Role of probiotic as adjuvant in treating various infections: a systematic review and meta-analysis.

BACKGROUND: Research on the advantages of probiotics has attracted increasing interest based on the number of publications, products, and public awareness of their benefits. This review evaluated the role of probiotics (single and multiple regimens) as an additional regimen to treat common infectious diseases, including Helicobacter. pylori, diarrheal infections, urinary tract infections (UTIs), upper respiratory tract infections (URTIs), and HIV infections. METHODS: We searched randomized controlled trials from PubMed, Scopus, Embase, and Cochrane and identified 6,950 studies. Duplicates were removed, and titles and abstracts were filtered. Bias was evaluated using the Cochrane Risk of Bias Tool for Randomized Trials (ROB 1.0 and 2.0). The certainty of the evidence was evaluated using GRADE. Data were extracted and meta-analysis was performed using RevMan. RESULTS: A total of 32 studies were included in this study (22 H. pylori studies, 2 diarrheal infection studies, 6 UTI studies, and 2 HIV infection studies). There was no study on URTI. Probiotics, in addition to primary treatment, could improve the eradication of H. pylori versus the control (RR: 1.09; 95% CI:1.04 - 1.13, p value = 0.001) and achieve a cure range of Nugent score in UTI patients (RR 1.38; 95% CI: 1.01 - 1.89, p value = 0.04). For eradicating H. pylori infection, subgroup analysis based on the therapy regimen showed that standard triple therapy was slightly superior compared to quadruple therapy in eradicating H. pylori (RR: 1.14 vs. 1.01, respectively). Single strain probiotics showed a similar effect to multiple strain probiotic regimens (both had an RR of 1.09). The effect estimates of the use of single strain probiotics as adjuvant therapy in eradicating H. pylori and the use of probiotics in UTI had a high certainty of evidence. Meta-analysis was not performed for infectious diarrheal because there were only two eligible studies with different probiotic supplementations and outcome parameters. Nonetheless, they showed that the diarrheal incidence was lower and complete remission of diarrheal was higher after the regimen of probiotics. Similarly, a meta-analysis was not performed for HIV infection because the two eligible studies used different designs and comparators with contradicting findings. CONCLUSION: This meta-analysis showed beneficial use of single strain probiotics as adjuvant therapy in eradicating H. pylori and the use of probiotics in UTI. Probiotic supplementation might not be beneficial for patients given a quadruple therapy. Single-strain and multi-strain probiotic regimens had similar effects in increasing the eradication rate of H. pylori. Our study also suggested that the benefits of probiotics as an additional regimen in infectious diarrheal and HIV infections remain unclear; more studies are needed to confirm the benefits.

Challenges of diagnosing severe malaria with complications in adult patients: a case report.

BACKGROUND: Malaria is known to be the main cause of death in malaria-endemic areas. The authors report a case of severe malaria in an adult with no history of travel from an endemic area with good outcomes after hospitalization. CASE PRESENTATION: A 46-year-old man was brought to the Emergency Room (ER) because of fever and chills for 6 days. Complaints were accompanied by nausea and vomiting three times a day. The patient also experienced headaches, weakness, coughing, and a runny nose after two days of admission. The patient had no history of traveling from a malaria-endemic area. The patient was transferred from the Emergency Department (ED) to the High Care Unit (HCU), and during 1 day of intensive care at the HCU, there was a clinical deterioration characterized by dyspnea, icteric sclerae, acral edema, tenderness in both calves, and rash in the abdominal area. Due to worsening respiratory function, the patient was placed on a ventilator. During intensive treatment, the patient continued to show deterioration. The clinical findings suggested a possible feature of Weil's disease or fulminant hepatitis, and although the patient was in intensive care, there was no clinically significant improvement. Furthermore, microscopic blood smear examination and rapid diagnostic tests (RDTs) for malaria were carried out on the 4th day of treatment with negative results. As there was no clinically significant improvement, it was decided to take a blood smear and repeat RDT on the twelfth day, which showed a positive result for falciparum malaria. Subsequently, artesunate was administered intravenously, and the patient's condition began to improve with a negative parasite count the following day. The patient was discharged in good clinical condition on day 25 of treatment. CONCLUSION: Good quality malaria diagnostic techniques are essential to diagnose malaria. A timely diagnosis of malaria has the potential to save the patient. Because Jakarta is not a malaria endemic area, it was concluded that this case was an introduced malaria case.

