Wastewater-based epidemiology surveillance as an early warning system for SARS-CoV-2 in Indonesia.

Background: Wastewater-based epidemiology (WBE) surveillance has been proposed as an early warning system (EWS) for community SARS-CoV-2 transmission. However, there is limited data from low-and middle-income countries (LMICs). This study aimed to assess the ability of WBE surveillance to detect SARS-CoV-2 in formal and informal environments in Indonesia using different methods of sample collection, to compare WBE data with patterns of clinical cases of COVID-19 within the relevant communities, and to assess the WBE potential to be used as an EWS for SARS-CoV-2 outbreaks within a community.

The association between high mobility group box 1 (HMGB1) and Interleukin-18 (IL-18) serum concentrations in COVID-19 inpatients.

Background: High mobility group box 1 (HMGB1) and interleukin-18 (IL-18) are involved in various non-coronavirus disease pathogenesis and are reported as potential biomarkers for coronavirus disease (COVID-19). However, their association with COVID-19 pathogenesis has not yet been explored.

Aim: This study aimed to investigate the association between HMGB1 and IL-18 concentrations in the sera of COVID-19 patients versus non-COVID-19 patients.

Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.

During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022.

Molecular Docking Study of the C-10 Massoia Lactone Compound as an Antimicrobial and Antibiofilm Agent against .

Antimicrobial resistance is now considered a global health problem because it reduces the effectiveness of antimicrobial drugs. According to the World Health Organization (WHO), the highest mortality rate is associated with infections caused by multidrug-resistant microorganisms, with approximately 700,000 deaths worldwide each year. The aim of this study was to determine the potential of C-10 massoia lactone to inhibit the growth of fungi and biofilm, and molecular docking studies were performed to determine the nature of the inhibition.

Prognostic factors for the outcomes of COVID-19 patients infected with SARS-CoV-2 Omicron and Delta variants.

Background: The SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Our study aimed to determine the prognostic factors for the outcomes of patients infected with SARS-CoV-2 Omicron and Delta variants, including age, sex, comorbidities, and smoking.

Antibiofilm Activity of Invasive Plants against Candida albicans: Focus on Baccharis halimifolia Essential Oil and Its Compounds.

The extracts of five invasive plants were investigated for antifungal and antibiofilm activities against Candida albicans, C. glabrata, C. krusei, and C.

Screening antibiofilm activity of invasive plants growing at the Slope Merapi Mountain, Central Java, against Candida albicans.

Background: Candida albicans causes high-mortality candidiasis. Antifungal drug resistance demands the development of virulence factor-targeting drugs, particularly antibiofilm. This study screened the effects of five invasive plants growing in Indonesia (Mimosa pudica, Lantana camara, Acacia mangium, Ageratina riparia, and Mikania micrantha) against C.

The high mutation rate at the D614G hotspot-furin cleavage site region increases the priming efficiency of the Spike protein by furin protease: analysis of Indonesian SARS-CoV-2 G614 variants obtained during the early COVID-19 pandemic.

Unlabelled: D614G mutation plays a significant role in the transmissibility of SARS-CoV-2. Identification of other mutations related to D614G mutation within the Spike protein is pivotal as they might contribute to the pathogenicity of SARS-CoV-2. This study aims to analyze the mutation rate of furin cleavage site (FCS) region of Indonesian origin SARS-CoV-2 and to predict the effect of mutation against Spike priming efficiency by furin.

Performance of Xpert MTB/RIF and sputum microscopy compared to sputum culture for diagnosis of tuberculosis in seven hospitals in Indonesia.

Introduction: Tuberculosis (TB) is a major public health concern in Indonesia, where the incidence was 301 cases per 100,000 inhabitants in 2020 and the prevalence of multi-drug resistant (MDR) TB is increasing. Diagnostic testing approaches vary across Indonesia due to resource limitations. Acid-fast bacilli (AFB) smear is widely used, though Xpert MTB/RIF has been the preferred assay for detecting TB and rifampicin resistance since 2012 due to higher sensitivity and ability to rapidly identify rifampicin resistance.

Characteristics of clinical isolates of nontuberculous mycobacteria in Java-Indonesia: A multicenter study.

Background: Nontuberculous mycobacterial (NTM) lung infections are a major public health concern. Diagnosis of NTM-pulmonary disease (NTM-PD) is difficult because its clinical, microbiological, and radiological features resemble to those of pulmonary tuberculosis (TB), leading to misdiagnosis. Identification at the species level is essential for diagnosis and determination of therapy, which is currently not performed routinely in Indonesian laboratories.

