Evaluation of SARS-CoV-2 quantification from oropharyngeal swabs, nasopharyngeal swabs, and naso-oropharyngeal swabs: A cross-sectional study

The current naso-oropharyngeal swab for SARS-CoV-2 detection faces several problems, such as waste issues and its use for quantitative studies. This study aimed to evaluate the total RNA and viral loads from different upper respiratory tract swabs types and whether SARS-CoV-2 quantification can use the current internal control for normalization. This cross-sectional study collected positive specimens with single oropharyngeal or nasopharyngeal swabs and naso-oropharyngeal swabs. The samples were extracted, tested with qualitative RT‒PCR, and then tested with quantitative RT‒PCR. The RNA eluate was measured for the total RNA concentration. The total RNA concentration, viral load, and RNaseP Ct values were collected and analysed statistically. The positive results came from 41 oropharyngeal swabs, 34 nasopharyngeal swabs, and 36 naso-oropharyngeal swabs. The total RNA increased significantly from oropharyngeal swabs to nasopharyngeal swabs to naso-oropharyngeal swabs. Significant differences in RNaseP Ct values between groups and their correlations with total RNA were found. In addition, the increase in the total RNA and the RNaseP Ct values were unrelated to the viral load. The physical features in the naso-oropharyngeal area and the swabbing procedures could affect the total RNA but not the viral load. However, since the virus particles could present inside and outside human cells, the increase in collected human cells may not always be followed by the viral load increase. Normalization using the RNaseP Ct value became unnecessary due to the factors mentioned above. Therefore, a careful approach is needed in viral load studies of swab specimens.

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.

Comparison of Culture Results between Specimens from Corneal Scraping with Microhomogenization and Corneal Swab in Moderate and Severe Bacterial Corneal Ulcers

The purpose of this study was to compare the bacterial culture results from corneal infiltrate specimens collected using two different methods, corneal scraping followed by microhomogenization and corneal swab. This is a comparative crosssectional study, with 18 participants undergoing corneal specimen collection using each of the 2 sampling techniques. The results from the scraping and swab methods were separated and then compared using data analysis. The proportion of Gram stain results that matched the culture results for the scraping-microhomogenization technique was 6/13 (46.2%), and the proportion of Gram stain results that matched the culture results for the swab technique was 5/13 (38.5%) (McNemar test P value, 1.000; P > 0.05). The proportion of positive cultures obtained using the scraping-microhomogenization technique was 13/18 (72.2%), and the proportion of positive cultures obtained using the swab technique was 9/18 (50%) (McNemar test P value, 0.219; P > 0.05). The Kappa suitability test value for comparison of the scraping-microhomogenization technique to the corneal swab was 0.333. The specimens collected by corneal scraping followed by microhomogenization had a higher positive bacterial culture rate than those collected by corneal swab, but the results were not statistically significant. IMPORTANCE This study aimed to compare the culture results between scraping specimens with microhomogenization and corneal smears in patients with moderate to severe bacterial corneal ulcers. This study could be a guideline for treating bacterial corneal ulcers.

Performance of Xpert MTB/RIF and sputum microscopy compared to sputum culture for diagnosis of tuberculosis in seven hospitals in Indonesia

Introduction

Tuberculosis (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, <1,000 Xpert instruments were available in Indonesia as of 2020 and the Xpert supply chain has suffered interruptions.

Methods

We compared the performance of Xpert MTB/RIF and AFB smear to facilitate optimization of TB case identification. We analyzed baseline data from a cohort study of adults with pulmonary TB conducted at seven hospitals across Indonesia. We evaluated sensitivity and specificity of AFB smear and Xpert MTB/RIF using Mycobacterium tuberculosis (Mtb) culture as the gold standard, factors associated with assay results, and consistency of Xpert MTB/RIF with drug susceptibility test (DST) in detecting rifampicin resistance.

Results

Sensitivity of AFB smear was significantly lower than Xpert MTB/RIF (86.2 vs. 97.4%, p-value <0.001), but specificity was significantly better (86.7 vs. 73.3%, p-value <0.001). Performance varied by hospital. Positivity rate for AFB smear and Mtb culture was higher in subjects with pulmonary cavities and in morning sputum samples. Consistency of Xpert MTB/RIF with DST was lower in those with rifampicin- sensitive TB by DST.

Discussion

Additional evaluation using sputa from primary and secondary Indonesian health centers will increase the generalizability of the assessment of AFB smear and Xpert MTB/RIF performance, and better inform health policy.

Clinical trial registration

[https://clinicaltrials.gov/], identifier [NCT027 58236].

