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Sun A, Vopařilová P, Liu X, Kou B, Řezníček T, Lednický T, Ni S, Kudr J, Zítka O, Fohlerová Z, Pajer P, Zhang H, Neužil P. An integrated microfluidic platform for nucleic acid testing. MICROSYSTEMS & NANOENGINEERING 2024; 10:66. [PMID: 38784376 PMCID: PMC11111744 DOI: 10.1038/s41378-024-00677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/30/2023] [Accepted: 01/07/2024] [Indexed: 05/25/2024]
Abstract
This study presents a rapid and versatile low-cost sample-to-answer system for SARS-CoV-2 diagnostics. The system integrates the extraction and purification of nucleic acids, followed by amplification via either reverse transcription-quantitative polymerase chain reaction (RT-qPCR) or reverse transcription loop-mediated isothermal amplification (RT-LAMP). By meeting diverse diagnostic and reagent needs, the platform yields testing results that closely align with those of commercial RT-LAMP and RT‒qPCR systems. Notable advantages of our system include its speed and cost-effectiveness. The assay is completed within 28 min, including sample loading (5 min), ribonucleic acid (RNA) extraction (3 min), and RT-LAMP (20 min). The cost of each assay is ≈ $9.5, and this pricing is competitive against that of Food and Drug Administration (FDA)-approved commercial alternatives. Although some RNA loss during on-chip extraction is observed, the platform maintains a potential limit of detection lower than 297 copies. Portability makes the system particularly useful in environments where centralized laboratories are either unavailable or inconveniently located. Another key feature is the platform's versatility, allowing users to choose between RT‒qPCR or RT‒LAMP tests based on specific requirements.
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Affiliation(s)
- Antao Sun
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 P. R. China
| | - Petra Vopařilová
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic
| | - Xiaocheng Liu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 P. R. China
| | - Bingqian Kou
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 P. R. China
| | - Tomáš Řezníček
- ITD Tech s.r.o, Osvoboditelů 1005, 735 81 Bohumín, Czech Republic
| | - Tomáš Lednický
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, Brno, 61200 Czech Republic
| | - Sheng Ni
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiří Kudr
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic
| | - Ondřej Zítka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic
| | - Zdenka Fohlerová
- Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 3058/10, Brno, 61600 Czech Republic
| | - Petr Pajer
- Military Health Institute, U Vojenské nemocnice 1200, 16200 Praha 6, Czech Republic
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049 P. R. China
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 P. R. China
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Kowalewicz C, Timmermans M, Fretin D, Wattiau P, Boland C. An in-house 45-plex array for the detection of antimicrobial resistance genes in Gram-positive bacteria. Microbiologyopen 2022; 12:e1341. [PMID: 36825880 PMCID: PMC9791161 DOI: 10.1002/mbo3.1341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022] Open
Abstract
Identifying antimicrobial resistance (AMR) genes and determining their occurrence in Gram-positive bacteria provide useful data to understand how resistance can be acquired and maintained in these bacteria. We describe an in-house bead array targeting AMR genes of Gram-positive bacteria and allowing their rapid detection all at once at a reduced cost. A total of 41 AMR probes were designed to target genes frequently associated with resistance to tetracycline, macrolides, lincosamides, streptogramins, pleuromutilins, phenicols, glycopeptides, aminoglycosides, diaminopyrimidines, oxazolidinones and particularly shared among Enterococcus and Staphylococcus spp. A collection of 124 enterococci and 62 staphylococci isolated from healthy livestock animals through the official Belgian AMR monitoring (2018-2020) was studied with this array from which a subsample was further investigated by whole-genome sequencing. The array detected AMR genes associated with phenotypic resistance for 93.0% and 89.2% of the individual resistant phenotypes in enterococci and staphylococci, respectively. Although linezolid is not used in veterinary medicine, linezolid-resistant isolates were detected. These were characterized by the presence of optrA and poxtA, providing cross-resistance to other antibiotics. Rarer, vancomycin resistance was conferred by the vanA or by the vanL cluster. Numerous resistance genes circulating among Enterococcus and Staphylococcus spp. were detected by this array allowing rapid screening of a large strain collection at an affordable cost. Our data stress the importance of interpreting AMR with caution and the complementarity of both phenotyping and genotyping methods. This array is now available to assess other One-Health AMR reservoirs.
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Affiliation(s)
| | | | - David Fretin
- Veterinary Bacteriology, SciensanoIxellesBelgium
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Gao W, Li B, Ling L, Zhang L, Yu S. MALDI-TOF MS method for differentiation of methicillin-sensitive and methicillin-resistant Staphylococcus aureus using (E)-Propyl α-cyano-4-Hydroxyl cinnamylate. Talanta 2022; 244:123405. [PMID: 35349841 DOI: 10.1016/j.talanta.2022.123405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 01/02/2023]
Abstract
Differentiating methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MRSA and MSSA) is crucial for clinical diagnosis and anti-microbial treatment. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is an efficient tool for identifying pathogenic microorganisms at the bacterial species level. Here, we found that MRSA and MSSA can be differentiated by MALDI-TOF MS by employing (E)-propylα-cyano-4-hydroxyl cinnamylate (CHCA-C3) as the matrix, which shows great performance for proteins/peptides, especially hydrophobic proteins. The results show that the mass spectra profile of standard MRSA (ATCC 43300) is significantly different from the profiles of standard MSSA strains (ATCC 25923 and 29213) when using CHCA-C3 as the matrix compared to traditional matrix. The mass profiles had great reproducibility and were scarcely influenced by the growth medium. Due to the enhanced discrimination ability of CHCA-C3, we collected the mass spectra of 62 clinical S. aureus strains and selected four representative peaks for principal component analysis, which showed great differentiation. Our results suggest that employing a suitable matrix could enhance the discrimination ability of antibiotic-resistant bacteria by MALDI-TOF MS.
