Characterization of SARS-CoV-2 East Java isolate, Indonesia.

Background: Incidents of SARS-CoV-2 in East Java increased steadily, and it became the second epicenter in Indonesia. The COVID-19 pandemic caused a dire multisectoral crisis all around the world. This study investigates and characterizes local isolates from East Java, Indonesia.   Methods: There were 54 patients suspected with SARS-COV-2 infection and 27 patients were COVID-19 positive. Virus isolates were obtained from COVID-19 inpatients' nasopharyngeal swabs at the Dr Soetomo Teaching Hospital, Surabaya. There were only three isolates (#6, #11, #35) with good growth characteristics. Serial blind passage and cytopathic effect observation in the Vero E6 cell line were performed for virus isolation. Confirmation of the SARS-CoV-2 infection was proven by means of reverse transcriptase-polymerase chain reactions using SARS-CoV-2 specific primers, scanning electron microscopy, and scanning transmission electron microscopy examination. Whole genome sequencing was performed using ARTIC protocol. Furthermore, SARS-CoV-2 characterization was identified through a western blot using rabbit serum immunized with inactive SARS-CoV-2 vaccine and human natural COVID-19 infection serum.   Results: Spike gene analysis of three samples (#6, #11, #35) found that the D614G mutation was detected in all isolates, although one isolate exhibited the D215Y and E484D mutation. Based on whole genome analysis, those three isolates were included in clade 20A, and two isolates were included in lineage B.1.6 with one isolate belongs to lineage B.1.4.7.   Conclusion: Based on molecular characterization and immunogenicity of SARS-CoV-2 East Java, Indonesia showed high titer and it has mutation in some regions.

Etiologies of severe acute respiratory infection (SARI) and misdiagnosis of influenza in Indonesia, 2013-2016.

BACKGROUND: Severe acute respiratory infection (SARI) accounts for a large burden of illness in Indonesia. However, epidemiology of SARI in tertiary hospitals in Indonesia is unknown. This study sought to assess the burden, clinical characteristics, and etiologies of SARI and concordance of clinical diagnosis with confirmed etiology. METHODS: Data and samples were collected from subjects presenting with SARI as part of the acute febrile Illness requiring hospitalization study (AFIRE). In tertiary hospitals, clinical diagnosis was ascertained from chart review. Samples were analyzed to determine the "true" etiology of SARI at hospitals and Indonesia Research Partnership on Infectious Diseases (INA-RESPOND) laboratory. Distribution and characteristics of SARI by true etiology and accuracy of clinical diagnosis were assessed. RESULTS: Four hundred and twenty of 1464 AFIRE subjects presented with SARI; etiology was identified in 242 (57.6%), including 121 (28.8%) viruses and bacteria associated with systemic infections, 70 (16.7%) respiratory bacteria and viruses other than influenza virus, and 51 (12.1%) influenza virus cases. None of these influenza patients were accurately diagnosed as having influenza during hospitalization. CONCLUSIONS: Influenza was misdiagnosed among all patients presenting with SARI to Indonesian tertiary hospitals in the AFIRE study. Diagnostic approaches and empiric management should be guided by known epidemiology. Public health strategies to address the high burden of influenza should include broad implementation of SARI screening, vaccination programs, clinician education and awareness campaigns, improved diagnostic capacity, and support for effective point-of-care tests.

Impact of a three-dose diphtheria outbreak response immunization in East Java, Indonesia, 6 months after completion.

Several outbreaks of diphtheria have occured in the East Java Province of Indonesia since 2011. The last effort to stop the outbreak in the province was a three round outbreak response immunization (ORI) in 2018.The aim of the this study was to evaluate the impact of the 2018 ORI in East Java province - 6 months following the completion of the program. Surveillance data was collected for 6 month period, from January to June 2019. The source of data was the district health offices, hospitals, community health centers, and private physician and paramedic practices. The data included demographic characteristics, involved health facilities, patient immunization history, clinical signs and symptoms, some laboratory test results and other additional examinations. All cases were evaluated by the East Java Provincial Diphtheria Expert Committee and not based on the individual physician decision. During the 6 month period, there were 97 diphtheria cases which approved by the Diphtheria Expert Committee. The reports came from 36 of 38 districts. One patient died, denoting a case fatality rate of 1%. The majority were 19 years of age or less, with uncomplete immunization. Patients above 19 years were 24%. Compared with 2017 (438 cases) and 2018 (310), 2019 saw a significant reduction in the number of reported cases. Only 4 positive culture results were collected (positivity rate 4,13%). Two patients had Mitis subtype and the other two had Gravis subtype. Diphtheria ORI in East Java had a significant impact during the first 6 months of 2019.

