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The AMR-ARRAY: A modular bead array detecting β-lactam, (fluoro) quinolone, colistin, aminoglycoside and macrolide resistance determinants in Gram-negative bacteria. J Microbiol Methods 2022; 196:106472. [DOI: 10.1016/j.mimet.2022.106472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/27/2022]
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The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives. Infect Dis Clin North Am 2017; 30:323-345. [PMID: 27208762 DOI: 10.1016/j.idc.2016.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.
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Thirty-minute screening of antibiotic resistance genes in bacterial isolates with minimal sample preparation in static self-dispensing 64 and 384 assay cards. Appl Microbiol Biotechnol 2015; 99:7711-22. [PMID: 26227406 PMCID: PMC4543423 DOI: 10.1007/s00253-015-6774-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/04/2015] [Accepted: 06/17/2015] [Indexed: 01/23/2023]
Abstract
In a clinical setting, molecular assays such as polymerase chain reaction offer a rapid means to infer or confirm identity and therapeutic decisions. Accordingly, a number of molecular assays targeting identity and antibiotic resistance (AR) genes have been developed; however, these methods can be technically complex and relatively expensive. Herein, we describe a diagnostic concept utilizing isothermal amplification technology with non-purified heat-lysed cells and self-dispensing cards for testing multiple primers in parallel. This proof-of-concept study, performed with Staphylococcus aureus isolates and associated AR genes, was compared with culture-based susceptibility and quantitative PCR (qPCR). Results demonstrate reduced sample processing steps resulting in a turnaround time (starting from bacterial culture to ending in the antibiotic resistance gene profile) in less than 30 min. For antibiotics tested in which an associated AR gene was targeted on the Gene-Z card, 69 % (18/26) of culture-based resistance events were positive for related AR genes. A comparison of loop-mediated isothermal amplification (LAMP) and qPCR assays targeting the same antibiotic resistance genes showed a 98.2 % agreement in terms of presence and absence calls. Identity-based discrepancies between conventional (phenotypic) and molecular (genotypic) results were further resolved, and we were able to demonstrate higher accuracy in identification with the molecular analysis.
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Koets M, van Ommering K, Wang L, Testori E, Evers TH, Prins MWJ. Influence of dsDNA fragment length on particle binding in an evanescent field biosensing system. Analyst 2014; 139:1672-7. [PMID: 24534803 DOI: 10.1039/c3an01999c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Particle labels are widely used in affinity-based biosensing due to the high detection signal per label, the high stability, and the convenient biofunctionalization of particles. In this paper we address the question how the time-course of particle binding and the resulting signals depend on the length of captured target molecules. As a model system we used fragments of dsDNA with lengths of 105 bp (36 nm), 290 bp (99 nm) and 590 bp (201 nm), detected in an evanescent-field optomagnetic biosensing system. On both ends the fragments were provided with small-molecule tags to allow binding of the fragments to protein-coated particles and to the capture molecules at the sensor surface. For isolated single particles bound to the surface, we observe that the optical scattering signal per particle depends only weakly on the fragment length, which we attribute to the pivoting motion that allows the particles to get closer to the surface. Our data show a strong influence of the fragment length on the particle binding: the binding rate of particles to the sensor surface is an order of magnitude higher for the longest dsDNA fragments compared to the smallest fragment studied in this paper. We attribute the enhanced binding rate to the length and motional freedom of the fragments. These results generate a new dimension for the design of assays and systems in particle-based biosensing.
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Affiliation(s)
- Marjo Koets
- Philips Research Europe, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands.