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Affiliation(s)
- Wenjing Gao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Bin Li
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ling Ling
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Li Zhang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Shaoning Yu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
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Antibiotic treatments to mothers during the perinatal period leaving hidden trouble on infants. Eur J Pediatr 2022; 181:3459-3471. [PMID: 35680662 PMCID: PMC9395442 DOI: 10.1007/s00431-022-04516-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/31/2022] [Indexed: 12/04/2022]
Abstract
UNLABELLED Antibiotic application during the perinatal period is unavoidable in the clinic, but the potential effects on mothers and infants remain unknown. Herein, 25 breast milk samples from mothers who received cefuroxime (CXM) or CXM + cefoxitin (CFX) treatments and fecal samples from their infants were collected to investigate the undesirable effects of antibiotics on the microbiota of mothers and neonates. Furthermore, five fecal samples of infants, whose mothers had antibiotic treatments, were collected at a 6-month postpartum follow-up visit to evaluate the long-term effects on infants' gut microbiota. Moreover, the relative abundance of antibiotic resistance genes (ARGs) in fecal samples was compared to investigate the transfer of ARGs in the infant gut microbiota. The results indicated that the antibiotic treatments had no influence on the microbiota of breast milk. The dominant bacterial phyla in the fecal samples changed to Firmicutes and Proteobacteria after antibiotic treatments, while the bacterial community showed a recuperative trend at the follow-up visits. In addition, the abundance of ARGs in the infant gut microbiota demonstrated a declining trend in the CXM- and CXM + CFX-treated groups, while ARG abundance presented a significant increasing trend after a 6-month recovery period. CONCLUSION Antibiotic treatments for mothers during the perinatal period disturb the gut microbiota in neonates. The infants' gut microbiota would partly return to their initial state after rehabilitation, but the transfer of ARGs would leave the hidden trouble of antibiotic resistance. Overall, the data presented here can help to guide the scientific use of antibiotics during the perinatal period and provide potential approaches to mitigate the negative consequences. WHAT IS KNOWN • Antibiotic application during the perinatal period is unavoidable in the clinic. • Misuse of antibiotics can cause various unintended consequences, especially for antibiotic resistance. WHAT IS NEW • Antibiotic treatments had no influence on the microbiota of breast milk but greatly disturbed the gut microbiota composition in infants. • The gut microbiota in infants would partly return to its initial state after rehabilitation but the transfer of ARGs would leave the hidden trouble of antibiotic resistance.
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Kaprou GD, Bergšpica I, Alexa EA, Alvarez-Ordóñez A, Prieto M. Rapid Methods for Antimicrobial Resistance Diagnostics. Antibiotics (Basel) 2021; 10:209. [PMID: 33672677 PMCID: PMC7924329 DOI: 10.3390/antibiotics10020209] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus, there is a growing demand for methods and technologies that enable rapid antimicrobial susceptibility testing (AST). The conventional methods and technologies addressing AMR diagnostics and AST employed in clinical microbiology are tedious, with high turnaround times (TAT), and are usually expensive. As a result, empirical antimicrobial therapies are prescribed leading to AMR spread, which in turn causes higher mortality rates and increased healthcare costs. This review describes the developments in current cutting-edge methods and technologies, organized by key enabling research domains, towards fighting the looming AMR menace by employing recent advances in AMR diagnostic tools. First, we summarize the conventional methods addressing AMR detection, surveillance, and AST. Thereafter, we examine more recent non-conventional methods and the advancements in each field, including whole genome sequencing (WGS), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and microfluidics technology. Following, we provide examples of commercially available diagnostic platforms for AST. Finally, perspectives on the implementation of emerging concepts towards developing paradigm-changing technologies and methodologies for AMR diagnostics are discussed.
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Affiliation(s)
- Georgia D. Kaprou
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Ieva Bergšpica
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia
| | - Elena A. Alexa
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
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Ren Y, Ji J, Sun J, Pi F, Zhang Y, Sun X. Rapid detection of antibiotic resistance in Salmonella with screen printed carbon electrodes. J Solid State Electrochem 2020. [DOI: 10.1007/s10008-020-04645-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Abstract
The study of hospital wastewater (HWW) microbiology is important to understand the pollution load, growth of particular pathogenic microbes, shift and drift in microbial community, development and spread of antibiotic resistance in microbes, and subsequent change in treatment efficiencies. This chapter investigates the potential microbes such as bacteria, viruses, fungi, and parasites present in HWW along with the diseases associated and methods of treatment used. Due to the indiscriminate release of antibiotics from hospitals, HWW serves as a hotspot for emergence of antibiotic-resistance genes (ARGs) and antibiotic-resistance bacteria. This chapter discusses the ARGs occurrence in HWW, their prevalence in the environment, the molecular tools used for identification, and different mechanisms of horizontal gene transfer. Thus better understanding of the microbiology of HWW could further help in development of advanced treatment technologies for effective removal of microbes and their bioproducts (toxins and infectious nucleic acid) from HWW and contaminated water.
