Dynamic antimicrobial resistance and phylogenomic structure of Salmonella Typhimurium from 2007 to 2019 in Shanghai, China

Abstract

Salmonella enterica serovar Typhimurium is an important foodborne pathogen associated with human salmonellosis worldwide. A retrospective screening was performed to elucidate the prevalence, antimicrobial resistance, and phylogenomic characterization of this pathogen in Shanghai, China. S. Typhimurium isolates were selected from 2,211 serotyped Salmonella isolates collected during 2007-2019. Two hundred and seventy-seven S. Typhimurium isolates were detected in 15 of 16 districts in Shanghai. It was noted that 214 (77.3%) isolates were multi-drug resistant and 32 (11.6%) isolates were resistant to ciprofloxacin and 5 (1.8%) isolates were further resistant to ceftriaxone. Poisson generalized linear mixed model results showed that the multi-drug resistance (MDR) in 2017 and 2018 was significantly higher than that in 2010 (P＜0.05), highlighting an increase in the risk of MDR. Phylogenetic results showed that a global data set of 401 sequenced S. Typhimurium isolates was classified into four clones (ST36, ST313, ST19, and ST34), which appeared in international clonal dissemination. The ST34 isolates from China fell into two clades, ST34C1 and ST34C2, the latter of which might originate from Shanghai, and then expanded nationally, accompanied by extended-spectrum β-lactamase gene bla_CTX-M-14 and a mutation in quinolone resistance-determining region of the gyrA 87 site. Furthermore, bla_CTX-M-14 linking to ISEcp1 upstream and ΔIS903B downstream was found in IncI (Gamma)-like plasmids, and the plasmid conjugation contributed to its horizontal transmission. To our knowledge, it is the first report of the epidemiological and phylogenetic characterization for S. Typhimurium including the emerged clade ST34C2 in Shanghai, warranting the necessity of surveillance for this high-risk pathogen.

Importance: Our study uncovered a widespread distribution of Salmonella enterica serovar Typhimurium isolates in Shanghai accompanied by the increase in antimicrobial resistance (AMR) especially MDR during a 10-year period, which filled in the gap about a long period of continuous monitoring of AMR in this pathogen in Shanghai. Meanwhile, we identified a new clade ST34C2 of S. Typhimurium with the acquisition of IncI (Gamma)-like plasmids mediated by extended-spectrum β-lactamase gene bla_CTX-M-14 as well as gyrA 87 mutation, which had not been reported before. It was noted that IncI (Gamma)-like plasmids were reported in S. Typhimurium for the first time and conjugation could accelerate the spread of antimicrobial resistance gene bla_CTX-M-14. These findings on the epidemic, antimicrobial resistance, and phylogenomic characterization for S. Typhimurium provide valuable insights into its potential risk to public health and also the basis for AMR prevention and control strategies in Shanghai in the future.

Keywords: IncI (Gamma) plasmids; Salmonella Typhimurium; antimicrobial resistance; phylogenomic analysis.

Fig 1

Prevalence of S. Typhimurium isolates in Shanghai, China. (A) The distribution of isolates in the districts of Shanghai city. The districts where S. Typhimurium isolates were identified are indicated in red, and the district where the isolate was not identified is indicated in blue-green. The number of isolates obtained from each district is shown. The initial map originated from DataV.GeoAtlas (http://datav.aliyun.com/portal/school/atlas/area_selector), followed by the use of Inkscape software to overlay different colored shades for representation. (B) The sample sources of isolates. The number of isolates obtained from different sources is shown.

Fig 2

(A) ST distribution of S. Typhimurium isolates bearing bla_CTX-M in Australia, China, Germany, Kenya, the United Kingdom, and the United States. (B) The prevalence of S. Typhimurium isolates bearing bla_CTX-M from 2005 to 2021. (C) Phylogenomic analysis of S. Typhimurium isolates bearing bla_CTX-M from 15 countries. Rings ①–⑨ from inside to outside along the tree represent metadata including STs, countries, sources, and bla_CTX-M variants (as shown in the inset legend).

Fig 3

Phylogenetic tree of S. Typhimurium isolates bearing bla_CTX-M in China. Leaf nodes are colored by provinces (see the key). The colors of isolate tips represent metadata columns including STs, provinces, years, sources, bla_CTX-M variants (bla_CTX-M-14, bla_CTX-M-15, bla_CTX-M-55, and bla_CTX-M-65), and mutations in QRDR of GyrA (as shown in the inset legend). Light-green and pink shading shows clades ST34C1 and ST34C2, respectively.

Fig 4

Sequence characterization of p11216B plasmid (A) and p10405B plasmid (B) in this study. Sequence comparison of IncI (Gamma) plasmids and IncI1-I (Alpha) plasmids (C). IncI (Gamma) plasmids included S. Enteritidis pSE115 (Accession number KT868530). IncI1-I (Alpha) plasmids included Escherichia coli pEK204 (Accession number NC_013120), Escherichia coli pEC32-IncI1 (Accession number CP085621), S. Heidelberg pSL476_91 (Accession number NC_011081), and S. Typhimurium pR17.1451_p102k (Accession number CP063296). Areas shaded in gray indicate homologies between the corresponding genetic loci.