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Wu B, Hu JS, Li Y. Development of an ultra-sensitive single-tube nested PCR assay for rapid detection of Campylobacter jejuni in ground chicken. Food Microbiol 2022; 106:104052. [DOI: 10.1016/j.fm.2022.104052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 04/10/2022] [Accepted: 04/22/2022] [Indexed: 11/04/2022]
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2
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Locher K, Belanger CR, Eckbo E, Caza M, Velapatino B, Charles MK. Automated 16S Sequencing Using an R-Based Analysis Module for Bacterial Identification. Microbiol Spectr 2022; 10:e0040822. [PMID: 35404089 PMCID: PMC9045293 DOI: 10.1128/spectrum.00408-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 12/26/2022] Open
Abstract
Sanger sequencing of the 16S rRNA gene is routinely used for the identification of bacterial isolates. However, this method is still performed mostly in more-specialized reference laboratories, and traditional protocols can be labor intensive. In this study, 99 clinical bacterial isolates were used to validate a fast, simplified, and largely automated protocol for 16S sequencing. The workflow combines real-time PCR of the first 500 bp of the bacterial 16S rRNA gene and amplicon sequencing on an automated, cartridge-based sequence analyzer. Sequence analysis, NCBI BLAST search, and result interpretation were performed using an automated R-based script. The automated workflow and R analysis described here produced results equal to those of manual sequence analysis. Of the 96 sequences with adequate quality, 90 were concordantly identified to the genus (n = 62) or species level (n = 28) compared with routine laboratory identification of the organism. One organism identification was discordant, and 5 resulted in an inconclusive identification. For sequences that gave a valid result, the overall accuracy of identification to at least the genus level was 98.9%. This simplified sequencing protocol provides a standardized approach to clinical 16S sequencing, analysis, and quality control that would be suited to frontline clinical microbiology laboratories with minimal experience. IMPORTANCE Sanger sequencing of the 16S rRNA gene is widely used as a diagnostic tool for bacterial identification, especially in cases where routine diagnostic methods fail to provide an identification, for organisms that are difficult to culture, or from specimens where cultures remain negative. Our simplified protocol is tailored toward use in frontline laboratories with little to no experience with sequencing. It provides a highly automated workflow that can deliver fast results with little hands-on time. Implementing 16S sequencing in-house saves additional time that is otherwise required to send out isolates/specimens for identification to reference laboratories. This makes results available much faster to physicians who can in turn initiate or adjust patient treatment accordingly.
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Affiliation(s)
- Kerstin Locher
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Corrie R. Belanger
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Eric Eckbo
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melissa Caza
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Billie Velapatino
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Marthe K. Charles
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Flipse J, von Wintersdorff CJH, van Niekerk JM, Jamin C, van Tiel FH, Hasman H, van Alphen LB. Appearance of vanD-positive Enterococcus faecium in a tertiary hospital in the Netherlands: prevalence of vanC and vanD in hospitalized patients. Sci Rep 2019; 9:6949. [PMID: 31061446 PMCID: PMC6502811 DOI: 10.1038/s41598-019-42824-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/14/2019] [Indexed: 02/06/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) can rapidly spread through hospitals. Therefore, our hospital employs a screening program whereby rectal swabs are screened for the presence of vanA and vanB, and only PCR-positive broths are cultured on VRE selection agar. Early November 2016, a clinical vanA-/vanB-negative VRE isolate was detected in a vanA/vanB-screening-negative patient, giving the possibility that an undetected VRE might be spreading within our hospital. Whole-genome-sequencing of the isolate showed that resistance was vanD-mediated and core genome multilocus sequence typing showed it was a rare type: ST17/CT154. To determine the prevalence of vanA/B/C/D-carrying enterococci, we designed a real-time PCR for vanC1/2/3 and vanD and screened rectal swabs from 360 patients. vanD was found in 27.8% of the patients, yet culture demonstrated only E. faecium from vanA-positive broths and E. gallinarum from vanC1-positive broths. No vanD-positive VRE were found, limiting the possibility of nosocomial spread of this VRE. Moreover, the high prevalence of non-VRE vanD in rectal swabs makes it unfeasible to include the vanD PCR in our VRE screening. However, having validated the vanC1/2/3 and vanD PCRs allows us to rapidly check future vanA/B-negative VRE for the presence of vanC and vanD genes.
