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Oriol Mitjà
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Anne Rompalo
- Department of Infectious Diseases, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Fiona Mulcahy
- Department of Genito Urinary Medicine and Infectious Diseases, St James’s Hospital, Dublin, Ireland
| | - Edward W. Hook
- Department of Medicine, University of Alabama, Birmingham, Birmingham, Alabama, United States of America
| | - Sheila A. Lukehart
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Amanda M. Casto
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Rojas PA, Timoteo OS, Barreto TV, Vila ZN, De Los Santos MB, Eguiluz M, Colarossi A, Ambulay J. Oil emulsion from Plukenetia huayllabambana (Sacha inchi) modifies nitric oxide and leptin in the liver and antioxidant and inflammation markers in the adipose tissue in obese rats. FFHD 2021. [DOI: 10.31989/ffhd.v11i3.778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Background: Obesity is characterized by excessive accumulation of adipose tissue and is associated with higher risk of metabolic diseases and other comorbidities. Efficacious strategies including a diet high in “functional foods” are promising. Plukenetia huayllabambana known as Sacha Inchi (SI), is a legume which seeds are rich in proteins, tocopherols, and fatty acids such as omega-3 (ω-3). The latter has emerged as a potential protective nutrient against the cardiometabolic risks associated with obesity. Omega-3 changes the membrane lipid profile of hepatic and adipose cells triggering the expression of antioxidant and anti-inflammatory genes. However, there are few reports in relation to the effect of these oils in inflammatory and stress response related to obesity. In this sense, the present study evaluated the effect of SI oil emulsion on nitric oxide and leptin levels in the liver and some markers of oxidative stress and inflammation in adipose tissue from the rodent obesity model.Methods: Six groups were formed: Not obese control group (Noc), obese control (Oc), two groups treated with the emulsion of SI oil (Os1:0.25g ω-3/day; Os2:0.5g ω-3/day), one obese group treated with atorvastatin (Oa) and one group treated with atorvastatin plus the emulsion of SI oil (Oas2).Results: Os1 and Os2 lowered nitric oxide and increased liver leptin levels. In the adipose tissue, the superoxide dismutase and reducing antioxidant power increased significantly in Os1 and Os2 groups. The anti-inflammatory marker IL-4 wasalso increased in Os2, Oa and Oas2 compared to the Oc and IL-10 increased in Oas2 group.Conclusion: Our study suggests that the emulsion of SI oil can modify the inflammatory and stress responses associated with obesity and it can be incorporated as a promising functional food.Keywords: Inflammation, leptin, obesity, nitric oxide, oxidative stress, SI oil emulsion.
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Haynes AM, Fernandez M, Romeis E, Mitjà O, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Giacani L. Transcriptional and immunological analysis of the putative outer membrane protein and vaccine candidate TprL of Treponema pallidum. PLoS Negl Trop Dis 2021; 15:e0008812. [PMID: 33497377 PMCID: PMC7864442 DOI: 10.1371/journal.pntd.0008812] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/05/2021] [Accepted: 01/09/2021] [Indexed: 11/29/2022] Open
Abstract
Background An effective syphilis vaccine should elicit antibodies to Treponema pallidum subsp. pallidum (T. p. pallidum) surface antigens to induce pathogen clearance through opsonophagocytosis. Although the combination of bioinformatics, structural, and functional analyses of T. p. pallidum genes to identify putative outer membrane proteins (OMPs) resulted in a list of potential vaccine candidates, still very little is known about whether and how transcription of these genes is regulated during infection. This knowledge gap is a limitation to vaccine design, as immunity generated to an antigen that can be down-regulated or even silenced at the transcriptional level without affecting virulence would not induce clearance of the pathogen, hence allowing disease progression. Principal findings We report here that tp1031, the T. p. pallidum gene encoding the putative OMP and vaccine candidate TprL is differentially expressed in several T. p. pallidum strains, suggesting transcriptional regulation. Experimental identification of the tprL transcriptional start site revealed that a homopolymeric G sequence of varying length resides within the tprL promoter and that its length affects promoter activity compatible with phase variation. Conversely, in the closely related pathogen T. p. subsp. pertenue, the agent of yaws, where a naturally-occurring deletion has eliminated the tprL promoter region, elements necessary for protein synthesis, and part of the gene ORF, tprL transcription level are negligible compared to T. p. pallidum strains. Accordingly, the humoral response to TprL is absent in yaws-infected laboratory animals and patients compared to syphilis-infected subjects. Conclusion The ability of T. p. pallidum to stochastically vary tprL expression should be considered in any vaccine development effort that includes this antigen. The role of phase variation in contributing to T. p. pallidum antigenic diversity should be further studied. Syphilis is still an endemic disease in many low- and middle-income countries and has been resurgent in high-income nations for almost two decades now. In endemic areas, syphilis still causes significant morbidity and mortality in patients, particularly when its causative agent, the bacterium Treponema pallidum subsp. pallidum is transmitted to the fetus during pregnancy. Although there are significant ongoing efforts to identify an effective syphilis vaccine to bring into clinical trials within the decade in the U.S., such efforts are partially hindered by the lack of knowledge on transcriptional regulation of many genes encoding vaccine candidates. Here, we start addressing this knowledge gap for the putative outer membrane protein (OMP) and vaccine candidates TprL, encoded by the tp1031 gene. As we previously reported for other putative OMP-encoding genes of the syphilis agent, tprL transcription level appears to be affected by the length of a homopolymeric sequence of guanosines (Gs) located within the gene promoter. This is a mechanism known as phase variation and often involved in altering the surface antigenic profile of a bacterial pathogen to facilitate immune evasion and/or adaptation to the host milieu.