Current Updates on Diagnosis and Management of Cholangiocarcinoma: from Surgery to Targeted Therapy.

Cholangiocarcinoma is commonly described as any malignancy arising from the lining of the bile duct and is recognized as one of the most common biliary malignancies. We conducted a literature review of current available evidences and guidelines.Based on the anatomical location of the origin of the mass, cholangiocarcinoma can be divided into intrahepatic, perihilar, and distal cholangiocarcinoma. Each of these subtypes has their own risk factors, best treatment options, and prognosis. The most common risk factors for cholangiocarcinoma also differs based on geography and population backgrounds. Histopathological biopsy remained the gold standard for cholangiocarcinoma diagnosis, however various advances has been made in diagnostic procedure, including MRCP, EUS, ERCP, EBUS, and cholangioscopy. Surgical resection is still the best treatment modality for cholangiocarcinoma, but it can only be done in few patients considering most patients were diagnosed in the unresectable state. Other treatment options includes conventional chemotherapy, locoregional therapy, systemic targeted therapy, and palliative best supportive care. Cholangiocarcinoma has an abundance of molecular targets and advances in biomolecular technologies bring further hope for future curative treatment options. Treatment options should be chosen individually based on each patient's condition and setting. Cholangiocarcinoma is still a major health problem in hepatobiliary malignancies. Multiple options are available for cholangiocarcinoma treatments.

Validation of the Nelwan Score as a screening tool for the diagnosis of typhoid fever in adults in Indonesia.

INTRODUCTION: Typhoid fever diagnosis is challenging for clinicians in areas with limited laboratory facilities. Scoring methods based on signs and symptoms are useful for screening for probable cases of typhoid fever. The Nelwan Score variables are derived from the clinical signs and symptoms of patients with suspected typhoid. We validated the Nelwan Score compared to laboratory tests as the gold standard. METHODS: This cross-sectional study was conducted between July 2017 and January 2018 in five hospitals and two primary health care centers in Jakarta and Tangerang, Indonesia. Patients with fever for 3-14 days and gastrointestinal symptoms were evaluated using the Nelwan Score. Blood cultures, samples for polymerase chain reaction testing, and additional rectal swab cultures were collected simultaneously to confirm the diagnosis of typhoid. Data were analyzed using a contingency table to measure sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), and the optimal cut-off of the Nelwan Score for typhoid diagnosis was determined using a receiver-operating characteristic curve. RESULT: Typhoid was confirmed in 11 of the 233 patients (4.7%) with suspected typhoid. Among laboratory-confirmed typhoid cases, the median Nelwan Score was 11 (range: 9-13) and the optimal cut-off value was 10, with an area under the curve of 71.3%, sensitivity of 81.8%, specificity of 60.8%, PPV of 9.3%, and NPV of 98.5%. CONCLUSION: A Nelwan Score of 10 is the best cut-off value for screening for typhoid fever. It is useful as screening tool for typhoid fever, where laboratory resources are limited, and could help to decrease irrational antibiotic use.

The role of CD4+, CD8+, CD4+/CD8+ and neutrophile to lymphocyte ratio in predicting and determining COVID-19 severity in Indonesian patients.

BACKGROUND: Biomarkers that are cost-effective and accurate for predicting severe coronavirus disease 2019 (COVID-19) are urgently needed. We would like to assess the role of various inflammatory biomarkers on admission as disease severity predictors and determine the optimal cut-off of the neutrophile-to-lymphocyte ratio (NLR) for predicting severe COVID-19. METHODS: We conducted a cross-sectional study in six hospitals in Bali and recruited real-time PCR-confirmed COVID-19 patients aged >18 y from June to August 2020. Data collection included each patient's demographic, clinical, disease severity and hematological data. Multivariate and receiver operating characteristic curve analyses were performed. RESULTS: A total of 95 Indonesian COVID-19 patients were included. The highest NLR among severe patients was 11.5±6.2, followed by the non-severe group at 3.3±2.8. The lowest NLR was found in the asymptomatic group (1.9±1.1). The CD4+ and CD8+ values were lowest in the critical and severe disease groups. The area under the curve of NLR was 0.959. Therefore, the optimal NLR cut-off value for predicting severe COVID-19 was ≥3.55, with sensitivity at 90.9% and a specificity of 16.7%. CONCLUSIONS: Lower CD4+ and CD8+ and higher NLR values on admission are reliable predictors of severe COVID-19 among Indonesian people. NLR cut-off ≥3.55 is the optimal value for predicting severe COVID-19.

