A narrative review of genomic characteristics, serotype, immunogenicity, and vaccine development of Streptococcus pneumoniae capsular polysaccharide

This narrative review describes genomic characteristic, serotyping, immunogenicity, and vaccine development of Streptococcus pneumoniae capsular polysaccharide (CPS). CPS is a primary virulence factor of S. pneumoniae. The genomic characteristics of S. pneumoniae CPS, including the role of biosynthetic gene and genetic variation within cps (capsule polysaccharide) locus which may lead to serotype replacement are still being investigated. One hundred unique serotypes of S. pneumoniae have been identified through various methods of serotyping using phenotypic and genotypic approach. The advantages and limitations of each method are various, emphasizing the need for accurate and comprehensive serotyping for effective disease surveillance and vaccine targeting. In addition, we elaborate the critical role of CPS in vaccine development by providing an overview of immunogenicity, ongoing research of pneumococcal vaccines, and the impact on disease burden.

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.

Metagenome and Resistome Analysis of Beta-Lactam-Resistant Bacteria Isolated from River Waters in Surabaya, Indonesia

Antimicrobial agents are administered to humans and livestock, and bacterial antimicrobial resistance (AMR) and antimicrobial agents are released into the environment. In this study, to investigate the trend of AMR in humans, livestock, and the environment, we performed a metagenomic analysis of multidrug-resistant bacteria with CHROMagar ESBL in environmental river water samples, which were collected using syringe filter units from waters near hospitals, downtown areas, residential areas, and water treatment plants in Surabaya, Indonesia. Our results showed that Acinetobacter, Pseudomonas, Aeromonas, Enterobacter, Escherichia, and Klebsiella grew in CHROMagar ESBL; they were most frequently detected in water samples from rivers surrounding hospitals contaminated with various AMR genes (ARGs) in high levels. These results identified bacteria as ARG reservoirs and revealed that hospitals could be sources for various ARGs disseminated into the environment. In conclusion, this study details a novel metagenomic analysis of collected bacteria in environmental water samples using a syringe filter unit for an AMR epidemiological study based on the One Health approach.

SUSCEPTIBILITY PATTERN OF METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS BACTERIA IN DR. SOETOMO GENERAL ACADEMIC HOSPITAL SURABAYA

Background: Methicillin-resistant Staphylococcus aureus (MRSA), Gram-positive bacteria causing infection in hospital-acquired infection, has increased worldwide, including in Indonesia. Currently, the updated data on MRSA in Indonesia is limited. Purpose: This study aims to explore the prevalence and susceptibility pattern of MRSA in Dr. Soetomo General Academic Hospital Surabaya, Indonesia. Methods: This study was a descriptive-analytic study with a retrospective design. All clinical isolates of Methicillin-sensitive Staphylococcus aureus (MSSA) and MRSA from January to December 2017 were included. All inpatients included one MSSA or MRSA, and colonized bacteria were excluded. Data were analyzed using Chi-Square or Fisher’s Exact Test. Results: A total of 503 Staphylococcus aureus isolates were identified, of which 126 (25.05%) were MRSA. The highest prevalence of MRSA was from pus, wound swab, and tissue,  59 (28.37%) from 333, and the highest prevalence of the ward was in the intensive care unit (50%). MRSA were highly sensitive to daptomycin (n=95/95; 100%), linezolid (n=123/125; 98.40%), vancomycin (n=120/125; 96.00%), nitrofurantoin (n=43/45; 95.56%), quinupristin-dalfopristin (n=112/121; 92.56%), fosfomycin (n=87/97; 89.69%), and moxifloxacin (n=104/117; 88.89%). The susceptibility of the other antibiotics such as rifampicin, clindamycin, erythromycin, chloramphenicol, cotrimoxazole, levofloxacin, gentamicin, and tetracycline was less than 80%. Conclusion: The prevalence of MRSA among hospitalized patients in Dr. Soetomo General Academic Hospital, Surabaya, is 25.05% and tends to decrease from January to December 2017. Most MRSA was sensitive/intermediate to daptomycin, linezolid, vancomycin, nitrofurantoin, quinupristin-dalfopristin, fosfomycin, and moxifloxacin.