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Feng J, Wang Y, Jin R, Hao G. A universal random DNA amplification and labeling strategy for microarray to detect multiple pathogens of aquatic animals. J Virol Methods 2019; 275:113761. [PMID: 31693912 DOI: 10.1016/j.jviromet.2019.113761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 11/28/2022]
Abstract
Diseases caused by bacteria, fungi, and viruses pose a great threat to aquaculture. As DNA microarrays can be used to detect multiple pathogens, here we reported an array with the potential to simultaneously detect 13 bacterial and 11 viral pathogens of aquatic animals. The array included 853 oligonucleotide probes (20-40 mer) complementary to various virus-specific sequences and four chromosomal loci (16S rRNA, gyrB, dnaJ, and recA) of bacteria. Multiplex PCR, phi29 DNA polymerase, and a Klenow fragment-based method were evaluated for amplifying and labeling the nucleic acid of pathogens. While array hybridization signals were most intense using pathogen sequences amplified by multiplex PCR, the phi29 DNA polymerase method was more convenient and ideal since it did not require sequence-specific primers that could bias against detecting novel pathogens. The feasibility of the phi29 DNA polymerase-based microarray strategy was also demonstrated by detecting multiple unknown pathogens from four samples of diseased fish and shrimps.
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Affiliation(s)
- Junli Feng
- Institute of Seafood, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yi Wang
- Institute of Seafood, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Renyao Jin
- Institute of Seafood, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Guijie Hao
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China.
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Abstract
Advances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multiomics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances toward such diagnostics. However, the inability to squeeze light with several hundred nanometer wavelengths into angstrom-scale volume for single-nucleotide measurements has hindered further progress. This limitation has been circumvented by analyzing the relative nucleobase content with Raman spectroscopy, in an optical sequencing method. Here, we performed optical sequencing measurements on positively charged silver nanoparticles to achieve 93.3% accuracy for predicting nucleobase content in label-free DNA k-mer blocks (where k = 10) as well as measurements on RNA and chemically modified nucleobases for extensions to transcriptomic and epigenetic studies. Our high-accuracy measurements were then used with a content-scoring database searching algorithm to correctly identify a β-lactamase gene from the MEGARes antibiotic resistance database and confirm the Pseudomonas aeruginosa pathogen of origin from <12 block content measurements (<15% coverage) of the gene. These results prove the feasibility of an optical sequencing platform as a diagnostic method. With the versatile range of available plasmonic substrates offering simple data acquisition, varying resolution (single-molecule to the ensemble), and multiplexing, this optical sequencing platform has potential as the rapid, cost-effective method needed for broad-spectrum biomarker detection.
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Typing of mecD Islands in Genetically Diverse Methicillin-Resistant Macrococcus caseolyticus Strains from Cattle. Appl Environ Microbiol 2019; 85:AEM.01496-19. [PMID: 31375493 DOI: 10.1128/aem.01496-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 07/29/2019] [Indexed: 11/20/2022] Open
Abstract
Macrococcus caseolyticus belongs to the normal bacterial flora of dairy cows and does not usually cause disease. However, methicillin-resistant M. caseolyticus strains were isolated from bovine mastitis milk. These bacteria had acquired a chromosomal island (McRI mecD -1 or McRI mecD -2) carrying the methicillin resistance gene mecD To gain insight into the distribution of McRI mecD types in M. caseolyticus from cattle, 33 mecD-containing strains from Switzerland were characterized using molecular techniques, including multilocus sequence typing, antibiotic resistance gene identification, and PCR-based McRI mecD typing. In addition, the same genetic features were analyzed in 27 mecD-containing M. caseolyticus strains isolated from bovine bulk milk in England/Wales using publicly available whole-genome sequences. The 60 strains belonged to 24 different sequence types (STs), with strains belonging to ST5, ST6, ST21, and ST26 observed in both Switzerland and England/Wales. McRI mecD -1 was found in different STs from Switzerland (n = 19) and England/Wales (n = 4). McRI mecD -2 was only found in 7 strains from Switzerland, all of which belonged to ST6. A novel island, McRI mecD -3, which contains a complete mecD operon (mecD-mecR1m-mecIm [where the subscript m indicates Macrococcus]) combined with the left part of McRI mecD -2 and the right part of McRI mecD -1, was found in heterogeneous STs from both collections (Switzerland, n = 7; England/Wales, n = 21). Two strains from England/Wales carried a truncated McRI mecD -3. Phylogenetic analyses revealed no clustering of strains according to geographical origin or carriage of McRI mecD -1 and McRI mecD -3. Circular excisions were also detected for McRI mecD -1 and McRI mecD -3 by PCR. The analyses indicate that these islands are mobile and may spread by horizontal gene transfer between genetically diverse M. caseolyticus strains.IMPORTANCE Since its first description in 2017, the methicillin resistance gene mecD has been detected in M. caseolyticus strains from different cattle sources and countries. Our study provides new insights into the molecular diversity of mecD-carrying M. caseolyticus strains by using two approaches to characterize mecD elements: (i) multiplex PCR for molecular typing of McRI mecD and (ii) read mapping against reference sequences to identify McRI mecD types in silico In combination with multilocus sequence typing, this approach can be used for molecular characterization and surveillance of M. caseolyticus carrying mecD.
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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] [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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Chanchaithong P, Perreten V, Am-In N, Lugsomya K, Tummaruk P, Prapasarakul N. Molecular Characterization and Antimicrobial Resistance of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates from Pigs and Swine Workers in Central Thailand. Microb Drug Resist 2019; 25:1382-1389. [PMID: 31361580 DOI: 10.1089/mdr.2019.0011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This study presents molecular characteristics of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) from pigs and swine workers in central Thailand. Sixty-three MRSA isolates were recovered from pigs (n = 60) and humans (n = 3). Two major LA-MRSA lineages, including sequence type (ST) 398 and clonal complex 9 (ST9 and ST4576, a novel single-locus variant of ST9), were identified. ST398 had spa type t034 (n = 55). ST9 and ST4576 had t337 (n = 8) and carried staphylococcal cassette chromosome mec (SCCmec) IX only. MRSA-ST398-t034 contained various SCCmec, including SCCmec V (n = 42), a novel SCCmec composite island (n = 12), and a nontypeable SCCmec (n = 1). All isolates were multidrug resistant and carried common resistance genes found in LA-MRSA. This is the first report of the presence of swine MRSA ST398 and multidrug resistance gene cfr in MRSA ST9 in Thailand. With identical molecular characteristics, pigs could be a source of MRSA ST398 spread to humans. A minor variation of genetic features and resistance gene carriage in both lineages represented a heterogeneous population and evolution of the endemic clones. A monitoring program and farm management, with prudent antimicrobial uses, should be implemented to reduce spreading. Strict hygiene and personal protection are also necessary to prevent transfer of LA-MRSA to humans.
