A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni
MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-05-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00818/full |
| _version_ | 1818513545277472768 |
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| author | Christian ePenny Beau eGrothendick Lin eZhang Connie eBorror Duane eBarbano Duane eBarbano Angela eCornelius Brent eGilpin Clifton eFagerquist William eZaragoza Michele T. Jay-Russell Albert eLastovica Catherine eRagimbeau Henry-Michel eCauchie Todd eSandrin Todd eSandrin |
| author_facet | Christian ePenny Beau eGrothendick Lin eZhang Connie eBorror Duane eBarbano Duane eBarbano Angela eCornelius Brent eGilpin Clifton eFagerquist William eZaragoza Michele T. Jay-Russell Albert eLastovica Catherine eRagimbeau Henry-Michel eCauchie Todd eSandrin Todd eSandrin |
| author_sort | Christian ePenny |
| collection | DOAJ |
| description | MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this study was to enhance strain level resolution for Campylobacter jejuni through the optimization of spectrum processing parameters using a series of designed experiments. A collection of 172 strains of C. jejuni were collected from Luxembourg, New Zealand, North America, and South Africa, consisting of four groups of antibiotic resistant isolates. The groups included: 1) 65 strains resistant to cefoperazone 2) 26 resistant to cefoperazone and beta-lactams 3) 5 strains resistant to cefoperazone, beta-lactams, and tetracycline, and 4) 76 strains resistant to cefoperazone, teicoplanin, amphotericin B and cephalothin. Initially, a model set of 16 strains (three biological replicates and three technical replicates per isolate, yielding a total of 144 spectra) of C. jejuni was subjected to each designed experiment to enhance detection of antibiotic resistance. The most optimal parameters were applied to the larger collection of 172 isolates (two biological replicates and three technical replicates per isolate, yielding a total of 1,031 spectra). We observed an increase in antibiotic resistance detection whenever either a curve based similarity coefficient (Pearson or ranked Pearson) was applied rather than a peak based (Dice) and/or the optimized preprocessing parameters were applied. Increases in antimicrobial resistance detection were scored using the jackknife maximum similarity technique following cluster analysis. From the first four groups of antibiotic resistant isolates, the optimized preprocessing parameters increased detection respective to the aforementioned groups by: 1) five percent 2) nine percent 3) ten percent, and 4) two percent. An additional second categorization was created from the collection consisting of 31 strains resistant to beta-lactams and 141 strains sensitive to beta-lactams. Applying optimal preprocessing parameters, beta-lactam resistance detection was increased by 34 percent. These results suggest that spectrum processing parameters, which are rarely optimized or adjusted, affect the performance of MALDI-TOF MS-based detection of antibiotic resistance and can be fine-tuned to enhance screening performance. |
| first_indexed | 2024-12-11T00:02:56Z |
| format | Article |
| id | doaj.art-694b85327cfd436486fd3a76ee9960e8 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-11T00:02:56Z |
| publishDate | 2016-05-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-694b85327cfd436486fd3a76ee9960e82022-12-22T01:28:24ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2016-05-01710.3389/fmicb.2016.00818187398A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuniChristian ePenny0Beau eGrothendick1Lin eZhang2Connie eBorror3Duane eBarbano4Duane eBarbano5Angela eCornelius6Brent eGilpin7Clifton eFagerquist8William eZaragoza9Michele T. Jay-Russell10Albert eLastovica11Catherine eRagimbeau12Henry-Michel eCauchie13Todd eSandrin14Todd eSandrin15Luxembourg Institute of Science and TechnologyArizona State UniversityArizona State UniversityArizona State UniversityArizona State UniversityArizona State UniversityInstitute of Environmental Science and Research (ESR)Institute of Environmental Science and Research (ESR)US Department of AgricultureUS Department of AgricultureUniversity of California, DavisUniversity of the Western CapeEpidemiological Surveillance of Infectious DiseasesLuxembourg Institute of Science and TechnologyArizona State UniversityArizona State UniversityMALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this study was to enhance strain level resolution for Campylobacter jejuni through the optimization of spectrum processing parameters using a series of designed experiments. A collection of 172 strains of C. jejuni were collected from Luxembourg, New Zealand, North America, and South Africa, consisting of four groups of antibiotic resistant isolates. The groups included: 1) 65 strains resistant to cefoperazone 2) 26 resistant to cefoperazone and beta-lactams 3) 5 strains resistant to cefoperazone, beta-lactams, and tetracycline, and 4) 76 strains resistant to cefoperazone, teicoplanin, amphotericin B and cephalothin. Initially, a model set of 16 strains (three biological replicates and three technical replicates per isolate, yielding a total of 144 spectra) of C. jejuni was subjected to each designed experiment to enhance detection of antibiotic resistance. The most optimal parameters were applied to the larger collection of 172 isolates (two biological replicates and three technical replicates per isolate, yielding a total of 1,031 spectra). We observed an increase in antibiotic resistance detection whenever either a curve based similarity coefficient (Pearson or ranked Pearson) was applied rather than a peak based (Dice) and/or the optimized preprocessing parameters were applied. Increases in antimicrobial resistance detection were scored using the jackknife maximum similarity technique following cluster analysis. From the first four groups of antibiotic resistant isolates, the optimized preprocessing parameters increased detection respective to the aforementioned groups by: 1) five percent 2) nine percent 3) ten percent, and 4) two percent. An additional second categorization was created from the collection consisting of 31 strains resistant to beta-lactams and 141 strains sensitive to beta-lactams. Applying optimal preprocessing parameters, beta-lactam resistance detection was increased by 34 percent. These results suggest that spectrum processing parameters, which are rarely optimized or adjusted, affect the performance of MALDI-TOF MS-based detection of antibiotic resistance and can be fine-tuned to enhance screening performance.http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00818/fullCampylobacter jejuniantibiotic resistanceantimicrobial resistanceMALDI-TOF MSDesigned experimentsSpectrum processing |
| spellingShingle | Christian ePenny Beau eGrothendick Lin eZhang Connie eBorror Duane eBarbano Duane eBarbano Angela eCornelius Brent eGilpin Clifton eFagerquist William eZaragoza Michele T. Jay-Russell Albert eLastovica Catherine eRagimbeau Henry-Michel eCauchie Todd eSandrin Todd eSandrin A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni Frontiers in Microbiology Campylobacter jejuni antibiotic resistance antimicrobial resistance MALDI-TOF MS Designed experiments Spectrum processing |
| title | A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni |
| title_full | A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni |
| title_fullStr | A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni |
| title_full_unstemmed | A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni |
| title_short | A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni |
| title_sort | designed experiments approach to optimizing maldi tof ms spectrum processing parameters enhances detection of antibiotic resistance in campylobacter jejuni |
| topic | Campylobacter jejuni antibiotic resistance antimicrobial resistance MALDI-TOF MS Designed experiments Spectrum processing |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00818/full |
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