Статті в журналах: "Faecal DNA"

1

Piggott, Maxine P. "Effect of sample age and season of collection on the reliability of microsatellite genotyping of faecal DNA." Wildlife Research 31, no. 5 (2004): 485. http://dx.doi.org/10.1071/wr03096.

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Individual identification of animals from DNA in field-collected faecal samples is becoming an increasingly important tool in wildlife population monitoring. A major issue relevant to the application of this technique is the reliability of the genotypes obtained. I investigated the effect of sample age and season of collection on amplification rates and reliability of microsatellite genotypes amplified from faecal DNA of a marsupial herbivore, the brush-tailed rock-wallaby (Petrogale penicillata) and a eutherian carnivore, the red fox (Vulpes vulpes). Comparison of DNA profiles from 1 day to 6 months for both species suggests that as the age of the faeces increases there is less good-quality DNA present on the surface of the faeces, resulting in significantly decreasing amplification rates and increasing genotyping error rates over time. No microsatellite PCR products were obtained from samples older than 3 months from any faecal DNA extract in either season. For both species, faeces collected during the summer trial yielded high-quality DNA for up to one week. Faeces collected in winter had significantly lower amplification rates and higher genotyping errors than the summer-collected samples. Computer simulations were used to estimate the probability of obtaining false genotypes when genotyping faecal samples of various ages. These revealed that three replicates is sufficient to prevent identification of false individuals for P. penicillata from faeces up to one week old in both summer and winter but more replicates may be required for older samples, particularly in winter. In contrast, up to eight replicates may be required for fox faeces collected in winter, particularly if more than one week old. These results also suggest that it is difficult to visually identify faecal age for V. vulpes, and any study using fox faeces would need to account for the likely inclusion of older faeces in a field collection. For P. penicillata, faecal age could be accurately assessed, particularly when less than one week old and targeting faeces that match the two most reliable appearance classes described here would be an efficient sampling strategy. It is recommended that the appropriate PCR replication protocol for any given study should be tailored to the error rates expected for the oldest samples likely to be collected. This study is the first to thoroughly investigate the effects of sample age and season of collection on microsatellite genotyping from faecal samples and provides guidelines for sampling and PCR repetition strategies for field-based non-invasive DNA studies.

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2

Inglis, G. D., L. D. Kalischuk, and H. W. Busz. "A survey ofCampylobacterspecies shed in faeces of beef cattle using polymerase chain reaction." Canadian Journal of Microbiology 49, no. 11 (November 1, 2003): 655–61. http://dx.doi.org/10.1139/w03-087.

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A polymerase chain reaction (PCR)-based survey of campylobacters associated with faeces collected from 382 beef cattle was undertaken. To ensure the removal of PCR inhibitors present in faeces and determine if adequate extraction was achieved, faeces were seeded with internal control DNA (i.e., DNA designed to amplify with the Campylobacter genus primer set, but provide a smaller amplicon) before the extraction procedure. In only two samples (0.5%) were the internal control or Campylobacter genus amplicons not detected. In the remaining 380 faecal samples, Campylobacter DNA was detected in 83% of the faecal samples (80% of the faecal samples were positive for Campylobacter genus DNA, and 3% of the samples were negative for Campylobacter genus DNA but positive for DNA of individual species). The most frequently detected species was Campylobacter lanienae (49%), a species only recently connected to livestock hosts. Campylobacter jejuni DNA was detected in 38% of the faecal samples, and Campylobacter hyointestinalis and Campylobacter coli DNA were detected in 8% and 0.5% of the samples, respectively. Campylobacter fetus DNA was not detected. Twenty-four percent of the faecal samples contained DNA of at least two species of Campylobacter. Of these samples, the majority (81%) contained DNA of C. jejuni and C. lanienae. The results of this study indicate that beef cattle commonly release a variety of Campylobacter species into the environment and may contribute to the high prevalence of campylobacteriosis in humans inhabiting areas of intensive cattle production, such as southern Alberta. Furthermore, this study demonstrates the utility of using PCR as a rapid and accurate method for simultaneously detecting the DNA of a diverse number of Campylobacter species associated with bovine faeces.Key words: campylobacters, detection, technique, Bos taurus.

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3

McMillan, M., W. G. MacKay, C. L. Williams, A. J. Shepherd, C. Malcolm, and L. T. Weaver. "Intrafamilial Genotyping ofHelicobacter pylorifrom Faecal DNA." Gastroenterology Research and Practice 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/491035.

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Helicobacter pyloriinfection, often acquired in early childhood, is a global cause of undernutrition, gastritis, peptic ulcer disease and gastric carcinoma. This study tested the feasibility of usingH. pylorished in the faeces as a source of DNA for non-invasive epidemiological studies.H. pyloriDNA was chemically recovered and isolated using a specific biotinylated oligonucleotide probe with magnetic capture from 28H. pyloripositive faecal samples obtained from children attending hospital for the investigation of suspectedH. pyloriinfection, together with close family members. Random amplification of polymorphic DNA (RAPD) was subsequently used to discriminate each isolate. 93% of stool samples selected were typeable. Parent, child and sibling samples were compared and similarities determined. Phylogenetic analysis showed thatH. pyloriDNA obtained from the faeces can be used to genotype individual strains, offering a means of studying intrafamilial transfer of this microorganism.

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4

Oberreuther-Moschner, Daniela L., Gerhard Jahreis, Gerhard Rechkemmer, and Beatrice L. Pool-Zobel. "Dietary intervention with the probiotics Lactobacillus acidophilus 145 and Bifidobacterium longum 913 modulates the potential of human faecal water to induce damage in HT29clone19A cells." British Journal of Nutrition 91, no. 6 (June 2004): 925–32. http://dx.doi.org/10.1079/bjn20041108.

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Probiotics reduce the risk of colon cancer by inhibiting carcinogen-induced DNA damage in animals, but there are no analogous data in human subjects. To enhance knowledge of the effects of probiotics in human subjects, we have investigated the genotoxicity of faecal water after dietary intervention with standard yoghurt or with probiotic yoghurt, which included the strains Lactobacillus acidophilus 145 and Bifidobacterium longum 913. Faeces were collected from nine healthy volunteers after intervention with probiotic yoghurt or standard yoghurt. Faecal water was isolated and incubated with human colon tumour cells HT29clone19A. DNA strand breaks, oxidised DNA bases and damage after challenge with H2O2 were determined by micro-gel-electrophoresis. Faecal water was genotoxic in comparison with NaCl, but protected against H2O2-induced DNA strand breaks. The intervention with probiotic yoghurt significantly lowered faecal water genotoxicity compared with standard yoghurt. However, probiotic intervention also increased oxidative damage; this either reflected prooxidative activity or stimulation of endogenous defence systems. Altogether, the balance of effects favoured protection, since faecal water from the probiotic group reduced overall genetic damage. Thus, there was a reduction of strand break-inducing compounds in human faeces after dietary intervention with probiotic bacteria. This protection reflected results from previous studies in carcinogen-exposed animals where probiotics reduced DNA damage in colon cells.

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5

Suehiro, Yutaka, Yibo Zhang, Shinichi Hashimoto, Taro Takami, Shingo Higaki, Yoshitaro Shindo, Nobuaki Suzuki, et al. "Highly sensitive faecal DNA testing of TWIST1 methylation in combination with faecal immunochemical test for haemoglobin is a promising marker for detection of colorectal neoplasia." Annals of Clinical Biochemistry: International Journal of Laboratory Medicine 55, no. 1 (January 12, 2017): 59–68. http://dx.doi.org/10.1177/0004563217691064.

