Genomic characterisation of the population structure and antibiotic resistance of Salmonella enterica serovar Infantis in Chile, 2009-2022

Abstract

Background: Multidrug-resistant (MDR) Salmonella Infantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases of Salmonella Infantis infections have substantially increased in recent years, this study aimed to characterise the genomic epidemiology and antimicrobial-resistance profiles of isolates obtained from different sources, aiming to inform effective surveillance and control measures.

Methods: We sequenced 396 Salmonella Infantis genomes and analysed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and antimicrobial resistance (AMR) profiles of Salmonella Infantis in the country.

Findings: The genomic and phylogenetic analyses showed that Salmonella Infantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. This was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial-susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended-spectrum β-lactamases and have intermediate fluoroquinolone resistance. HC20_343 Salmonella Infantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity.

Interpretation: Our findings show a widespread dissemination of MDR Salmonella Infantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first-line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL-producing Salmonella Infantis with intermediate fluoroquinolone resistance in the continent.

Funding: Partially supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services as part of an award, FDU001818, with 30% percent funded by FDA/HHS; and by Agencia de Investigación y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID-Millennium Science Initiative Program-ICN2021_044.

Keywords: Americas; Antibiotic resistance; CTX-M-65; Chile; Fluoroquinolones; Megaplasmid; Salmonella Infantis; pESI.

Fig. 1

Region of origin, isolation source, and collection year of the Salmonella Infantis isolates analysed in this study. A) Location of continental Chile in South America and distribution of its human population, poultry production, and collected Salmonella Infantis isolates among the 16 Regions (first-level administrative divisions). Note the concentration of these three variables in central Chile, especially in the Metropolitan Region. Population and poultry data were obtained from the corresponding last population and agricultural censuses carried out in 2017 and 2021, respectively (available at http://resultados.censo2017.cl/ and https://www.ine.gob.cl/censoagropecuario/resultados-finales/graficas-regionales. The administrative Regions from which the Salmonella Infantis isolates were collected are indicated. RM: Región Metropolitana. B) Salmonella Infantis isolates distribution per isolation source and per C) collection year.

Fig. 2

Phylogenetic analysis of Chilean Salmonella Infantis genomes. A core SNP-based maximum likelihood phylogeny (2008 variant sites; 95% presence) was constructed with 440 Chilean Salmonella Infantis genomes using Salmonella Infantis N55391 (Enterobase barcode SAL_EA1888AA), a USA strain isolated from poultry in 2014, as the reference. Additionally, metadata regarding the HC20 clusters (clade colours and first ring), isolation source (second ring), isolation year (third ring), and presence of antibiotic-resistance genes/mutations as determined by AMRFinderPlus (coloured squares/stars) were incorporated into the phylogenetic tree.

Fig. 3

Antibiotic-resistance determinants and pESI-like megaplasmid presence among Salmonella Infantis from the HC20_343 cluster. A) Frequency of individual antibiotic-resistant genes/mutations in the HC20_343 coloured by antibiotic class. B) Frequency of overall antibiotic-resistance genes/mutations per genome (blue bars) and antibiotic classes targeted per genome (red bars). C) Presence of pESI-like megaplasmids among the Chilean Salmonella Infantis genomes. A vertical representation of the same phylogenetic tree of Fig. 2 is coloured according to the HC20 clusters. The presence of each of the 315 genes from the pESI-like megaplasmid pN55391 was assessed by ABRicate using a custom database (blue squares). Black horizontal bars above the presence/absence matrix indicate the backbone regions of the megaplasmid (genes in black font) or the antibiotic-resistance regions (genes in red font). A red dashed line rectangle delimits the most variable region among the Chilean pESI-like megaplasmids relative to pN55391. K88-lf (K88-like fimbria), Ipf (Infantis plasmid-encoded fimbria, Ybt (Yersiniabactin synthesis cluster), mer (mercury-resistance cluster), T4P (type-IV pili encoding cluster), Tra (transfer region).

Fig. 4

Population structure of Chilean Salmonella Infantis and intra-source genomic diversity within cluster HC20_343. A) Minimum spanning tree depicting the population structure of Salmonella Infantis in Chile based on the cgMLST profiles of 3002 alleles. Nodes are coloured according to the HC20 clusters determined by HierCC or the isolation source, and their size is proportional to the number of isolates included in each node. The legends indicate the different HC20 clusters present, the isolation sources, and the number of isolates. B) Zoom-in view of the HC20_343 cluster structure with nodes coloured according to the isolation source. The legend also indicates the number of isolates per source within HC20_343. The shaded area and numbers indicate subclusters evidencing transmission of Salmonella Infantis between different sources. C) PAD between unique cgSTs from cluster HC20_343 per isolation source. Each violin plot, truncated at the highest and smallest values, represents the frequency distribution of PADs. The black unbroken and dashed lines represent the median PAD, and the 25th and 75th percentiles, respectively. The n_ST value indicates the number of isolates with unique cgSTs within each isolation source. Only isolates representing unique cgSTs were included in the analysis. Note: In panel 4B, the links and node sizes are the same as in panel 4A. However, panel 4B is presented at a different scale, and some branches were adjusted to prevent overlapping and improve subcluster visualization.