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Affiliation(s)
- Jacky Flipse
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands. .,Laboratory for Medical Microbiology and Infectious Diseases, Isala Clinics, Zwolle, The Netherlands.
| | - Christian J H von Wintersdorff
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Julius M van Niekerk
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Casper Jamin
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Frank H van Tiel
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lieke B van Alphen
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands.
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Muhamadali H, Subaihi A, Mohammadtaheri M, Xu Y, Ellis DI, Ramanathan R, Bansal V, Goodacre R. Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms via multiple vibrational spectroscopic fingerprinting. Analyst 2018; 141:5127-36. [PMID: 27414261 DOI: 10.1039/c6an00883f] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Despite the fact that various microorganisms (e.g., bacteria, fungi, viruses, etc.) have been linked with infectious diseases, their crucial role towards sustaining life on Earth is undeniable. The huge biodiversity, combined with the wide range of biochemical capabilities of these organisms, have always been the driving force behind their large number of current, and, as of yet, undiscovered future applications. The presence of such diversity could be said to expedite the need for the development of rapid, accurate and sensitive techniques which allow for the detection, differentiation, identification and classification of such organisms. In this study, we employed Fourier transform infrared (FT-IR), Raman, and surface enhanced Raman scattering (SERS) spectroscopies, as molecular whole-organism fingerprinting techniques, combined with multivariate statistical analysis approaches for the classification of a range of industrial, environmental or clinically relevant bacteria (P. aeruginosa, P. putida, E. coli, E. faecium, S. lividans, B. subtilis, B. cereus) and yeast (S. cerevisiae). Principal components-discriminant function analysis (PC-DFA) scores plots of the spectral data collected from all three techniques allowed for the clear differentiation of all the samples down to sub-species level. The partial least squares-discriminant analysis (PLS-DA) models generated using the SERS spectral data displayed lower accuracy (74.9%) when compared to those obtained from conventional Raman (97.8%) and FT-IR (96.2%) analyses. In addition, whilst background fluorescence was detected in Raman spectra for S. cerevisiae, this fluorescence was quenched when applying SERS to the same species, and conversely SERS appeared to introduce strong fluorescence when analysing P. putida. It is also worth noting that FT-IR analysis provided spectral data of high quality and reproducibility for the whole sample set, suggesting its applicability to a wider range of samples, and perhaps the most suitable for the analysis of mixed cultures in future studies. Furthermore, our results suggest that while each of these spectroscopic approaches may favour different organisms (sample types), when combined, they would provide complementary and more in-depth knowledge (structural and/or metabolic state) of biological systems. To the best of our knowledge, this is the first time that such a comparative and combined spectroscopic study (using FT-IR, Raman and SERS) has been carried out on microbial samples.
