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Indrihutami K, Chand K, Fahmia R, Rahardjani M, Wulandari F, Subekti D, Noviyanti R, Soebandrio A, Mallisa NT, Mardika IM, Budiman W, Suriswan I, Ertanto Y, Chen MC, Murshedkar T, Abebe Y, Sim BKL, Hoffman SL, Richie TL, Chen S, Elyazar IRF, Ekawati LL, Baird JK, Nelwan EJ. Implementation of a Randomized, Placebo-Controlled Trial of Live Attenuated Malaria Sporozoite Vaccines in an Indonesian Military Study Population. Am J Trop Med Hyg 2024; 110:892-901. [PMID: 38531102 PMCID: PMC11066349 DOI: 10.4269/ajtmh.23-0597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/24/2023] [Indexed: 03/28/2024] Open
Abstract
Malaria eradication efforts prioritize safe and efficient vaccination strategies, although none with high-level efficacy against malaria infection are yet available. Among several vaccine candidates, Sanaria® PfSPZ Vaccine and Sanaria PfSPZ-CVac are, respectively, live radiation- and chemo-attenuated sporozoite vaccines designed to prevent infection with Plasmodium falciparum, the leading cause of malaria-related morbidity and mortality. We are conducting a randomized normal saline placebo-controlled trial called IDSPZV1 that will analyze the safety, tolerability, immunogenicity, and efficacy of PfSPZ Vaccine and PfSPZ-CVac administered pre-deployment to malaria-naive Indonesian soldiers assigned to temporary duties in a high malaria transmission area. We describe the manifold challenges of enrolling and immunizing 345 soldier participants at their home base in western Indonesia before their nearly 6,000-km voyage to eastern Indonesia, where they are being monitored for incident P. falciparum and Plasmodium vivax malaria cases during 9 months of exposure. The unique regulatory, ethical, and operational complexities of this trial demonstrate the importance of thorough planning, frequent communication, and close follow-up with stakeholders. Effective engagement with the military community and the ability to adapt to unanticipated events have proven key to the success of this trial.
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Affiliation(s)
| | - Krisin Chand
- Oxford University Clinical Research Unit Indonesia, Jakarta, Indonesia
| | - Rizka Fahmia
- Oxford University Clinical Research Unit Indonesia, Jakarta, Indonesia
| | - Mutia Rahardjani
- Oxford University Clinical Research Unit Indonesia, Jakarta, Indonesia
| | - Fitria Wulandari
- Oxford University Clinical Research Unit Indonesia, Jakarta, Indonesia
| | - Decy Subekti
- Oxford University Clinical Research Unit Indonesia, Jakarta, Indonesia
| | - Rintis Noviyanti
- Eijkman Research Center for Molecular Biology, National Research & Innovation Agency, Cibinong, West Java, Indonesia
- EXEINS Health Initiative, Jakarta, Indonesia
| | - Amin Soebandrio
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Noch T. Mallisa
- Presidential Staff Office, Republic of Indonesia, Jakarta, Indonesia
| | | | - Waras Budiman
- Muhammadiyah University, Surabaya, East Java, Indonesia
| | | | - Yogi Ertanto
- Army Medical Center, Army of the Republic of Indonesia, Jakarta, Indonesia
| | | | | | | | | | | | | | | | | | - Lenny L. Ekawati
- Oxford University Clinical Research Unit Indonesia, Jakarta, Indonesia
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - J. Kevin Baird
- Oxford University Clinical Research Unit Indonesia, Jakarta, Indonesia
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Erni J. Nelwan
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Division of Tropical Medicine and Infectious Disease, Department of Internal Medicine, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
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2
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Khoeri MM, Maladan Y, Salsabila K, Alimsardjono L, Vermasari N, Puspitasari I, Yunita R, Tafroji W, Sarassari R, Sari RF, Balqis SA, Wahid GA, Purwanto DS, Harimurti K, Soebandrio A, Safari D. Whole genome sequencing data of Streptococcus pneumoniae isolated from Indonesian population. Data Brief 2024; 53:110251. [PMID: 38533114 PMCID: PMC10964051 DOI: 10.1016/j.dib.2024.110251] [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: 10/02/2023] [Revised: 12/21/2023] [Accepted: 02/20/2024] [Indexed: 03/28/2024] Open
Abstract
Streptococcus pneumoniae is the leading cause of bacterial pneumonia, bacteremia, and meningitis. Indonesia introduced the pneumococcal conjugate vaccine (PCV) nationwide in 2022. In this study, we present whole genome sequence (WGS) data of 94 S. pneumoniae isolates that were obtained from hospitalized patients, healthy children, and adult groups from different regions prior to PCV program in Indonesia. DNA sequences of S. pneumoniae were obtained using the TruSeq Nano DNA kit (Illumina NovaSeq6000 Platform). The genome data of S. pneumoniae features a 1,969,562 bp to 2,741,371 bp circular chromosome with 39-40% G+C content. The genome includes 1935-3319 coding sequences (CDS), 2 to 5 rRNA genes, 43 to 49 tRNA genes, and 56 to 71 ncRNA. These data will be useful for analyzing the serotype, sequence type, virulence genes, antimicrobial resistance genes, and the impact of pneumococcal vaccination in Indonesia. The FASTQ raw files of these sequences are available under BioProject accession number PRJNA995903 and Sequence Read Archive accession numbers SRR25316461-SRR25316554.
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Affiliation(s)
- Miftahuddin Majid Khoeri
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
- Doctoral program in Biomedical, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Yustinus Maladan
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Korrie Salsabila
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | | | | | | | - Rina Yunita
- Haji Adam Malik Hospital, Medan, North Sumatera, Indonesia
- Department of Microbiology, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Wisnu Tafroji
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Rosantia Sarassari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Ratna Fathma Sari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Sarah Azhari Balqis
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Ghina Athyah Wahid
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Diana Shinta Purwanto
- Department of Biochemistry, Faculty of Medicine, Sam Ratulangi University, Manado, North Sulawesi, Indonesia
| | - Kuntjoro Harimurti
- Departement of Internal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Amin Soebandrio
- Departement of Clinical Microbiology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Dodi Safari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
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Safari D, Daningrat WOD, Milucky JL, Khoeri MM, Paramaiswari WT, Tafroji W, Salsabila K, Winarti Y, Soebandrio A, Hadinegoro SR, Prayitno A, Childs L, Pimenta FC, Carvalho MDG, Pilishvili T. Nasopharyngeal carriage of Streptococcus pneumoniae among children <5 years of age in Indonesia prior to pneumococcal conjugate vaccine introduction. PLoS One 2024; 19:e0297041. [PMID: 38206916 PMCID: PMC10783721 DOI: 10.1371/journal.pone.0297041] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/27/2023] [Indexed: 01/13/2024] Open
Abstract
Pneumococcal conjugate vaccines (PCVs) prevent nasopharyngeal colonization with vaccine serotypes of Streptococcus pneumoniae, leading to reduced transmission of pneumococci and stronger population-level impact of PCVs. In 2017 we conducted a cross-sectional pneumococcal carriage study in Indonesia among children aged <5 years before 13-valent PCV (PCV13) introduction. Nasopharyngeal swabs were collected during visits to community integrated health service posts at one peri-urban and one rural study site. Specimens were analyzed by culture, and isolates were serotyped using sequential multiplex polymerase chain and Quellung reaction. Antibiotic susceptibility was performed by broth microdilution method. We enrolled 1,007 children in Gunungkidul District, Yogyakarta (peri-urban) and 815 in Southwest Sumba, East Nusa Tenggara (rural). Pneumococcal carriage prevalence was 30.9% in Gunungkidul and 87.6% in Southwest Sumba (combined: 56.3%). PCV13 serotypes (VT) carriage was 15.0% in Gunungkidul and 52.6% in Southwest Sumba (combined: 31.8%). Among pneumococcal isolates identified, the most common VT were 6B (16.4%), 19F (15.8%), and 3 (4.6%) in Gunungkidul (N = 323) and 6B (17.6%), 19F (11.0%), and 23F (9.3%) in Southwest Sumba (N = 784). Factors associated with pneumococcal carriage were age (1-2 years adjusted odds ratio (aOR) 1.9, 95% CI 1.4-2.5; 3-4 years aOR 1.5, 95% CI 1.1-2.1; reference <1 year), other children <5 years old in the household (aOR 1.5, 95% CI 1.1-2.0), and presence of ≥1 respiratory illness symptom (aOR 1.8, 95% CI 1.4-2.2). Overall, 61.5% of the pneumococcal isolates were non-susceptible to ≥1 antibiotic class and 13.2% were multi-drug non-susceptible (MDNS) (non-susceptible to ≥3 classes of antibiotics). Among 602 VT isolates, 73.9% were non-susceptible and 19.9% were MDNS. These findings are critical to establish a pre-PCV13 carriage prevalence and demonstrate the complexity in evaluating the impact of PCV13 introduction in Indonesia given the wide variability in the carriage prevalence as shown by the two study sites.
