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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Leski TA, Spangler JR, Wang Z, Schultzhaus Z, Taitt CR, Dean SN, Stenger DA. Machine learning for design of degenerate Cas13a crRNAs using lassa virus as a model of highly variable RNA target. Sci Rep 2023; 13:6506. [PMID: 37081092 PMCID: PMC10119381 DOI: 10.1038/s41598-023-33494-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023] Open
Abstract
The design of minimum CRISPR RNA (crRNA) sets for detection of diverse RNA targets using sequence degeneracy has not been systematically addressed. We tested candidate degenerate Cas13a crRNA sets designed for detection of diverse RNA targets (Lassa virus). A decision tree machine learning (ML) algorithm (RuleFit) was applied to define the top attributes that determine the specificity of degenerate crRNAs to elicit collateral nuclease activity. Although the total number of mismatches (0-4) is important, the specificity depends as well on the spacing of mismatches, and their proximity to the 5' end of the spacer. We developed a predictive algorithm for design of candidate degenerate crRNA sets, allowing improved discrimination between "included" and "excluded" groups of related target sequences. A single degenerate crRNA set adhering to these rules detected representatives of all Lassa lineages. Our general ML approach may be applied to the design of degenerate crRNA sets for any CRISPR/Cas system.
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Affiliation(s)
- T A Leski
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA.
| | - J R Spangler
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
| | - Z Wang
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
| | - Z Schultzhaus
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
- U.S. Department of Agriculture, Riverdale, MD, USA
| | - C R Taitt
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
- Nova Research Inc., Alexandria, VA, USA
| | - S N Dean
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
| | - D A Stenger
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
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Leski TA, Taitt CR, Colston SM, Bangura U, Holtz A, Yasuda CY, Reynolds ND, Lahai J, Lamin JM, Baio V, Ansumana R, Stenger DA, Vora GJ. Prevalence of malaria resistance-associated mutations in Plasmodium falciparum circulating in 2017–2018, Bo, Sierra Leone. Front Microbiol 2022; 13:1059695. [DOI: 10.3389/fmicb.2022.1059695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
IntroductionIn spite of promising medical, sociological, and engineering strategies and interventions to reduce the burden of disease, malaria remains a source of significant morbidity and mortality, especially among children in sub-Saharan Africa. In particular, progress in the development and administration of chemotherapeutic agents is threatened by evolved resistance to most of the antimalarials currently in use, including artemisinins.MethodsThis study analyzed the prevalence of mutations associated with antimalarial resistance in Plasmodium falciparum from 95 clinical samples collected from individuals with clinically confirmed malaria at a hospital in Bo, Sierra Leone between May 2017 and December 2018. The combination of polymerase chain reaction amplification and subsequent high throughput DNA sequencing was used to determine the presence of resistance-associated mutations in five P. falciparum genes – pfcrt, pfmdr1, pfdhfr, pfdhps and pfkelch13. The geographic origin of parasites was assigned using mitochondrial sequences.ResultsRelevant mutations were detected in the pfcrt (22%), pfmdr1 (>58%), pfdhfr (100%) and pfdhps (>80%) genes while no resistance-associated mutations were found in the pfkelch13 gene. The mitochondrial barcodes were consistent with a West African parasite origin with one exception indicating an isolate imported from East Africa.DiscussionDetection of the pfmdr1 NFSND haplotype in 50% of the samples indicated the increasing prevalence of strains with elevated tolerance to artemeter + lumefantrine (AL) threatening the combination currently used to treat uncomplicated malaria in Sierra Leone. The frequency of mutations linked to resistance to antifolates suggests widespread resistance to the drug combination used for intermittent preventive treatment during pregnancy.
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Spangler JR, Leski TA, Schultzhaus Z, Wang Z, Stenger DA. Large scale screening of CRISPR guide RNAs using an optimized high throughput robotics system. Sci Rep 2022; 12:13953. [PMID: 35977955 PMCID: PMC9385653 DOI: 10.1038/s41598-022-17474-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
All CRISPR/CAS systems utilize CRISPR guide RNAs (crRNAs), the design of which depend on the type of CAS protein, genetic target and the environment/matrix. While machine learning approaches have recently been developed to optimize some crRNA designs, candidate crRNAs must still be screened for efficacy under relevant conditions. Here, we demonstrate a high-throughput method to screen hundreds of candidate crRNAs for activation of Cas13a collateral RNA cleavage. Entire regions of a model gene transcript (Y. pestis lcrV gene) were tiled to produce overlapping crRNA sets. We tested for possible effects that included crRNA/target sequence, size and secondary structures, and the commercial source of DNA oligomers used to generate crRNAs. Detection of a 981 nt target RNA was initially successful with 271 out of 296 tested guide RNAs, and that was improved to 287 out of 296 (97%) after protocol optimizations. For this specific example, we determined that crRNA efficacy did not strongly depend on the target region or crRNA physical properties, but was dependent on the source of DNA oligomers used for RNA preparation. Our high-throughput methods for screening crRNAs has general applicability to the optimization of Cas12 and Cas13 guide RNA designs.
