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.

Specifications table

Subject	Bacterial Sequencing
Specific subject area	Genomics
Type of data	Genome sequences (DNA-Seq raw reads)
How data were acquired	Illumina MiSeq sequencing platform (Illumina, San Diego, CA, USA)
Data format	Raw sequences (FASTQ)
Parameters for data collection	Genomic DNA was extracted from purified cultures of Escherichia coli and quantified, following which libraries were prepared and quality checked for sequencing.
Description of data collection	DNA extraction was performed using the Geneaid Presto™ Mini gDNA Bacteria Kit (with lysozyme) (Geneaid, New Taipei City, Taiwan). DNA isolate purity was quantified with a Qubit® 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) using a target-specific Qubit assay (dsDNA BR Assay Kit, Thermo Fisher Scientific). Libraries were prepared using the Nextera™ DNA Flex Library Prep Kit (Illumina®) and library quality was examined using The Agilent 4200 TapeStation system (G2991AA) (Agilent, Santa Clara, CA, USA). Sequencing was performed using the Illumina MiSeq system.
Data source location	Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
Data accessibility	Raw data (FASTQ) files of Escherichia coli have been deposited in the National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/, under BioProject database: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA596854, BioSample database: (https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=596854), and Sequence Read Archive (SRA) database: https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=596854 with accession number: SRR10761126–SRR10761147.

Value of the data

• •These data shed light on the molecular biology of E. coli found in bloodstream infections.
• •These data provide insights into antibiotic resistance in E. coli, which will be beneficial to clinicians and patients.
• •The data will help us understand the genomic mechanisms underlying the severity of E. coli-caused bloodstream infections.

1. Data Description

E. coli (Gram-negative bacterial commensals) naturally exists in the human gastrointestinal tract. Pathogenicity, virulence, and multidrug resistance features of pathogenic E. coli are routinely obtained by commensal E. coli through horizontal transfer and other mechanisms. Virulent E. coli share pathogenic factors, virulence, and resistance with less virulent strains, causing overlapping pathogenesis beyond their natural capability [1].

We present whole genome sequence data of 22 E. coli isolates obtained from bloodstream infection patients admitted to Cipto Mangunkusumo National Hospital, Jakarta, Indonesia. Purified E. coli DNA was quantified using Qubit 3.0 (Table 1). The quality of library preparations was checked using the Agilent 4200 TapeStation system and found to be equal to that of the reference (Fig. 1 and Table 2). Electrophoresis strengthened these results (Fig. 2). Sequencing was performed using the Illumina MiSeq system.

Table 1.

DNA library purification and concentrations using Qubit 3.0.

Sample	Purity 260/280	Qubit 3.0 (C) (μg/ml)
RSCM_EC_0102	2	25.9
RSCM_EC_0203	2.028	42.5
RSCM_EC_0305	1.808	19.7
RSCM_EC_0406	1.939	28.1
RSCM_EC_0507	1.914	40.7
RSCM_EC_0608	1.9	30.2
RSCM_EC_0709	2.038	30.5
RSCM_EC_0911	2	19.6
RSCM_EC_1013	2.043	33
RSCM_EC_1114	2.05	49.3
RSCM_EC_1316	1.943	57
RSCM_EC_1418	1.955	21.7
RSCM_EC_1526	2.059	29.7
RSCM_EC_1628	1.95	16.3
RSCM_EC_1732	2.053	51
RSCM_EC_1833	2	42.6
RSCM_EC_1935	1.944	39.9
RSCM_EC_2036	1.864	49.3
RSCM_EC_2137	2	30
RSCM_EC_2240	2	36.9
RSCM_EC_2341	2	36
RSCM_EC_2442	2	43.2

Fig. 1.

Library size profiles using the Agilent 4200 TapeStation system. A) Reference Guide [2] and B) Experimental E. coli libraries.

Table 2.

E. coli library regions quality-checked using the Agilent 4200 TapeStation system.

Sample	From (bp)	To (bp)	Average Size (bp)	Conc. (μg/μl)	Region Molarity (nmol/l)	% of Total
RSCM_EC_0203 (A1)	314	1016	593	3.15	8.69	67.5
RSCM_EC_0305 (B1)	254	910	489	4.95	16.5	79.2
RSCM_EC_0911 (C1)	253	877	459	4.57	16.2	79.7
RSCM_EC_1114 (D1)	280	928	509	5.53	17.7	84.9
RSCM_EC_1316 (E1)	248	919	504	4.41	14.3	82.4

Fig. 2.

Electrophoresis of five E. coli DNA library samples. EL1: Genomic DNA ladder (as reference); A1: RSCM_EC_0203; B1: RSCM_EC_0305; C1: RSCM_EC_0911; D1: RSCM_EC_1114; E1: RSCM_EC_1316).