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Affiliation(s)
- Dodi Safari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Wa Ode Dwi Daningrat
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer L. Milucky
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Miftahuddin Majid Khoeri
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Wisiva Tofriska Paramaiswari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Wisnu Tafroji
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Korrie Salsabila
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Yayah Winarti
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Amin Soebandrio
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | | | - Ari Prayitno
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Lana Childs
- CDC Foundation, Atlanta, GA, United States of America
| | - Fabiana C. Pimenta
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Maria da Gloria Carvalho
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Tamara Pilishvili
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Kurnia RS, Soebandrio A, Harun VH, Nugroho CMH, Krisnamurti DGB, Poetri ON, Indrawati A, Tarigan S, Natih KKN, Ibrahim F, Sudarmono PP, Silaen OSM. Clostridium perfringens sialidase interaction with Neu5Ac α-Gal sialic acid receptors by in-silico observation and its impact on monolayers cellular behavior structure. J Adv Vet Anim Res 2023; 10:667-676. [PMID: 38370892 PMCID: PMC10868698 DOI: 10.5455/javar.2023.j722] [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: 07/26/2023] [Revised: 08/02/2023] [Accepted: 08/20/2023] [Indexed: 02/20/2024] Open
Abstract
Objective This study aims to evaluate the effect of Clostridium perfringens sialidase treatment on monolayer cell behavior using computational screening and an in vitro approach to demonstrate interaction between enzyme-based drugs and ligands in host cells. Materials and Methods The in silico study was carried out by molecular docking analysis used to predict the interactions between atoms that occur, followed by genetic characterization of sialidase from a wild isolate. Sialidase, which has undergone further production and purification processes exposed to chicken embryonic fibroblast cell culture, and observations-based structural morphology of cells compared between treated cells and normal cells without treatment. Results Based on an in silico study, C. perfringens sialidase has an excellent binding affinity with Neu5Acα (2.3) Gal ligand receptor with Gibbs energy value (∆G)-7.35 kcal/mol and Ki value of 4.11 µM. Wild C. perfringens isolates in this study have 99.1%-100% similarity to the plc gene, NanH, and NanI genes, while NanJ shows 93.18% similarity compared to the reference isolate from GenBank. Sialidase at 750 and 150 mU may impact the viability, cell count, and cell behavior structure of fibroblast cells by significantly increasing the empty area and perimeter of chicken embryo fibroblast (CEF) cells, while at 30 mU sialidase shows no significant difference compared with mock control. Conclusion Sialidase-derived C. perfringens has the capacity to compete with viral molecules for attachment to host sialic acid based on in silico analysis. However, sialidase treatment has an impact on monolayer cell fibroblasts given exposure to high doses.
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Affiliation(s)
- Ryan Septa Kurnia
- Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Amin Soebandrio
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Vivi Hardianty Harun
- Biotechnology/Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Indonesia
| | | | | | - Okti Nadia Poetri
- Department of Animal Disease and Veterinary Health, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Agustin Indrawati
- Department of Animal Disease and Veterinary Health, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Simson Tarigan
- National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | | | - Fera Ibrahim
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | | | - Otto Sahat Martua Silaen
- Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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Setiadi W, Effendi Q, Johar E, Yohan B, Wibowo DP, Syahrani L, Pramono AA, Kartapradja HH, Yudhaputri FA, Dewi BE, Malik SG, Myint KSA, Soebandrio A, Safari D. Significant increase in anti-SARS-CoV-2 antibodies after administration of heterologous mRNA-based vaccine booster in individuals receiving two doses of inactivated COVID-19 vaccine: A single-center study in healthcare workers in Jakarta, Indonesia. J Infect Public Health 2023; 16:1848-1851. [PMID: 37837920 DOI: 10.1016/j.jiph.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Vaccine plays an important role in breaking SARS-CoV-2 transmission and accelerating the path to pandemic recovery. Currently, there is still limited data on heterologous COVID-19 booster vaccination efficacy and effectiveness in Indonesia. METHODS Antibody response was retrospectively analyzed from 156 serum collected from healthcare workers that have received mRNA-1273 vaccine as the booster against SARS-CoV-2. These individuals had previously received the full two doses of inactivated anti-SARS-CoV-2 vaccine. Serological analysis was performed to measure total antibody, as well as IgA and IgG antibodies specific to spike (S) protein using ECLIA and ELISA methods. RESULTS A significant increase in total, IgA, and IgG antibody titers was reported in vaccine receiving a third heterologous booster dose of mRNA-based COVID-19 vaccine following two doses of inactivated type. CONCLUSION The third heterologous booster dose of vaccine may be beneficial to individuals with or without previous history of SARS-CoV-2 infection.
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Affiliation(s)
- Wuryantari Setiadi
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Qothrunnada Effendi
- Graduate Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Edison Johar
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Exeins Health Initiative, Jakarta, Indonesia
| | - Benediktus Yohan
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Lepa Syahrani
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Hannie H Kartapradja
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | | | - Beti Ernawati Dewi
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Safarina G Malik
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Mochtar Riady Institute for Nanotechnology, Tangerang, Banten, Indonesia
| | - Khin Saw Aye Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Exeins Health Initiative, Jakarta, Indonesia
| | - Amin Soebandrio
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Dodi Safari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia.
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Sutanto I, Soebandrio A, Ekawati LL, Chand K, Noviyanti R, Satyagraha AW, Subekti D, Santy YW, Crenna-Darusallam C, Instiaty I, Budiman W, Prasetya CB, Lardo S, Elyazar I, Duparc S, Cedar E, Rolfe K, Fernando D, Berni A, Jones S, Kleim JP, Fletcher K, Sharma H, Martin A, Taylor M, Goyal N, Green JA, Tan LK, Baird JK. Tafenoquine co-administered with dihydroartemisinin-piperaquine for the radical cure of Plasmodium vivax malaria (INSPECTOR): a randomised, placebo-controlled, efficacy and safety study. Lancet Infect Dis 2023; 23:1153-1163. [PMID: 37236221 PMCID: PMC10533414 DOI: 10.1016/s1473-3099(23)00213-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Tafenoquine, co-administered with chloroquine, is approved for the radical cure (prevention of relapse) of Plasmodium vivax malaria. In areas of chloroquine resistance, artemisinin-based combination therapies are used to treat malaria. This study aimed to evaluate tafenoquine plus the artemisinin-based combination therapy dihydroartemisinin-piperaquine for the radical cure of P vivax malaria. METHODS In this double-blind, double-dummy, parallel group study, glucose-6-phosphate dehydrogenase-normal Indonesian soldiers with microscopically confirmed P vivax malaria were randomly assigned by means of a computer-generated randomisation schedule (1:1:1) to dihydroartemisinin-piperaquine alone, dihydroartemisinin-piperaquine plus a masked single 300-mg dose of tafenoquine, or dihydroartemisinin-piperaquine plus 14 days of primaquine (15 mg). The primary endpoint was 6-month relapse-free efficacy following tafenoquine plus dihydroartemisinin-piperaquine versus dihydroartemisinin-piperaquine alone in all randomly assigned patients who received at least one dose of masked treatment and had microscopically confirmed P vivax at baseline (microbiological intention-to-treat population). Safety was a secondary outcome and the safety population comprised all patients who received at least one dose of masked medication. This study is registered with ClinicalTrials.gov, NCT02802501 and is completed. FINDINGS Between April 8, 2018, and Feb 4, 2019, of 164 patients screened for eligibility, 150 were randomly assigned (50 per treatment group). 6-month Kaplan-Meier relapse-free efficacy (microbiological intention to treat) was 11% (95% CI 4-22) in patients treated with dihydroartemisinin-piperaquine alone versus 21% (11-34) in patients treated with tafenoquine plus dihydroartemisinin-piperaquine (hazard ratio 0·44; 95% CI [0·29-0·69]) and 52% (37-65) in the primaquine plus dihydroartemisinin-piperaquine group. Adverse events over the first 28 days were reported in 27 (54%) of 50 patients treated with dihydroartemisinin-piperaquine alone, 29 (58%) of 50 patients treated with tafenoquine plus dihydroartemisinin-piperaquine, and 22 (44%) of 50 patients treated with primaquine plus dihydroartemisinin-piperaquine. Serious adverse events were reported in one (2%) of 50, two (4%) of 50, and two (4%) of 50 of patients, respectively. INTERPRETATION Although tafenoquine plus dihydroartemisinin-piperaquine was statistically superior to dihydroartemisinin-piperaquine alone for the radical cure of P vivax malaria, the benefit was not clinically meaningful. This contrasts with previous studies in which tafenoquine plus chloroquine was clinically superior to chloroquine alone for radical cure of P vivax malaria. FUNDING ExxonMobil, Bill & Melinda Gates Foundation, Newcrest Mining, UK Government all through Medicines for Malaria Venture; and GSK. TRANSLATION For the Indonesian translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Inge Sutanto
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | | | - Lenny L Ekawati
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; University of Oxford Clinical Research Unit-Indonesia, Jakarta, Indonesia
| | - Krisin Chand
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; University of Oxford Clinical Research Unit-Indonesia, Jakarta, Indonesia
