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Abstract 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. Methods In this retrospective cross-sectional study, we involved 352 patients with COVID-19 from Yogyakarta and Central Java provinces, Indonesia, from May 2021 to February 2022, consisting of 164 males and 188 females. We included all patients with the PCR’s Ct value of less than 30 for further whole-genome sequencing. Results Ct value and mean age of COVID-19 patients were not significantly different between both groups (p = 0.146 and 0.273, respectively). Patients infected with Omicron (n = 139) and Delta (n = 213) variants showed similar hospitalization (p = 0.396) and mortality rates (p = 0.565). Multivariate analysis of both groups showed that older age (≥ 65 years) had a higher risk for hospitalization (OR = 3.86 [95% CI = 1.29–11.5]; p = 0.015) and fatalities (OR = 3.91 [95% CI = 1.35–11.42]; p = 0.012). In both groups, patients with cardiovascular disease had a higher risk for hospitalization (OR = 5.36 [95% CI = 1.08–26.52]; p = 0.039), whereas patients with diabetes revealed a higher risk for fatalities (OR = 9.47 [95% CI = 3.23–27.01]; p =

Abstract 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. albicans biofilms. Antifungal activity, antiphospholipase activity, biofilm morphology of C. albicans, and cytotoxic capacity were also evaluated. Methods Maceration was used to extract the plants, and the most active extract inhibiting the biofilms was fractionated using liquid–liquid fractionation. Antibiofilm activity was determined by a colorimetric assay, MTT. Antifungal activity was tested using the broth microdilution method. A phospholipase assay was performed using the egg-yolk agar method. Influence on the C. albicans morphology was assessed using scanning electron microscopy (SEM). The cytotoxic effect was carried out against Vero and HeLa cell lines. Results M. pudica extracts showed the most potent antifungal efficacy with minimum inhibitory concentration (MIC) of 15.62 µg/mL and 7.81 µg/mL for aerial parts and roots, respectively. At high concentrations (500 µg/mL and 250 µg/mL), ethanol extract of M. pudica aerial parts strongly inhibited the phospholipase activity. Ethyl-acetate fraction of M. pudica aerial parts demonstrated the most potent antibiofilm activity against 24 h old biofilm of C. albicans with an inhibitory concentration (53.89%) of 62.5 µg/mL showed no cytotoxicity in both Vero and HeLa cells. This fraction affected the morphology of C. albicans and contained promising compounds for inhibiting the 24 h old biofilm of C. albicans. Conclusions Invasive M. pudica plant inhibited the growth of planktonic C. albicans cells and its ethyl acetate fraction decreased the metabolic activity of C. albicans biofilms. This result demonstrates the potential of invasive M. pudica plant to reduce biofilm-associated candida infection.

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. Material and methods: We used stored serum samples obtained from 30 COVID-19 patients and 30 non-COVID-19 patients. We collected data on age, gender, treatment status, principal diagnosis, and comorbidity from patient medical records. HMGB1 and IL-18 concentrations were analyzed in the serum by enzyme-linked immunosorbent assay (ELISA). The swab samples’ RT-PCR cycle threshold (CT) values were obtained from the laboratory database. Results: HMGB1 concentrations were increased in the COVID-19 inpatients and non-COVID-19 inpatients compared to non-COVID-19 outpatients (COVID-19 inpatients vs. non-COVID-19 outpatients: 151.33 (90.27–192.38) vs. 80.75 (54.16–128.72) ng/ml; p = 0.0316; non-COVID-19 inpatients vs. non-COVID-19 outpatients: 152.66 (104.04–288.51) vs. 80.75 (54.16–128.72) ng/ml; p = 0.0199). IL-18 concentrations were also higher in the COVID-19 inpatients and non-COVID-19 inpatients compared to non-COVID-19 outpatients (COVID-19 inpatients vs. non-COVID-19 outpatients: 620.00 (461.50–849.6) vs. 403.10 (372.70–556.90) pg/ml; p = 0.0376; non-COVID-19 inpatients vs. non-COVID-19 outpatients: 835.70 (558.30–1602.00) vs. 403.10 (372.70–556.90) pg/ml; p = 0.0026). Moreover, HMGB1 was associated with IL-18 concentrations in the sera of COVID-19 inpatients (p = 0.0337; r = 0.5500). Conclusion: The association of HMGB1 and IL-18 in COVID-19 might indicate the potential for a dangerous cycle leading to a cytokine storm to occur.

