Antibiotic Resistance in Salmonella Typhimurium Isolates Recovered From the Food Chain Through National Antimicrobial Resistance Monitoring System Between 1996 and 2016

Abstract

Salmonella is a major foodborne pathogen which causes widespread contamination and infection worldwide. Salmonella Typhimurium is one of the leading serovars responsible for human and animal salmonellosis, globally. The increasing rate of antibiotic resistance in Salmonella Typhimurium poses a significant global concern, and an improved understanding of the distribution of antibiotic resistance patterns in Salmonella Typhimurium is essential for choosing the suitable antibiotic for the treatment of infections. To evaluate the roles of animal and human in antibiotic resistance dissemination, this study aims to categorize 11,447 S. Typhimurium strains obtained across the food-chain, including food animals, retail meats and humans for 21 years in the United States by analyzing minimum inhibitory concentrations (MICs) values for 27 antibiotics. Random Forest Algorithm and Hierarchical Clustering statistics were used to group the strains according to their minimum inhibitory concentration values. Classification and Regression Tree analysis was used to identify the best classifier for human- and animal-populations' isolates. We found the persistent population or multi-drug resistant strains of S. Typhimurium across the four time periods (1996∼2000, 2001∼2005, 2006∼2010, 2011∼2016). Importantly, we also detected that there was more diversity in the MIC patterns among S. Typhimurium strains isolated between 2011 and 2016, which suggests significant emergence of diversified multi-drug resistant strains. The most frequently observed (43%) antibiotic resistance patterns found in S. Typhimurium were tetra-resistant pattern ASSuT (ampicillin, streptomycin, sulfonamides, and tetracycline) and the penta-resistant pattern ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline). Animals (mainly swine and bovine) are the major source for these two frequently found antibiotic resistance patterns. The occurrence of antibiotic resistant strains from humans and chicken is alarming. Strains were mostly susceptible to fluoroquinolones. Together, this study helped in understanding the expansion of dynamics of antibiotic resistance of S. Typhimurium and recommended fluoroquinolones as a possible treatment options against S. Typhimurium infection.

Keywords: Salmonella Typhimurium; antibiotic resistance; fluoroquinolones; foodborne pathogen; minimum inhibitory concentration; population diversity.

FIGURE 1

General trend analysis of antibiotic resistance for some certain commonly used molecules (denoted by the color of the lines as given in legend). (A) The resistance pattern in animal isolates, (B) the resistance pattern in meat isolates and (C) the resistance pattern for the human isolates. The XX’ presents the time of data collection while YY’ gives the resistance percent. [Tetracycline (TET), Ampicillin (AMP), Streptomycin (STR), Chloramphenicol (CHL), Sulfamethoxazole-trimethoprim (COT)].

FIGURE 2

The dynamics of antibiotic resistance features of Salmonella Typhimurium strains across 21 years in the United States. The multidimensional scaling plot of 11,447 Salmonella Typhimurium strains with MIC values for each bacterial isolate were used for producing the proximity matrices, where x-, y- and z- axes are the multidimensional scaling coordinates. Bacterial isolates with similar MIC values are represented by points close one to the other, whereas isolates with dissimilar antibiotic resistant MIC values are represented by separated points. Each bacterium was indicated as individual dot, where colors represented four different periods. (A) The dynamics of antibiotic resistance for four separate time periods. Time period 1 from the year 1996 to 2000, time period 2 from the year 2001 to 2005, time period 3 from the year 2006 to 2010 and time period 4 from the year 2011 to 2016. (B) The dynamics of antibiotic resistance for all four time periods describing together.

FIGURE 3

The population diversity of 11,447 S. Typhimurium strains from humans, animals, and retail meats. (A) Population diversity of S. Typhimurium strains grouped by hierarchical clustering. A hierarchical tree with 200 bootstrapping, by using the MIC value of 27 antibiotics, was used to group different population. (B) The antibiogram for individual S. Typhimurium strains were shown, with blue indicating the susceptibility, and yellow indicating the resistance, based on the MICs interpreted by the CLSI-2017 standards. Gray color indicates strains without MIC value.

