Plasmid-driven clonal expansion of multidrug-resistant monophasic Salmonella Typhimurium in a Global Food Trade Hub

Abstract

Shenzhen, a major port city with a heavily imported food supply, offers a critical setting to examine the spread and adaptation of multidrug-resistant Salmonella 1,4,[5],12:i: - (S. 1,4,[5],12:i:-). This study integrates 17 years of genomic, epidemiological, and food safety data. We explored the serovar's population structure, antibiotic resistance gene (ARG) patterns, and transmission dynamics locally and globally. Our analyses revealed substantial rise in S. 1,4,[5],12:i: - prevalence among non-typhoidal Salmonella isolates over the past 17 years, from 2.27% in 2007 to 24.79% in 2023. S. 1,4,[5],12:i: - was predominated by ST34 (97.9%), with high genotypic resistance to aminoglycosides (100%), tetracyclines (96.6%), β-lactams (89.3%), and sulphonamides (88.5%). Phylogenetic analysis separated S. 1,4,[5],12:i: - into four clades. Clade 4, first detected in Shenzhen in 2013, emerged as the predominant lineage by 2023 (56.9%). This clade exhibited minimal genetic diversity (≤ 38 core SNPs), with adaptive traits linked to the acquisition of resistance-associated plasmids. Notably, plasmid-driven ARGs, including carbapenem resistance genes, have emerged as a growing concern. Transmission analysis identified two key transmission dynamics: transient outbreaks primarily involving food handlers and persistent lineages sustained through local and international spread, often facilitated by the food supply chain. These findings underscore the role of occupational carriers and imported food products in the dissemination of ARGs, emphasizing the need for enhanced surveillance and improved health and hygiene practices for food handlers. This study provides a comprehensive molecular epidemiological framework for addressing multidrug-resistant Salmonella in globalized urban food hubs, offering a foundation for future surveillance and control efforts.

Keywords: Salmonella Typhimurium monophasic variant; food handlers; multidrug resistance (MDR); plasmid; transmission routes.

Figure 1.

The detection situation of non-typhoidal Salmonella in Shenzhen from 2007 to 2023. The bar charts indicate the total counts of Salmonella and the total counts of non-typhoidal Salmonella from different sources. The top of the bar chart indicates the total NTS isolates per year. The line charts depict the proportions of Salmonella Typhimurium and S.1,4,[5],12:i:- among non-typhoidal Salmonella. (Abbreviations: IDDS = Infectious Diarrhoea Disease Surveillance; FSS = Food Safety Surveillance; OFHS = Occupational Food Handler Screening.).

Figure 2.

Population structure and epidemiology of S. 1,4,[5],12:i:- strains. (A) Population structure of S. 1,4,[5],12:i:-. Maximum-likelihood phylogenetic tree constructed based on the 1908 genome sequences reported in this study and 1,523 publicly available S. 1,4,[5],12:i:- strains with genotypic information and metadata. The scale bar indicates the number of substitutions per site per genome. Metadata is visualized on the concentric rings according to the legend, from inside to outside;1. Clade branch, 2. Sequence type (ST), 3. Source of isolates, 4–5. Country and City, 6–9. Presence of multidrug resistance genes markers (QRDR mutation, quinolone, ESBL, and AmpC), 10–12. Presence of plasmid replicons (IncHI2/2A, Col_pHAD28, p0111). (B) The time-scaled phylogeny of S. 1,4,[5],12:i:- strains, derived from time divergence analysis conducted with TreeTime. The illustration depicts the phylogenetic estimation of the evolutionary rate of isolates using TreeTime on a time-scaled phylogeny. The X-axis represents time, and the Y-axis indicates root-to-tip regression. (C) Epidemiological prevalence of clade branches in Shenzhen. The X-axis represents time, and the Y-axis shows the stacked percentage.

Figure 3.

Strains were grouped into clusters based on an SNP threshold of ≤3. Only clusters containing more than two strains are shown. (A) Timing and Size of S. 1,4,[5],12:i:- Genetic Clusters. Clusters are plotted on separate horizontal lines according to the date of isolation. The size of each point represents the relative frequency of strains within the cluster. Blue points indicate clusters with a frequency of ≥ 5 strains, while red points represent clusters with a frequency of < 5 strains. (B) Geographic Dissemination of S. 1,4,[5],12:i:- Clusters. The grey nodes represent Clusters, and the colours in the legend indicate clusters from the corresponding regions as shown in the legend. Among them, yellow represents Asia excluding China, green represents China excluding Guangdong Province, and blue represents Guangdong Province excluding Shenzhen City. (C) Transmission Dynamics and Demographics of S. 1,4,[5],12:i:- Genetic Clusters. The yellow “Human” includes isolates from other regions and those from Shenzhen IDDS and OHFS sources, while the purple “Food” includes foodborne isolates from other regions and those from Shenzhen FSS sources.

Figure 4.

ARGs-related antibiotic types and plasmid replicon carriage associated with S. 1,4,[5],12:i:- in Shenzhen. The dashed line on the Y-axis indicates the point from 2011 where the number of S. 1,4,[5],12:i:- isolates identified in Shenzhen exceeded 20 strains.(A) Prevalence of main ARGs related to antibiotics among S. 1,4,[5],12:i:- in Shenzhen.(B) Prevalence of main plasmid replicons among S. 1,4,[5],12:i:- in Shenzhen.

Figure 5.

Analysis of the association and co-linearity between resistance genes and plasmids. (A,B) Network diagrams showing the association between resistance genes and plasmids in S. 1,4,[5],12:i:- isolates from Shenzhen (ρ > 0, p < 0.05). Blue dots represent resistance genes, and red dots represent plasmid replicons. Red lines indicate strong associations (ρ > 0.7), orange lines indicate moderate associations (0.3 < ρ ≤ 0.7), and grey lines indicate weak associations (ρ ≤ 0.3). Panel A presents the overall association network between resistance genes and plasmids. Panel B presents the strong association network between resistance genes and plasmids. (C) Co-occurrence relationships between resistance genes and plasmids in S. 1,4,[5],12:i:- from Shenzhen analysed using the Kleit method. Gradient colours are used to represent the proportion, with the X-axis indicating plasmids and chromosomes (chr), the Y-axis on the left side indicating types of antibiotics, and the labels on the right side corresponding to the resistance genes.