Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica

Abstract

Salmonella enterica is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on Salmonella isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of Salmonella pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:– and the Salmonella genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between Salmonella isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the spv operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed Salmonella genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.

Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the blaCTX-M-65 Gene with or without fosA3 in pESI-like Plasmids

“…However, there was also considerable variation, as shown by their comparison with some key examples ( Figure 1 ), which include the original pESI plasmid, detected in a human isolate from Israel (119944), which lacks most of the R1 region [ 7 , 8 ]. A higher degree of similarity was found with two bla CTX-M-65 -positive plasmids, with or without fosA3 (FSIS1502169 and CVM N18S2198, respectively; [ 14 , 24 ]), identified in isolates from chicken samples in the USA.…”

“…Infantis ([ 13 , 16 ]; Figure 2 ). They have been reported in humans and along the poultry production chain in the USA and South America, with only a limited number of isolates being detected in other livestock animals [ 14 , 24 , 42 , 43 , 44 , 45 , 46 ]. Isolates carrying pESI-like plasmids positive for bla CTX-M-65 ± fosA3 have also been associated with human clinical cases in Europe, specifically in patients with a travel history to America [ 10 , 12 , 16 ].…”

Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

“…We found that the genomic regions of A. cerana symbionts were essentially identical to two plasmids belonging to the IncQ-1 subgroup. This finding indicates that the IncQ plasmids are integrated into the chromosome of bee gut bacteria, as found in Salmonella enterica [ 47 ] and Vibrio cholerae [ 48 ]. Interestingly, we detected sequence deletions in the integrated plasmid fragments, especially in the strB and replicon modules.…”

Five Complete Salmonella enterica Serotype Reading Genomes Recovered from Patients in the United States

“…Clade 2 primarily contained human isolates, and its pangenome was considerably smaller than those of the other clades, but further analysis to understand these differences was not performed ( 2 ). Closed sequences of Reading are required for pangenome exploration and to further understand the novel “emergent” subclade, but only 11 are currently available ( 3 , 4 ), and none are from US patients. Here, we generated five complete clinical Reading sequences from Clades 1 and 2 to serve as references.…”