Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates

Abstract

Over 100 years ago, Robert Koch introduced his ideas about how to prove a causal relationship between a microorganism and a disease. Koch's postulates created a scientific standard for causal evidence that established the credibility of microbes as pathogens and led to the development of modern microbiology. In more recent times, Koch's postulates have evolved to accommodate a broader understanding of the host-parasite relationship as well as experimental advances. Techniques such as in situ hybridization, PCR, and representational difference analysis reveal previously uncharacterized, fastidious or uncultivated, microbial pathogens that resist the application of Koch's original postulates, but they also provide new approaches for proving disease causation. In particular, the increasing reliance on sequence-based methods for microbial identification requires a reassessment of the original postulates and the rationale that guided Koch and later revisionists. Recent investigations of Whipple's disease, human ehrlichiosis, hepatitis C, hantavirus pulmonary syndrome, and Kaposi's sarcoma illustrate some of these issues. A set of molecular guidelines for establishing disease causation with sequence-based technology is proposed, and the importance of the scientific concordance of evidence in supporting causal associations is emphasized.

Direct sputum analysis of Pseudomonas aeruginosa macrorestriction fragment genotypes in patients with cystic fibrosis

“…Of the patients 9 were homozygous for the most frequent disease-causing CFTR mutation ∆F508, 3 patients were ∆F508 compound heterozygotes and 1 patient carried the two exon 11 mutations G551D and R553X on her CF chromosomes (Table 1) [6,48]. The group covered the whole spectrum of mild (forced vital capacity (FVC) >80% predicted, patients 2, 6,8,9,10,13), moderate (FVC 60 -80% predicted, patients 1, 5, 12) and severe pulmonary disease (FVC <60% predicted, patients 3, 4, 7, 11) [36,48]. On the day of sampling all patients were in a clinically stable condition with no signs of pulmonary exacerbation.…”

“…Direct examination of bacterial DNA by PFGE: impact on clinical microbiology Direct analysis of bacterial chromosomal DNA from clinical sources in vivo was confined to small genomic portions which were detected either by hybridization with probes or by PCR-mediated amplification [2,9,45,50]. All other nucleic acid methodology requires the cultivation of bacterial isolates in vitro.…”

“…Patients' selection was based on their ability to drain at least 5 ml of bron- Sputum-derived agarose blocks (lanes 3, 6,9,13,15,17,19,22) and the corresponding blocks of subcultured isolates obtained from the same sputum specimen were applied on adjacent lanes. Sputa were provided from eight patients with CF in 1996.…”

Progression of Infection and Tumor Development in Damselfish

“…In such cases, identifying etiologic agents must often rely on determining the distribution of microbial nucleic acid sequences rather than manipulating cultured microbes (Fredricks and Relman, 1996). Perhaps the strongest evidence supporting the hypothesis that DVLA is the etiologic agent of DNF is the presence of high levels of this DNA in the tumors of fish with experimentally induced DNF.…”

A PCR-ELISA Method for Direct Detection of the Oyster Pathogen Haplosporidium nelsoni

“…The technique of polymerase chain reaction (PCR) has been widely used in pathogen detection, even for species that cannot be cultured (Fredricks and Relman, 1996). In the area of oyster research, PCR-agarose gel electrophoresis has been used for detection of the bacterial pathogen Vibrio cholerae in C. virginica (DePaola and Hwang, 1995).…”