Draft genome sequencing data of Enterococcus faecium BT22, a vancomycin-resistant opportunistic pathogen isolated from hospital effluents

A vancomycin-resistant Gram-positive bacterium of the genus Enterococcus, designated as BT22, was isolated from untreated hospital effluents at Chettia Chlef Hospital. The complete genome of strain BT22 was sequenced using the Illumina MiSeq platform, revealing a total length of 2,577,707 bp, with 2462 coding sequences (CDS) and an average G+C content of 38.00 mol%. Phylogenomic analyses confirmed that strain BT22 belongs to the same species as Enterococcus faecium AVS0243, with a similarity of 99.79 %. The study identified 12 antibiotic resistance genes and one virulence gene in strain BT22. These genes confer resistance to various classes of antibiotics, including aminoglycosides, macrolides, tetracyclines, and vancomycin. However, the virulence gene identified codes for adhesion. Furthermore, mobile genetic elements, such as IS elements carried by a conjugative plasmid, were detected. The genomic sequencing data of E. faecium BT22 will be of great value to the scientific community, enabling comparative genomic analyses and a better understanding of antibiotic resistance mechanisms, particularly towards vancomycin. The genomic information has been deposited in the DDBJ/EMBL/GenBank databases under accession number JASSVD010000000, providing an essential resource in the fight against antibiotic resistance and the spread of resistant bacterial strains.


a b s t r a c t
A vancomycin-resistant Gram-positive bacterium of the genus Enterococcus , designated as BT22, was isolated from untreated hospital effluents at Chettia Chlef Hospital.The complete genome of strain BT22 was sequenced using the Illumina MiSeq platform, revealing a total length of 2,577,707 bp, with 2462 coding sequences (CDS) and an average G + C content of 38.00 mol%.Phylogenomic analyses confirmed that strain BT22 belongs to the same species as Enterococcus faecium AVS0243, with a similarity of 99.79 %.The study identified 12 antibiotic resistance genes and one virulence gene in strain BT22.These genes confer resistance to various classes of antibiotics, including aminoglycosides, macrolides, tetracyclines, and vancomycin.However, the virulence gene identified codes for adhesion.Furthermore, mobile genetic elements, such as IS elements carried by a conjugative plasmid, were detected.The genomic sequencing data of E. faecium BT22 will be of great value to the scientific community, enabling comparative genomic analyses and a better understanding of antibiotic resistance mechanisms, particularly towards vancomycin.The genomic information has been deposited in the DDBJ/EMBL/GenBank databases under accession number JASSVD010 0 0 0 0 0 0, providing an essential resource in the fight against antibiotic resistance and the spread of resistant bacterial strains.
© 2023 The Author(s

Value of the Data
• Preliminary genomic data of Enterococcus faecium strain BT22, isolated from untreated hospital effluents, provide a valuable opportunity to deepen our understanding of antibiotic resistance mechanisms, especially vancomycin resistance, developed in a hospital setting.• These data are crucial, essential for exploring the virulence of BT22 and the mechanisms of acquisition and horizontal transfer of resistance, thus offering perspectives on combating infections.• These data hold significant importance for obtaining information on antimicrobial resistance genes in vancomycin-resistant Enterococcus faecium strains, benefiting researchers and the fields of medicine and health.
• By unraveling the genome of this strain, these data can serve as a reference sequence for detecting antibiotic resistance genes in other isolates with unknown genomic information.

Objectives
The primary objective of this study is to provide the complete genome sequence of E. faecium strain BT22, thereby facilitating an in-depth exploration of genes associated with vancomycin resistance, as well as the identification of virulence genes and those involved in horizontal transfer.

