#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Determining an optimal pool size for testing beef herds for Johne’s disease in Australia


Autoři: Anna Ly aff001;  Navneet K. Dhand aff001;  Evan S. G. Sergeant aff002;  Ian Marsh aff003;  Karren M. Plain aff001
Působiště autorů: Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia aff001;  Ausvet Pty Ltd., Canberra, Australia aff002;  Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, Australia aff003
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0225524

Souhrn

Bovine Johne’s disease (JD) is a chronic debilitating disease affecting cattle breeds worldwide. Pooled faecal samples are routinely tested by culture to detect Mycobacterium avium subsp. paratuberculosis (Mptb) infection. More recently, a direct high throughput molecular test has been introduced in Australia for the detection of Mptb in faeces to circumvent the long culture times, however, the optimal pool size for beef cattle faeces is not known. This study aimed to determine the optimal pool size to achieve the highest test sensitivity and specificity for beef cattle. Individual archived faecal samples with low, medium and high quantities of Mptb (n = 30) were pooled with faecal samples from confirmed JD negative animals to create pool sizes of 5, 10, 15 and 20, to assess the diagnostic sensitivity relative to individual faecal qPCR. Samples from JD-free cattle (n = 10) were similarly evaluated for diagnostic specificity. Overall, 160 pools were created, with Mptb DNA extracted using magnetic bead isolation method prior to Mptb-specific IS900 quantitative PCR (qPCR). The pool size of 10 yielded the highest sensitivity 73% (95% CI: 54–88%), regardless of the quantity of Mptb DNA present in the faeces. There was no significant differences between the four different pool sizes for positive pool detection, however, there was statistical significance between low, medium and high quantities of Mptb. Diagnostic specificity was determined to be 100%. The increase in pool size greater than 10 increased the chances of PCR inhibition, which was successfully relieved with the process of DNA dilution. The results of this study demonstrate that the pool size of 10 performed optimally in the direct faecal qPCR. The results from this study can be applied in future simulation modelling studies to provide suggestions on the cost-effective testing for JD in beef cattle.

Klíčová slova:

Beef – Cattle – DNA extraction – Molting – Paratuberculosis – Polymerase chain reaction – Simulation and modeling – Veterinary diseases


Zdroje

1. Chiodini RJ, Van Kruiningen HJ, Merkal RS. Ruminant paratuberculosis (Johne's disease): the current status and future prospects. Cornell Vet. 1984;74(3):218–62. 6375961.

2. Clarke CJ. The pathology and pathogenesis of paratuberculosis in ruminants and other species. J Comp Pathol. 1997;116(3):217–61. doi: 10.1016/s0021-9975(97)80001-1 9147244

3. Mitchell RM, Schukken Y, Koets AP, Weber M, Bakker D, Stabel J, et al. Differences in intermittent and continuous fecal shedding patterns between natural and experimental Mycobacterium avium subspecies paratuberculosis infections in cattle. Vet Res. 2015;46(1):66. doi: 10.1186/s13567-015-0188-x 26092571

4. Sweeney RW. Transmission of Paratuberculosis. Veterinary Clinics of North America: Food Animal Practice. 1996;12(2):305–12. doi: 10.1016/s0749-0720(15)30408-4 8828107

5. Whittington RJ, Reddacliff LA, Marsh I, McAllister S, Saunders V. Temporal patterns and quantification of excretion of Mycobacterium avium subsp paratuberculosis in sheep with Johne's disease. Aust Vet J. 2000;78(1):34–7. doi: 10.1111/j.1751-0813.2000.tb10355.x 10736683

6. Geraghty T, Graham DA, Mullowney P, More SJ. A review of bovine Johne's disease control activities in 6 endemically infected countries. Prev Vet Med. 2014;116(1–2):1–11. doi: 10.1016/j.prevetmed.2014.06.003 24997766

7. Animal Health Australia. BJD—Where to from here? 2015. Available from: https://animalhealthaustralia.com.au/wp-content/uploads/2016/02/BJD-Framework-Document_final.pdf.

8. Animal Health Australia. JD in cattle tools 2019 [updated February 25, 2019]. Available from: https://animalhealthaustralia.com.au/jd-cattle-tools/.

9. Plain KM, Marsh IB, Waldron AM, Galea F, Whittington A-M, Saunders VF, et al. High-throughput direct fecal PCR assay for detection of Mycobacterium avium subsp. paratuberculosis in sheep and cattle. J Clin Microbiol. 2014;52(3):745–57. doi: 10.1128/JCM.03233-13 24352996

10. Whittington RJ. Cultivation of Mycobacterium avium subsp. paratuberculosis. Paratuberculosis: Organism, Disease, Control. Wallingford: CABI; 2010. p. 244–66.