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Affiliation(s)
- Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Diagnosis and Monitoring of Animal Pathogen Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nutthee Am-In
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Kittitat Lugsomya
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Padet Tummaruk
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Diagnosis and Monitoring of Animal Pathogen Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Uddin MJ, Ma CJ, Kim JC, Ahn J. Proteomics-based discrimination of differentially expressed proteins in antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium, Klebsiella pneumoniae, and Staphylococcus aureus. Arch Microbiol 2019; 201:1259-1275. [PMID: 31240342 DOI: 10.1007/s00203-019-01693-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 06/06/2019] [Accepted: 06/13/2019] [Indexed: 01/25/2023]
Abstract
This study was designed to compare the differentially expressed proteins between antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium, Klebsiella pneumonia, and Staphylococcus aureus. The susceptibilities of wild-type (WT), ciprofloxacin (CIP) and/or oxacillin (OXA)-induced, and clinically isolated resistant (CCARM) S. Typhimurium (STWT, STCIP, and STCCARM), K. pneumoniae (KPWT, KPCIP, and KPCCARM), and S. aureus (SAWT, SACIP, SAOXA, and SACCARM) to antibiotics were determined using broth microdilution assay. STCIP was highly resistant to piperacillin (MIC > 512 μg/ml), KPCIP was resistant to chloramphenicol (128 μg/ml) and norfloxacin (16 μg/ml), SACIP was resistant to fluoroquinolones (32 μg/ml), and SAOXA was resistant to ceftriaxone (32 μg/ml). The protein profiles of antibiotic-sensitive and antibiotic-resistant strains were determined using 2-DE analysis followed by LC-MS/MS. The commonly expressed proteins of STWT-STCIP, STWT-STCCARM, KPWT-KPCIP, KPWT-KPCCARM, SAWT-SACIP, SAWT-SAOXA, and SAWT-SACCARM were 763, 677, 677, 469, 261, 259, and 226, respectively. The unique protein spots were observed 57 (6.5%), 80 (11.5%), and 68 (13.9%), respectively, for STCCARM, KPCCARM, and SACCARM. The highly up-regulated protein, PrsA (10-fold), was observed in STCIP resistant to ciprofloxacin (128-fold), levofloxacin (32-fold), norfloxacin (64-fold), and piperacillin (> 16-fold). The up-regulated proteins (YadC, FimA, and RplB) in KPCIP resistant to chloramphenicol (> 32-fold), ciprofloxacin (32-fold), levofloxacin (6-fold), norfloxacin (128-fold), and sparfloxacin (64-fold). AcrB and RpoB were up-regulated in SACCARM resistant to multiple antibiotics. The differentially expressed proteins were related to the antibiotic resistance of STWT, STCIP, STCCARM, KPWT, KPCIP, KPCCARM, SAWT, SACIP, SAOXA, and SACCARM. The resistance-associated proteins could be useful biomarkers for detecting antibiotic-resistant pathogens.
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Affiliation(s)
- Md Jalal Uddin
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Choong Je Ma
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Jin-Chul Kim
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Juhee Ahn
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea.
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Korshoj LE, Nagpal P. BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage. Comput Biol Med 2019; 110:196-206. [PMID: 31173943 DOI: 10.1016/j.compbiomed.2019.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/10/2023]
Abstract
A single, inexpensive diagnostic test capable of rapidly identifying a wide range of genetic biomarkers would prove invaluable in precision medicine. Previous work has demonstrated the potential for high-throughput, label-free detection of A-G-C-T content in DNA k-mers, providing an alternative to single-letter sequencing while also having inherent lossy data compression and massively parallel data acquisition. Here, we apply a new bioinformatics algorithm - block optical content scoring (BOCS) - capable of using the high-throughput content k-mers for rapid, broad-spectrum identification of genetic biomarkers. BOCS uses content-based sequence alignment for probabilistic mapping of k-mer contents to gene sequences within a biomarker database, resulting in a probability ranking of genes on a content score. Simulations of the BOCS algorithm reveal high accuracy for identification of single antibiotic resistance genes, even in the presence of significant sequencing errors (100% accuracy for no sequencing errors, and >90% accuracy for sequencing errors at 20%), and at well below full coverage of the genes. Simulations for detecting multiple resistance genes within a methicillin-resistant Staphylococcus aureus (MRSA) strain showed 100% accuracy at an average gene coverage of merely 0.515, when the k-mer lengths were variable and with 4% sequencing error within the k-mer blocks. Extension of BOCS to cancer and other genetic diseases met or exceeded the results for resistance genes. Combined with a high-throughput content-based sequencing technique, the BOCS algorithm potentiates a test capable of rapid diagnosis and profiling of genetic biomarkers ranging from antibiotic resistance to cancer and other genetic diseases.
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Affiliation(s)
- Lee E Korshoj
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Prashant Nagpal
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA.
