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Taitt CR, Leski TA, Compton JR, Chen A, Berk KL, Dorsey RW, Sozhamannan S, Dutt DL, Vora GJ. Impact of template denaturation prior to whole genome amplification on gene detection in high GC-content species, Burkholderia mallei and B. pseudomallei. BMC Res Notes 2024; 17:70. [PMID: 38475810 DOI: 10.1186/s13104-024-06717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
OBJECTIVE 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). RESULTS 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), blaBP/MBL-3, blaABPS, penA-BP, and qacE, in both BM and BP while blaBP/MBL-1, macB, blaOXA-42/43 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. BlaTEM was detected in nearly a third of BM and BP amplicons derived from thermally, but not chemically denatured templates. BlaTEM 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 blaTEM 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.
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Affiliation(s)
- Chris R Taitt
- Nova Research Inc., Alexandria, VA, 22308, USA
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Tomasz A Leski
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Jaimee R Compton
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Karle's Fellow, US Naval Research Laboratory, Washington, DC, USA
| | - Kimberly L Berk
- US Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Robert W Dorsey
- US Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Frederick, MD, USA
- Joint Research and Development, Inc., Stafford, VA, USA
| | - Dianne L Dutt
- Defense Threat Reduction Agency, Joint Science and Technology Office, Ft. Belvoir, VA, USA
| | - Gary J Vora
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA.
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Markowicz A, Bondarczuk K, Cycoń M, Sułowicz S. Land application of sewage sludge: Response of soil microbial communities and potential spread of antibiotic resistance. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116317. [PMID: 33383416 DOI: 10.1016/j.envpol.2020.116317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/03/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
The effect of land application of sewage sludge on soil microbial communities and the possible spread of antibiotic- and metal-resistant strains and resistance determinants were evaluated during a 720-day field experiment. Enzyme activities, the number of oligotrophic bacteria, the total number of bacteria (qPCR), functional diversity (BIOLOG) and genetic diversity (DGGE) were established. Antibiotic and metal resistance genes (ARGs, MRGs) were assessed, and the number of cultivable antibiotic- (ampicillin, tetracycline) and heavy metal- (Cd, Zn, Cu, Ni) resistant bacteria were monitored during the experiment. The application of 10 t ha-1 of sewage sludge to soil did not increase the organic matter content and caused only a temporary increase in the number of bacteria, as well as in the functional and structural biodiversity. In contrast to expectations, a general adverse effect on the tested microbial parameters was observed in the fertilized soil. The field experiment revealed a significant reduction in the activities of alkaline and acid phosphatases, urease and nitrification potential. Although sewage sludge was identified as the source of several ARGs and MRGs, these genes were not detected in the fertilized soil. The obtained results indicate that the effect of fertilization based on the recommended dose of sewage sludge was not achieved.
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Affiliation(s)
- Anna Markowicz
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Poland.
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Białystok, Białystok, Poland.
| | - Mariusz Cycoń
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences, Medical University of Silesia, Sosnowiec, Poland.
| | - Sławomir Sułowicz
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Poland.
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