Examination of Acid-Fast Bacilli in Sputum Using Modified Light Microscope with Homemade Light Emitting Diode Additional Attachment

Typical clinical symptoms and chest X-ray is a marker of Tuberculosis (TB) sufferers. However, the diagnosis of TB in adults should be supported by microscopic examination. Currently, Bacilli microscopic examination of acid-fast bacilli (AFB) in sputum by Ziehl-Neelsen (ZN) coloring is the most widely used. However, for reasons of convenience, especially for laboratories with a considerable amount of smear samples, and due to higher sensitivity compared with ZN staining, the World Health Organization (WHO) has recommended the use of auramine-O-staining (fluorochrome  staining), which is visualized by light emitting diode (LED) fluorescence microscopy. The aim of this study was to evaluate the performance of modified light microscope with homemade LED additional attachment for examination of AFB in sputum using auramine-O-staining method. We compared the sensitivity and specificity of 2 kinds of AFB in sputum methods: ZN and fluorochrome, using culture on Lowenstein-Jensen media as the gold standard. The results showed auramine-O-staining gives more proportion of positive findings (81%) compared to the ZN method (70%). These results demonstrated that the sensitivity of auramine-O-staining was higher than ZN, however it gives more potential false positive results than ZN. The sensitivity of auramine-O-staining in detecting AFB in sputum was 100% while the specificity was 88%

Faktor-faktor yang Mempengaruhi Produksi Susu Sapi Perah di Kecamatan Megamendung Kabupaten Bogor Provinsi Jawa Barat

The dairy cow is one of the lifestock commodity still have potential to develop in Indonesia. The domestic milk production only cover 1/3 of domestic demand so the most of milk remains were still imported. Cipayung village, District Megamendung, Bogor regency is one of the central production for fresh milk. The problems that faced by the most of farmers in this region are the low productivity of milk, it's about 8-10 litre/day so it's can influence to the income level of farmers too. The purpose of this research are to analyze about factors that have affected to the production of milk and to analyze income of dairy cow farm. This research used Cobb Douglas production function with the respondents were 35 dairy farmers members of Mekar Jaya Farmer Group. The respondents in this research were chosen by purposive sampling method where leader of the farmer group has an estimation to choose the farmers that have qualification become a respondent. Based on the results of analyzed research showed that period of lactation, forages, water and labors were factors that have significantly affected to the production of dairy cows. This analyze also showed that the value of farm R/C ratio of the cash cost was1,64 and R/C ratio of the total cost was 1,25

Direct PCR: Alternative Diagnostic Method for Diagnosis of Diphtheria Rapidly, Easily and Cost Effective

Some diseases require immediate and appropriate treatment to decrease the fatality risk patients incident, for example diphtheria. Time to help patients is very crucial since delay of therapy may increase the mortality cases up to 20 times. In other hands, conventional diagnostic methods (the gold standard) for diagnosis of diphtheria is time consuming and laborious. Therefore, an alternative diagnostic method which is rapid, easy and inexpensive is needed. In this case, direct PCR has been proved to reduce time and cost in laboratory examination. This study aimed to develop direct PCR as alternative diagnostic method for diagnosis of diphtheria rapidly, easily, and inexpensive. Fifteen samples include 10 isolates of Corynebacterium diphtheriae (toxigenic) and 3 isolates of Corynebacterium non- diphtheriae (nontoxigenic) and 2 clinical specimens (throat swab) was examined by performing direct PCR method and a standard PCR method was used for optimizing the protocols. Result showed that direct PCR can be used to amplify target genes correctly as well as standard PCR. All of C. diphtheriae samples showed bands at 168 bp (dtxR gene marker) and 551 bp (tox gene marker) while no band appeared in others. Direct PCR detected at least 71 CFU/uL of bacterial cells in samples. We concluded that direct PCR can be used for alternative diagnostic method for diagnosis of diphtheria which is rapid, easy and cost effective

