Nasopharyngeal carriage rate, serotype distribution, and antimicrobial profiles of Streptococcus pneumoniae among patients with acute respiratory tract infection in Manado, North Sulawesi, Indonesia.

We studied the carriage rate, distribution of serotype, and antimicrobial profile of Streptococcus pneumoniae (S. pneumoniae) among patients with acute respiratory tract infections (ARTI) in two primary health centres and a tertiary referral hospital from 2019 to 2020 in Manado, North Sulawesi, Indonesia before 13-valent pneumococcal conjugate vaccine (PCV13) introduction. A total of 106 nasopharyngeal swab samples were collected from children and adult patients. Serotyping of S. pneumoniae strain was performed by sequential multiplex PCR and Quellung reaction. Antimicrobial profile was performed by the disc diffusion method. We identified thirty-one patients carried S. pneumoniae strains (29 %). The S. pneumoniae carriage rate was found to be higher among children aged 2-5 years (13/32; 40.6 %) than in children under 1 year (8/27; 29.6 %), children and adolescents under 18 years of age (5/20; 25.0 %) and adult patients (5/27; 18.5 %). The distribution of serotypes varied, including 14, 18C, 19A, 23F, 19F and 35B (two strains each) and 1, 3, 6B, 6C, 31, 9V, 15C, 16F, 17F, 23A, 35F (one strain each) and non-typeable (9/31; 29 %). We found S. pneumoniae isolates were susceptible to vancomycin (30/31; 97 %), chloramphenicol (29/31; 94 %), clindamycin (29/31; 94 %), erythromycin (22/31; 71 %), azithromycin (22/31; 71 %), tetracycline (14/31; 45 %), penicillin (11/31; 35 %), and sulfamethoxazole/trimethoprim (10/31; 32 %). This study provides supporting baseline data on distribution of serotype and antimicrobial profile of S. pneumoniae among patients with ARTI before PCV13 introduction in Manado, North Sulawesi, Indonesia.

Whole genome sequencing data of Streptococcus pneumoniae isolated from Indonesian population.

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.

Nasopharyngeal carriage of Streptococcus pneumoniae among children <5 years of age in Indonesia prior to pneumococcal conjugate vaccine introduction.

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.

Antibacterial activity of medicinal plants in Indonesia on Streptococcus pneumoniae.

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.

Nasopharyngeal carriage rate, serotype distribution, and antimicrobial susceptibility profile of Streptococcus pneumoniae isolated from children under five years old in Kotabaru, South Kalimantan, Indonesia.

BACKGROUND: Streptococcus pneumoniae is a bacterial pathogen that colonizes the human nasopharynx. Colonization is frequently reported to be high in young children. In this study, we investigated the nasopharyngeal (NP) carriage rate, serotype distribution, and antibiotic susceptibility of S. pneumoniae in children under five years of age in Kotabaru, South Kalimantan, Indonesia. METHODS: NP swab specimens were collected from 399 young children (mean age: 30 months) who participated in the Rampa Village Community Health Center, with 74% of the participants being Bajau children. S. pneumoniae was identified using optochin susceptibility and bile solubility tests. Serotyping was performed by sequential multiplex PCR, and antimicrobial susceptibility profiling was performed by disk diffusion and microdilution methods. RESULTS: The NP carriage rate of S. pneumoniae was 45% (180/399). The most commonly serotypes were 6A/6B (18%), followed by 15B/15C (17%), 19F (16%), 34 (8%), and 23F (5%); 46% of them were identified as strains of the PCV13 vaccine type. Additionally, almost half of the pneumococcal isolates were non-susceptible to penicillin (40%), whereas non-susceptibility to tetracycline (36.8%), trimethoprim/sulfamethoxazole (29.7%), erythromycin (16.8%), chloramphenicol (9.7%), and clindamycin (8.6%) was also found. We identified 18% (n = 34) of S. pneumoniae isolates as multidrug-resistant (MDR) strains, and serotype 19F was the most common (74%) among them. CONCLUSIONS: MDR S. pneumoniae vaccine type strains were dominated by serotype 19F. The implementation of a pneumococcal conjugate vaccine program in Indonesia might reduce MDR strains circulating in the community in the future.

Genetic characterization of co-trimoxazole non-susceptible Streptococcus pneumoniae isolates from Indonesia.

