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References - Pathogen DNA Isolation

Marin MJ, Ambrosio N, Virto L, Diz P, Álvarez M, Herrera D, Figuero E (2017) Detection and quantification of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Streptococcus oralis in blood samples with different microbiological identification methods: An in vitro study. Arch Oral Biol 74, 55-62.

Sánchez MC, Fernández E, Llama-Palacios A, Figuero E, Herrera D, Sanz M (2017) Response to antiseptic agents of periodontal pathogens in in vitro biofilms on titanium and zirconium surfaces. Dent Mat doi.org/10.1016/j.dental.2017.01.013.

Ružić-Sabljić E, Cerar T (2017) Progress in the molecular diagnosis of Lyme disease. Exp Rev Mol Diagn 17, 19-30.

Ruppé E, Greub G, Schrenzel J (2017) Messages from the first International Conference on Clinical Metagenomics (ICCMg). Microbes Inf, doi.org/10.1016/j.micinf.2017.01.005.

Rose G, Shaw AG, Sim K, Wooldridge DJ, Li MS, Gharbia S, Kroll J S (2017) Antibiotic resistance potential of the healthy preterm infant gut microbiome. PeerJ 5, e2928.

Czurda S, Lion T (2017) Broad-spectrum molecular detection of fungal nucleic acids by PCR-based amplification techniques. In: Lion T (ed.), Human Fungal Pathogen Identification: Methods and Protocols, Methods in Molecular Biology, vol. 1508, p. 257-266. DOI 10.1007/978-1-4939-6515-1_4, © Springer Science+Business Media New York.

Czurda S, Lion T (2017) Prerequisites for control of contamination in fungal diagnosis. In: Lion T (ed.), Human Fungal Pathogen Identification: Methods and Protocols, Methods in Molecular Biology, vol. 1508, p. 249-255. DOI 10.1007/978-1-4939-6515-1_4, © Springer Science+Business Media New York.

Votintseva AA, Bradley P, Pankhurst L, del    Ojo Elias C,    Loose M, Nilgiriwala K, Chatterjee A, Grace Smith E, Sanderson N, Walker TM, Morgan MR, Wyllie DH, Walker AS, Peto TEA, Crook DW,  Iqbal Z (2017) Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples. http://biorxiv.org/content/biorxiv/early/2016/12/16/094789.full.pdf.

Vutukuru MR, Sharma DK, Ragavendar MS, Schmolke S, Huang Y, Gumbrecht W, Mitra N (2016) A rapid, highly sensitive and culture-free detection of pathogens from blood by positive enrichment. J Microbiol Meth 131, 105-109.

Ziegler I, Fagerström A, Strålin K, Mölling P (2016) Evaluation of a commercial multiplex PCR assay for detection of pathogen DNA in blood from patients with suspected sepsis. PLoS ONE 11, e0167883. doi:10.1371/journal.

Gyarmati P, Kjellander C, Aust C, Song Y, Öhrmalm L, Giske CG (2016) Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia. Sci Rep. 6, 23532. doi:  10.1038/srep 23532.

Marín MJ, Figuero E, González I, O´Connor A, Diz P, Álvarez M, Herrera D, Sanz M (2016) Comparison of the detection of periodontal pathogens in bacteraemia after tooth brushing by culture and molecular techniques. Med Oral Patol Oral Cir Bucal 21, e276-84. doi:10.4317/medoral.20842.

Thoendel M, Jeraldo PR, Greenwood-Quaintance KE, Yao JZ, Chia N, Hanssen AD, Abdel MP, Patel R (2016) Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. J Microbiol Meth 21, 141-145.

Knabl L, Mutschlechner W, Orth-Höller D (2016) Evaluation of a multiplex OnSpot Primer-Extension PCR assay in the diagnosis of sepsis. J Microbiol Meth 120, 91-93.

