Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State

Abstract

Salmonella enterica serotype typhimurium (S. typhimurium) boasts a broad host range and can be transmitted between livestock and humans. While members of this serotype can acquire resistance to antimicrobials, the temporal dynamics of this acquisition is not well understood. Using new York State (NYS) and its dairy cattle farms as a model system, 87 S. Typhimurium strains isolated from 1999 to 2016 from either human clinical or bovine-associated sources in NYS were characterized using wholegenome sequencing. More than 91% of isolates were classified into one of four major lineages, two of which were largely susceptible to antimicrobials but showed sporadic antimicrobial resistance (AMR) gene acquisition, and two that were largely multidrug-resistant (MDR). All four lineages clustered by presence and absence of elements in the pan-genome. the two MDR lineages, one of which resembled S. Typhimurium DT104, were predicted to have emerged circa 1960 and 1972. The two largely susceptible lineages emerged earlier, but showcased sporadic AMR determinant acquisition largely after 1960, including acquisition of cephalosporin resistance-conferring genes after 1985. These results confine the majority of AMR acquisition events in NYS S. typhimurium to the twentieth century, largely within the era of antibiotic usage. Salmonella enterica subsp. enterica serotype Typhimurium (S. Typhimurium) consistently ranks as one of the serotypes most commonly isolated from human clinical cases in the United States; in 2016, it was reported as being responsible for 4,581 culture-confirmed human infections in the U.S. alone 1. Additionally, S. Typhimurium is capable of infecting a broad range of hosts: it is frequently isolated not only from humans, but from animals as well, including livestock, rodents, and birds 2-4. Within the serotype, numerous S. Typhimurium lineages have been identified, several of which are notable due to their propensity for resistance to antimicrobials 5. Many of these lineages have been assigned using phage typing, a practice by which S. Typhimurium can be differentiated based on its susceptibility to lysis by phages of varying specificity 6. Host range can vary within phage type, as some phage types (e.g. DT104, DT204, DT49) are commonly associated with epidemics among livestock and humans 2,6,7 , while others exhibit a narrower host range (e.g. DT2 and DT99, which are highly virulent in pigeons) 6-9. Additionally, a number of S. Typhimurium lineages are often associated with distinct antimicrobial resistance (AMR) profiles; for example, S. Typhimurium DT104 is often characterized by its resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline (ACSSuT), although AMR profiles within a lineage can vary 10-13. While whole-genome sequencing (WGS) is being increasingly employed to characterize S. Typhimurium from diverse sources at high resolution, the bulk of the effort has focused on characterizing distinct lineages that have been responsible for human epidemics (e.g. DT104) 12,14. Furt...

Genomic characterization of endemic and ecdemic non-typhoidalSalmonella entericalineages circulating among animals and animal products in South Africa

“…The strain isolated in this study possessed five AMR genes: streptomycin resistance-conferring aadA2 , beta lactamase bla CARB-2 , chloramphenicol resistance-conferring floR , sulfonamide resistance-conferring sul1 , and tetracycline resistance-conferring tet(G) (Figure 7). Notably, when compared to genomes from a previous study of S. Typhimurium in the United States (New York State) (32), this isolate clustered among DT104 strains isolated from dairy cattle and humans, sharing a common ancestor dated circa 1975 (95% CI [1467.42, 1999.00]; Supplemental Figure S6).…”

“…Notably, some African S. Typhimurium lineages were distributed across the African continent, while others were strongly associated with a particular region/country (Figure 7 and Supplemental Text). When compared to genomes from a previous study of S. Typhimurium from New York State that have been shown to be representative of the human- and bovine-associated S. Typhimurium population in the United States as a whole (32), only five of 24 S. Typhimurium strains sequenced here (20.8%) shared a common ancestor with one or more New York State strains after 1900 (Supplemental Figure S6 and Supplemental Text). This indicates that many of the strains sequenced here are not closely related to S. Typhimurium lineages circulating among cattle and humans in the United States.…”

“…The resulting phylogeny was annotated using the bactaxR package in R (Figure 7). All aforementioned S. Typhimurium SNP calling and phylogeny construction steps were repeated to construct an additional time-scaled ML phylogeny, using the 24 isolates sequenced here and 87 human- and bovine-associated S. Typhimurium isolates from a previous study of the serotype in New York State in the United States (32) ( n = 111; Supplemental Figure S6).…”

Monitoring the Antimicrobial Resistance Dynamics of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing

“…GFF files produced by Prokka (see section "In Silico Antimicrobial Resistance Determinant Detection" above) were used as input for Roary version 3.12.0 (Page et al, 2015), which was used to identify orthologous gene clusters at a 70% protein BLAST (blastp) identity threshold. The resulting gene presence/absence matrix produced by Roary was used as input for besPLOT (https://github.com/lmc297/besPLOT) (Carroll et al, 2020a), which was used to perform non-metric multidimensional scaling (NMDS) (Kruskal, 1964) and construct plots in two dimensions using a Jaccard distance metric and the following dependencies in R: vegan version 2.5-6 (Oksanen et al, 2019), shiny version 1.4.0.2 (Chang et al, 2020), ggplot2 version 3.3.0 (Wickham, 2016), plyr version 1.8.6 (Wickham, 2011), dplyr version 0.8.5 (Wickham et al, 2020), cluster version 2.1.0 (Maechler et al, 2019), and ggrepel version 0.8.2 (Slowikowski, 2020).…”

“…This is a provisional file, not the final typeset article One particularly notable observation is represented by multiple, independent acquisitions of the betalactamase blaCMY among S. Typhimurium and S. Typhimurium Copenhagen, as all blaCMY acquisition events within this serotype group were confined to the 2000s. blaCMY can confer resistance to cephalosporins, including (i) ceftriaxone, which has been used in human medicine since the early 1980s, and is used to treat invasive salmonellosis cases when fluoroquinolones cannot be used (e.g., for pediatric salmonellosis cases), and (ii) ceftiofur, which has been used in veterinary settings since the late 1980s to treat disease cases among dairy cattle and other animals (Hornish and Kotarski, 2002;Alcaine et al, 2005;Liebana et al, 2013;Yang et al, 2016;Carroll et al, 2017b;Carroll et al, 2020a). Because blaCMY often confers resistance to both ceftriaxone and ceftiofur, there has been concern that the use of ceftiofur in livestock can contribute to the dissemination of blaCMY and thus yield bacterial populations that are co-resistant to ceftriaxone (Alcaine et al, 2005;Tragesser et al, 2006;Carroll et al, 2017b;Carroll et al, 2020a).…”