BackgroundWastewater-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.Materials and methodsWe conducted WBE surveillance in three districts in Yogyakarta province, Indonesia, over eleven months (27 July 2021 to 7 January 2022 [Delta wave]; 18 January to 3 June 2022 [Omicron wave]). Water samples using grab, and/or passive sampling methods and soil samples were collected either weekly or fortnightly. RNA was extracted from membrane filters from processed water samples and directly from soil. Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the SARS-CoV-2 N and ORF1ab genes.ResultsA total of 1,582 samples were collected. Detection rates of SARS-CoV-2 in wastewater reflected the incidence of community cases, with rates of 85% at the peak to 2% at the end of the Delta wave and from 94% to 11% during the Omicron wave. A 2-week lag time was observed between the detection of SARS-CoV-2 in wastewater and increasing cases in the corresponding community.ConclusionWBE surveillance for SARS-CoV-2 in Indonesia was effective in monitoring patterns of cases of COVID-19 and served as an early warning system, predicting the increasing incidence of COVID-19 cases in the community.

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 C. tropicalis biofilm, and molecular docking studies were performed to determine the nature of the inhibition. The study was conducted using the microdilution method for antifungal and antibiofilm testing and designed with a molecular docking approach. Furthermore, an analysis using the scanning electron microscope (SEM) was performed to evaluate the mechanism of effect. The results obtained showed that C-10 massoia lactone can inhibit the growth of fungi by 84.21% w/v. Meanwhile, the growth of C. tropicalis biofilm in the intermediate phase was 80.23% w/v and in the mature phase was 74.23% w/v. SEM results showed that C-10 massoia lactone damaged the EPS matrix of C. tropicalis so that hyphal formation was hindered due to damage to fungal cells, resulting in a decrease in attachment, density, and lysis of C. tropicalis fungal cells. Based on molecular docking tests, C-10 massoia lactone was able to inhibit biofilm formation without affecting microbial growth, while docking C-10 massoia lactone showed a significant binding and has the potential as an antifungal agent. In conclusion, the C-10 massoia lactone compound has the potential as an antibiofilm against C. tropicalis, so it can become a new antibiofilm agent.

IntroductionTuberculosis (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. However,

Abstract 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. Whole-genome sequencing of 170 full-genomes of SARS-CoV-2 was conducted with the Illumina MiSeq sequencer. Most patients (47%) had mild symptoms of COVID-19 followed by moderate (19.6%), no symptoms (13.7%), severe (4%), and critical (2%). Mortality was found in 13.7% of the COVID-19 patients. There was a significant difference between the age of hospitalized patients (53.4 ± 18 years) and the age of non-hospitalized patients (34.6 ± 19) (p = 0.001). The patients’ hospitalization was strongly associated with hypertension, diabetes, and anticoagulant and were strongly significant with the OR of 17 (95% CI 2–144; p = 0.001), 4.47 (95% CI 1.07–18.58; p = 0.039), and 27.97 (95% CI 1.54–507.13; p = 0.02), respectively; while the patients’ mortality was significantly correlated with patients’ age, anticoagulant, steroid, and diabetes, with OR of 8.44 (95% CI 1.5–47.49; p = 0.016), 46.8 (95% CI 4.63–472.77; p = 0.001), 15.75 (95% CI 2–123.86; p = 0.009), and 8.5 (95% CI 1.43–50.66; p = 0.019), respectively. This study found the clade: L (2%), GH (84.3%), GR (11.7%), and O (2%). Besides the D614G mutation, we found L5F (18.8%), V213A (18.8%), and S689R (8.3%). No significant association between multiple S protein mutations and the patients’ hospitalization or mortality. Multivariate analysis revealed that hypertension and anticoagulant were the significant factors influencing the hospitalization and mortality of patients with COVID-19 with an OR of 17.06 (95% CI 2.02–144.36; p = 0.009) and 46.8 (95% CI 4.63–472.77; p = 0.001), respectively. Moreover, the multiple S protein mutations almost reached a strong association with patients’ hospitalization (p = 0.07). We concluded that hypertension and anticoagulant therapy have a significant impact on COVID-19 outcomes. This study also suggests that multiple S protein mutations may impact the COVID-19 outcomes. This further emphasized the significance of monitoring SARS-CoV-2 variants through genomic surveillance, particularly those that may impact the COVID-19 outcomes.