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Affiliation(s)
- Austin M. Haynes
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Mark Fernandez
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Oriol Mitjà
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias I Pujol, Badalona, Barcelona, Spain
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- David Geffen School of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, United States of America
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- School of Public Health and Administration “Carlos Vidal Layseca”, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- David Geffen School of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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7
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Brandão JHSG, Rodrigues NF, Eguiluz M, Guzman F, Margis R. Araucaria angustifolia chloroplast genome sequence and its relation to other Araucariaceae. Genet Mol Biol 2019; 42:671-676. [PMID: 31188933 PMCID: PMC6905450 DOI: 10.1590/1678-4685-gmb-2018-0213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 07/18/2018] [Accepted: 11/28/2018] [Indexed: 11/30/2022] Open
Abstract
Araucaria angustifolia is endemic to southern Brazil. Known as Brazilian pine, A. angustifolia is the only native conifer species with economic and social relevance in this country. Due to massive exploitation, it has suffered a significant population decline and currently is classified as critically endangered. This encouraged the scientific community to investigate genetic features in Brazilian pine to increase resources for management and preservation. In this work, RNA-Seq data was used to determine the complete nucleotide sequence of the A. angustifolia chloroplast genome (cpDNA). The cpDNA is 146,203 bp in length and contains 122 genes, including 80 protein-coding genes, 5 ribosomal RNA genes, and 37 tRNA genes. Coding regions comprise 45.02%, 4.96% correspond to rRNAs and tRNAs, and 50.02% of the genome encompasses non-coding regions. Genes found in the inverted repeat (IR) are present as single copy, with exception of the rrn5 and trnI-CAU loci. The typical LSC, SSC, IRa and IRb organization reported in several land-plant groups is not present in A. angustifolia cpDNA. Phylogenetic analyses using Bayesian and Maximum Likelihood methods clustered A. angustifolia in the Araucariaceae family, with A. heterophylla and A. columnaris as congeneric species. The screening of A. angustifolia cpDNA reveled 100 SSRs, 14 of them corresponding to tetrapolymer loci.
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Affiliation(s)
- José Henrique S G Brandão
- PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, (UFRGS), Porto Alegre, RS, Brazil
| | - Nureyev F Rodrigues
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Maria Eguiluz
- PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, (UFRGS), Porto Alegre, RS, Brazil
| | - Frank Guzman
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rogerio Margis
- PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, (UFRGS), Porto Alegre, RS, Brazil.,PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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8
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Eguiluz M, Kulcheski FR, Margis R, Guzman F. De novo assembly of Vriesea carinata leaf transcriptome to identify candidate cysteine-proteases. Gene 2019; 691:96-105. [PMID: 30630096 DOI: 10.1016/j.gene.2018.12.053] [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: 10/10/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 11/30/2022]
Abstract
Vriesea carinata is an endemic bromeliad from the Brazilian Atlantic Forest. It has trichome and tank system in their leaves which allows to absorb water and nutrients. It belongs to Bromeliaceae family, which includes several species highly enriched of cysteine-proteases (CysPs). These proteolytic enzymes regulate processes as senescence, cell differentiation, pathogen-linked programmed cell death and mobilization of proteins. Although, their biological importance, there are not genomic resources in V. carinata that can help to identify and understand their molecular mechanisms involved in different biological processes. Thus high-throughput transcriptome sequencing of V. carinata is necessary to generate sequences for the purpose of gene discovery and functional genomic studies. In the present study, we sequenced and assembled the V. carinata transcriptome to the identification of CysPs. A total of 43,232 contigs were assembled for the leaf tissue. BLAST analysis indicated that 23,803 contigs exhibited similarity to non-redundant Viridiplantae proteins. 28.24% of the contigs were classified into the COG database, and gene ontology categorized them into 61 functional groups. A metabolic pathway analysis with KEGG revealed 9679 contigs assigned to 31 metabolic pathways. Among 16 full-length CysPs identified, 11 were evaluated in respect to their expression patterns in the leaf apex, base and inflorescence tissues. The results showed differential expression levels of legumain, metacaspase, pyroglutamyl and papain-like CysPs depending of the leaf region. These results provide a global overview of V. carinata gene functions and expression activities of CysPs in those tissues.