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Affiliation(s)
- J R Spangler
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA.
| | - T A Leski
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - Z Schultzhaus
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Z Wang
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - D A Stenger
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
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Leski TA, Taitt CR, Bangura U, Lahai J, Lamin JM, Baio V, Koroma MS, Swaray AG, Jacobsen KH, Jackson O, Jones BW, Phillips CL, Ansumana R, Stenger DA. Comparison of capillary and venous blood for malaria detection using two PCR-based assays in febrile patients in Sierra Leone. Malar J 2021; 20:133. [PMID: 33676502 PMCID: PMC7936501 DOI: 10.1186/s12936-021-03644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background Rapid and sensitive diagnostics are critical tools for clinical case management and public health control efforts. Both capillary and venous blood are currently used for malaria detection and while diagnostic technologies may not be equally sensitive with both materials, the published data on this subject are scarce and not conclusive. Methods Paired clinical samples of venous and capillary blood from 141 febrile individuals in Bo, Sierra Leone, were obtained between January and May 2019 and tested for the presence of Plasmodium parasites using two multiplexed PCR assays: the FilmArray-based Global Fever Panel (GFP) and the TaqMan-based Malaria Multiplex Sample Ready (MMSR) assay. Results No significant differences in Plasmodium parasite detection between capillary and venous blood for both assays were observed. The GFP assay was more sensitive than MMSR for all markers that could be compared (Plasmodium spp. and Plasmodium falciparum) in both venous and capillary blood. Conclusions No difference was found in malaria detection between venous and capillary blood using two different PCR-based detection assays. This data gives support for use of capillary blood, a material which can be obtained easier by less invasive methods, for PCR-based malaria diagnostics, independent of the platform.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA.
| | - Chris Rowe Taitt
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Umaru Bangura
- Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | - Joseph Lahai
- Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | | | - Victoria Baio
- Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | | | - Abdulai G Swaray
- College of Science, George Mason University, Fairfax, Virginia, USA
| | - Kathryn H Jacobsen
- Department of Global & Community Health, George Mason University, Fairfax, Virginia, USA
| | | | | | | | - Rashid Ansumana
- Mercy Hospital Research Laboratory, Bo, Sierra Leone.,Njala University, Bo, Sierra Leone
| | - David A Stenger
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
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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: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Taitt CR, Leski TA, Colston SM, Bernal M, Canal E, Regeimbal J, Rios P, Vora GJ. A comparison of methods for DNA preparation prior to microarray analysis. Anal Biochem 2019; 585:113405. [PMID: 31445900 DOI: 10.1016/j.ab.2019.113405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/21/2019] [Accepted: 08/21/2019] [Indexed: 01/30/2023]
Abstract
Microarrays are a valuable tool for analysis of both bacterial and eukaryotic nucleic acids. As many of these applications use non-specific amplification to increase sample concentration prior to analysis, the methods used to fragment and label large amplicons are important to achieve the desired analytical selectivity and specificity. Here, we used eight sequenced ESKAPE pathogens to determine the effect of two methods of whole genome amplicon fragmentation and three methods of subsequent labeling on microarray performance; nick translation was also assessed. End labeling of both initial DNase I-treated and sonication-fragmented amplicons failed to provide detectable material for a significant number of sequence-confirmed genes. However, processing of amplicons by nick translation, or by sequential fragmentation and labeling by Universal Labeling System or Klenow fragment/random primer provided good sensitivity and selectivity, with marginally better results obtained by Klenow fragment labeling. Nick-translation provided 91-100% sensitivity and 100% specificity in the tested strains, requiring half as many manipulations and less than 4h to process samples for hybridization; full sample processing from whole genome amplification to final data analysis could be performed in less than 10h. The method of template denaturation before amplification did affect detection sensitivity/selectivity of nick-labeled amplicons, however.
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Affiliation(s)
- Chris R Taitt
- 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
| | - Sophie M Colston
- National Research Council Research Associateship Program, Washington, DC, 20001, USA
| | | | | | | | | | - Gary J Vora
- Center for BioMolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
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8
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Ansumana R, Dariano DF, Jacobsen KH, Leski TA, Lamin JM, Lahai J, Bangura U, Bockarie AS, Taitt CR, Yasuda C, Bockarie MJ, Stenger DA. Seroprevalence of hepatitis B surface antigen (HBsAg) in Bo, Sierra Leone, 2012-2013. BMC Res Notes 2018; 11:113. [PMID: 29422083 PMCID: PMC5806241 DOI: 10.1186/s13104-018-3218-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/01/2018] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE The aim of this study was to determine the prevalence of hepatitis B surface antigen (HBsAg) among febrile individuals tested at Mercy Hospital Research Laboratory (MHRL) in Bo, Sierra Leone. RESULTS A total of 860 febrile individuals ages 5 years and older were tested by MHRL between July 2012 and June 2013 with a Standard Diagnostics Bioline HBsAg rapid diagnostic test. The overall HBsAg prevalence rate was 13.7%, including a rate of 15.5% among males and 12.6% among females. The HBsAg rate did not differ by child or adult age group (p > 0.5). The prevalence rate in Bo was similar to the 11-15% HBsAg prevalence rates reported in the past decade from other studies across West Africa. Scaling up the infant hepatitis B vaccination program in Sierra Leone will be important for reducing the future burden of disease and premature death attributable to chronic viral hepatitis B disease.
