Virulence-associated Genome Sequences of Pasteurella canis and Unique Toxin Gene Prevalence of P. canis and Pasteurella multocida Isolated from Humans and Companion Animals
2023; 43(3): 263-272
Ann Lab Med 2024; 44(1): 47-55
Published online September 4, 2023 https://doi.org/10.3343/alm.2024.44.1.47
Copyright © Korean Society for Laboratory Medicine.
Takashi Takahashi , M.D., Ph.D.1, Hyaekang Kim , Ph.D.2, Han-Sung Kim , M.D.3, Hyun Soo Kim , M.D.3, Wonkeun Song , M.D., Ph.D.3, and Jae-Seok Kim, M.D., Ph.D.3
1Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan; 2Bioresources Collection and Research Division, Bioresources Collection and Bioinformation Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Korea; 3Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea
Correspondence to: Jae-Seok Kim, M.D., Ph.D.
Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Kangdong-gu, Seoul 05355, Korea
E-mail: jaeseok@hallym.ac.kr
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Background: Staphylococcal cassette chromosome mec type V (SCCmec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock. Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCCmec V after transmission from overseas donor strains to Korean recipient strains.
Methods: Sixty-three complete MRSA SCCmec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Ranger-dtl was applied to 818 SCCmec V strains using publicly available whole-genome data.
Results: The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCCmec V clinical isolates was traced to 2000–2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCCmec V donors.
Conclusions: Most Korean SCCmec V strains may have emerged during 2000–2010. A unique MRSA SCCmec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.
Keywords: Clades, Comparative genomic analysis, Donor–recipient, Horizontal gene transfer, Korea, Methicillin, One Health, Phylogeny, SCCmec V, Staphylococcus, Whole genome sequence
Methicillin-resistant
Methicillin resistance is conferred by
SCC
Colonization or infection with livestock-associated MRSA has been reported in several domesticated livestock animals [14]. Carrier animals not only serve as reservoirs for opportunistic infections but can also transmit livestock-associated MRSA to other animal species or humans [15]. In Korea, livestock-associated SCC
Recently, we analyzed six SCC
We evaluated the possible phylogenetic emergence of SCC
We screened the SCC
Strain information
Strain | Isolation date | Host | Isolation source | MLST | SCC | PVL | Antibiotic resistance genes | Antibiotic resistance phenotypes | Virulence genes | |
---|---|---|---|---|---|---|---|---|---|---|
HL20709 | August 23, 2017 | Blood | ST59 | t437 | V | PVL+ | Phenicol, β-lactam, fosfomycin, macrolide, aminoglycoside, tetracycline, efflux | |||
HL23187 | May 8, 2019 | Blood | ST59 | t437 | V | PVL+ | β-Lactam, tetracycline, fosfomycin, efflux | |||
HL25274 | June 10, 2020 | Blood | ST45 | t1081 | V | PVL– | Quinolone, β-lactam, fosfomycin, macrolide, aminoglycoside, tetracycline, efflux | |||
HL24830 | March 6, 2020 | Blood | ST72 | t3092 | V | PVL– | Quinolone, β-lactam, fosfomycin, trimethoprim, mupirocin, macrolide, aminoglycoside, tetracycline, efflux | |||
HL25870 | September 9, 2020 | Blood | ST1232 | t034 | V | PVL+ | β-Lactam, fosfomycin, macrolide, aminoglycoside, tetracycline, efflux | |||
HL2018_N011 | January 10, 2018 | Pus | ST59 | t437 | V | PVL+ | Tetracycline, phenicol, macrolide, efflux, fosfomycin, aminoglycoside, β-lactam |
Abbreviations: MLST, multilocus sequence type; PVL, Panton–Valentine leucocidin.
The presence of a gene encoding methicillin resistance was confirmed via PCR screening for
Six SCC
For the MiSeq reads, adapter sequences were removed, and quality-filtering was performed using Trimmomatic v.0.39 [21]. For the MinION reads, base calling and demultiplexing were conducted using the Guppy GPU basecaller v.6.0.6, and sequencing artifacts were removed using Porechop v.0.2.4. Genome sequences were constructed from the MiSeq and MinION data using SPAdes v.3.14.0. Hybrid assembly was performed using Unicycler v.0.4.8, as previously described [20]. Genome assembly completeness was assessed using BUSCO v.5.3.2 with the lineage dataset bacillales_odb10. The complete genome sequences were annotated using the Prokaryotic Genome Annotation Pipeline v.4.3.
A genome map of the constructed MRSA genome was generated using CGView v.2.0.3. The CGView Comparison Tool (CCT) was used for visual comparison of the CGH comprising six WGS datasets, as described previously [22, 23]. All five other WGS datasets were aligned with the complete genome of strain HL24830 as a reference sequence. Clusters of orthologous gene (COG) functional categories were assigned based on the NCBI COG database (https://www.ncbi.nlm.nih.gov/research/cog) and are displayed using different colors.