Peterson SW, Knox NC, Golding GR, Tyler SD, Tyler AD, Mabon P, Embree JE, Fleming F, Fanella S, Van Domselaar G, Mulvey MR, Graham MR (2016) A study of the infant nasal microbiome development over the first year of life and in relation to their primary adult caregivers using cpn60 universal target (UT) as a phylogenetic marker. PLoS ONE 11, e0152493. doi:10.1371/journal.pone.0152493.

Arrazuria R, Elguezabal N, Juste RA, Derakhshani H, Khafipour E (2016) Mycobacterium avium subspecies paratuberculosis infection modifies gut microbiota under different dietary conditions in a rabbit model. Front Microbiol 7, 446. doi: 10.3389/fmicb.2016.00446.

Moore MS, McCarroll MG, McCann CD, May L, Younes N, Jordan JA (2016) Direct screening of blood by PCR and pyrosequencing for a 16S rRNA gene target from emergency department and intensive care unit patients being evaluated for bloodstream infection. J Clin Microbiol 54, 99–105.

Bwanga F, Disqué C, Lorenz MG, Allerheiligen V, Worodria W, Luyombya A, Najjingo I, Weizenegger M (2015) Higher blood volumes improve the sensitivity of direct PCR diagnosis of blood stream tuberculosis among HIV-positive patients: an observation study. BMC Infect Dis 15, 48. DOI 10.1186/s12879-015-0785-3.

Rose G, Wooldridge DJ, Anscombe C, Mee ET, Misra RV, Gharbia S (2015) Challenges of the unknown: clinical application of microbial metagenomics. Int J Genomics vol. 2015, Article ID 292950, 10 pages, doi:10.1155/2015/292950.

Gyarmati P, Kjellander C, Aust C, Kalin M, Öhrmalm L, Giske CG (2015) Bacterial landscape of bloodstream infections in neutropenic patients via high throughput sequencing. PLoS ONE 10, e0135756. doi:10.1371/journal.pone.0135756.

Risso A, Carlo C, Mezzabotta L, Elia C, Andrealli A, Spandre M, Di Luigi P, Barbui A, Evangelista A, Morgando A, Serra R, Ciccone G, Marzano A, Rizzetto M (2015) Adrenal function and microbial DNA in noninfected cirrhotic patients with ascites: relationship and effect on survival. Digest Liver Dis 47, 702-708.

Aghamollaei H, Moghaddam MM, Kooshki H, Heiat M, Mirnejad R, Barzi NS (2015) Detection of Pseudomonas aeruginosa by a triplex polymerase chain reaction assay based on lasI/R and gyrB genes. J Infect Pub Health 418; doi.org/10.1016/j.jiph.2015.03.003.

Lorenz MG, Mühl H, Disqué C (2015) Bacterial and fungal DNA extraction from blood samples: manual protocols. Sepsis: diagnostic methods and protocols. Methods in Molecular Biology (Mancini N, ed.), p. 109-119. Springer New York.

Lorenz MG, Disqué C, Mühl H (2015) Bacterial and fungal DNA extraction from blood samples: automated protocols. Sepsis: diagnostic methods and protocols. Methods in Molecular Biology, vol. 1237 (Mancini N, ed.), p. 121-128. Springer New York.

Leitner E, Kessler HH (2015) Broad-range PCR for the identification of bacterial and fungal pathogens from blood: a sequencing approach. Sepsis: diagnostic methods and protocols. Methods in Molecular Biology (Mancini N, ed.), p. 129-138. Springer New York.

Sánchez MC, Llama-Palacios A, Fernández E, Figuero E, Marín MJ, León R, Blanc V, Herrera D, Sanz M (2014) An in vitro biofilm model associated to dental implants: Structural and quantitative analysis of in vitro biofilm formation on different dental implant surfaces, Dental Materials; doi.org/10.1016/j.dental.2014.07.008.

Duran-Pinedo AE, Chen T, Teles R, R Starr JR, Wang X, Krishnan K, Frias-Lopez J (2014) Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis. The ISME Journal, doi:10.1038/ismej.2014.23.

Fricke WF, Maddox C, Song Y, Bromberg JS (2014), Human microbiota characterization in the course of renal transplantation. Am J Transplant 14, 416–427.

