Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources

Abstract

Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.

Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates

“…On the other hand, all isolates carried an IncFIB plasmid that could increase colonization in the chicken cecum, which may help to explain its persistence in the food animal population [52]. Within the plasmid IncFIB, some of the common resistance genes identified were similar to those previously reported [53], including AAC(3)-IV, aadA2, APH(4)-Ia, cmlA1, dfrA12, floR, sul1, sul3, and tet(A), which encode resistance to gentamicin, streptomycin, hygromycin B, chloramphenicol, trimethoprim, florphenicol, sulfonamides, and tetracycline, respectively. It should be noted that gentamicin is a critically important antimicrobial, while chloramphenicol, trimethoprim, sulfonamides, and tetracycline are highly important antibiotics in human medicine, according to the latest WHO publication [54].…”

Virulence and Antibiotic Resistance Genes in Listeria monocytogenes Strains Isolated From Ready-to-Eat Foods in Chile

“… Gygli et al (2019) reported that the possible discrepancy between gene detection by WGS and antibiotic susceptibility testing of Mycobacterium tuberculosis strains could arise because the clinical concentrations established to classify it as resistant have cutoff scores that are too high, thus misclassifying strains as susceptible. Aljahdali et al (2020) , found a positive concordance between the presence of resistance genes and resistance phenotypes in various in Salmonella strains; however, they also observed that some strains with beta-lactamase resistance genes were still phenotypically susceptible to amoxicillin-clavulanic acid. Therefore, the difference between genotype and phenotype in these strains could be due to exceptional mutations that reduce gene expression and can confer susceptibility to antimicrobial agents used in susceptibility tests.…”

Prevalence and Characteristics of Phenicol-Oxazolidinone Resistance Genes in Enterococcus Faecalis and Enterococcus Faecium Isolated from Food-Producing Animals and Meat in Korea

“…Twenty-two E. faecalis and E. faecium isolates harboring phenicol-oxazolidinone resistance genes were used as the donor cells, and with Escherichia coli strain J53 served as the recipient strain for the conjugation experiments using methods previously described by Aljahdali et al with minor modifications [ 32 ]. Briefly, each donor and recipient cells were cultured on TSA agar and incubated at 37 °C for 24 h. Cultured donor and recipient cells were mixed in 500 µL LB broth (1:1) and incubated at 37 °C for 3 h. Transconjugants were streaked on LB agar containing 200 mg/L sodium azide and incubated at 37 °C for 24 h. Several colonies were picked and plated on MacConkey agar at 37 °C for 24 h. Transconjugants from MacConkey agar were subcultured on TSA, incubated at 37 °C for 24 h, and subjected to PCR for the optrA , poxtA , cfr , and fexA genes, respectively, according to Table 6 .…”