An evaluation of the clinical features of measles virus infection for diagnosis in children within a limited resources setting.

BACKGROUND: Measles is a recurrent health problem in both advanced and developed countries. The World Health Organization (WHO) recommends anti-measles immunoglobulin M (Ig M) as the standard method of detecting the virus; however, many areas still present the inability to perform a serology test of anti-measles IgM. Therefore, a typical clinical feature is necessary to establish the diagnosis of measles. The objective of this study was to evaluate hyperpigmented rash and other clinical features as the diagnostic tools with respect to measles, especially in an outbreak setting. METHODS: In this observational diagnostic study, the inclusion criteria were as follows: between 6 and 144 months of age, fever, maculopapular rash for 3 days or more, accompanied by a cough, or coryza, or conjunctivitis. Those with a prior history of measles vaccination (1-6 weeks) were excluded, in addition to those with histories of corticosteroid for 2 weeks or more and immunocompromised conditions. The samples were taken from Dr. Soetomo General Academic Hospital in Surabaya, Indonesia. We evaluated the sensitivity, specificity, the positive predictive value, and the negative predictive value of such clinical features. Hyperpigmented rash was validated using Kappa and Mc Nemar tests. Anti-measles Ig M was considered as the gold standard. RESULTS: This study gathered 82 participants. The clinical manifestations of all subjects included fever, cough, coryza, conjunctivitis, Koplik spots, and maculopapular rash (which turns into hyperpigmented rash along the course of the illness). Most maculopapular rashes turn out to be hyperpigmented (89%). Sensitivity, specificity, positive predictive value, and negative predictive values ​​of the combination of fever, maculopapular rash, and hyperpigmented rash were found to be at 90.7, 28.6, 93.2, and 22.2%, respectively. The Mc Nemar and Kappa tests showed p values of 0.774 and 0.119, respectively. CONCLUSION: The combination of fever, maculopapular rash, and hyperpigmented rash can be used as a screening tool regarding measles infection in an outbreak setting, which can then be confirmed by anti-measles Ig M. Cough, coryza, and Koplik's spot can be added to this combination, albeit with a slight reduction of sensitivity value.

First-line antibiotic susceptibility pattern of toxigenic Corynebacterium diphtheriae in Indonesia.

BACKGROUND: Diphtheria has been reported as an outbreak in some regions in Indonesia, most especially in East Java Province. Resistance to penicillin, erythromycin, and other antibiotics, single or multiple, has been reported in several studies. This study aims to evaluate the first-line antibiotic susceptibility pattern of toxigenic Corynebacterium diphtheriae isolates. METHODS: This descriptive observational study was performed from August to November 2018. C. diphtheriae isolates were collected from diphtheria patients and carriers in East Java from 2012 to 2017 and kept at the Balai Besar Laboratorium Kesehatan Daerah Surabaya or the Public Health Laboratory of Surabaya. Sample selection was done by random cluster sampling. The sensitivity test by E-test®of the five antibiotics (penicillin, oxacillin, erythromycin, azithromycin, and clarithromycin) was done to determine the minimum inhibitory concentration (MIC). The Clinical and Laboratory Standards Institute M45A (2015) Corynebacterium spp. for penicillin and erythromycin was used as standard. RESULTS: From 114 targeted isolates, 108 were viable and toxigenic. The E-test was performed on the viable isolates. The majority of the hosts were male (58.3%), with median (range) age of 6.5 (1-14) years. Half of the samples were from the 1 to 5-year-old age group. The isolates were acquired much more from patients (78.7%) than carriers (21.3%) and from pharyngeal swab (74.1%). Most of these isolates were from Madura Island (47.2%) and the northern and eastern parts of the province (horseshoe area). Mitis isolates were the major variant (76.9%). The susceptibility pattern of C. diphtheriae to erythromycin was better than that to penicillin. The E-test result for penicillin was 68.52% susceptible, 31.48% intermediate, and 0% resistant (MIC range, < 0.016 to 2 µg/L) and for erythromycin (MIC range, < 0.016 to > 256 µg/L) was 85.2% susceptible, 12% intermediate, and 2.8% resistant The MIC range for oxacillin was 1 to 96 µg/L, while for both azithromycin and clarithromycin were <  0.016 to > 256 µg/L. CONCLUSION: The susceptibility rate of C. diphtheriae to erythromycin is higher than that to penicillin. The regular update of antibiotic selection to the national guidelines is recommended. The MIC reference standard to azithromycin and clarithromycin is also needed.