The Vascular Access Related Infections: Have We Anticipated Them Adequately?

The number of patients in need of haemodialysis (HD) is increasing from time to time. In 2018, the Indonesian Renal Registry documented more than 130,000 active patients from 651 registered HD centres. Twenty percent are diabetic patients with end-stage renal disease (ESDR) equal to 8,633 patients. Diabetes Mellitus accounts for 2% of all diabetes cases in the age of 15 year-old and above. Hence, the increasing need for HD is inevitable and is parallel with the need for vascular access procedures.One of the major problems that occurs with vascular access is the risk of infection. Among HD patients, mortality and morbidity are predominantly associated with infection; about one-fifth as a cause of hospital admissions, one-fourth of the infection-related admissions are due to infection of vascular access. Susilo et.al, reported around 40% of patients with temporary vascular access had an infection. Data is limited and might be also underestimated.Unfortunately, the available studies examining risk factors for vascular access-associated infection are scarce and mostly collected with substandard methodology. It is to be highlighted that the study of Susilo et al. may represent the population of a  referral hospital for HD, yet as a reader it is worth noting that heterogeneity among centres and populations should be acknowledged. A comprehensive in-depth review and further research of these studies are crucial for a greater level of understanding for the cause of infection and therefore inform effective early detection and prevention strategies to reduce morbidity and mortality among haemodialysis patients, especially at-risk patients.

Association of leukocyte nadir with complete remission in Indonesian acute myeloid leukemia patients undergoing 7+3 remission induction chemotherapy.

Background: The 7+3 regimen is still the main choice of remission induction chemotherapy in acute myeloid leukemia (AML). Successfully achieving complete remission (CR) and the time required to achieve it determine patient's survival. Hence, bone marrow examination on 14 th day of chemotherapy is recommended to predict CR. However, the examination is invasive and still inaccurate. Methods: A prognostic study with retrospective cohort design was conducted at two central hospitals in Indonesia based on medical record data of AML patients who underwent 7+3 induction chemotherapy from January 1st, 2015, to December 31st, 2019. The association of nadir leukocyte level and the time required to achieve it with CR occurrence was assessed. Results: One hundred and one subjects were recruited with median age 39 years and 55% men. A total of 55.4% subjects achieved CR. Nadir leukocyte level below 200/mcl was the most optimal cut-off point and independently associated with CR (OR 2.48; 95% CI 1.03-5.97) while time required to achieve it was not. Conclusions: The nadir leukocyte level is associated with an increase probability of CR but not for the time required to achieve it in AML patients undergoing 7+3 induction chemotherapy.

Clinical characteristics and outcomes of COVID-19 patients in Bali, Indonesia.

INTRODUCTION: The spectrum of illness and outcomes of coronavirus disease 2019 (COVID-19) patients may vary. This study reports the characteristics of COVID-19 patients in Bali, Indonesia, and evaluates the diagnostic value of their clinical symptoms. METHOD: This observational study was conducted in eight hospitals. The patients were classified as non-severe COVID-19, severe COVID-19, and non-COVID-19. Demographics, clinical, laboratory, and radiologic characteristics, and outcomes of COVID-19 patients were collected. Factors associated with the severity and outcomes were assessed using the chi-squared test or ANOVA when appropriate. We also compared the clinical features of non-severe COVID-19 and non-COVID-19 patients to evaluate the diagnostic accuracy. RESULTS: This study included 92 patients: 41 non-COVID-19 and 51 COVID-19 patients, comprising 45 non-severe and six severe cases. The most common symptoms of COVID-19 were cough (47.1%), fever (31.0%), and dyspnea (25.3%). Cough, fatigue, and anosmia have high accuracy, and combining these complaints in clinical diagnostics offered a higher accuracy in predicting COVID-19 patients (60.1%). We found lower lymphocyte counts and interleukin-1R levels and higher levels of C-reactive protein, interleukin-6, and interleukin-8 in severe compared than in non-severe COVID-19 patients. Lactate dehydrogenase was associated with intensive care unit admission and ventilator use, while other markers such as neutrophil-lymphocyte ratio, C-reactive protein, and interleukin-6 were not. CONCLUSION: A battery of symptoms, including cough, fatigue, and anosmia, is likely associated with COVID-19 in Bali. Clinicians should be aware of these symptoms to ensure a prompt diagnostic test for COVID-19, beyond other causes of acute febrile illnesses.