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Affiliation(s)
- Rashid Ansumana
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone. .,Department of Community Health and Clinical Studies, Njala University, Bo, Sierra Leone.
| | - Donald F Dariano
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Kathryn H Jacobsen
- Department of Global & Community Health, George Mason University, Fairfax, VA, USA
| | - Tomasz A Leski
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Joseph M Lamin
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone
| | - Joseph Lahai
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone
| | - Umaru Bangura
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone
| | - Alfred S Bockarie
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone.,Department of Community Health and Clinical Studies, Njala University, Bo, Sierra Leone
| | - Chris R Taitt
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Chadwick Yasuda
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | | | - David A Stenger
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
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9
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Ansumana R, Dariano DF, Jacobsen KH, Leski TA, Taitt CR, Lamin JM, Lahai J, Bangura U, Bockarie AS, Yasuda C, Bockarie MJ, Stenger DA. Prevalence of markers of HIV infection among febrile adults and children in Bo, Sierra Leone, 2012-2013. BMC Res Notes 2017; 10:565. [PMID: 29110721 PMCID: PMC5674775 DOI: 10.1186/s13104-017-2912-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The goal of this study was to examine the prevalence of HIV among febrile patients seeking care in Mercy Hospital, Bo, Sierra Leone, in 2012-2013. RESULTS A total of 1207 febrile persons were tested for HIV with Determine™ and SD Bioline rapid diagnostic tests kits that detect the presence of HIV antibodies and HIV p24 antigens. The overall prevalence of HIV among the tested patients was 8.9%, which is considerably higher than the < 2% prevalence of HIV reported previously in the general population. While these results are not sufficient to prove a causal relationship, the obtained data imply that HIV positive individuals may be more likely to suffer from febrile infectious diseases than individuals without HIV infection. Increasing the availability and use of HIV testing services will allow antiretroviral therapy to be accessed in a timely manner and improve health status among people living with HIV.
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Affiliation(s)
- Rashid Ansumana
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone. .,Department of Community Health and Clinical Studies, Njala University, Bo, Sierra Leone.
| | - Donald F Dariano
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Kathryn H Jacobsen
- Department of Global & Community Health, George Mason University, Fairfax, VA, USA
| | - Tomasz A Leski
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Chris R Taitt
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Joseph M Lamin
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone
| | - Joseph Lahai
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone
| | - Umaru Bangura
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone
| | - Alfred S Bockarie
- Mercy Hospital Research Laboratory, Kulanda Town, Bo, Sierra Leone.,Department of Community Health and Clinical Studies, Njala University, Bo, Sierra Leone
| | - Chadwick Yasuda
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Moses J Bockarie
- Liverpool School of Tropical Medicine, 5 Pembroke Place, Liverpool, L35QA, United Kingdom
| | - David A Stenger
- Center for Biomolecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
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Dariano DF, Taitt CR, Jacobsen KH, Bangura U, Bockarie AS, Bockarie MJ, Lahai J, Lamin JM, Leski TA, Yasuda C, Stenger DA, Ansumana R. Surveillance of Vector-Borne Infections (Chikungunya, Dengue, and Malaria) in Bo, Sierra Leone, 2012-2013. Am J Trop Med Hyg 2017; 97:1151-1154. [PMID: 29031286 DOI: 10.4269/ajtmh.16-0798] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malaria remains a significant cause of morbidity and mortality in West Africa, but the contribution of other vector-borne infections (VBIs) to the burden of disease has been understudied. We used rapid diagnostic tests (RDTs) for three VBIs to test blood samples from 1,795 febrile residents of Bo City, Sierra Leone, over a 1-year period in 2012-2013. In total, 24% of the tests were positive for malaria, fewer than 5% were positive for markers of dengue virus infection, and 39% were positive for IgM directed against chikungunya virus (CHIKV) or a related alphavirus. In total, more than half (55%) of these febrile individuals tested positive for at least one of the three VBIs, which highlights the very high burden of vector-borne diseases in this population. The prevalence of positives on the Chikungunya IgM and dengue tests did not vary significantly with age (P > 0.36), but higher rates of malaria were observed in children < 15 years of age (P < 0.001). Positive results on the Chikungunya IgM RDTs were moderately correlated with rainfall (r2 = 0.599). Based on the high prevalence of positive results on the Chikungunya IgM RDTs from individuals Bo and its environs, there is a need to examine whether an ecological shift toward a greater burden from CHIKV or related alphaviruses is occurring in other parts of Sierra Leone or the West African region.