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Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Abdu Subaihi
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Mahsa Mohammadtaheri
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - David I Ellis
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Rajesh Ramanathan
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Vipul Bansal
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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Wan Y, Song F, Wang G, Liu H, An M, Wang A, Wu X, Ma C, Wang N. Electrical Signal Reporter, Pore-Forming Protein, for Rapid, Miniaturized, and Universal Identification of Microorganisms. Anal Chem 2018; 90:9853-9858. [DOI: 10.1021/acs.analchem.8b01933] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
- Marine College, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
| | - Fengge Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
- Marine College, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
| | - Guoqing Wang
- College of Materials and Chemical Engineering, Hainan University No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
| | - Hong Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
- Marine College, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
| | - Meng An
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
- Marine College, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
- Marine College, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
| | - Xi Wu
- Shenzhen Institute for Drug Control, No.28, Gaoxinzhong Second Road, Shenzhen, Guangdong Province, China, 518057
| | - Chunxin Ma
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, No. 58, Renmin Avenue, Haikou, Hainan Province, China, 570228
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Su L, Yang L, Huang S, Su X, Li Y, Wang F, Wang E, Kang N, Xu J, Song A. Comparative Gut Microbiomes of Four Species Representing the Higher and the Lower Termites. JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew081. [PMID: 27638955 PMCID: PMC5026480 DOI: 10.1093/jisesa/iew081] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 07/30/2016] [Indexed: 05/12/2023]
Abstract
Aiming at learning the association between the gut microbiota and termites with different diet habits and phylogenetic positions, the gut bacteria of three populations for each of the two higher termites (wood-feeding Mironasutitermes shangchengensis and fungus-feeding Odontotermes formosanus) and two wood-feeding lower termites (Tsaitermes ampliceps and Reticulitermes flaviceps) were analyzed by high-throughput 454 pyrosequencing of 16S V1-V3 amplicons. As results, 132 bacterial genera and some unidentified operational taxonomic units within 29 phyla in the gut bacteria were detected, with Spirochaetes (11-55%), Firmicutes (7-18%), Bacteroidetes (7-31%), and Proteobacteria (8-14%) as the main phyla, and Treponema, TG5, Dysgonomonas, Tannerella, za29, Lactococcus, Pseudomonas, and SJA-88 as the common genera in all the four termites. The diversity of gut bacterial communities in the higher termite guts was significantly greater than that in the lower termites; while the gut microbiota in M. shangchengensis (wood-feeding higher termite) was more similar to those of the wood-feeding lower termites rather than that of O. formosanus (fungus-feeding higher termite), and phylum Spirochaetes and nitrogen-fixing bacteria were super-dominant in the wood-feeding termites, despite of their phylogenetic relations. This study reported for the first time the gut bacterial communities for the termites of M. shangchengensis and T. ampliceps and the comparative analyses showed that the gut microbial communities varied according to the phylogeny and the diet habits of termites.
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Affiliation(s)
- LiJuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - LeLe Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Shi Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - XiaoQuan Su
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - Yan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - FengQin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan 450002, China
| | - EnTao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México, DF 11340, México
| | - Ning Kang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - Jian Xu
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - AnDong Song
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan 450002, China
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7
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von Wintersdorff CJH, Penders J, Stobberingh EE, Oude Lashof AML, Hoebe CJPA, Savelkoul PHM, Wolffs PFG. High rates of antimicrobial drug resistance gene acquisition after international travel, The Netherlands. Emerg Infect Dis 2014; 20:649-57. [PMID: 24655888 DOI: 10.3201/eid.2004.131718] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We investigated the effect of international travel on the gut resistome of 122 healthy travelers from the Netherlands by using a targeted metagenomic approach. Our results confirm high acquisition rates of the extended-spectrum β-lactamase encoding gene blaCTX-M, documenting a rise in prevalence from 9.0% before travel to 33.6% after travel (p<0.001). The prevalence of quinolone resistance encoding genes qnrB and qnrS increased from 6.6% and 8.2% before travel to 36.9% and 55.7% after travel, respectively (both p<0.001). Travel to Southeast Asia and the Indian subcontinent was associated with the highest acquisition rates of qnrS and both blaCTX-M and qnrS, respectively. Investigation of the associations between the acquisitions of the blaCTX-M and qnr genes showed that acquisition of a blaCTX-M gene was not associated with that of a qnrB (p = 0.305) or qnrS (p = 0.080) gene. These findings support the increasing evidence that travelers contribute to the spread of antimicrobial drug resistance.