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Fu Y, Pan Y, Pan M, Wang Y, Liu W, Li Y. Development of a high-throughput DNA microarray for drug-resistant gene detection and its preliminary application. J Microbiol Methods 2012; 89:110-8. [PMID: 22619747 DOI: 10.1016/j.mimet.2012.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Most bacteria are resistant to a wide variety of antibiotics and other drugs, which decrease the effectiveness of clinical drug therapies. The present study developed a high-throughput DNA microarray for drug-resistant gene detection. A total of 115 specific oligonuclieotide probes with lengths of 42 nt to 45 nt and comparable Tm values were selected from 17 categories of drug-resistant genes in the National Center for Biotechnology Information database and were chemically synthesized. The entire bacterial DNA was extracted, randomly amplified, and labeled using Cy3-dCTP. The hybridization conditions of the microarray test were optimized to improve sensitivity and specificity. The drug-resistant genes were detected and genotyped using microarray analysis after hydration at 42°C for 4h with 2× hybridization solution. The microarray test sensitivity was 20ng/μL DNA. The performance of the microarray was validated using reference strains and clinical isolates. The results were consistent with direct DNA sequence analysis and drug susceptibility tests. The developed DNA microarray could be used to detect and screen drug-resistant bacteria rapidly and simultaneously. Thus, the present study could be helpful in effectively using antibiotics and controlling infectious diseases.
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Affiliation(s)
- Yali Fu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 210029, PR China
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Kakatkar A, Pansare L, Gautam R, Shashidhar R, Karani M, Bandekar J. Molecular characterization of antibiotic resistant Salmonella isolates from Indian foods. Food Res Int 2011. [DOI: 10.1016/j.foodres.2011.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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7
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Delgado S, Fracchetti F, Mayo B, Torriani S. Development and validation of a multiplex PCR-based DNA microarray hybridisation method for detecting bacterial antibiotic resistance genes in cheese. Int Dairy J 2011. [DOI: 10.1016/j.idairyj.2010.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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A multiplex ligation detection assay for the characterization of Salmonella enterica strains. Int J Food Microbiol 2010; 145 Suppl 1:S68-78. [PMID: 21093086 DOI: 10.1016/j.ijfoodmicro.2010.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 09/28/2010] [Accepted: 10/17/2010] [Indexed: 11/22/2022]
Abstract
A proof of principle of a multi-target assay for genotyping Salmonella has been developed targeting 62 genomic marker sequences of Salmonella related to pathogenicity. The assay is based on multiplex ligation detection reaction (LDR) followed by customized ArrayTube® microarray detection. The feasibility of the developed assay was verified in a method comparison study with conventional PCR using 16 Salmonella 'test' strains comprising eight serovars. Subsequently, the feasibility of the LDR microarray assay was also tested by analyzing 41 strains belonging to 23 serovars. With the exception of four serovars each serovar was characterized by a unique virulence associated gene repertoire. The LDR microarray platform proved to be a convenient, rapid and easy to use tool with potential in tracing a Salmonella contamination in the food chain, for outbreak studies, and to provide data for risk assessors that support bio-traceability models.
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Discovery of a gene conferring multiple-aminoglycoside resistance in Escherichia coli. Antimicrob Agents Chemother 2010; 54:2666-9. [PMID: 20368404 DOI: 10.1128/aac.01743-09] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine-origin Escherichia coli isolates were tested for resistance phenotypes using a disk diffusion assay and for resistance genotypes using a DNA microarray. An isolate with gentamicin and amikacin resistance but with no corresponding genes detected yielded a 1,056-bp DNA sequence with the closest homologues for its inferred protein sequence among a family of 16S rRNA methyltransferase enzymes. These enzymes confer high-level aminoglycoside resistance and have only recently been described in Gram-negative bacteria.