Case series in Indonesia: B.1.617.2 (delta) variant of SARS-CoV-2 infection after a second dose of vaccine

BACKGROUND

The B.1.617.2 (delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first discovered in Maharashtra in late 2020 and has rapidly expanded across India and worldwide. It took only 2 mo for this variant to spread in Indonesia, making the country the new epicenter of the delta variant as of July 2021. Despite efforts made by accelerating massive rollouts of current vaccines to protect against infection, cases of fully-vaccinated people infected with the delta variant have been reported.

AIM

To describe the demographic statistics and clinical presentation of the delta variant infection after the second dose of vaccine in Indonesia.

METHODS

A retrospective, single-centre case series of the general consecutive population that worked or studied at Faculty of Medicine, Universitas Indonesia with confirmed Delta Variant Infection after a second dose of vaccine from 24 June and 25 June 2021. Cases were collected retrospectively based on a combination of author recall, reverse transcription-polymerase chain reaction (RT-PCR), and whole genome sequencing results from the Clinical Microbiology Laboratory, Faculty of Medicine, Universitas Indonesia.

RESULTS

Between 24 June and 25 June 2021, 15 subjects were confirmed with the B.1.617.2 (delta) variant infection after a second dose of the vaccine. Fourteen subjects were vaccinated with CoronaVac (Sinovac) and one subject with ChAdOx1 nCoV-19 (Oxford-AstraZeneca). All of the subjects remained in home isolation, with fever being the most common symptom at the onset of illness (n = 10, 66.67%). The mean duration of symptoms was 7.73 d (± 5.444). The mean time that elapsed from the first positive swab to a negative RT-PCR test for SARS-CoV-2 was 17.93 d (± 6.3464). The median time that elapsed from the second dose of vaccine to the first positive swab was 87 d (interquartile range: 86-128).

CONCLUSION

Although this case shows that after two doses of vaccine, subjects are still susceptible to the delta variant infection, currently available vaccines remain the most effective protection. They reduce clinical manifestations of COVID-19, decrease recovery time from the first positive swab to negative swab, and lower the probability of hospitalization and mortality rate compared to unvaccinated individuals.

Gaps in antimicrobial stewardship programmes in Asia: a survey of 10 countries

OBJECTIVES

To determine antimicrobial stewardship (AMS) programme practices in Asian secondary- and tertiary-care hospitals.

METHODS

AMS programme team members within 349 hospitals from 10 countries (Cambodia, India, Indonesia, Japan, Malaysia, Pakistan, the Philippines, Taiwan, Thailand and Vietnam) completed a questionnaire via a web-based survey link. The survey contained questions as to whether 12 core components deemed essential for AMS programmes were implemented.

RESULTS

Overall, 47 (13.5%) hospitals fulfilled all core AMS programme components. There was a mean positive response rate (PRR) of 85.6% for the responding countries in relation to a formal hospital leadership statement of support for AMS activities, but this was not matched by budgeted financial support for AMS activities (mean PRR 57.1%). Mean PRRs were ≥80.0% for the core AMS team comprising a physician or other leader responsible for AMS activities, a pharmacist and infection control and microbiology personnel. Most hospitals had access to a timely and reliable microbiology service (mean PRR 90.4%). Facility-specific antibiotic treatment guidelines for common infections (mean PRR 78.7%) were in place more often than pre-authorization and/or prospective audit and feedback systems (mean PRR 66.5%). In terms of AMS monitoring and reporting, PRRs of monitoring specific antibiotic use, regularly publishing AMS outcome measures, and the existence of a hospital antibiogram were 75.1%, 64.4% and 77.9%, respectively.

CONCLUSIONS

Most hospitals participating in this survey did not have AMS programmes fulfilling the requirements for gold standard AMS programmes in hospital settings. Urgent action is required to address AMS funding and resourcing deficits.

Characteristics of Drug-sensitive and Drug-resistant Tuberculosis Cases among Adults at Tuberculosis Referral Hospitals in Indonesia

