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.

Association of blood isolate's multi antibiotic resistance-index on laboratory-confirmed bloodstream infection: A cross-sectional study.

BACKGROUND: A not optimal way of the insertion of the intravenous catheter can be one of the factors that cause bloodstream infection (BSI) that should be confirmed with blood culture, and if positive it is called Laboratory-Confirmed Bloodstream Infection (LCBI). One of the surveillance methods of nosocomial infection that is commonly used is the Multi Antibiotic Resistance (MAR)-Index. The aimed of study was association of MAR-index from blood isolates on LCBI category. METHOD: This study used a cross-sectional study with a consecutive sampling method. Data collection for this study includes identification of micromaterial profile, antimicrobial test, MAR-Index, and LCBI category. The analysis used is the Mann Whitney test with p < 0.05. RESULT: There were 43 isolates of LCBI 1, 26 isolates of LCBI 2, and none of the LCBI 3. Microorganisms in the LCBI category 1 were Staphylococcus aureus (53.4%), Acinetobacter baumannii (20.9%), Escherichia coli (9.3%), Klebsiella pneumonia (7.0%), Pseudomonas aeruginosa (4.7%), and Enterococcus faecalis (4.7%) with the MAR-Index ranged from 0.22 to 0.91. Microorganisms in the LCBI category 2 were Staphylococcus haemolyticus (69.3%), Staphylococcus epidermidis (19.3%), Staphylococcus hominis (3.8%), Streptococcus viridans (3.8%), and Corynebacterium jeikeium (3.8%) with the MAR-Index ranging between 0.11 and 0.79. There is no significant difference of MAR-index between LCBI 1 and 2 (p = 0.424) and no association of MAR-index on LCBI (p = 0.571). CONCLUSION: Most LCBI type 1 is Staphylococcus aureus and LCBI type 2 is Staphylococcus haemolyticus which there is no significant association of MAR-index on LCBIs.

Apoptosis-Inducing Factor, Protein Expression, and Apoptosis Changes with Glutamine in Podocytes Cells Exposed with Cisplatin.

Cisplatin is a well-known chemotherapeutic drug. It is one of the most effective anticancer agents and is widely used for the treatment of several types of tumors. However, side effects in normal tissues and organs, such as nephrotoxicity that induces apoptosis in epithelial cells in the kidney, limit the use of cisplatin. Glutamine is a substrate for the synthesis of glutathione as an antioxidant and promotes HSP70 release, protecting cells from apoptosis induced by different stimuli. In the present study, we investigated the protective effect of glutamine on cisplatin nephrotoxicity in the kidney. Mice were divided into three groups such as a group of control (P0), a group of intraperitoneal injection of a single dose cisplatin 20 mg/kg BW at 7th day (P1), and a group of intravenous glutamine injection 100 mg/kg BW at days 1-7 and given an intraperitoneal injection of single dose cisplatin 20 mg/kg BW at 7th day (P2). Measurement of AIF expression and apoptotic cells was carried out by immunohistochemical methods. The number of AIF expressions and apoptotic cells is expressed in the Allred score. AIF expression result is as follows: P0: 3.29 ± 0.79, P1: 5.32 ± 0.68, and P2: 4.49 ± 0.47. Apoptosis result is as follows: P0: 3.04 ± 0.70, P1: 5.26 ± 0.53, and P2: 4.44 ± 0.41. There is a decreased expression of AIF on intravenous glutamine administration, followed by a decrease in apoptosis in the podocyte. In conclusion, glutamine administration might represent the treatment of nephrotoxic-induced cisplatin.

International Comparison of Causative Bacteria and Antimicrobial Susceptibilities of Urinary Tract Infections between Kobe, Japan, and Surabaya, Indonesia.