BackgroundNontuberculous 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.Methodology and principal findingsFrom January 2020 to May 2021, 94 NTM isolates were collected from three TB referral centers in Java Province. Species were identified using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). Tests were performed to determine antibiotic susceptibility, biofilm formation ability, sliding motility characteristics, and the ability to adhere to and invade pneumocytes. After identifying the species of all the isolates, we found nine groups of NTMs: M. fortuitum group 51% (48/94), M. abscessus 38.3% (36/94), M. intracellulare 3.1% (3/94), M. neoaurum 2.1% (2/94), M. chelonae 1.1% (1/94), M. gordonae 1.1% (1/94), M. szulgai 1.1% (1/94), M. mucogenicum 1.1% (1/94), and M. arupense 1.1% (1/94). Amikacin was the most effective antibiotic against M. fortuitum group and M. abscessus. The M. fortuitum group was significantly better at forming biofilms than M. abscessus, but both had the same sliding motility capability. The ability of the M. fortuitum group to adhere to and invade pneumocytes was better than that of M. abscessus, with the number isolates of the M. fortuitum group capable of superior adhesion and invasion to that of M. abscessus.Conclusions/significanceThis study shows that M. fortuitum group and M. abscessus were the most common NTM found in Java, Indonesia. The M. fortuitum group and M. abscessus were the most susceptible to amikacin; therefore, this was the empirical treatment of choice. The ability to form biofilms is directly proportional to the ability to adhere to and invade pneumocytes but not to the susceptibility profile or sliding motility characteristics.

Abstract 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. We determined the full-genome sequences of SARS-CoV-2 using the Illumina MiSeq next-generation sequencer. Phylogenetic analysis was performed using a dataset of 142 full-genomes of SARS-CoV-2 from different regions. Results Ninety-four SNPs were detected throughout the open reading frame (ORF) of SARS-CoV-2 samples with 58% (54/94) of the nucleic acid changes resulting in amino acid mutations. About 94% (16/17) of the virus samples showed D614G on spike protein and 56% of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. The virus samples from family cluster-1 (n = 3) belong to the same clade GH, in which two were collected from deceased patients, and the other from the survived patient. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation. Conclusions Our study is the first comprehensive report associating the full-genome sequences of SARS-CoV-2 with the epidemiological data within family clusters. Phylogenetic analysis revealed that the three viruses from family cluster-1 formed a monophyletic group, whereas viruses from family cluster-2 formed a polyphyletic group indicating there is the possibility of different sources of infection. This study highlights how the same spike protein mutations among members of the same family might show different disease outcomes.

Background: Klebsiella pneumoniae is a Gram-negative bacterium that often causes nosocomial infections. Use of broad-spectrum antibiotics as an empiric therapy has contributed to increases of K. Pneumoniae strains that are resistant to antibiotics. Therefore, a test on antibiotic susceptibility of K. pneumoniae is needed as a guide in treating a definitive therapy. Objective: This study aimed to measure the percentages of multidrug-resistant (MDR) of K. pneumoniae and its susceptibility at dr. Soeradji Tirtonegoro Central Hospital, Klaten, Central Java in 2017. Methods: This study was a descriptive study using secondary data at the Clinical Microbiology Laboratorium of dr. Soeradji Tirtonegoro Central Hospital, Klaten. The K. pneumoniae was isolated from patients hospitalized in the hospital from January 1, 2017, to December 31 2017. Identifications of the K. pneumoniae were conducted by a colony morphology observation, a gram staining, and a biochemical test. The test of antibiotics susceptibility used Kirby-Bauer method based on Clinical and Laboratory Standards Institute (CLSI). The data were analyzed by univariate analysis. Results: In 2017, there were 213 K. pneumoniae isolates from various clinical samples. Among them, 122 isolates were MDR K. pneumoniae (57.28%). The majority of MDR K. pneumoniae were resistant to a wide range of antibiotics. The MDR K. pneumoniae had only a good sensitivity to meropenem (98.43%), amikacin (93.75%), nitrofurantoin (88.89%), and fosfomycin (88.89%). In contrast, all non-MDR K. pneumoniae had good sensitivity to all tested antibiotics, except to ampicillin. Conclusion: The percentage of MDR K. pneumoniae isolates at the dr. Soeradji Tirtonegoro Cental in 2017 was 57%. Meropenem and amikacin could be considered as empirical therapies to cure an MDR K. pneumoniae infection.