As Indonesia's rifampin resistance testing rates are lower than global testing rates per the 2020 WHO global tuberculosis (TB) report, prevalence of multidrug-resistant TB may be underestimated. Our study aimed to evaluate prevalence and patterns of TB drug resistance (DR) within Indonesia. We conducted a cross-sectional analysis of baseline data collected from 2017-2018 as part of a cohort study of adults with presumed pulmonary TB at 7 DR-TB referral hospitals in Indonesia. Bacteriological examinations (acid-fast bacilli, GeneXpert, sputum culture) and drug-susceptibility testing were performed following the guidelines of the National TB Program. Of 447 participants with complete bacteriological examinations, 312 (69.8%) had positive sputum cultures for Mycobacterium tuberculosis. The proportion of MDR and pre-extensively drug-resistant was higher in previously treated compared with newly diagnosed participants (52.5% [73/139] versus 15% [26/173]). Compared with drug-sensitive case, drug-resistant TB was associated with cavities. Given the difference between rates of DR in TB referral hospitals from our study compared with the WHO survey in 2019 that showed 17.7% and 3.3% DR among previously treated and newly diagnosed participants globally, further characterization of Indonesia's TB epidemiology in the general population is needed. Strategies, including public policies to optimize case finding, strengthen capacity for resistance testing, and prevent loss to follow-up will be critical to reduce the burden of TB in Indonesia.

Antimicrobial activity of homemade WHO ethanol-based hand rub solution in pediatric department, Dr. Cipto Mangunkusumo National Referral Hospital

Background Hand hygiene is essential in reducing healthcare-associated infections. Alcohol-based hand rub solutions have been reported to have superior antimicrobial efficacy on both bacteria and lipophilic viruses compared to washing with hand soap. In low- and middle-income countries, the cost of infection control poses a challenge. Our hospital produced an ethanol-based hand rub based on a WHO formulation to reduce the infection prevention costs. Objectives To identify the antimicrobial activity of a WHO ethanol-based hand rub solution against bacterial contamination on the hands of healthcare workers at the Department of Child Health, Dr. Cipto Mangunkusumo National Referral Hospital. Methods This cross-sectional study was performed on the hands of healthcare workers (physicians and nurses) working in the Department of Child Health, Dr. Cipto Mangunkusumo National Referral Hospital, Jakarta. A total of 225 specimens from 75 subjects were obtained by collecting swabs on both hands before and after participants worked in the Department of Child Health, Dr. Cipto Mangunkusumo General Hospital. Bacterial culture tests were performed to identify gram-positive and gram-negative bacteria. Bacteria were grouped into no-growth/Bacillus sp, Enterobacteriaceae, cocci, and non-fermenter groups. Results The use of our WHO ethanol-based hand rub solution, generally resulted in a statistically significant decrease in bacterial growth from 84 to 54.6%, before compared to after the hand rub was performed. In more detail, there was a 72.7% decrease in Enterobacteriaceae, a 71.4% decrease in non-fermenters, an 8.6% decrease in cocci and a 44.1% increase in the number of specimens showing no growth bacteria/Bacillus sp. Conclusion Our WHO ethanol-based hand rub has significant antimicrobial activity for common nosocomial pathogens (e.g., Staphylococcus aureus, P. aeruginosa, and K. pneumoniae).

Optimizing antibiotic use in Indonesia: A systematic review and evidence synthesis to inform opportunities for intervention

Background

A major driver of antimicrobial resistance (AMR) and poor clinical outcomes is suboptimal antibiotic use, although data are lacking in low-resource settings. We reviewed studies on systemic antibiotic use (WHO ATC/DDD category J01) for human health in Indonesia, and synthesized available evidence to identify opportunities for intervention.

Methods

We systematically searched five international and national databases for eligible peer-reviewed articles, in English and Indonesian, published between 1 January 2000 and 1 June 2021 including: (1) antibiotic consumption; (2) prescribing appropriateness; (3) antimicrobial stewardship (AMS); (4) consumers' and providers' perceptions. Two independent reviewers included studies and extracted data. Study-level data were summarized using random-effects model meta-analysis for consumption and prescribing appropriateness, effect direction analysis for antimicrobial stewardship (AMS) interventions, and qualitative synthesis for perception surveys. (PROSPERO: CRD42019134641).

Findings

Of 9323 search hits, we included 100 reports on antibiotic consumption (20), prescribing appropriateness (49), AMS interventions (13), and/or perception (25) (8 categorized in >1 domain). The pooled estimate of overall antibiotic consumption was 134.8 DDD per 100 bed-days (95%CI 82.5-187.0) for inpatients and 121.1 DDD per 1000 inhabitants per day (10.4-231.8) for outpatients. Ceftriaxone, levofloxacin, and ampicillin were the most consumed antibiotics in inpatients, and amoxicillin, ciprofloxacin, and cefadroxil in outpatients. Pooled estimates for overall appropriate prescribing (according to Gyssens method) were 33.5% (18.1-53.4) in hospitals and 49.4% (23.7-75.4) in primary care. Pooled estimates for appropriate prescribing (according to reference guidelines) were, in hospitals, 99.7% (97.4-100) for indication, 84.9% (38.5-98.0) for drug choice, and 6.1% (0.2-63.2) for overall appropriateness, and, in primary care, 98.9% (60.9-100) for indication, 82.6% (50.5-95.7) for drug choice and 10.5% (0.8-62.6) for overall appropriateness. Studies to date evaluating bundled AMS interventions, although sparse and heterogeneous, suggested favourable effects on antibiotic consumption, prescribing appropriateness, guideline compliance, and patient outcomes. Key themes identified in perception surveys were lack of community antibiotic knowledge, and common non-prescription antibiotic self-medication.

