Large-scale genomic analysis places Chinese CC398 as a persistent human-associated MSSA lineage apart from the dominant global LA-MRSA clade
5 affiliations
- 1Changshu Hospital Affiliated to Soochow University, Changshu No.1 People's Hospital, Soochow University, Changshu, Jiangsu, China
- 2Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
- 3The Second Affiliated Hospital of Soochow University, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
- 4National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- 5Suzhou BenQ Medical Center, Suzhou, Jiangsu, China
Abstract
Staphylococcus aureus clonal complex (CC)398 has emerged as a dominant livestock-associated methicillin-resistant S. aureus (LA-MRSA) lineage worldwide; however, its evolutionary trajectory and regional diversification remain incompletely understood. We developed a core-genome multilocus sequence typing (cgMLST) scheme with hierarchical clustering and applied it to over 30,000 S. aureus genomes, revealing frequent cross-border transmission of CC398. Subsequent time-calibrated phylogenetic analysis placed the most recent common ancestor at 1942 (95% CI: 1939–1945), with the human-to-livestock host jump around 1969 (95% CI: 1968–1972). Chinese CC398 exhibits a distinct trajectory: unlike the LA-MRSA lineages dominating Europe and North America, Chinese isolates are predominantly human-associated methicillin-susceptible S. aureus (HA-MSSA), forming unique East Asia-specific phylogroups (SAP1, SAP2, and AP1–AP3), with distinct resistance and virulence profiles. The LA lineage remains limited in China, with multinational mixed clusters emerging only after 2019. Analysis of global transmission networks revealed a significant correlation between LA-CC398 spread and international trade in fresh swine products, while no such correlation was observed for the human-associated lineage. Beyond the established lineage markers tet(M) and scn, our analysis identified additional differentially distributed genes, including cadC—a chromosomal cadmium resistance regulator—as a novel HA-lineage-enriched gene whose functional role in host adaptation remains to be determined. This study reveals that CC398 followed fundamentally different evolutionary paths in China versus Western countries, challenging a one-size-fits-all model of its dissemination.
IMPORTANCE: This study illustrates how large-scale microbial genomics can resolve the evolutionary origins and regional diversification of bacterial pathogens. By applying a novel cgMLST scheme to over 30,000 S. aureus genomes, we show that CC398 followed fundamentally different evolutionary paths in China versus Western countries—challenging the prevailing model of uniform global dissemination—and that livestock-associated MRSA expansion is closely linked to international trade in fresh pork products. These findings highlight the need for integrated surveillance across human, animal, and trade interfaces to anticipate the emergence and spread of zoonotic pathogens.
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BibTeX
@article{jiang2026largescale,
title = {{Large-scale genomic analysis places Chinese CC398 as a persistent human-associated MSSA lineage apart from the dominant global LA-MRSA clade}},
author = {Guilai Jiang and Changyuan Guo and Yulin Hua and Chaoshen Wu and Shengkai Li and Yuezhuo Wang and Jun Zhao and Linli Ji and Yijie Cheng and Zhemin Zhou and Xuejie Wu and Heng Li},
journal = {mSystems},
year = {2026},
month = sep,
doi = {10.1128/msystems.00621-26},
url = {https://doi.org/10.1128/msystems.00621-26},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Large-scale genomic analysis places Chinese CC398 as a persistent human-associated MSSA lineage apart from the dominant global LA-MRSA clade
AU - Guilai Jiang
AU - Changyuan Guo
AU - Yulin Hua
AU - Chaoshen Wu
AU - Shengkai Li
AU - Yuezhuo Wang
AU - Jun Zhao
AU - Linli Ji
AU - Yijie Cheng
AU - Zhemin Zhou
AU - Xuejie Wu
AU - Heng Li
PY - 2026
DA - 2026/09/11
JO - mSystems
DO - 10.1128/msystems.00621-26
UR - https://doi.org/10.1128/msystems.00621-26
AB - Staphylococcus aureus clonal complex (CC)398 has emerged as a dominant livestock-associated methicillin-resistant S. aureus (LA-MRSA) lineage worldwide; however, its evolutionary trajectory and regional diversification remain incompletely understood. We developed a core-genome multilocus sequence typing (cgMLST) scheme with hierarchical clustering and applied it to over 30,000 S. aureus genomes, revealing frequent cross-border transmission of CC398. Subsequent time-calibrated phylogenetic analysis placed the most recent common ancestor at 1942 (95% CI: 1939–1945), with the human-to-livestock host jump around 1969 (95% CI: 1968–1972). Chinese CC398 exhibits a distinct trajectory: unlike the LA-MRSA lineages dominating Europe and North America, Chinese isolates are predominantly human-associated methicillin-susceptible S. aureus (HA-MSSA), forming unique East Asia-specific phylogroups (SAP1, SAP2, and AP1–AP3), with distinct resistance and virulence profiles. The LA lineage remains limited in China, with multinational mixed clusters emerging only after 2019. Analysis of global transmission networks revealed a significant correlation between LA-CC398 spread and international trade in fresh swine products, while no such correlation was observed for the human-associated lineage. Beyond the established lineage markers tet(M) and scn, our analysis identified additional differentially distributed genes, including cadC—a chromosomal cadmium resistance regulator—as a novel HA-lineage-enriched gene whose functional role in host adaptation remains to be determined. This study reveals that CC398 followed fundamentally different evolutionary paths in China versus Western countries, challenging a one-size-fits-all model of its dissemination. IMPORTANCE: This study illustrates how large-scale microbial genomics can resolve the evolutionary origins and regional diversification of bacterial pathogens. By applying a novel cgMLST scheme to over 30,000 S. aureus genomes, we show that CC398 followed fundamentally different evolutionary paths in China versus Western countries—challenging the prevailing model of uniform global dissemination—and that livestock-associated MRSA expansion is closely linked to international trade in fresh pork products. These findings highlight the need for integrated surveillance across human, animal, and trade interfaces to anticipate the emergence and spread of zoonotic pathogens.
SN - 2379-5077
ER -