Background The Xpert MTB/RIF assay demonstrated a better diagnostic value than sputum smear for TB in adults and children. Objective To evaluate the use of Xpert MTB/RIF for TB diagnosis in children. Methods We conducted a prospective study in Yogyakarta, Indonesia, involving 19 primary health centers (PHCs) and one provincial hospital. Children aged 0-14 years with suspected TB who visited the study sites were screened. Subjects underwent history-taking, physical examination, tuberculin skin test, chest X-ray, as well as sputum induction for Xpert MTB/RIF assay, sputum smear, and TB culture. The diagnosis of TB was made by doctors based on the results of investigations, as follows: certain TB (bacteriological confirmation), probable TB, and possible TB. Results Of 80 subjects, 21 (26%) were diagnosed with TB disease (4 certain TB and 17 probable TB). Sputum induction was successfully performed in 79 children. None of the children had positive sputum smears. Mycobacterium tuberculosis was detected by Xpert MTB/RIF in 4 children, accounting for 5% of all children with suspected TB, or 19% among children with TB disease. The 4 Xpert MTB/RIF-positive subjects had severe TB disease and were rifampicin-sensitive. Conclusion Xpert MTB/RIF may improve case finding among children with severe TB disease with negative sputum smear.

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. Materials and methods We initiated a routine surveillance of wastewater and environmental sampling at three predetermined districts in Special Region of Yogyakarta Province. Water samples were collected from central and community wastewater treatment plants (WWTPs), including manholes flowing to the central WWTP, and additional soil samples were collected for the near source tracking (NST) locations (i.e., public spaces where people congregate). Results We began collecting samples in the Delta wave of the COVID-19 pandemic in Indonesia in July 2021. From a 10-week period, 54% (296/544) of wastewater and environmental samples were positive for SARS-CoV-2 RNA. The sample positivity rate decreased in proportion with the reported incidence of COVID-19 clinical cases in the community. The highest positivity rate of 77% in week 1, was obtained for samples collected in July 2021 and decreased to 25% in week 10 by the end of September 2021. Conclusion A WBE surveillance system for SARS-CoV-2 in Indonesia is feasible to monitor the community burden of infections. Future studies testing the potential of WBE and EWS for signaling early outbreaks of SARS-CoV-2 transmissions in this setting are required.

Background: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) has been responsible for the current increase in Coronavirus disease 2019 (COVID-19) infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia.Methods: In this cross-sectional study, we ascertained 161 patients, 69 with the Delta variant and 92 with the non-Delta variant. The Illumina MiSeq next-generation sequencer was used to perform the whole-genome sequences of SARS-CoV-2.Results: The mean age of patients with the Delta variant and the non-Delta variant was 27.3 ± 20.0 and 43.0 ± 20.9 (p = 3 × 10−6). The patients with Delta variant consisted of 23 males and 46 females, while the patients with the non-Delta variant involved 56 males and 36 females (p = 0.001). The Ct value of the Delta variant (18.4 ± 2.9) was significantly lower than that of the non-Delta variant (19.5 ± 3.8) (p = 0.043). There was no significant difference in the hospitalization and mortality of patients with Delta and non-Delta variants (p = 0.80 and 0.29, respectively). None of the prognostic factors were associated with the hospitalization, except diabetes with an OR of 3.6 (95% CI = 1.02–12.5; p = 0.036). Moreover, the patients with the following factors have been associated with higher mortality rate than the patients without the factors: age ≥65 years, obesity, diabetes, hypertension, and cardiovascular disease with the OR of 11 (95% CI = 3.4–36; p = 8 × 10−5), 27 (95% CI = 6.1–118; p = 1 × 10−5), 15.6 (95% CI = 5.3–46; p = 6 × 10−7), 12 (95% CI = 4–35.3; p = 1.2 × 10−5), and 6.8 (95% CI = 2.1–22.1; p = 0.003), respectively. Multivariate analysis showed that age ≥65 years, obesity, diabetes, and hypertension were the strong prognostic factors for the mortality of COVID-19 patients with the OR of 3.6 (95% CI = 0.58–21.9; p = 0.028), 16.6 (95% CI = 2.5–107.1; p = 0.003), 5.5 (95% CI = 1.3–23.7; p = 0.021), and 5.8 (95% CI = 1.02–32.8; p = 0.047), respectively.Conclusions: We show that the patients infected by the SARS-CoV-2 Delta variant have a lower Ct value than the patients infected by the non-Delta variant, implying that the Delta variant has a higher viral load, which might cause a more transmissible virus among humans. However, the Delta variant does not affect the COVID-19 outcomes in our patients. Our study also confirms that older age and comorbidity increase the mortality rate of patients with COVID-19.