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Background As TWIST1 methylation is specific to colorectal neoplasia, detection of TWIST1 methylation from faeces samples might be useful for colorectal neoplasia screening. However, because the content of human DNA in faeces is very small, it is very difficult to detect TWIST1 methylation by conventional bisulphite-based methylation assays. Therefore, we developed a new methylation assay without bisulphite treatment, the combined restriction digital PCR assay, and evaluated its sensitivity and specificity in combination with and without the faecal immunochemical test for haemoglobin for colorectal neoplasia detection from faeces samples. Methods For the combined restriction digital PCR assay, DNA was treated with three methylation-sensitive restriction enzymes and an exonuclease, followed by measurement of TWIST1 methylation level by droplet digital PCR. Faecal DNA testing and faecal immunochemical test for haemoglobin were performed on 109 patients with colorectal neoplasia and 10 control individuals. Results Basic performance testing showed that the combined restriction digital PCR assay enabled detection of 0.14% of the TWIST1 methylation level for the lymphocyte DNA. The combined restriction digital PCR assay from faeces samples had a sensitivity of 22.2% (95% confidence interval, 2.8–60.0%) for non-advanced adenoma, 47.1% (95% confidence interval, 23.0–72.2%) for advanced adenoma, and 33.7% (95% confidence interval, 23.7–45.0%) for colorectal cancer, and a specificity of 100.0%. Combination of faecal immunochemical test for haemoglobin and faecal combined restriction digital PCR assay increased sensitivity to 82.4% (95% confidence interval, 56.6–96.2%) for the detection of advanced adenoma. Conclusions We developed the combined restriction digital PCR assay, a possible highly sensitive methylation assay. Combination of faecal combined restriction digital PCR assay with faecal immunochemical test for haemoglobin may provide an alternative screening strategy for colorectal neoplasia, especially for potentially precancerous lesions.

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6

Carpenter, Fiona M., and Martin A. Dziminski. "Breaking down scats: degradation of DNA from greater bilby (Macrotis lagotis) faecal pellets." Australian Mammalogy 39, no. 2 (2017): 197. http://dx.doi.org/10.1071/am16030.

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Isolating DNA from scats (faeces) of threatened species is a valuable, non-invasive method for identifying individuals. To establish whether genotyping of greater bilby (Macrotis lagotis) individuals from faecal pellets collected in the field can be useful for population monitoring, an understanding of the DNA degradation rates is necessary. To determine the relationship between time and degradation of bilby faecal DNA, and assess whether a two-step elution process during extraction results in better-quality DNA, faecal pellets were collected from captive individuals, maintained under seminatural conditions, then harvested at known periods. DNA was amplified from faecal pellets with a 99% success rate and error rates of less than 5% up to 14 days after deposition. The amplification rate decreases, and the rate of allelic dropout increases with time, but DNA can still be amplified at rates above 60% and error rates below 15% at 90–180 days. We found that a second elution step was unnecessary, with more DNA amplified over a longer period using the first eluate. Viable DNA exists on bilby faecal pellets for a long period after deposition, which is useful for obtaining genetic samples for population monitoring programs and studies on population genetics.

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7

Afonso, E., and A. C. Goydadin. "Molecular detection of Anaplasma phagocytophilum DNA in the lesser horseshoe bat (Rhinolophus hipposideros) guano." Epidemiology and Infection 146, no. 10 (May 30, 2018): 1253–58. http://dx.doi.org/10.1017/s0950268818001279.

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AbstractAlthough bats are increasingly recognised as potential reservoir hosts of human zoonotic pathogens, bacteria in bats are still poorly studied. To investigate the DNA faecal prevalence of the bacterium Anaplasma phagocytophilum, we sampled 23 lesser horseshoe bat (Rhinolophus hipposideros) maternity colonies located in buildings (churches, barns) in rural villages of eastern France. A total of 552 faecal samples were collected from 278 individuals. Anaplasma phagocytophilum DNA was detected in the faeces of 63 individuals (22.7%). Such high prevalence might suggest persistent infection in bats and/or a frequent consumption of insect preys carrying bacteria. Faecal DNA prevalence varied highly among colonies but was not related to the colony size. Faecal DNA prevalence was the highest in the Jura Department, where the density of ticks is known to be the highest across the study area. Because the sampled bats live in close proximity to humans, we discuss how concerning the presence of A. phagocytophilum DNA in bat guano is for humans frequenting places of worship that shelter bats. We also advocate future research to understand what a high faecal DNA prevalence in bat guano really implicates in terms of bacteria transmission.

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8

Baker-Austin, Craig, Rachel Rangdale, James Lowther, and David N. Lees. "Application of mitochondrial DNA analysis for microbial source tracking purposes in shellfish harvesting waters." Water Science and Technology 61, no. 1 (January 1, 2010): 1–7. http://dx.doi.org/10.2166/wst.2010.767.

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We present a method for the reliable detection and source characterisation of faecal pollution in water and shellfish matrices, utilising real-time PCR analysis of mitochondrial DNA targets. In this study we designed real-time PCR (TaqMan) probes to target human, bovine, ovine and swine mtDNA. PCR amplification using species-specific TaqMan probes on faecal matter and mixed effluent slurries revealed no cross-reactions between species of interest and other vertebrate faecal matter. Performed as a single blind experiment we were able to correctly identify faecal material in 17/20 effluents (85% correct). mtDNA degrades relatively quickly in faecally-spiked water samples (∼2 weeks), a similar timeframe of environmental persistence to several bacterial faecal indictors, highlighting its applicability. The procedure described here is specific, rapid (<5 hours) and sensitive. These results confirm the suitability of using species-specific mtDNA as an indicator in source tracking studies in surface waters, shellfish harvesting areas and shellfish matrices.

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9

Parsons, Kim M., John F. Dallas, Diane E. Claridge, John W. Durban, Kenneth C. Balcomb Iii, Paul M. Thompson, and Les R. Noble. "Amplifying dolphin mitochondrial DNA from faecal plumes." Molecular Ecology 8, no. 10 (October 1999): 1766–68. http://dx.doi.org/10.1046/j.1365-294x.1999.00723-8.x.

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10

MARCET, P. L., T. DUFFY, M. V. CARDINAL, J. M. BURGOS, M. A. LAURICELLA, M. J. LEVIN, U. KITRON, R. E. GÜRTLER, and A. G. SCHIJMAN. "PCR-based screening and lineage identification ofTrypanosoma cruzidirectly from faecal samples of triatomine bugs from northwestern Argentina." Parasitology 132, no. 1 (September 15, 2005): 57–65. http://dx.doi.org/10.1017/s0031182005008772.

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This study applied improved DNA extraction and polymerase chain reaction strategies for screening and identification ofTrypanosoma cruzilineages directly from faeces of triatomines collected in a well-defined rural area in northwestern Argentina. Amplification of the variable regions of the kinetoplastid minicircle genome (kDNA-PCR) was performed in faecal lysates from 33 microscope (MO)-positive and 93 MO-negativeTriatoma infestans, 2 MO-positive and 38 MO-negativeTriatoma guasayanaand 2 MO-positive and 73 MO-negativeTriatoma garciabesi. kDNA-PCR detectedT. cruziin 91% MO-positive and 7·5% MO-negativeT. infestans, which were confirmed by amplification of the minicircle conserved region. In contrast, kDNA-PCR was negative in all faecal samples from the other triatomine species. A panel of PCR-based genomic markers (intergenic region of spliced-leader DNA, 24Sα and 18S rRNA genes and A10 sequence) was implemented to identify the parasite lineages directly in DNA lysates from faeces and culture isolates from 28 infected specimens. Two were found to be infected with TCI, 24 with TCIIe, 1 with TCIId and 1 revealed a mixed TCI+TCII infection in the faecal sample whose corresponding culture only showed TCII, providing evidence of the advantages of direct typing of biological samples. This study provides an upgrade in the current diagnosis and lineage identification ofT. cruziin field-collected triatomines and showsT. cruziII strains as predominant in the region.

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11

Tende, Talatuxs, Bengt Hansson, Ulf Ottosson, and Staffan Bensch. "Evaluating preservation medium for the storage of DNA in African lion Panthera leo faecal samples." Current Zoology 60, no. 3 (June 1, 2014): 351–58. http://dx.doi.org/10.1093/czoolo/60.3.351.

