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Identifikasi Serotipe dan Sensitivitas Antibiotik S. pneumoniae yang Dibawa Nasofaring Penderita Oma di Kabupaten Banyumas Oviani, Miranti; Wahyono, Daniel Joko; Safari, Dodi
BioEksakta : Jurnal Ilmiah Biologi Unsoed Vol 2 No 1 (2020): BioEksakta
Publisher : Fakultas Biologi Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.bioe.2020.2.1.1779

The aims of this study are to detect S. pneumoniae carried by nasopharnyx of children in primary school (aged 6-12 years) that diagnosed with AOM, to identify sensitivity of S. pneumoniae to antibiotics. The design of this study is nonexperimental survey with the descriptive analysis. Sampling was conducted in September - December 2018 in Banyumas district primary schools. Detection of S. pneumoniae was performed with microbiology methods. Meanwhile, serotype was determined by multiplex PCR and sensitivity to antibiotics was deduced using disc diffusion. The result of this study showed that carriage rate of S. pneumoniae carried by nasopharynx in children aged over 5 years that diagnosed with AOM in the Banyumas district was 35%. Serotype of S. pneumoniae obtainend from this study were 6A/6B, 6C/6D, 17F, 3, 13, 14, 23B, and untypeable. In addition, isolates of S. pneumoniae were highly susceptible to clindamycin (100%), erythromycin (100%), sulphametaxazole/trimethoprim (100%), chloramphenicol (88%), oxacillin (77%), and tetracycline (66%).

Gut Microbiota Profile of Infants with Breastfeeding and Mixed Feeding Patterns Kusumaningrum, Tina; Tafroji, Wisnu; Gultom, Septiani Madonna; Putri, Nina Dwi; Hafifah, Cut Nurul; Safari, Dodi
HAYATI Journal of Biosciences Vol. 31 No. 3 (2024): May 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.3.530-538

We explore the gut microbiota profiles of 103 stool samples collected from infants at the age of 4 and 6 months in Jakarta, Indonesia. We performed 16S rRNA gene sequencing with Illumina MiSeq to identify the diversity, structure, and composition of the gut microbiota from those stool samples. Among 103 stool samples, 55 and 48 samples were collected from infants with breastfeeding and mixed feeding patterns, respectively. We found that the most abundant bacteria were Bifidobacteriales from the phylum of Actinobacteria (43.05%), Lactobacillales from the phylum of Firmicutes (28.39%), and Enterobacterales from the phylum of Proteobacteria (13.75%). The alpha and beta diversity analysis showed that the association between feeding patterns and differences in the microbial communities was not statistically significant (p-value >0.05). Our study did not show a difference in the gut microbiota pattern between the two feeding pattern groups. This result contributed to the variety of the world gut microbiota profile data in infants.

Bacterial Profile and Antimicrobial Resistance Patterns of Pleural Empyema in Pekanbaru Hospitals Yovi, Indra; Safari, Dodi; Syah, Nur Afrainin; Anggraini, Dewi; Hanifah, Zulfa Nur; Shapira, Vanesya Zahrani; Elliyanti, Aisyah
Jurnal Respirologi Indonesia Vol 44, No 1 (2024)
Publisher : Perhimpunan Dokter Paru Indonesia (PDPI)/The Indonesian Society of Respirology (ISR)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36497/jri.v44i1.590

Background: Empyema is a problem worldwide due to its high incidence, mortality, and morbidity rates. So, administering antibiotics is mandatory to treat the disease. It should be sensitive to the causal microorganisms and avoid resistant ones for treatment efficacy. This research aimed to determine bacterial profile and antimicrobial resistance, which can be fundamental foundations for clinical practices in the treatment of patients, especially in Pekanbaru.Methods: This was a cross-sectional study from medical records at Arifin Achmad and Eka Hospitals from January 1, 2015, to December 31, 2022, including culture and antibiotic resistance test results with samples from pleural fluid and antibiotic susceptibility test using VITEK 2.0.Results: A total of 197 pleural fluid specimens were obtained. Gram-negative bacteria were found to be the most prevalent at 79.7%, namely Klebsiella pneumoniae (18.5%), Escherichia coli (12.0%), and Pseudomonas aeruginosa (11.0%). Gram-positive bacteria were found at 12.2%, the most common being Staphylococcus aureus (6.1%) and Enterococcus faecalis (2.0%). Antibiotic sensitivity tests for Gram-negative bacteria showed that amikacin and tigecycline were the most sensitive, and Gram-positive bacteria showed the most sensitivity to linezolid, tigecycline, and vancomycin. The resistance of Klebsiella pneumoniae and Escherichia coli to cephalosporins was 18.5% and 75.0%, respectively. The resistance of Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa to carbapenems was 8.0%, 13.0%, and 53.0%, respectively.Conclusion: Gram-negative is the most common microorganism found in pleural empyema. The resistance of multiresistant bacteria to antibiotics is high and requires supervision to apply appropriate antibiotic administration based on local antimicrobial patterns and the need to strengthen antimicrobial stewardship programs.