Dengue viral infection in Indonesia: Epidemiology, diagnostic challenges, and mutations from an observational cohort study.

BACKGROUND: Dengue virus (DENV) infection is a major cause of acute febrile illness in Indonesia. Diagnostic inaccuracy may occur due to its varied and non-specific presentation. Characterization of DENV epidemiology, clinical presentation, and virology will facilitate appropriate clinical management and public health policy. METHODOLOGY/PRINCIPAL FINDINGS: A multicenter observational cohort study was conducted in Indonesia to assess causes of acute fever requiring hospitalization. Clinical information and specimens were collected at enrollment, 14-28 days, and 3 months from 1,486 children and adults. Total of 468 (31.9%) cases of DENV infection were confirmed by reference laboratory assays. Of these, 414 (88.5%) were accurately diagnosed and 54 had been misdiagnosed as another infection by sites. One hundred initially suspected dengue cases were finally classified as 'non-dengue'; other pathogens were identified in 58 of those cases. Mortality of DENV infection was low (0.6%). Prior DENV exposure was found in 92.3% of subjects >12 years. DENV circulated year-round in all cities, with higher incidence from January to March. DENV-3 and DENV-1 were the predominant serotypes. This study identified DENV-1 with TS119(C→T) substitution in the serotyping primer annealing site, leading to failure of serotype determination. CONCLUSIONS/SIGNIFICANCE: DENV is a common etiology of acute febrile illness requiring hospitalization in Indonesia. Diagnostic accuracy at clinical sites merits optimization since misdiagnosis of DENV infection and over-estimation of dengue can negatively impact management and outcomes. Mutation at the annealing site of the serotyping primer may confound diagnosis. Clinicians should consider following diagnostic algorithms that include DENV confirmatory testing. Policy-makers should prioritize development of laboratory capacity for diagnosis of DENV.

Effect of Lactobacillus plantarum IS-10506 on blood lipopolysaccharide level and immune response in HIV-infected children.

BACKGROUND AND OBJECTIVES: HIV enteropathy may cause disruption of the intestinal barrier, leading to a loss of CD4+ T cells, increased intestinal permeability, and microbial translocation. Lactobacillus plantarum IS-10506 has the ability to improve gut barrier function. This study investigated the effect of L. plantarum IS-10506 on a number of biomarkers of enteropathy-related damage in HIV-infected paediatric patients undergoing antiretroviral therapy (ARV). MATERIALS AND METHODS: A randomized, double-blind, placebo-controlled study was conducted on 2-18 year-old children, diagnosed as HIV infected according to the WHO 2007 criteria who had received ARV for ≥ 6 months. Subjects were excluded if ARV therapy was discontinued or the patients took probiotics ≥ 2 weeks prior to the study or during the study period. Subjects were randomized into a probiotic group and placebo group. The probiotic group received L. plantarum IS-10506 2.86 × 1010 cfu/day for 6 days. Blood lipopolysaccharide (LPS) level, serum CD4+ T cell count, serum CD8+ T cell count, CD4+/CD8+ T cell ratio, and faecal sIgA level were assessed as biomarkers. RESULTS: Twenty-one subjects completed this study. The blood LPS level decreased significantly in the probiotic group (p = 0.001). There was no significant difference in absolute CD4+ T cell count, percent CD4+ cells, absolute CD8+ T cell count, CD4+/CD8+ T cell ratio, or faecal sIgA. No serious adverse events were reported. CONCLUSION: The probiotic L. plantarum IS-10506 reduced the blood LPS level but showed no effect on the humoral mucosa and systemic immune response in HIV-infected children undergoing ARV therapy.