Objectives: Monitoring the spread of the G614 in specific locations is critical as this variant is highly transmissible and can trigger the emergence of other mutations. Therefore, a rapid and accurate method that can reliably detect the D614G mutation will be beneficial. This study aims to analyze the potential use of the two-step Reverse Transcriptase quantitative polymerase chain reaction - high resolution melting analysis (RT-qPCR-HRM) to detect a specific mutation in the SARS-CoV-2 genome. Methods: Six SARS-CoV-2 RNA samples were synthesized into cDNA and analyzed with the qPCR-HRM method in order to detect the D614G mutation in Spike protein of SARS-CoV-2. The primers are designed to target the specific Spike region containing the D614G mutation. The qPCR-HRM analysis was conducted simultaneously, and the identification of the SARS-CoV-2 variant was confirmed by conventional PCR and Sanger sequencing methods. Results: The results showed that the melting temperature (Tm) of the D614 variant was 79.39 ± 0.03 °C, which was slightly lower than the Tm of the G614 variant (79.62 ± 0.015 °C). The results of the HRM analysis, visualized by the normalized melting curve and the difference curve were able to discriminate the D614 and G614 variant samples. All samples were identified as G614 variants by qPCR-HRM assay, which was subsequently confirmed by Sanger sequencing. Conclusions: This study demonstrated a sensitive method that can identify the D614G mutation by a simple two-step RT-qPCR-HRM assay procedure analysis, which can be useful for active surveillance of the transmission of a specific mutation.

Abstract Background Klebsiella pneumoniae (K. pneumoniae) 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 K. pneumoniae isolated from clinical samples in a tertiary care hospital in Klaten, Indonesia. Methods K. pneumoniae was isolated from inpatients in Soeradji Tirtonegoro Hospital Klaten from June 2017 to May 2018. Identification of K. pneumoniae isolate was done by analyzing colony morphology, microscopic examination, and by performing biochemical testing. Testing of antibiotics susceptibility and biofilm-producing capacity used the Kirby-Bauer disk diffusion method and adherence quantitative assays, respectively. Results A total of 167 (17.36%) K. pneumoniae isolates were isolated from 962 total clinical bacterial isolates during the study. Most of them were collected from patients aged more than 60 years old and were mainly obtained from respiratory specimens (51.50%). Most of K. pneumoniae isolates were extensively resistant to antibiotics. A more favorable profile was found only towards meropenem, amikacin, and piperacillin-tazobactam, showing 1.20%; 4.79% and 10.53% of resistance, respectively. The overall proportion of multidrug-resistant K. pneumoniae isolates was 54.49%. In addition, 148 (85.63%) isolates were biofilm producers, with 45 (26.95%) isolates as strong, 48 (28.74%) isolates as moderate, and 50 (29.94%) isolates as weak biofilm producers. Conclusion Most of the K. pneumoniae isolates demonstrated resistance to a wide range of antibiotics and are biofilm producers.

Abstract Background Biofilm is one of the causes of antibiotic resistance. One of the biofilm-producing bacteria is Staphylococcus epidermidis 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. However, its effect on clinical isolates of S. epidermidis in producing biofilm has not been established. This study was conducted to investigate the effect of 1-monolaurin towards biofilm forming clinical isolates of S. epidermidis. Methods The experiment used micro broth dilution technique which consists of test group (1-monolaurin), positive control group (rifampicin), solvent group, negative control group (clinical isolate of S. epidermidis), and media group (TSB media). The Minimal Inhibition Concentration (MIC) was determined by incubating bacteria added with 1-monolaurin (1000–1953 μg/mL) or rifampicin (250–0,488 μg/mL) for 24 h. The MIC was determined visually. After that, the incubated bacteria was cultured in TSA media to determine Minimal Bactericidal Concentration (MBC). The assessment of Biofilm inhibitory Concentration (BIC) and Biofilm Eradication Concentration (BEC) was conducted with the same way, the difference was BIC intervened directly with compound meanwhile BEC was incubated for 24 h in 37 °C before the intervention. Then, the specimen was reincubated to grow biofilm at the microplate, washed with PBS and stained with 1% of crystal violet. The optical density (OD) was measured at a wavelength of 595 nm. The percentage of BIC and BEC then were calculated, continued to probit analysis regression to determine the BIC50, BIC80, BEC50, and BEC80. Results The MIC dan MBC of 1-monolaurin and rifampicin were > 1000 μg/mL, > 1000 μg/mL, ≤0.488 μg/mL, and 1.953 μg/mL respectively. BIC50 and BIC80 of 1-monolaurin and rifampicin were 26.669 μg/mL, 168.688 μg/mL, 0.079 μg/mL, and 0.974 μg/mL respectively. The BEC50 and BEC80 of 1-monolaurin and rifampicin were 322.504 μg/mL, 1338.681 μg/mL, 5.547 μg/mL, dan 17.910 μg/mL respectively. Conclusion The 1-monolaurin can inhibit growth and eradicate the biofilm formed by clinical isolates of S. epidermidis, however, it has neither inhibit nor kill planktonic cells of S. epidermidis.