We investigated the genetic variation of folA and folP genes encoding dihydropteroate synthase (DHPS) and dihydrofolate reductase (DHFR) enzymes amongst trimethoprim/sulfamethoxazole (co-trimoxazole) non-susceptible Streptococcus pneumoniae isolated from the Indonesian population. Archived S. pneumoniae isolates were screened for the presence and analysis of folA and folP genes using the polymerase chain reaction sequencing method. We found that 80 % of co-trimoxazole non-susceptible isolates (n=30/39) showed a 6 bp insertion in the sulphonamide-binding site of DHPS. The Asp-92-Ala and Ile-100-Leu substitutions were more common on DHFR (42 %; 22/53) followed by the Asp-92-Ala, Glu-94-Asp and Ile-100-Leu substitutions (32 %; 17/53). The combination of the Ile-100-Leu substitution at the DHFR region and the 6 bp insertion was the most dominant combination among isolates having both folA and folP genes.

Isolation and Identification of Optochin-Resistant Viridans Group Streptococci from the Sputum Samples of Adult Patients in Jakarta, Indonesia.

AIM: To investigate optochin-resistant viridans group streptococci (VGS) strains isolated from the sputum sample of adult patients with different clinical symptoms. MATERIALS AND METHODS: Optochin-resistant VGS isolates were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). recA sequencing was used to confirm identified isolates at the genus level by MALDI-TOF MS. Finding. We identified 79% of tested isolates (148/187) at the species-level identification using the MALDI-TOF MS tool. We identified that the most common species isolated from sputum specimens were S. oralis (44.9%) followed by S. mitis (25.7%), S. infantis (9.1%), S. parasanguinis (7.5%), S. peroris (3.7%), S. anginosus (2.7%), and S. sanguinis (2.1%). Discussion. The S. oralis strains were majority of optochin-resistant VGS isolates obtained from sputum of adult patients in Jakarta, Indonesia. MALDI-TOF MS showed potential for the rapid identification tool to identify optochin-resistant VGS isolates. Although there were discrepancies in identifying isolates at the genus/species level, the performance could be improved by expanding its database.

Serotypes and antibiotic susceptibility profile of Streptococcus pneumoniae isolated from nasopharynges of children infected with HIV in Jakarta, Indonesia, pre- and post-pneumococcal vaccination.

The aim of this prospective study was to investigate the serotypes and antibiotic susceptibility of S. pneumoniae carried by children infected with HIV before and after vaccination with the seven-valent pneumococcal conjugate vaccine in Jakarta, Indonesia in 2013. We collected nasopharyngeal swab specimens from 52 children pre-vaccination and 6 months post-vaccination. Serotyping was performed by conventional multiplex polymerase chain reaction and Quellung reaction. The antibiotic susceptibility profile was obtained by disc diffusion. We determined that 27 (52%) and 24 (46%) of the 52 children carried S. pneumoniae during pre- and post-vaccination periods, respectively with the majority of the isolates being non-vaccine type strains (85% pre-vaccination and 75% post-vaccination). Serotypes 34, 6C, and 16F (two strains each) were the most commonly identified serotypes at pre-vaccination. Serotypes 23A (three strains) and 19F (two strains) were the most commonly identified serotypes post-vaccination. In general, isolates were most commonly susceptible to chloramphenicol (88%) and clindamycin (88%), followed by erythromycin (84%), trimethoprim-sulphamethoxazole (69%), tetracycline (61%), and penicillin (59%). In conclusion, serotypes of S. pneumoniae isolated from the nasopharynges of children infected with HIV varied and were more likely to be non-vaccine type strains both before and after vaccination.

Prevalence, serotype and antibiotic susceptibility of Group B Streptococcus isolated from pregnant women in Jakarta, Indonesia.

Group B Streptococcus (GBS) is a bacterial pathogen which is a leading cause of neonatal infection. Currently, there are limited GBS data available from the Indonesian population. In this study, GBS colonization, serotype distribution and antimicrobial susceptibility profile of isolates were investigated among pregnant women in Jakarta, Indonesia. Demographics data, clinical characteristics and vaginal swabs were collected from 177 pregnant women (mean aged: 28.7 years old) at 29-40 weeks of gestation. Bacterial culture identification tests and latex agglutination were performed for GBS. Serotyping was done by conventional multiplex PCR and antibiotic susceptibility testing by broth microdilution. GBS colonization was found in 53 (30%) pregnant women. Serotype II was the most common serotype (30%) followed by serotype III (23%), Ia and IV (13% each), VI (8%), Ib and V (6% each), and one non-typeable strain. All isolates were susceptible to vancomycin, penicillin, ampicillin, cefotaxime, daptomycin and linezolid. The majority of GBS were resistant to tetracycline (89%) followed by clindamycin (21%), erythromycin (19%), and levofloxacin (6%). The serotype III was more resistant to erythromycin, clindamycin, and levofloxacin and these isolates were more likely to be multidrug resistant (6 out of 10) compared to other serotypes. This report provides demographics of GBS colonization and isolate characterization in pregnant women in Indonesia. The results may facilitate preventive strategies to reduce neonatal GBS infection and improve its treatment.