| | | | | | - Decy Subekti
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; University of Oxford Clinical Research Unit-Indonesia, Jakarta, Indonesia
| | - Yulia Widya Santy
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; University of Oxford Clinical Research Unit-Indonesia, Jakarta, Indonesia
| | - Chelzie Crenna-Darusallam
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Mochtar Riady Institute for Nanotechnology, Banten, Indonesia
| | | | - Waras Budiman
- Health Service, Army of the Republic of Indonesia, Jakarta, Indonesia
| | | | - Soroy Lardo
- Health Service, Army of the Republic of Indonesia, Jakarta, Indonesia
| | - Iqbal Elyazar
- University of Oxford Clinical Research Unit-Indonesia, Jakarta, Indonesia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - J Kevin Baird
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; University of Oxford Clinical Research Unit-Indonesia, Jakarta, Indonesia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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7
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Tafroji W, Margyaningsih NI, Khoeri MM, Paramaiswari WT, Winarti Y, Salsabila K, Putri HFM, Siregar NC, Soebandrio A, Safari D. Antibacterial activity of medicinal plants in Indonesia on Streptococcus pneumoniae. PLoS One 2022; 17:e0274174. [PMID: 36099236 PMCID: PMC9469987 DOI: 10.1371/journal.pone.0274174] [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: 04/28/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is a human pathogenic bacterium able to cause invasive pneumococcal diseases. Some studies have reported medicinal plants having antibacterial activity against pathogenic bacteria. However, antibacterial studies of medicinal plants against S. pneumoniae remains limited. Therefore, this study aims to describe the antibacterial activity of medicinal plants in Indonesia against S. pneumoniae. Medicinal plants were extracted by maceration with n-hexane, ethanol, ethyl acetate and water. Antibacterial activity was defined by inhibition zone and minimum inhibitory concentration (MIC). Bactericidal activity was measured by culture and time-killing measurement. Methods used to describe the mechanism of action of the strongest extract were done by absorbance at 595 nm, broth culture combined with 1% crystal violet, qRT-PCR targeting lytA, peZT and peZA, and transmission electron microscope to measure bacterial lysis, antibiofilm, LytA and peZAT gene expression, and ultrastructure changes respectively. Among 13 medicinal plants, L. inermis Linn. ethyl acetate extract showed the strongest antibacterial activity against S. pneumoniae with an MIC value of 0,16 mg/ml. Bactericidal activity was observed at 0,16 mg/ml for 1 hour incubation. Lawsonia inermis extract showed some mechanism of actions including bacterial lysis, antibiofilm, and ultrastructure changes such as cell wall disruption, decreasing cell membrane integrity and morphological disorder. Increasing of lytA and decreasing of peZA and peZT expression were also observed after incubation with the extract. In addition, liquid chromatography mass spectrophotometer showed phenolic compounds as the commonest compound in L. inermis ethyl acetate extract. This study describes the strong antibacterial activity of L. inermis with various mechanism of action including ultrastructure changes.
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Affiliation(s)
- Wisnu Tafroji
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- * E-mail:
| | | | - Miftahuddin Majid Khoeri
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | | | - Yayah Winarti
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Korrie Salsabila
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | | | - Nurjati Chairani Siregar
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Amin Soebandrio
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Dodi Safari
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
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8
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Nugroho CMH, Kurnia RS, Tarigan S, Silaen OSM, Triwidyaningtyas S, Wibawan IWT, Natalia L, Takdir AK, Soebandrio A. Screening and purification of NanB sialidase from Pasteurella multocida with activity in hydrolyzing sialic acid Neu5Acα(2–6)Gal and Neu5Acα(2–3)Gal. Sci Rep 2022; 12:9425. [PMID: 35676312 PMCID: PMC9177577 DOI: 10.1038/s41598-022-13635-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
Study on sialidases as antiviral agents has been widely performed, but many types of sialidase have not been tested for their antiviral activity. Pasteurella multocida NanB sialidase is one such sialidase that has never been isolated for further research. In this study, the activity of NanB sialidase was investigated in silico by docking the NanB sialidase of Pasteurella multocida to the Neu5Acα(2–6)Gal and Neu5Acα(2–3)Gal ligands. Additionally, some local isolates of Pasteurella multocida, which had the NanB gene were screened, and the proteins were isolated for further testing regarding their activity in hydrolyzing Neu5Acα(2–6)Gal and Neu5Acα(2–3)Gal. Silico studies showed that the NanB sialidase possesses an exceptional affinity towards forming a protein–ligand complex with Neu5Acα(2–6)Gal and Neu5Acα(2–3)Gal. NanB sialidase of Pasteurella multocida B018 at 0.129 U/mL and 0.258 U/mL doses can hydrolyze Neu5Acα(2–6)Gal and Neu5Acα(2–3)Gal better than other doses. In addition, those doses can inhibit effectively H9N2 viral binding to red blood cells. This study suggested that the NanB sialidase of Pasteurella multocida B018 has a potent antiviral activity because can hydrolyze sialic acid on red blood cells surface and inhibit the H9N2 viral binding to the cells.
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Setiadi W, Rozi IE, Safari D, Daningrat WOD, Johar E, Yohan B, Yudhaputri FA, Lestari KD, Oktavianthi S, Myint KSA, Malik SG, Soebandrio A. Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study. PLoS One 2022; 17:e0268241. [PMID: 35550635 PMCID: PMC9098020 DOI: 10.1371/journal.pone.0268241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 04/25/2022] [Indexed: 12/28/2022] Open
Abstract
We determined the prevalence and epidemiological characteristics of COVID-19 in Jakarta and neighboring areas, Indonesia from March 2020 to February 2021, based on nasopharyngeal/oropharyngeal (NP/OP) swab specimens that were tested at the Eijkman Institute for Molecular Biology, Jakarta. NP/OP swab specimens were collected from COVID-19 suspects or individuals in contact tracing programs from primary healthcare centers (PHC) and hospitals. The specimens were screened for the SARS-CoV-2 by qRT-PCR. Demography data and clinical symptoms were collected using national standardized laboratory form. Of 64,364 specimens, 10,130 (15.7%) were confirmed positive for SARS-CoV-2, with the peak prevalence of infection in March 2020 (26.3%) follow by in January 2021 (23.9%) and February 2021 (21.8%). We found that the positivity rate of the specimens from Jakarta, West Java, and Banten was 16.3%, 13.3%, and 16.8%, respectively. Positivity rate was higher in specimens from hospitals (16.9%) than PHC (9.4%). Of the positive specimens, 29.6% were from individuals aged >60 years old, followed by individuals aged 41-60 years old (24.2%). Among symptomatic cases of SARS-CoV-2, the most common symptoms were cough, fever, and a combination of both cough & fever. In conclusion, this study illustrates the prevalence and epidemiological characteristics from one COVID-19 diagnostic center in Jakarta and neighbouring areas in Indonesia.
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Affiliation(s)
- Wuryantari Setiadi
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Ismail Ekoprayitno Rozi
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Dodi Safari
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Wa Ode Dwi Daningrat
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Edison Johar
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Benediktus Yohan
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | | | - Karina Dian Lestari
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Sukma Oktavianthi
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Khin Saw Aye Myint
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Safarina G. Malik
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Amin Soebandrio
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
- * E-mail:
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10
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Ariyanto IA, Estiasari R, Karim B, Wijaya IP, Bela B, Soebandrio A, Price P, Lee S. Which NK cell populations mark the high burden of CMV present in all HIV patients beginning ART in Indonesia? AIDS Res Ther 2022; 19:16. [PMID: 35292053 PMCID: PMC8922863 DOI: 10.1186/s12981-022-00439-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background Cytomegalovirus (CMV) has been linked with cardiovascular disease (CVD) in populations where some individuals are seronegative. However, effects of CMV are unclear in HIV patients who all have high levels of CMV antibodies. Other metrics of their CMV burden are needed. Amongst transplant recipients, CMV drives the expansion of NK cell populations expressing NKG2C and/or LIR1 and lacking FcRγ. Methods Indonesian HIV patients (n = 40) were tested before ART and after 6 months, with healthy local controls (n = 20). All patients had high CMV antibody titres. 52% started therapy with CMV DNA detectable by qPCR, providing a crude measure of CMV burden. Proportions of CD56Hi or CD56Lo NK cells expressing FcRγ, NKG2C or LIR1 were determined flow cytometrically. CVD was predicted using carotid intimal media thickness (cIMT). Values were correlated with levels of CMV antibodies on ART. Results Patients had low proportions of CD56Lo and more CD56Hi NK cells. However proportions of FcRγ− NK cells were lowest in patients with CMV DNA, and cIMT values related inversely with FcRγ− NK cells in these patients. Percentages of NKG2C+CD56Lo NK cells were similar in patients and controls, but rose in patients with CMV DNA. Proportions of NKG2C+ CD56Hi NK cells correlated with levels of CMV antibodies in CMV DNA-negative patients. Conclusions We show that the very high burdens of CMV in this population confound systems developed to study effects of CMV in other populations. FcRγ− NK cells may be depleted by very high CMV burdens, but NKG2C and antibody levels may be informative in patients on ART. Supplementary Information The online version contains supplementary material available at 10.1186/s12981-022-00439-2.