Metode Cepat Ekstraksi Dna Corynebacterium Diphtheriae Untuk Pemeriksaan Pcr

Diagnosis of diphtheria caused byCorynebacterium diphtheriaeshould be done immediately since delay of therapy may cause 20-fold increase rate of death. One method of rapid diagnostic to identify diphtheria is by using polymerase chain reaction (PCR). The fundamental issue of this method depends on the DNA, either its quality or quantity. The simple DNA extraction method, which is using mechanical/physical principles with a little of chemical reagents (such as boiling method and the use of sodium hydroxide (NAOH)), will have some benefits, such as easy to be performed, low cost, fast, and environmentally friendly. This study aimed to evaluate effectivity and efficiency of boiling method with NaOH to extract DNA of C. diphtheriae compared to the use of a commercial diagnostic kit for PCR assay. We used C. diphtheriae toxygenic(NCTC 10648) isolates, which are grown in blood agar plates. We then prepared the suspensions of cell/colony in aquadest with several dilutions. Each dilution was extracted using boiling method, NaOH and controlled with the use of a commercial diagnostic kit (QiAmp DNA Minikit). The results were evaluated quantitatively with spectrophotometer and qualitatively with gel electrophoresis. The results showed that the extracted DNA from boiling method with NaOH has an adequate quality and quantity for PCR assay (up to 9 CFU/uL cell/reaction). Therefore, it can be summarized that boiling method with NaOH is effective and efficient to be applied in PCR assay forC. diphtheriae.Key words: boiling extraction method, NaOH, C.diphtheriae, PCRAbstrakKematian kasus difteri yang disebabkan oleh Corynebacterium diphtheriaedapat meningkat 20 kali lipat karena keterlambatan pengobatan sehingga penegakan diagnosis harus dilakukan sesegera mungkin. Salah satu metode diagnostik yang cukup cepat untuk mendeteksi penyakit difteri adalah pemeriksaan polymerase chain reaction(PCR). Keberhasilan pemeriksaan PCR dipengaruhi oleh kualitas dan kuantitas DNA. Metode ekstraksi DNA sederhana menggunakan prinsip mekanik/fisika dengan reagen kimia minimalis, seperti metode pemanasan (boiling)dan penggunaan (NAOH) memiliki beberapa kelebihan, diantaranya mudah dilakukan, biaya murah, waktu yang dibutuhkan singkat dan lebih ramah lingkungan. Penelitian ini bertujuan untuk menilai efektifitas dan efisiensi metode boilingdan NAOH untuk ekstraksi DNA C.diphtheriae dibandingkan dengan penggunaan kit komersial dalam pemeriksaan PCR. Sampel berupa isolat C.diphtheriae toksigenik (NCTC 10648), ditumbuhkan dalam blood agar, kemudian dibuat suspensi sel/koloni dalam aquadest dengan beberapa kali pengenceran. Masing-masing pengenceran diekstraksi dengan metode boilingdan NaOH yang terkontrol dengan kit komersial (QiAmp DNA Minikit). Hasil ekstraksi dinilai secara kuantitatif dengan spektrofotometer dan secara kualitatif dengan gel elektroforesis. Hasil penelitian menunjukkan bahwa DNA hasil ekstraksi dengan metode boilingdan NaOH mempunyai kualitas dan kuantitas yang cukup untuk pemeriksaan PCR hingga 9 CFU/uL sel bakteri/reaksi sehingga dapat disimpulkan bahwa metode boiling dan NaOH cukup efektif dan efisien untuk diaplikasikan pada metode PCR untuk C.diphtheriae.Kata Kunci: boiling, NaOH, C.diphtheriae, PC

Infections and antimicrobial resistance in intensive care units in lower-middle income countries: a scoping review

Background: Intensive care units (ICUs) in lower-middle income countries (LMICs) are suspected to constitute a special risk for patients of acquiring infection due to multiple antibiotic resistant organisms. The aim of this systematic scoping review was to present the data published on ICU-acquired infections and on antimicrobial resistance observed in ICUs in LMICs over a 13-year period. A systematic scoping review was conducted according to the PRISMA extension guideline for scoping reviews and registered in the Open Science Framework. Main body of the abstract: Articles were sought that reported on ICU-acquired infection in LMICs between 2005 and 2018. Two reviewers parallelly reviewed 1961 titles and abstracts retrieved from five data banks, found 274 eligible and finally included 51. Most LMICs had not produced reports in Q1 or Q2 journals in this period, constituting a large gap in knowledge. However, from the reported evidence it is clear that the rate of ICU-acquired infections was comparable, albeit approximately 10% higher, in LMICs compared to high income countries. In contrast, ICU mortality was much higher in LMICs (33.6%) than in high income countries (< 20%). Multidrug-resistant Gram-negative species, especially Acinetobacter baumannii and Pseudomonas aeruginosa, and Klebsiella pneumoniae played a much more dominant role in LMIC ICUs than in those in high income countries. However, interventions to improve this situation have been shown to be feasible and effective, even cost-effective. Conclusions: Compared to high income countries the burden of ICU-acquired infection is higher in LMICs, as is the level of antimicrobial resistance; the pathogen distribution is also different. However, there is evidence that interventions are feasible and may be quite effective in these settings. Protocol Registration The protocol was registered with Open Science Framework (https://osf.io/c8vjk

Clinical impact of endemic NDM-producing Klebsiella pneumoniae in intensive care units of the national referral hospital in Jakarta, Indonesia