Zha Y, Armeanu E, DiVerniero T, Lewis TA, Dobson RC, Kontoyiannis DP, Roilides E, Walsh TJ, Perlin DS (2014) Fungal DNA detected in blood samples of patients who received contaminated methylprednisolone injections reveals increased complexity of causative agents. J Clin Microbiol 52, 2212-2215.

Krohn S, Böhm S, Engelmann C, Hartmann J, Brodzinski A, Chatzinotas A, Zeller K, Prywerek D, Fetzer I, Berg T (2014) Application of qualitative and quantitative real-time PCR, direct sequencing, and terminal restriction fragment length polymorphism analysis for detection and identification of polymicrobial 16S rRNA genes in ascites. J Clin Microbiol 52, 1754-1757.

Masek BJ, Hardick J, Won H, Yang S, Hsieh YH, Rothman RE, Gaydos CA (2014) Sensitive detection and serovar differentiation of typhoidal and nontyphoidal Salmonella enterica species using 16S rRNA Gene PCR coupled with high-resolution melt analysis. J Mol Diagn 16, 261–266.

Rudkjøbing VB, Aanaes K, Wolff TY, von Buchwald C, Johansen HK, Thomsen TR (2014) An exploratory study of microbial diversity in sinus infections of cystic fibrosis patients by molecular methods. J Cys Fibrosis doi:10.1016/j.jcf.2014.02.008.

McCann CD, Jordan JJ (2014) Evaluation of MolYsis™Complete5 DNA extraction method for detecting Staphylococcus aureus DNA from whole blood in a sepsis model using PCR/pyrosequencing. J Microbiol Meth 99, 1-7.

Hansen WLJ, Bruggeman CA, Wolffs PFG (2013) Pre-analytical sample treatment and DNA extraction protocols for the detection of bacterial pathogens from whole blood. Meth Mol Biol 943, 81-90.

Laakso S, Mäki M (2013) Assessment of a semi-automated protocol for multiplex analysis of sepsis-causing bacteria with spiked whole blood samples. MicrobiologyOpen 2, 284–292.

Benítez-Páez A, Álvarez M, Belda-Ferre P, Rubido S, Mira A, Tomás I (2013) Detection of transient bacteraemia following dental extractions by 16S rDNA pyrosequencing: A pilot study. PLoS ONE 8, e57782. doi:10.1371/journal.pone.0057782.

Loonen AJM, Jansz AR, Stalpers J, Wolffs PFG, van den Brule AJC (2012) An evaluation of three processing methods and the effect of reduced culture times for faster direct identification of pathogens from BacT/ALERT blood cultures by MALDI-TOF MS. Eur J Clin Microbiol Infect Dis 31, 1575-1583.

Thomsen TR, Xu Y, Lorenzen J, Nielsen PH, Schønheyder HC (2012) Improved diagnosis of biofilm infections using various molecular methods. Culture negative orthopedic biofilm infections. Springer Series on Biofilms 7, 29-41.

Richardson LJ, Kaestlia M, Mayoa M, Bowers JR, Tuanyok A, Schupp J, Engelthaler D, Wagner DM, Keim PS, Currie BJ (2012) Towards a rapid molecular diagnostic for melioidosis: Comparison of DNA extraction methods from clinical specimens. J Microbiol Meth 88, 179–181.

Xu Y, Børsholt Rudkjøbing V, Simonsen O, Pedersen C, Lorenzen J, Schønheyder HC, Nielsen PH, Rolighed Thomsen T (2012) Bacterial diversity in suspected prosthetic joint infections: an exploratory study using 16S rRNA gene analysis. FEMS Immunol Med Microbiol 65, 291–304.

Esteban J, Alonso-Rodriguez N, del-Prado G, Ortiz-Pérez A, Molina-Manso D, Cordero-Ampuero J, Sandova E, Fernández-Roblas R, Gómez-Barrena E (2012) PCR-hybridization after sonication improves diagnosis of implant-related infection. Acta Orthopaedica 3, 299-304.

