Draft genome sequence of Enterobacter chengduensis ECC445, isolated from fresh water in the West Indies
BMC Genomic Data volume 24, Article number: 16 (2023)
The Enterobacter cloacae complex is considered an important opportunistic pathogen. It comprises many members that remain difficult to delineate by phenotypic approaches. Despite its importance in human infection, there is a lack of information on associated members in other compartments. Here we report the first de novo assembled and annotated whole-genome sequence of a E. chengduensis strain isolated from the environment.
ECC445 specimen was isolated in 2018 from a drinking water catchment point in Guadeloupe. It was clearly related to E. chengduensis species according to hsp60 typing and genomic comparison. Its whole-genome sequence is 5,211,280-bp long divided into 68 contigs, and presents a G + C content of 55.78%. This genome and associated datasets provided here will serve as a useful resource for further analyses of this rarely reported Enterobacter species.
Members of the E. cloacae complex (ECC) are ubiquitous Enterobacteriaceae involved in various opportunistic infections in animals, humans and plants . The taxonomy of this bacterial complex has been re-evaluated regularly [1,2,3]. There are to date 24 species and 22 Enterobacter genomospecies in this bacterial complex . In parallel to whole-genome sequencing, different typing approaches have been proposed to help in identify them, such as the amplification of the partial gene coding for the heat-shock protein 60 (hsp60) .
The objective of this study is to report a draft genome sequence of an environmentally isolated E. chengduensis. We also provided a global overview of this species which is rarely described in the scientific literature. ECC445 strain is associated with a broader analysis of Enterobacter population diversity and was isolated from a water sample . This sample was collected in June 2018 during prospective control of a catchment point in Petit-Bourg, Guadeloupe (French overseas territory; 16.188009 N, 61.659017 W). After serial dilutions, 100 mL were filtered (0.45 μm, Millipore, Guyancourt, France). The membrane was placed in 9 mL of buffered peptone water solution for overnight pre-enrichment at 37 °C. Then, 100 μL of broth were cultured aerobically onto chromogenic agar supplemented with ceftriaxone at 4 mg/L (CCA, CHROMagar, Paris, France).
ECC445 strain was isolated from this selective plate after overnight growth at 37 °C. It was initially identified as E. cloacae (97.7% ID) with the API-20E system (BioMérieux, Marcy-l'Étoile, France), and as E. hormaechei (99.9% ID) by matrix assisted laser desorption/ionization time–of–flight mass spectrometry (VITEK MS, BioMérieux, Marcy-l'Étoile, France) . This strain was resistant to third-generation cephalosporins by chromosomal overproduction of AmpC (CA-SFM/EUCAST guideline 2018, disc diffusion method; DataFile 1; Table 1) [5, 7, 8].
Upon isolation and to better identify this bacterium, DNA analysis was conducted. Unless otherwise stated on the detailed methodology file, default parameters were used for all software tools (DataFile 2) . DNA was extracted from a pure isolate with the QIAamp DNA minikit (Qiagen, Hilden, Germany). We conducted the hsp60 typing approach and obtained a 273-bp amplicon that was sequenced at Eurofins (Eurofins Genomic SAS, Les Ullis, France; DataSet 1) [4, 5, 10]. BLASTn submission to the NCBI nucleotide collection database indicated 100% coverage and a maximum percentage identity with the E. chengduensis reference (v2.11.0; 99.27%; CP043318) [11,12,13].
The second sequencing step was performed with a NextSeq 500 system (Illumina; 150-bp paired-end configuration; Nextera XT Kit; DataSet 2) . Raw reads (n = 7,941,390) were trimmed and filtered with AlienTrimmer v0.4.0 . De novo assembly and annotation were performed with SPAdes (v3.12.0; –careful) and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP v5.3; DataSet 3) [23, 25, 26]. Whole-genome sequence of ECC445 strain has a 95-fold coverage and BUSCO single-copy completeness of 98.60% (v5.3.2) . It is 5,211,280-bp long divided onto 68 contigs, and presents a G + C content of 55.78% (QUAST v5.0.2; DataFile 3) [14, 28].