Paired-end libraries were obtained from sequencing runs (Table 3). FASTQ raw data files have been deposited in the NCBI database under BioProject accession number PRJNA596854 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA596854), BioSample database: (https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=596854) and Sequence Read Archive (SRA) accession numbers: SRR10761126–SRR10761147 (https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=596854). These data will be useful for analysing the serotypes, virulence genes, and antimicrobial resistance genes of E. coli.

Table 3.

Descriptive information for whole genome sequencing of raw E. coli data.

Sample	Total Raw Reads (Mb)	Total bases (Mbp)	GC Content (%)	BioSample Accession Number	SRA Accession Number
RSCM_EC_0102	0.56	311.8	50.4	SAMN13640292	SRS5880528
RSCM_EC_0203	0.97	503.1	50.2	SAMN13640311	SRS5880529
RSCM_EC_0305	1.7	883.5	50.2	SAMN13640332	SRS5880540
RSCM_EC_0406	1.6	875.3	50.3	SAMN13640527	SRS5880543
RSCM_EC_0507	2.2	1200	50.3	SAMN13640528	SRS5880544
RSCM_EC_0608	1.3	655.2	49.6	SAMN13640529	SRS5880545
RSCM_EC_0709	1.6	879.5	50.8	SAMN13640533	SRS5880546
RSCM_EC_0911	1.6	835	50.5	SAMN13640535	SRS5880547
RSCM_EC_1013	0.9	465.6	50.5	SAMN13640581	SRS5880548
RSCM_EC_1114	1.8	971.4	50.2	SAMN13640826	SRS5880549
RSCM_EC_1316	1.1	592.9	50.3	SAMN13640832	SRS5880530
RSCM_EC_1418	0.90	512.7	50.0	SAMN13640834	SRS5880531
RSCM_EC_1526	1.3	661.5	50.8	SAMN13640837	SRS5880532
RSCM_EC_1628	0.93	492.0	49.9	SAMN13640838	SRS5880533
RSCM_EC_1732	2.7	1500	50.0	SAMN13640846	SRS5880534
RSCM_EC_1833	1.0	562.0	50.0	SAMN13640847	SRS5880535
RSCM_EC_1935	0.92	466.6	50.7	SAMN13640849	SRS5880536
RSCM_EC_2036	1.27	665.5	50.4	SAMN13640850	SRS5880537
RSCM_EC_2137	0.46	254.2	50.4	SAMN13640852	SRS5880538
RSCM_EC_2240	0.84	476.6	50.4	SAMN13640877	SRS5880539
RSCM_EC_2341	1.4	749.6	50.6	SAMN13640878	SRS5880541
RSCM_EC_2442	2.3	1100	49.9	SAMN13640880	SRS5880542

2. Experimental Design, Materials, and Methods

2.1. Sample collection and bacteria culturing

E. coli were isolated from blood samples of bloodstream infection patients, who varied in gender and age and were admitted to Cipto Mangunkusumo National Hospital in 2018. After isolation, the E. coli were cultured in Lactose Broth medium in the laboratory facilities at the Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Indonesia.

2.2. DNA isolation and quantification

DNA extraction was performed using a Geneaid Presto™ Mini gDNA Bacteria Kit (with lysozyme). DNA sample purity was determined from the 260/280 nm absorbance values with a ratio of 1.8–2.0 indicating a pure DNA sample [2]. Pure DNA isolates were then quantified using a Qubit® 3.0 Fluorometer (Thermo Fisher Scientific) and a target-specific Qubit assay (dsDNA BR Assay Kit, Thermo Fisher Scientific). Initially, 43 DNA samples were prepared; however, 22 samples were chosen for DNA sequencing based on their high purity and adequate concentration (Table 1).

2.3. Library preparation and quality checking

DNA libraries were prepared using the Nextera™ DNA Flex Library Prep Kit (Illumina) according to the manufacturer's protocol. Five random libraries were quality checked using the Agilent 4200 TapeStation system (G2991AA). The E. coli library profile showed similarities with that of the Reference Guide of the Nextera™ DNA Flex Library Prep Kit [2]. Fig. 1 shows typical library size profiles with an average fragment size of 600 bp when analysed with a size range of 150–1500 bp. Specific region details are shown in Table 2. The library quality was also strengthened by the electrophoresis results that showed each of the five libraries having a fragment size of approximately 300–1000 bp (Fig. 2). Thus, it was demonstrated that the quality of the E. coli libraries met the Illumina MiSeq platform requirements.

2.4. Whole genome sequencing and data

The E. coli libraries were sequenced using the Illumina MiSeq platform according to the following steps: 1) Denaturing the libraries; 2) Diluting the libraries; 3) Preparing the optional PhiX control; 4) Loading the libraries onto the reagent cartridge; and 5) Setting up the sequencing run [3]. Paired-end libraries were obtained from sequencing runs (Table 3). The data sequences were deposited in the SRA under BioProject accession number PRJNA596854.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.