Abstract
Antimicrobial resistance (AMR) has become an urgent public health issue, as pathogens are becoming increasingly resistant to commonly used antimicrobials. While AMR isolate data are available in the NCBI Pathogen Detection Isolates Browser (NPDIB) database, few researches have been performed to compare antimicrobial resistance detected in environmental and clinical isolates. To address this, this work conducted the first multivariate statistical analysis of antimicrobial-resistance pathogens detected in NPDIB clinical and environmental isolates for the US from 2013 to 2018. The highly occurring AMR genes and pathogens were identified for both clinical and environmental settings, and the historical profiles of those genes and pathogens were then compared for the two settings. It was found that Salmonella enterica and E. coli and Shigella were the highly occurring AMR pathogens for both settings. Additionally, the genes fosA, oqxB, ble, floR, fosA7, mcr-9.1, aadA1, aadA2, ant(2”)-Ia, aph(3”)-Ib, aph(3')-Ia, aph(6)-Id, blaTEM-1, qacEdelta1, sul1, sul2, tet(A), and tet(B) were mostly detected for both clinical and environmental settings. Ampicillin, ceftriaxone, gentamicin, tetracycline, and cefoxitin were the antimicrobials which got the most resistance in both settings. The historical profiles of these genes, pathogens, and antimicrobials indicated that higher occurrence frequencies generally took place earlier in the environmental setting than in the clinical setting.
Highlights
Every year, foodborne pathogens cause the sicknesses of one in six Americans, hospitalize 128,000, and cause the deaths of 3,000 [1]
Comparing Antimicrobial resistance (AMR) Pathogens Found in Environmental and Clinical Samples
Major pathogens were detected from the hierarchical clustering result (Figure 1), along with the visualization of the pathogens in the two-dimensional space created from principal component analysis (Supplementary Figure 1)
Summary
Foodborne pathogens cause the sicknesses of one in six Americans, hospitalize 128,000, and cause the deaths of 3,000 [1]. There are 31 known pathogens that cause foodborne illness, and several unspecified agents that have yet to be identified [2, 3]. These pathogens obtain resistance to commonly used antimicrobials [4]. In order to combat AMR foodborne pathogens, the National Antimicrobial Resistance Monitoring System (NARMS) has been gathering data from human clinical samples, animal slaughter samples, and retail meat samples [5, 6]. NPDIB contains useful information on AMR pathogen isolates throughout the countries in the world, including sampling locations, date, isolation sources, isolate types, and antimicrobial-resistance genotypes. Useful information on antimicrobial resistance should be obtained by analyzing the data from NPDIB
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