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Albert E, Biksi I, Német Z, Csuka E, Kelemen B, Morvay F, Bakos Z, Bodó G, Tóth B, Collaud A, Rossano A, Perreten V. Outbreaks of a Methicillin-Resistant Staphylococcus aureus Clone ST398-t011 in a Hungarian Equine Clinic: Emergence of Rifampicin and Chloramphenicol Resistance After Treatment with These Antibiotics. Microb Drug Resist 2019; 25:1219-1226. [PMID: 31066624 DOI: 10.1089/mdr.2018.0384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Between July 2011 and May 2016, a total of 40 Staphylococcus aureus strains originating from 36 horses were confirmed as methicillin resistant (methicillin-resistant Staphylococcus aureus [MRSA]) in a university equine clinic. An additional 10 MRSA strains from 36 samples of clinic workers were obtained in October 2017. The first equine isolate represented the sequence type ST398, spa-type t011, and SCCmec IV. This isolate was resistant to a wide spectrum of antimicrobial agents. MRSA strains with the same genotype and with very similar resistance profiles were isolated on 21 more occasions from September 2013 to September 2014. A second outbreak occurred from May 2015 until May 2016. The first isolate in this second outbreak shared the same genotype, but was additionally resistant to chloramphenicol. The second isolate from August 2015 also showed resistance to rifampicin. The clone was isolated 18 times. Most of the human isolates shared the same genotype as the isolates from horses and their resistance patterns showed only slight differences. We can conclude that the MRSA-related cases at the Department and Clinic of Equine Medicine were all nosocomial infections caused by the same clonal lineage belonging to the clonal complex 398. The clonal complex 398 of equine origin is reported for the first time in Hungary. In addition, our observation of the emergence of new resistance to antimicrobial agents within the clonal lineage after treatment with antibiotics is of concern. Strict hygiene regulations have been introduced to lower the incidence of MRSA isolation and the related clinical disease.
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Affiliation(s)
- Ervin Albert
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Imre Biksi
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Zoltán Német
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Edit Csuka
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Bernadett Kelemen
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Flóra Morvay
- Department and Clinic of Equine Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Zoltán Bakos
- Department and Clinic of Equine Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Gábor Bodó
- Department and Clinic of Equine Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Balázs Tóth
- Department and Clinic of Equine Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Alexandra Collaud
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Alexandra Rossano
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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Chen QL, An XL, Zheng BX, Ma YB, Su JQ. Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1230-1237. [PMID: 30248848 DOI: 10.1016/j.scitotenv.2018.07.260] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Phyllosphere contains various microorganisms that may harbor diverse antibiotic resistance genes (ARGs). However, we know little about the composition of antibiotic resistome and the factors influencing the diversity and abundance of ARGs in the phyllosphere. In this study, 16S rRNA gene amplicon sequencing and high-throughput quantitative PCR approaches were employed to investigate the effects of long-term (over 10 years) organic fertilization on the phyllosphere bacterial communities and antibiotic resistome. Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes dominated in the phyllosphere bacterial communities. Long-term application of sewage sludge and chicken manure altered the phyllosphere bacterial community composition, with a remarkable decrease in bacterial alpha-diversity. A total of 124 unique ARGs were detected in the phyllosphere. The application of sewage sludge and chicken manure significantly increased the abundance of ARGs, with a maximum 2638-fold enrichment. Variation partitioning analysis (VPA) together with network analysis indicated that the profile of ARGs is strongly correlated with bacterial community compositions. These results improve the knowledge about the diversity of plant-associated antibiotic resistome and factors influencing the profile of ARGs in the phyllosphere.
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Affiliation(s)
- Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Bang-Xiao Zheng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Bing Ma
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Nutrient Cycling, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole-Genome Sequences. J Clin Microbiol 2018; 56:JCM.01815-17. [PMID: 29925638 DOI: 10.1128/jcm.01815-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 05/09/2018] [Indexed: 01/08/2023] Open
Abstract
In principle, whole-genome sequencing (WGS) can predict phenotypic resistance directly from a genotype, replacing laboratory-based tests. However, the contribution of different bioinformatics methods to genotype-phenotype discrepancies has not been systematically explored to date. We compared three WGS-based bioinformatics methods (Genefinder [read based], Mykrobe [de Bruijn graph based], and Typewriter [BLAST based]) for predicting the presence/absence of 83 different resistance determinants and virulence genes and overall antimicrobial susceptibility in 1,379 Staphylococcus aureus isolates previously characterized by standard laboratory methods (disc diffusion, broth and/or agar dilution, and PCR). In total, 99.5% (113,830/114,457) of individual resistance-determinant/virulence gene predictions were identical between all three methods, with only 627 (0.5%) discordant predictions, demonstrating high overall agreement (Fleiss' kappa = 0.98, P < 0.0001). Discrepancies when identified were in only one of the three methods for all genes except the cassette recombinase, ccrC(b). The genotypic antimicrobial susceptibility prediction matched the laboratory phenotype in 98.3% (14,224/14,464) of cases (2,720 [18.8%] resistant, 11,504 [79.5%] susceptible). There was greater disagreement between the laboratory phenotypes and the combined genotypic predictions (97 [0.7%] phenotypically susceptible, but all bioinformatic methods reported resistance; 89 [0.6%] phenotypically resistant, but all bioinformatics methods reported susceptible) than within the three bioinformatics methods (54 [0.4%] cases, 16 phenotypically resistant, 38 phenotypically susceptible). However, in 36/54 (67%) cases, the consensus genotype matched the laboratory phenotype. In this study, the choice between these three specific bioinformatic methods to identify resistance determinants or other genes in S. aureus did not prove critical, with all demonstrating high concordance with each other and phenotypic/molecular methods. However, each has some limitations; therefore, consensus methods provide some assurance.