Interpretation

Context-specific intervention strategies are urgently needed to improve appropriate antibiotic use in Indonesian hospitals and communities, with critical evidence gaps concerning the private and informal healthcare sectors.

Funding

Wellcome Africa Asia Programme Vietnam.

91. Gaps and Opportunities in Antimicrobial Stewardship Programs in Asia: A Survey of 10 Countries

Background

Most studies on hospital antimicrobial stewardship (AMS) status and practices are conducted in the west, and there is a lack of such data from Asian countries. The objective of this survey was to determine existing AMS practices and gaps, and challenges in implementing AMS programs in secondary and tertiary acute-care hospitals in 10 Asian countries.

Methods

A 70-item questionnaire was disseminated to hospitals fulfilling inclusion criteria and responses were collected from 10 April 2020 to 9 April 2021. The survey, specific to the Asian hospital setting, enquired about hospital leadership support for AMS; AMS team membership and training; AMS interventions; AMS monitoring and reporting; hospital infrastructure; and education. These were subdivided into core and supplementary components, adapted from the Transatlantic Taskforce on Antimicrobial Resistance set of core and supplementary indicators for hospital AMS programs, and the US Centers for Disease Control and Prevention checklist for core elements of hospital AMS programs.

Results

A total of 349 hospitals from Cambodia, India, Indonesia, Japan, Malaysia, Pakistan, Philippines, Taiwan, Thailand and Vietnam responded. Overall, only 47 hospitals fulfilled all 12 core components, and there were inter-country differences in terms of performance. The hospitals generally did well in terms of the AMS team (ie, comprising at least a physician leader responsible for AMS activities, a pharmacist, and infection control and microbiology personnel), and access to a timely and reliable microbiology service, with mean positive response rates (PRR) of ≥ 80% for these indicators (Figure 1). In the core components of AMS program interventions, and AMS monitoring and reporting, the lower mean PRR ( > 60%) revealed that Asia has wider gaps in these areas versus gold standards. Although many hospitals had formal hospital leadership statements to support AMS (mean PPR 85.6%), this was not always matched by allocated financial support for AMS activities (mean PPR 57.1%).

Figure 1

Conclusion

For all core components of an AMS program, most Asian hospitals participating in this survey fell short of international gold standards. Inter-country differences in gaps highlight that country-specific solutions are needed to improve current standards in AMS.

Disclosures

Tetsuya Matsumoto, MD; PhD, MSD (Speaker's Bureau)Pfizer (Speaker's Bureau)

Procalcitonin (PCT)-guided antibiotic stewardship in Asia-Pacific countries: adaptation based on an expert consensus meeting

Introduction Recently, an expert consensus on optimal use of procalcitonin (PCT)-guided antibiotic stewardship was published focusing mainly on Europe and the United States. However, for Asia-Pacific countries, recommendations may need adaptation due to differences in types of infections, available resources and standard of clinical care. Methods Practical experience with PCT-guided antibiotic stewardship was discussed among experts from different countries, reflecting on the applicability of the proposed Berlin consensus algorithms for Asia-Pacific. Using a Delphi process, the group reached consensus on two PCT algorithms for the critically ill and the non-critically ill patient populations. Results The group agreed that the existing evidence for PCT-guided antibiotic stewardship in patients with acute respiratory infections and sepsis is generally valid also for Asia-Pacific countries, in regard to proposed PCT cut-offs, emphasis on diagnosis, prognosis and antibiotic stewardship, overruling criteria and inevitable adaptations to clinical settings. However, the group noted an insufficient database on patients with tropical diseases currently limiting the clinical utility in these patients. Also, due to lower resource availabilities, biomarker levels may be measured less frequently and only when changes in treatment are highly likely. Conclusions Use of PCT to guide antibiotic stewardship in conjunction with continuous education and regular feedback to all stakeholders has high potential to improve the utilization of antibiotic treatment also in Asia-Pacific countries. However, there is need for adaptations of existing algorithms due to differences in types of infections and routine clinical care. Further research is needed to understand the optimal use of PCT in patients with tropical diseases.