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11
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Soebandrio A, Kusumaningrum T, Yudhaputri FA, Oktavianthi S, Malik SG, Myint KSA. Characteristics of children with confirmed SARS-CoV-2 infection in Indonesia. J Clin Virol Plus 2022; 1:100027. [PMID: 35262013 PMCID: PMC8193971 DOI: 10.1016/j.jcvp.2021.100027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/26/2022] Open
Abstract
Objective COVID-19 in children poses a significant challenge due to the atypical/asymptomatic presentations. The study is aimed to help understand clinical characteristics in Indonesian children for better management and control of transmission. Methods clinical characteristics of children with confirmed COVID-19 were retrospectively analysed from the database dating from March to November 2020. Results the study revealed a high prevalence (67.3%) of asymptomatic cases from contact tracing population. The most common symptoms in children with confirmed COVID-19 were cough and fatigue. Among symptomatic patients, 14/21 (66.7%) had either radiological and/or clinical evidence of pneumonia. Conclusion children with respiratory symptoms especially those with contact history should be screened for possible COVID-19 infection regardless of disease severity.
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Affiliation(s)
- Amin Soebandrio
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
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12
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Hartawan R, Pujianto DA, Dharmayanti NLPI, Soebandrio A. Improving siRNA design targeting nucleoprotein gene as antiviral against the Indonesian H5N1 virus. J Vet Sci 2022; 23:e24. [PMID: 35187881 PMCID: PMC8977538 DOI: 10.4142/jvs.21174] [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: 06/16/2021] [Revised: 11/08/2021] [Accepted: 12/07/2021] [Indexed: 12/05/2022] Open
Abstract
Background Small interfering RNA technology has been considered a prospective alternative antiviral treatment using gene silencing against influenza viruses with high mutations rates. On the other hand, there are no reports on its effectiveness against the highly pathogenic avian influenza H5N1 virus isolated from Indonesia. Objectives The main objective of this study was to improve the siRNA design based on the nucleoprotein gene (siRNA-NP) for the Indonesian H5N1 virus. Methods The effectiveness of these siRNA-NPs (NP672, NP1433, and NP1469) was analyzed in vitro in Marbin-Darby canine kidney cells. Results The siRNA-NP672 caused the largest decrease in viral production and gene expression at 24, 48, and 72 h post-infection compared to the other siRNA-NPs. Moreover, three serial passages of the H5N1 virus in the presence of siRNA-NP672 did not induce any mutations within the nucleoprotein gene. Conclusions These findings suggest that siRNA-NP672 can provide better protection against the Indonesian strain of the H5N1 virus.
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Affiliation(s)
- Risza Hartawan
- Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesian Research Center for Veterinary Science, Ministry of Agriculture, Bogor 16114, Indonesia
| | - Dwi Ari Pujianto
- Department of Medical Biology Pre Clinic, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | | | - Amin Soebandrio
- Eijkman Institute, Ministry of Research, Technology and Higher Education, Jakarta 10430, Indonesia
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13
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Soebandrio A, Kusumaningrum T, Yudhaputri FA, Oktavianthi S, Safari D, Malik SG, Myint KSA. COVID-19 prevalence among healthcare workers in Jakarta and neighbouring areas in Indonesia during early 2020 pandemic. Ann Med 2021; 53:1896-1904. [PMID: 34783269 PMCID: PMC8604529 DOI: 10.1080/07853890.2021.1975309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/27/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The COVID-19 disease has overwhelmed and disrupted healthcare services worldwide, particularly healthcare workers (HCW). HCW are essential workers performing any job in a healthcare setting who are potentially directly or indirectly exposed to infectious materials. Our retrospective cohort study aimed to determine the prevalence of COVID-19 infections among HCW in Jakarta and neighbouring areas during the first three months of the pandemic. METHODS Nasopharyngeal/oropharyngeal swab specimens from HCW working at private and public hospitals in Jakarta and neighbouring areas were screened for SARS-CoV-2 between March and May 2020. Data on demography, clinical symptoms, contact history, and personal protective equipment (PPE) use were collected using standardised forms. RESULTS Among 1201 specimens, 7.9% were confirmed positive for SARS-CoV-2 with the majority coming from medical doctors (48.4%) and nurses (44.2%). 64.2% of the positive cases reported to have contact with suspect/confirmed COVID-19 cases, including 32 (52.2%) with patient and 3 (6.6%) with co-worker. The symptomatic HCW had a significantly lower median Ct value as compared to their asymptomatic counterpart (p < .001). Tendency to have a higher prevalence of pneumonia was observed in the age group of 40 - 49 and ≥50 years old. CONCLUSION Our findings highlighted the necessity to implement proper preventive and surveillance strategies for this high-risk population including adherence to strict PPE protocol and appropriate training.Key MessageHealthcare workers (HCW), defined as those handling any job in a healthcare setting, are at the frontline of risk of infection as SARS-CoV-2 is easily transmitted through airborne droplets and direct contact with contaminated surfaces. The aim of our study is to attain a more comprehensive and accurate picture of the impact of COVID-19 on HCW during the earlier phase of the outbreak in Indonesia to develop effective strategies that protect the health and safety of this workforce. Our findings highlighted that COVID-19 infections in HCW were mostly acquired in healthcare settings, with significant consequences of pneumonia and hospitalisation occurring across all age groups.
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Affiliation(s)
- Amin Soebandrio
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | | | | | | | - Dodi Safari
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
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14
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Nugroho CMH, Silaen OSM, Kurnia RS, Soejoedono RD, Poetri ON, Soebandrio A. Isolation and molecular characterization of the hemagglutinin gene of H9N2 avian influenza viruses from poultry in Java, Indonesia. J Adv Vet Anim Res 2021; 8:423-434. [PMID: 34722740 PMCID: PMC8520164 DOI: 10.5455/javar.2021.h530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 12/01/2022] Open
Abstract
Objective: The avian influenza virus (AIV) subtype H9N2 circulating in Indonesia has raised increasing concern about its impact on poultry and its public health risks. In this study, the H9N2 virus from chicken poultry farms in Java was isolated and characterized molecularly. Materials and Methods: Thirty-three pooled samples of chicken brain, cloacal swab, trachea, and oviduct were taken from multiple chickens infected with AIV in five regions of Java, Indonesia. The samples were isolated from specific pathogenic-free embryonated eggs that were 9 days old. Reverse transcription polymerase chain reaction and sequencing were used to identify H9N2 viruses. Results: This study was successful in detecting and characterizing 13 H9N2 isolates. The sequencing analysis of hemagglutinin genes revealed a 96.9%–98.8% similarity to the H9N2 AIV isolated from Vietnam in 2014 (A/muscovy duck/Vietnam/LBM719/2014). According to the phylogenetic analysis, all recent H9N2 viruses were members of the lineage Y280 and clade h9.4.2.5. Nine of the H9N2 isolates studied showed PSKSSR↓GLF motifs at the cleavage site, while four had PSKSSR↓GLF. Notably, all contemporary viruses have leucine (L) at position 216 in the receptor-binding region, indicating that the virus can interact with a human-like receptor. Conclusion: This study described the features of recent H9N2 viruses spreading in Java’s poultry industry. Additionally, H9N2 infection prevention and management must be implemented to avoid the occurrence of virus mutations in the Indonesian poultry industry.
