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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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Reddy Banda S, Klapproth H, Smit N, Bednar S, Brandstetter T, Rühe J. An advanced and efficient asymmetric PCR method for microarray applications. Front Bioeng Biotechnol 2022; 10:1045154. [PMID: 36532575 PMCID: PMC9748121 DOI: 10.3389/fbioe.2022.1045154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/09/2022] [Indexed: 06/18/2024] Open
Abstract
The sensitivity of a PCR based biochip assay relies on the efficiency of PCR amplicons in binding to the microarray spots. The essential factor determining the sensitivity is the amount of single stranded (ss) amplicons available for biochip hybridization. Asymmetric PCR can generate ss-amplicons depending on the ratio of primers used in the amplification process, but this process is often inefficient. We report a novel variant of PCR called the Asymmetric Exponential and Linear Amplification (AELA) which can overcome these issues and generate large amounts of single stranded amplicons. AELA-PCR introduces an amplification strategy that makes use of both exponential and linear amplification of the target nucleic acid. This is done by specifically designed primers and choice of adequate thermal profiles. In conventional PCR with a classical thermal profile, these specifically designed primers will work normally and contribute to an exponential increase of amplicons. A designed sequence extension of one of the primers and a very specific thermal profile, will result in a situation that the extended primer will be the only functional one for amplification, resulting in a linear phase of the amplification process. That is why during this step only one of the two strands of the target is amplified linearly and no longer exponentially. The result of the whole process is an amplification product enriched very strongly in one of the two single strands of the target. These adaptions in PCR are particularly favorable where the generation of ss-DNA/RNA is required. We demonstrate the higher biochip sensitivity of AELA-PCR compared to conventional amplification methods with an example of the Staphylococcus aureus detection on a DNA oligonucleotide microarray.
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Affiliation(s)
- Suresh Reddy Banda
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Holger Klapproth
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Nicolaas Smit
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Sonja Bednar
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Thomas Brandstetter
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Jürgen Rühe
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
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Z-Guggulsterone alleviated oxidative stress and inflammation through inhibiting the TXNIP/NLRP3 axis in ischemic stroke. Int Immunopharmacol 2020; 89:107094. [PMID: 33129097 DOI: 10.1016/j.intimp.2020.107094] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/25/2020] [Accepted: 10/09/2020] [Indexed: 01/05/2023]
Abstract
Ischemic stroke is a serious and life-threatening cerebrovascular thrombotic disease; however, the therapeutic strategy is limited for the complicated mechanism and narrow therapeutic window. Our previous study suggested that Z-Guggulsterone (Z-GS), an active component derived from myrrh, is a good candidate for cerebral injury. The object of this study is to investigate the exact mechanisms of Z-GS in cerebral ischemic stroke. Rats were used to conduct middle cerebral artery occlusion (MCAO) model and were treated with different dosage of Z-GS. Morphological results showed that Z-GS significantly alleviated neurological deficits, infarct volume and histopathological damage in MCAO rats. A total of 8276 differentially expressed genes were identified based on microarray analysis. Oxidation-reduction process and inflammatory response were enriched as the significant gene ontology items. TXNIP and NLRP3 were screened as the potential target genes by Series Test of Cluster (STC) analysis. The results were validated by immunohistochemistry and immunofluorescence staining. Besides, Z-GS successfully inhibited oxidative stress and inflammatory response in oxygen-glucose deprivation (OGD) treated neurons. Knockdown of TXNIP significantly decreased the expression of NLRP3 in OGD-induced neurons. In addition, Z-GS treatment scarcely changed the expressions of NLRP3 in siRNA-TXNIP pretreated cells compared with the siRNA-TXNIP alone treatment group, suggesting that the neuroprotective effect of Z-GS was dependent on TXNIP-NLRP3 axis. Taken together, this study revealed that Z-GS exerted neuroprotective property through alleviated oxidative stress and inflammation via inhibiting the TXNIP/NLRP3 axis. Z-GS could be considered as a promising candidate for the treatment of ischemic stroke.