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Davis MA, Lim JY, Soyer Y, Harbottle H, Chang YF, New D, Orfe LH, Besser TE, Call DR. Development and validation of a resistance and virulence gene microarray targeting Escherichia coli and Salmonella enterica. J Microbiol Methods 2010; 82:36-41. [PMID: 20362014 DOI: 10.1016/j.mimet.2010.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 03/23/2010] [Accepted: 03/24/2010] [Indexed: 11/19/2022]
Abstract
A microarray was developed to simultaneously screen Escherichia coli and Salmonella enterica for multiple genetic traits. The final array included 203 60-mer oligonucleotide probes, including 117 for resistance genes, 16 for virulence genes, 25 for replicon markers, and 45 other markers. Validity of the array was tested by assessing inter-laboratory agreement among four collaborating groups using a blinded study design. Internal validation indicated that the assay was reliable (area under the receiver-operator characteristic curve=0.97). Inter-laboratory agreement, however, was poor when estimated using the intraclass correlation coefficient, which ranged from 0.27 (95% confidence interval 0.24, 0.29) to 0.29 (0.23, 0.34). These findings suggest that extensive testing and procedure standardization will be needed before bacterial genotyping arrays can be readily shared between laboratories.
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Affiliation(s)
- Margaret A Davis
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-7040, United States.
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11
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Zou W, Frye J, Chang CW, Liu J, Cerniglia C, Nayak R. Microarray analysis of antimicrobial resistance genes inSalmonella entericafrom preharvest poultry environment. J Appl Microbiol 2009; 107:906-14. [DOI: 10.1111/j.1365-2672.2009.04270.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Lu H, Wang X, Lang X, Wang Y, Dang Y, Zhang F, Tang J, Li X, Feng X. Preparation and application of microarrays for the detection of antibiotic resistance genes in samples isolated from Changchun, China. Mol Biol Rep 2009; 37:1857-65. [DOI: 10.1007/s11033-009-9621-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 07/03/2009] [Indexed: 11/27/2022]
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13
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Koets M, van der Wijk T, van Eemeren J, van Amerongen A, Prins M. Rapid DNA multi-analyte immunoassay on a magneto-resistance biosensor. Biosens Bioelectron 2009; 24:1893-8. [DOI: 10.1016/j.bios.2008.09.023] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 09/19/2008] [Accepted: 09/23/2008] [Indexed: 12/01/2022]
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Poultry-associated Salmonella enterica subsp. enterica serovar 4,12:d:- reveals high clonality and a distinct pathogenicity gene repertoire. Appl Environ Microbiol 2008; 75:1011-20. [PMID: 19114530 DOI: 10.1128/aem.02187-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A European baseline survey during the years 2005 and 2006 has revealed that the monophasic Salmonella enterica subsp. enterica serovar 4,12:d:- was, with a prevalence of 23.6%, the most frequently isolated serovar in German broiler flocks. In Denmark and the United Kingdom, its serovar prevalences were 15.15% and 2.8%, respectively. Although poultry is a major source of human salmonellosis, serovar 4,12:d:- is rarely isolated in humans (approximately 0.09% per year). Molecular typing studies using pulsed-field gel electrophoresis and DNA microarray analysis show that the serovar is highly clonal and lacks genes with known contributions to pathogenicity. In contrast to other poultry-associated serovars, all strains were susceptible to 17 antimicrobial agents tested and did not encode any resistance determinant. Furthermore, serovar 4,12:d:- lacked the genes involved in galactonate metabolism and in the glycolysis and glyconeogenesis important for energy production in the cells. The conclusion of the study is that serovar 4,12:d:- seems to be primarily adapted to broilers and therefore causes only rare infections in humans.