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Abstract Lion faecal samples, collected in the field between 1 hour to 1 week after defecation were preserved in three different media (ethanol, ASL buffer and Two-step storage). The aim was to determine which faecal DNA field preservation method best enhances PCR amplification success. Samples stored in ethanol showed a significantly higher amplification success of microsatellite loci than samples stored in the other two media. In contrast, amplification success of a mitochondrial locus was similar among the samples stored in the three types of media. We reviewed twelve previous studies that employed different media for the storage of faeces, although patterns of success were not fully consistent among different media, ethanol storage was scored highest in the majority of these tests.

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12

Mancianti, Francesca, Simona Nardoni, Gaetano Ariti, Dario Parlanti, Giovanna Giuliani, and Roberto A. Papini. "Cross-sectional survey of Toxoplasma gondii infection in colony cats from urban Florence (Italy)." Journal of Feline Medicine and Surgery 12, no. 4 (April 2010): 351–54. http://dx.doi.org/10.1016/j.jfms.2009.09.001.

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Cats are the key species in the epidemiology of Toxoplasma gondii infection, even if the proportion of subjects excreting oocysts is low. The aim of the present paper was to obtain information about seroprevalence, oocyst shedding rate and presence of T gondii DNA in faeces collected from an urban population of colony cats in Florence (Tuscany). Fifty European shorthair feral cats were examined for anti- T gondii specific antibodies by a modified agglutination test (MAT), and for oocysts by microscopic examination and for faecal protozoal DNA, by means of a nested polymerase chain reaction (n-PCR) protocol. Twenty-two out of 50 serum samples (44%) were MAT positive. T gondii oocysts were not detected in any of the examined faecal samples. Eight out of 50 faecal specimens (16%) were n-PCR positive and sequencing of the bands was specific for T gondii. Detection by combination of the two methods was higher than single techniques and enhanced the detection of T gondii up to 48%. Our results suggest that the use of MAT plus PCR in faeces may be the best choice for diagnosis of feline toxoplasmosis. Further studies to ascertain the real infectivity of the copro-PCR positive subjects are required.

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13

Lee, Chang Soo, Jason W. Marion, and Jiyoung Lee. "A novel genetic marker for the rapid detection of Bacteroides fragilis in recreational water as a human-specific faecal indicator." Journal of Water and Health 9, no. 2 (April 25, 2011): 253–64. http://dx.doi.org/10.2166/wh.2011.120.

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Bacteroides spp. has gained substantial interest among the suggested potential candidates for alternative faecal indicators for untreated recreational waters by the US EPA. Interest in Bacteroides as a faecal indicator is based upon the relative abundance of selected members of the Bacteroides genus in the human colon and human faeces. In this study, we developed a real-time PCR detection system based on gyrase B subunit genes (gyrB) specific to Bacteroides fragilis. The gryB-based method was compared with previously described 16S rRNA-based real-time qPCR methods and evaluated for specificity, sensitivity and robustness in detecting B. fragilis from untreated recreational water impacted by human and non-human faecal sources. The new gyrB-based system only detected B. fragilis, whereas the 16S rRNA-based methods generated cross-amplifications with other Bacteroides and Prevotella species. We used a procedure of prefiltration, filtration, sonication and DNA concentration in order to improve the DNA extraction efficiency and the sensitivity of the real-time PCR while removing interference. The amplification and sequencing of PCR products generated by the gyrB-based method confirmed that gyrB-amplified sequences only contained B. fragilis. This rapid method is useful for quantifying faecal contamination and may assist beach and watershed managers in elucidating possible contamination sources.

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Edge, T. A., S. Hill, G. Stinson, P. Seto, and J. Marsalek. "Experience with the antibiotic resistance analysis and DNA fingerprinting in tracking faecal pollution at two lake beaches." Water Science and Technology 56, no. 11 (December 1, 2007): 51–58. http://dx.doi.org/10.2166/wst.2007.757.

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Posting or closing of swimming beaches because of faecal contamination is a widespread problem reported in many locations. In a risk-based approach to this problem, the risk to swimmers' health is assessed by field monitoring of indicator bacteria and the associated risks are managed by source controls and other remedial measures. In risk assessment, great advances have been made in recent years with the introduction of microbial source tracking (MST) techniques. Two such techniques, antibiotic resistance analysis and DNA fingerprinting, were applied in a study of causes of faecal contamination at two lake beaches in Toronto, Ontario. Both methods identified bird faeces as the dominant sources of E. coli. Coping with this type of pollution presents a major environmental challenge.

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15

Haag, Taiana, Anelisie S. Santos, Fernanda P. Valdez, Dênis A. Sana, Leandro Silveira, Laury Cullen, Carlos De Angelo, et al. "Molecular tracking of jaguar melanism using faecal DNA." Conservation Genetics 11, no. 3 (April 30, 2009): 1239–42. http://dx.doi.org/10.1007/s10592-009-9933-x.

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16

Wilson, G. J., A. C. Frantz, L. C. Pope, T. J. Roper, T. A. Burke, C. L. Cheeseman, and R. J. Delahay. "Estimation of badger abundance using faecal DNA typing." Journal of Applied Ecology 40, no. 4 (August 2003): 658–66. http://dx.doi.org/10.1046/j.1365-2664.2003.00835.x.

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17

FRANTZEN, M. A. J., J. B. SILK, J. W. H. FERGUSON, R. K. WAYNE, and M. H. KOHN. "Empirical evaluation of preservation methods for faecal DNA." Molecular Ecology 7, no. 10 (October 1998): 1423–28. http://dx.doi.org/10.1046/j.1365-294x.1998.00449.x.

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18

Dimitrov, Zh. "Assessment of lactobacillus bulgaricus strain in human intestinal samples by denaturation gradient gel electrophoresis." Trakia Journal of Sciences 17, no. 4 (2019): 312–17. http://dx.doi.org/10.15547/tjs.2019.04.003.

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PURPOSE. The purpose of this work was to evaluate the content of Lactobacillus bulgaricus in faecal samples of volunteers after consumption of yoghurt produced with selected L. bulgaricus strain. METHODS. Using Denaturation Gradient Gel Electrophoresis (DGGE) the DNA band corresponding to L. bulgaricus was well separated from the DNA bands of other lactobacilli. RESULTS. Faecal samples of all four volunteers consumed yoghurt contained a major DNA band indicating the presence of L. bulgaricus, unlike the faecal samples from the three volunteers no consumed yoghurt where the specific for L. bulgaricus DNA band was absent. The differences in the intensity of the electrophoretic band of L. bulgaricus are influenced by the individuality of the volunteers and the duration of yoghurt consumption. By help of DGGE it was possible to assay the presence of L. bulgaricus in faecal samples and on the base of the intensity of the specific DNA fragment to evaluate the dynamics of L. bulgaricus content during 10 days consumption of yoghurt. CONCLUSIONS. DGGE proved to be an applicable tool to monitor the presence of L. bulgaricus strains in human intestinal samples.

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19

Naser, Sabri M., Marc Vancanneyt, Evelyne De Graef, Luc A. Devriese, Cindy Snauwaert, Karen Lefebvre, Bart Hoste, et al. "Enterococcus canintestini sp. nov., from faecal samples of healthy dogs." International Journal of Systematic and Evolutionary Microbiology 55, no. 5 (September 1, 2005): 2177–82. http://dx.doi.org/10.1099/ijs.0.63752-0.

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The taxonomic position of strain LMG 13590T, originally isolated from dog faeces and classified as Enterococcus dispar in the BCCM/LMG Bacteria Catalogue, was reinvestigated. This strain and 12 recent isolates from faecal samples of healthy dogs occupied a clearly separate position when investigated with multilocus sequence analysis (MLSA) of the genes encoding the alpha subunit of ATP synthase (atpA), RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase alpha subunit (pheS). The 16S rRNA gene sequence of one representative strain showed highest similarities of 98–99 % with E. dispar LMG 13521T, Enterococcus canis LMG 12316T and Enterococcus asini LMG 18727T. A further polyphasic taxonomic study based on whole-cell protein fingerprinting, DNA–DNA hybridization and biochemical features demonstrated that the 13 enterococcal dog faecal strains represent a single, novel Enterococcus species for which the name Enterococcus canintestini sp. nov. is proposed. The type strain is LMG 13590T (=CCM 7285T).