Frekuensi Karier Streptococcus pneumoniae pada Populasi Dewasa Suku Akit Provinsi Riau Rosdiana, Dani; Veronica, R. Merlinda; Harahap, Sari; Esha, Indi; Mardhatilah, Ashifa; Putri, Nabila; Safitri, Nuridha Audinia; Safari, Dodi; Sarassari, Rosantia; Ilmiawati, Cimi; Elliyanti, Aisyah
Jurnal Ilmu Kedokteran Vol 18, No 2 (2024): Jurnal Ilmu Kedokteran
Publisher : Fakultas Kedokteran Universitas Riau

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26891/JIK.v18i2.2024.137-143

Stretococcus pneumoniae (S.pneumoniae) is a commonly colonized in healthy people that potentially to be transmitted directly to other individuals through droplets and as an invasive pathogen. The prevalence/ frequency of S. pneumoniae carriage in children is around 20-60%, while data of carriage’s frequency in adult population is still limited. Akit tribe is a tribe who lives in a group in the coastal rural area of Rupat Island. The high incidence of upper respiratory tract infection among Akit tribe and the location can be risk for S. pneumoniae carriage. Study aimed is to identify the frequency of carriage in the adult population of the Akit tribe. Nasopharyngeal swab was collected from healthy adults, then cultivated on agar media. Colonies suspected as S. pneumoniae then selected, then subjected to optochin test. S. pneumoniae confirmation were using automatic machine VITEK. We reported S. pneumoniae carriage rate was 7.8% (12 of 153 participants) among Akit tribe.

Immune Response to Capsular Polysaccharide of Streptococcus pneumoniae in Rabbits Immunized with Pneumococcal Conjugate Vaccine Zaenab; Tafroji, Wisnu; Salsabila, Korrie; Winarti, Yayah; Wulandari, I Gusti Ayu Inten; Yasmon, Andi; Safari, Dodi
HAYATI Journal of Biosciences Vol. 32 No. 3 (2025): May 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.3.642-648

To evaluate the immune response of a rabbit model to polysaccharide capsules of Streptococcus pneumoniae after primary and booster immunization with pneumococcal conjugate vaccine. Rabbits were immunized with 0.25 ml of the 13-valent pneumococcal conjugate vaccine (PCV13) on Day 0, 7, and 14. Blood of rabbits was collected to measure the specific antibodies against the native polysaccharide capsules of S. pneumoniae serotypes 6B (Anti-Pn6BPS antibodies) and 19F (Anti-19FPS antibodies) using enzyme-linked immunosorbent assay (ELISA). The specific anti-Pn6BPS and anti-Pn19FPS antibodies in the immunized group increased significantly compared to the control rabbit after immunization (P<0.05). The highest titer of anti-Pn6BPS and anti-Pn19FPS antibodies were obtained on Day 21 and Day 28, respectively. The third immunization on Day 21 is a fairly high increase in specific antibodies against polysaccharide type 6B and type 19F. The highest antibody titers against polysaccharide capsules of S. pneumoniae were obtained after booster immunization.

Mortality and associated factors among community-acquired pneumonia patients: A cross-sectional study in a provincial referral hospital in Indonesia Rosdiana, Dani; Siregar, Fajri M.; Ediwi, Nabila C.; Putri, Rahmi T.; Nurrahma, Zuyyina ER.; Elisabet, Adinda; Sarassari, Rosantia; Safari, Dodi; Ilmiawati, Cimi; Elliyanti, Aisyah
Narra J Vol. 5 No. 2 (2025): August 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i2.1649

Community-acquired pneumonia (CAP) poses a significant impact on the healthcare system due to rehospitalization and mortality. About one-third of hospitalized CAP patients died within one year. In addition to advanced age, vulnerable groups with comorbidities such as cancer, diabetes, and cerebrovascular disease (CVD) are more likely to suffer from severe CAP. The aim of this study was to investigate the factors linked to mortality in adult hospitalized CAP patients. The study extracted the medical records of patients aged ≥18 years, admitted to a referral hospital in Riau Province, who were diagnosed with CAP between January and December 2023. Multiple logistic regression step-wise analysis was employed to determine the factors associated with mortality in CAP patients. The study involved 334 patients with a median age of 58 years. Based on the confusion, urea, respiratory rate, blood pressure, and age ≥65 years (CURB-65) score, 11.9% of patients had severe CAP (CURB-65 scores 3 and 4). Age was a significant predictor of severe CAP (p≤0.001). The most prevalent comorbidities were malignancy (33.2%), CVD (30.2%), and diabetes (28.4%). Mortality incidence during hospitalization reached 35.9%. Significant factors associated with mortality in hospitalized CAP patients included renal dysfunction/elevated serum urea levels (p=0.031), CURB-65 score (p=0.023), vasopressor use (p≤0.001), mechanical ventilator use (p≤0.01) and steroid use (p=0.029). However, CVD was associated with a decreased risk of mortality (p=0.019). Gram-negative bacteria predominated, accounting for 50.6% of all positive isolates. Several significant factors were associated with mortality in adult patients hospitalized with CAP at referral Hospital in Riau, including renal dysfunction, CURB-65 score, vasopressor use, mechanical ventilator use, and steroid use. This finding underscored the importance of early identification factors in CAP patients.