Multimodal intervention to reduce acquisition of carbapenem-non-susceptible Gram-negative bacteria in intensive care units in the National Referral Hospital of Indonesia: An interrupted time series study

PURPOSE

To evaluate a low-cost multimodal intervention on the acquisition of carbapenem-non-susceptible Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa by patients in low-resource intensive care units.

MATERIALS AND METHODS

We performed a quasi-experimental study in a referral hospital in Jakarta, Indonesia: pre-intervention phase 1 (2013-2014), intervention phase 2 (2014-2015) and post-intervention phase 3 (2015-2016). The intervention was hand hygiene promotion and environmental cleaning and disinfection combined with patient disinfection and cohorting. The primary outcome was acquisition of resistant bacteria per 100 patient-days at risk, which was assessed by active microbiological surveillance and analysed with a multilevel Poisson segmented regression model.

RESULTS

In phase 1 (387 patients), the acquisition rate was 4.3/100 days for carbapenem-non-susceptible A. baumannii versus 1.1/100 days for both K. pneumoniae and P. aeruginosa. There was a significant step change from phase 1 to phase 3 (361 patients) in the acquisition of carbapenem-non-susceptible strains, the incidence rate ratio (IRR) was 0.343 (99%CI: 0.164-0.717). This significant change was mainly due to reduced acquisitions of resistant A. baumannii (IRR 0.4, 99%CI: 0.181-1.061). Negative confounding was observed.

CONCLUSION

A multimodal intervention to prevent acquisition of resistant pathogens is feasible and may be effective in ICUs in lower-middle income countries.

New approach for the identification of potentially toxigenic Corynebacterium sp. using a multiplex PCR assay

In diphtheria laboratory examinations, the PCR test can be applied to isolates and clinical specimens. This study aimed to develop a PCR assay to identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types. Seven reference isolates, four synthetic DNA samples, 36 stored isolates, and 487 clinical samples used for PCR optimization. The PCR results was confirmed by DNA sequence analysis. The results of the PCR examination of the 7 reference isolates and 36 stored isolates were similar to the results obtained using conventional methods as gold standard, both for diphtheria-causing and non-diphtheria-causing bacteria. The validation of the PCR results using DNA sequence analysis showed that there was no mispriming or misamplification. The multiplex PCR assay developed in this study could correctly identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types not yet covered by established PCR methods.

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)

Consideration of the Cycle Threshold Values from Real-Time RT-PCR SARS-CoV-2 Interpretation for the Clinicians: Analysis of 339 Positive Cases from a Referral Laboratory in Jakarta, Indonesia

BACKGROUND

real-time RT-PCR was recommended by WHO for COVID-19 diagnosis. The cycle threshold (Ct) values were expected to have an association with clinical manifestation. However, the diagnostic modalities such as quantitative molecular detection and virus isolation were not yet available for the routine test. This study has been conducted to analyze the relationship between the Ct values of qualitative rRT-PCR and the clinical manifestation and to describe the factors determining the result.

METHODS

from March to April 2020, specimens were sent to our laboratory from different healthcare centers in Jakarta. The patient's characteristic and clinical manifestation were extracted from the specimen's epidemiology forms. The specimens extracted and tested using rRT-PCR, and the Ct value were collected. The data were analyzed using the appropriate statistic test.

RESULTS

from 339 positive results, the mild to moderate case was 176 (52%) and the severe cases was 163 (48%). Female was dominant in the mild to moderate cases (58%), while the male was prevalent in the severe cases (60%). The median age for mild to moderate case was 35 years old and severe cases was 49 years old. Statistical analysis found relationship between both group with gender (p = 0.001) and age (p < 0.001), but not with the Ct value.

CONCLUSION

many variables in specimen sampling and processing could affect the Ct value result. In addition, the disease's severity was depended with the host immune response, regardless the number of virus. There was suggested no significant difference between the Ct values of mild-moderate and severe COVID-19, and thus should not be loosely interpreted.

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 bla_NDM. 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.

Clinical Practice Guidelines in Complicated Intra-Abdominal Infection 2018: An Indonesian Perspective

BACKGROUND

The occurrence of complicated intra-abdominal infections (cIAI) remains high despite system improvement in accordance with Joint Commission International because of heterogeneity of management. However, published clinical practice guidelines (CPGs) were not feasible to be implemented because these guidelines were not specific to Indonesian characteristics. Thus, a national CPG should be developed to minimize heterogeneity in the management of cIAI in Indonesia.