Rare cardiac complication of toxoplasmosis in immunocompetent host.

Myocarditis is a rare complication of toxoplasmosis, especially in immunocompetent individuals. We present a case of a 28-year-old man with a history of fever and chest pain suggestive of myocarditis. Fever, along with lymphadenopathy, electrocardiography, imaging, and serologic testing, showed Toxoplasma gondii as the probable etiology. An excellent response to treatment confirmed the diagnosis.

Perceptions, views and practices regarding antibiotic prescribing and stewardship among hospital physicians in Jakarta, Indonesia: a questionnaire-based survey.

OBJECTIVES: Antibiotic overuse is one of the main drivers of antimicrobial resistance (AMR), especially in low-income and middle-income countries. This study aimed to understand the perceptions and views towards AMR, antibiotic prescribing practice and antimicrobial stewardship (AMS) among hospital physicians in Jakarta, Indonesia. DESIGN: Cross-sectional, self-administered questionnaire-based survey, with descriptive statistics, exploratory factor analysis (EFA) to identify distinct underlying constructs in the dataset, and multivariable linear regression of factor scores to analyse physician subgroups. SETTING: Six public and private acute-care hospitals in Jakarta in 2019. PARTICIPANTS: 1007 of 1896 (53.1% response rate) antibiotic prescribing physicians. RESULTS: Physicians acknowledged the significance of AMR and contributing factors, rational antibiotic prescribing, and purpose and usefulness of AMS. However, this conflicted with reported suboptimal local hospital practices, such as room cleaning, hand hygiene and staff education, and views regarding antibiotic decision making. These included insufficiently applying AMS principles and utilising microbiology, lack of confidence in prescribing decisions and defensive prescribing due to pervasive diagnostic uncertainty, fear of patient deterioration or because patients insisted. EFA identified six latent factors (overall Crohnbach's α=0.85): awareness of AMS activities; awareness of AMS purpose; views regarding rational antibiotic prescribing; confidence in antibiotic prescribing decisions; perception of AMR as a significant problem; and immediate actions to contain AMR. Factor scores differed across hospitals, departments, work experience and medical hierarchy. CONCLUSIONS: AMS implementation in Indonesian hospitals is challenged by institutional, contextual and diagnostic vulnerabilities, resulting in externalising AMR instead of recognising it as a local problem. Appropriate recognition of the contextual determinants of antibiotic prescribing decision making will be critical to change physicians' attitudes and develop context-specific AMS interventions.

Recent advances in the diagnosis of intestinal tuberculosis.

BACKGROUND: Intestinal tuberculosis still has a high incidence, especially in developing countries. The biggest challenge of this disease is the establishment of the diagnosis because the clinical features are not typical. Investigations such as culture, acid-fast bacilli (AFB) staining, and histopathology have low sensitivity, so other investigations are needed. Latest molecular-based diagnostic modalities such as GeneXpert, interferon-gamma (IFN-γ) release assays (IGRA), polymerase chain reaction (PCR), multiplex-PCR, and immunological markers are expected to help diagnose intestinal tuberculosis. This article review will examine the latest diagnostic modalities that can be used as a tool in establishing the diagnosis of intestinal tuberculosis. RESULTS: Through a literature search, we were able to review the diagnostic values of various available diagnostic modalities as the appropriate additional test in intestinal tuberculosis. Culture as a gold standard has a sensitivity and specificity value of 9.3% and 100% with the MGIT BACTEC system as the most recommended medium. The sensitivity values of AFB staining, histopathology examination, GeneXpert, IGRA, PCR, multiplex-PCR and, immunological markers were ranged between 17.3 and 31%; 68%; 81-95.7%; 74-88%; 21.6-65%; 75.7-93.1%; and 52-87%, respectively. Meanwhile the specificity values were 100%; 77.1%; 91-100%; 74-87%; 93-100%; 96.4-100%; and 70-95%, respectively. CONCLUSION: The combination of clinical examination, conventional examination, and the latest molecular-based examination is the best choice for establishing the diagnosis of intestinal tuberculosis. Most recent modalities such as multiplex PCR and immunological marker examinations are diagnostic tools that deserve to be used in diagnosing intestinal tuberculosis as their sensitivity and specificity values are quite high and more evidences are expected to support the application of these examinations shortly soon.

