Salmonella enterica is one of the most common bacterial pathogens in humans and animals. Systematic studies on the trends and geographical distribution of antimicrobial-resistant Salmonella and dominant serovars have been well studied in European and American countries while not in China. Here, taking the One-Health strategy, we used >35 000 Salmonella enterica isolates to explore the temporal and spatial dynamics of dominant serovars in China. We found that Salmonella Typhimurium was the dominant serovar causing human infection in China, which was consistent with Australia but inconsistent with North American and European countries. The proportion of Salmonella serovars Typhimurium, London, Rissen, Corvallis, Meleagridis, Kentucky, and Goldcoast showed an increasing trend during 2006–2019. We randomly selected 1962 isolates for comparative genomics and antimicrobial resistance studies and found that the number of antibiotic resistance genes (ARGs) per isolate increased 1.84 and 2.69 times of human and non-human origins, respectively, spanning 14 years. The proportion of antimicrobial-resistant Salmonella isolates had an increasing trend during 2006–2019, especially beta-lactam, quinolone, tetracycline, and rifampicin resistance. Moreover, we found that higher diversity of sequence types (STs) in S. Typhimurium than in other serovars, ST34 from pig and ST19 from chicken origin, were mainly associated with isolates causing child and adult gastro-infection, respectively. Our results fill in the data gap on the trends of dominant serovars and antimicrobial resistance of Salmonella enterica in China. These data provide useful information for public health decision-makers prioritizing interventions for foodborne diseases and food safety.

Although previous studies using phenotypic or/and genomic approaches monitoring have revealed the spatiotemporal distribution of antimicrobial resistance (AMR) in Salmonella in local areas, their geographical patterns and driving factors remain largely unknown at a global scale. Here, we performed an analysis of publicly available data of 208,233 Salmonella genomes in 148 countries/regions between 1900 and 2023 and explored driving indicators of AMR. Overall, we found that the geographic distribution of AMR varied depending on the location, source, and serovar. The proportion of AMR levels increased across six continents, especially in serovars Agona, Dublin, I 1,4,[5],12:i:-, Muenchen, Senftenberg, Mbandaka mainly from chickens, food, wild animals, and the environment, while decreased in Schwarzengrund and Saintpaul mainly from cattle, pigs, and turkeys. We also found that S. Typhimurium exhibiting macro, red, dry, and rough was detected as early as 1992 in the USA, earlier than in China. Moreover, we identified that antibiotic consumption, agriculture, climate, urban, health, and socioeconomic factors contribute to the development of AMR in Salmonella. We present a globally high-resolution genetic atlas of Salmonella and also identify some factors driving the rise of AMR, which can provide valuable information for understanding the transmission dynamics and evolutionary trajectories of Salmonella.

Colistin resistance mediated by mcr-1-harbouring plasmids is an emerging threat in Enterobacteriaceae, like Salmonella. Based on its major contribution to the diarrhoea burden, the epidemic state and threat of mcr-1-harbouring Salmonella in community-acquired infections should be estimated. This retrospective study analysed the mcr-1 gene incidence in Salmonella strains collected from a surveillance on diarrhoeal outpatients in Shanghai Municipality, China, 2006-2016. Molecular characteristics of the mcr-1-positive strains and their plasmids were determined by genome sequencing. The transfer abilities of these plasmids were measured with various conjugation strains, species, and serotypes. Among the 12,053 Salmonella isolates, 37 mcr-1-harbouring strains, in which 35 were serovar Typhimurium, were detected first in 2012 and with increasing frequency after 2015. Most patients infected with mcr-1-harbouring strains were aged <5 years. All strains, including fluoroquinolone-resistant and/or extended-spectrum β-lactamase-producing strains, were multi-drug resistant. S. Typhimurium had higher mcr-1 plasmid acquisition ability compared with other common serovars. Phylogeny based on the genomes combined with complete plasmid sequences revealed some clusters, suggesting the presence of mcr-1-harbouring Salmonella outbreaks in the community. Most mcr-1-positive strains were clustered together with the pork strains, strongly suggesting pork consumption as a main infection source. The mcr-1-harbouring Salmonella prevalence in community-acquired diarrhoea displays a rapid increase trend, and the ESBL-mcr-1-harbouring Salmonella poses a threat for children. These findings highlight the necessary and significance of prohibiting colistin use in animals and continuous monitoring of mcr-1-harbouring Salmonella.

Little attention has been paid to heavy metal resistance (HMR) to pathogenic bacteria with the wide use of heavy metals as feed additives in food animals. Therefore, present study was constructed to investigate the presence of HMR in Escherichia coli and Salmonella, and its correlation with disinfectant resistance genes (DRGs) and antibiotic resistance genes (ARGs). The heavy metal resistance genes (HMRGs) of 178 E. coli and 294 Salmonella isolated from chicken farms and retail meats were detected by polymerase chain reaction (PCR). The minimal inhibitory concentrations (MICs) of heavy metals were determined by broth micro-dilution method. The complete-genome of E. coli E308 which had indications of multi-resistance was recovered and assembled using third-generation sequencing. Results showed that frequency of different HMRGs in E. coli and Salmonella ranged 0.60 - 77.0% and 0.30 - 87.1%, respectively. MICs of heavy metals for E. coli and Salmonella ranged widely from ≤ 12.5 mg/L to 1600 mg/L. Moreover, the HMRGs (zntA, arsB, merA, pcoR, pcoA, pcoC and chrA) were found to be significantly associated with one or more DRGs (sugE(c), emrE, mdfA, ydgE/ydgF, qacF, sugE(p) and qacEΔ1) and ARGs (sul1, sul2, sul3, tetA, tetB, tetC, bla_TEM, bla_SHV and bla_CTX) (p < 0.05). The present study demonstrated that HMRGs were widely present in E. coli and Salmonella isolated from chicken farm and retail meats, and the association between HMRGs with DRGs and ARGs may lead to the co-resistance of heavy metals and other antimicrobials.

In this study, we report a novel mcr-1 gene variant, named mcr-1.6 , carried by an IncP plasmid in a colistin-resistant Salmonella enterica serovar Typhimurium isolate from a healthy person. Compared with mcr-1 , the mcr-1.6 gene contains two single-nucleotide polymorphisms, one of which results in an arginine to histidine variation (Arg536→His). The plasmid carrying the mcr-1.6 gene was designated pMCR1.6_P053 and is similar to a recently discovered mcr-1 -bearing plasmid found in Klebsiella pneumoniae .