METHODS

We developed a CPG on cIAI through the adaptation of published CPGs. The process proceeded in steps recommended by ADAPTE. Published CPGs were critically appraised using Appraisal of Guidelines for Research and Evaluation (AGREE) II critical appraisal tools. For a specific updated CPG, the analysis was performed using Checklist for the Reporting of Updated Guidelines (CheckUp). Appropriate statements and recommendations in selected CPGs were adapted into our CPG with consideration of Indonesian characteristics. The recommendations were established by the hierarchy of evidence on Grading of Recommendations Assessment, Development and Evaluation (GRADE). The approval of the recommendation draft was performed using the Delphi method.

RESULTS

Sixty-eight full-text guidelines were downloaded from several sites. Thirty-three CPGs were related to intra-abdominal infection and 18 others were specific on CPG on intra-abdominal infection and cIAI. On review of these 18 CPGs, 13 were strongly recommended, three were recommended, and two were not recommended. On review updated CPGs, five updated CPGs were found, all with the same score. Two of the strongly recommended updated CPGs had been published in 2016 and 2017, i.e. recommendations by the World Society of Emergency Surgery 2016 consensus conference and revised CPG of the Surgical Site Infection Society. There were a total of 84 statements and recommendations developed and approved by the task force through using the Delphi method.

CONCLUSIONS

This guideline summarizes the definition, classification, pathophysiology, etiology, risk factors, assessments, and management of cIAI. Evidence-based recommendations have been developed with consideration of Indonesian-specific characteristics.

Presentation, etiology, and outcome of brain infections in an Indonesian hospital: A cohort study

Background

Little detailed knowledge is available regarding the etiology and outcome of CNS infection, particularly in HIV-infected individuals, in low-resource settings.

Methods

From January 2015 to April 2016, we prospectively included all adults with suspected CNS infection in a referral hospital in Jakarta, Indonesia. Systematic screening included HIV testing, CSF examination, and neuroimaging.

Results

A total of 274 patients with suspected CNS infection (median age 26 years) presented after a median of 14 days with headache (77%), fever (78%), seizures (27%), or loss of consciousness (71%). HIV coinfection was common (54%), mostly newly diagnosed (30%) and advanced (median CD4 cell count 30/µL). Diagnosis was established in 167 participants (65%), including definite tuberculous meningitis (TBM) (n = 44), probable TBM (n = 48), cerebral toxoplasmosis (n = 48), cryptococcal meningitis (n = 14), herpes simplex virus/varicella-zoster virus/cytomegalovirus encephalitis (n = 10), cerebral lymphoma (n = 1), neurosyphilis (n = 1), and mucormycosis (n = 1). In-hospital mortality was 32%; 6-month mortality was 57%. The remaining survivors had either moderate or severe disability (36%) according to Glasgow Outcome Scale.

Conclusion

In this setting, patients with CNS infections present late with severe disease and often associated with advanced HIV infection. Tuberculosis, toxoplasmosis, and cryptococcosis are common. High mortality and long-term morbidity underline the need for service improvements and further study.

Endemic carbapenem-nonsusceptible Acinetobacter baumannii-calcoaceticus complex in intensive care units of the national referral hospital in Jakarta, Indonesia

Background

Carbapenem-nonsusceptible A. baumannii-calcoaceticus complex have emerged worldwide, but the epidemiology in Indonesian hospitals has not been studied.

Methods

A prospective observational study was performed on the intensive care units (ICUs) of the national referral hospital in Jakarta-Indonesia, in 2013 and 2014. All consecutive adult patients admitted and hospitalized for >48 h in ICUs were included. Basic and clinical data at admission were recorded. Carbapenem-nonsusceptible A. baumannii-calcoaceticus complex from clinical cultures and standardized screening were included. Environmental niches and healthcare workers (HCWs) were also screened. PCR was used to detect carbapenemase genes, and Raman spectroscopy as well as multilocus sequence typing (MLST) for typing.

Results

Of 412 included patients, 69 (16.7%) carried carbapenem-nonsusceptible A. baumannii-calcoaceticus complex on admission, and 89 (25.9%) became positive during ICU stay. The acquisition rate was 43 per 1000 patient-days at risk. Six isolates were cultured from environment and one from a HCW. Acquisition of carbapenem-nonsusceptible A. baumannii-calcoaceticus complex was associated with longer ICU stay (median interquartile range [IQR]: 11 days [5-18], adjusted hazard ratio [aHR]: 2.56 [99% confidence interval (CI):1.76-3.70]), but not with mortality (adjusted odds ratio: 1.59 [99%CI: 0.74-3.40] at the chosen level of significance). The bla_OXA-23-like gene was detected in 292/318 (91.8%) isolates, including isolates from the environment and HCW. Typing revealed five major clusters. Sequence types (ST)195, ST208, ST218, ST642 as well as new STs were found. The dominant clone consisted of isolates from patients and environment throughout the study period.