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Affiliation(s)
| | - Chris R Taitt
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, Washington, District of Columbia
| | - Kathryn H Jacobsen
- Department of Global and Community Health, George Mason University, Fairfax, Virginia
| | - Umaru Bangura
- Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | - Alfred S Bockarie
- Njala University, Bo Campus, Sierra Leone.,Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | - Moses J Bockarie
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Joseph Lahai
- Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | | | - Tomasz A Leski
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, Washington, District of Columbia
| | - Chadwick Yasuda
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, Washington, District of Columbia
| | - David A Stenger
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, Washington, District of Columbia
| | - Rashid Ansumana
- Mercy Hospital Research Laboratory, Bo, Sierra Leone.,Njala University, Bo Campus, Sierra Leone.,Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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11
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Hebert CG, Hart S, Leski TA, Terray A, Lu Q. Label-Free Detection of Bacillus anthracis Spore Uptake in Macrophage Cells Using Analytical Optical Force Measurements. Anal Chem 2017; 89:10296-10302. [PMID: 28876903 DOI: 10.1021/acs.analchem.7b01983] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Understanding the interaction between macrophage cells and Bacillus anthracis spores is of significant importance with respect to both anthrax disease progression, spore detection for biodefense, as well as understanding cell clearance in general. While most detection systems rely on specific molecules, such as nucleic acids or proteins and fluorescent labels to identify the target(s) of interest, label-free methods probe changes in intrinsic properties, such as size, refractive index, and morphology, for correlation with a particular biological event. Optical chromatography is a label free technique that uses the balance between optical and fluidic drag forces within a microfluidic channel to determine the optical force on cells or particles. Here we show an increase in the optical force experienced by RAW264.7 macrophage cells upon the uptake of both microparticles and B. anthracis Sterne 34F2 spores. In the case of spores, the exposure was detected in as little as 1 h without the use of antibodies or fluorescent labels of any kind. An increase in the optical force was also seen in macrophage cells treated with cytochalasin D, both with and without a subsequent exposure to spores, indicating that a portion of the increase in the optical force arises independent of phagocytosis. These results demonstrate the capability of optical chromatography to detect subtle biological differences in a rapid and sensitive manner and suggest future potential in a range of applications, including the detection of biological threat agents for biodefense and pathogens for the prevention of sepsis and other diseases.
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Affiliation(s)
- Colin G Hebert
- Naval Research Laboratory , Chemistry Division, Bio/Analytical Chemistry Section, Code 6112, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Sean Hart
- LumaCyte, LLC , 1145 River Road, Suite 16, Charlottesville, Virginia 22901, United States
| | - Tomasz A Leski
- Naval Research Laboratory , Center for Bio/Molecular Science and Engineering, Code 6910, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Alex Terray
- Naval Research Laboratory , Chemistry Division, Bio/Analytical Chemistry Section, Code 6112, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Qin Lu
- Naval Research Laboratory , Chemistry Division, Bio/Analytical Chemistry Section, Code 6112, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
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12
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Taitt CR, Leski TA, Erwin DP, Odundo EA, Kipkemoi NC, Ndonye JN, Kirera RK, Ombogo AN, Walson JL, Pavlinac PB, Hulseberg C, Vora GJ. Antimicrobial resistance of Klebsiella pneumoniae stool isolates circulating in Kenya. PLoS One 2017; 12:e0178880. [PMID: 28575064 PMCID: PMC5456380 DOI: 10.1371/journal.pone.0178880] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/19/2017] [Indexed: 01/08/2023] Open
Abstract
We sought to determine the genetic and phenotypic antimicrobial resistance (AMR) profiles of commensal Klebsiella spp. circulating in Kenya by testing human stool isolates of 87 K. pneumoniae and three K. oxytoca collected at eight locations. Over one-third of the isolates were resistant to ≥3 categories of antimicrobials and were considered multidrug-resistant (MDR). We then compared the resistance phenotype to the presence/absence of 238 AMR genes determined by a broad-spectrum microarray and PCR. Forty-six genes/gene families were identified conferring resistance to β-lactams (ampC/blaDHA, blaCMY/LAT, blaLEN-1, blaOKP-A/OKP-B1, blaOXA-1-like family, blaOXY-1, blaSHV, blaTEM, blaCTX-M-1 and blaCTX-M-2 families), aminoglycosides (aac(3)-III, aac(6)-Ib, aad(A1/A2), aad(A4), aph(AI), aph3/str(A), aph6/str(B), and rmtB), macrolides (mac(A), mac(B), mph(A)/mph(K)), tetracyclines (tet(A), tet(B), tet(D), tet(G)), ansamycins (arr), phenicols (catA1/cat4, floR, cmlA, cmr), fluoroquinolones (qnrS), quaternary amines (qacEΔ1), streptothricin (sat2), sulfonamides (sul1, sul2, sul3), and diaminopyrimidines (dfrA1, dfrA5, dfrA7, dfrA8, dfrA12, dfrA13/21/22/23 family, dfrA14, dfrA15, dfrA16, dfrA17). This is the first profile of genes conferring resistance to multiple categories of antimicrobial agents in western and central Kenya. The large number and wide variety of resistance genes detected suggest the presence of significant selective pressure. The presence of five or more resistance determinants in almost two-thirds of the isolates points to the need for more effective, targeted public health policies and infection control/prevention measures.