Before conducting comparative genomic analysis, we retrieved all publicly available genome sequences of the genera
Sixty-three complete circular genome sequences of SCC
WGS datasets on 818 methicillin-resistant staphylococcal strains (including MRSA and other staphylococci) were retrieved from NCBI, and the strains were typed as SCC
Among the six SCC
Table 2 presents the MinION and MiSeq sequencing metrics of the two assemblies from both WGS datasets. Table 3 summarizes the metrics of the six circularly assembled and annotated SCC
Sequencing metrics for the two assemblies from two whole-genome sequencing datasets
Strain | MinION sequencing* | MiSeq sequencing† | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Read length N50 (bp) | Mean read quality | N of reads | Total bases (bp) | Coverage (X) | N of reads | Total bases (bp) | Coverage (X) | ||||
HL20709 | 13,266 | 11.3 | 112,634 | 1,220,990,317 | 426.9 | 1,947,068 | 288,474,163 | 100.9 | |||
HL23187 | 16,867 | 11.2 | 42,440 | 557,671,576 | 196.4 | 1,837,608 | 272,537,071 | 96.0 | |||
HL25274 | 3,247 | 12.6 | 329,151 | 762,618,177 | 271.4 | 3,027,274 | 445,604,778 | 158.6 | |||
HL24830 | 7,148 | 8.7 | 132,592 | 528,929,395 | 181.5 | 1,881,702 | 278,662,641 | 95.6 | |||
HL25870 | 7,928 | 8.7 | 335,981 | 1,402,136,279 | 479.1 | 1,720,578 | 255,003,766 | 87.1 | |||
HL2018_N011 | 8,616 | 8.7 | 81,207 | 325,914,573 | 116.0 | 1,613,702 | 238,922,352 | 85.0 |
*Oxford Nanopore Technologies, Oxford, UK.
†Illumina, San Diego, CA, USA.
Summarized metrics for the six circularly assembled and annotated genomes
Metric | HL20709 | HL23187 | HL25274 | HL24830 | HL25870 | HL2018_N011 |
---|---|---|---|---|---|---|
Completeness, %* | 450 (100%) | 450 (100%) | 450 (100%) | 450 (100%) | 450 (100%) | 450 (100%) |
N of chromosomes | 1 | 1 | 1 | 1 | 1 | 1 |
N of plasmids | 0 | 1 | 2 | 1 | 1 | 1 |
Total length, bp | 2,860,303 | 2,860,005 | 2,913,602 | 2,926,847 | 2,809,575 | 2,881,027 |
GC, % | 32.5 | 32.5 | 32.5 | 32.5 | 32.5 | 32.5 |
N of protein-coding genes | 2,706 | 2,695 | 2,714 | 2,790 | 2,626 | 2,705 |
N of non-coding genes | 66 | 82 | 83 | 82 | 82 | 81 |
*Genome assembly completeness was assessed using BUSCO v.5.3.2 with the lineage dataset bacillales_odb10.
Fig. 1 shows the circular map of the six complete SCC
Fig. 2 shows the dated phylogenetic tree of the six Korean MRSA SCC
Possible
Computational analysis of possible
Donor strain | Host | Collection year | Oversea country | Recipient strain | Host (specimen) | Collection year | Location | Support value |
---|---|---|---|---|---|---|---|---|
Pig | 2010 | The USA | Pig (nasal cavity) | 2017 | Chungcheongnam-do | 1 | ||
Human | 2006 | Taiwan, Germany, and the Netherlands | Human | 2019 | Unknown location | 1 | ||
Human (pus) | 2017 | Hong Kong | Human (pus) | 2018 | Seoul | 1 | ||
Human (pus) | 2017 | Hong Kong | Human (blood) | 2017 | Seoul | 1 | ||
Human | 2008 | Unknown | Dog (ear) | 2017 | Seongnam-si | 1 | ||
Food | 2011 | China | Human (blood) | 2020 | Seoul | 1 | ||
Human (nasal cavity and prosthetic joint) | 2011 and 2018 | Australia and Germany | Human (skin) | 2017 | Seoul | 0.92 |
Recipient strains isolated in Korea are presented, and the methicillin-resistant
*Donor strain (
Abbreviation: HGT, horizonal gene transfer.
MRSA strains with SCC
Human invasive MRSA isolates harboring SCC
The current study had two limitations. First, although
In conclusion, we estimated the possible clades and donor–recipient relationships among MRSA SCC
SCC
None.
Kim J-S and Takahashi T conceptualized the study. Kim H and Kim J-S were involved in the investigation. Kim H, Kim H-S, Kim HS, Song W, and Kim J-S were involved in the formal analysis. Kim H-S, Kim HS, Song W, and Kim J-S provided resources. Takahashi T and Kim J-S drafted the manuscript. Kim J-S, Kim H, and Takahashi T reviewed and edited the manuscript.
None declared.
This work was supported in part by the Bio & Medical Technology Development Program of the National Research Foundation funded by the Ministry of Science and ICT, Korea (2017M3A9E 4077225) to Prof. Kim J-S.