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Cotting K, Strauss C, Rodriguez-Campos S, Rostaher A, Fischer NM, Roosje PJ, Favrot C, Perreten V. Macrococcus canis and M. caseolyticus in dogs: occurrence, genetic diversity and antibiotic resistance. Vet Dermatol 2017; 28:559-e133. [PMID: 28748533 DOI: 10.1111/vde.12474] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND The discovery of a new Macrococcus canis species isolated from skin and infection sites of dogs led us to question if Macrococcus spp. are common in dogs and are resistant to antibiotics. HYPOTHESIS/OBJECTIVES To evaluate the occurrence of Macrococcus spp. in dogs, determine antibiotic resistance profiles and genetic relationships. ANIMALS One hundred and sixty two dogs (mainly West Highland white terriers and Newfoundland dogs) were screened for the presence of Macrococcus, including six dogs with Macrococcus infections. METHODS Samples were taken from skin, ear canal and oral mucosa using swabs. Macrococci were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry, 16S rRNA sequencing and nuc-PCR. Minimal inhibitory concentrations of 19 antibiotics were determined using broth microdilution. Resistance mechanisms were identified by microarray and sequencing of the fluoroquinolone-determining region of gyrA and grlA. Sequence type (ST) was determined by multilocus sequence typing. RESULTS Out of the 162 dogs, six harboured M. caseolyticus (n = 6) and 13 harboured M. canis (n = 16). Six isolates of M. canis and one of M. caseolyticus were obtained from infection sites. The 22 M. canis strains belonged to 20 different STs and the seven M. caseolyticus strains to three STs. Resistance to antibiotics was mostly associated with the detection of known genes, with mecB-mediated meticillin resistance being the most frequent. CONCLUSION AND CLINICAL IMPORTANCE This study gives some insights into the occurrence and genetic characteristics of antibiotic-resistant Macrococcus from dogs. Presence of M. canis in infection sites and resistance to antibiotics emphasized that more attention should be paid to this novel bacteria species.
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Affiliation(s)
- Kerstin Cotting
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Länggassstrasse 122, Bern, CH-3001, Switzerland
| | - Christian Strauss
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Länggassstrasse 122, Bern, CH-3001, Switzerland
| | - Sabrina Rodriguez-Campos
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Länggassstrasse 122, Bern, CH-3001, Switzerland
| | - Ana Rostaher
- Clinic for Small Animal Internal Medicine, Dermatology unit, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 260, Zurich, CH-8057, Switzerland
| | - Nina M Fischer
- Clinic for Small Animal Internal Medicine, Dermatology unit, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 260, Zurich, CH-8057, Switzerland
| | - Petra J Roosje
- Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, University of Bern, Länggassstrasse 128, Bern, CH-3001, Switzerland
| | - Claude Favrot
- Clinic for Small Animal Internal Medicine, Dermatology unit, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 260, Zurich, CH-8057, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Länggassstrasse 122, Bern, CH-3001, Switzerland
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New Macrolide-Lincosamide-Streptogramin B Resistance Gene erm(48) on the Novel Plasmid pJW2311 in Staphylococcus xylosus. Antimicrob Agents Chemother 2017; 61:AAC.00066-17. [PMID: 28438941 DOI: 10.1128/aac.00066-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/14/2017] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequencing of Staphylococcus xylosus strain JW2311 from bovine mastitis milk identified the novel 49.3-kb macrolide-lincosamide-streptogramin B (MLSB) resistance plasmid pJW2311. It contained the macrolide resistance gene mph(C), the macrolide-streptogramin B resistance gene msr(A), and the new MLSB resistance gene erm(48) and could be transformed into Staphylococcus aureus by electroporation. Functionality of erm(48) was demonstrated by cloning and expression in S. aureus.
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22
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Hulme J. Recent advances in the detection of methicillin resistant Staphylococcus aureus (MRSA). BIOCHIP JOURNAL 2017. [DOI: 10.1007/s13206-016-1201-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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23
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Bojang E, Jafali J, Perreten V, Hart J, Harding-Esch EM, Sillah A, Mabey DCW, Holland MJ, Bailey RL, Roca A, Burr SE. Short-term increase in prevalence of nasopharyngeal carriage of macrolide-resistant Staphylococcus aureus following mass drug administration with azithromycin for trachoma control. BMC Microbiol 2017; 17:75. [PMID: 28351345 PMCID: PMC5371190 DOI: 10.1186/s12866-017-0982-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/11/2017] [Indexed: 11/27/2022] Open
Abstract
Background Mass drug administration (MDA) with azithromycin is a corner-stone of trachoma control however it may drive the emergence of antimicrobial resistance. In a cluster-randomized trial (Clinical trial gov NCT00792922), we compared the reduction in the prevalence of active trachoma in communities that received three annual rounds of MDA to that in communities that received a single treatment round. We used the framework of this trial to carry out an opportunistic study to investigate if the increased rounds of treatment resulted in increased prevalence of nasopharyngeal carriage of macrolide-resistant Staphylococcus aureus. Three cross-sectional surveys were conducted in two villages receiving three annual rounds of MDA (3 × treatment arm). Surveys were conducted immediately before the third round of MDA (CSS-1) and at one (CSS-2) and six (CSS-3) months after MDA. The final survey also included six villages that had received only one round of MDA 30 months previously (1 × treatment arm). Results In the 3 × treatment arm, a short-term increase in prevalence of S. aureus carriage was seen following MDA from 24.6% at CSS-1 to 38.6% at CSS-2 (p < 0.001). Prevalence fell to 8.8% at CSS-3 (p < 0.001). A transient increase was also seen in prevalence of carriage of azithromycin resistant (AzmR) strains from 8.9% at CSS-1 to 34.1% (p < 0.001) in CSS-2 and down to 7.3% (p = 0.417) in CSS-3. A similar trend was observed for prevalence of carriage of macrolide-inducible-clindamycin resistant (iMLSB) strains. In CSS-3, prevalence of carriage of resistant strains was higher in the 3 × treatment arm than in the 1 × treatment (AzmR 7.3% vs. 1.6%, p = 0.010; iMLSB 5.8% vs. 0.8%, p < 0.001). Macrolide resistance was attributed to the presence of msr and erm genes. Conclusions Three annual rounds of MDA with azithromycin were associated with a short-term increase in both the prevalence of nasopharyngeal carriage of S. aureus and prevalence of carriage of AzmR and iMLSBS. aureus. Trial registration This study was ancillary to the Partnership for the Rapid Elimination of Trachoma, ClinicalTrials.gov NCT00792922, registration date November 17, 2008.