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von Wintersdorff CJH, Penders J, Stobberingh EE, Oude Lashof AML, Hoebe CJPA, Savelkoul PHM, Wolffs PFG. High rates of antimicrobial drug resistance gene acquisition after international travel, The Netherlands. Emerg Infect Dis 2014. [PMID: 24655888 PMCID: PMC3966371 DOI: 10.3201/eid2004.131718] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated the effect of international travel on the gut resistome of 122 healthy travelers from the Netherlands by using a targeted metagenomic approach. Our results confirm high acquisition rates of the extended-spectrum β-lactamase encoding gene blaCTX-M, documenting a rise in prevalence from 9.0% before travel to 33.6% after travel (p<0.001). The prevalence of quinolone resistance encoding genes qnrB and qnrS increased from 6.6% and 8.2% before travel to 36.9% and 55.7% after travel, respectively (both p<0.001). Travel to Southeast Asia and the Indian subcontinent was associated with the highest acquisition rates of qnrS and both blaCTX-M and qnrS, respectively. Investigation of the associations between the acquisitions of the blaCTX-M and qnr genes showed that acquisition of a blaCTX-M gene was not associated with that of a qnrB (p = 0.305) or qnrS (p = 0.080) gene. These findings support the increasing evidence that travelers contribute to the spread of antimicrobial drug resistance.
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9
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Role of the siderophore transporter SirABC in the Staphylococcus aureus resistance to oxidative stress. Curr Microbiol 2014; 69:164-8. [PMID: 24682218 DOI: 10.1007/s00284-014-0567-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
Abstract
In Staphylococcus aureus, the intracellular siderophore staphyloferrin B, which has been shown to chelate iron-bound to serum transferrin, is transported into cells by the SirABC system. In this work, we have analysed the role of the Sir transporter under stress conditions that resemble those imposed by the mammalian innate immune system. We show that exposure of S. aureus to oxidative and nitrosative stress generated by hydrogen peroxide and S-nitrosoglutathione, respectively, induced the expression of the sirA gene. The disruption of the sir operon led to a strain with lower viability and decreased resistance to oxidative stress. S. aureus sir null mutant was also analysed during infection of murine macrophages and shown to contribute to S. aureus survival inside macrophages. Altogether, our results indicate that the Sir transport system confers protection against reactive oxygen species, therefore, contributing to the virulence of S. aureus.
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Chen L, Cai Y, Zhou G, Shi X, Su J, Chen G, Lin K. Rapid Sanger sequencing of the 16S rRNA gene for identification of some common pathogens. PLoS One 2014; 9:e88886. [PMID: 24551186 PMCID: PMC3925228 DOI: 10.1371/journal.pone.0088886] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 01/09/2014] [Indexed: 02/05/2023] Open
Abstract
Conventional Sanger sequencing remains time-consuming and laborious. In this study, we developed a rapid improved sequencing protocol of 16S rRNA for pathogens identification by using a new combination of SYBR Green I real-time PCR and Sanger sequencing with FTA® cards. To compare the sequencing quality of this method with conventional Sanger sequencing, 12 strains, including three kinds of strains (1 reference strain and 3 clinical strains, which were previously identified by biochemical tests), which have 4 Pseudomonas aeruginosa, 4 Staphyloccocus aureus and 4 Escherichia coli, were targeted. Additionally, to validate the sequencing results and bacteria identification, expanded specimens with 90 clinical strains, also comprised of the three kinds of strains which included 30 samples respectively, were performed as just described. The results showed that although statistical differences (P<0.05) were found in sequencing quality between the two methods, their identification results were all correct and consistent. The workload, the time consumption and the cost per batch were respectively light versus heavy, 8 h versus 11 h and $420 versus $400. In the 90 clinical strains, all of the Pseudomonas aeruginosa and Staphyloccocus aureus strains were correctly identified, but only 26.7% of the Escherichia coli strains were recognized as Escherichia coli, while 33.3% as Shigella sonnei and 40% as Shigella dysenteriae. The protocol described here is a rapid, reliable, stable and convenient method for 16S rRNA sequencing, and can be used for Pseudomonas aeruginosa and Staphyloccocus aureus identification, yet it is not completely suitable for discriminating Escherichia coli and Shigella strains.
