A Survey of Antimicrobial Resistance Determinants in Category A Select Agents, Exempt Strains, and Near-Neighbor Species

Abstract

A dramatic increase in global antimicrobial resistance (AMR) has been well documented. Of particular concern is the dearth of information regarding the spectrum and prevalence of AMR within Category A Select Agents. Here, we performed a survey of horizontally and vertically transferred AMR determinants among Category A agents and their near neighbors. Microarrays provided broad spectrum screening of 127 Francisella spp., Yersinia spp., and Bacillus spp. strains for the presence/absence of 500+ AMR genes (or families of genes). Detecting a broad variety of AMR genes in each genus, microarray analysis also picked up the presence of an engineered plasmid in a Y. pestis strain. High resolution melt analysis (HRMA) was also used to assess the presence of quinolone resistance-associated mutations in 100 of these strains. Though HRMA was able to detect resistance-causing point mutations in B. anthracis strains, it was not capable of discriminating these point mutations from other nucleotide substitutions (e.g., arising from sequence differences in near neighbors). Though these technologies are well-established, to our knowledge, this is the largest survey of Category A agents and their near-neighbor species for genes covering multiple mechanisms of AMR.

Tracking Antimicrobial Resistance Determinants in Diarrheal Pathogens: A Cross-Institutional Pilot Study

“…Understanding that the microarray used here requires approx. 85–90% sequence identity for detection of similar genes (or families of genes) [ 43 , 44 ], it is unclear whether the redesign of probes for this gene will improve microarray specificity.…”

Impact of template denaturation prior to whole genome amplification on gene detection in high GC-content species, Burkholderia mallei and B. pseudomallei

“…Equivalent amounts (3.2 µg) of thermal or chemical amplicons were fragmented and labeled using Bionick DNA-Labeling System (ThermoFisher). Fragmented, biotinylated amplicons were then applied without purification to the ARDM v.3.1 (Customarray, USA), and hybridized overnight at 60 ℃ as previously described [ 15 , 16 ]. Hybridized microarrays were processed, labeled, and interrogated using the Electrasense Reader (Customarray) and previously established positive/negative thresholds [ 15 ].…”

“…Fragmented, biotinylated amplicons were then applied without purification to the ARDM v.3.1 (Customarray, USA), and hybridized overnight at 60 ℃ as previously described [ 15 , 16 ]. Hybridized microarrays were processed, labeled, and interrogated using the Electrasense Reader (Customarray) and previously established positive/negative thresholds [ 15 ]. Burkholderiales-specific ARDM content is found in Additional File 1 .…”

“…This work is an extension to a previously published survey of Category A Select Agents and exempt strains for horizontally and vertically transferred AMR determinants [ 15 ]. Here, we use the Antimicrobial Resistance Determinant Microarray (ARDM) v.3.1 for broad spectrum screening of > 500 AMR determinants in 22 BM and 37 BP strains, with PCR as an orthogonal detection method.…”

Plague Prevention and Therapy: Perspectives on Current and Future Strategies

“…In addition, Cabanel, et al, 2018 cited that independent horizontal transfer may be the reason for unrelated plasmids among these MDR strains. Other drug-resistant strains and antimicrobial resistance mechanisms have been reported and all aspects of drug-resistance in Y. pestis must remain an important research priority [110,111].…”