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Affiliation(s)
- Chris Rowe Taitt
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC United States of America
| | - Tomasz A. Leski
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC United States of America
| | - Daniel P. Erwin
- US Army Medical Research Directorate-Kenya, Walter Reed Army Institute of Research, Kericho, Kenya
| | - Elizabeth A. Odundo
- KEMRI/US Army Medical Research Directorate-Kenya, Walter Reed Army Institute of Research, Kericho, Kenya
| | - Nancy C. Kipkemoi
- KEMRI/US Army Medical Research Directorate-Kenya, Walter Reed Army Institute of Research, Kericho, Kenya
| | - Janet N. Ndonye
- KEMRI/US Army Medical Research Directorate-Kenya, Walter Reed Army Institute of Research, Kericho, Kenya
| | - Ronald K. Kirera
- KEMRI/US Army Medical Research Directorate-Kenya, Walter Reed Army Institute of Research, Kericho, Kenya
| | - Abigael N. Ombogo
- KEMRI/US Army Medical Research Directorate-Kenya, Walter Reed Army Institute of Research, Kericho, Kenya
| | - Judd L. Walson
- Department of Global Health, University of Washington, Seattle, WA, United States of America
- Departments of Pediatrics, Medicine, and Epidemiology, University of Washington, Seattle, WA, United States of America
| | - Patricia B. Pavlinac
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Christine Hulseberg
- US Army Medical Research Directorate-Kenya, Walter Reed Army Institute of Research, Kericho, Kenya
| | - Gary J. Vora
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC United States of America
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13
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Leski TA, Taitt CR, Bangura U, Stockelman MG, Ansumana R, Cooper WH, Stenger DA, Vora GJ. High prevalence of multidrug resistant Enterobacteriaceae isolated from outpatient urine samples but not the hospital environment in Bo, Sierra Leone. BMC Infect Dis 2016; 16:167. [PMID: 27090787 PMCID: PMC4836052 DOI: 10.1186/s12879-016-1495-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 04/06/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The rising level of antimicrobial resistance among bacterial pathogens is one of the most significant public health problems globally. While the antibiotic resistance of clinically important bacteria is closely tracked in many developed countries, the types and levels of resistance and multidrug resistance (MDR) among pathogens currently circulating in most countries of sub-Saharan Africa are virtually unknown. METHODS From December 2013 to April 2014, we collected 93 urine specimens from all outpatients showing symptoms of urinary tract infection (UTI) and 189 fomite swabs from a small hospital in Bo, Sierra Leone. Culture on chromogenic agar combined with biochemical and DNA sequence-based assays was used to detect and identify the bacterial isolates. Their antimicrobial susceptibilities were determined using a panel of 11 antibiotics or antibiotic combinations. RESULTS The 70 Enterobacteriaceae urine isolates were identified as Citrobacter freundii (n = 22), Klebsiella pneumoniae (n = 15), Enterobacter cloacae (n = 15), Escherichia coli (n = 13), Enterobacter sp./Leclercia sp. (n = 4) and Escherichia hermannii (n = 1). Antimicrobial susceptibility testing demonstrated that 85.7 % of these isolates were MDR while 64.3 % produced an extended-spectrum ß-lactamase (ESBL). The most notable observations included widespread resistance to sulphonamides (91.4 %), chloramphenicol (72.9 %), gentamycin (72.9 %), ampicillin with sulbactam (51.4 %) and ciprofloxacin (47.1 %) with C. freundii exhibiting the highest and E. coli the lowest prevalence of multidrug resistance. The environmental cultures resulted in only five Enterobacteriaceae isolates out of 189 collected with lower overall antibiotic resistance. CONCLUSIONS The surprisingly high proportion of C. freundii found in urine of patients with suspected UTI supports earlier findings of the growing role of this pathogen in UTIs in low-resource countries. The isolates of all analyzed species showed worryingly high levels of resistance to both first- and second-line antibiotics as well as a high frequency of MDR and ESBL phenotypes, which likely resulted from the lack of consistent antibiotic stewardship policies in Sierra Leone. Analysis of hospital environmental isolates however suggested that fomites in this naturally ventilated hospital were not a major reservoir for Enterobacteriaceae or antibiotic resistance determinants.
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Affiliation(s)
- Tomasz A Leski
- Naval Research Laboratory, Code 6910, 4555 Overlook Avenue SW, Washington, DC, 20375, USA.
| | - Chris R Taitt
- Naval Research Laboratory, Code 6910, 4555 Overlook Avenue SW, Washington, DC, 20375, USA
| | - Umaru Bangura
- Mercy Hospital Research Laboratory, Bo, Sierra Leone.,Njala University, Bo, Sierra Leone
| | - Michael G Stockelman
- Naval Research Laboratory, Code 6910, 4555 Overlook Avenue SW, Washington, DC, 20375, USA
| | - Rashid Ansumana
- Mercy Hospital Research Laboratory, Bo, Sierra Leone.,Liverpool School of Tropical Medicine, Liverpool, UK.,Njala University, Bo, Sierra Leone
| | | | - David A Stenger
- Naval Research Laboratory, Code 6910, 4555 Overlook Avenue SW, Washington, DC, 20375, USA
| | - Gary J Vora
- Naval Research Laboratory, Code 6910, 4555 Overlook Avenue SW, Washington, DC, 20375, USA
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14
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Leski TA, Stockelman MG, Moses LM, Park M, Stenger DA, Ansumana R, Bausch DG, Lin B. Sequence variability and geographic distribution of Lassa virus, Sierra Leone. Emerg Infect Dis 2015; 21:609-18. [PMID: 25811712 PMCID: PMC4378485 DOI: 10.3201/eid2104.141469] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Lassa virus (LASV) is endemic to parts of West Africa and causes highly fatal hemorrhagic fever. The multimammate rat (Mastomys natalensis) is the only known reservoir of LASV. Most human infections result from zoonotic transmission. The very diverse LASV genome has 4 major lineages associated with different geographic locations. We used reverse transcription PCR and resequencing microarrays to detect LASV in 41 of 214 samples from rodents captured at 8 locations in Sierra Leone. Phylogenetic analysis of partial sequences of nucleoprotein (NP), glycoprotein precursor (GPC), and polymerase (L) genes showed 5 separate clades within lineage IV of LASV in this country. The sequence diversity was higher than previously observed; mean diversity was 7.01% for nucleoprotein gene at the nucleotide level. These results may have major implications for designing diagnostic tests and therapeutic agents for LASV infections in Sierra Leone.