Conclusions

Carbapenem-nonsusceptible A. baumannii-calcoaceticus complex are endemic in this setting. Prevention requires source control and limiting transmission of strains.

Trial registration

The study was retrospectively registered at www.trialregister.nl (No:5541). Candidate number: 23,527, NTR number: NTR5541, Date registered NTR: 22nd December 2015.

Optimal Amikacin Levels for Patients with Sepsis in Intensive Care Unit of Cipto Mangunkusumo Hospital, Jakarta, Indonesia

BACKGROUND

Amikacin is one of the antibiotics of choice for sepsis and septic shock. Pharmacokinetic of amikacin can be influenced by septic condition with subsequent effect on its pharmacodynamic. At Cipto Mangunkusumo Hospital (RSCM), Jakarta, adult patients in the ICU were given standard amikacin dose of 1 g/day, however the achievement of optimal plasma level had never been evaluated. This study aimed to evaluate whether the optimal plasma level of amikacin was achieved with the use of standard dose in septic conditions.

METHODS

all septic patients admitted to the intensive care unit of a national tertiary hospital receiving standard dose of 1g/day IV amikacin during May-September 2015 were included in this study. Information of minimum inhibitory concentration MIC was obtained from microbial culture. Cmax of amikacin was measured 30 minutes after administration and optimal level was calculated. Optimal amikacin level was considered achieved when Cmax/MIC ratio >8.

RESULTS

average Cmax achieved for all patients was 86.4 (43.5-238) µg/mL with 87% patients had Cmax of >64 µg/mL.MIC data were available for 7 of 23 patients. MICs for identified pathogens were 0.75 - >256 µg/mL (K. pneumonia), 0.75 - >256 µg/mL(A. baumanii), 1.5 - >256 µg/mL (P. aeruginosa)and 0.75 - 16 µg/mL(E. coli). Four out of seven patients achieved optimal amikacin level.

CONCLUSION

despite high Cmax, only half of the patients achieved optimal amikacin level with highly variable Cmax. This study suggests that measurement of Cmax and MIC are important to optimize septic patients management.

Comparison of minimal inhibitory and bactericidal capacity of oral penicillin V with benzathine penicillin G to Streptococcus beta--hemolyticus group A in children with rheumatic heart disease

Background Injection ofbenzatine penicillin G (BPG) every 28days is still the drug of choice for secondary prevention of rheu-matic heart disease (RHD). BPG sometimes poses problems dueto pain at the injection site, possible anaphylaxis, and is not alwaysavailable. Some centers choose oral penicillin over BPG.Objectives To compare minimal inhibitory capacity (MIC) andminimal bactericidal capacity (MBC) of oral penicillin V serumwith those of BPG among SGA infected RHD.Methods This was a clinical trial with crossover design study tocompare MIC of penicillin V and BPG. Outcome measures wereMIC and MBC. Statistical analysis was performed using pairedt-test and wilcoxon test.Result There were 32 subjects consisted of 17 males and 15females. The mean value of MIC and MBC serum of penicillinV were 0.031 and 0.125. The mean value of MIC and MBCserum of BPG3 were 0.094 and 0.031. Respectively the MICof penicillin V was similar to that of BPGy The mean value ofMIC and MBC of BPG4 were 0.125 and 0.250. Respectively theMIC of penicillin V was significantly higher than that of BPG 4.The MBC of penicillin V was significantly higher than that ofBPG 4. The MIC ofBPG 3 was similar to that ofBPG 4• The MBCof BPG 3 was similar to that of BPG 4.Conclusions The MIC of penicillin V was similar to that ofBPG 3,the MBC of oral penicillin V was higher than that ofBPG 3• TheMIC and MBC of penicillin V was higher than those of BPG 4.

Detection of carbapenemase encoding genes in Enterobacteriace, Pseudomonas aeruginosa, and Acinetobacter baumanii isolated from patients at Intensive Care Unit Cipto Mangunkusumo Hospital in 2011

AIM

to determine the prevalence of carbapenemase encoding genes (blaIMP-1, blaVIM-2, blaKPC-2, blaOXA-48, and blaNDM-1) of carbapenem-resistant Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumanii isolated from the intensive care unit patients as pathogens, in Cipto Mangunkusumo hospital (ICU-RSCM) in 2011.

