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

ABSTRACT: 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.

SUBMITTER: Nelwan EJ

PROVIDER: S-EPMC7210415 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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

Nelwan Erni Juwita EJ Puspandari Nelly N Paramita Rafika Indah RI Erlina Linda L Renesteen Editha E Fadilah Fadilah F

Data in brief 20200430

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, Ja ...[more]

PMID: 32395590

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Project description: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 blaOXA-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.

Project description:BackgroundHand hygiene (HH) is considered to be the single most effective measure in preventing healthcare-associated infections. However, HH compliance rates among nurses and doctors in hospitals are often very low. Few studies have addressed HH compliance in Indonesia, performed interventions to increase HH compliance, and none have had long-term follow-up. We, therefore, addressed this issue by performing long-term follow-up after a multifaceted intervention in the intensive care unit (ICU) setting.MethodsThis was an observational, prospective, before-and-after intervention study (May-September 2014, February-April 2017). We measured HH knowledge and HH compliance before (at baseline) and directly after a multifaceted improvement program (post-intervention) and performed a re-evaluation three years later. The multifaceted improvement program included education, feedback, reminders, interviews and the use of role models. The study involved nurses and physicians working in two ICUs of the Dr. Cipto Mangunkusumo Hospital in Jakarta.ResultsA total of 97 at baseline, and 72 at post-intervention HH knowledge questionnaires were completed. There was a statistically significant improvement in the median overall HH knowledge score at post-intervention (from 15 to 22, p < 0.001). There was no significant difference between the two ICUs. The overall HH compliance was 27% at baseline and significantly improved to 77% post-intervention (p < 0.001). For all five HH moments, the compliance of nurses and physicians separately improved significantly from the baseline phase to the post-intervention phase (p < 0.001), except for 'moment 3' (after body fluid exposure), for which baseline rates were already high. Most of the compliance rates were significantly lower in both groups of healthcare workers upon follow-up three years later. Overall, the HH compliance of the nurses was significantly better than the physicians' compliance (p = 0.005).ConclusionsOur multifaceted improvement program, for nurses and physicians of the ICUs in the largest hospital of Indonesia, resulted in a significant improvement of the HH knowledge and HH compliance, but HH compliance levels waned over time after the intervention, indicating a need for continued monitoring and repeated interventions.Trial registrationThe study was registered at www.trialregister.nl (No: 5541). Candidate number: 23527, NTR number: NTR5541, Date registered NTR: 22-DECEMBER-2015.

Project description:ObjectiveA 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/methodsAdult 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.ResultsTwenty-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.ConclusionsNDM-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 registrationThe 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.

Project description:BackgroundPre-hospital and emergency services in Indonesia are still developing. Despite recent improvements in the Indonesian healthcare system, issues with the provision of pre-hospital and emergency services persist. The demand for pre-hospital and emergency services has not been the subject of previous research and, therefore, has not been fully understood. Our research explored the utilization of emergency medical services by patients attending hospital emergency departments in Jakarta, Indonesia.MethodsThe study used a cross-sectional survey design involving five general hospitals (four government-funded and one private). Each patient's demographic profile, medical conditions, time to treatment, and mode of transport to reach the hospital were analysed using descriptive statistics.ResultsA total of 1964 (62%) patients were surveyed. The median age of patients was 44 years with an interquartile range (IQR) of 26 to 58 years. Life-threatening conditions such as trauma and cardiovascular disease were found in 8.6 and 6.6% of patients, respectively. The majority of patients with trauma travelled to the hospital using a motorcycle or car (59.8%). An ambulance was used by only 9.3% of all patients and 38% of patients reported that they were not aware of the availability of ambulances. Ambulance response time was longer as compared to other modes of transportation (median: 24 minutes and IQR: 12 to 54 minutes). The longest time to treatment was experienced by patients with neurological disease, with a median time of 120 minutes (IQR: 78 to 270 minutes). Patients who used ambulances incurred higher costs as compared to those patients who did not use ambulances.ConclusionThe low utilization of emergency ambulances in Jakarta could be contributed to patients' lack of awareness of medical symptoms and the existence of ambulance services, and patients' disinclination to use ambulances due to high costs and long response times. The emergency ambulance services can be improved by increasing population awareness on symptoms that warrant the use of ambulances and reducing the cost burden related to ambulance use.

Dataset Information

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

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

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