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Affiliation(s)
- Linxiang Chen
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Molecular Biology, Shantou Entry-Exit Inspection and Quarantine Bureau, Shantou, Guangdong, China
| | - Ying Cai
- Laboratory of Molecular Biology, Shantou Entry-Exit Inspection and Quarantine Bureau, Shantou, Guangdong, China
| | - Guangbiao Zhou
- Laboratory of Molecular Biology, Shantou Entry-Exit Inspection and Quarantine Bureau, Shantou, Guangdong, China
| | - Xiaojun Shi
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
| | - Jianhui Su
- Laboratory of Molecular Biology, Shantou Entry-Exit Inspection and Quarantine Bureau, Shantou, Guangdong, China
| | - Guanwu Chen
- Laboratory of Molecular Biology, Shantou Entry-Exit Inspection and Quarantine Bureau, Shantou, Guangdong, China
| | - Kun Lin
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
- * E-mail:
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Lal D, Jindal S, Kumari H, Jit S, Nigam A, Sharma P, Kumari K, Lal R. Bacterial diversity and real-time PCR based assessment oflinAandlinBgene distribution at hexachlorocyclohexane contaminated sites. J Basic Microbiol 2013; 55:363-73. [DOI: 10.1002/jobm.201300211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/21/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Devi Lal
- Department of Zoology; Molecular Biology Laboratory; University of Delhi; Delhi India
| | - Swati Jindal
- Department of Zoology; Molecular Biology Laboratory; University of Delhi; Delhi India
| | - Hansi Kumari
- Department of Zoology; Molecular Biology Laboratory; University of Delhi; Delhi India
| | - Simran Jit
- Department of Zoology; Molecular Biology Laboratory; University of Delhi; Delhi India
| | - Aeshna Nigam
- Department of Zoology; Molecular Biology Laboratory; University of Delhi; Delhi India
| | - Pooja Sharma
- Department of Zoology; Molecular Biology Laboratory; University of Delhi; Delhi India
| | - Kirti Kumari
- Department of Zoology; Molecular Biology Laboratory; University of Delhi; Delhi India
| | - Rup Lal
- Department of Zoology; Molecular Biology Laboratory; University of Delhi; Delhi India
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12
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Beuving J, Verbon A, Gronthoud FA, Stobberingh EE, Wolffs PFG. Antibiotic susceptibility testing of grown blood cultures by combining culture and real-time polymerase chain reaction is rapid and effective. PLoS One 2011; 6:e27689. [PMID: 22194790 PMCID: PMC3237415 DOI: 10.1371/journal.pone.0027689] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/21/2011] [Indexed: 11/19/2022] Open
Abstract
Background Early administration of appropriate antibiotic therapy in bacteraemia patients dramatically reduces mortality. A new method for RApid Molecular Antibiotic Susceptibility Testing (RAMAST) that can be applied directly to positive blood cultures was developed and evaluated. Methodology/Principal Findings Growth curves and antibiotic susceptibility of blood culture isolates (Staphylococcus aureus, enterococci and (facultative) aerobic Gram-negative rods) were determined by incubating diluted blood cultures with and without antibiotics, followed by a quantitative universal 16S PCR to detect the presence or absence of growth. Testing 114 positive blood cultures, RAMAST showed an agreement with microbroth dilution of 96.7% for Gram-negative rods, with a minor error (false-susceptibility with a intermediate resistant strain) rate of 1.9%, a major error (false resistance) rate of 0.8% and a very major error (false susceptibility) rate of 0.6%. Agreement for S.aureus was 97.9%, with a very major error rate of 2.1%. Enterococcus species showed 95.0% agreement, with a major error rate of 5.0%. These agreements are comparable with those of the Phoenix system. Starting from a positive blood culture, the test was completed within 9 hours. Conclusions/Significance This new rapid method for antibiotic susceptibility testing can potentially provide accurate results for most relevant bacteria commonly isolated from positive blood cultures in less time than routine methods.