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20

Meier, H., C. Koob, W. Ludwig, R. Amann, E. Frahm, S. Hoffmann, U. Obst, and K. H. Schleifer. "Detection of enterococci with rRNA targeted DNA probes and their use for hygienic drinking water control." Water Science and Technology 35, no. 11-12 (June 1, 1997): 437–44. http://dx.doi.org/10.2166/wst.1997.0774.

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Enterococci are useful indicators of faecal contamination with their high abundance in faeces and long survival in the environment and the possibility of indicating the source of contamination by species identification has lead to discussion of whether enterococci would be more reliable faecal indicators than E. coli. In an attempt to facilitate rapid and accurate identification of enterococci, 16S rRNA targeted oligonucleotide probes were designed by computer-aided analysis of more than 4,000 rRNA sequences. Probes were labelled non-isotopically with digoxigenin and fluorescent dyes. Conditions for specific hybridisation were optimised for dot blot hybridisation and whole cell hybridisation for all probes. With a combination of two probes, all hygienically important enterococci could be detected and 24 biochemically identified environmental isolates also hybridised with one of these probes. A quantitative detection method with a high sensitivity was developed based on filtration of water samples through polycarbonate filters, a short incubation on agar and microcolony filter hybridisation with fluorescently labelled probes followed by epifluorescence microscopy. Within 8–20h sampling a specific identification of enterococcal microcolonies was possible. With this method 15/32 well- and tap-water sources from the Mainz area were identified as being of substandard quality. The proposed method detects faecal contamination significantly earlier than conventional methods and could be helpful in the hygienic monitoring of drinking water.

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Redd, K. S., S. N. Jarman, S. D. Frusher, and C. R. Johnson. "A molecular approach to identify prey of the southern rock lobster." Bulletin of Entomological Research 98, no. 3 (April 28, 2008): 233–38. http://dx.doi.org/10.1017/s0007485308005981.

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AbstractWe demonstrate the use of molecular techniques to detect specific prey consumed by the southern rock lobster (Jasus edwardsii). A quick and non-lethal method was used to collect rock lobster faecal material and a molecular protocol was employed to isolate prey DNA from faecal samples. The isolated DNA was amplified using the polymerase chain reaction (PCR) with PCR primers designed to target specific prey items. Feeding experiments determined that DNA from black-lipped abalone (Haliotis rubra) and sea urchins (Centrostephanus rodgersii and Heliocidaris erythrogramma) can be detected in rock lobster faecal samples within seven hours and remains present for up to 60 h after ingestion.

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Hooda, Seema, Brittany M. Vester Boler, Katherine R. Kerr, Scot E. Dowd, and Kelly S. Swanson. "The gut microbiome of kittens is affected by dietary protein:carbohydrate ratio and associated with blood metabolite and hormone concentrations." British Journal of Nutrition 109, no. 9 (August 31, 2012): 1637–46. http://dx.doi.org/10.1017/s0007114512003479.

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High-protein, low-carbohydrate (HPLC) diets are common in cats, but their effect on the gut microbiome has been ignored. The present study was conducted to test the effects of dietary protein:carbohydrate ratio on the gut microbiota of growing kittens. Male domestic shorthair kittens were raised by mothers fed moderate-protein, moderate-carbohydrate (MPMC; n 7) or HPLC (n 7) diets, and then weaned at 8 weeks onto the same diet. Fresh faeces were collected at 8, 12 and 16 weeks; DNA was extracted, followed by amplification of the V4–V6 region of the 16S rRNA gene using 454 pyrosequencing. A total of 384 588 sequences (average of 9374 per sample) were generated. Dual hierarchical clustering indicated distinct clustering based on the protein:carbohydrate ratio regardless of age. The protein:carbohydrate ratio affected faecal bacteria. Faecal Actinobacteria were greater (P< 0·05) and Fusobacteria were lower (P< 0·05) in MPMC-fed kittens. Faecal Clostridium, Faecalibacterium, Ruminococcus, Blautia and Eubacterium were greater (P< 0·05) in HPLC-fed kittens, while Dialister, Acidaminococcus, Bifidobacterium, Megasphaera and Mitsuokella were greater (P< 0·05) in MPMC-fed kittens. Principal component analysis of faecal bacteria and blood metabolites and hormones resulted in distinct clusters. Of particular interest was the clustering of blood TAG with faecal Clostridiaceae, Eubacteriaceae, Ruminococcaceae, Fusobacteriaceae and Lachnospiraceae; blood ghrelin with faecal Coriobacteriaceae, Bifidobacteriaceae and Veillonellaceae; and blood glucose, cholesterol and leptin with faecal Lactobacillaceae. The present results demonstrate that the protein:carbohydrate ratio affects the faecal microbiome, and highlight the associations between faecal microbes and circulating hormones and metabolites that may be important in terms of satiety and host metabolism.

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Bowles, Ella, and Andrew W. Trites. "Faecal DNA amplification in Pacific walruses (Odobenus rosmarus divergens)." Polar Biology 36, no. 5 (March 21, 2013): 755–59. http://dx.doi.org/10.1007/s00300-013-1296-6.

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Rochet, Violaine, Lionel Rigottier-Gois, Maléne Sutren, Marie-Noëlle Krementscki, Claude Andrieux, Jean-Pierre Furet, Patrick Tailliez, et al. "Effects of orally administeredLactobacillus caseiDN-114 001 on the composition or activities of the dominant faecal microbiota in healthy humans." British Journal of Nutrition 95, no. 2 (February 2006): 421–29. http://dx.doi.org/10.1079/bjn20051625.

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The composition and activities of the faecal microbiota in twelve healthy subjects analysed in a single open study were monitored before (1-week baseline step), during (10d supplementation step) and after (10d follow-up step) the ingestion of a fermented milk containingLactobacillus caseiDN-114001. Fluorescentin situhybridisation with group-specific DNA probes, real-time PCR usingL. paracaseigroup-specific primers and temporal temperature gradient gel electrophoresis (TTGE) using group-specific primers were carried out, together with bacterial enzyme activity and metabolite analyses to monitor the structure and activities of the faecal microbiota.L. caseiDNA was detected in the faeces of all of the subjects by TTGE after 10d supplementation. Its quantification by real-time PCR showed a 1000-fold increase during the test step compared with initial levels. No major modification in either the dominant members of the faecal microbiota or their activities was observed during the trial. In conclusion, the short-term consumption of a milk product containingL. caseiDN-114001 was accompanied by a high, transient increase in the quantity of this strain in the faeces of all of the subjects without markedly affecting biochemical or bacteriological factors.

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Starkey, Bryan J. "Screening for colorectal cancer." Annals of Clinical Biochemistry: International Journal of Laboratory Medicine 39, no. 4 (July 1, 2002): 351–65. http://dx.doi.org/10.1258/000456302760042470.

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Colorectal cancer (CRC) causes 20 000 deaths per annum in the UK alone. Screening has been shown to reduce mortality but debate exists as to which approach to use. Direct visualization of the colorectum has the advantage that it detects lesions most effectively and is required at less frequent intervals, but the procedure is invasive and at present too costly for screening purposes. Faecal occult blood measurement, despite its limitations, is currently the recommended screening method, with follow-up of positive tests by colonoscopy or other visualization techniques. This strategy has been shown to reduce mortality from CRC by about 20% and screening trials directed towards individuals in the over 50 years age group are underway in the UK and elsewhere. Future developments in CRC screening include colorectal visualization by computed colonography - a less-invasive alternative to colonoscopy. Developments in stool analysis are also occurring. Examination of faecal samples for cellular products derived from neoplasms (e.g. calprotectin) may prove more sensitive and specific than faecal occult blood measurements. In addition, detection of altered DNA in faeces is being investigated by molecular biology techniques. Using a multi-target assay panel to detect point mutations and other neoplasia-associated DNA abnormalities may be an effective strategy for CRC screening in the future.

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Nowland, Tanya L., Valeria A. Torok, Wai Y. Low, Mary D. Barton, Kate J. Plush, and Roy N. Kirkwood. "Faecal Microbiota Analysis of Piglets During Lactation." Animals 10, no. 5 (April 27, 2020): 762. http://dx.doi.org/10.3390/ani10050762.