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Affiliation(s)
| | | | - Ryan Septa Kurnia
- Doctoral Program Biomedical Science, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Retno Damajanti Soejoedono
- Department of Animal Diseases and Public Health, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia
| | - Okti Nadia Poetri
- Department of Animal Diseases and Public Health, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia
| | - Amin Soebandrio
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Microbiology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
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15
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Sasmono RT, Johar E, Yohan B, Ma'roef CN, Soebandrio A, Myint KS, Pronyk P, Hadinegoro SR, Soepardi EJ, Bouckenooghe A, Hawley W, Rosenberg R, Powers AM. Stability of Zika Virus Antibodies in Specimens from a Retrospective Serological Study. Am J Trop Med Hyg 2021; 105:853. [PMID: 34314374 PMCID: PMC8592325 DOI: 10.4269/ajtmh.21-0564b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- R Tedjo Sasmono
- Eijkman Institute for Molecular Biology Jakarta, Indonesia E-mails:, , , , ,
| | - Edison Johar
- Eijkman Institute for Molecular Biology Jakarta, Indonesia E-mails:, , , , ,
| | - Benediktus Yohan
- Eijkman Institute for Molecular Biology Jakarta, Indonesia E-mails:, , , , ,
| | | | - Amin Soebandrio
- Eijkman Institute for Molecular Biology Jakarta, Indonesia E-mails:, , , , ,
| | - Khin Sa Myint
- Eijkman Institute for Molecular Biology Jakarta, Indonesia E-mails:, , , , ,
| | | | | | | | | | - William Hawley
- Centers for Disease Control and Prevention Atlanta, Georgia E-mail:
| | - Ronald Rosenberg
- Centers for Disease Control and Prevention Fort Collins, Colorado E-mails:@cdc.hhs.gov
| | - Ann M Powers
- Centers for Disease Control and Prevention Fort Collins, Colorado E-mails:@cdc.hhs.gov
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16
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Sasmono RT, Johar E, Yohan B, Ma’roef CN, Pronyk P, Hadinegoro SR, Soepardi EJ, Bouckenooghe A, Hawley WA, Rosenberg R, Powers AM, Soebandrio A, Myint KSA. Spatiotemporal Heterogeneity of Zika Virus Transmission in Indonesia: Serosurveillance Data from a Pediatric Population. Am J Trop Med Hyg 2021; 104:2220-2223. [PMID: 33939632 PMCID: PMC8176489 DOI: 10.4269/ajtmh.21-0010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 01/05/2021] [Accepted: 03/08/2021] [Indexed: 11/23/2022] Open
Abstract
The presence of Zika virus (ZIKV) in Indonesia has been recognized since the 1970s, but its transmission dynamics there have been poorly understood. To understand more fully the geographic distribution and burden of ZIKV infection, we performed retrospective serological tests on specimens collected from asymptomatic children age 5 to 9 years old living at 30 sites in 14 provinces. Of 870 serum samples tested, 9.2% were found to be positive for anti-ZIKV antibodies, as confirmed by plaque reduction neutralization assays. This was the same overall prevalence reported previously for 1- to 4-year-old children collected at the same sites at the same time. Together with geographic differences in seroprevalence between the age groups, these data suggest that, although ZIKV might be endemic in Indonesia, its occurrence has been focal and episodic.
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Affiliation(s)
| | - Edison Johar
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | | | - Sri Rezeki Hadinegoro
- Faculty of Medicine and Cipto Mangunkusumo Hospital, Universitas Indonesia, Jakarta, Indonesia
| | | | | | | | - Ronald Rosenberg
- Centers for Disease Control and Prevention, Fort Collins, Colorado
| | - Ann M. Powers
- Centers for Disease Control and Prevention, Fort Collins, Colorado
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Sunarno, Khariri, Muna F, Sariadji K, Rukminiati Y, Febriyana D, Febrianti T, Saraswati RD, Susanti I, Puspandari N, Karuniawati A, Malik A, Soebandrio A. New approach for the identification of potentially toxigenic Corynebacterium sp. using a multiplex PCR assay. J Microbiol Methods 2021; 184:106198. [PMID: 33713727 DOI: 10.1016/j.mimet.2021.106198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 10/22/2022]
Abstract
In diphtheria laboratory examinations, the PCR test can be applied to isolates and clinical specimens. This study aimed to develop a PCR assay to identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types. Seven reference isolates, four synthetic DNA samples, 36 stored isolates, and 487 clinical samples used for PCR optimization. The PCR results was confirmed by DNA sequence analysis. The results of the PCR examination of the 7 reference isolates and 36 stored isolates were similar to the results obtained using conventional methods as gold standard, both for diphtheria-causing and non-diphtheria-causing bacteria. The validation of the PCR results using DNA sequence analysis showed that there was no mispriming or misamplification. The multiplex PCR assay developed in this study could correctly identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types not yet covered by established PCR methods.
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Affiliation(s)
- Sunarno
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia.
| | - Khariri
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Fauzul Muna
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Kambang Sariadji
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Yuni Rukminiati
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Dwi Febriyana
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Tati Febrianti
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Ratih Dian Saraswati
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Ida Susanti
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Nelly Puspandari
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | | | - Amarila Malik
- Division of Microbiology and Biotechnology Pharmacy, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia
| | - Amin Soebandrio
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Eijkman Institute for Molecular Biology, Jakarta, Indonesia
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Ariyanto IA, Lee S, Estiasari R, Edmands J, Bela B, Soebandrio A, Price P. Understanding the effects of CMV on γδ T-cell populations in HIV patients starting antiretroviral therapy. Clin Immunol 2021; 226:108696. [PMID: 33621667 DOI: 10.1016/j.clim.2021.108696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/17/2021] [Accepted: 02/16/2021] [Indexed: 12/14/2022]
Abstract
Cytomegalovirus (CMV) affects γδ T-cell profiles in healthy individuals and transplant recipients, but the effects of HIV and CMV have not been distinguished in HIV patients. CMV-seropositive Indonesian HIV patients (n = 40) were studied before ART and after six months, alongside healthy controls (n = 20). 50% of patients started ART with detectable CMV DNA. Proportions of Vδ2- γδ T-cells were high in patients and declined on ART, whilst proportions of Vδ2+ γδ T-cells were uniformly low, and correlated inversely with levels of CMV DNA and CMV-reactive antibody. Residual Vδ2+ cells were enriched for markers of terminal differentiation, but this did not associate with CMV metrics. Patients with CMV DNA at baseline showed a direct correlation between CMV reactive-antibody and CD8+ γδ T-cells. Our data are consistent with a role for CMV in the depletion of Vδ2+ γδ T-cells in HIV patients beginning ART, with no consistent evidence of a role for CMV in γδ T-cell activation or differentiation.
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Affiliation(s)
- Ibnu A Ariyanto
- Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Virology and Cancer Pathobiology Research Center, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Silvia Lee
- Department of Microbiology, Pathwest Laboratory Medicine, Perth, Australia; School of Pharmacy & Biomedical Science, Curtin University, Perth, Australia
| | - Riwanti Estiasari
- Department of Neurology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Jeanne Edmands
- School of Pharmacy & Biomedical Science, Curtin University, Perth, Australia
| | - Budiman Bela
- Virology and Cancer Pathobiology Research Center, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | | | - Patricia Price
- Virology and Cancer Pathobiology Research Center, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; School of Pharmacy & Biomedical Science, Curtin University, Perth, Australia.
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Widhidewi NW, Wiyatno A, Dewantari AK, Paramasatiari L, Aryastuti SA, Artika IN, Setiawan WD, Soebandrio A, Aye Myint KS, safari D. Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia. Access Microbiol 2020; 2:acmi000120. [PMID: 32974585 PMCID: PMC7494194 DOI: 10.1099/acmi.0.000120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 12/04/2022] Open
Abstract
Acute respiratory tract infection (ARTI) is the most common infectious disease in humans worldwide. The morbidity and mortality rates are high, especially in developing countries from Southeast Asia and Africa. While ARTI is commonly associated with viruses, there is limited data on the spectrum of viruses causing ARTI in developing countries, including Indonesia. This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In total, 98 out of 200 samples (49.0 %) tested positive for viruses. Our study confirmed 64.3 % viral etiology in children and 12.2 % in adults. Viruses that were detected were Herpesviridae (15.0 %) followed by enteroviruses (12.0 %), influenza A virus (11.5 %), respiratory syncytial virus (8.0 %), Adenoviridae (6.5 %), human metapneumovirus (3.5 %), Paramyxoviridae (2.0 %), bocavirus (1.0 %) and Coronaviridae (0.5 %). The study sheds light on the viral spectrum of ARTI in children and adults in Tabanan, Bali, Indonesia.