Biofilm acts as the mediator for infection nowadays. Approximately, more than 80% infection incidents are biofilm-formation related. Biofilm as bacteria's defense system is more difficult to eradicate by antibiotic; therefore, pathogen bacteria on their biofilm forms can make serious problems for human health. The invention of a new candidate for polymicrobial biofilm can be an essential challenge to be studied, in order to prevent infections related to biofilm. Tannin is a polyphenol compound with anti-bacterial and anti-fungal potential. This study aims to acknowledge the effectiveness of tannin in inhibition and degradation of C. albicans, P. aeruginosa, E. coli, S. aureus, and polymicrobial biofilm. The assay for biofilm inhibition and degradation were determined with microtiter broth method. The effectivity of tannin antibiofilm against polymicrobial biofilm were analyzed by calculating minimum biofilm inhibitory concentration (MBIC50) and minimum biofilm eradication concentration (MBEC50) values. The mechanism of action of tannin against polymicrobial biofilm was tested using scanning electron microscopy (SEM). The data were analyzed using the Statistical Package for the Social Sciences (SPSS) with a 95% confidence level. Tannin 1% gave inhibition activity of mono-species biofilm formation S. aureus in the middle phase and maturation of 79.04±0.01, 61.48±0.03, E. coli 74.56±0.01, 67.91±0.02, P. aeruginosa 67.32±0.05, 35.13± 0.01, C. albicans 60.62±0.01, 47.16±0.01. The results also provide evidence that tannin activity can degrade and damage the matrix of extracellular polymeric substance (EPS) polymicrobial biofilms. Hence, tannins can be a potential candidate for new antibiofilm for polymicrobial biofilm.

BackgroundTuberculosis 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. Candida spp., which are yeast-like fungi and a constituent of normal flora in humans, are notoriously reported to be one of the most common opportunistic nosocomial infections. This study aimed to measure the proportion of presumptive MDR-TB patients colonized with Candida spp. and to characterize its susceptibility against azole group antifungal agents.MethodsSputum from presumptive MDR-TB patients were collected and examined for the presence of Mycobacterium tuberculosis and its rifampicin resistant status using GeneXpert. It was further cultured on Sabouroud's Dextrose Agar (SDA) to isolate the Candida spp. The Candida species were determined using HiCrome™ Candidal Differential Agar. Antifungal susceptibility was tested using microbroth dilution methods. Checkerboard microdilution assays were performed to measure the interaction between rifampicin and fluconazole to C. albicans.ResultsThere were 355 presumptive MDR-TB patients enrolled. A total of 101 (28.4%) patients were confirmed to have M. tuberculosis. There were 113 (31.8%) sputum positive for Candida spp., which corresponded to 149 Candida spp. isolates. Candida albicans was the most frequent (53.7%) species isolated from all patients. The susceptibility of Candida spp. against fluconazole, itraconazole, and ketoconazole were 38.3%, 1.3%, and 10.7% respectively. There was significant association between rifampicin exposure history and susceptibility of Candida albicans against fluconazole (Odds Ratio: 9.96; 95% CI: 1.83-54.19; p ConclusionThere was high frequency of azole resistant Candida spp. isolates colonizing the respiratory tract of presumptive MDR-TB patients. This presence might indicate the association of chronic exposure to rifampicin, the main drug for tuberculosis therapy, with the induction of azole resistance.

