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Çevresel Örneklerde Bulunan Canlı Patojen Mikroorganizmaları Saptama ve Miktarlarını Belirlemede Yeni Yaklaşımlar

Year 2017, Volume: 27 Issue: 2, 285 - 291, 30.06.2017
https://doi.org/10.29133/yyutbd.292851

Abstract

Gıda endüstrisi, çevre endüstrisi, tıp ve tarım gibi pek çok endüstri ve
bilimsel alanda ürün kontaminasyonu halk sağlığı açısından çok kötü sonuçlar
doğurabilmektedir. Bu nedenle çevresel ve endüstriyel örneklerde indikatör
mikroorganizmaların saptanması ve miktarlarının belirlenmesi halk sağlığı ve
güvencesi açısından çok büyük önem taşımaktadır. Patojen mikroorganizmaların
canlı olanları büyük ölçüde halk sağlığını tehdit ettiği için sadece canlı
hücreleri saptayan ve miktarlarını belirleyen yeni tekniklerin geliştirilmesi
çok önemlidir. Bu derleme, bir örnek içerisinde bulunan sadece patojen
mikroorganizmaları değil aynı zamanda istenilen diğer canlı hücreleri saptamakta
ve miktarlarını belirlemekte kullanılan geleneksel yöntemler ile yeni, güncel
moleküler gelişmeleri avantaj ve dezavantajları ile birlikte özetlemektedir.