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Antimicrobial use in animals and the potential development of antimicrobial resistance is a global concern. So, non-antimicrobial techniques for animal disease control are needed. This study aimed to determine whether neonatal ceftiofur (CF) treatment affects piglet faecal microbiomes and whether faecal microbiome transplantation (FMT) can correct it. Two focal piglets per sow were assigned to treatments as follows: cffresh (n = 6) received CF (3 mg/kg intramuscular) at 7 d and fresh FMT at 13 d; cffrozen (n = 7) received CF at 7 d and frozen FMT at 13 d; CF (n = 8) received CF at 7 d and no FMT; and no CF (n = 5) received no CF or FMT. DNA was extracted from faecal samples collected on days 7, 13, and 18 for 16S rRNA amplicon analysis. All faecal blends used for the FMT consisted of pooled donor pig faeces at 1:2 ratio with saline, delivered orally at 3 mL/kg. Alpha and beta diversity metrics increased with age (p < 0.05). However, no effect of antibiotic or FMT treatment was evident in 13 and 18 d old piglets (p > 0.05). Although no effect of treatment was observed, information regarding microbial membership during lactation was gained.

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Young, Melanie J., Ludovic Dutoit, Fiona Robertson, Yolanda van Heezik, Philip J. Seddon, and Bruce C. Robertson. "Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin." Wildlife Research 47, no. 6 (2020): 509. http://dx.doi.org/10.1071/wr19246.

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Abstract Context. Diet variability is a significant driver of seabird decline; however, data on seabird diet composition and trends have been affected by changes in precision and resolution owing to the evolution of different sampling methods over time. We investigated the effectiveness of applying a passive molecular diet method using faeces obtained from the endangered yellow-eyed penguin. Aims. To assess the feasibility of applying DNA metabarcoding methods to yellow-eyed penguin faeces to evaluate diet, and to compare the reliability of diet results derived from adults and chicks, and from latrine versus fresh faecal samples. Methods. We collected 313 faecal samples from yellow-eyed penguins resident on the Otago coast of New Zealand from October 2016 to August 2017. We used polymerase chain reaction (PCR) with mitochondrial 16S cephalopod and chordate primers to amplify prey DNA present in the faecal samples, and tested the completeness of our assembled reference databases based on previous diet research. Amplified prey DNA sequences were then assigned to taxa from our reference databases by using QIIME2. Key results. Mitochondrial 16S chordate PCR primers were effective at identifying 29 fish taxa, with 98.3% of amplified sequences being identified to species or genus level in 193 samples (61.7% collected). There was no significant difference in the number, occurrence or proportion of ray-finned fish prey DNA sequences derived from fresh samples or latrines. Mitochondrial 16S cephalopod PCR primers classified 1.98% of amplified DNA sequences as targets, with 96.5% of these target sequences being identified to species or genus level in 48 samples (15.3% collected), and five taxa identified. Conclusions. We recommend the collection of latrine samples to enable long-term monitoring of the diet of yellow-eyed penguins, which will optimise the trade-off between wildlife disturbance and dietary resolution. Further refinement is needed to identify cephalopod dietary components for yellow-eyed penguins, because our cephalopod primers were not as specific as those used for ray-finned fishes, amplifying a large number (>98%) of non-cephalopod species. Implications. DNA metabarcoding offers a robust and comprehensive alternative to other, more intrusive, seabird diet-assessment methods, but still requires parallel studies to provide critical information on prey size, true diet composition and diet quality.

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Chiriboga, Adriana E. C. Nascimento, Walter V. Guimarães, Maria Cristina D. Vanetti, and Elza F. Araújo. "Detection ofLawsonia intracellularisin faeces of swine from the main producing regions in Brazil." Canadian Journal of Microbiology 45, no. 3 (March 1, 1999): 230–34. http://dx.doi.org/10.1139/w98-234.

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Swine proliferative enteropathy is an enteric disease caused by Lawsonia intracellularis which affects animals between 6 and 20 weeks of age, causing diarrhea, anorexia, and poor growth. The presence of L. intracellularis was evaluated in the faecal samples of 636 swine from 75 randomly chosen herds in the main swine-producing regions of Brazil. The pathogen was detected by the polymerase chain reaction method (PCR) using L. intracellularis specific primers. A 319-bp DNA fragment specific for L. intracellularis was produced on amplification of DNA from the faeces of pigs with proliferative enteropathy. Equal amounts of DNA extracted from the faeces of animals from the same herd were pooled together and, once L. intracellularis was detected, the faecal material of each animal was analyzed separately. The incidence of L. intracellularis was 33.4% in the state of Santa Catarina, 29.4% in Paraná, 26.3% in Minas Gerais, 16.7% in Mato Grosso, and 7.1% in São Paulo. The presence of the pathogenic agent was detected in samples from 15 farms, representing a total incidence of 20%. Although 46 animals (7.2%) were shown to be infected, 11% did not present any symptoms of swine proliferative enteropathy. The use of PCR allowed the detection of L. intracellularis in swine farms and the evaluation of the incidence of proliferative enteropathy in different regions of Brazil.Key words: proliferative enteropathy, diagnosis, Lawsonia intracellularis, PCR, incidence.

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Husakova, Marketa, Petr Kralik, Vladimir Babak, and Iva Slana. "Efficiency of DNA Isolation Methods Based on Silica Columns and Magnetic Separation Tested for the Detection of Mycobacterium avium Subsp. Paratuberculosis in Milk and Faeces." Materials 13, no. 22 (November 12, 2020): 5112. http://dx.doi.org/10.3390/ma13225112.

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Timely and reliable detection of animals shedding Mycobacterium avium subsp. paratuberculosis (MAP) should help to effectively identify infected animals and limit infection transmission at early stages to ensure effective control of paratuberculosis. The aim of the study was to compare DNA extraction methods and evaluate isolation efficiency using milk and faecal samples artificially contaminated by MAP with a focus on modern instrumental automatic DNA isolation procedures based on magnetic separation. In parallel, an automatic and manual version of magnetic separation and two methods of faecal samples preparation were compared. Commercially available DNA isolation kits were evaluated, and the selected kits were used in a trial of automatic magnetic beads-based isolation and compared with the manual version of each kit. Detection of the single copy element F57 was performed by qPCR to quantify MAP and determine the isolation efficiency. The evaluated kits showed significant differences in DNA isolation efficiencies. The best results were observed with the silica column Blood and Tissue kit for milk and Zymo Research for faeces. The highest isolation efficiency for magnetic separation was achieved with MagMAX for both matrices. The magnetic separation and silica column isolation methods used in this study represent frequently used methods in mycobacterial diagnostics.

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Meekan, M. G., S. N. Jarman, C. McLean, and M. B. Schultz. "DNA evidence of whale sharks (Rhincodon typus) feeding on red crab (Gecarcoidea natalis) larvae at Christmas Island, Australia." Marine and Freshwater Research 60, no. 6 (2009): 607. http://dx.doi.org/10.1071/mf08254.

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Whale sharks (Rhincodon typus) are thought to aggregate in nearshore waters around Christmas Island (105°37′E, 10o29′S) to consume the marine larvae of the endemic red land crab (Gecarcoidea natalis). However, there have been no direct observations of sharks feeding on crab larvae. Whale shark faeces were analysed using genetic testing to confirm the presence of crab larvae in their diet. Primers were designed for amplifying two Gecarcoidea natalis mitochondrial small-subunit (mtSSU) rDNA regions. Gel electrophoresis of polymerase chain reaction (PCR) products amplified from whale shark faecal DNA produced bands of the expected size for G. natalis templates. Specificity of both primer sets for G. natalis mtSSU rDNA was expected to be high from comparisons with mtSSU rDNA regions from closely related crabs and we confirmed their specificity empirically. The amplification of fragments from faecal DNA of the same size as those produced from G. natalis DNA indicates that the whale shark had been feeding on G. natalis and that enough of the crab DNA survived digestion to be detected by these PCRs. Our study provides further evidence that aggregations of whale sharks in coastal waters occur in response to ephemeral but predictable increases in planktonic prey.

