ABSTRACT
Pasteurella multocida is a rare cause of human infection most often associated with animal bites or scratches. We report the complete genome sequence of Pasteurella multocida subsp. septica strain 0092 recovered from the blood culture of a sepsis patient in Nakhon Phanom, Thailand in 2022. The genome totals 2,392,800 bp.
KEYWORDS: sepsis, Pasteurella
ANNOUNCEMENT
Pasteurella multocida is an anaerobic gram-negative coccobacillus known as oral commensal in cats and dogs. P. multocida can be divided into five capsular serotypes (A, B, D, E, and F) (1). Up until now, over 2,500 genomes are publicly available; however, approximately 10% of the genome was from human. Among human-associated isolates, subspecies septica has been reported as one of the most prevalent (2).
Strain 0092 was isolated from the blood culture drawn from a patient with sepsis at Nakhon Phanom Hospital, Thailand in 2022. The primary blood culture isolate was recovered on 5% sheep blood agar at 35 ± 2°C in ambient air for 18 h and identified to the species level by the BD Phoenix Automated Identification System (BD Diagnostic Systems, Sparks, MD).
For the isolate preparation, colonies were revived from −80°C frozen stock in rich media with 15% glycerol and sub-cultured on a blood agar plate. The plate was incubated at 35 ± 2°C in ambient air for 20–24 h to ensure colony purity and viability prior to subsequent steps. Antimicrobial susceptibility testing interpreted according to Clinical and Laboratory Standards Institute (CLSI) M45 (3rd edition) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) (version 16) showed susceptibility to co-trimoxazole and ceftriaxone; otherwise, it showed non-susceptible phenotypes.
Genomic DNA was extracted from approximately 1 × 10⁹ bacterial cells, adjusted to McFarland standard 3.5–4.0, and suspended in 1 mL of phosphate-buffered saline (PBS) using the ZymoBIOMICS DNA Miniprep Kit (Zymo Research, Irvine, CA, USA) following the manufacturer’s instructions. Libraries were prepared with the Rapid Barcoding Kit SQK-RBK004 (Oxford Nanopore Technologies). Because SQK-RBK004 is a rapid, transposase-based kit (not a ligation kit), the genomic DNA was neither mechanically sheared nor size-selected prior to library preparation. The library was sequenced on a FLO-MIN106 V9.4.1 flow cell using a MinION Mk1C (Oxford Nanopore Technology). Base-calling was performed in MinKNOW software using high-accuracy model. Sequencing produced 126,562 reads, with a read N50 of 10,425 bp, corresponding to approximately 300× coverage.
De novo assembly was generated with Flye v2.9.5-b1801 (3). Genome contamination and the completeness were assessed with CheckM2 version 1.1.0 (4) and BUSCO version 6.1.0 (5), respectively. Annotation was performed with Bakta version 1.9.4 (6). Default parameters were used unless otherwise specified. Taxonomic assignment was confirmed by average nucleotide identity (ANI). The strain 0092 shared 98.73% ANI with P. multocida subsp. septica calculated with EZBioCloud above 96% threshold.
The draft genome consists of a circular chromosome and a circular plasmid with a total length of 2,351,053 bp and 41,747. The guanine-cytosine (GC) content was 40.3% (chromosome) and 32.9% (plasmid) (Table 1).
TABLE 1.
Genome characteristics of P. multocida subsp. septica strain 0092
| Strain | Strain 0092 | |
|---|---|---|
| ANI hit | Pasteurella multocida subsp. septica | |
| Chromosome | Plasmid | |
| GC content (%) | 40.3 | 32.9 |
| Size (bp) | 2,351,053 | 41,747 |
| tRNAs | 58 | 0 |
| rRNAs | 19 | 0 |
| CDSs | 3,436 | 71 |
| CRISPR region | 3 | 0 |
Screening for antibiotic resistance determinants using CARD (7), AMRprofiler (8), and AMRfinder (9),identified a cAMP-activated global transcriptional regulator, with 98% sequence coverage and 86% identity. In Escherichia coli, this regulator modulates expression of mdtEF efflux pump (10). Its presence may contribute to the reduced susceptibility observed for several antimicrobial agents tested.
Strain 0092 expands the small set of human-derived P. multocida subsp. septica genomes from mainland Southeast Asia and provides a regional reference for genomic surveillance of invasive pasteurellosis.
ACKNOWLEDGMENTS
We would like to express our sincere gratitude to Dr. Woradee Luechachaiwong and Dr. Pongpun Sawatwong of the Division of Global Health Protection Program, Thailand Ministry of Public Health—U.S. Centers for Disease Control and Prevention Collaboration, as well as the project staff and Nakhon Phanom Provincial Hospital, for their valuable support and collaboration. We also extend our appreciation to all study participants for their contribution to this research.
This work was supported by the U.S. CDC and Thailand Ministry of Public Health Cooperative Agreement no. U01GH002366 under the program “Conducting Public Health Research in Thailand: Technical Collaboration with the Ministry of Public Health (MOPH).”
Contributor Information
Pisut Pongchaikul, Email: pisut.pon@mahidol.ac.th.
Daria Van Tyne, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
DATA AVAILABILITY
The draft genome for P. multocida subsp. septica strain 0092 has been deposited to NCBI under BioProject accession number PRJNA1444785 (BioSample accession number SAMN56769409; Sequence Read Archive accession number SRR39247279).
ETHICS APPROVAL
All procedures involving human samples were approved by the Institute for the Development of Human Research Protections Review Board (COA no. IHRP2024108).
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Associated Data
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Data Availability Statement
The draft genome for P. multocida subsp. septica strain 0092 has been deposited to NCBI under BioProject accession number PRJNA1444785 (BioSample accession number SAMN56769409; Sequence Read Archive accession number SRR39247279).