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

Nelwan, Erni Juwita; Puspandari, Nelly; Paramita, Rafika Indah; Erlina, Linda; Renesteen, Editha; Fadilah, Fadilah

doi:10.1016/j.dib.2020.105631

Cited by 5 publications

(3 citation statements)

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“…The ages (25-34), 34 (49.3%), where more prevalence in women has cervicitis than other ages. These findings disagree with (Zhang, et al, 2018) who reported that among women with cervical intraepithelial lesions aged 65-69 years (38.8%) was significantly higher than that of the other age groups [11]. The mean± SD, of tumor marker Ca125 there were a highly significant differences between patient (30.33±1.09) and the healthy control (19.40±0.68), these results were matched with who reported that the tumors biomarker CA125 has been used as the primary ovarian cancer marker for the past four decades and gave a highly significant levels [12].…”

Section: Discussioncontrasting

confidence: 77%

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The Sequence of Prostaglandin-Endoperoxide Synthase 2 Gene in Women with Cervicitis

Ahlial

Mohammed

Khalaf

2022

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Cervicitis is a clinical syndrome characterized by inflammation of primarily the columnar epithelium of the uterine endocervix. It can be acute or chronic. Prostaglandin endo peroxide synthase2 (Cyclooxygenase-2) is a key enzyme in prostaglandin synthesis, which is coded by the PTGS2 gene, and recognized as the master switch that activates the inflammatory response; its induction leads to the biosynthesis of prostaglandins. The current study aims to determine the CA125, CA 19.9, and, CA 15.3 markers level and their relationship with the COX-2 gene. Venous blood samples were obtained from 100 women with cervicitis whose ages ranged from 18 to 60 years, and 100 healthy women as a control group. Detection of CA19-9, CA- 125 and CA 15-3 markers was performed by using Cobas E411 analyzer while the CRP test was detected by using Afias CRP instrument. The conventional PCR was used for gene detection and DNA sequencing. The mean± SD of Ca125, CA15.3 and CRP showed a highly significant differences between patient (30.33±1.09), (22.82±1.07), (88.06±5.88) respectively and the healthy control (19.40±0.68), (18.34±0.77), (6.73±0.12) respectively-value >0.001. The mutation in PTGS2 gene with highly CA125 marker 100(100%) and CRP levels 20(80%), while in CA15.3 marker 3(15%) and CA19.9 marker 1(5%). The mutation occurrence in analysis of rs20417 NSP of PTGS2 gene with wild CC GG and the variation C>G G>C.

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Section: Discussioncontrasting

confidence: 77%

“…Genomic DNA was isolated from Blood Sample according to the protocol of Geneaid Extraction (Presto™ Mini g DNA Kit Geneaid, Taiwan) [11].…”

Section: Dna Extractionmentioning

confidence: 99%

The Sequence of Prostaglandin-Endoperoxide Synthase 2 Gene in Women with Cervicitis

Ahlial

Mohammed

Khalaf

2022

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“…coli u sing a Geneaid Presto TM Mini gDNA Bacteria Kit. All of the isolation and whole genome sequencing methods of 22 samples of Escherichia coli were described in Nelwan, et al , 2020 [ 15 ]. This research was performed in strict conformity with the suggestions in the guide of Helsinki Declaration and the research protocol was approved by Health Research Ethics Committee, National Institute of Health Research and Development (HREC-NIHRD) with protocol approval number: LB.02.01/KE.014/2019.…”

Section: Methodsmentioning

confidence: 99%

Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing

et al. 2020

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Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

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Genomic and functional potential of the immobilized microbial consortium MCSt-1 for wastewater treatment

Jha

Dafale

Hathi

et al. 2021

Science of The Total Environment

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

Cited by 5 publications

References 1 publication

The Sequence of Prostaglandin-Endoperoxide Synthase 2 Gene in Women with Cervicitis

The Sequence of Prostaglandin-Endoperoxide Synthase 2 Gene in Women with Cervicitis

Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing

Genomic and functional potential of the immobilized microbial consortium MCSt-1 for wastewater treatment

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