METHODS

we examined the carbapenemase encoding genes in the clinical microbiology laboratory (LMK FKUI/RSCM). Duplex- and simplex PCR methods were conducted to detect the resistant genes.

RESULTS

we found 4 (5%) P. aeruginosa strains carry blaIMP-1 gene and all were isolated from sputum specimens. The prevalence of carbapenem resistant among Gram-negative bacilli isolated from ICU-RSCM, are Enterobacteriaceae 27.6%, P. aeruginosa 21.9%, and A. baumannii 50.5%. The New Delhi Metallo--lactamase encoding gene (blaNDM-1) was detected in 1 K. pneumonia isolated from sputum as well. The other genes, i.e. blaKPC-2, blaVIM-2, and blaOXA-48 were not found in any isolates. The absence of other genes indicated that other mechanisms may play a role in the occurrence of carbapenem resistance in pathogens isolated in ICU-RSCM.

CONCLUSION

this study confirmed that the prevalence of carbapenems resistant Gram-negative bacilli in ICU-RSCM in 2011 was high. The carbapenemase encoding genes, which were detected among the carbapenems resistant Gram-negative bacilli, were blaIMP-1 and blaNDM-1.

Invasive pneumococcal disease among hospitalized children aged 28 days to 60 months in Jarkarta

Streptococcus pneumoniae is a leading cause of morbidity and mortality among children worldwide. Prevention of invasive pneumococcal disease (IPD) with a pneumococcal conjugate vaccine (PCV) is an effective approach to reduce the burden of pneumococcal disease. Nationwide epidemiological data is required prior to considering universal pneumococcal immunization for Indonesia. This preliminary study aimed to quantify the burden of IPD among hospitalized children at Cipto Mangunkusumo Hospital and Fatmawati Hospital, Jakarta. We studied 205 subjects aged 28 days to 60 months who were admitted with the diagnosis of pneumonia, meningitis, sepsis, and suspected occult bacteremia. Streptococcus pneumoniae was isolated from 1 of 205 blood specimens, giving an IPD proportion of 0.5%. The IPD case in this study was a 3-month-old baby with meningitis and bilateral lobar pneumonia. The Quellung test demonstrated serotype 7F. The isolate was susceptible to amoxicillin and Cotrimoxazole. Incidence of IPD could not be calculated due to low number of cases; this underscores the importance of surveillance of pneumococcal disease in Indonesia.

Trends in antimicrobial susceptibility of gram-negative bacteria isolated from blood in Jakarta from 2002 to 2008

BACKGROUND

This study examined the susceptibility of Gram-negative bacteria in the bloodstream to antimicrobials with the aim of providing information relevant to the guidance of therapy.

METHODOLOGY

Blood specimens received by the Laboratory of Clinical Microbiology, Faculty of Medicine, University of Indonesia, from 2002 to 2008, were analyzed for the presence of Gram-negative bacteria and their susceptibility to four antibiotic groups frequently administered in hospitals and community settings.

RESULTS

During the seven-year period leading up to 2008, approximately 68% of Gram-negative bacteria were identified among all positive isolates from blood specimens. The eight most frequent species found were Acinetobacter anitratus (25.8%), Pseudomonas aeruginosa (19.5%), Klebsiella pneumoniae subsp. pneumoniae (14.5%), Enterobacter aerogenes (8%), Salmonella Typhi (7.5%), Escherichia coli (6.2%), Alcaligenes faecalis (5.6%) and Klebsiella oxytoca (3.2%). At 80% susceptibility or greater, Ceftriaxone and Cefotaxime were active only on E. coli and S. Typhi. Cefepime demonstrated activity on all eight species tested except K. pneumonia while Amikacin showed activity against five species, A. faecalis, E. aerogenes, E. coli, K. pneumoniae subsp. pneumoniae and S. Typhi. Gentamycin was active against three species: E. aerogenes, K. oxytoca and S. Typhi. Ciprofloxacin and Levofloxacin significantly differed in their spectrum: while Ciprofloxacin was active against four of the eight species tested (E. aerogenes, E. coli, K. oxytoca, and S. Typhi ), Levofloxacin was similar to Cefepime and was active against all eight species except K. pneumoniae subsp. pneumonia.

CONCLUSIONS

Since antimicrobials are broadly used in Jakarta, it is important that the information captured in this study be disseminated.