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Affiliation(s)
- Ni Wayan Widhidewi
- Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya, No. 6 Jakarta, Indonesia
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - Ageng Wiyatno
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | | | - Lila Paramasatiari
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - Sri Agung Aryastuti
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - I Nengah Artika
- Tabanan General Hospital, Jl. Pahlawan, Tabanan, Bali, Indonesia
| | | | - Amin Soebandrio
- Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya, No. 6 Jakarta, Indonesia
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | - Khin Saw Aye Myint
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | - Dodi safari
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
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Mawuntu AHP, Johar E, Anggraeni R, Feliana F, Bernadus JBB, Safari D, Yudhaputri FA, Dhenni R, Dewi YP, Kato C, Powers AM, Rosenberg R, Soebandrio A, Myint KSA. Rickettsia felis identified in two fatal cases of acute meningoencephalitis. PLoS Negl Trop Dis 2020; 14:e0007893. [PMID: 32069292 PMCID: PMC7048312 DOI: 10.1371/journal.pntd.0007893] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 08/08/2019] [Revised: 02/28/2020] [Accepted: 10/31/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Rickettsia felis has recently emerged worldwide as a cause of human illness. Typically causing mild, undifferentiated fever, it has been implicated in several cases of non-fatal neurological disease in Mexico and Sweden. Its distribution and pathogenicity in Southeast Asia is poorly understood. METHODOLOGY/PRINCIPAL FINDINGS We retroactively tested cerebrospinal fluid (CSF) or sera from 64 adult patients admitted to hospital in North Sulawesi, Indonesia with acute neurological disease. Rickettsia felis DNA was identified in the CSF of two fatal cases of meningoencephalitis using multi-locus sequence typing semi-nested PCR followed by Sanger sequencing. DNA from both cases had 100% sequence homologies to the R. felis reference strain URRWXCal2 for the 17-kDa and ompB genes, and 99.91% to gltA. CONCLUSION/SIGNIFICANCE The identification of R. felis in the CSF of two fatal cases of meningoencephalitis in Indonesia suggests the distribution and pathogenicity of this emerging vector-borne bacteria might be greater than generally recognized. Typically Rickettsia are susceptible to the tetracyclines and greater knowledge of R. felis endemicity in Indonesia should lead to better management of some acute neurological cases.
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Affiliation(s)
| | - Edison Johar
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Riane Anggraeni
- Faculty of Medicine, Sam Ratulangi University, Manado, Indonesia
| | - Feliana Feliana
- Faculty of Medicine, Sam Ratulangi University, Manado, Indonesia
| | | | - Dodi Safari
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Rama Dhenni
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Yora P. Dewi
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Cecilia Kato
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Ann M. Powers
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Ronald Rosenberg
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Amin Soebandrio
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Khin S. A. Myint
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
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21
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Abdullah M, Maulahela H, Utari AP, Kusumo PD, Soebandrio A, Achmad I, William A, Makmun D. Patient assessment of constipation quality of life questionnaire: validity and reliability for Indonesian population. Med J Indones 2019. [DOI: 10.13181/mji.v28i4.3353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Constipation is a condition commonly encountered by physicians, causing a significant reduction in patients’ quality of life. Therefore, successful management of constipation should also include increase the quality of life. The Patient Assessment of Constipation Quality of Life (PAC-QOL) questionnaire is a questionnaire developed to address this issue. However, this questionnaire had not been translated into the Indonesian language. This study was aimed to adapt PAC-QOL into Indonesian culture and perform the psychometric evaluation.
METHODS Translation and cultural adaptation were performed based on the linguistic validation guidelines by Acquadro et al in 2012. To perform the psychometric evaluation, a total of 64 subjects in Petamburan district in Jakarta, Indonesia, were recruited from February to March 2018. Test-retest reliability was assessed by completing the PACQOL twice with one-week interval. Subjects also completed the Short Form 36 (SF-36) Health Survey Questionnaire to assess concurrent validity. Internal consistency was analyzed with Cronbach’s alpha value (>0.7) and the intraclass correlation coefficient.
RESULTS The mean (standard deviation) overall average score was 1.52 (0.66), while the Cronbach’s alpha value for the overall average score was 0.910. Concurrently, the intraclass correlation coefficient for the overall score was 0.87. Simultaneously, several experts judged content validity to be adequate. All the questions had significant correlations with their respective domains. Moreover, each domain of PAC-QOL also had a significant correlation with several SF-36 domains.
CONCLUSIONS The psychometric evaluation performed in this study demonstrated that the Indonesian version of the PAC-QOL was valid and reliable, suggesting that this questionnaire can be used in daily clinical practice.
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22
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Cicero A, Meyer D, Shearer MP, AbuBakar S, Bernard K, Carus WS, Chong CK, Fischer J, Hynes N, Inglesby T, Kwa CG, Makalinao I, Pangestu T, Sitompul R, Soebandrio A, Sudarmono P, Tjen D, Wibulpolprasert S, Yunus Z. Southeast Asia Strategic Multilateral Dialogue on Biosecurity. Emerg Infect Dis 2019; 25. [PMID: 31002062 PMCID: PMC6478199 DOI: 10.3201/eid2505.181659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A strategic multilateral dialogue related to biosecurity risks in Southeast Asia, established in 2014, now includes participants from Singapore, Malaysia, Indonesia, Thailand, Philippines, and the United States. This dialogue is conducted at the nonministerial level, enabling participants to engage without the constraints of operating in their official capacities. Participants reflect on mechanisms to detect, mitigate, and respond to biosecurity risks and highlight biosecurity issues for national leadership. Participants have also identified factors to improve regional and global biosecurity, including improved engagement and collaboration across relevant ministries and agencies, sustainable funding for biosecurity programs, enhanced information sharing for communicable diseases, and increased engagement in international biosecurity forums.
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23
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Kusumo PD, Maulahela H, Utari AP, Surono IS, Soebandrio A, Abdullah M. Probiotic Lactobacillus plantarum IS 10506 supplementation increase SCFA of women with functional constipation. Iran J Microbiol 2019; 11:389-396. [PMID: 32148669 PMCID: PMC7049320] [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] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND AND OBJECTIVES Gut microbiota influences our health via multiple mechanisms. Microbiota produced Short Chain Fatty Acid (SCFA) as an energy to maintain gut ecosystem and physiology. Dysbiosis is correlated with SCFA imbalance which in turn resulted in physiological abnormalities in the intestine, such as functional constipation. MATERIALS AND METHODS Randomized Double-Blind Controlled Trial (RCT) was conducted on women with functional constipation (n=37) in the community of Jakarta and profile of SCFA was assessed by using GC-MS from the stool after 21 days supplementation of fermented milk (placebo and probiotic). RESULTS Probiotic supplementation significantly influenced acetate titer (p=0,032) marginally significant for propionate and butyrate (p=0.063 and p=0.068, respectively) and the respondent with increasing SCFA's metabolite are higher in probiotic group compared to the respondents in placebo group. Acetate is the highest SCFA titer found in faeces samples of women with functional constipation. CONCLUSION Probiotic Lactobacillus plantarum IS 10506 supplementation influenced all the SCFA parameter (acetate, propionate and butyrate).
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Affiliation(s)
- Pratiwi Dyah Kusumo
- Biomedic Doctoral Programme, School of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Biomedic, School of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Hasan Maulahela
- Department of Gastroenterology, School of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Amanda Pitarini Utari
- Department of Gastroenterology, School of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Ingrid S. Surono
- Department of Food Technology, Faculty of Engineering, Bina Nusantara University, Jakarta, Indonesia
| | - Amin Soebandrio
- Eijkman Biology Molecular Institute, Jakarta, Indonesia
- Department of Microbiology, School of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Murdani Abdullah
- Department of Gastroenterology, School of Medicine, Universitas Indonesia, Jakarta, Indonesia
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24
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Sasmono RT, Dhenni R, Yohan B, Pronyk P, Hadinegoro SR, Soepardi EJ, Ma'roef CN, Satari HI, Menzies H, Hawley WA, Powers AM, Rosenberg R, Myint KSA, Soebandrio A. Zika Virus Seropositivity in 1-4-Year-Old Children, Indonesia, 2014. Emerg Infect Dis 2019; 24. [PMID: 30125240 PMCID: PMC6106422 DOI: 10.3201/eid2409.180582] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We assessed Zika virus seroprevalence among healthy 1–4-year-old children using a serum sample collection assembled in 2014 representing 30 urban sites across Indonesia. Of 662 samples, 9.1% were Zika virus seropositive, suggesting widespread recent Zika virus transmission and immunity. Larger studies are needed to better determine endemicity in Indonesia.