Uncommon Pathogen Bacillus Cereus Causing Subdural Empyema in a Child.

BACKGROUND: Subdural empyema (SDE) in children is a severe intracranial infection. Many pathogens can cause SDE. CASE DETAILS: In this articlewe present a 15-month old Indonesian boy diagnosed as SDE based on the clinical symptoms and neuroimaging. A complete blood count showed white blood cell count of 13.800/mm3 and the CRP level was 8.3 mg/L. Craniotomy following burr hole drainage procedure was performed to decrease intracranial pressure. The liquor culture indicated Bacillus cereus. A meropenem injection and metronidazole infusion were administered appropriately with antibiotic sensitivity for several weeks. Immediate initiation of appropriate antibiotic therapy related to an accelerated surgical drainage can improve the outcome. CONCLUSION: The combination of medication and surgery treatment for Bacillus cereus in SDE resulted in a good response, leaving neurological sequelae.

Clinical and virological characteristics of dengue in Surabaya, Indonesia.

Dengue disease is still a major health problem in Indonesia. Surabaya, the second largest city in the country, is endemic for dengue. We report here on dengue disease in Surabaya, investigating the clinical manifestations, the distribution of dengue virus (DENV) serotypes, and the relationships between clinical manifestations and the genetic characteristics of DENV. A total of 148 patients suspected of having dengue were recruited during February-August 2012. One hundred one (68%) of them were children, and 47 (32%) were adults. Dengue fever (DF) and Dengue hemorrhagic fever (DHF) were equally manifested in all of the patients. We performed DENV serotyping on all of the samples using real-time RT-PCR. Of 148, 79 (53%) samples were detected as DENV positive, with DENV-1 as the predominant serotype (73%), followed by DENV-2 (8%), DENV-4 (8%), and DENV-3 (6%), while 5% were mixed infections. Based on the Envelope gene sequences, we performed phylogenetic analyses of 24 isolates to genotype the DENV circulating in Surabaya in 2012, and the analysis revealed that DENV-1 consisted of Genotypes I and IV, DENV-2 was of the Cosmopolitan genotype, the DENV-3 viruses were of Genotype I, and DENV-4 was detected as Genotype II. We correlated the infecting DENV serotypes with clinical manifestations and laboratory parameters; however, no significant correlations were found. Amino acid analysis of Envelope protein did not find any unique mutations related to disease severity.

Application of revised dengue classification criteria as a severity marker of dengue viral infection in Indonesia.

A prospective study of dengue infected patients at Dr.Soetomo Hospital pediatric ward was carried out from October 2008 to April 2009 to evaluate the revised dengue classification system proposed by the Dengue Control (DENCO), for early detection of severe dengue infected patients using the WHO classification system for comparison, with the addition of clinical interventions as a tool to grade for severity. One hundred forty-five patients were included in the study. Using the WHO classification system, 122 cases (84.1%) were classified as having non-severe dengue, of which 70 (48.3%) were classified as having dengue fever (DF), 39 (26.9%) as having dengue hemorrhagic fever (DHF) grade I, and 13 (9%) as having DHF grade II. Twenty-three (15.9%) were classified as having severe dengue, of which 16 (11%) were classified as having DHF grade III and 7 (4.8%) as having DHF grade IV. With clinical interventions included, 8 cases (6.6%) originally classified as having non-severe dengue infection were reclassified as having severe infection (sensitivity = 74%, specificity = 100%, likelihood ratio (-) = 0.26). Using the new dengue classification system, 117 cases (80.7%) were classified as having non-severe dengue infection, of which 79 (54.5%) were classified as having dengue without warning signs and 38 (26.2%) were classified as having dengue with warning signs, while 28 (19.3%) were classified as having severe dengue infection. Using clinical intervention, 4 cases (3.4%) which were originally classified as having non-severe dengue infection were reclassified as having severe dengue infection (sensitivity = 88%, specificity = 99%, likelihood ratio (+) = 98.88, likelihood ratio (-) = 0.13). Binary logistic regression showed the revised dengue classification system (p = 0.000, Wald:22.446) was better in detecting severe dengue infections than the WHO classification system (p = 0.175, Wald:6.339).