Distribution of Carbapenemase Genes among Carbapenem-Non-Susceptible Acinetobacter baumanii Blood Isolates in Indonesia: A Multicenter Study

Carbapenem non-susceptible Acinetobacter baumannii (CNSAB) is an important pathogen that causes nosocomial bacteremia among critically ill patients worldwide. The magnitude of antibiotic resistance of A. baumanii in Indonesia is expected to be significant; however, the data available are limited. The aim of this study was to analyze the genetic profiles of CNSAB isolates from patients with bacteremia in Indonesia. CNSAB isolates from blood cultures of bacteremia patients in 12 hospitals in Indonesia were included. The blood cultures were conducted using the BacT/Alert or BACTEC automated system. The CNSAB were identified with either Vitek 2 system or Phoenix platform followed by a confirmation test using a multiplex polymerase chain reaction (PCR) assay, targeting the specific gyrB gene. The carbapenemase genes were detected by multiplex PCR. In total, 110 CNSAB isolates were collected and were mostly resistant to nearly all antibiotic classes. The majority of CNSAB isolates were susceptible to tigecycline and trimethoprim-sulfamethoxazole (TMP-SMX), 45.5% and 38.2%, respectively. The bla_OXA-51-like gene was identified in all CNSAB isolates. Out of the total, 83.6% of CNSAB isolates had bla_OXA-23-like gene, 37.3% bla_OXA-24-like gene, 4.5% bla_NDM-1 gene, 0.9% bla_IMP-1 gene, and 0.9% bla_VIM gene. No bla_OXA-48-like gene was identified. The bla_OXA-23-like gene was the predominant gene in all except two hospitals. The presence of the bla_OXA-24-like gene was associated with resistance to tigecycline, amikacin, TMP-SMX and cefoperazone-sulbactam, while bla_OXA-23-like gene was associated with resistance to TMP-SMX and cefoperazone-sulbactam. In conclusion, the bla_OXA-23-like gene was the predominant gene among CNSAB isolates throughout Indonesia. A continuous national surveillance system needs to be established to further monitor the genetic profiles of CNSAB in Indonesia.

Analysis of the upstream genetic structures of the ISEcp1-blaCTX-M transposition units in Escherichia coli isolates carrying blaCTX-M obtained from the Indonesian and Vietnamese communities

Extended spectrum β-lactamase (ESBL)-producing Escherichia coli have been found in healthy individuals in Indonesia and Vietnam. The ISEcp1-bla_CTX-M transposition unit of ESBL-producing bacterial isolates has been considered responsible for the production of CTX-M type ESBL and it is important for the dissemination of bla_CTX-M . This study aimed to characterize the upstream genetic structure (UGS) of E. coli isolates possessing bla_CTX-M-1 group and/or bla_CTX-M-9 group genes obtained from healthy individuals in Indonesia and Vietnam. A total of 501 CTX-M type ESBL-producing E. coli isolates possessing bla_CTX-M-1 group and/or bla_CTX-M-9 group genes were obtained from healthy individuals of the two countries in 2018. The UGSs of the ISEcp1-bla_CTX-M transposition unit of the 501 ESBL-producing E. coli isolates were amplified by barcode-adaptor-ligation-mediated PCR and analyzed using the Nanopore sequencer. The obtained sequence information was used to classify the UGSs of the ISEcp1-bla_CTX-M transposition unit. From the 501 ESBL-producing E. coli isolates, 502 UGSs were obtained, which were classified into 85 UGS types based on the sequence. ISEcp1 of 359 (71.5%) of the 502 UGSs was disrupted by gene insertion, and ISEcp1-bla_CTX-M transposition unit of most (87.1%) of the determined UGSs was confirmed as plasmidic. Only 6 (7.1%) of the 85 UGS types were common to both countries. Our results indicated that many different UGSs of ISEcp1-bla_CTX-M transposition units were detected in Indonesia and Vietnam; hence, we suggest that structurally different kinds of plasmids harboring bla_CTX-M were separately distributed in the two countries.