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Affiliation(s)
- Judith Beuving
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Annelies Verbon
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Firza A. Gronthoud
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ellen E. Stobberingh
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Petra F. G. Wolffs
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
- * E-mail:
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Hsi SC, Sun JR, Chiueh TS. Evaluation of the alkaline wash/lysis procedure for the molecular diagnosis of a positive bacterial blood culture in clinical routine practice. J Clin Lab Anal 2011; 24:139-44. [PMID: 20486192 DOI: 10.1002/jcla.20396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Blood culture is commonly used to detect microorganisms in patients with a suspected blood infection. This study evaluated the alkaline wash/lysis procedure to extract DNA of microorganisms in a clinical blood culture. A multiplex polymerase chain reaction (PCR) targeting the 16S rDNA (ribosomal DNA) gene and the fungal ITS (internal transcribed spacer) gene was used as a reliable indicator for the presence of microorganism DNA in the extracts. A total of 535 BacT/ALERT positive blood culture bottles were evaluated. Multiplex PCR showed positive results in 530 DNA extracts, but 5 DNA extracts gave negative results. We conclude that the alkaline wash/lysis procedure in combination with the multiplex PCR is a simple and sensitive method, which can be used in a standard diagnostic laboratory to detect microorganisms in blood culture material.
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Affiliation(s)
- Sheng-Chuan Hsi
- Hsin Sheng College of Medical Care and Management, Taoyuan, Taiwan
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Dubois D, Leyssene D, Chacornac JP, Kostrzewa M, Schmit PO, Talon R, Bonnet R, Delmas J. Identification of a variety of Staphylococcus species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2010; 48:941-5. [PMID: 20032251 PMCID: PMC2832446 DOI: 10.1128/jcm.00413-09] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 08/05/2009] [Accepted: 12/11/2009] [Indexed: 11/20/2022] Open
Abstract
Whole-cell fingerprinting by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) in combination with a dedicated bioinformatic software tool (MALDI Biotyper 2.0) was used to identify 152 staphylococcal strains corresponding to 22 staphylococcal species. Spectra of the 152 isolates, previously identified at the species level using a sodA gene-based oligonucleotide array, were analyzed against the main spectra of 3,030 microorganisms. A total of 151 strains out of 152 (99.3%) were correctly identified at the species level; only one strain was identified at the genus level. The MALDI-TOF MS method revealed different clonal lineages of Staphylococcus epidermidis that were of either human or environmental origin, which suggests that the MALDI-TOF MS method could be useful in the profiling of staphylococcal strains. The topology of the dendrogram generated by the MALDI Biotyper 2.0 software from the spectra of 120 Staphylococcus reference strains (representing 36 species) was in general agreement with that inferred from the 16S rRNA gene-based analysis. Our findings indicate that the MALDI-TOF MS technology, associated with a broad-spectrum reference database, is an effective tool for the swift and reliable identification of Staphylococci.
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Affiliation(s)
- Damien Dubois
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - David Leyssene
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Jean Paul Chacornac
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Markus Kostrzewa
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Pierre Olivier Schmit
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Régine Talon
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Richard Bonnet
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Julien Delmas
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
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Doud M, Zeng E, Schneper L, Narasimhan G, Mathee K. Approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung. Hum Genomics 2009; 3:246-56. [PMID: 19403459 PMCID: PMC3500232 DOI: 10.1186/1479-7364-3-3-246] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microbial communities play vital roles in many aspects of our lives, although our understanding of microbial biogeography and community profiles remains unclear. The number of microbes or the diversity of the microbes, even in small environmental niches, is staggering. Current microbiological methods used to analyse these communities are limited, in that many microorganisms cannot be cultured. Even for the isolates that can be cultured, the expense of identifying them definitively is much too high to be practical. Many recent molecular technologies, combined with bioinformatic tools, are raising the bar by improving the sensitivity and reliability of microbial community analysis. These tools and techniques range from those that attempt to understand a microbial community from their length heterogeneity profiles to those that help to identify the strains and species of a random sampling of the microbes in a given sample. These technologies are reviewed here, using the microbial communities present in the lungs of cystic fibrosis patients as a paradigm.
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Affiliation(s)
- Melissa Doud
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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