Revisiting the Overlooked Infection: Rickettsioses.

The prevalence of human Rickettsioses cases in Indonesia is unknown and could probably be underestimated. The high prevalence of seropositive Rickettsia sp. was reported in small mammals (as vectors) and humans. In Indonesia, a recent study in patients with acute fever revealed that the prevalence of Rickettsioses is 10%. Many cases of Rickettsioses were often misdiagnosed with dengue fever, enteric fever, or leptospirosis due to their overlapping clinical manifestation. The limitation of point of care testing in Indonesia hindered the adequacy of diagnosis confirmation. Appropriate empirical or definitive treatment with macrolide, mainly doxycycline, is preferable compared to other broad-spectrum antibiotics, such as cephalosporin or quinolones. Moreover, when left untreated, Rickettsioses may deteriorate progressively to fatal outcomes, such as meningitis, sepsis, and even death. The awareness of health care practitioners, the availability of confirmatory rapid diagnostic tests and adequate treatment choices are important in eradicating this disease.

Vaccine-Associated Disease Enhancement (VADE): Considerations in Postvaccination COVID-19.

INTRODUCTION: The COVID-19 pandemic has entered a new phase with the roll-out of several vaccines worldwide at an accelerated phase. The occurrence of a more severe presentation of COVID-19 after vaccination may affect policymakers' decision-making and vaccine uptake by the public. Vaccine-associated disease enhancement (VADE) is the modified presentation of infections in individuals after having received a prior vaccination. Currently, little is known about the potential of vaccine-associated disease enhancement (VADE) following COVID-19 immunization. Case Illustration. We herewith report two patients admitted with confirmed COVID-19 pneumonia with a history of CoronaVac vaccination. The first patient with a relatively milder course of the disease had received two doses of CoronaVac, whereas the second patient with a more progressive course of the disease received only one dose before developing symptoms and being admitted to the hospital. Our observations suggest that vaccination could act in boosting the inflammatory process and reveal the previously asymptomatic COVID-19 illness. Theoretically, vaccines could induce VADE, where only suboptimal, nonprotective titers of neutralizing antibodies were produced or proinflammatory T-helper type 2 response was induced. Secondly, enhanced respiratory disease (ERD) could manifest, where pulmonary symptoms are more severe due to peribronchial monocytic and eosinophilic infiltration. Understanding VADE is important for the decision-making by the public, clinicians, and policymakers and is warranted for successful vaccination uptake. CONCLUSION: We report two cases of patients developing COVID-19 shortly after CoronaVac vaccination in which VADE is likely. We recommend that current vaccination strategies consider the measurement of neutralizing antibody titer as a guide in ensuring the safest strategy for mass immunization. Studies are needed to investigate the true incidence of VADE on vaccinated individuals as well as on how to differentiate between VADE and severe manifestations of COVID-19 that are unrelated to vaccination.

Extended spectrum beta-lactamase-producing Escherichia coli surveillance in the human, food chain, and environment sectors: Tricycle project (pilot) in Indonesia.

The World Health Organization (WHO) has been implementing antimicrobial surveillance with a "One Health" approach, known as the Global Surveillance ESBL E. coli Tricycle Project. We describe the implementation of the Tricycle Project (pilot) in Indonesia, focusing on its results, challenges and recommendations. The samples were 116 patients with bloodstream infections caused by ESBL E. coli, 100 rectal swabs collected from pregnant women, 240 cecums of broiler, and 119 environmental samples, using the standardized method according to the guidelines. ESBL-producing E. coli was found in 40 (40%) of the 100 pregnant women, while the proportion of ESBL-producing E. coli was 57.7% among the total E. coli-induced bloodstream infections. ESBL-producing E. coli was isolated from 161 (67.1%) out of 240 broilers. On the other hand, the average concentration of E. coli in the water samples was 2.0 × 108 CFU/100 mL, and the ratio of ESBL-producing E. coli was 12.8% of total E. coli. Unfortunately, 56.7% of questionnaires for patients were incomplete. The Tricycle Project (pilot) identified that the proportion of ESBL-producing E. coli was very high in all types of samples, and several challenges and obstacles were encountered during the implementation of the study in Indonesia. The finding of this study have implication to health/the antimicrobial resistance (AMR) surveillance. We recommend continuing this project and extending this study to other provinces to determine the AMR burden as the baseline in planning AMR control strategies in Indonesia. We also recommend improving the protocol of this study to minimize obstacles in the field.

