Epidemiologic and genomic insights on mcr-1-harbouring Salmonella from diarrhoeal outpatients in Shanghai, China, 2006-2016

Abstract

Background: 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.

Methods: 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.

Findings: 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.

Interpretation: 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.

Keywords: Children; Multi-drug resistant; Outbreak; Salmonella; Swine; mcr-1.

Fig. 1

Epidemiological description of the Salmonella isolates used in this study. From top to bottom: (1) the amount of isolates in each year from 2006 to 2016; (2) the serotype composition ratios of S. Typhimurium, S. Enteritidis, and the group of other serotypes in each year; (3) the composition ratios of each age group in each year.

Fig. 2

The rate of mcr-1-harbouring isolates grouped by different factors. (a–b) The rates of mcr-1-harbouring isolates among the total Salmonella sp. strains in different years (a) and in different age groups (b). (c) The rates of mcr-1-harbouring S. Typhimurium strains among just the S. Typhimurium isolates in different age groups. (d) The rates of mcr-1-harbouring isolates among the total Salmonella sp. strains in different serotypes.

Fig. 3

Phylogenetic analysis of the mcr-1-harbouring S. Typhimurium isolates obtained in this study. From left to right: (1) Maximum likelihood (ML) tree of mcr-1-harbouring S. Typhimurium isolates. The font colour of the labels in the tree represents the replicon sequence type of the mcr-1-harbouring plasmids (blue: IncI2, red: IncHI2, green: IncX4); (2) The sampling dates of the outpatients; (3) The length of the mcr-1-harbouring plasmids; (4) A heatmap of the antimicrobial resistance genes on the mcr-1-harbouring plasmids. The yellowish shade indicates close genomic clonal clusters. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 4

Distribution of the replicon sequence types of mcr-1-harbouring plasmids, based on the sampling dates.

Fig. 5

The conjugation rates of the mcr-1-harbouring plasmids isolated in this study. (a–c) The 37 mcr-1-harbouring Salmonella strains were used as the donors, and E. coli J53 strain (a), S. Typhi CT18 strain (b), or K. pneumoniae BJ1988 strain (c) was used as the recipient. (d) Five E. coli J53 strains (two carrying the mcr-1 IncHI2 plasmid, two carrying the mcr-1 IncI2 plasmid, and one carrying the mcr-1 IncX4 plasmid) were used as the donors, and four S. Derby strains, four S. Enteritidis strains, and five S. Typhimurium strains were used as the recipients. The grey triangles and circles are the log₁₀-transformation of the transfer frequency data after incubation at 37 °C for 4 h and 24 h, respectively.

Fig. 6

Heatmap of mcr-1-harbouring plasmids based on the presence of coding sequences (cds). (a–b) Heatmap of mcr-1-harbouring IncHI2 plasmids (a) and mcr-1-harbouring IncI2 plasmids (b). Red represents the presence of similar cds. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 7

Dendrograms of mcr-1-positive S. Typhimurium isolates from different hosts. In addition to the 35 mcr-1-harbouring S. Typhimurium strains from humans found in this study, another 10 mcr-1-positive S. Typhimurium strains from swine obtained by our team and 55 mcr-1-negative S. Typhimurium genomic sequences retrieved from GenBank (comprised of 19 from poultry, 11 from swine, and 25 from humans) were also included in this analysis. Red: mcr-1-harbouring S. Typhimurium strains isolated from humans; Green: S. Typhimurium strains isolated from swine; Purple: S. Typhimurium strains isolated from poultry; Blue: mcr-1-negative S. Typhimurium strains isolated from humans. Right phylogenetic tree: the strains carrying mcr-1 plasmids are marked with light-brown spots, the branches containing swine-source strains are marked with light green boxes as the background, and the branches containing poultry-source strains are marked with light purple boxes. Bottom-left phylogenetic tree: the branches containing strains from different sources are marked with the same colour format as the phylogenetic tree on the right, to more clearly present the separation of the branches and locations of the mcr-1-harbouring strains. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)