Antimicrobial Sensitivity Pattern from Hospitalized Pneumonia Patients in National Referral Infectious Disease Hospital in Indonesia.

Background: Pneumonia is still a major global problem with high morbidity and mortality. The increasing number of pneumonia cases caused by bacteria, especially multidrug-resistant pathogens, increasing age of the population, patients with chronic disease (comorbid), and inappropriate antimicrobial therapy at initial administration make the treatment become less effective. These issues finally contribute to higher morbidity and mortality in cases of hospitalized pneumonia patients. Therefore, it is crucial to know the microbial pattern and select the therapy according to local antimicrobial sensitivity patterns. Method: A cross-sectional study was conducted for hospitalized pneumonia patients between January 2015 and December 2016 in Indonesia National Referral Infectious Disease Hospital. Data were collected from medical records to show patient characteristics, antimicrobial treatment data, culture examination, and bacterial sensitivity. Results: A total of 99 pneumonia patients required hospitalization and underwent sputum culture examination. The patients were mostly above 65 years old (32.3%) and male (57.6%). The most common comorbidities were pulmonary tuberculosis (21%), and the others were heart failure, chronic obstructive pulmonary disease (COPD), and HIV/AIDS. Based on the sputum culture, fungi were identified in most specimens (56%), while the bacteria identified were Klebsiella pneumoniae (14%), Acinetobacter sp. (12%), and Pseudomonas sp. (8%). Third-generation cephalosporin, such as ceftriaxone (50%), was commonly used as an antibiotic for pneumonia treatment. Conclusion: Most common bacteria isolated from sputum culture were Klebsiella pneumoniae which were more sensitive to the beta-lactam and aminoglycoside groups. The higher risk factors were age above 65 years old, being male, and having tuberculosis.

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.

Detection of toxin-producing Corynebacterium diphtheriae from throat swabs of diphtheria patients using duplex real-time PCR.

BACKGROUND AND OBJECTIVES: Diphtheria is a potentially fatal disease caused by toxigenic bacterial infection, particularly from Corynebacterium diphtheriae (C. diphtheriae). Isolation of C. diphtheriae is technically lacking in sensitivity, and Elek's test to detect toxin production has several difficulties associated with its application. Duplex real-time PCR to throat swab of suspected diphtheria patients can detect both bacteria and toxin-encoding genes simultaneously, faster, with higher sensitivity and specificity. MATERIALS AND METHODS: A total of 89 consecutive throat swabs from suspected diphtheria patients were collected from Sulianti Saroso Infectious Disease Hospital, Jakarta, during 2018 to 2019. Two pairs of primers and probes, targeting the rpoB gene of C. diphtheriae and the A-subunit of the diphtheria toxin gene, were used in this study. Parameters including annealing temperature, concentration of primers and probes, inhibitors, cross-reaction and detection limit were all optimized. Elek's toxigenicity test and clinical data were analyzed for comparison. RESULTS: The optimum annealing temperature was 55°C. The concentrations of Cd primer, Tox primer, Cd probe and Tox probe were 0.4, 0.6, 0.5 and 0.625 µM, respectively. DNA elution and template volumes were 50 µL and 5 µL. The detection limit was 2 CFU/mL. No cross-reaction with other microorganisms was observed. Of the 89 samples, duplex real-time PCR gave better results than the standard test, with 19 (21.3%) and 10 (11.2%) patients diagnosed with diphtheria, respectively. CONCLUSION: Duplex real-time PCR increases the rate of laboratory diagnosis of diphtheria, compared to the standard method to detect potentially toxigenic C. diphtheriae.

Detection of multiple viral sequences in the respiratory tract samples of suspected Middle East respiratory syndrome coronavirus patients in Jakarta, Indonesia 2015-2016.

OBJECTIVES: The identification and analysis of viral etiological agents from suspected Middle East respiratory syndrome coronavirus (MERS-CoV) cases admitted to Prof. Dr. Sulianti Saroso Infectious Disease Hospital (IDH) using molecular assays. METHODS: Biological samples were collected from 13 hospitalized patients suspected of MERS-CoV infection in Prof. Dr. Sulianti Saroso IDH from July 2015 to December 2016. The majority of patients presented with pneumonia, with symptoms including fever (≥37.5 °C), labored breathing, and cough, and with a history of travel to the Middle East. Viral RNA was isolated and converted to cDNA, which was used as a template for the detection of 12 viral panels using conventional PCR and sequencing. RESULTS: Viral etiological agents detected in the patients were enterovirus D68, dengue virus type 3, rhinovirus C, human coronavirus 229E, herpes simplex virus type 1, influenza virus H1N1, influenza virus H3N2, human metapneumovirus, and rhinovirus A60. CONCLUSIONS: The sequences of nine viral agents under different taxa were detected in suspected MERS-CoV patients, including influenza virus, paramyxovirus, coronavirus, enterovirus, human metapneumovirus, and herpesvirus.