11. Whittington RJ, Whittington A-M, Waldron A, Begg DJ, Silva Kd, Purdie AC, et al. Development and validation of a liquid medium (M7H9C) for routine culture of Mycobacterium avium subsp. paratuberculosis to replace modified Bactec 12B medium. J Clin Microbiol. 2013;51(12):3993. doi: 10.1128/JCM.01373-13 24048541

12. McKenna SLB, Ritter C, Dohoo I, Keefe GP, Barkema HW. Comparison of fecal pooling strategies for detection of Mycobacterium avium ssp. paratuberculosis in cattle. J Dairy Sci. 2018;101(8):7463–70. doi: 10.3168/jds.2018-14458 29803424

13. Kalis CH, Hesselink JW, Barkema HW, Collins MT. Culture of strategically pooled bovine fecal samples as a method to screen herds for paratuberculosis. J Vet Diagn Investig. 2000;12(6):547–51. doi: 10.1177/104063870001200609 11108455

14. Messam LLM, O’Brien JM, Hietala SK, Gardner IA. Effect of changes in testing parameters on the cost-effectiveness of two pooled test methods to classify infection status of animals in a herd. Prev Vet Med. 2010;94(3):202–12. doi: 10.1016/j.prevetmed.2010.01.005 20207038

15. van Schaik G, Pradenas F M, Mella N A, Kruze V J. Diagnostic validity and costs of pooled fecal samples and individual blood or fecal samples to determine the cow- and herd-status for Mycobacterium avium subsp. paratuberculosis. Prev Vet Med. 2007;82(1):159–65. doi: 10.1016/j.prevetmed.2007.05.018 17597241

16. van Schaik G, Stehman SM, Schukken YH, Rossiter CR, Shin SJ. Pooled fecal culture sampling for Mycobacterium avium subsp. paratuberculosis at different herd sizes and prevalence. J Vet Diagn Investig. 2003;15(3):233–41. doi: 10.1177/104063870301500304 12735345

17. Wells SJ, Godden SM, Lindeman CJ, Collins JE. Evaluation of bacteriologic culture of individual and pooled fecal samples for detection of Mycobacterium paratuberculosis in dairy cattle herds. J Am Vet Med Assoc. 2003;223(7):1022–5. doi: 10.2460/javma.2003.223.1022 14552493

18. Whittington RJ, Fell S, Walker D, McAllister S, Marsh I, Sergeant E, et al. Use of pooled fecal culture for sensitive and economic detection of Mycobacterium avium subsp. paratuberculosis infection in flocks of sheep. J Clin Microbiol. 2000;38(7):2550–6. 10878042

19. Cao Y, Griffith JF, Dorevitch S, Weisberg SB. Effectiveness of qPCR permutations, internal controls and dilution as means for minimizing the impact of inhibition while measuring Enterococcus in environmental waters. J Appl Microbiol. 2012;113(1):66–75. doi: 10.1111/j.1365-2672.2012.05305.x 22497995

20. Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, et al. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 2008;8(1):125–. doi: 10.1186/1471-2180-8-125 18652685

21. Rapp D. DNA extraction from bovine faeces: current status and future trends. J Appl Microbiol. 2010;108(5):1485–93. doi: 10.1111/j.1365-2672.2009.04606.x 19912432

22. Acharya KR, Dhand NK, Whittington RJ, Plain KM. PCR inhibition of a quantitative PCR for detection of Mycobacterium avium subspecies paratuberculosis DNA in feces: Diagnostic implications and potential solutions. Frontiers in microbiology. 2017;8.

23. Christensen J, Gardner IA. Herd-level interpretation of test results for epidemiologic studies of animal diseases. Prev Vet Med. 2000;45(1):83–106. doi: 10.1016/S0167-5877(00)00118-5

24. Eamens GJ, Marsh I.M., Plain K.M., Whittington R.J.,. The Australian and New Zealand standard diagnostic procedure (ANZSDP) for Johne’s disease 2015.

25. Eamens GJ, Whittington RJ, Turner MJ, Austin SL, Fell SA, Marsh IB. Evaluation of radiometric faecal culture and direct PCR on pooled faeces for detection of Mycobacterium avium subsp. paratuberculosis in cattle. Vet Microbiol. 2007;125(1):22–35. doi: 10.1016/j.vetmic.2007.04.043 17560743

26. Wells SJ, Whitlock RH, Lindeman CJ, Fyock T. Evaluation of bacteriologic culture of pooled fecal samples for detection of Mycobacterium paratuberculosis. Am J Vet Res. 2002;63(8):1207–11. doi: 10.2460/ajvr.2002.63.1207 12171178

27. Begg DJ, Plain KM, de Silva K, Gurung R, Gunn A, Purdie AC, et al. Immunopathological changes and apparent recovery from infection revealed in cattle in an experimental model of Johne's disease using a lyophilised culture of Mycobacterium avium subspecies paratuberculosis. Vet Microbiol. 2018;219:53–62. doi: 10.1016/j.vetmic.2018.03.029 29778205

28. Kawaji S, Taylor DL, Mori Y, Whittington RJ. Detection of Mycobacterium avium subsp. paratuberculosis in ovine faeces by direct quantitative PCR has similar or greater sensitivity compared to radiometric culture. Vet Microbiol. 2007;125(1):36–48. doi: 10.1016/j.vetmic.2007.05.002 17582709

29. Sergeant E. Epitools epidemiological calculators—Calculate test Sensitivity and Specificity and ROC curves: Ausvet Pty Ltd; 2019. Available from: http://epitools.ausvet.com.au/content.php?page=ROC_curves.