OBJECTIVE: A prospective observational study was performed to assess the epidemiology and clinical impact of carbapenem-non-susceptible Klebsiella pneumoniae (CNKP) in intensive care units (ICUs) of the national referral hospital in Jakarta, Indonesia. MATERIALS/METHODS: Adult patients consecutively hospitalized for > 48 h in two ICUs of the national referral hospital were included from April until October 2013 and from April until August 2014. K. pneumoniae from clinical cultures and standardized screening of rectum and throat on admission, discharge and weekly if hospitalized > 7 days were collected. Environmental niches and healthcare workers (HCWs) were also screened. Susceptibility was determined phenotypically and the presence of carbapenemase genes by PCR. Raman spectroscopy as well as multiple-locus variable number tandem repeat analysis (MLVA) were used for typing. RESULTS: Twenty-two out of 412 (5.3%) patients carried CNKP on admission and 37/390 (9.5%) acquired CNKP during ICU stay. The acquisition rate was 24.7/1000 patient-days at risk. One out of 31 (3.2%) environmental isolates was a CNKP. None of the HCWs carried CNKP. Acquisition of CNKP was associated with longer ICU stay (adjusted Hazard Ratio: 2.32 [CI99: 1.35-3.68]). ICU survival was lower among patients with CNKP compared to patients with carbapenem-susceptible K. pneumoniae (aHR 2.57, p = 0.005). Ninety-six of the 100 (96%) CNKP isolates carried a carbapenemase gene, predominantly blaNDM. Raman typing revealed three major clusters among 48 Raman types identified, whereas MLVA distinguished six major clusters among a total of 30 different genotypes. CONCLUSIONS: NDM-producing CNKP are introduced into these ICUs and some strains expand clonally among patients and the environment, resulting in endemic CNKP. CNKP acquisition was associated with prolonged ICU stay and may affect ICU survival. TRIAL REGISTRATION: The study was registered at Netherlands Trial Register http://www.trialregister.nl. Candidate number: 23527, NTR number: NTR5541, NL number: NL5425 (https://www.trialregister.nl/trial/5424), Retrospectively registered: NTR: 22 December 2015

Diagnostic and antibiotic use practices among COVID-19 and non-COVID-19 patients in the Indonesian National Referral Hospital.

BACKGROUND: Little is known about diagnostic and antibiotic use practices in low and middle-income countries (LMICs) before and during COVID-19 pandemic. This information is crucial for monitoring and evaluation of diagnostic and antimicrobial stewardships in healthcare facilities. METHODS: We linked and analyzed routine databases of hospital admission, microbiology laboratory and drug dispensing of Indonesian National Referral Hospital from 2019 to 2020. Patients were classified as COVID-19 cases if their SARS-CoV-2 RT-PCR result were positive. Blood culture (BC) practices and time to discontinuation of parenteral antibiotics among inpatients who received a parenteral antibiotic for at least four consecutive days were used to assess diagnostic and antibiotic use practices, respectively. Fine and Grey subdistribution hazard model was used. RESULTS: Of 1,311 COVID-19 and 58,917 non-COVID-19 inpatients, 333 (25.4%) and 18,837 (32.0%) received a parenteral antibiotic for at least four consecutive days. Proportion of patients having BC taken within ±1 calendar day of parenteral antibiotics being started was higher in COVID-19 than in non-COVID-19 patients (21.0% [70/333] vs. 18.7% [3,529/18,837]; p<0.001). Cumulative incidence of having a BC taken within 28 days was higher in COVID-19 than in non-COVID-19 patients (44.7% [149/333] vs. 33.2% [6,254/18,837]; adjusted subdistribution-hazard ratio [aSHR] 1.71, 95% confidence interval [CI] 1.47-1.99, p<0.001). The median time to discontinuation of parenteral antibiotics was longer in COVID-19 than in non-COVID-19 patients (13 days vs. 8 days; aSHR 0.73, 95%Cl 0.65-0.83, p<0.001). CONCLUSIONS: Routine electronic data could be used to inform diagnostic and antibiotic use practices in LMICs. In Indonesia, the proportion of timely blood culture is low in both COVID-19 and non-COVID-19 patients, and duration of parenteral antibiotics is longer in COVID-19 patients. Improving diagnostic and antimicrobial stewardship is critically needed

Epidemiology and characterisation of carbapenem-non-susceptible Pseudomonas aeruginosa in a large intensive care unit in Jakarta, Indonesia

The aim of this study was to describe the epidemiology and clinical impact of carbapenem-non-susceptible Pseudomonas aeruginosa (CNPA) in intensive care units (ICUs) of the national refer