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Taitt CR, Leski TA, Prouty MG, Ford GW, Heang V, House BL, Levin SY, Curry JA, Mansour A, Mohammady HE, Wasfy M, Tilley DH, Gregory MJ, Kasper MR, Regeimbal J, Rios P, Pimentel G, Danboise BA, Hulseberg CE, Odundo EA, Ombogo AN, Cheruiyot EK, Philip CO, Vora GJ. Tracking Antimicrobial Resistance Determinants in Diarrheal Pathogens: A Cross-Institutional Pilot Study. Int J Mol Sci 2020; 21:ijms21165928. [PMID: 32824772 PMCID: PMC7460656 DOI: 10.3390/ijms21165928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Infectious diarrhea affects over four billion individuals annually and causes over a million deaths each year. Though not typically prescribed for treatment of uncomplicated diarrheal disease, antimicrobials serve as a critical part of the armamentarium used to treat severe or persistent cases. Due to widespread over- and misuse of antimicrobials, there has been an alarming increase in global resistance, for which a standardized methodology for geographic surveillance would be highly beneficial. To demonstrate that a standardized methodology could be used to provide molecular surveillance of antimicrobial resistance (AMR) genes, we initiated a pilot study to test 130 diarrheal pathogens (Campylobacter spp., Escherichia coli, Salmonella, and Shigella spp.) from the USA, Peru, Egypt, Cambodia, and Kenya for the presence/absence of over 200 AMR determinants. We detected a total of 55 different determinants conferring resistance to ten different categories of antimicrobials: genes detected in ≥ 25 samples included blaTEM, tet(A), tet(B), mac(A), mac(B), aadA1/A2, strA, strB, sul1, sul2, qacEΔ1, cmr, and dfrA1. The number of determinants per strain ranged from none (several Campylobacter spp. strains) to sixteen, with isolates from Egypt harboring a wider variety and greater number of genes per isolate than other sites. Two samples harbored carbapenemase genes, blaOXA-48 or blaNDM. Genes conferring resistance to azithromycin (ere(A), mph(A)/mph(K), erm(B)), a first-line therapeutic for severe diarrhea, were detected in over 10% of all Enterobacteriaceae tested: these included >25% of the Enterobacteriaceae from Egypt and Kenya. Forty-six percent of the Egyptian Enterobacteriaceae harbored genes encoding CTX-M-1 or CTX-M-9 families of extended-spectrum β-lactamases. Overall, the data provide cross-comparable resistome information to establish regional trends in support of international surveillance activities and potentially guide geospatially informed medical care.
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Affiliation(s)
- Chris R. Taitt
- US Naval Research Laboratory, Center for Biomolecular Science & Engineering, Washington, DC 20375, USA; (T.A.L.); (G.J.V.)
- Correspondence: ; Tel.: +1-011-202-404-4208
| | - Tomasz A. Leski
- US Naval Research Laboratory, Center for Biomolecular Science & Engineering, Washington, DC 20375, USA; (T.A.L.); (G.J.V.)
| | - Michael G. Prouty
- US Naval Medical Research Unit No. 2-Phnom Penh, Blvd Kim Il Sung, Khan Toul Kork, Phnom Penh, Cambodia; (M.G.P.); (G.W.F.); (V.H.)
| | - Gavin W. Ford
- US Naval Medical Research Unit No. 2-Phnom Penh, Blvd Kim Il Sung, Khan Toul Kork, Phnom Penh, Cambodia; (M.G.P.); (G.W.F.); (V.H.)
| | - Vireak Heang
- US Naval Medical Research Unit No. 2-Phnom Penh, Blvd Kim Il Sung, Khan Toul Kork, Phnom Penh, Cambodia; (M.G.P.); (G.W.F.); (V.H.)
| | - Brent L. House
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Samuel Y. Levin
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Jennifer A. Curry
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Adel Mansour
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Hanan El Mohammady
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Momtaz Wasfy
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Drake Hamilton Tilley
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Michael J. Gregory
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Matthew R. Kasper
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - James Regeimbal
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Paul Rios
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Guillermo Pimentel
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Brook A. Danboise
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Christine E. Hulseberg
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Elizabeth A. Odundo
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Abigael N. Ombogo
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Erick K. Cheruiyot
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Cliff O. Philip
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Gary J. Vora
- US Naval Research Laboratory, Center for Biomolecular Science & Engineering, Washington, DC 20375, USA; (T.A.L.); (G.J.V.)
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A Survey of Antimicrobial Resistance Determinants in Category A Select Agents, Exempt Strains, and Near-Neighbor Species. Int J Mol Sci 2020; 21:ijms21051669. [PMID: 32121349 PMCID: PMC7084191 DOI: 10.3390/ijms21051669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/02/2023] Open
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.
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