Zhou L, Pollard AJ (2012) A novel method of selective removal of human DNA improves PCR sensitivity for detection of Salmonella Typhi in blood samples. BMC Inf Dis 12, 164 doi:10.1186/1471-2334-12-164.

Loonen AJM, Jansz AR, Kreeftenberg H, Bruggeman CA, Wolffs PFG, van den Brule AJC (2011) Acceleration of the direct identification of Staphylococcus aureus versus coagulase-negative staphylococci from blood culture material: a comparison of six bacterial DNA extraction methods. Eur J Clin Microbiol Infect Dis 30, 337-342.

Mayr A, Lass-Flörl C (2011) Non–culture-based methods for the diagnosis of invasive candidiasis. Curr Fungal Infect Reports 5, 151-156.

Wolff TY, Moser C, Bundgaard H, Høiby N, Nielsen PH, Thomsen TR (2011) Detection of microbial diversity in endocarditis using cultivation-independent molecular techniques. Scand J Infect Dis 43, 857-869.

Meurs KM, Heaney AM, Atkins CE, DeFrancesco TC, Fox PR, Keene BW, Kellihan HB, Miller MW, Oyama MA, Oaks JL (2011) Comparison of polymerase chain reaction with bacterial 16S primers to blood culture to identify bacteremia in dogs with suspected bacterial endocarditis. J Vet Inter Med 25, 959–962.

Wiesinger-Mayr H, Jordana-Lluch E, Martró E, Schoenthaler S, Noehammer C (2011) Establishment of a semi-automated pathogen DNA isolation from whole blood and comparison with commercially available kits. J Microbiol Meth 85, 206–213.

Kemp M, Jensen KH, Dargis R, Christensen JJ (2010) Routine ribosomal PCR and DNA sequencing for detection and identification of bacteria. Future Microbiol 5, 1101-1107.

Downey LC, Smith BP, Benjamin DK, Cohen-Wolkowiez (2010) Recent advances in the detection of neonatal candidiasis. Curr Fungal Infect Rep 4, 17-22.

Bille J (2010) New nonculture-based methods for the diagnosis of invasive candidiasis. Curr Opin Crit Care 16, 460-464.

Leggieri N (2010) Molecular diagnosis of bloodstream infections: planning to (physically) reach the bedside. Curr Opin Infect Dis 23, 311-319.

Horz HP, Scheer S, Vianna ME, Conrads G (2010) New methods for selective isolation of bacterial DNA from human clinical specimens. Anaerobe 16, 47-53.

Hansen WLJ, Bruggeman CA, Wolffs PFG (2009) Evaluation of new preanalysis sample treatment tools and DNA isolation protocols to improve bacterial pathogen detection in whole blood. J Clin Microbiol 47, 2629-2631.

Wellinghausen N, Siegel D, Gebert S, Winter J (2009) Rapid detection of Staphylococcus aureus bacteremia and methicillin resistance by real-time PCR in whole blood samples. Eur J Clin Microbiol Infect Dis 28, 1001-1005.

Wellinghausen N, Siegel D, Winter J, Gebert S (2009) Rapid diagnosis of candidaemia by real-time PCR detection of Candida DNA in blood samples. J Med Microbiol 58, 1106-1111.

Handschur M, Karlic H, Hertl C, Pfeilstöcker M, Haslberger AG (2009) Preanalytic removal of human DNA eliminates false signals in general 16S rDNA PCR monitoring of bacterial pathogens in blood. Comp Immunol Microbiol Infect Dis 32, 207-219.

Gebert S, Siegel D, Wellinghausen N (2008) Rapid detection of pathogens in blood culture bottles by real-time PCR in conjunction with the pre-analytic tool MolYsis. J Infect 57, 307-316.

Horz HP, Scheer S, Huenger F, Vianna ME, Conrads G (2008) Selective isolation of bacterial DNA from human clinical specimens. J Microbiol Meth 72, 98-102.

Disqué C (2007) Einfluss der DNA-Extraktion auf die PCR-Detektion von Sepsiserregern. BIOspektrum 06, 627-629.