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Taitt CR, Leski TA, Heang V, Ford GW, Prouty MG, Newell SW, Vora GJ. Antimicrobial resistance genotypes and phenotypes from multidrug-resistant bacterial wound infection isolates in Cambodia. J Glob Antimicrob Resist 2015; 3:198-204. [DOI: 10.1016/j.jgar.2015.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/25/2015] [Accepted: 05/18/2015] [Indexed: 11/24/2022] Open
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16
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Ansumana R, Jacobsen KH, Leski TA, Covington AL, Bangura U, Hodges MH, Lin B, Bockarie AS, Lamin JM, Bockarie MJ, Stenger DA. Reemergence of chikungunya virus in Bo, Sierra Leone. Emerg Infect Dis 2014; 19:1108-10. [PMID: 23764023 PMCID: PMC3713974 DOI: 10.3201/eid1907.121563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We diagnosed 400 possible IgM-positive cases of chikungunya virus in Bo, Sierra Leone, during July 2012–January 2013 by using lateral flow immunoassays. Cases detected likely represent only a small fraction of total cases. Further laboratory testing is required to confirm this outbreak and characterize the virus.
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17
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Leski TA, Bangura U, Jimmy DH, Ansumana R, Lizewski SE, Stenger DA, Taitt CR, Vora GJ. Multidrug-resistant tet(X)-containing hospital isolates in Sierra Leone. Int J Antimicrob Agents 2013; 42:83-6. [PMID: 23688520 DOI: 10.1016/j.ijantimicag.2013.04.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 04/01/2013] [Accepted: 04/09/2013] [Indexed: 11/26/2022]
Abstract
The tet(X) gene encodes a flavin-dependent monooxygenase that confers resistance to all clinically relevant tetracycline antibiotics including tigecycline. It has only previously been identified in environmental and non-human pathogenic bacteria. To investigate levels of multidrug resistance in Bo, Sierra Leone, a molecular epidemiological study was conducted using an antimicrobial resistance determinant microarray (ARDM), PCR and DNA sequencing. The study found that 21% of isolates from Mercy Hospital (Bo, Sierra Leone) were tet(X)-positive, all of which originated from urinary specimens. Use of molecular epidemiological surveillance tools has provided the first evidence of tet(X)-containing multidrug-resistant Gram-negative hospital isolates in a hospital in Sierra Leone.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
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18
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Jimmy DH, Sundufu AJ, Malanoski AP, Jacobsen KH, Ansumana R, Leski TA, Bangura U, Bockarie AS, Tejan E, Lin B, Stenger DA. Water quality associated public health risk in Bo, Sierra Leone. Environ Monit Assess 2013; 185:241-51. [PMID: 22350346 DOI: 10.1007/s10661-012-2548-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 01/19/2012] [Indexed: 05/10/2023]
Abstract
Human health depends on reliable access to safe drinking water, but in many developing countries only a limited number of wells and boreholes are available. Many of these water resources are contaminated with biological or chemical pollutants. The goal of this study was to examine water access and quality in urban Bo, Sierra Leone. A health census and community mapping project in one neighborhood in Bo identified the 36 water sources used by the community. A water sample was taken from each water source and tested for a variety of microbiological and physicochemical substances. Only 38.9% of the water sources met World Health Organization (WHO) microbial safety requirements based on fecal coliform levels. Physiochemical analysis indicated that the majority (91.7%) of the water sources met the requirements set by the WHO. In combination, 25% of these water resources met safe drinking water criteria. No variables associated with wells were statistically significant predictors of contamination. This study indicated that fecal contamination is the greatest health risk associated with drinking water. There is a need to raise hygiene awareness and implement inexpensive methods to reduce fecal contamination and improve drinking water safety in Bo, Sierra Leone.
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Leski TA, Lin B, Malanoski AP, Stenger DA. Application of resequencing microarrays in microbial detection and characterization. Future Microbiol 2012; 7:625-37. [PMID: 22568717 DOI: 10.2217/fmb.12.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Microarrays are powerful, highly parallel assays that are transforming microbiological diagnostics and research. The adaptation of microarray-based resequencing technology for microbial detection and characterization resulted in the development of a number assays that have unique advantages over other existing technologies. This technological platform seems to be especially useful for sensitive and high-resolution multiplexed diagnostics for clinical syndromes with similar symptoms, screening environmental samples for biothreat agents, as well as genotyping and whole-genome analysis of single pathogens.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, SW, Washington, DC 20375, USA.