Whole-genome sequencing allowed accurate species identification using FastANI v1.3 and Genome-to-Genome Distance Calculator (GGDC; v3.0) against last Enterobacter references panel provided by Feng Y. and colleagues [3, 29,30,31]. Results confirmed that ECC445 strain is closely related to E. chengduensis with the novel Sequence Type ST1533 (Average Nucleotide Identity – ANI: 98.48%; in silico DNA-DNA Hybridization – isDDH formula 2: 88.20%) [5, 11, 29, 32, 33].
On June 29, 2022, a total of 19 E. chengduensis with complete metadata was retrieved from the NCBI database . All these whole-genome sequences have passed our quality control (DataFile 4) . To place ECC445 isolate in a global context, a core-genome alignment with Roary v3.13.0 was performed using reference sequences of Enterobacter, including all previous E. chengduensis (DataFile 5) [3, 13, 16, 34]. If only fastqs were available, de novo assembly was performed with SPAdes . All additional sequences were annotated with PGAP as described above . Maximum-likelihood phylogenetic reconstructions were performed by IQ-TREE (v2.1.2) and associated dependencies (i.e. ModelFinder and UFBoot2; –merit BIC: GTR + F + R8 –ufboot 1,000 –bnni; DataFile 6) [17, 35,36,37]. The tree was drawn with iTOL v6.4.2 (DataFile 7) [18, 38].
To date, ECC445 strain is the first E. chengduensis described in the natural environment and is a probable human pathogen (81.9%; PathogenFinder v1.1; DataFile 8) [19, 39]. The remaining 19 E. chengduensis isolates were recovered from human samples (i.e. ST414 n = 18; ST1535 n = 1). Most of them were described from China (10/19, 52.6%). Unlike ECC445, many of these strains had acquired resistance genes and plasmids (ResFinder v4.1, PlasmidFinder v2.1; details in the DataFile 4) [15, 40, 41].
The CRISPRCasFinder tool v1.1.2 identified a CRISPR/Cas system in the strain ECC445 genome (3 array sequences; Cas type I-F with evidence level of 4; DataFile 9) [20, 42]. As shown in DataFile 10 , none of the 46 CRISPR spacer sequences from strain ECC445 were found in the other E. chengduensis isolates using the CRISPR Comparison ToolKit (CCTK; v0.8.4) . In contrast, some spacer arrays were identical between ST1535 and ST414 strains. These observations are consistent with the evolution of ECC445 ST1533 isolate in a different ecosystem than other E. chengduensis STs.
This Data note was limited to a single draft genome sequence. To overcome this limitation and place this strain in a global context, an extensive analysis of E. chengduensis strains was performed. Its correct identification by the hsp60 approach was confirmed here by whole-genome sequencing. However, further analysis on a larger collection is needed to appreciate the robustness of this technique to identify E. chengduensis among other ECC members.
Availability of data and materials
The genomic data described in this Data note can be freely and openly accessed on GenBank of NCBI. The partial hsp60 coding sequence of this E. chengduensis strain is available on OM687483 . In addition, the SRA accession of the ECC445 strain is SRR16640525 , and the annotated assembly is version JAKLRZ000000000.1 . Associated DataFiles are available on Figshare: antibiotic resistance profile and analysis of the sequence quality of the ECC445 strain [8, 14]; PathogenFinder and CrisprCasFinder [19, 20]; and global analysis of E. chengduensis from Genbank [15,16,17,18, 21]. The detailed methodology is available on the reference .
Average Nucleotide Identity
CRISPR Comparison ToolKit
Enterobacter cloacae Complex
Genome-to-Genome Distance Calculator
Heat-shock protein 60
in silico DNA-DNA Hybridization
Prokaryotic Genome Annotation Pipeline
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We thank the Pasteur International Bioresources network for whole-genome sequencing. We are also grateful to ARS Guadeloupe and the team of the PubMLST E. cloacae typing database for their collaboration. M. Pot extends special thanks to N. Bougrer for her involvement in the curation of the associated data.
The initial project was supported by a FEDER grant (2018-FED-1084), financed by the European Union and the Guadeloupe Region . The funders had no role in the design of the study, in the collection and analyses of data, in the writing of the manuscript, or in the decision to publish the paper.
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Pot, M., Ducat, C., Reynaud, Y. et al. Draft genome sequence of Enterobacter chengduensis ECC445, isolated from fresh water in the West Indies. BMC Genom Data 24, 16 (2023). https://doi.org/10.1186/s12863-023-01116-7
- CRISPR spacer
- Enterobacter cloacae complex