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Affiliation(s)
- M Eguiluz
- PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Brazil; Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - F R Kulcheski
- PPGBCD, Departamento de Biologia Celular, Genética e Embriologia, Universidade Federal de Santa Catarina-UFSC, Florianópolis, Brazil
| | - R Margis
- PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Brazil; PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Brazil
| | - F Guzman
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Brazil.
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9
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Galdino JH, Eguiluz M, Guzman F, Margis R. Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms. Front Genet 2019; 10:222. [PMID: 30984236 PMCID: PMC6448024 DOI: 10.3389/fgene.2019.00222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 12/12/2018] [Accepted: 02/28/2019] [Indexed: 01/01/2023] Open
Abstract
The knowledge about plant miRNAs has increased exponentially, with thousands of miRNAs been reported in different plant taxa using high throughput sequencing technologies and bioinformatic tools. Nevertheless, several groups of plants remain unexplored, and the gap of knowledge about conifer miRNAs is considerable. There is no sequence or functional information available on miRNAs in Araucariaceae. This group is represented in Brazil by only one species, Araucaria angustifolia, an endangered species known as Brazilian pine. In the present study, Brazilian pine has its transcriptome explored with respect to small RNAs, representing the first description in a member of the Araucariaceae family. The screening for conserved miRNAs in Brazilian pine revealed 115 sequences of 30 miRNA families. A total of 106 precursors sequences were predicted. Forty one comprised conserved miRNAs from 16 families, whereas 65 were annotated as novel miRNAs. The comparison of Brazilian pine precursors with sRNA libraries of other five conifer species indicates that 9 out 65 novel miRNAs are conserved among gymnosperms, while 56 seems to be specific for Brazilian pine or restricted to Araucariaceae family. Analysis comparing novel Brazilian pine miRNAs precursors and Araucaria cunninghamii RNA-seq data identified seven orthologs between both species. Mature miRNA identified by bioinformatics predictions were validated using stem-loop RT-qPCR assays. The expression pattern of conserved and novel miRNAs was analyzed in five different tissues of 3-month-old Araucaria seedlings. The present study provides insights about the nature and composition of miRNAs in an Araucariaceae species, with valuable information on miRNAs diversity and conservation in this taxon.
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Affiliation(s)
- José Henrique Galdino
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Maria Eguiluz
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Frank Guzman
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Rogerio Margis
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
- Departamento de Biofísica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
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10
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Eguiluz M, Yuyama PM, Guzman F, Rodrigues NF, Margis R. Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora. Genet Mol Biol 2017; 40:871-876. [PMID: 29111566 PMCID: PMC5738614 DOI: 10.1590/1678-4685-gmb-2017-0096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 04/18/2017] [Accepted: 07/13/2017] [Indexed: 12/02/2022] Open
Abstract
Plinia trunciflora is a Brazilian native fruit tree from the
Myrtaceae family, also known as jaboticaba. This species has great potential by
its fruit production. Due to the high content of essential oils in their leaves
and of anthocyanins in the fruits, there is also an increasing interest by the
pharmaceutical industry. Nevertheless, there are few studies focusing on its
molecular biology and genetic characterization. We herein report the complete
chloroplast (cp) genome of P. trunciflora using high-throughput
sequencing and compare it to other previously sequenced Myrtaceae genomes. The
cp genome of P. trunciflora is 159,512 bp in size, comprising
inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and
18,587 bp (SSC). The genome contains 111 single-copy genes (77 protein-coding,
30 tRNA and four rRNA genes). Phylogenetic analysis using 57 cp protein-coding
genes demonstrated that P. trunciflora, Eugenia uniflora and
Acca sellowiana form a cluster with closer relationship to
Syzygium cumini than with Eucalyptus. The
complete cp sequence reported here can be used in evolutionary and population
genetics studies, contributing to resolve the complex taxonomy of this species
and fill the gap in genetic characterization.
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Affiliation(s)
- Maria Eguiluz
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Priscila Mary Yuyama
- Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Frank Guzman
- Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Nureyev Ferreira Rodrigues
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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