References

  • Alonso JL, Amorós I, Guy RA (2014). Quantification of viable Giardia cysts and Cryptosporidium oocysts in wastewater using propidium monoazide quantitative real-time PCR. Parasitol. Res. 113: 2671–2678
  • Ayrapetyan M and Oliver JD (2016). The viable but non-culturable state and its relevance in food safety. Curr Opin Food Sci. 2016, 8:127–133
  • Bae S and Wuertz S (2012). Survival of host-associated Bacteroidales cells and their relationship with Enterococcus spp., Campylobacter jejuni, Salmonella enterica serovar Typhimurium, and Adenovirus in freshwater microcosms as measured by propidium monoazide-quantitative PCR. Appl. Environ. Microbiol. 78: 922–932
  • Bae S and Wuertz S (2009). Discrimination of viable and dead fecal Bacteroidales bacteria by quantitative PCR with propidium monoazide. Appl. Environ. Microbiol. 75:2940-2944.
  • Berney M, Hammes F, Bosshard F, Weilenmann H-U, Thomas Egli T (2007). Assessment and interpretation of bacterial viability by using the LIVE/DEAD BacLight Kit in combination with flow cytometry. Appl. Environ. Microbiol. 73: 3283-3290.
  • Boulos L, Prévost M, Barbeau B, Coallier J, Desjardins R (1999). LIVE/DEAD BacLight : application of a new rapid staining method for direct enumeration of viable and total bacteria in drinking water. J. Microbiol. Methods; 37:77-86.
  • Epstein E (2003). Land application of sewage sludge and biosolids. Published by Lewis Publishers.
  • Fournier PE, Dubourg G, Raoult D (2014). Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med. 6: 114
  • Ginzinger DG (2002). Gene quantification using real-time quantitative PCR:An emerging technology hits the mainstream. Exp. Hematol. 30:503-12.
  • Hazen TC, Rocha AM, Techtmann SM (2013). Advances in monitoring environmental microbes. Curr Opin Biotech. 24:526–533.
  • Heise J, Nega M, Alawi M and Wagner D (2016). Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples. J. Microbiol. Methods 121: 11-23.
  • Higgins MJ, Chen YC, Murthy SN, Hendrickson D, Farrel J, Schafer P (2007). Reactivation and growth of non-culturable indicator bacteria in anaerobically digested biosolids after centrifuge dewatering. Water Res. 41:665-673.
  • Higgins MJ, Chen YC, Hendrickson D, Murthy SN (2008). Evaluation of Bacterial Pathogen and Indicator Densities After Dewatering of Anaerobically Digested Biosolids Phase II and III. WERF 04-CTS-3T, IWA, London, UK.
  • Hoefel D, Grooby WL, Monis PT, Andrews S, Saint C P (2003). Enumeration of water-borne bacteria using viability assays and flow cytometry: a comparison to culture-based techniques. J. Microbiol. Methods 55:585-597.
  • Josephson KL, Gerba CP, Pepper IL (1993). Polymerase chain reaction detection of nonviable bacterial pathogens. Appl. Environ. Microb. 59:3513–3515.
  • Koch WH (2004). Technology platforms for pharmacogenomic diagnostic assays. Nat. Rev. Drug Discov.3:749-61.
  • Lazcka O, Del Campo FJ, Muñoz FX (2007). Pathogen detection: a perspective of traditional methods and biosensors. Biosens. Bioelectron. 22:1205-17.
  • Levsky JM and Singer RH (2003). Fluorescence in situ hybridization: past, present and future. J Cell Sci. 116:2833-8
  • Lin WT, Luo JF, Guo Y (2011). Comparison and Characterization of Microbial Communities in Sulfide-rich Wastewater with and without Propidium Monoazide Treatment. Curr. Microbiol. 62:374-81.
  • Masters CI, Shallcross JA, Mackey BM (1994). Effect of stress treatments on the detection of Listeria monocytogenes and enterotoxigenic Escherichia coli by the polymerase chain reaction. J. Appl.Bacteriol.77:73–79.
  • Nocker A, Cheung CY, Camper AK (2006). Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J. Microbiol. Methods 67:310-320.