Pneumonia is a threat to all States. CAP treatment in hospitals typically uses empirical antibiotic therapy with IDSA/ATS guidelines. This research aimed to compare empirical antibiotic therapy of CAP patients in types A and B hospital and to analyze the variations that occur and compare the outcome of the therapy. The research was conducted retrospectively by collecting data from the medical records of patients diagnosed with CAP. The inclusion criteria in this research were male and female adult patients aged ≥18 years who had complete medical record data. Patients who underwent inpatient care in the in-patient wards (non ICU) of type A and B hospital received empirical antibiotic therapy. Data from type A hospital (RS A) were taken within the period of January 2014-December 2016, while data from type B hospital (RS B) were taken in January 2013-December 2016. The number of patients with CAP in hospital A is 72, whereas in hospital B, it is 34. Patients with malignancy and immunocompromise were excluded from this research. In this research, germs found in hospital A were mapped, while no gynecologic examination/culture was performed in hospital B. The outcome of the treatment was an improvement in response 5-7 days after empirical antibiotics was given, as reported by a physician and/or by an improvement in the x-ray thorax results. Patient demographic data and antibiotic therapy pattern were analyzed descriptively. Outcome of patient therapy was analyzed using Chi square statistics with 95% confidence level.The results showed that empirical antibiotic therapy in CAP patients in type A hospital were largely based on IDSA/ATS guidelines, whereas in it is the opposite for type B hospital. Outcomes of patient therapy in A and B hospitals showed patient improvement of about 76%. In type A hospital, the cause of CAP is largely negativeGram bacteria which are still sensitive to cephalosporin/carbapenem (cefpirom, ceftasidim, cefepim, and imipenem) and aminogicosida (amikacin, netilmisin, and tobramisin).

Summary In real‐life situations, bacteria are often transmitted from biofilms growing on donor surfaces to receiver ones. Bacterial transmission is more complex than adhesion, involving bacterial detachment from donor and subsequent adhesion to receiver surfaces. Here, we describe a new device to study shear‐induced bacterial transmission from a (stainless steel) pipe to a (silicone rubber) tube and compare transmission of EPS‐producing and non‐EPS‐producing staphylococci. Transmission of an entire biofilm from the donor to the receiver tube did not occur, indicative of cohesive failure in the biofilm rather than of adhesive failure at the donor‐biofilm interface. Biofilm was gradually transmitted over an increasing length of receiver tube, occurring mostly to the first 50 cm of the receiver tube. Under high‐shearing velocity, transmission of non‐EPS‐producing bacteria to the second half decreased non‐linearly, likely due to rapid thinning of the lowly lubricious biofilm. Oppositely, transmission of EPS‐producing strains to the second tube half was not affected by higher shearing velocity due to the high lubricity and stress relaxation of the EPS‐rich biofilms, ensuring continued contact with the receiver. The non‐linear decrease of ongoing bacterial transmission under high‐shearing velocity is new and of relevance in for instance, high‐speed food slicers and food packaging.

Tuberculosis (TB), in which caused by pathogenic bacteria, Mycobacterium tuberculosis, has become the major causes of death among all of infectious diseases. The increasing incidence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) has created a need to discover a new antituberculosis drug candidate. The aim of this study was to screen extract and fractions of Tinospora crispa for activity against Mycobacterium tuberculosis H37Rv using the Microplate Alamar Blue Assay (MABA) method. T. crispa extract was prepared by maceration in ethanol (96%) and antituberculosis activity was carried out using MABA method. The result of this study showed that ethanolic extract of T. crispa exhibit antituberculosis activity with minimum inhibition concentration of 12.5 mg/ml.

Meningitis bacterial merupakan infeksi sistem saraf pusat (SSP), terutama menyerang anak pada usia

Multidrug-resistant (MDR) adalah suatu keadaan dimana bakteri resisten terhadap minimal satu jenis antibiotik dari ≥3 golongan antibiotik. MDR ini dapat disebabkan karena beberapa hal antara lain pemakaian antibiotik yang tidak tepat dosis, tidak tepat diagnostik dan tidak tepat bakteri penyebab. Multidrug-resistant organisms (MDRO) adalah mikroorganisme, terutama bakteri yang mengalami MDR. Saat ini resistensi antibiotik merupakan masalah global, data pada tahun 2009, Indonesia menduduki peringkat ke 8 dari 27 negara dengan predikat multidrug-resistant tertinggi di dunia . Penelitian ini bertujuan mengidentifikasi pola MDRO dan infeksi MDRO pada pasien yang dirawat di bangsal NICU RSUP dr. Soeradji Tirtonegoro Klaten selama periode Desember 2013 sampai dengan Desember 2014. Desain penelitian ini adalah deskriftif dengan data yang dikumpulkan secara retrospektif. Empat puluh enam pasien yang menjadi subyek penelitian karakteristiknya homogen dalam hal usia, lama perawatan dan luaran kliniknya, Semua pasien dilakukan kultur dan tes sensitivitas terhadap antibiotik. Hasil : bakteri yang menginfeksi pasien NICU RSUP dr. Soeradji Tirtonegoro adalah Pseudomonas sp, Klebsiella sp, Serratia sp, Enterobacter sp, Acinetobacter dan Edwardsiella sp (diurutkan dari proporsi tertinggi ke terendah). Ditemukan bahwa 98% dari keseluruhan isolat bakteri tersebut termasuk kategori MDRO. Jenis infeksi bakterial yang ditemukan adalah sepsis, pneumonia dan komplikasi sepsis dengan pneumonia. Antibiotik yang masih poten untuk semua bakteri ini adalah cotrimoxazole, ciprofloxasin, chloramphenicol, levofloxasin, amikasin and meropenem (diurutkan dari antibiotik dengan sensitivitas terendah).

