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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
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mra00052-24
10.1128/mra.00052-24
mra.00052-24
Genome Sequences
clinical-microbiologyClinical MicrobiologyComplete genome sequence of Streptococcus intermedius strain XH2169
https://orcid.org/0009-0006-6070-7077
Zhang Yisha 1 2 3
Yao Yue 1 2 3
Zhao Feng 4 5
https://orcid.org/0000-0003-2903-918X
Yu Yunsong 1 2 3 yvys119@zju.edu.cn

https://orcid.org/0000-0001-8215-916X
Hua Xiaoting 1 2 3 xiaotinghua@zju.edu.cn

1 Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, China
2 Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province , Hangzhou, China
3 Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou, China
4 Department of Clinical Laboratory, Sir Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, Zhejiang, China
5 Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang, China
Editor Dunning Hotopp Julie C. University of Maryland School of Medicine , Baltimore, Maryland, USA

Address correspondence to Xiaoting Hua, xiaotinghua@zju.edu.cn
Address correspondence to Yunsong Yu, yvys119@zju.edu.cn
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00052-2418 1 2024
28 6 2024
Copyright © 2024 Zhang et al.
2024
Zhang et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

Here, we report the complete genome sequence of Streptococcus intermedius strain XH2169 isolated from a blood sample in China. The genome comprises a single circular chromosome with a length of 1,944,282 bp. It harbored 1,891 coding gene sequences, 16 rRNA genes, 60 tRNA genes, and 3 noncoding RNA genes.

KEYWORDS

Streptococcus intermedius
whole-genome sequencing
MOST | National Key Research and Development Program of China (NKPs) 2023YFC2307100 Yu Yunsong National Natural Science Foundation of China (NSFC) U22A20338, 32270183 Yu Yunsong Hua Xiaoting cover-dateSeptember 2024
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pmcANNOUNCEMENT

Streptococcus intermedius is a β-hemolytic Gram-positive member of the Streptococcus anginosus group (1). Despite being part of the normal microbiota, S. intermedius is a common pathogen associated with brain abscesses, liver abscesses, and thoracic empyema (2, 3), contributing to the elevated incidence and mortality rates (4). As the available genome sequences are limited on the National Center for Biotechnology Information (NCBI), our knowledge of the genomic factors which contribute to its dissemination to the brain and liver abscess is hindered. Thus, we conducted a detailed genome analysis of S. intermedius XH2169.

On 15 August 2021, a 44-year-old woman with septic shock and liver abscesses was admitted to Sir Run Run Shaw Hospital in Zhejiang to undergo intensive care unit (ICU) monitoring. After being admitted to the ICU, percutaneous puncture and drainage of hepatoma were performed in the emergency department on that day. The postoperative drainage was smooth, but the patient suffered from recurrent fever after surgery. S. intermedius XH2169 was isolated from the patient’s blood during routine diagnostic analysis (consent for sampling was obtained from the patient) and cultured on a Columbia blood agar plate for 24 hours. Genomic DNA extraction was performed using the QIAamp DNA Mini kit (Qiagen, Germany) and subsequently analyzed on a 1% agarose gel. The identical genomic DNA preparation was employed for both Illumina and Oxford Nanopore Technologies (ONT) sequencing. Illumina sequencing libraries were generated using the Nextflex rapid DNA sequencing kit. For Nanopore sequencing, libraries were conducted by native barcoding expansion set (EXP-NBD104) and SQK-LSK109 ligation sequencing kit without any size selection or trimming. The individual libraries were quantitated using a Qubit version 3.0 fluorometer (Invitrogen, Carlsbad, CA, USA). Finally, the library was loaded onto an R version 9.4.1 flow cell and sequenced on the MinION platform (Oxford Nanopore Technologies, UK).

Whole-genome sequencing was performed on the Illumina HiSeq X Ten platform, as well as on the ONT, UK. The long reads were generated using Guppy v.5.1.2 from ONT (5), with the parameters “–flowcell FLO-MIN106 –kit SQK-LSK109 –barcode_kits ‘EXP-NBD104 EXP-NBD114’,” and the default mode was set to “high accuracy.” Trimmomatic v.0.30 was used to trim the Illumina reads (6). We assembled the filtered MinION reads with Raven v.1.1.10 (7) and subsequently polished the genome sequence with Illumina reads using Polypolish (8). Illumina sequencing achieved an averaged depth of 536×, generating a total of 6,887,896 150-bp paired-end reads. Nanopore sequencing coverage averaged 399×, and a total of 152,875 reads were obtained, with an N50 value of 8,763. After Polypolish, a total of 1,944,282 bp was obtained (Table 1). A total of 16 rRNAs and 60 tRNAs were identified, as well as three noncoding RNAs. Antibiotic resistance genes were identified using ABRicate v.0.8.13 (https://github.com/tseemann/abricate). The analysis revealed the presence of two resistance genes: tet(M) and erm(B). Unless specified, default parameters were utilized for all software. The resulting complete genome sequence was annotated by the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). For XH2169, the minimum inhibitory concentration (MIC) of penicillin was determined using the broth microdilution method. Escherichia coli (American Type Culture Collection) ATCC 25922 was used as quality control. The strain was susceptible to penicillin (MIC = 0.125 µg/mL), according to the Clinical and Laboratory Standards Institute breakpoints (9).

TABLE 1 Genome annotation features of S. intermedius XH2169a

Genome features	Value	
Genome size (bp)	1,944,282	
GC content	37.74	
No. of genes (total)	1,966	
No. of CDSs (total)	1,891	
No. of CDSs (with protein)	1,816	
No. of rRNAs	16	
No. of tRNAs	60	
No. of noncoding RNAs	3	
Accession no.	CP136799	
a GC, guanine-cytosine content; CDS, Coding sequence.

The complete genome sequence of S. intermedius XH2169 will promote the understanding of its genetic characterization and offer new insight into liver abscesses caused by this species.

ACKNOWLEDGMENTS

This work was supported by the National Key Research and Development Program of China (grant number 2023YFC2307100) and the National Natural Science Foundation of China (grant numbers U22A20338 and 32270183).

DATA AVAILABILITY

The whole-genome sequence of XH2169 is available in GenBank under accession number CP136799. The BioSample and BioProject accession numbers are SAMN37717071and PRJNA1025243, respectively. The raw sequence data have been deposited in the Sequence Read Archive under accession numbers SRR26319261 (Nanopore) and SRR26319260 (Illumina).

ETHICS

Ethical approval and informed consent were obtained by the ethics committee of the Sir Run Run Shaw Hospital, Zhejiang University School of Medicine (approval number 20201217–33).
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