Hospital-acquired Skin and Skin-structure Infection in COVID-19 Infected Patient with Prolonged Hospitalization.

Acute bacterial skin and skin-structure infections (ABSSSI) is defined in 2013 by the US Food and Drug Administration as a bacterial cellulitis/erysipelas, major skin abscesses, and wound infections. The Infectious Diseases Society of America (IDSA) in 2014 classifies skin and soft-tissue infection (SSTI) as either non-purulent (which includes cellulitis, erysipelas, and necrotizing infection) or purulent (including furuncle, carbuncle, and abscess). Among hospitalized patients with SSTI, healthcare-associated infections account for 73.5% of all cases. Notably, skin and skin-structure infections caused by Pseudomonas aeruginosa, a common hospital pathogen, was reported to cause higher total cost and longer hospital length of stay compared to non-P. aeruginosa cases, despite causing only approximately 5.7% of all healthcare-associated SSTIs. Infection with P. aeruginosa should always be considered in non-healing skin infections in patients with prolonged hospitalization and antibiotic exposure. Tissue culture, preferably taken by surgical debridement, should be promptly performed; and when hospital-infection is suspected, appropriate antibiotics should be started along with removal of all devitalized tissue and to promote skin and soft tissue healing. Expedited discharge should be considered when possible, with adequate antibiotic treatment and follow up for definitive wound treatment.

Correlation of miR-150, hsa-let-7e, and miR- 146a and gene expression of IL-6, IL-8, IP-10, and MIP-1ß during dengue virus infection.

Growing evidence suggests that microRNAs (miRNAs) play a pivotal role in viral infection. The objective of this study was to assess the association between the expression of miR- 150, hsa-let-7e, and miR-146a on cytokine expression during dengue infection. Dengue virus (DENV) strain SJN-006, a serotype 2 DENV strain of the Cosmopolitan genotype, isolated in Bali, Indonesia, was used to infect peripheral blood mononuclear cells (PBMCs) isolated from healthy individuals. The relative gene expressions of miR-150, hsa-let-7e, and miR-146a as well as the gene expression of cytokines (IL-6, IL-8, IP-10, and MIP-1ß) were determined using quantitative real time - polymerase chain reaction (qRT-PCR) at 6, 12 and 24 hours post infection (hpi). Correlations between the microRNAs and cytokines were analyzed by means of causality tests. Our data suggests that miR-150 and hsa-let-7e were significantly higher in infected-PBMCs after 12 hpi compared to the uninfected-PBMCs (p<0.05). The causality tests demonstrated that miR-150 and has-let- 7e were negatively correlated with IL-8 expression, meanwhile miR-146a was the contrast. DENV infection was negatively and positively correlated with miR-150 and hsa-let-7e, respectively, after 24 hpi. In conclusion, our data demonstrates the vital role of miR-150, hsa-let-7e, and miR-146a in regulating IL-8 expression with possible different pathways.

Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing.

Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

Whole genome sequencing data of Escherichia coli isolated from bloodstream infection patients in Cipto Mangunkusumo National Hospital, Jakarta, Indonesia.

Bloodstream infections (BSIs) are some of the most devastating preventable complications in critical care units. Of the bacterial causes of BSIs, Escherichia coli is the most common among Enterobacteriaceae. Bacteria resistant to therapeutic antibiotics represent a significant global health challenge. In this study, we present whole genome sequence data of 22 E. coli isolates that were obtained from bloodstream infection patients admitted to Cipto Mangunkusumo National Hospital, Jakarta, Indonesia. These data will be useful for analysing the serotypes, virulence genes, and antimicrobial resistance genes of E. coli. DNA sequences of E. coli were obtained using the Illumina MiSeq platform. The FASTQ raw files of these sequences are available under BioProject accession number PRJNA596854 and Sequence Read Archive accession numbers SRR10761126-SRR10761147.

The Threat of Emerging and Re-emerging Infections in Indonesia.