Pneumococcal nasopharyngeal carriage in Indonesia infants and toddlers post-PCV13 vaccination in a 2+1 schedule: A prospective cohort study.

BACKGROUND: The PCV13 immunization demonstration program began in October 2017 in Indonesia. The aim of this study is to assess the dynamic changes of pneumococcal serotype before and after PCV13 administration, with two primary and one booster doses. METHODS: The prospective cohort study was conducted as a follow up study measuring the impact of PCV13 demonstration program by the Indonesian Ministry of Health in Lombok Island, West Nusa Tenggara, Indonesia, from March 2018 to June 2019. The subjects were two-month-old healthy infants who were brought to the primary care facility for routine vaccination and followed until 18 months of age. We use convenience sampling method. There were 115 infants in the control group and 118 infants in the vaccine group, and the PCV immunization was given on a 2+1 schedule. Nasopharyngeal (NP) swabs were collected four times during the vaccination periods by trained medical staff. Specimens were analyzed by culture methods to detect S. pneumonia colonization and multiplex polymerase chain reaction (mPCR) to determine serotype. The most frequently detected serotypes will be named as dominant serotypes. Descriptive analysis of demographic characteristics, the prevalence of overall and serotype colonization, and the distribution of serotypes were performed. The prevalence of both cohort groups were compared using chi-square test. Statistical significance was set at p < 0.05. RESULTS: Two hundred and thirty three infants age two months old were recruited, with 48.9% of the subjects were male and 51.1% of the subjects were female. Sociodemographic data in both cohort groups were relatively equal. Nasopharyngeal pneumococcal colonization before PCV13 administration occurred in 19.1% of the control and 22.9% of the vaccine group. The prevalence increased with increasing age in both groups. The prevalence of VT serotypes in control groups aged 2 months, 4 months, 12 months, and 18 months was 40.9%, 44.2%, 53.8%, and 54.3%, respectively, and in the vaccine group, 25.9%, 40.4%, 38.0%, and 22.6%, respectively. The most common VT serotypes in both groups were 6A/6B, 19F, 23F, and 14. The prevalence of VT serotypes decreased significantly compared to non-vaccine type serotypes after three doses of the PCV13 vaccine (p < 0.001). Another notable change was the decline in prevalence of serotype 6A/6B after PCV13 administration using the 2+1 schedule. CONCLUSIONS: This study shows lower prevalence of VT and 6A/6B serotypes in the nasopharynx among children who were PCV13 vaccinated compared with those who were unvaccinated. The result from this study will be the beginning of future vaccine evaluation in larger population and longer period of study.

Streptococcus pneumoniae carriage and antibiotic susceptibility among Indonesian pilgrims during the Hajj pilgrimage in 2015.

The Hajj is an annual pilgrimage to Mecca and one of the largest gathering of people in the world. Most Indonesian pilgrims are senior adults and elderly adults, who are more prone to acquire infections during the Hajj ritual. The aims of this study are to investigate the dynamics of Streptococcus pneumoniae colonization and to investigate antibiotic susceptibility of pneumococcal strains in Indonesian pilgrims. This was a prospective multi-site longitudinal study in Indonesian hajj pilgrims aged >18 years old in the year 2015. Nasopharyngeal swabs were collected from the same subject before departure and upon arrival at the airport. S. pneumoniae was identified using conventional and molecular approach, while antibiotic susceptibility was determined using a disk diffusion method. Among 813 Hajj pilgrims who were enrolled from five sites in this study, the prevalence of S. pneumoniae carriage rates before- and after-the Hajj were 8.6% (95% CI 6.7-10.5%) and 8.2% (95% CI 6.4-10.1%), (p value: 0.844) respectively. Serotype 16F, 6A/6B, 3, 18, and 23F were the five most prevalent serotypes before Hajj, whereas serotypes 3, 34, 13, 4, and 23F were the most prevalent serotypes after Hajj. Serotype 3 was identified as most acquired serotype during Hajj in Indonesian pilgrim. There was an increase in the percentage of isolates susceptible to co-trimoxazole after Hajj (42.9% versus 57.4%). The study provided an overview of the change of dynamics of S. pneumoniae serotype acquisition in Indonesian Hajj Pilgrims. Along with data of vaccination serotypes coverage and antimicrobial susceptibility, these findings may contribute to recommendation of vaccination and treatment policies in the future.

Nasopharyngeal carriage and antimicrobial susceptibility profile of Haemophilus influenzae among patients infected with HIV in Jakarta, Indonesia.