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Affiliation(s)
- Ebrima Bojang
- Disease Control and Elimination Theme, Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia
| | - James Jafali
- Disease Control and Elimination Theme, Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, CH-3012, Bern, Switzerland
| | - John Hart
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Emma M Harding-Esch
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Ansumana Sillah
- National Eye Health Programe, Ministry of Health and Social Welfare, Kanifing, The Gambia
| | - David C W Mabey
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Martin J Holland
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Robin L Bailey
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Anna Roca
- Disease Control and Elimination Theme, Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia.,Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Sarah E Burr
- Disease Control and Elimination Theme, Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia. .,Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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A Novel erm(44) Gene Variant from a Human Staphylococcus saprophyticus Isolate Confers Resistance to Macrolides and Lincosamides but Not Streptogramins. Antimicrob Agents Chemother 2016; 61:AAC.01655-16. [PMID: 27799208 DOI: 10.1128/aac.01655-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/23/2016] [Indexed: 01/30/2023] Open
Abstract
A novel erm(44) gene variant, erm(44)v, has been identified by whole-genome sequencing in a Staphylococcus saprophyticus isolate from the skin of a healthy person. It has the particularity to confer resistance to macrolides and lincosamides but not to streptogramin B when expressed in S. aureus The erm(44)v gene resides on a 19,400-bp genomic island which contains phage-associated proteins and is integrated into the chromosome of S. saprophyticus.
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Su JQ, Cui L, Chen QL, An XL, Zhu YG. Application of genomic technologies to measure and monitor antibiotic resistance in animals. Ann N Y Acad Sci 2016; 1388:121-135. [DOI: 10.1111/nyas.13296] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
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Feichtinger M, Mayrhofer S, Kneifel W, Domig KJ. Tetracycline Resistance Patterns of Lactobacillus buchneri Group Strains. J Food Prot 2016; 79:1741-1747. [PMID: 28221841 DOI: 10.4315/0362-028x.jfp-15-577] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Lactobacilli are applied as starter cultures for controlled fermentation in the production of food and feed. Among other lactobacilli, members of the Lactobacillus buchneri group are used in fermented milk, wine, and silage. Most of the L. buchneri species used for the manufacturing of food or feed are already on the list for qualified presumption of safety status and are recommended as biological agents by the European Food Safety Authority. Consequently, new strains intended as food or feed additives do not require any additional safety check than confirming the absence of transferable antibiotic resistance determinants. Of these determinants, tetracycline resistance genes are especially predominant in lactobacilli. Within this study, a total of 128 strains belonging to the L. buchneri group ( L. buchneri , L. diolivorans , L. farraginis , L. hilgardii , L. kefiri , L. kisonensis , L. otakiensis , L. parabuchneri , L. parafarraginis , L. parakefiri , L. rapi , L. senioris , and L. sunkii ) were examined for their susceptibility to tetracycline. Tetracycline MICs were assessed by the broth microdilution method according to ISO 10932/IDF 223. Subsequently, the presence of tetracycline resistance genes was investigated by using PCR. In addition, selected strains were tested for a broader range of tetracycline resistance genes by using a microarray technique. Applying the tetracycline cutoff values defined by European Food Safety Authority for heterofermentative and obligately homofermentative lactobacilli, 96.9% of the strains would have been categorized as tetracycline resistant. However, none of the tested tetracycline resistance genes could be detected by PCR or microarray analysis. Furthermore, the MIC distribution of all strains was unimodal and at the high end of the tested tetracycline concentration range (4 to 256 μg/ml). Thus, these data suggest that tetracycline resistance in the L. buchneri group strains is intrinsic, which complies with the requirements defined in the qualified presumption of safety outline.
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Affiliation(s)
- Marlies Feichtinger
- BOKU-University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, A-1190 Vienna, Austria
| | - Sigrid Mayrhofer
- BOKU-University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, A-1190 Vienna, Austria
| | - Wolfgang Kneifel
- BOKU-University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, A-1190 Vienna, Austria
| | - Konrad J Domig
- BOKU-University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, A-1190 Vienna, Austria
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Discovery of Novel MLSB Resistance Methylase Genes and Their Associated Genetic Elements in Staphylococci. CURRENT CLINICAL MICROBIOLOGY REPORTS 2016. [DOI: 10.1007/s40588-016-0030-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abstract
Worldwide infectious disease is one of the leading causes of death. Despite improvements in technology and healthcare services, morbidity and mortality due to infections have remained unchanged over the past few decades. The high and increasing rate of antibiotic resistance is further aggravating the situation. Growing resistance hampers the use of conventional antibiotics, and substantial higher mortality rates are reported in patients given ineffective empiric therapy mainly due to resistance to the agents used. These infections cause suffering, incapacity, and death and impose an enormous financial burden on both healthcare systems and on society in general. The accelerating development of multidrug resistance is one of the greatest diagnostic and therapeutic challenges to modern medicine. The lack of new antibiotic options underscores the need for optimization of current diagnostics, therapies, and prevention of the spread of multidrug-resistant organisms. The so-called -omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have yielded large-scale datasets that advanced the search for biomarkers of infectious diseases in the last decade. One can imagine that in the future the implementation of biomarker-driven molecular test systems will transform diagnostics of infectious diseases and will significantly accelerate the identification of the bacterial pathogens at the infected host site. Furthermore, molecular tests based on the identification of markers of antibiotic resistance will dramatically change resistance profiling. The replacement of culturing methods by molecular test systems for early diagnosis will provide the basis not only for a prompt and targeted therapy, but also for a much more effective stewardship of antibiotic agents and a reduction of the spread of multidrug resistance as well as the appearance of new antibiotic resistances.