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Tankouo-Sandjong B, Sessitsch A, Stralis-Pavese N, Liebana E, Kornschober C, Allerberger F, Hächler H, Bodrossy L. Development of an oligonucleotide microarray method for Salmonella serotyping. Microb Biotechnol 2008; 1:513-22. [PMID: 21261872 PMCID: PMC3815293 DOI: 10.1111/j.1751-7915.2008.00053.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Adequate identification of Salmonella enterica serovars is a prerequisite for any epidemiological investigation. This is traditionally obtained via a combination of biochemical and serological typing. However, primary strain isolation and traditional serotyping is time‐consuming and faster methods would be desirable. A microarray, based on two housekeeping and two virulence marker genes (atpD, gyrB, fliC and fljB), has been developed for the detection and identification of the two species of Salmonella (S. enterica and S. bongori), the five subspecies of S. enterica (II, IIIa, IIIb, IV, VI) and 43 S. enterica ssp. enterica serovars (covering the most prevalent ones in Austria and the UK). A comprehensive set of probes (n = 240), forming 119 probe units, was developed based on the corresponding sequences of 148 Salmonella strains, successfully validated with 57 Salmonella strains and subsequently evaluated with 35 blind samples including isolated serotypes and mixtures of different serotypes. Results demonstrated a strong discriminatory ability of the microarray among Salmonella serovars. Threshold for detection was 1 colony forming unit per 25 g of food sample following overnight (14 h) enrichment.
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Affiliation(s)
- B Tankouo-Sandjong
- Austrian Research Centers GmbH, Department of Bioresources, Seibersdorf, Austria
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16
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Eijkelkamp JM, Aarts HJM, van der Fels-Klerx HJ. Suitability of Rapid Detection Methods for Salmonella in Poultry Slaughterhouses. FOOD ANAL METHOD 2008. [DOI: 10.1007/s12161-008-9040-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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18
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19
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Ammor MS, Gueimonde M, Danielsen M, Zagorec M, van Hoek AHAM, de Los Reyes-Gavilán CG, Mayo B, Margolles A. Two different tetracycline resistance mechanisms, plasmid-carried tet(L) and chromosomally located transposon-associated tet(M), coexist in Lactobacillus sakei Rits 9. Appl Environ Microbiol 2008; 74:1394-401. [PMID: 18192429 PMCID: PMC2258611 DOI: 10.1128/aem.01463-07] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Accepted: 12/26/2007] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus sakei is extensively used as functional starter culture in fermented meat products. One of the safety criteria of a starter culture is the absence of potentially transferable antibiotic resistance determinants. However, tetracycline-resistant L. sakei strains have already been observed. In this paper, we show that tetracycline resistance in L. sakei Rits 9, a strain isolated from Italian Sola cheese made from raw milk, is mediated by a transposon-associated tet(M) gene coding for a ribosomal protection protein and a plasmid-carried tet(L) gene coding for a tetracycline efflux pump. pLS55, the 5-kb plasmid carrying the tet(L) gene, is highly similar to the pMA67 plasmid recently described for Paenibacillus larvae, a species pathogenic to honeybees. pLS55 could be transferred by electroporation into the laboratory strain L. sakei 23K. While the L. sakei 23K transformant containing pLS55 displayed an intermediate tetracycline resistance level (MIC, <32 microg/ml), L. sakei Rits 9, containing both tetracycline-resistant determinants, had a MIC of <256 microg/ml, suggesting that Tet L and Tet M confer different levels of resistance in L. sakei. Remarkably, in the absence of tetracycline, a basal expression of both genes was detected for L. sakei Rits 9. In addition, subinhibitory concentrations of tetracycline affected the expression patterns of tet(M) and tet(L) in different ways: the expression of tet(M) was induced only at high tetracycline concentrations, whereas the expression of tet(L) was up-regulated at lower concentrations. This is the first time that two different mechanisms conferring resistance to tetracycline are characterized for the same strain of a lactic acid bacterium.
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Affiliation(s)
- Mohammed Salim Ammor
- Instituto de Productos Lácteos de Asturias (CSIC), Carretera de Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
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Mosaic tetracycline resistance genes and their flanking regions in Bifidobacterium thermophilum and Lactobacillus johnsonii. Antimicrob Agents Chemother 2007; 52:248-52. [PMID: 17967912 DOI: 10.1128/aac.00714-07] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For the first time, mosaic tetracycline resistance genes were identified in Lactobacillus johnsonii and in Bifidobacterium thermophilum strains. The L. johnsonii strain investigated contains a complex hybrid gene, tet(O/W/32/O/W/O), whereas the five bifidobacterial strains possess two different mosaic tet genes: i.e., tet(W/32/O) and tet(O/W). As reported by others, the crossover points of the mosaic tet gene segments were found at similar positions within the genes, suggesting a hot spot for recombination. Analysis of the sequences flanking these genes revealed that the upstream part corresponds to the 5' end of the mosaic open reading frame. In contrast, the downstream region was shown to be more variable. Surprisingly, in one of the B. thermophilum strains a third tet determinant was identified, coding for the efflux pump Tet(L).
