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

• Published in: BMC research notes Vol. 17; no. 1; p. 70
• Main Authors: Taitt, Chris R, Leski, Tomasz A, Compton, Jaimee R, Chen, Amy, Berk, Kimberly L, Dorsey, Robert W, Sozhamannan, Shanmuga, Dutt, Dianne L, Vora, Gary J
• Format: Journal Article
• Language: English
• Published: England BioMed Central 12.03.2024; BMC
• Subjects: Anti-Infective Agents; Antimicrobial agents; Antimicrobial resistance; Burkholderia; Burkholderia - genetics; Burkholderia mallei - genetics; Burkholderia pseudomallei; Denaturation; DNA microarrays; Drug resistance; ESBL; Extended-spectrum β-lactamase; Genes; Genomes; Humans; Public health; Research Note; Resistome; Respiratory Distress Syndrome; Select agents; United States > US; ESBL; Antimicrobial resistance; Resistome; Select agents; Extended-spectrum β-lactamase
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-024-06717-8

In this study, we sought to determine the types and prevalence of antimicrobial resistance determinants (ARDs) in Burkholderia spp. strains using the Antimicrobial Resistance Determinant Microarray (ARDM). Whole genome amplicons from 22 B. mallei (BM) and 37 B. pseudomallei (BP) isolates were tested for > 500 ARDs using ARDM v.3.1. ARDM detected the following Burkholderia spp.-derived genes, aac(6), bla , blaA , penA-BP, and qacE, in both BM and BP while bla , macB, bla  and penA-BC were observed in BP only. The method of denaturing template for whole genome amplification greatly affected the numbers and types of genes detected by the ARDM. Bla was detected in nearly a third of BM and BP amplicons derived from thermally, but not chemically denatured templates. Bla results were confirmed by PCR, with 81% concordance between methods. Sequences from 414-nt PCR amplicons (13 preparations) were 100% identical to the Klebsiella pneumoniae reference gene. Although bla sequences have been observed in B. glumae, B. cepacia, and other undefined Burkholderia strains, this is the first report of such sequences in BM/BP/B. thailandensis (BT) clade. These results highlight the importance of sample preparation in achieving adequate genome coverage in methods requiring untargeted amplification before analysis.