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Fluorescence-based bioassays for the detection and evaluation of food materials. SENSORS 2015; 15:25831-67. [PMID: 26473869 PMCID: PMC4634490 DOI: 10.3390/s151025831] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022]
Abstract
We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.
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A long downstream probe-based platform for multiplex target capture. Anal Biochem 2015; 491:4-9. [PMID: 26344895 DOI: 10.1016/j.ab.2015.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 11/20/2022]
Abstract
A simple and rapid detection platform was established for multiplex target capture through generating single-strand long downstream probe (ssLDP), which was integrated with the ligase detection reaction (LDR) method for the purpose of multiplicity and high specificity. To increase sensitivity, the ladder-like polymerase chain reaction (PCR) amplicons were generated by using universal primers that complement ligated products. Each of the amplicons contained a stuffer sequence with a defined yet variable length. Thus, the length of the amplicon is an index of the specific suppressor, allowing its identification via electrophoresis. The multiplexed diagnostic platform was optimized using standard plasmids and validated by using potato virus suppressors as a detection model. This technique can detect down to 1.2 × 10(3) copies for single or two mixed target plasmids. When compared with microarray results, the electrophoresis showed 98.73-100% concordance rates for the seven suppressors in the 79 field samples. This strategy could be applied to detect a large number of targets in field and clinical surveillance.
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Nian Q, Zhang Z, Wei C, Kuang X, Wang X, Wang L. Gene expression profiling in myelodysplastic syndrome after SPARC overexpression associated with Ara-C. Oncol Rep 2015; 34:2072-82. [PMID: 26238482 DOI: 10.3892/or.2015.4139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/30/2015] [Indexed: 12/11/2022] Open
Abstract
Secreted protein acidic and rich in cysteine (SPARC) is involved in many biological processes, including erythropoiesis and cell proliferation. However, the role of SPARC in myelodysplastic syndrome (MDS) remains to be elucidated. Pyrimidine analogue cytosine arabinoside (Ara-C) is among the most effective agents used in the treatment of acute leukemia. The aim of the present study was to determine whether the chemotherapeutic activity of Ara-C was enhanced by the overexpression of SPARC. DNA microarray technology and RNA sequencing were employed to examine differential gene expression in the apoptosis signaling pathway after gene change occurred in cells following drug treatment. The results showed that upregulation of the expression of SPARC induced SKM-1 cell death and inhibited proliferation. Additionally, the apoptotic rate of SPARC overexpression combined with Ara-C increased significantly. Transcription factors CPBP and ZNF333 regulated the 69 genes and long non-coding RNA (lncRNA). Moreover, the mRNA and protein expression of apoptosis-related genes in the DNA microarray results were increased. These results suggest that SPARC expression changes with Ara-C, revealing a possible application in the treatment of MDS.
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Affiliation(s)
- Qing Nian
- Department of Emergency, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Zhiqiang Zhang
- Department of Emergency, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Chunmei Wei
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Xingyi Kuang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Xingyong Wang
- Department of Emergency, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
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The new macrolide-lincosamide-streptogramin B resistance gene erm(45) is located within a genomic island in Staphylococcus fleurettii. Antimicrob Agents Chemother 2015; 59:3578-81. [PMID: 25779586 DOI: 10.1128/aac.00369-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/11/2015] [Indexed: 01/02/2023] Open
Abstract
Genome alignment of a macrolide, lincosamide, and streptogramin B (MLSB)-resistant Staphylococcus fleurettii strain with an MLSB-susceptible S. fleurettii strain revealed a novel 11,513-bp genomic island carrying the new erythromycin resistance methylase gene erm(45). This gene was shown to confer inducible MLSB resistance when cloned into Staphylococcus aureus. The erm(45)-containing island was integrated into the housekeeping gene guaA in S. fleurettii and was able to form a circular intermediate but was not transmissible to S. aureus.
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Anjum MF. Screening methods for the detection of antimicrobial resistance genes present in bacterial isolates and the microbiota. Future Microbiol 2015; 10:317-20. [DOI: 10.2217/fmb.15.2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Alcaine SD, Pacitto D, Sela DA, Nugen SR. Phage & phosphatase: a novel phage-based probe for rapid, multi-platform detection of bacteria. Analyst 2015; 140:7629-36. [DOI: 10.1039/c5an01181g] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A bacteriophage-based biosensing platform forE. coliis proposed. The bacteriophage T7 was genetically engineered to carry the alkaline phosphatase genephoA. The overexpression of the gene was quantified with colorimetric, fluorescent, and chemiluminescent methods.
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Affiliation(s)
- S. D. Alcaine
- Department of Food Science
- University of Massachusetts
- Amherst
- USA
| | - D. Pacitto
- Department of Microbiology
- University of Massachusetts
- Amherst
- USA
| | - D. A. Sela
- Department of Food Science
- University of Massachusetts
- Amherst
- USA
- Department of Microbiology
| | - S. R. Nugen
- Department of Food Science
- University of Massachusetts
- Amherst
- USA
- Department of Microbiology
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