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20
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Leski TA, Ansumana R, Malanoski AP, Jimmy DH, Bangura U, Barrows BR, Alpha M, Koroma BM, Long NC, Sundufu AJ, Bockarie AS, Lin B, Stenger DA. Leapfrog diagnostics: Demonstration of a broad spectrum pathogen identification platform in a resource-limited setting. Health Res Policy Syst 2012; 10:22. [PMID: 22759725 PMCID: PMC3418216 DOI: 10.1186/1478-4505-10-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 07/04/2012] [Indexed: 11/16/2022] Open
Abstract
Background Resource-limited tropical countries are home to numerous infectious pathogens of both human and zoonotic origin. A capability for early detection to allow rapid outbreak containment and prevent spread to non-endemic regions is severely impaired by inadequate diagnostic laboratory capacity, the absence of a “cold chain” and the lack of highly trained personnel. Building up detection capacity in these countries by direct replication of the systems existing in developed countries is not a feasible approach and instead requires “leapfrogging” to the deployment of the newest diagnostic systems that do not have the infrastructure requirements of systems used in developed countries. Methods A laboratory for molecular diagnostics of infectious agents was established in Bo, Sierra Leone with a hybrid solar/diesel/battery system to ensure stable power supply and a satellite modem to enable efficient communication. An array of room temperature stabilization and refrigeration technologies for reliable transport and storage of reagents and biological samples were also tested to ensure sustainable laboratory supplies for diagnostic assays. Results The laboratory demonstrated its operational proficiency by conducting an investigation of a suspected avian influenza outbreak at a commercial poultry farm at Bo using broad range resequencing microarrays and real time RT-PCR. The results of the investigation excluded influenza viruses as a possible cause of the outbreak and indicated a link between the outbreak and the presence of Klebsiella pneumoniae. Conclusions This study demonstrated that by application of a carefully selected set of technologies and sufficient personnel training, it is feasible to deploy and effectively use a broad-range infectious pathogen detection technology in a severely resource-limited setting.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington DC, 20375, USA.
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21
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Wang Z, Malanoski AP, Lin B, Long NC, Leski TA, Blaney KM, Hansen CJ, Brown J, Broderick M, Stenger DA, Tibbetts C, Russell KL, Metzgar D. Broad spectrum respiratory pathogen analysis of throat swabs from military recruits reveals interference between rhinoviruses and adenoviruses. Microb Ecol 2010; 59:623-634. [PMID: 20217405 DOI: 10.1007/s00248-010-9636-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 01/13/2010] [Indexed: 05/28/2023]
Abstract
Military recruits experience a high incidence of febrile respiratory illness (FRI), leading to significant morbidity and lost training time. Adenoviruses, group A Streptococcus pyogenes, and influenza virus are implicated in over half of the FRI cases reported at recruit training center clinics, while the etiology of the remaining cases is unclear. In this study, we explore the carriage rates and disease associations of adenovirus, enterovirus, rhinovirus, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis in military recruits using high-density resequencing microarrays. The results showed that rhinoviruses, adenoviruses, S. pneumoniae, H. influenzae, and N. meningitidis were widely distributed in recruits. Of these five agents, only adenovirus showed significant correlation with illness. Among the samples tested, only pathogens associated with FRI, such as adenovirus 4 and enterovirus 68, revealed strong temporal and spatial clustering of specific strains, indicating that they are transmitted primarily within sites. The results showed a strong negative association between adenoviral FRI and the presence of rhinoviruses in recruits, suggesting some form of viral interference.
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Affiliation(s)
- Zheng Wang
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA.
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22
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Abstract
Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification. This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques. The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA and Nova Research Inc., 1900 Elkin Street, Suite 230, Alexandria, VA, USA
| | - Anthony P Malanoski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - David A Stenger
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
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23
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Abstract
Optical chromatography, used for particle separation, involves loosely focusing a laser into a fluid flowing opposite the direction of laser propagation. When microscopic particles in the flow path encounter this beam they are trapped axially along the beam and are pushed upstream from the laser focal point to rest at a point where the optical and fluid forces on the particle balance. Because optical and fluid forces are sensitive to differences in the physical and chemical properties of a particle, separations are possible. An optical chromatography beam which completely fills a fluid channel can operate as an optically tunable filter for the preparative separation of polymeric/colloidal and biological samples. We show how the technique can be used to separate injected samples containing large numbers of colloids. The power of optical chromatographic separations is illustrated through combination with epi-fluorescence microscopy and sample purification for real-time polymerase chain reaction (RT-PCR) detection of Bacillus anthracis spores.
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Affiliation(s)
- Sean J Hart
- Naval Research Laboratory, Chemistry Division, Bio/Analytical Chemistry, Washington, DC 20375, USA.
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24
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Abstract
Optical chromatography is a technique for the separation of particles that capitalizes on the balance between optic and fluidic forces. When microscopic particles in a fluid flow encounter a laser beam propagating in the opposite direction, they are trapped axially along the beam. They are then optically pushed upstream from the laser focal point to rest at a point where the optic and fluidic forces on the particle balance. Because optical and fluid forces are sensitive to differences in the physical and chemical properties of a particle, both coarse and fine separations are possible. We describe how an optical chromatography beam directed into a tailored flow environment, has been adapted to operate as an optical filter for the concentration / bioenrichment of colloidal and biological samples. In this work, the demonstrated ability to concentrate spores of the biowarfare agent, Bacillus anthracis, may have significant impact in the biodefense arena. Application of these techniques and further design of fluidic and optical environments will allow for more specific identification, concentration and separation of many more microscopic particle and biological suspensions.