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25
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Sasmono R, Dhenni R, Yohan B, Pronyk P, Hadinegoro S, Soepardi E, Ma’roef C, Satari H, Menzies H, Hawley W, Powers A, Rosenberg R, Myint K, Soebandrio A. Endemicity of Zika virus in Indonesia: serological evidence in pediatric population. Int J Infect Dis 2019. [DOI: 10.1016/j.ijid.2018.11.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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26
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Danquah L, Sulo J, Mersini K, Bino S, Huda N, Adisasmito W, Soebandrio A, Karimuribo E, Sindato C, Beda E, Rweyemamu M, Were W, Lutwama J, Yishai R, Cohen D, Thajeen J, Nyein S, Oo MK, Libel M, Gresham L, Japra N, Burke C, Orefuwa E, Asquith P, Longuet C. Assessment of event based surveillance in cross border areas of six regional networks. Int J Infect Dis 2019. [DOI: 10.1016/j.ijid.2018.11.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Suwarto S, Adlani H, Nainggolan L, Rumende CM, Soebandrio A. Laboratory parameters for predicting Salmonella bacteraemia: a prospective cohort study. Trop Doct 2017; 48:124-127. [PMID: 28959915 DOI: 10.1177/0049475517734118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Blood cultures for a definitive diagnosis of typhoid fever takes time and are not routinely available. We thus investigated laboratory parameters to predict Salmonella bacteraemia. We conducted a prospective cohort study in Jakarta, Indonesia. Patients with suspected typhoid fever admitted to hospital from October 2014 to December 2016 were included. Out of 187 individuals, 27 had Salmonella typhi and 12 had S. paratyphi in blood cultures. Absolute eosinopenia, elevated aspartate aminotransferase and elevated C-reactive protein > 40 mg/L were positive predictors.
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Affiliation(s)
- Suhendro Suwarto
- 1 Senior Lecturer, Division of Tropical and Infectious Diseases, Department of Internal Medicine, Faculty of Medicine Universitas Indonesia, Dr. Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia
| | - Hadianti Adlani
- 2 Associate Lecturer, Department of Internal Medicine, Faculty of Medicine Universitas Indonesia, Dr. Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia
| | - Leonard Nainggolan
- 3 Lecturer, Division of Tropical and Infectious Diseases, Department of Internal Medicine, Faculty of Medicine Universitas Indonesia, Dr. Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia
| | - Cleopas Martin Rumende
- 4 Senior Lecturer, Department of Internal Medicine, Faculty of Medicine Universitas Indonesia, Dr. Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia
| | - Amin Soebandrio
- 5 Professor, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,5 Professor, Department of Microbiology, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
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Bentley K, Soebandrio A. Dietary exposure assessment for arsenic and mercury following submarine tailings placement in Ratatotok Sub-district, North Sulawesi, Indonesia. Environ Pollut 2017; 227:552-559. [PMID: 28501769 DOI: 10.1016/j.envpol.2017.04.081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/22/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
The Mesel gold mine in the Ratatotok Sub-district operated between 1996 and 2004 with tailings disposal via an engineered submarine tailings placement (STP) into Buyat Bay. This operation raised concerns of increased levels of arsenic (As) and mercury (Hg) associated disease in the local communities from consumption of seafood contaminated with anthropogenic As and Hg. This report uses the dietary exposure to As and Hg, from local fishermen and market-purchased Codex "as consumed" and environmental fish results from the pre-mining baseline (1990-1995), the mine operational (1996-2004) and post-closure monitoring (2007-2016) to examine the potential health effects. The Ratatotok Sub-district consumers total As average daily intake from fish was between 152 and 317 μg/day (adults) and 58 and 105 μg/day (infants). The average daily intake of inorganic arsenic (Asi) from the dietary staples fish and rice and drinking water consumption was 77 μg/day (adults) and 35 μg/day (infants) at Buyat Pantai and 39 μg/day (adults) and 19 μg/day (infants) at Ratatotok township. Fish consumption contributed 8.2% (adults) and 6.5% (infants) to total daily Asi intake. Average Hg intake from fish consumption, exceeded the FAO WHO PTWI for methylmercury (MeHg) for all age and gender groups at Buyat Pantai 4.6 μg/kg bw/wk (adults) and 7.3 μg/kg bw/wk (infants) and for the infants at Buyat village and Ratatotok township (2.5 and 2.8 μg/kg bw/wk respectively). The Manado City consumers had average intakes below the MeHg PTWI. The Hg exceedances resulted from the high fish consumption in coastal communities and not elevated levels of Hg in fish. Hg exposure levels from the pre-mining baseline, Mesel STP operation and post-closure monitoring, confirmed that exceedances were unrelated to the tailings deposited into Buyat Bay.
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Affiliation(s)
- Keith Bentley
- Centre for Environmental Health, Canberra, ACT 2606, Australia.
| | - Amin Soebandrio
- Eijkman Institute for Molecular Biology, Ministry for Research, Technology and Higher Education, Jakarta, Indonesia
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29
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Yudhaputri FA, Trimarsanto H, Perkasa A, Yohan B, Haryanto S, Wiyatno A, Soebandrio A, Myint KS, Ledermann JP, Rosenberg R, Powers AM, Sasmono RT. Genomic characterization of Zika virus isolated from Indonesia. Virology 2017; 510:248-251. [PMID: 28755588 DOI: 10.1016/j.virol.2017.07.026] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 01/06/2023]
Abstract
Zika virus (ZIKV) JMB-185 strain was isolated from a febrile patient in Jambi, Indonesia in 2014. To understand its genetic characteristics, we performed whole genome sequencing using the Ion Torrent PGM platform on the supernatant of the first passage. The phylogenetic analysis showed that the isolate was not closely related to the Brazilian ZIKV associated with microcephaly or isolates from the recent Singapore Zika outbreak. Molecular evolution analysis indicated that JMB-185 strain may have been circulating in the Southeast Asia region, including Indonesia since 2000. We observed high nucleotide sequence identity between Indonesia, Thailand, Singapore, and American strains although unique amino acid substitutions were also observed. This report provides information on the genomic characteristics of Indonesian ZIKV which may be used for further studies.
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Affiliation(s)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Agency for Assessment and Application of Technology, Jakarta, Indonesia
| | - Aditya Perkasa
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Ageng Wiyatno
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Khin Saw Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Ronald Rosenberg
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Ann M Powers
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
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30
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Bentley K, Soebandrio A. Arsenic and mercury concentrations in marine fish sourced from local fishermen and fish markets in mine-impacted communities in Ratatotok Sub-district, North Sulawesi, Indonesia. Mar Pollut Bull 2017; 120:75-81. [PMID: 28479145 DOI: 10.1016/j.marpolbul.2017.04.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/21/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Mesel gold mine, Ratatotok Sub-district, North Sulawesi, Indonesia deposited about 4.5millionm3 of detoxified tailings containing arsenic (As) and mercury (Hg) via a submarine pipeline into Buyat Bay. As and Hg analysis of 216 fish muscle tissue composites from subsistence fishermen, local markets and a reference market confirmed that mean As levels were comparable between locations (range 1.71 to 2.12mg/kg wet weight (ww)) and <10% of the Australia New Zealand standard. Mean Hg concentrations were highest for the artisanal fishermen group (0.23mg/kg ww), similar between the local markets (0.11-0.14mg/kg ww) and lower at the reference market (0.04mg/kg ww). A 12-month fish availability study identified that the results were due to the different coral and deep ocean species assemblages. All mean values were <50% of the FAO/WHO/Codex standard for Hg. The results confirmed that there was no contamination from the deposited submarine tailings.
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Affiliation(s)
- Keith Bentley
- Centre for Environmental Health, Canberra, ACT 2606, Australia.
| | - Amin Soebandrio
- Eijkman Institute for Molecular Biology, Ministry for Research, Technology and Higher Education, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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31
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Haryanto S, Hayati RF, Yohan B, Sijabat L, Sihite IF, Fahri S, Meutiawati F, Halim JAN, Halim SN, Soebandrio A, Sasmono RT. The molecular and clinical features of dengue during outbreak in Jambi, Indonesia in 2015. Pathog Glob Health 2016; 110:119-29. [PMID: 27215933 DOI: 10.1080/20477724.2016.1184864] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dengue is hyperendemic in Indonesia. In 2015, reported cases of dengue fever doubled those of 2014 in the Jambi municipality of Sumatra. We examined viral aetiology and its relationship with disease outcome in Jambi. Dengue-suspected patients' sera were collected and NS1 detection and IgM/IgG serology were performed. Dengue virus (DENV) serotyping was performed using real-time RT-PCR. Envelope genes were sequenced to determine the genotypes of DENV. Clinical, haematologic, and demographic data were recorded. Of 210 dengue-suspected patients, 107 were confirmed. The disease manifested as Dengue Fever (62%), Dengue Haemorrhagic Fever (36%), and Dengue Shock Syndrome (2%). The serotypes of 94 DENV were determined. All DENV serotypes were detected with DENV-1 as the predominant serotype (66%). Genotypically, the DENV-1 viruses belong to Genotype I, DENV-2 was of Cosmopolitan genotype, DENV-3 as Genotype I, and DENV-4 belonged to Genotype II. Comparison with historical data revealed serotype predominance switched from DENV-3 to DENV-1, and the replacement of Genotype IV of DENV-1 with Genotype I. In summary, DENV-1 predominated during the 2015 dengue outbreak in Jambi. The full spectrum of dengue disease occurred and was characterized by a switch in predominant serotypes.