Detection of Pathogenic Leptospira in Sputum of Leptospirosis Patient with Pulmonary Hemorrhage. Handayani, Farida Dwi; Novipuspitasari, Lisa; Ahmed, Ahmed; Safari, Dodi; Hidajat, Muhammad Choirul; Soebandrio, Amin; Gasem, Muhammad Hussein
Journal of Biomedicine and Translational Research Vol 11, No 2 (2025): August 2025
Publisher : Faculty of Medicine, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jbtr.v11i2.28259

Background: The pathogenic Leptospira species is the causative agent of leptospirosis, an endemic zoonotic disease in Indonesia. Misdiagnosis of the disease frequently occurs, as confirmatory diagnosis confined to highly specialized laboratories. As well, the pulmonary involvement of leptospirosis with hemoptysis is scarcely reported.Case Presentation: A 49 years-old male patient was admitted to the district hospital with acute febrile illness and a history of traveling to a malaria-endemic area in Borneo, Indonesia. Based on a chest X-ray result, the patient was clinically suspected to have pulmonary tuberculosis. However, the clinical manifestations of leptospirosis i.e. conjunctival suffusion, calf pain, and oliguria were present, and later hemoptysis was also reported. A clinical diagnosis of leptospirosis with pulmonary involvement was proposed. Immunochromatographic test (ICT)-rapid test for vivax/falciparum malaria and Ziehl-Neelsen (ZN) staining of sputum for tuberculosis results were both negative. Microscopic Agglutination Test (MAT), the IgM anti-Leptospira rapid test (lateral flow assay), and PCR amplification of both conventional and real-time (qPCR) were performed using various samples (serum, urine, and sputum). The MAT of acute single serum sample and rapid test were negative. Intriguingly, the PCR showed positive results in sputum and urine samples but not in the serum sample, highlighting the usefulness of leptospiral molecular detection to confirm further diagnosis.Conclusion: Molecular detection of pathogenic Leptospira in sputum samples can be considered for confirmatory diagnosis of leptospirosis patients with pulmonary hemorrhage. Likewise, the urine sample can be used as an option in the examination of severe leptospirosis.

Bacterial Profile and Antimicrobial Resistance Patterns of Pleural Empyema in Pekanbaru Hospitals Yovi, Indra; Safari, Dodi; Syah, Nur Afrainin; Anggraini, Dewi; Hanifah, Zulfa Nur; Shapira, Vanesya Zahrani; Elliyanti, Aisyah
Jurnal Respirologi Indonesia Vol 44 No 1 (2024)
Publisher : Perhimpunan Dokter Paru Indonesia (PDPI)/The Indonesian Society of Respirology (ISR)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36497/jri.v44i1.590

Background: Empyema is a problem worldwide due to its high incidence, mortality, and morbidity rates. So, administering antibiotics is mandatory to treat the disease. It should be sensitive to the causal microorganisms and avoid resistant ones for treatment efficacy. This research aimed to determine bacterial profile and antimicrobial resistance, which can be fundamental foundations for clinical practices in the treatment of patients, especially in Pekanbaru.Methods: This was a cross-sectional study from medical records at Arifin Achmad and Eka Hospitals from January 1, 2015, to December 31, 2022, including culture and antibiotic resistance test results with samples from pleural fluid and antibiotic susceptibility test using VITEK 2.0.Results: A total of 197 pleural fluid specimens were obtained. Gram-negative bacteria were found to be the most prevalent at 79.7%, namely Klebsiella pneumoniae (18.5%), Escherichia coli (12.0%), and Pseudomonas aeruginosa (11.0%). Gram-positive bacteria were found at 12.2%, the most common being Staphylococcus aureus (6.1%) and Enterococcus faecalis (2.0%). Antibiotic sensitivity tests for Gram-negative bacteria showed that amikacin and tigecycline were the most sensitive, and Gram-positive bacteria showed the most sensitivity to linezolid, tigecycline, and vancomycin. The resistance of Klebsiella pneumoniae and Escherichia coli to cephalosporins was 18.5% and 75.0%, respectively. The resistance of Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa to carbapenems was 8.0%, 13.0%, and 53.0%, respectively.Conclusion: Gram-negative is the most common microorganism found in pleural empyema. The resistance of multiresistant bacteria to antibiotics is high and requires supervision to apply appropriate antibiotic administration based on local antimicrobial patterns and the need to strengthen antimicrobial stewardship programs.

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