Biofilm formation and the expression of icaA gene can be induced by environment conditions that are potentially toxic for bacterial cells. The effect of green flies maggots secretion to biofilm was studied some years ago to investigate in vitro effect of secretion of Chloroprocta sp. maggots on the formation of Staphylococcus epidermidis biofilm (phenotype) and the expression level of icaA gene (genotype) for indicating its mechanism on bacterial biofilm eradication. Microtiter plate biofilm assay was used to measure the effect of Chloroprocta sp. maggots secretion at various concentration on S. epidermidis biofilm. The expression level of icaA gene was performed by Real TimePCR using lightcycler method. The biofilm susceptibility test was done against maggots excretion/secretion using MTT assay. Whereas planktonic susceptibility testing was carried out using Kirby Bauer method. In the presence of maggots secretion at low concentration (5%), biofilm formation of S. epidermidis 734 was induced. In contrast, the expression level of icaA gene in production of maggots excretion/ secretion at concentration of 5% was lower than that of without maggots secretion (1/2 Fold). Eradication of bacterial biofilm was demonstrated after 48h incubation (MD=-0,011;P

Staphylococcus epidermidis has been shown to undergo a phase variation correlating with expression of the icaADBC operon which contributes to biofilm formation. Biofilm formation of Enterococcus faecalis is related to heterogeneity in electrophoretic mobility. Here the relationship between phase variants of clinical isolates of S. epidermidis, icaADBC presence and electrophoretic mobility distributions is investigated. Of 105 S. epidermidis clinical isolates, 5 showed phase variation on Congo Red agar plate. Biofilm forming capability of the blackcolonies and inability of the red colonies were confirmed using a microtiter plate assay and confocal laser scanning microscopy. Upon analysis of electrophoretic mobility distributions, the black colonies displayed heterogeneity at pH 2 which was absent in the red colonies of the same strain. Surprisingly, it was shown that in all red colonies had lost the icaADBC genes. Determination of gene copy number using Real Time PCR targeting icaA showed reduction of gene copy within a culture with phase variation. In conclusion, using three fundamentally different approaches phase variation of the five clinical isolates was observed. Variants appeared through loss of icaA and icaC gens. To our knowledge this is the first report indicating S. epidermidis strains irreversible switching from biofilm + to biofilm – phenotype by deletion of ica genes. Key words: deletion, ica genes, Staphylococcus epidermidis, IcaADBC operon

Staphylococcus epidermidis has been shown to undergo a phase variation correlating with expression of the icaADBC operon which contributes to biofilm formation. Biofilm formation of Enterococcus faecalis is related to heterogeneity in electrophoretic mobility. Here the relationship between phase variants of clinical isolates of S. epidermidis, icaADBC presence and electrophoretic mobility distributions is investigated. Of 105 S. epidermidis clinical isolates, 5 showed phase variation on Congo Red agar plate. Biofilm forming capability of the black colonies and inability of the red colonies were confirmed using a microtiter plate assay and confocal laser scanning microscopy. Upon analysis of electrophoretic mobility distributions, the black colonies displayed heterogeneity at pH 2 which was absent in the red colonies of the same strain. Surprisingly, it was shown that in all red colonies had lost the icaADBC genes. Determination of gene copy number using Real Time PCR targeting icaA showed reduction of gene copy within a culture with phase variation. In conclusion, using three fundamentally different approaches phase variation of the five clinical isolates was observed. Variants appeared through loss of icaA and icaC gens. To our knowledge this is the first report indicating S. epidermidis strains irreversible switching from biofilm + to biofilm – phenotype by deletion of ica genes. Key words: deletion, ica genes, Staphylococcus epidermidis, IcaADBC operon