The Prevalence of Extended Spectrum Beta-Lactamase (ESBL) Producing Gut Bacterial Flora Among Patients in Dr. Soetomo Hospital and Primary Health Centre in Surabaya

The extended-spectrum b-lactamase (ESBL) producer bacteria until now were mostly identified in hospital environment. The aim of this study was to analyze the prevalence of ESBL-producing gut flora and distribution of ESBL encoding genes between hospitalized patient in Tropical Wards of Dr. Soetomo Hospital and patient from a primary health centre (PHC) as community environment in Surabaya. Thiry rectal swab samples from hospital of Dr. Soetomo patients and from PHC (60 samples in total) were collected for this study. Samples were screened in MacConkey agar supplemented with 2 mg/L of cefotaxim, incubated at 37ºC for 24 hours. Then the growing colony were confirmed with Disk Diffusion Synergy test (DDST) for diagnosis of ESBL producer. The identified ESBL producers were then identified the bacteria species by biochemical method. ESBL gene were detected by PCR with specific primers. The results showed that there was not difference of positif nuber of ESBL-producing bacteria gut floral between patients of Dr.Soetomo Hospital, 25/30 (83.3%) and PHC, 11/30 (36.7%) (p=1). The pattern of ESBL gene distributions among samples from hospital showed that SHV was 12%, TEM was 36%, and CTX-M was 80%, and from PHC were SHV 18.2%, TEM 27,3% and CTX-M 81,8%. Statistical analysis showed that the pattern was not significantly different among hospitals and PHC samples as shown by SHV gene (p=0,631), TEM (p= 0.715), and CTX -M (p=1). From each ESBL gene, the dominant genes that found producing ESBL were the CTX-M genes followed by TEM and SHV genes. The prevalence of ESBL producersin intestinal flora of both the hospital (83,3%) and the PHC (36,7%) was very high. There was not significant difference between the prevalence of ESBL producer in gut flora of hospitalized patients compared to PHC. There was found other patterns of ESBL gene combinations in the hospital of SHV+CTX-M genes, TEM+CTX-M, SHV+TEM+CTX-M genes and PHC, the combination pattern of SHV+CTX-M, TEM+CTX-M.

Characterization of CTX-M type ESBL-producing Enterobacteriaceae isolated from asymptomatic healthy individuals who live in a community of the Okinawa prefecture, Japan

This study was performed to characterize CTX-M type extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae carriage in asymptomatic health individuals, which has not been well investigated, in a community of the Okinawa prefecture, Japan. Fecal samples were voluntary collected from asymptomatic healthy individuals who were going to take a routine medical checkup. The collected fecal samples were inoculated on MacConkey agar supplemented with 2 μg/ml of cefotaxime and incubated at 37 °C. Randomly selected three lactose-fermented colonies per each sample were analyzed. Genetic relatedness among the CTX-M type ESBL-producing Enterobacteriaceae isolates were performed by pulsed-field gel electrophoresis (PFGE) after confirmation of ESBL phenotype and determination of bacterial species. Location of bla_CTX-M was confirmed by S1-PFGE, I-CeuI-PFGE and the Southern blotting hybridization. ESBL-producing Enterobacteriaceae was isolated from 32 (12.2%) of the collected 263 fecal samples, and 96 ESBL-producing Enterobacteriaceae isolates were obtained. CTX-M type ESBL-producing Escherichia coli B2 were major (67 isolates, 72.0%) and 40 (59.7%) of the 67 CTX-M type ESBL -producing E. coli B2 were E. coli B2-ST131. Three CTX-M type ESBL-producing E. coli B2-ST131 isolates from asymptomatic healthy individuals showed similar PFGE band patterns as five CTX-M type ESBL -producing E. coli B2-ST131 isolates from a hospital locates in the same area of the target community. Chromosomally-transferred bla_CTX-M was observed in 10.0% of the examined CTX-M type ESBL-producing Enterobacteriaceae isolates. We report current situation CTX-M type ESBL-producing Enterobacteriaceae carriage in asymptomatic healthy individuals of the Okinawa prefecture, Japan. In addition, our results indicated that worldwide distributed CTX-M type ESBL-producing E. coli B2-ST131 has been spread in a community. Therefore monitoring of ESBL-producing Enterobacteriaceae in healthy individuals is important.