  • Nocker A and Camper AK (2006). Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide. Appl. Environ. Microbiol. 72:1997-2004.
  • Nocker A, Fernandez PS, Burr MD, Camper AK (2007). Use of propidium monoazide for live/dead distinction in microbial ecology. Appl. Environ. Microbiol. 73: 5111-5117
  • Oliver SP, Jayarao BM, Almeida RA (2005). Foodborne pathogens in milk and the dairy farm environment: food safety and public health implications. Foodborne Pathog Dis. 2:115-29.
  • Oliver JD (2010). Recent findings on the viable but nonculturable state in pathogenic bacteria. FEMS Microbiol Rev. 34: 415-25.
  • Qi Y, Dentel SK, Herson DS (2007). Increases in fecal coliform bacteria resulting from centrifugal dewatering of digested biosolids. Water Res. 41: 571-580.
  • Rawsthorne H, Dock CN, Jaykus LA (2009). PCR-based method using propidium monoazide to distinguish viable from nonviable Bacillus subtilis spores. Appl. Environ. Microbiol. 75: 2936–2939.
  • Sánchez G, Elizaquível P, Aznar R (2012). Discrimination of infectious hepatitis A viruses by propidium monoazide real-time RT-PCR. Food Environ. Virol. 4: 21–25.
  • Smith CJ and Osborn AM (2009). Advantages and limitations of quantitative PCR (Q-PCR) based approaches in microbial ecology. FEMS Microbiol. Ecol., 67: 6–20
  • Takahashi H, Gao Y, Miya S, Kuda T, Kimura B (2017). Discrimination of live and dead cells of Escherichia coli using propidium monoazide after sodium dodecyl sulfate treatment. Food Control 71: 79-82.
  • Tantikachornkiat M, Sakakibara S, Neuner M, Durall DM (2016). The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria. Int J Food Microbiol. 234: 53–59.
  • Taskin B, Gozen AG, Duran M (2011). Selective quantification of viable Escherichia coli bacteria in biosolids by quantitative PCR with propidium monoazide modification. Appl. Environ. Microbiol. 77: 4329–4335.
  • Taylor MJ, Bentham RH, Ross KE (2014). Limitations of using propidium monoazide with qPCR to discriminate between live and dead Legionella in biofilm samples. Microbiol. Insights 7: 15–24
  • ThermoFisher (2017). http://www.thermofisher.com/tr/en/home/technical-resources/research-tools/image-gallery.html (Access Date: February 15, 2017)
  • USEPA (2003). Control of Pathogens and Vector Attraction in Sewage Sludge, EPA/625/R-92/013, Revised July 2003, U.S. Environmental protection Agency, Washington.
  • USEPA (2006). Multi-Stage Anaerobic Digestion, EPA/832/F-06/031, U.S. Environmental protection Agency, Washington D.C.
  • Veal DA, Deere D, Ferrari B, Piper J, Attfield PV (2000). Fluorescence staining and flow cytometry for monitoring microbial cells. J. Immunol. Methods 243:191-210.
  • Vesper S, McKinstry C, Hartmann C, Neace M, Yoder S, Vesper A (2008). Quantifying fungal viability in air and water samples using quantitative PCR after treatment with propidium monoazide (PMA). J. Microbiol. Methods 72: 180–184.
  • Virta M, Lineri S, Kankaanpää P, Karp M, Peltonen K, Nuutila J, Lilius E-M (1998). Determination of complement-mediated killing of bacteria by viability staining and bioluminescence. Appl. Environ. Microbiol. 64:515-519.
  • Wagner AO, Praeg N, Reitschuler C, Illmer P (2015) Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil. Appl Soil Ecol 93:56–64
  • Wagner AO, Malin C, Knapp BA, Illmer P (2008). Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide. Appl. Environ. Microbiol. 74:2537-2539.
  • Wang LK, Shammas NK, Hung, YT (2008). Biosolids Engineering and Management, Volume 7. Published by Humana Press.
  • Zhou Z, Pons MN, Raskin L, Zilles JL (2007). Automated image analysis for quantitative fluorescence in situ hybridization with environmental samples. Appl. Environ. Microbiol. 73: 2956-2962.