The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia.

Background: Wastewater-based epidemiology (WBE) surveillance as an early warning system (EWS) for monitoring community transmission of SARS-CoV-2 in low- and middle-income country (LMIC) settings, where diagnostic testing capacity is limited, needs further exploration. We explored the feasibility to conduct a WBE surveillance in Indonesia, one of the global epicenters of the COVID-19 pandemic in the middle of 2021, with the fourth largest population in the world where sewer and non-sewered sewage systems are implemented. The feasibility and resource capacity to collect samples on a weekly or fortnightly basis with grab and/or passive sampling methods, as well as to conduct qualitative and quantitative identification of SARS-CoV-2 ribonucleic acid (RNA) using real-time RT-PCR (RT-qPCR) testing of environmental samples were explored.

Co-infection of SARS-CoV-2 with other viral respiratory pathogens in Yogyakarta, Indonesia: A cross-sectional study.

Background: Growing evidence shows that viral co-infection is found repeatedly in patients with Coronavirus Disease-2019 (COVID-19). This is the first report of SARS-CoV-2 co-infection with viral respiratory pathogens in Indonesia.

Methods: Over a one month period of April to May 2020, SARS-CoV-2 positive nasopharyngeal swabs in our COVID-19 referral laboratory in Yogyakarta, Indonesia, were tested for viral respiratory pathogens by real-time, reverse transcription polymerase chain reaction (RT-PCR).

Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations.

The outcome of SARS-CoV-2 infection is determined by multiple factors, including the viral, host genetics, age, and comorbidities. This study investigated the association between prognostic factors and disease outcomes of patients infected by SARS-CoV-2 with multiple S protein mutations. Fifty-one COVID-19 patients were recruited in this study.

Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters.

Background: Transmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2. We aimed to: (1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and (2) conduct phylogenetic analysis of all samples from Yogyakarta and Central Java, Indonesia and other countries.

Methods: The study involved 17 patients with COVID-19, including two family clusters.

Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia.

Background: Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia ( = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia.

Methods: Whole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument.

High frequency of azole resistant Candida spp. colonization among presumptive multidrug resistant tuberculosis (MDR-TB) patients.

Background: Tuberculosis is one of the major causes of death globally. The problems become even more complicated with the rise in prevalence of multidrug resistant tuberculosis (MDR-TB). Many diseases have been reported to occur with tuberculosis making it more difficult to manage.

Biofilm formation and antibiotic resistance of isolated from clinical samples in a tertiary care hospital, Klaten, Indonesia.

Background: is a common cause of health-care associated infections (HAIs) and has high levels of antibiotic resistance. These bacteria are well-known for their ability to produce biofilm. The purpose of this study was to identify the antibiotic resistance pattern and biofilm-producing capacity of isolated from clinical samples in a tertiary care hospital in Klaten, Indonesia.

The 1-monolaurin inhibit growth and eradicate the biofilm formed by clinical isolates of .

Background: Biofilm is one of the causes of antibiotic resistance. One of the biofilm-producing bacteria is which has been proven to infect long-term users of urinary catheters and implant devices. The 1-monolaurin compound has been known to have an antimicrobial effect.

Pan-drug-resistant and biofilm-producing strain of : first report of melioidosis from a diabetic patient in Yogyakarta, Indonesia.

Melioidosis, an infectious disease caused by , has recently gained importance as an emerging infectious disease in Indonesia. Reports of this infection in Indonesia are limited, although cases have been reported in Makassar, South Sulawesi. We report a case of cutaneous melioidosis caused by pan-drug-resistant, moderate biofilm-producer strain of in a diabetic patient.

Detection of bla genes and identification of biofilm-producing capacity of Acinetobacter baumannii in a tertiary teaching hospital, Klaten, Indonesia.

Introduction: Acinetobacter baumannii (A. baumannii) is commonly found as an agent of nosocomial infections and demonstrates a high antibiotic resistance due to its carbapenemase production. The objectives of this study were to explore the antibiotic resistance pattern, the presence of OXAs genes and the biofilm-producing capacity of A.

Transmission of Monospecies and Dual-Species Biofilms from Smooth to Nanopillared Surfaces.

The transmission of bacteria in biofilms from donor to receiver surfaces precedes the formation of biofilms in many applications. Biofilm transmission is different from bacterial adhesion, because it involves biofilm compression in between two surfaces, followed by a separation force leading to the detachment of the biofilm from the donor surface and subsequent adhesion to the receiver surface. Therewith, the transmission depends on a balance between donor and receiver surface properties and the cohesiveness of the biofilm itself.