Variation by country in urinary tract infection (UTI)-causative bacteria is partly due to the differences in the use of antibiotics. We compared their frequencies and antibiotic susceptibilities in the treatment of patients with UTI from 2 cities, Kobe, Japan, and Surabaya, Indonesia. We retrospectively analyzed 1,804 urine samples collected from patients with UTI in 2014 (1,251 collected in 11 months at Kobe University Hospital in Kobe and 544 collected in 2 months at Dr. Soetomo Hospital in Surabaya). Surabaya data were divided into adult and pediatric patients because a substantial number of specimens from pediatric-patients had been collected. The results indicated that Escherichia coli was the most common uropathogen (24.1% in Kobe and 39.3% in Surabaya) and was significantly resistant to ampicillin and substantially to first- and third-generation cephalosporins in Surabaya adults but not in Kobe adults (p ＜ 0.01). Enterococcus faecalis was often isolated in Kobe (14.0%), but not in Surabaya (5.3%). Klebsiella spp. were isolated at a higher rate in Surabaya pediatric patients (20.3%) than in Surabaya adults (13.6%) and Kobe adults (6.6%). The antibiotic susceptibilities of the isolates form Surabaya isolates tended to be lower than the ones from Kobe. Extended-spectrum ß-lactamase-producing Gram-negative bacteria were detected at a significantly higher rate in Surabaya than in Kobe (p ＜ 0.001). These results showed that the antimicrobial resistance patterns of UTI-causative bacteria are highly variable among 2 countries, and the continuous surveillance of trends in antibiotic resistance patterns of uropathogens is necessary for the future revision of antibiotic use.

High rate of seronegative HCV infection in HIV-positive patients.

Co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) is a significant global health problem. The two viruses are transmitted with high efficacy via blood-to-blood contact, mainly intravenous drug use (IVDU), whereas HCV is less easily transmitted sexually. Antibody testing is the main screening method for HCV infection, although it may not be the optimal option for HIV infection. The aim of this study was to investigate HCV infection in HIV-positive patients, with and without a detectable anti-HCV antibody response. A total of 187 plasma samples were obtained from HIV-positive patients in Surabaya, Indonesia and examined for anti-HCV [HCV enzyme immunoassay (EIA) 3.0], HCV genotype/subtype [reverse transcription-polymerase chain reaction (RT-PCR) using primers targeting a part of NS5B/5'UTR followed by sequencing] and HCV viral load (quantitative RT-PCR). A total of 119 patients (63.6%) were found to be anti-HCV-positive and, among these, HCV RNA was detected in 73 (61.3%), with HCV-1a as the predominant subtype (31.5%). Of the 68 anti-HCV-negative samples, HCV RNA was detected in 26/68 (38.2%) mostly as the HCV-3a subtype (50%). High HCV viral loads were more common among the HCV-seropositive patients. The HCV-seropositive samples with detected HCV RNA were mostly obtained from HIV-positive patients with parenteral transmission (IVDU) (76.7%); however, the HCV-seronegative samples with detected HCV RNA were mostly from patients who had acquired HCV through heterosexual transmission (61.5%). In conclusion, HIV-positive patients were at high risk of becoming co-infected with HCV and several remained HCV-seronegative. Furthermore, there may exist differences in HCV seropositivity and subtypes between HIV-positive patients who acquired HCV sexually and those who acquired HCV parenterally.

Emergence of fluoroquinolone-resistant strains of Salmonella enterica in Surabaya, Indonesia.

Typhoid fever remains a major health problem in developing countries. Fluoroquinolones such as ciprofloxacin emerged as the 1st-choice treatment of enteric fever, including typhoid, in the 1990s. Recently, Salmonella typhi strains with resistance to ciprofloxacin have been increasingly reported in several countries, although the fluoroquinolone-resistant clinical strain has not been reported in Indonesia. In the present study, we examined the drug susceptibility and the presence of gyrA mutations in 17 clinical strains of S. typhi isolated from Surabaya, Indonesia, in 2006 (9 strains) and 2008 (8 strains). Although all 9 isolates from 2006 were sensitive to all tested antibiotics and had no mutation in the gyrA gene, all 8 isolates from 2008 were resistant to nalidixic acid and ampicillin and had a gyrA mutation at codon 87. In addition, 3 of 8 strains from 2008 showed multiple drug resistance, including resistance to chloramphenicol, trimethoprim-sulfamethoxazole, and ciprofloxacin. Therefore, newer drugs, such as ceftriaxone, cefixime, and azithromycin, might be effective in this situation. This is the 1st report of the emergence of fluoroquinolone-resistant clinical strains of S. typhi with a gyrA mutation, and it reveals a health risk due to multidrug-resistant strains in Indonesia.