Novel Approaches for Monitoring Viable Pathogenic Microorganisms in Environmental Samples

Year 2017, Volume: 27 Issue: 2, 285 - 291, 30.06.2017
https://doi.org/10.29133/yyutbd.292851

Abstract

In many industries and
scientific fields, for example, food industry, medicine, ecological business
and agriculture, contamination of products
may have terrible consequences in the manner of public
health.
Therefore, detection and quantification of
indicator microorganisms in many environmental sample and industrial products
are the keys for counteractive action and identification of problems related to
health issues. Also, since viable portion of the pathogenic microorganisms is
likely a threat to public health, developing a novel method to quantify only
viable cells is imperative.
This review considers the traditional methods and the novel molecular
developments with their advantages and drawbacks for detection and quantification
of not only pathogenic microorganisms but also any living cells in a sample.

References

  • Alonso JL, Amorós I, Guy RA (2014). Quantification of viable Giardia cysts and Cryptosporidium oocysts in wastewater using propidium monoazide quantitative real-time PCR. Parasitol. Res. 113: 2671–2678
  • Ayrapetyan M and Oliver JD (2016). The viable but non-culturable state and its relevance in food safety. Curr Opin Food Sci. 2016, 8:127–133
  • Bae S and Wuertz S (2012). Survival of host-associated Bacteroidales cells and their relationship with Enterococcus spp., Campylobacter jejuni, Salmonella enterica serovar Typhimurium, and Adenovirus in freshwater microcosms as measured by propidium monoazide-quantitative PCR. Appl. Environ. Microbiol. 78: 922–932
  • Bae S and Wuertz S (2009). Discrimination of viable and dead fecal Bacteroidales bacteria by quantitative PCR with propidium monoazide. Appl. Environ. Microbiol. 75:2940-2944.
  • Berney M, Hammes F, Bosshard F, Weilenmann H-U, Thomas Egli T (2007). Assessment and interpretation of bacterial viability by using the LIVE/DEAD BacLight Kit in combination with flow cytometry. Appl. Environ. Microbiol. 73: 3283-3290.
  • Boulos L, Prévost M, Barbeau B, Coallier J, Desjardins R (1999). LIVE/DEAD BacLight : application of a new rapid staining method for direct enumeration of viable and total bacteria in drinking water. J. Microbiol. Methods; 37:77-86.
  • Epstein E (2003). Land application of sewage sludge and biosolids. Published by Lewis Publishers.
  • Fournier PE, Dubourg G, Raoult D (2014). Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med. 6: 114
  • Ginzinger DG (2002). Gene quantification using real-time quantitative PCR:An emerging technology hits the mainstream. Exp. Hematol. 30:503-12.
  • Hazen TC, Rocha AM, Techtmann SM (2013). Advances in monitoring environmental microbes. Curr Opin Biotech. 24:526–533.
  • Heise J, Nega M, Alawi M and Wagner D (2016). Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples. J. Microbiol. Methods 121: 11-23.
  • Higgins MJ, Chen YC, Murthy SN, Hendrickson D, Farrel J, Schafer P (2007). Reactivation and growth of non-culturable indicator bacteria in anaerobically digested biosolids after centrifuge dewatering. Water Res. 41:665-673.
  • Higgins MJ, Chen YC, Hendrickson D, Murthy SN (2008). Evaluation of Bacterial Pathogen and Indicator Densities After Dewatering of Anaerobically Digested Biosolids Phase II and III. WERF 04-CTS-3T, IWA, London, UK.
  • Hoefel D, Grooby WL, Monis PT, Andrews S, Saint C P (2003). Enumeration of water-borne bacteria using viability assays and flow cytometry: a comparison to culture-based techniques. J. Microbiol. Methods 55:585-597.
  • Josephson KL, Gerba CP, Pepper IL (1993). Polymerase chain reaction detection of nonviable bacterial pathogens. Appl. Environ. Microb. 59:3513–3515.
  • Koch WH (2004). Technology platforms for pharmacogenomic diagnostic assays. Nat. Rev. Drug Discov.3:749-61.
  • Lazcka O, Del Campo FJ, Muñoz FX (2007). Pathogen detection: a perspective of traditional methods and biosensors. Biosens. Bioelectron. 22:1205-17.
  • Levsky JM and Singer RH (2003). Fluorescence in situ hybridization: past, present and future. J Cell Sci. 116:2833-8
  • Lin WT, Luo JF, Guo Y (2011). Comparison and Characterization of Microbial Communities in Sulfide-rich Wastewater with and without Propidium Monoazide Treatment. Curr. Microbiol. 62:374-81.
  • Masters CI, Shallcross JA, Mackey BM (1994). Effect of stress treatments on the detection of Listeria monocytogenes and enterotoxigenic Escherichia coli by the polymerase chain reaction. J. Appl.Bacteriol.77:73–79.