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Hart SJ, Terray A, Leski TA, Arnold J, Stroud R. Discovery of a Significant Optical Chromatographic Difference between Spores of Bacillus anthracis and Its Close Relative, Bacillus thuringiensis. Anal Chem 2006; 78:3221-5. [PMID: 16643018 DOI: 10.1021/ac052221z] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A significant difference between two closely related Bacillus spores has been discovered using optical chromatography. This difference can be harnessed for the separation of microscopic particles using opposing laser and fluid flow forces. Particles of different size, composition, and shape experience different optical and fluid forces and come to rest at unique equilibrium positions where the two forces balance. Separations in excess of 600 mum have been observed between Bacillus anthracis Sterne strain and its genetic relative, Bacillus thuringiensis. These findings open new possibilities for detection and characterization of the biological warfare agent, B. anthracis, the causative agent of anthrax, the deadly mammalian disease. The large optical separation between these species is surprising given their close genetic relationship but may be explained by differences in their shape and exosporium morphology, which may result in differences in fluid drag force. The observation of large differences due to less common variables indicates the complex nature of the force balance in optical chromatography, which may in the future be used to separate and characterize microbiological samples. In general, the discovery of such large differences between such closely related biological species suggests new possibilities for the separation and characterization of microorganisms using the full range of emerging techniques that employ radiation pressure (optical filtering, laser tweezers, optical chromatography, etc.).
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Affiliation(s)
- Sean J Hart
- Chemistry Division, Bio/Analytical Chemistry, Naval Research Laboratory, Code 6112, 4555 Overlook Avenue, S.W., Washington, DC 20375, USA.
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Leski TA, Gniadkowski M, Skoczyńska A, Stefaniuk E, Trzciński K, Hryniewicz W. Outbreak of mupirocin-resistant staphylococci in a hospital in Warsaw, Poland, due to plasmid transmission and clonal spread of several strains. J Clin Microbiol 1999; 37:2781-8. [PMID: 10449452 PMCID: PMC85378 DOI: 10.1128/jcm.37.9.2781-2788.1999] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/1999] [Accepted: 06/09/1999] [Indexed: 11/20/2022] Open
Abstract
An outbreak of mupirocin-resistant (MuR) staphylococci was investigated in two wards of a large hospital in Warsaw, Poland. Fifty-three MuR isolates of Staphylococcus aureus, S. epidermidis, S. haemolyticus, S. xylosus, and S. capitis were identified over a 17-month survey which was carried out after introduction of the drug for the treatment of skin infections. The isolates were collected from patients with infections, environmental samples, and carriers; they constituted 19.5% of all staphylococcal isolates identified in the two wards during that time. Almost all the MuR isolates were also resistant to methicillin (methicillin-resistant S. aureus and methicillin-resistant coagulase-negative staphylococci). Seven of the outbreak isolates expressed a low-level-resistance phenotype (MuL), whereas the remaining majority of isolates were found to be highly resistant to mupirocin (MuH). The mupA gene, responsible for the MuH phenotype, has been assigned to three different polymorphic loci among the strains in the collection analyzed. The predominant polymorph, polymorph I (characterized by a mupA-containing EcoRI DNA fragment of about 16 kb), was located on a specific plasmid which was widely distributed among the entire staphylococcal population. All MuR S. aureus isolates were found to represent a single epidemic strain, which was clonally disseminated in both wards. The S. epidermidis population was much more diverse; however, at least four clusters of closely related isolates were identified, which suggested that some strains of this species were also clonally spread in the hospital environment. Six isolates of S. epidermidis were demonstrated to express the MuL and MuH resistance mechanisms simultaneously, and this is the first identification of such dual MuR phenotype-bearing strains. The outbreak was attributed to a high level and inappropriate use of mupirocin, and as a result the dermatological formulation of the drug has been removed from the hospital formulary.
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Affiliation(s)
- T A Leski
- Sera & Vaccines Central Research Laboratory, 00-725 Warsaw, Poland.
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Leski TA, Gniadkowski M, Trzciński K, Hryniewicz W. Comparison of genetic characteristics of MRSA strains present in a Warsaw hospital in 1992 and 1996. Zentralbl Bakteriol 1998; 287:363-73. [PMID: 9638866 DOI: 10.1016/s0934-8840(98)80172-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nine isolates of methicillin-resistant Staphylococcus aureus (MRSA) collected in a Warsaw hospital in 1996 were typed by phenotypic (resistograms) and genotypic (PFGE and plasmid restriction analysis-REAP) methods. Twenty-four (MRSA) strains collected in this hospital during a period of the same duration in 1992 and typed earlier using resistograms and PFGE were also typed by REAP. Comparison of typing results obtained for isolates from 1992 and 1996 showed that strains characterised by PFGE patterns of two distinct types described as specific of the two clonally related groups of Polish MRSA in a multicentre study in 1992 are continuously present in the hospital. However, MRSA strains representing PFGE patterns not observed before were also found within the collection from 1996. REAP typing has proved to have a discriminatory power similar to that of PFGE analysis. Nevertheless, due to the lack of plasmids or difficulties in plasmid DNA isolation in 3 out of 33 studied strains, the typability of REAP turned out to be lower than that of PFGE.
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Affiliation(s)
- T A Leski
- Sera and Vaccines Central Research Laboratory, Warszawa, Poland
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