In this study, the prevalence of nasopharyngeal carriage and the antimicrobial susceptibility profile of Haemophilus influenzae were investigated in children and adults with HIV infection in Jakarta, Indonesia. Thirty-four H. influenzae isolates were identified in the children (n=16/90; 18%) and adults (n=18/200; 9%) infected with HIV. All isolates were nontypeable H. influenzae and were less susceptible to ampicillin (62%) and trimethoprim/sulfamethoxazole (41%). In this study, the H. influenzae strains carried by patients infected with HIV were dominated by non-capsulated types.

NASOPHARYNGEAL CARRIAGE OF STREPTOCOCCUS PNEUMONIAE IN HEALTHY CHILDREN UNDER FIVE YEARS OLD IN CENTRAL LOMBOK REGENCY, INDONESIA.

Colonization with Streptococcus pneumoniae is mostly symptomless, but can progress to respiratory or even systemic disease. We investigated nasopharyngeal carriage of Streptococcus pneumoniae in healthy children under five years of age in Central Lombok Regency, Indonesia. This cross sectional study was carried out in 2012 among 1,200 healthy children aged 2 to 60 months. A multiplex sequential PCR was employed to determine serotype of cultured S. pneumoniae and a disk diffusion method to assess susceptibility to antimicrobial drugs. S. pneumoniae was cultured from 554 children and the most frequent serotypes found were 6A/B (22% of pneumococcal strains), 19F (11%), 23F (10%), 15B/C (8%), and 19A and 14 (4% each). The majority of strains were still susceptible to clindamycin (97%), erythromycin (87%), chloramphenicol (81%), and penicillin (72%), with only 41% and 38% susceptible to tetracycline and sulfamethoxazole/trimethoprim, respectively. Continuous surveillance of S. pneumoniae carriage is important for future pneumococcal vaccination programs in Indonesia.

STAPHYLOCOCCUS AUREUS AND STREPTOCOCCUS PNEUMONIAE PREVALENCE AMONG ELDERLY ADULTS IN JAKARTA, INDONESIA.

We studied Staphylococcus aureus and Streptococcus pneumoniae carriage among elderly adults in Jakarta, Indonesia. Nasopharyngeal swabs were collected from 149 adults aged 60-97 years. Both S. aureus and S. pneumoniae were identified by conventional and molecular methods. Methicillin-resistant Staphylococcus aureus (MSRA) was determined by PCR and antibiotic susceptibility using the disk diffusion method. Pneumococcal serotyping was performed with sequential multiplex PCR. We found S. aureus and S. pneumoniae present in 42 and 4 elderly adults respectively, and MRSA prevalence of 6%. Serotypes 3, 6A/B, 15B/C and 35F were identified among the four pneumococcal isolates. The majority of S. aureus isolates were susceptible to chloramphenicol (93%) and sulfamethoxazole/trimethoprim (93%), followed by gentamicin (88%), erythromycin (83%), penicillin (79%) and tetracycline (74%). Thus S. aureus prevalence is higher than that of S. pneumoniae, and a high frequency of MRSA carried by elderly adults in Jakarta, Indonesia.

Serotype distribution and antibiotic susceptibility of Streptococcus pneumoniae strains carried by children infected with human immunodeficiency virus.

BACKGROUND: We studied the serotype distribution and antibiotic susceptibility of Streptococcus pneumoniae isolates carried by children infected with HIV in Jakarta, Indonesia. METHODS: Nasopharyngeal swabs were collected from 90 HIV infected children aged 4 to 144 months. S. pneumoniae was identified by conventional and molecular methods. Serotyping was performed with sequential multiplex PCR and antibiotic susceptibility with the disk diffusion method. RESULTS: We identified S. pneumoniae carriage in 41 children (46%). Serotype 19 F was most common among 42 cultured strains (19%) followed by 19 A and 6A/B (10% each), and 23 F (7%). Most isolates were susceptible to chloramphenicol (86%), followed by clindamycin (79%), erythromycin (76%), tetracycline (43%), and sulphamethoxazole/trimethoprim (41%). Resistance to penicillin was most common with only 33% of strains being susceptible. Strains of serotypes targeted by the 13-valent pneumococcal conjugate polysaccharide vaccine (PCV13) were more likely to be multidrug resistant (13 of 25 or 52%) compared to non-PCV13 serotype isolates (3 of 17 or 18%; Fisher exact test p = 0.05). CONCLUSION: Our study provides insight into the epidemiology of pneumococcal carriage in young HIV patients in Indonesia. These findings may facilitate potential preventive strategies that target invasive pneumococcal disease in Indonesia.