Koch’s postulates: An interventionist perspective

Ross, Lauren N.; Woodward, James

doi:10.1016/j.shpsc.2016.06.001

Cited by 35 publications

(26 citation statements)

References 11 publications

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“…Decayed tissue samples from lesion margins were transferred to fresh PDA plates, the fungus was re‐isolated each time and identified as the inoculated strain by morphological, microscopic and molecular analysis. The analysis was performed strictly in line with Koch's postulates (Ross & Woodward, ).…”

Section: Resultsmentioning

confidence: 99%

Isolation and identification of pathogenic fungi causing postharvest fruit rot of kiwifruit (Actinidia chinensis) in China

Pan

Chen

et al. 2017

Journal of Phytopathology

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Kiwifruit is a very important commercial crop in China, which is the largest producer of the fruit in the world. The rapid expansion of areas of kiwifruit cultivation has resulted in the spread of postharvest rot diseases. To clarify the pathogens causing kiwifruit postharvest rots in China, 76 pure strains were isolated from 138 rotten fruits during the shelf-life period, with fruit collected from the 11 main regions of kiwifruit cultivation (Shaanxi, Sichuan, Henan, Guizhou, Hubei, Anhui, Jiangxi, Hunan, Fujian, Zhejiang and Jiangsu provinces) during 2014-2015. By examining the morphological and microscopic characteristics together with the results of pathogenicity testing and ITS (internal transcribed spacer) sequencing, four species were identified as the main pathogens causing kiwifruit postharvest rots in China. They were Phomopsis sp., Botryosphaeria dothidea, Alternaria alternata and Pestalotiopsis microspora, with identification rates of 52.6%, 23.7%, 13.2% and 10.5%, respectively. All isolates inoculated on wounded fruit were pathogenic but non-pathogenic when peels were unwounded except B. dothidea. These findings have important implications for resistance breeding and control of kiwifruit postharvest rots in China. K E Y W O R D S internal transcribed spacer identification, kiwifruit fungal postharvest rots, morphological analysis, pathogenicity tests

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Section: Resultsmentioning

confidence: 99%

Isolation and identification of pathogenic fungi causing postharvest fruit rot of kiwifruit (Actinidia chinensis) in China

Pan

Chen

et al. 2017

Journal of Phytopathology

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show abstract

“…He emphasised that a non-specific relationship does not undermine causality. Specificity originated in Robert Koch's postulates to evaluate causality in infectious diseases, but is rare in epidemiology and usually arises when the outcome is defined based on the exposure status (e.g., tuberculosis being defined by the presence of the tubercle bacillus) [17,51,52]. Comparisons highlighted how multiple causation (where one exposure may affect many outcomes and one outcome may be effected by many exposures) limits the utility of directly applying specificity in epidemiological practice, but extending the concept to the related idea of 'falsification' may improve its usefulness.…”

Section: Specificitymentioning

confidence: 99%

Assessing causality in epidemiology: revisiting Bradford Hill to incorporate developments in causal thinking

et al. 2020

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The nine Bradford Hill (BH) viewpoints (sometimes referred to as criteria) are commonly used to assess causality within epidemiology. However, causal thinking has since developed, with three of the most prominent approaches implicitly or explicitly building on the potential outcomes framework: directed acyclic graphs (DAGs), sufficient-component cause models (SCC models, also referred to as ‘causal pies’) and the grading of recommendations, assessment, development and evaluation (GRADE) methodology. This paper explores how these approaches relate to BH’s viewpoints and considers implications for improving causal assessment. We mapped the three approaches above against each BH viewpoint. We found overlap across the approaches and BH viewpoints, underscoring BH viewpoints’ enduring importance. Mapping the approaches helped elucidate the theoretical underpinning of each viewpoint and articulate the conditions when the viewpoint would be relevant. Our comparisons identified commonality on four viewpoints: strength of association (including analysis of plausible confounding); temporality; plausibility (encoded by DAGs or SCC models to articulate mediation and interaction, respectively); and experiments (including implications of study design on exchangeability). Consistency may be more usefully operationalised by considering an effect size’s transportability to a different population or unexplained inconsistency in effect sizes (statistical heterogeneity). Because specificity rarely occurs, falsification exposures or outcomes (i.e., negative controls) may be more useful. The presence of a dose-response relationship may be less than widely perceived as it can easily arise from confounding. We found limited utility for coherence and analogy. This study highlights a need for greater clarity on BH viewpoints to improve causal assessment.

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“…Traditional methods to establish causation are grounded in designing interventions that show a direct connection between an entity and a phenomenon. For instance, one can experimentally show how a pathogen causes a disease using Koch's postulates [52,53] or how microbiota affects the physiological functions of their host. While some microbiota therapies cure disease through the inoculation of "healthy" microbiota into "unhealthy" patients (for example, fecal transplantation; see "Microbiota and health" section), the level of analysis for microbiota research is not precise enough to establish a causal pathway as the agents (microbial taxa) that bring about the cure are never identified.…”

Section: Microbiota and Causation: Should Microbiota Research Considementioning

confidence: 99%

“Microbiota, symbiosis and individuality summer school” meeting report

et al. 2020

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How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science.

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Koch’s postulates: An interventionist perspective

Cited by 35 publications

References 11 publications

Isolation and identification of pathogenic fungi causing postharvest fruit rot of kiwifruit (Actinidia chinensis) in China

Isolation and identification of pathogenic fungi causing postharvest fruit rot of kiwifruit (Actinidia chinensis) in China

Assessing causality in epidemiology: revisiting Bradford Hill to incorporate developments in causal thinking

“Microbiota, symbiosis and individuality summer school” meeting report

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