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Wu, Wen-Tzu, Han-Chung Cheng та Hsiao-Ling Chen. "Ameliorative effects of konjac glucomannan on human faecal β-glucuronidase activity, secondary bile acid levels and faecal water toxicity towards Caco-2 cells". British Journal of Nutrition 105, № 4 (10 грудня 2010): 593–600. http://dx.doi.org/10.1017/s0007114510004009.

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Konjac glucomannan (KGM) has been shown to increase human colon microbial ecology and reduce faecal toxicity in mice. The main goal of the present study was to assess the effects of a KGM supplement into a low-fibre diet on precancerous markers of colon cancer in a double-blind, placebo- and diet-controlled study. Adult volunteers consumed defined diets supplemented with konjac (4·5 g/d) or placebo (maize starch) for 4 weeks. Stools collected before and at the end of the supplementation were analysed for β-glucosidase, β-galactosidase and β-glucuronidase activities, microflora and bile acids. Faecal water was co-incubated with Caco-2 cells, a model of human colonocytes, to determine the cytotoxicity and DNA-damaging effect as assessed by the comet assay. The results indicated that the KGM supplement significantly decreased faecal β-glucuronidase activity by 25·6 (se7·8) % and faecal secondary bile acid level by 42·4 (se11·8) %. In contrast, consuming the defined diet supplemented with placebo for 4 weeks did not improve these determinants. The KGM-supplemented diet, but not the placebo diet, significantly increased the survival rate (%) of Caco-2 cells co-incubated with faecal water for 1 and 3 h, respectively. In addition, KGM significantly reduced the DNA damage induced by the faecal water alone or in combination with H2O2. The faecal bifidobacteria and lactobacilli levels increased only with the KGM-supplemented diet. Therefore, we conclude that supplementation of KGM into a low-fibre diet improved the faecal microbial ecology and metabolites, which may contribute to the reduced toxicity of faecal water and precancerous risk factors of human colon cancer.

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Osaki, Takako, Masumi Okuda, Junko Ueda, Mutsuko Konno, Hideo Yonezawa, Fuhito Hojo, Kiyoko Yagyu, et al. "Multilocus sequence typing of DNA from faecal specimens for the analysis of intra-familial transmission of Helicobacter pylori." Journal of Medical Microbiology 62, no. 5 (May 1, 2013): 761–65. http://dx.doi.org/10.1099/jmm.0.053140-0.

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This study used multilocus sequence typing (MLST) of total DNA extracted from faecal specimens to genotype Helicobacter pylori to analyse intra-familial transmission. Faecal DNA was extracted and amplified by nested PCR. The products were analysed by direct sequencing and the allele type was determined using an MLST website. Mother-to-child transmission was suspected in at least two of three families, and father-to-child transmission was suspected in one family.

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Ghaly, Simon, Nadeem Kaakoush, Frances Lloyd, Lavinia Gordon, Cynthia Forest, Ian Lawrance, and Prue Hart. "Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice." Nutrients 10, no. 8 (August 11, 2018): 1069. http://dx.doi.org/10.3390/nu10081069.

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Reduced sunlight exposure has been associated with an increased incidence of Crohn’s disease and ulcerative colitis. The effect of ultraviolet radiation (UVR) on the faecal microbiome and susceptibility to colitis has not been explored. C57Bl/6 female mice were fed three different vitamin D-containing diets for 24 days before half of the mice in each group were UV-irradiated (1 kJ/m2) for each of four days, followed by twice-weekly irradiation of shaved dorsal skin for 35 days. Faecal DNA was extracted and high-throughput sequencing of the 16S RNA gene performed. UV irradiation of skin was associated with a significant change in the beta-diversity of faeces compared to nonirradiated mice, independently of vitamin D. Specifically, members of phylum Firmicutes, including Coprococcus, were enriched, whereas members of phylum Bacteroidetes, such as Bacteroidales, were depleted. Expression of colonic CYP27B1 increased by four-fold and IL1β decreased by five-fold, suggesting a UVR-induced anti-inflammatory effect. UV-irradiated mice, however, were not protected against colitis induced by dextran sodium sulfate (DSS), although distinct faecal microbiome differences were documented post-DSS between UV-irradiated and nonirradiated mice. Thus, skin exposure to UVR alters the faecal microbiome, and further investigations to explore the implications of this in health and disease are warranted.

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Piggott, Maxine P., Rebecca Wilson, Sam C. Banks, Clive A. Marks, Frank Gigliotti, and Andrea C. Taylor. "Evaluating exotic predator control programs using non-invasive genetic tagging." Wildlife Research 35, no. 7 (2008): 617. http://dx.doi.org/10.1071/wr08040.

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Carnivorous predators are difficult to detect using conventional survey methods, especially at low levels of abundance. The introduced red fox (Vulpes vulpes) in Australia is monitored to determine the effectiveness of control programs, but assessing population parameters such as abundance and recruitment is difficult. We carried out a feasibility study to determine the effectiveness of using faecal DNA analysis methods to identify individual foxes and to assess abundance before and after lethal control. Fox faeces were collected in two sampling periods over four separate transects, and genotyped at five microsatellite loci. Two transects were subject to lethal control between collection periods. DNA was extracted from 170 fox faeces and, in total, 54 unique genotypes were identified. Fifteen biopsy genotypes from 30 foxes killed during lethal control were detected among the faecal genotypes. Overall, a similar number of genotypes were detected in both sampling periods. The number of individuals sampled in both periods was low (n = 6) and new individuals (n = 24) were detected in the second collection period. We were also able to detect animals that avoided lethal control, and movement of individuals between transects. The ability to identify individual foxes using these DNA techniques highlighted the shortcomings of the sample design, in particular the spatial scale and distances between transects. This study shows that non-invasive DNA sampling can provide valuable insight into pre and post fox abundance in relation to lethal control, individual behaviour and movement, as well as sample design. The information gained from this study will contribute to the design of future studies and, ultimately, control strategies.

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Smith, Steve, Peter McRae, and Jane Hughes. "Faecal DNA analysis enables genetic monitoring of the species recovery program for an arid-dwelling marsupial." Australian Journal of Zoology 57, no. 2 (2009): 139. http://dx.doi.org/10.1071/zo09035.

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The greater bilby, Macrotis lagotis, is a species of conservation significance in the arid and semiarid zones of Australia. A species recovery program has been underway since the mid-1990s but the incorporation of molecular genetic data within the program has been difficult due to the problems of obtaining regular, population-wide samples of this trap-shy and sparsely distributed species. In this study, we demonstrate that faecal pellets collected from around burrows in the dry, arid habitat of western Queensland provide a viable source for DNA extraction and analysis. Faecal DNA was used to generate population-level estimates of microsatellite and mtDNA diversity for comparison with previous estimates for the natural population derived from tissue samples. Data were used to assess both the reliability of faecal-derived genotypes and the extent of any diversity loss since the previous study. Microsatellite diversity recorded from eight polymorphic markers for the natural population (A = 4.31 ± 0.30, HE = 0.76 ± 0.03) was comparable with the previous study, indicating little change in genetic diversity for the natural population in the 10-year interim. Faecal genotypes generated for the recently reintroduced population matched the known number of founders as well as a known genotype, providing support for the reliability of the faecal DNA approach. The captive and reintroduced populations had significantly lower diversity levels than the natural population (A = 3.59 ± 0.28, HE = 0.68 ± 0.03; A = 3.57 ± 0.20, HE = 0.65 ± 0.03 respectively). Mitochondrial control region analysis, incorporating nested clade phylogeographic analysis (NCPA), agrees with earlier findings that populations of bilbies across the arid zone in Australia have only recently become fragmented, but the case for Queensland bilbies being strongly differentiated from other regions is diminished. Implications from this study include the need to further supplement the captive and reintroduced populations with additional out-bred individuals and that faecal DNA can be used effectively for ongoing monitoring and management of this species.