FIGURE 4

Graphical representations of four antibiotic resistance patterns (ASSuT, ACSSuT, ACSSuTAmc and ACSSuTAmcAxoTio) found in S. Typhimurium strains through 1996–2016 in United States. (A) ASSuT (Ampicillin, Streptomycin, Sulfonamides, and Tetracycline) resistance patterns found in S. Typhimurium isolates from animals, meat and humans. Though the ASSuT resistance in animal and human isolates of Typhimurium declined sharply during 2002–2008, the resistance is on rise in the recent years. The ASSuT resistance in meat isolates showed increasing pattern with time. (B) ACSSuT (Ampicillin, Chloramphenicol, Streptomycin, Sulfonamides, and Tetracycline) resistance patterns found in S. Typhimurium isolates from animals, meat and humans. The ACSSuT resistance in human and meat isolates of Typhimurium showing decreasing pattern but the same resistance in animal isolates showing increasing trend with the time. (C) ACSSuTAmc (Ampicillin, Chloramphenicol, Streptomycin, Sulfonamides, Tetracycline, and Amoxicillin-clavulanic acid) resistance patterns found in S. Typhimurium isolates from animals, meat and humans. The ACSSuTAmc resistance in human and meat isolates of Typhimurium showing decreasing pattern but in animal isolates the resistance remained high with time. (D) ACSSuTAmcAxoTio (Ampicillin, Chloramphenicol, Streptomycin, Sulfonamides, Tetracycline, Amoxicillin-clavulanic acid, Ceftriaxone, and Ceftiofur) resistance patterns found in S. Typhimurium isolates from animals, meat and humans. ACSSuTAmcAxoTio resistance in animal isolates showed increasing tendency in the recent years. The XX’ presents the time of data collection while YY’ gives the percent of resistance. (E) Pie chart showing the percentage of distribution of four different resistance patterns among 7237 isolates of S. Typhimurium from animals, meat and humans.

FIGURE 5

Graphical representations of four antibiotic resistance patterns (ASSuT, ACSSuT, ACSSuTAmc and ACSSuTAmcAxoTio) found in S. Typhimurium isolates through 1996–2016 in United States obtained from five different hosts (bovine, chicken, swine, turkey, and human). (A) ASSuT (Ampicillin, Streptomycin, Sulfonamides, and Tetracycline) resistance patterns found in S. Typhimurium isolates from bovine, chicken, swine, turkey and human. S. Typhimurium isolates from bovine, swine and turkey showed higher percentage of this resistance pattern than the isolates from chicken and human. (B) ACSSuT (Ampicillin, Chloramphenicol, Streptomycin, Sulfonamides, and Tetracycline) resistance patterns found in S. Typhimurium isolates from bovine, chicken, swine, turkey and human. Swine and bovine isolates showed more ACSSuT resistance pattern than other host isolates. (C) ACSSuTAmc (Ampicillin, Chloramphenicol, Streptomycin, Sulfonamides, Tetracycline, and Amoxicillin-clavulanic acid) resistance patterns found in S. Typhimurium isolates from bovine, chicken, swine, turkey and human. Swine and bovine isolates showed more percentage of resistance pattern among all host isolates. (D) ACSSuTAmcAxoTio (Ampicillin, Chloramphenicol, Streptomycin, Sulfonamides, Tetracycline, Amoxicillin-clavulanic acid, Ceftriaxone, and Ceftiofur) resistance patterns found in S. Typhimurium isolates from bovine, chicken, swine, turkey and human. Percentage of this resistance pattern found high in bovine Typhimurium isolates. The XX’ presents the time of data collection while YY’ gives the percent of resistance.

FIGURE 6

The dynamics of antibiotic resistance features of Salmonella Typhimurium isolates according to the all sources (A) such as animal (C), meat (B) and human (D) used in this study. The diversity of antimicrobial resistance is greater in the isolates from the human population than in those from animals and animal meat.

FIGURE 7

The dynamics of antibiotic resistance features of Salmonella Typhimurium isolates by host population (A) such as Human (B), Chicken (C), Bovine (D), Porcine (E), Turkey (F). S. Typhimurium strains from human and chicken showed high antibiotic resistance diversity more than bovine, porcine and turkey strains.