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Ojha S, Kostrzynska M. Examination of animal and zoonotic pathogens using microarrays. Vet Res 2007; 39:4. [DOI: 10.1051/vetres:2007042] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 07/27/2007] [Indexed: 01/13/2023] Open
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Ammor MS, Flórez AB, van Hoek AH, de los Reyes-Gavilán CG, Aarts HJ, Margolles A, Mayo B. Molecular Characterization of Intrinsic and Acquired Antibiotic Resistance in Lactic Acid Bacteria and Bifidobacteria. J Mol Microbiol Biotechnol 2007; 14:6-15. [DOI: 10.1159/000106077] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Majtan T, Majtanova L, Timko J, Majtan V. Oligonucleotide microarray for molecular characterization and genotyping of Salmonella spp. strains. J Antimicrob Chemother 2007; 60:937-46. [PMID: 17897936 DOI: 10.1093/jac/dkm326] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES To characterize and subtype multidrug-resistant Salmonella isolates by determining the virulence factors, prophage sequences and antimicrobial resistance genes using a novel Salmonella-specific oligonucleotide microarray. METHODS Preliminary screening of 24 Salmonella clinical isolates was carried out by using susceptibility testing, plasmid profiling and class 1 integron PCR. Subsequently, oligonucleotide microarray was involved in genotypic characterization and localization of monitored genetic markers. The presence of antimicrobial resistance genes was also detected and confirmed by PCR and subsequent sequencing. The potential spread of emerging bla(SHV-2) was investigated by bacterial conjugation. RESULTS All Salmonella strains revealed resistance to two or more (up to nine) antibiotics. Nineteen of them carried class 1 integrons including dfrA1, dfrA12, aadA1, aadA2, bla(PSE-1) and bla(TEM-1) gene cassettes, respectively. Twenty-three out of 24 Salmonella isolates possessed one or more plasmids. Oligonucleotide microarray characterization and typing revealed the conserved character of Salmonella pathogenicity island virulence factors among three Salmonella enterica serovars, significant variability in prophage sequences and many different antimicrobial resistance gene patterns. Differential labelling of genomic and plasmid DNA, respectively, and hybridization to the microarray made it possible to localize important resistance determinants. Microarray results were successfully confirmed and verified by using PCR. The emerging bla(SHV-2) gene from Salmonella Kentucky SK10944 conferring resistance to ceftriaxone and cefotaxime was transferred via bacterial conjugation to Escherichia coli K-12 3110. CONCLUSIONS Salmonella isolates were quickly and thoroughly characterized by a novel oligonucleotide microarray, which could become a useful tool for detection of virulence and resistance genes and monitoring of their dissemination among salmonellae and closely related bacteria.
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Affiliation(s)
- T Majtan
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 84551 Bratislava 45, Slovakia.