Data Description
The strain BT22 originates from untreated hospital effluent samples collected at Chettia Chlef Hospital.This strain has been identified as Vancomycin-Resistant Enterococcus (VRE), with a minimum inhibitory concentration (MIC) reaching up to 1024 μg/mL.Based on the complete genome sequence, isolate BT22 was closely related to Enterococcus faecium AVS0243 with a similarity of 99.79 %.The phylogenomic tree also confirmed that strain BT22 belongs to E. faecium ( Fig. 1 ).The preliminary genome consists of 91 contigs, with a total length of 2,577,707 base   1 ).Among these genes, aac(6 )-Ii and str confer resistance to aminoglycosides, while msrC, tet(M), and eatA are responsible for resistance to macrolides, tetracyclines, and LSAP (Lincosamides, Streptogramins A, and Pleuromutilins), respectively.Additionally, we identified seven other genes associated with vancomycin resistance, such as vanZ-A, vanY-A, vanX-A, vanA, vanH-A, vanS-A, and vanR-A .We also detected a virulence gene "acm " that plays an important role in the adhesion of Enterococcus bacteria.
The genome of BT22 revealed three sequences showing strong homology with plasmid sequences, as identified using PlasmidFinder 2.0 ( Table 2 ).Additionally, during the search for prophages using PHAST, we identified an intact prophage region within contig 18, located between positions 420-40866.This prophage region contains all the necessary elements for a functional phage, including the attL and attR attachment sites of the phage, the integrase, tail, head, capsid, portal, and genes encoding the terminase.
VRprofile2 allowed us to highlight the presence of mobile genetic elements, such as Tn/IS, some of which were carried by plasmid replicons ( Table 3 ).These elements could be involved Fig. 2. Circular Genome Map of E. faecium BT22 (JASSVD010 0 0 0 0 0 0): Tracks from the inside out include GC skew, GC content, contigs, forward genes, reverse genes, antibiotic resistance genes, virulence genes, IS elements, plasmid regions, and prophage regions.This circular genomic map was constructed using Proksee. in the mobilization of resistance genes, particularly IS1297, which has been associated with the transfer of the str resistance gene related to Streptomycin, as well as the VanHAX genes related to Vancomycin and Teicoplanin resistance.An additional analysis of the replicon containing IS1297, the rep1 plasmid, conducted with the help of OriTfinder, revealed that it is conjugative.This plasmid possesses all the necessary genes for conjugation, including the relaxase, oriT, T4SS gene cluster, and a T4CP coupling protein.
The circular genome map of E. faecium BT22 shows the genome distribution ( Fig. 2 )

Processing of raw sequences and assembly, annotation, and analysis
Strain BT22 was isolated from untreated hospital effluent samples collected at Chettia Chlef Hospital.It was obtained using a dilution method on Slanetz and Bartley agar plates containing vancomycin at a concentration of 8 μg/mL.Identification was performed through experiments involving colony morphology, physiological and biochemical experiments, as well as MALDI-TOF identification.After obtaining a pure colony of strain BT22, we conducted a subculture in 2 mL of BHI broth medium, followed by incubation at 37 °C for 18 hours.Subsequently, we extracted the total genomic DNA following the manufacturer's instructions of the DNAMITE DNA bacterial kit from Microzone Ltd (United Kingdom).Before proceeding further, we verified the concentration of the purified DNA using Qubit (Qubit 2.0 Fluorometer) and Nanodrop (NanoDrop 20 0 0) measurement devices.For the subsequent analysis, we sent the purified DNA sample to the service provider Microsynth AG, Schützenstrasse 15, 9436 Balgach, Switzerland.Their expertise in genomic sequencing was utilized to perform the sequencing on the Illumina MiSeq platform.To prepare the DNA library for sequencing, we used the Nextera XT DNA Library Prep 2 × 300 bp v3 reagent kits provided by Illumina (San Diego, CA).

Whole genome sequencing, assembly annotation and analysis
The raw sequences underwent quality checking using FASTQC [1] .Poor-quality reads and adapters were removed using Trimmomatic [2] , leaving only filtered reads for assembly with MIRA v4.9.6 [3] .The consensus was improved by aligning Illumina reads to the contigs using Pilon [4] .CONTIGuator [5] was used to determine the order and orientation of the contigs, while Quast 5.0.2 [6] was utilized to examine and statistically assess the assembly quality.The predicted genes were used as the input for BUSCO [7] to estimate genome completeness based on the lactobacillales_odb10 dataset.
Genome annotation was performed using PGAP from NCBI [8] , and OAT [9] was employed to establish phylogenetic relationships and genome similarity, resulting in the construction of a phylogenetic tree and a heatmap.The search for antibiotic resistance genes and virulence genes in strain BT22 was conducted in the AMRFinderPlus [10] and VFDB [11] databases using ABRicate [12] .The search for plasmids, prophages, and detection of the mobilome associated with antibiotic resistance were conducted using PlasmidFinder 2.0 [13] , PHASTER [14] , and VRprofile2 [15] , respectively.Furthermore, OriTfinder [16] was employed to rapidly locate the origin sites for DNA transfer in mobile genetic elements.Finally, a circular genomic map was generated using Proksee [17]

Fig. 1 .
Fig. 1.Heat Map and Phylogenetic Tree of Average Nucleotide Identity (ANI) for BT22 Genome and Closely Related Enterococcus spp.The heat map on the right is shown as an oblique 10 × 10 matrix, where each cell represents the ANI value between the row and the corresponding genome of the column, The color keys represent the identity of strains with lower (blue), and higher (red) ANI values and the phylogenetic tree on the left is a distance tree constructed by the UPGMA method.

Table 1
Antibiotic resistance genes and virulence factors found in BT22 genome.

Table 2
Plasmid Sequences Identified in the Genome of E. faecium BT22.

Table 3
Mobilome associated with antibiotic resistance in the Genome of E. faecium BT22.