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Faridi, F., D. Suchitra Sena, and V. Sharma. "Comparative evaluation of faecal community DNA isolation methods in camels." Journal of Camel Practice and Research 21, no. 2 (2014): 183. http://dx.doi.org/10.5958/2277-8934.2014.00031.9.

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37

Traverso, Giovanni, Anthony Shuber, Louise Olsson, Bernard Levin, Constance Johnson, Stanley R. Hamilton, Kevin Boynton, Kenneth W. Kinzler, and Bert Vogelstein. "Detection of proximal colorectal cancers through analysis of faecal DNA." Lancet 359, no. 9304 (February 2002): 403–4. http://dx.doi.org/10.1016/s0140-6736(02)07591-8.

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Eggert, Lori S., Gareth Patterson, and Jesús E. Maldonado. "The Knysna elephants: a population study conducted using faecal DNA." African Journal of Ecology 46, no. 1 (March 2008): 19–23. http://dx.doi.org/10.1111/j.1365-2028.2007.00794.x.

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Piggott, Maxine P., and Andrea C. Taylor. "Extensive evaluation of faecal preservation and DNA extraction methods in Australian native and introduced species." Australian Journal of Zoology 51, no. 4 (2003): 341. http://dx.doi.org/10.1071/zo03012.

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We evaluated and compared sixteen combinations of commonly used storage and extraction methods for faecal DNA from two Australian marsupial herbivores, two marsupial carnivores and an introduced carnivorous mammal. For all species the highest amplification and lowest genotyping error rates were achieved using dried faeces extracted via a surface wash followed by spin column purification. The highest error rates were seen in the two Dasyurus spp. and the lowest in Vulpes vulpes. The rates observed for each species were incorporated into computer simulations to identify the number of PCR replicates required to achieve accurate genotyping of DNA isolated via the optimised protocol. Three replicates per sample were sufficient for V. vulpes, Thylogale billardierii and Petrogale penicillata. However, further replicates may be required for marsupial carnivores, as their faeces yielded DNA that amplified substantially less often and less reliably, for all preservation and extraction methods tested, than did the other species. Although pilot studies remain vital for evaluating the feasibility of non-invasive sampling prior to undertaking any in-depth study the availability of a thoroughly tested storage and DNA extraction combination protocol known to be optimal for five different species should make that process much simpler.

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Bergmann, Michèle, Stephanie Schwertler, Stephanie Speck, Uwe Truyen, Sven Reese, and Katrin Hartmann. "Faecal shedding of parvovirus deoxyribonucleic acid following modified live feline panleucopenia virus vaccination in healthy cats." Veterinary Record 185, no. 3 (April 30, 2019): 83. http://dx.doi.org/10.1136/vr.104661.

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Positive canine parvovirus (CPV) faecal test results have been reported in dogs after modified live virus (MLV) vaccination. Thus, the aim was to investigate feline panleucopenia virus (FPV) shedding in recently vaccinated, adult, clinically healthy cats and to assess related factors. Forty cats were vaccinated with an FPV MLV vaccine. Faeces of cats were tested for presence of parvovirus DNA on days 7, 14, 21 and 28 by quantitative real-time PCR; DNA-positive samples were subjected to partial VP2 gene sequencing. Virus isolation was performed whenever sufficient amounts of faeces were available. Serum antibody titres were measured by haemagglutination inhibition on days 0, 7 and 28. Overall, 30.0 per cent (12/40; 95% CI 18.0 to 45.6) of cats shed parvovirus DNA. Sequencing revealed FPV vaccine virus DNA in three cats, FPV field virus DNA in four cats and CPV field virus DNA in one cat. Shedding was significantly associated with lack of prevaccination antibody titres (40) (P=0.016; OR: 6.44; 95% CI 1.44 to 28.89) and with postvaccination titre increases (fourfold) (P=0.029; OR: 5.00; 95% CI 1.17 to 21.39). Shedding of field or vaccine virus DNA seems to be common in healthy cats which can be a concern in shelters and catteries. Diagnostic tools should be developed to facilitate differentiation of vaccine and field virus shedding.

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Rosellini, Stefano, Enrique Osorio, Aritz Ruiz-González, Ana Piñeiro, and Isabel Barja. "Monitoring the small-scale distribution of sympatric European pine martens (Martes martes) and stone martens (Martes foina): a multievidence approach using faecal DNA analysis and camera-traps." Wildlife Research 35, no. 5 (2008): 434. http://dx.doi.org/10.1071/wr07030.

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The European pine marten (Martes martes) and stone marten (Martes foina) are two closely related mustelids that live sympatrically over a large area of Europe. In the northern Iberian Peninsula, the distribution ranges of both species overlap extensively. The objectives of this study were (1) to verify whether, on a small scale, both species also live sympatrically and (2) to compare camera traps and scat DNA as methods for detecting marten species. The study was conducted in a protected area (province of Ourense, north-west Spain), which covers 6700 ha. To test the sympatry hypothesis, 90 fresh faecal samples, identified as faeces of genus Martes on the basis of their morphology, were collected from June 2004 to August 2006. The specific identification of faecal samples was conducted using polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) techniques. In addition, 20 camera-traps (916 camera-trap-nights) were in operation during the study period. Of the faecal samples collected, 88.8% were attributed to the European pine marten, while the remaining 11.2% were not amplified by PCR and thus could not be assigned. The European pine marten was identified in 57.9% of the photos of carnivores and the stone marten was not detected in any. The faecal DNA analysis and camera-trap results supported previous conclusions about habitat preferences and the distribution of the two species obtained using other methods. The two non-invasive methods that were used in this study were shown to be reliable techniques that can be employed simultaneously, because each method has advantages and disadvantages that are influenced by the size of the area inventoried, sampling effort, and cost and efficiency of the method. The data gathered using these methods provided important information on the understanding of trophic and competitive interactions between the species.

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Berry, Oliver, Stephen D. Sarre, Lachlan Farrington, and Nicola Aitken. "Faecal DNA detection of invasive species: the case of feral foxes in Tasmania." Wildlife Research 34, no. 1 (2007): 1. http://dx.doi.org/10.1071/wr06082.

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Анотація:

Early detection of biological invasions is critical to reducing their impact, but because invading organisms are initially at low densities, detection and eradication can be challenging. Here, we demonstrate the utility of faecal DNA analysis for the detection of an elusive invasive species – the red fox, Vulpes vulpes, which was illegally introduced to the island of Tasmania in the late 1990s. Foxes are a devastating pest to both wildlife and agriculture on the Australian mainland, and would have a similarly serious impact in Tasmania if they became established. Attempts to eradicate foxes from Tasmania have been hampered by unreliable distribution data derived mostly from public sightings. In response, we developed a highly accurate and reliable DNA-based PCR-multiplex test that identifies foxes from field-collected faeces. We also developed a sexing test, but it was reliable only for faeces less than three weeks old. Faeces are a useful target for DNA-based diagnostics in foxes because they are deposited in prominent locations and are long-lasting. The species identification test formed a key component of a Tasmania-wide detection and eradication program. In all, 1160 geo-referenced carnivore scats were analysed; of these, 78% contained DNA of sufficient quality for species identification. A single scat from the north-east of the island was identified as belonging to fox, as was a nine-week-old roadkill carcass from the north coast, and a blood sample from near Hobart, triggering increased control and surveillance in these regions. The accuracy, reliability, and cost-effectiveness of non-invasive tests make them a critical adjunct to traditional tools for monitoring cryptic invasive species that are at low density in the early stages of invasion and when eradication is still an option.

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43

HUNG, G. C., R. B. GASSER, I. BEVERIDGE, and N. B. CHILTON. "Species-specific amplification by PCR of ribosomal DNA from some equine strongyles." Parasitology 119, no. 1 (July 1999): 69–80. http://dx.doi.org/10.1017/s0031182099004497.