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24
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Susceptibility of human and probiotic Bifidobacterium spp. to selected antibiotics as determined by the Etest method. Int Dairy J 2007. [DOI: 10.1016/j.idairyj.2007.01.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Ma M, Wang H, Yu Y, Zhang D, Liu S. Detection of antimicrobial resistance genes of pathogenic Salmonella from swine with DNA microarray. J Vet Diagn Invest 2007; 19:161-7. [PMID: 17402610 DOI: 10.1177/104063870701900204] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A glass-based microarray was developed to detect 11 antimicrobial resistance genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, and chloramphenicols. The target genes for microarray were generated from Salmonella isolates by PCR and confirmed by sequencing. The specificity of the microarray was tested using 11 positive DNA probes. The sensitivity was tested with tetA gene and Salmonella isolates. Using detection threshold of signal-to-noise ratio (S/N) > or = 1.5 or median pixel intensity > or =1000, antimicrobial resistance genes carried by 30 Salmonella isolates were detected. Common genes included sul I(76.7%, 23/30), aph(3')-IIa (60%, 18/30), tetC (60%, 18/30), cat] (43.3%, 13/30), tetA (40%, 12/30) and aadA1 (36.7%, 11/30), and the results were confirmed to be correct by PCR.
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Affiliation(s)
- Menggen Ma
- College of Life Science, Sichuan University, 29 Wangjiang Rd, Wuhou District, Chengdu 610064, China.
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Strommenger B, Schmidt C, Werner G, Roessle-Lorch B, Bachmann TT, Witte W. DNA microarray for the detection of therapeutically relevant antibiotic resistance determinants in clinical isolates of Staphylococcus aureus. Mol Cell Probes 2007; 21:161-70. [PMID: 17123780 DOI: 10.1016/j.mcp.2006.10.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 10/07/2006] [Accepted: 10/12/2006] [Indexed: 11/20/2022]
Abstract
An oligonucleotide microarray was constructed for the rapid and sensitive molecular detection of antibiotic resistance determinants in Staphylococcus aureus. The array is equipped with oligonucleotide capture probes for the detection of 10 clinically and therapeutically relevant antibiotic resistance genes and -mutations (mecA, aacA-aphD, tetK, tetM, vat(A), vat(B), vat(C), erm(A), erm(C), grlA-mutation) as well as several control probes. A microarray concept was established including multiplexed PCR amplification, DNA labeling, hybridization and data processing. This concept was applied to clinical Staphylococcus aureus isolates and results were concordant with those from standard genotypic and phenotypic resistance testing. Our microarray concept offers rapid and accurate identification of antibiotic resistance profiles. It is easily expandable and thus can be adapted to changing clinical and epidemiological requirements in clinical diagnosis as well as in epidemiological studies.
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Affiliation(s)
- Birgit Strommenger
- Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855 Wernigerode, Germany.
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Patterson AJ, Colangeli R, Spigaglia P, Scott KP. Distribution of specific tetracycline and erythromycin resistance genes in environmental samples assessed by macroarray detection. Environ Microbiol 2007; 9:703-15. [PMID: 17298370 DOI: 10.1111/j.1462-2920.2006.01190.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A macroarray system was developed to screen environmental samples for the presence of specific tetracycline (Tc(R)) and erythromycin (erm(R)) resistance genes. The macroarray was loaded with polymerase chain reaction (PCR) amplicons of 23 Tc(R) genes and 10 erm(R) genes. Total bacterial genomic DNA was extracted from soil and animal faecal samples collected from different European countries. Macroarray hybridization was performed under stringent conditions and the results were analysed by fluorescence scanning. Pig herds in Norway, reared without antibiotic use, had a significantly lower incidence of antibiotic resistant bacteria than those reared in other European countries, and organic herds contained lower numbers of resistant bacteria than intensively farmed animals. The relative proportions of the different genes were constant across the different countries. Ribosome protection type Tc(R) genes were the most common resistance genes in animal faecal samples, with the tet(W) gene the most abundant, followed by tet(O) and tet(Q). Different resistance genes were present in soil samples, where erm(V) and erm(E) were the most prevalent followed by the efflux type Tc(R) genes. The macroarray proved a powerful tool to screen DNA extracted from environmental samples to identify the most abundant Tc(R) and erm(R) genes within those tested, avoiding the need for culturing and biased PCR amplification steps.