Human immunodeficiency virus (HIV) is one example of an emerging infection with total of 386 district of all province in Indonesia reported having such infection; with cumulative number of HIV infected patient from the year 1987 to 2014 is 150,296 while AIDS is 55,799 patients. The access to care only available for 153,887 patients among all HIV/AIDS patients of whom 70% are eligible for anti-retroviral (ARV) treatment and of these only half adhered to ARV treatment. In addition to that, there is an increased risk of other emerging diseases such as Zika virus, Monkey pox or Hanta pulmonary syndrome since a sporadic cases were reported around the region.Beside new diseases, tuberculosis, dengue virus, malaria and diphteria are continuously reported in Indonesia and classified as re-emerging illnesses. On this edition data on diphteria epidemiology in Indonesia will be shown by Karyanti et al.6 A recent outbreak of diphteria in Indonesia which involved almost all province in the country has led to a response named ORI (outbreak response of Immunization). Regardless of immunization, proper treatment including the distribution of anti-toxin and antibiotics are needed to stop the spread of this particular bacteria, further decreasing the mortality rate. In conclusion, the author of this paper mentioned that immunization gap needs to be handle systematically. Immunization data released on 2017 showed that complete immunization was given only to 20% of targeted group, while almost 75% were either unvaccinated or unknown. During the outbreak of diphteria in Indonesia, the WHO also reported several countries with similar problem such as Bangladesh, Haiti and Yamen. It was shown that a coordination between doctors in clinic/hospital with public health officer to conduct an epidemiological investigation, in conjunction with giving prophylaxis and assuring the logistics of anti-diphteria toxin and antibiotics were accessible were  the key of success in eliminating diphteria like it was in Bangladesh.Adherence to treatment are multifactorial for all illnesses. First, is the duration of treatment and the potential adverse event due to the medication. The Ministry of Health of the Republic of Indonesia has support the early diagnosis of HIV and delivering treatment as soon as possible, in order to avoid transmission of the disease. Second, looking at another side of the story for HIV infected patients, receiving ARV treatment as a long life treatment could possibly cause an adverse event somewhere along the line. Budiman et.al reported factors that might contribute to liver injury. His study shows that measuring baseline liver function test AST routinely might minimize the toxicity of ARV to patients particularly with a low body mass index. Last, despite the adherence to treatment and procedures in minimizing the risk of adverse event to medication, we are now facing the primary resistance virus that transmitted in the community as mentioned by Megasari et al.8 on her report regarding the transmission of drug resistance HIV virus to naïve patients in Bali.The Indonesian government through the Indonesian Ministry of Health has established a collaboration and one health approaches to tackle the threat of diseases in the country, particularly in infectious diseases.

Diphtheria Epidemiology in Indonesia during 2010-2017.

BACKGROUND: in recent years, diphtheria has reemerged in several countries including Venezuela, Yemen, Bangladesh, and Haiti. Similarly, Indonesia also showed an increased number of diphtheria cases in 2010-2017 despite the Diphteria, Tetanus, Pertussis (DTP) immunization program applied in Indonesia for children. This study aimed to evaluate the epidemiology of diphtheria cases which occurred in Indonesia during 2010-2017. METHODS: this was a retrospective study of diphtheria cases in Indonesia. The following source of data about diphtheria disease burden and vaccine coverage was obtained from Ministry of Health Republic of Indonesia, Indonesian Pediatric Society and World Health Organization South East Asia Regional Office. RESULTS: the number of diphtheria cases in Indonesia were distributed across 30 provinces with a total of 811 cases in 2011; 1,192 cases in 2012; 296 cases in 2014; and 939 cases in 2017. Based on age group, the highest number of case fatality rate were in age group of 5-9 years old. Diphtheria immunization coverage in Indonesia among children was fluctuated, reported as 67.7 % in 2007, 61.9 % in 2010, 75.6% in 2013 and 61.3% in 2018. In addition to that, the organization of internal medicine has recommend booster of DPT immunization every 10 years for those children that had received complete DPT vaccination during childhood, however this was not applied. As the countermeasure towards this trend, the Ministry of Health implemented three rounds of Outbreak Response Immunization (ORI) targeted for the age group of 0-1-6 months old and 1-18 years old in 2017 and tailor approached for adults that had exposed to cases. Banten, DKI Jakarta and West Java were the first three provinces to implement this program considering their condensed population and high risk of disease transmission. CONCLUSION: in Indonesia, there was dramatic increase of diphtheria case in 2010-2017, where immunization in children should be reinforced by increasing coverage more than 95% and adult boosted vaccination approaches should be initiated to prevent the spread of these fatal diphtheria diseases in Indonesia.