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Affiliation(s)
- Sotianingsih Haryanto
- a Siloam Hospital , Jambi , Indonesia.,d Faculty of Medicine , Jambi University , Jambi , Indonesia
| | - Rahma F Hayati
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
| | | | | | | | - Sukmal Fahri
- c Health Polytechnic , Jambi Provincial Health Office , Jambi , Indonesia
| | | | | | - Stefanie N Halim
- e Faculty of Medicine , Diponegoro University , Semarang , Indonesia
| | - Amin Soebandrio
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
| | - R Tedjo Sasmono
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
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Apriyanto DR, Aoki C, Hartati S, Hanafi M, Kardono LBS, Arsianti A, Louisa M, Sudiro TM, Dewi BE, Sudarmono P, Soebandrio A, Hotta H. Anti-Hepatitis C Virus Activity of a Crude Extract from Longan (Dimocarpus longan Lour.) Leaves. Jpn J Infect Dis 2015; 69:213-20. [PMID: 26255732 DOI: 10.7883/yoken.jjid.2015.107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Infection with hepatitis C virus (HCV) results in hepatitis C, a disease characterized by chronic infection, cirrhosis, and hepatocellular carcinoma. Currently, the standard therapy is a combination of pegylated interferon-α plus ribavirin with NS3 protease inhibitors. Addition of NS3 protease inhibitors to the standard therapy improves response rates; however, use of NS3 protease inhibitors is also associated with significant adverse effects and an increase in the overall cost of treatment. Therefore, there is a need to develop safe and inexpensive drugs for the treatment of HCV infections. In this study, we examined the antiviral activity of a crude extract from Dimocarpus longan leaves against HCV (genotype 2a strain JFH1). The D. longan crude extract (DL-CE) exhibited anti-HCV activity with a 50% effective concentration (EC50) of 19.4 μg/ml without cytotoxicity. A time-of-addition study demonstrated that DL-CE has anti-HCV activity at both the entry and post-entry steps and markedly blocks the viral entry step through direct virucidal activity with marginal inhibition of virion assembly. Co-treatment of DL-CE with cyclosporine A, an immunosuppressant or telaprevir, an NS3 protease inhibitor, resulted in additive and synergistic antiviral effects, respectively. Our findings suggest that DL-CE may be useful as an add-on therapy candidate for treating HCV infections.
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Abstract
Influenza A (H5N1) virus, has spread to several countries in the world and has a high mortality rate. Meanwhile, the virus has evolved into several clades. The human influenza A (H5N1) virus circulating in Indonesia is a member of clade 2.1, which is different in antigenicity from other clades of influenza A (H5N1). An analysis of the antigenic variation in the H5 hemagglutinin gene (HA) of the influenza A (H5N1) virus strains circulating in Indonesia has been undertaken. Several position of amino acid mutations, including mutations at positions 35, 53, 141, 145, 163, 174, 183, 184, 189, and 231, have been identified. The mutation Val-174-Iso appears to play an important role in immunogenicity and cross-reactivity with rabbit antisera. This study shows that the evolution of the H5HA antigenic variation of the influenza A (H5N1) virus circulating in Indonesia from 2005 to 2011 may affect the immunogenicity of the virus.
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Affiliation(s)
- Vivi Setiawaty
- Center for Biomedical and Basic Technology of Health, National Institute of Health Research and Development, Ministry of Health. ; Doctoral Program of Faculty of Medicine, University of Indonesia
| | - Eka Pratiwi
- Center for Biomedical and Basic Technology of Health, National Institute of Health Research and Development, Ministry of Health
| | - Hana A Pawestri
- Center for Biomedical and Basic Technology of Health, National Institute of Health Research and Development, Ministry of Health
| | - Fera Ibrahim
- Department of Microbiology, Faculty of Medicine, University of Indonesia
| | - Amin Soebandrio
- Department of Microbiology, Faculty of Medicine, University of Indonesia
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Bijie H, Kulpradist S, Manalaysay M, Soebandrio A. In vitro activity, pharmacokinetics, clinical efficacy, safety and pharmacoeconomics of ceftriaxone compared with third and fourth generation cephalosporins: review. J Chemother 2005; 17:3-24. [PMID: 15828439] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Due to their wide spectrum of activity, good pharmacokinetics, established clinical efficacy and high tolerability, cephalosporins are among the most widely used antibiotics worldwide. The third and fourth generation cephalosporins are predominantly parenteral agents, administered two or three times daily, used in the treatment of a wide range of moderate to severe infections. Ceftriaxone, a third generation cephalosporin, is unique in exhibiting an unusually long elimination half-life that allows for once-daily administration. Among third generation cephalosporins, ceftazidime and cefoperazone are unusual among cephalosporins in possessing activity, albeit moderate, against Pseudomonas aeruginosa. However, both of these agents also exhibit marked loss of activity against Gram-negative organisms producing high levels of Class A or C beta-lactamases. Sulperazone, a 1:1 combination of cefoperazone and the beta-lactamase inhibitor sulbactam, is more resistant to attack by Class A beta-lactamases but remains vulnerable to isolates producing Class C beta-lactamases. Ceftriaxone exhibits the widest antibacterial spectrum of third generation cephalosporins and this is reflected in clinical responses. Cefoperazone and sulperazone exhibit the poorest clinical responses. Although the fourth generation cephalosporins cefpirome and cefepime exhibit enhanced stability to bacterial beta-lactamases and marginally enhanced in vitro antibacterial activity over ceftriaxone, there is no clinical advantage in terms of clinical or bacteriological success. The cephalosporins are well tolerated, with few and generally transient adverse effects; the major exception being haematological abnormalities including blood coagulation disorders associated with cefoperazone. Several pharmacoeconomic studies indicate that the once-daily dosing regimen required for ceftriaxone is the major factor responsible for its cost-effectiveness over third and fourth generation cephalosporins.
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Affiliation(s)
- H Bijie
- Institute of Respiratory Diseases, Medical Center of Fudan University, Shanghai 200932, China.
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Soebandrio A, Sri-Budayanti NN, Widayati A, Wiwing V, Nusatya MA. Role of β−lactamase in the susceptibility of clinical isolates to β−lactam antibiotics. Med J Indones 2004. [DOI: 10.13181/mji.v13i3.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Sudiro TM, Soebandrio A, Prawoto P, Sudarmono P. Resistance pattern of <em>Mycobacterium tuberculosis</em> to first-line antituberculosis drugs. Med J Indones 2000. [DOI: 10.13181/mji.v9i3.628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Soebandrio A. Development of Elisa for rapid detection of anti-dengue antibody. Med J Indones 1992. [DOI: 10.13181/mji.v1i2.3583] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
[no abstract available]
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Abstract
Change in the specificity of anti-(4-hydroxy-3-nitrophenyl)acetyl (NP) antibodies (Abs) with time after immunization was studied. The early anti-NP Abs was specific to the ionized (phenolate) form of NP. The specificity changed with time and the late Abs became able to bind to the protonated (phenolic) form as well as the phenolate form of NP. The nucleotide sequences of mRNA coding for variable regions of heavy and light chains suggested that somatic hypermutation contributed to this change of the specificity.
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Fujio H, Takagaki Y, Ha YM, Doi EM, Soebandrio A, Sakato N. Native and non-native conformation-specific antibodies directed to the loop region of hen egg-white lysozyme. J Biochem 1985; 98:949-62. [PMID: 2416741 DOI: 10.1093/oxfordjournals.jbchem.a135375] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Two types of antibodies were differentiated in conventional guinea pig anti-hen egg-white lysozyme (HEL) antisera. The specificities of both antibodies were directed to the loop I region (mainly directed to Cys64--Cys80 loop) but the antibodies were distinct in respect of reactivities with native HEL. One type of antibody reacted with HEL and loop-peptides of HEL but not with the completely reduced and carboxymethylated form of loop-peptides (native conformation specific antibody: NC-Ab). On the other hand, the other type of antibody did not react with HEL but reacted with loop-peptides and also with the completely reduced and carboxymethylated form of loop-peptides (non-native conformation specific antibody: NNC-Ab). The percentage of NNC-Ab in loop I reactive antibody fraction from pooled guinea pig anti-HEL antisera obtained by two different immunization methods was about 25%. Since the affinities of the NNC-Ab to loop-related peptides were higher by one order of magnitude than those of the NC-Ab to the same peptides, care is necessary in evaluating antigenic determinants in native protein. The immunization of guinea pigs with Ploop I . II [sequence 57-107 (Cys64-Cys80, Cys76-Cys94)] evoked an antibody population having specificity similar to but not identical with that of the NNC-Ab type anti-loop I antibody in conventional anti-HEL antisera.
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