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Affiliation(s)
- Andrea J Patterson
- Gut Health Division, Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, UK
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Malorny B, Bunge C, Guerra B, Prietz S, Helmuth R. Molecular characterisation of Salmonella strains by an oligonucleotide multiprobe microarray. Mol Cell Probes 2006; 21:56-65. [PMID: 17029709 DOI: 10.1016/j.mcp.2006.08.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 07/26/2006] [Accepted: 08/03/2006] [Indexed: 10/24/2022]
Abstract
A DNA microarray has been developed for the simultaneous characterisation and typing of Salmonella enterica subsp. enterica isolates. One-hundred and nine 35-40 mer oligonucleotides probes detect flagellar and somatic antigen encoding genes (serogroup or serotype specific), important virulence genes located within or outside the pathogenicity islands, phage-associated genes and antibiotic resistance determinants. The probes were printed on glass slides and whole genomic Cy5-labelled Salmonella DNA was hybridised to the substrate. A set of 19 different Salmonella strains and one Escherichia coli strain has been selected as positive and negative controls for each probe. The validity of the results is confirmed by gene-specific PCRs or phenotypic methods (serotyping, MIC determination for various antimicrobial agents). Of 2071 data points generated, an agreement of 97.4% has been obtained between microarray and PCR/phenotypic results. Twenty-six data points (1.3%) were classified as uncertain and, similarly, 1.3% showed a discordant result. The microarray described here is a new tool to study the epidemiology of Salmonella strains on the genotypic level and might become a powerful method in risk assessment studies.
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Affiliation(s)
- Burkhard Malorny
- National Salmonella Reference Laboratory, Federal Institute for Risk Assessment, Diedersdorfer Weg 1, D-12277 Berlin, Germany
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29
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Hermans APHM, Beuling AM, van Hoek AHAM, Aarts HJM, Abee T, Zwietering MH. Distribution of prophages and SGI-1 antibiotic-resistance genes among different Salmonella enterica serovar Typhimurium isolates. MICROBIOLOGY-SGM 2006; 152:2137-2147. [PMID: 16804187 DOI: 10.1099/mic.0.28850-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recently, the authors identified Salmonella enterica serovar Typhimurium (S. Typhimurium) definitive type (DT)104-specific sequences of mainly prophage origin by genomic subtractive hybridization. In the present study, the distribution of the prophages identified, ST104 and ST64B, and the novel prophage remnant designated prophage ST104B, was tested among 23 non-DT104 S. Typhimurium isolates of different phage types and 19 isolates of the DT104 subtypes DT104A, DT104B low and DT104L, and the DT104-related type U302. The four S. Typhimurium prophages Gifsy-1, Gifsy-2, Fels-1 and Fels-2 were also included. Analysis of prophage distribution in different S. Typhimurium isolates may supply additional information to enable development of a molecular method as an alternative to phage typing. Furthermore, the presence of the common DT104 antibiotic resistance genes for the penta-resistance type ACSSuT, aadA2, floR, pse-1, sul1 and tet(G), was also studied because of the authors' focus on this emerging type. Based on differences in prophage presence within their genome, it was possible to divide S. Typhimurium isolates into 12 groups. Although no clear relationship was found between different phage type and prophage presence, discrimination could be made between the different DT104 subtypes based on diversity in the presence of prophages ST104, ST104B and ST64B. The novel prophage remnant ST104B, which harbours a homologue of the Escherichia coli O157 : H7 HldD LPS assembly-related protein, was identified only in the 14 DT104L isolates and in the DT104-related U302 isolate. In conclusion, the presence of the genes for penta-resistance type ACSSuT, the HldD homologue containing ST104 prophage remnant and phage type DT104L are most likely common features of the emerging subtype of S. Typhimurium DT104.