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The first and second internal transcribed spacer sequences of 28 morphologically-defined species of horse strongyle were characterized, and specific oligonucleotide primers were designed for some species based on the nucleotide differences. Utilizing these primers, a PCR approach was developed for the specific amplification of ribosomal DNA of Strongylus vulgaris, Cyathostomum catinatum, Cylicocyclus nassatus, Cylicostephanus longibursatus or Cylicostephanus goldi. The method allowed the species-specific amplification of parasite DNA derived from faecal samples and/or copro-cultures, demonstrating the potential of the approach for the diagnosis of equine strongyloidosis. The establishment of this PCR assay also has implications for studying the biology and epidemiology of equine strongyles and anthelmintic resistance using faecal egg count reduction tests.

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Yan, HongBin, XinWen Bo, Youyu Liu, Zhongzi Lou, XingWei Ni, WanGui Shi, Fang Zhan, HongKean Ooi, and WanZhong Jia. "Differential diagnosis of Moniezia benedeni and M. expansa (Anoplocephalidae) by PCR using markers in small ribosomal DNA (18S rDNA)." Acta Veterinaria Hungarica 61, no. 4 (December 1, 2013): 463–72. http://dx.doi.org/10.1556/avet.2013.035.

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Moniezia benedeniandM. expansaare common ruminant tapeworms of worldwide distribution, causing gastrointestinal disorders and even death in sheep and goats. In this study, a polymerase chain reaction- (PCR-) based approach for precise species identification was developed and also applied to faecal DNA diagnosis of the tapeworm infection. Since nuclear ribosomal DNA (rDNA) appears to be a useful target for species and/or strain markers, the 18S regions of the rDNA ofM. benedeniandM. expansawere amplified and sequenced. The lengths and GC contents of the regions sequenced were 2476–2487 bp and 51.9–52.1% forM. benedeniand 2473 bp and 51.9–52.0% forM. expansa, respectively. Alignment and comparison of the 18S sequences of the two species showed 92.5–93.3% homology. No matches for the 18S regions ofM. benedeniandM. expansawere found with other species by BLAST search, which made the 18S sequences appropriate markers for the design of distinctive primers for the twoMonieziaspecies. Our 18S-based PCR could detect as low levels as 0.5 pg genomic DNA or the DNA extracted from 0.2 g faecal sample collected from the rectum of anM. expansa-infected goat. The results indicate that this PCR approach is a reliable alternative for the differential diagnosis ofMonieziaspecies in faecal samples.

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Vierheilig, J., D. Savio, R. E. Ley, R. L. Mach, A. H. Farnleitner, and G. H. Reischer. "Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring." Water Science and Technology 72, no. 11 (August 10, 2015): 1962–72. http://dx.doi.org/10.2166/wst.2015.407.

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The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multi-compartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems.

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46

Mathis, A., P. Deplazes, and J. Eckert. "An improved test system for PCR-based specific detection ofEchinococcus multiloculariseggs." Journal of Helminthology 70, no. 3 (September 1996): 219–22. http://dx.doi.org/10.1017/s0022149x00015443.

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AbstractFor the sensitive detection of eggs ofEchinococcus multilocularisin fox faeces by PCR we have evaluated a method based on the previous concentration of helminth eggs by a combination of sequential sieving of faecal samples and flotation of the eggs in zinc chloride solution. The eggs were microscopically detected in the fractions retained in 40 and 20µm mesh sieves. DNA of the taeniid eggs retained in the 20 µm sieve was obtained after alkaline lysis and PCR was performed usingE. multilocularisspecies-specific primers. Compared to the parasitological findings after examination of the small intestines of the foxes, the specificity of the PCR was 100% (no false-positive result with 20 foxes free ofE. multilocularis) and the sensitivity was 94% (33 positive results from total 35 foxes proven to be infected withE. multilocularis). Both false-negative results were obtained with faeces from foxes harbouring immature worms. Using faecal volumes between 2 and 20 ml, no inhibition of PCR was observed as was demonstrated by the amplification of size-modified target in parallel reactions. The tests were undertaken with fresh faeces stored in 70% ethanol, but egg detection by PCR was also possible after inactivation of eggs by freezing the faeces at −80°C for one week or by incubation at +70°C for 2 h.

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47

Slinger, K. R., A. H. Stewart, Z. C. T. R. Daniel, H. Hall, H. V. Masey O’Neill, M. R. Bedford, T. Parr, and J. M. Brameld. "The association between faecal host DNA or faecal calprotectin and feed efficiency in pigs fed yeast-enriched protein concentrate." Animal 13, no. 11 (2019): 2483–91. http://dx.doi.org/10.1017/s1751731119000818.

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OLSEN, B., K. PERSSON, and K. A. BROHOLM. "PCR detection of Chlamydia psittaci in faecal samples from passerine birds in Sweden." Epidemiology and Infection 121, no. 2 (October 1998): 481–84. http://dx.doi.org/10.1017/s0950268898001320.

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To investigate to what extent wild passerine birds are carriers of Chlamydia psittaci, 312 faecal samples from 18 bird species were collected. Using the PCR technique and subsequent DNA sequencing, C. psittaci DNA was demonstrated in faecal samples from 9 (2·9%) birds of 6 different species. Sera from 65 bird-ringers, highly exposed to wild birds, were tested by microimmunofluorescence assay for the occurrence of IgG and IgM antibodies to C. psittaci. No such antibodies were found. This results indicate that a significant proportion of wild passerine birds are carriers of C. psittaci, but rarely infectious to humans.

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Anggita, Marla, Okti Herawati, and Sidna Artanto. "Molecular Screening of Salmonella sp. from fecal sample of Sparrows (Passer domesticus) in Yogyakarta, Indonesia." BIO Web of Conferences 33 (2021): 07003. http://dx.doi.org/10.1051/bioconf/20213307003.

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Wild birds is one of the reservoir agent of some of various zoonotic diseases. The study was aim to see the potential of sparrow as the reservoir agent of Salmonella sp. using polymerase chain reaction (PCR) method. We detected the invA gene of Salmonella sp. from faecal sample of sparrows (Passer domesticus) in local area of Yogyakarta, Indonesia. A total of 30 faecal dropping samples were collected from sparrows. DNA was extracted from the faecal samples, then amplified by PCR for the target genes. The amplicons were electrophorized to see the visualization of DNA on the agarose gel. The result showed the prevalence of the positive result of Salmonella sp. was 3,3%. The study indicated that sparrows can spread zoonotic pathogens and this necessitates monitoring for the epidemiologic status of these pathogens among birds, also applying the appropriate intervention measures to prevent the transmission of zoonotic diseasesfrom birds to humans.

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50

Bretagne, S., J. P. Guillou, M. Morand, and R. Houin. "Detection ofEchinococcus multilocularisDNA in fox faeces using DNA amplification." Parasitology 106, no. 2 (February 1993): 193–99. http://dx.doi.org/10.1017/s0031182000074990.

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SUMMARYIn order to identifyEchinococcus multilocularisDNA in fox faeces for epidemiological purposes, we have developed a new method to prepare DNA suitable for PCR amplification. DNA isolation from fox excrement was performed according to a novel procedure involving lysis in KOH, phenol–chloroform extraction and a purification step on a matrix (Prep-A-Gene®). The target sequence for amplification was theE. multilocularisU1 snRNA gene. PCR products were indistinguishable for 32 differentE. multilocularisisolates and no signal was observed after ethidium bromide staining with DNAs from other tapeworm species, includingE. granulosus.The sensitivity of amplification was monitored by the addition ofE. multilocularisDNA or eggs to faeces free ofE. multilocularisand was estimated to be 1 egg per 4 g of faeces. PCR products were blotted onto nylon membranes and hybridized with an internal oligonucleotide probe in order to confirm the results. Twenty nine faecal samples from foxes shot in Franche-Comté (East France) were tested. Out of 10 samples from foxes in which noE. multilocularisadult worms could be observed after necropsy, 7 were PCR positive, showing that the PCR test is more sensitive than microscopical examination. Out of 19 samples from foxes harbouringE. multilocularisadult worms, 18 were PCR positive. The remaining PCR-negative sample could be due either to the misidentification of the species of adult worm (E. granulosusandE. multilocularis), or to DNA variation between different isolates ofE. multilocularis. Further work in the field should be initiated in order to confirm these results.

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