Genomic analysis of almost 8,000 Salmonella genomes reveals drivers and landscape of antimicrobial resistance in China.

Foodborne infection remains a major public health concern worldwide. With rising antimicrobial resistance, genomic surveillance is key to tracking outbreaks and monitoring transmission, but there is no comprehensive national surveillance scheme for involving humans, food, animals, and the environment in China. Moreover, the association between antimicrobial resistance and climate, social, and economic factors has rarely been investigated. Here, we use 1,962 isolates collected from 22 Chinese provinces and add 6,035 publicly available genomes to build a Chinese local genome database version 2 (CLSGDB v2) representing 30 Chinese provinces, covering 1905-2022. Using the CLSGDB v2, we mapped the landscape and spatiotemporal dynamics of antimicrobial resistance markers, virulome, and mobilome in . We identified 317 positive and 745 azithromycin resistance genes positive isolates out of 7,997 isolates. We further uncovered the geographic distribution veil of , , , , and genes in China, all of them resistant to the critically important antimicrobials including colistin, fosfomycin, azithromycin, and the third-generation cephalosporins. Interestingly, economic, climatic, and social factors can drive the rise of antimicrobial resistance was observed. Finally, we release the CLSGDB v2 as an open-access database and thus can assist surveillance studies tracking 164 serovars and 295 sequence types across the globe. The CLSGDB v2 is freely available at https://nmdc.cn/clsgdbv2.IMPORTANCEWe established the largest Salmonella genome database from China and presented the landscape and spatiotemporal dynamics of antimicrobial resistance genes. We also found that economic, climatic, and social factors can drive the rise of antimicrobial resistance. The Chinese local Salmonella genome database version 2 was released as an open-access database (https://nmdc.cn/clsgdbv2) and thus can assist surveillance studies across the globe. This database will help inform interventions for AMR, food safety, and public health.