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Affiliation(s)
- Armand P H M Hermans
- Laboratory of Food Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
- RIKILT Institute of Food Safety, PO Box 230, 6700 AE Wageningen, The Netherlands
| | - Annelien M Beuling
- Laboratory of Food Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
- RIKILT Institute of Food Safety, PO Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Henk J M Aarts
- RIKILT Institute of Food Safety, PO Box 230, 6700 AE Wageningen, The Netherlands
| | - Tjakko Abee
- Laboratory of Food Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Marcel H Zwietering
- Laboratory of Food Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
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30
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Francois P, Charbonnier Y, Jacquet J, Utinger D, Bento M, Lew D, Kresbach GM, Ehrat M, Schlegel W, Schrenzel J. Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification. J Microbiol Methods 2006; 65:390-403. [PMID: 16216356 DOI: 10.1016/j.mimet.2005.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Revised: 08/16/2005] [Accepted: 08/17/2005] [Indexed: 11/18/2022]
Abstract
Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta(2)O(5)-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing >54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 h. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription.
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Affiliation(s)
- Patrice Francois
- University Hospitals of Geneva, Genomic Research Laboratory, Service of Infectious Diseases, Switzerland.
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31
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Frye JG, Jesse T, Long F, Rondeau G, Porwollik S, McClelland M, Jackson CR, Englen M, Fedorka-Cray PJ. DNA microarray detection of antimicrobial resistance genes in diverse bacteria. Int J Antimicrob Agents 2006; 27:138-51. [PMID: 16427254 DOI: 10.1016/j.ijantimicag.2005.09.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 09/17/2005] [Indexed: 11/26/2022]
Abstract
High throughput genotyping is essential for studying the spread of multiple antimicrobial resistance. A test oligonucleotide microarray designed to detect 94 antimicrobial resistance genes was constructed and successfully used to identify antimicrobial resistance genes in control strains. The microarray was then used to assay 51 distantly related bacteria, including Gram-negative and Gram-positive isolates, resulting in the identification of 61 different antimicrobial resistance genes in these bacteria. These results were consistent with their known gene content and resistance phenotypes. Microarray results were confirmed by polymerase chain reaction and Southern blot analysis. These results demonstrate that this approach could be used to construct a microarray to detect all sequenced antimicrobial resistance genes in nearly all bacteria.
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Affiliation(s)
- Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. Department of Agriculture, Agriculture Research Service, Richard B. Russell Research Center, 950 College Station Road, Athens, GA 30605, USA.
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32
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Kastner S, Perreten V, Bleuler H, Hugenschmidt G, Lacroix C, Meile L. Antibiotic susceptibility patterns and resistance genes of starter cultures and probiotic bacteria used in food. Syst Appl Microbiol 2005; 29:145-55. [PMID: 16464696 DOI: 10.1016/j.syapm.2005.07.009] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Indexed: 11/24/2022]
Abstract
A survey of starter and probiotic cultures was carried out to determine the current antibiotic resistance situation in microbial food additives in Switzerland. Two hundred isolates from 90 different sources were typed by molecular and other methods to belong to the genera Lactobacillus (74 samples), Staphylococcus (33 samples), Bifidobacterium (6 samples), Pediococcus (5 samples), or were categorized as lactococci or streptococci (82 samples). They were screened for phenotypic resistances to 20 antibiotics by the disk diffusion method. Twenty-seven isolates exhibiting resistances that are not an intrinsic feature of the respective genera were further analyzed by microarray hybridization as a tool to trace back phenotypic resistances to specific genetic determinants. Their presence was finally verified by PCR amplification or Southern hybridization. These studies resulted in the detection of the tetracycline resistance gene tet(K) in 5 Staphylococcus isolates used as meat starter cultures, the tetracycline resistance gene tet(W) in the probiotic cultures Bifidobacterium lactis DSM 10140 and Lactobacillus reuteri SD 2112 (residing on a plasmid), and the lincosamide resistance gene lnu(A) (formerly linA) in L. reuteri SD 2112.
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Affiliation(s)
- Sabine Kastner
- Laboratory of Food Biotechnology, Institute of Food Science and Nutrition, Swiss Federal Institute of Technology (ETH), ETH-Zentrum, CH-8092 Zurich, Switzerland
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