30. Lehnert B. BlandAltmanLeh: Plots (Slightly Extended) Bland-Altman Plots. 0.3.1 ed. R package 2015.

31. Pedersen KS, Johansen M, Jorsal SE, Nielsen JP, Bækbo P, Angen Ø. Pooling of porcine fecal samples for quantification of Lawsonia intracellularis by real-time polymerase chain reaction. J Vet Diagn Investig. 2014;26(3):342–5. doi: 10.1177/1040638714524572 24621847

32. Herd Health Pty Ltd. Review of the Australian Johne’s Disease Market Assurance Program for cattle (CattleMAP) 2016. Available from: https://www.animalhealthaustralia.com.au/wp-content/uploads/2015/09/CattleMAP-Review-2016_Exec-summary.pdf.

33. Monteiro L, Bonnemaison D, Vekris A, Petry KG, Bonnet J, Vidal R, et al. Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J Clin Microbiol. 1997;35(4):995–8. 9157172

34. Thornton CG, Passen S. Inhibition of PCR amplification by phytic acid, and treatment of bovine fecal specimens with phytase to reduce inhibition. J Microbiol Methods. 2004;59(1):43–52. Epub 2004/08/25. doi: 10.1016/j.mimet.2004.06.001 15325752.

35. Morre SA, van Dijk R, Meijer CJ, van den Brule AJ, Kjaer SK, Munk C. Pooling cervical swabs for detection of Chlamydia trachomatis by PCR: sensitivity, dilution, inhibition, and cost-saving aspects. J Clin Microbiol. 2001;39(6):2375–6. Epub 2001/06/21. 11414248; PubMed Central PMCID: PMC88155.

36. Sergeant ESG, McAloon CG, Tratalos JA, Citer LR, Graham DA, More SJ. Evaluation of national surveillance methods for detection of Irish dairy herds infected with Mycobacterium avium ssp. paratuberculosis. J Dairy Sci. 2019;102(3):2525–38. doi: 10.3168/jds.2018-15696 30692009

37. Meyer A, McAloon CG, Tratalos JA, More SJ, Citer LR, Graham DA, et al. Modeling of alternative testing strategies to demonstrate freedom from Mycobacterium avium ssp. paratuberculosis infection in test-negative dairy herds in the Republic of Ireland. J Dairy Sci. 2019;102:2427–42. doi: 10.3168/jds.2018-14883 30639002

38. Kralik P, Pribylova-Dziedzinska R, Kralova A, Kovarcik K, Slana I. Evidence of passive faecal shedding of Mycobacterium avium subsp. paratuberculosis in a Limousin cattle herd. Veterinary journal (London, England : 1997). 2014;201(1):91–4. doi: 10.1016/j.tvjl.2014.02.011 24836889

39. Logar K, Kopinč R, Bandelj P, Starič J, Lapanje A, Ocepek M. Evaluation of combined high-efficiency DNA extraction and real-time PCR for detection of Mycobacterium avium subsp. paratuberculosis in subclinically infected dairy cattle: comparison with faecal culture, milk real-time PCR and milk ELISA. BMC Veterinary Research. 2012;8(1):49. doi: 10.1186/1746-6148-8-49 22551054

40. Dhand NK, Sergeant E, Toribio J-AL, Whittington RJ. Estimation of sensitivity and flock-sensitivity of pooled faecal culture for Mycobacterium avium subsp. paratuberculosis in sheep. Prev Vet Med. 2010;95(3):248–57.

41. Cannon RM, Nicholls TJ. Relationship between sample weight, homogeneity, and sensitivity of fecal culture for Salmonella enterica. J Vet Diagn Investig. 2002;14(1):60–2. doi: 10.1177/104063870201400112 12680646

42. Mita A, Mori Y, Nakagawa T, Tasaki T, Utiyama K, Mori H. Comparison of fecal pooling methods and DNA extraction kits for the detection of Mycobacterium avium subspecies paratuberculosis. MicrobiologyOpen. 2016;5(1):134–42. doi: 10.1002/mbo3.318 26666871

43. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55(4):611–22. doi: 10.1373/clinchem.2008.112797 19246619


Článek vyšel v časopise

PLOS One


2019 Číslo 11
Nejčtenější tento týden
Nejčtenější v tomto čísle
Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

KOST
Koncepce osteologické péče pro gynekology a praktické lékaře
nový kurz
Autoři: MUDr. František Šenk

Sekvenční léčba schizofrenie
Autoři: MUDr. Jana Hořínková

Hypertenze a hypercholesterolémie – synergický efekt léčby
Autoři: prof. MUDr. Hana Rosolová, DrSc.

Svět praktické medicíny 5/2023 (znalostní test z časopisu)

Imunopatologie? … a co my s tím???
Autoři: doc. MUDr. Helena Lahoda Brodská, Ph.D.

Všechny kurzy
Kurzy Podcasty Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se

#ADS_BOTTOM_SCRIPTS#