  • Nocker A, Cheung CY, Camper AK (2006). Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J. Microbiol. Methods 67:310-320.
  • Nocker A and Camper AK (2006). Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide. Appl. Environ. Microbiol. 72:1997-2004.
  • Nocker A, Fernandez PS, Burr MD, Camper AK (2007). Use of propidium monoazide for live/dead distinction in microbial ecology. Appl. Environ. Microbiol. 73: 5111-5117
  • Oliver SP, Jayarao BM, Almeida RA (2005). Foodborne pathogens in milk and the dairy farm environment: food safety and public health implications. Foodborne Pathog Dis. 2:115-29.
  • Oliver JD (2010). Recent findings on the viable but nonculturable state in pathogenic bacteria. FEMS Microbiol Rev. 34: 415-25.
  • Qi Y, Dentel SK, Herson DS (2007). Increases in fecal coliform bacteria resulting from centrifugal dewatering of digested biosolids. Water Res. 41: 571-580.
  • Rawsthorne H, Dock CN, Jaykus LA (2009). PCR-based method using propidium monoazide to distinguish viable from nonviable Bacillus subtilis spores. Appl. Environ. Microbiol. 75: 2936–2939.
  • Sánchez G, Elizaquível P, Aznar R (2012). Discrimination of infectious hepatitis A viruses by propidium monoazide real-time RT-PCR. Food Environ. Virol. 4: 21–25.
  • Smith CJ and Osborn AM (2009). Advantages and limitations of quantitative PCR (Q-PCR) based approaches in microbial ecology. FEMS Microbiol. Ecol., 67: 6–20
  • Takahashi H, Gao Y, Miya S, Kuda T, Kimura B (2017). Discrimination of live and dead cells of Escherichia coli using propidium monoazide after sodium dodecyl sulfate treatment. Food Control 71: 79-82.
  • Tantikachornkiat M, Sakakibara S, Neuner M, Durall DM (2016). The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria. Int J Food Microbiol. 234: 53–59.
  • Taskin B, Gozen AG, Duran M (2011). Selective quantification of viable Escherichia coli bacteria in biosolids by quantitative PCR with propidium monoazide modification. Appl. Environ. Microbiol. 77: 4329–4335.
  • Taylor MJ, Bentham RH, Ross KE (2014). Limitations of using propidium monoazide with qPCR to discriminate between live and dead Legionella in biofilm samples. Microbiol. Insights 7: 15–24
  • ThermoFisher (2017). http://www.thermofisher.com/tr/en/home/technical-resources/research-tools/image-gallery.html (Access Date: February 15, 2017)
  • USEPA (2003). Control of Pathogens and Vector Attraction in Sewage Sludge, EPA/625/R-92/013, Revised July 2003, U.S. Environmental protection Agency, Washington.
  • USEPA (2006). Multi-Stage Anaerobic Digestion, EPA/832/F-06/031, U.S. Environmental protection Agency, Washington D.C.
  • Veal DA, Deere D, Ferrari B, Piper J, Attfield PV (2000). Fluorescence staining and flow cytometry for monitoring microbial cells. J. Immunol. Methods 243:191-210.
  • Vesper S, McKinstry C, Hartmann C, Neace M, Yoder S, Vesper A (2008). Quantifying fungal viability in air and water samples using quantitative PCR after treatment with propidium monoazide (PMA). J. Microbiol. Methods 72: 180–184.
  • Virta M, Lineri S, Kankaanpää P, Karp M, Peltonen K, Nuutila J, Lilius E-M (1998). Determination of complement-mediated killing of bacteria by viability staining and bioluminescence. Appl. Environ. Microbiol. 64:515-519.
  • Wagner AO, Praeg N, Reitschuler C, Illmer P (2015) Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil. Appl Soil Ecol 93:56–64
  • Wagner AO, Malin C, Knapp BA, Illmer P (2008). Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide. Appl. Environ. Microbiol. 74:2537-2539.
  • Wang LK, Shammas NK, Hung, YT (2008). Biosolids Engineering and Management, Volume 7. Published by Humana Press.
  • Zhou Z, Pons MN, Raskin L, Zilles JL (2007). Automated image analysis for quantitative fluorescence in situ hybridization with environmental samples. Appl. Environ. Microbiol. 73: 2956-2962.
There are 43 citations in total.

Details

Subjects Engineering
Journal Section Articles
Authors

Bilgin Taşkın

Publication Date June 30, 2017
Acceptance Date April 1, 2017
Published in Issue Year 2017 Volume: 27 Issue: 2

Cite

APA Taşkın, B. (2017). Novel Approaches for Monitoring Viable Pathogenic Microorganisms in Environmental Samples. Yuzuncu Yıl University Journal of Agricultural Sciences, 27(2), 285-291. https://doi.org/10.29133/yyutbd.292851
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Yuzuncu Yil University Journal of Agricultural Sciences by Van Yuzuncu Yil University Faculty of Agriculture is licensed under a Creative Commons Attribution 4.0 International License.