Microbiology: Ditch the term pathogen

Casadevall, Arturo; Pirofski, Liise Anne

doi:10.1038/516165a

Cited by 108 publications

(73 citation statements)

References 6 publications

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“…Thus, the manifestation of CV-B3 infection might be driven by the host-virus interaction. Other factors such as viral load during the infection and host immune status may also influence the outcome of CV-B3 infections and need to be examined (Casadevall & Pirofski, 2014;Kishimoto et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Genomic characterization of coxsackievirus type B3 strains associated with acute flaccid paralysis in south-western India

Laxmivandana

Cherian

Yergolkar

et al. 2016

Journal of General Virology

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Acute flaccid paralysis (AFP) associated with coxsackievirus type B3 (CV-B3) of the species Enterovirus B is an emerging concern worldwide. Although CV-B3-associated AFP in India has been demonstrated previously, the genomic characterization of these strains is unreported. Here, CV-B3 strains detected on the basis of the partial VP1 gene in 10 AFP cases and five asymptomatic contacts identified from different regions of south-western India during 2009-2010 through the Polio Surveillance Project were considered for complete genome sequencing and characterization. Phylogenetic analysis of complete VP1 gene sequences of global CV-B3 strains classified Indian CV-B3 strains into genogroup GVI, along with strains from Uzbekistan and Bangladesh, and into a new genogroup, GVII. Genomic divergence between genogroups of the study strains was 14.4 % with significantly lower divergence (1.8 %) within GVI (n512) than that within GVII (8.5 %) (n53). The strains from both AFP cases and asymptomatic contacts, identified mainly in coastal Karnataka and Kerala, belonged to the dominant genogroup GVI, while the GVII strains were recovered from AFP cases in north interior Karnataka. All study strains carried inter-genotypic recombination with the structural region similar to reference CV-B3 strains, and 59 non-coding regions and non-structural regions closer to other enterovirus B types. Domain II structures of 59 non-coding regions, described to modulate virus replication, were predicted to have varied structural folds in the two genogroups and were attributed to differing recombination patterns. The results indicate two distinct genomic compositions of CV-B3 strains circulating in India and suggest the need for concurrent analysis of viral and host factors to further understand the varied manifestations of their infections.

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Section: Discussionmentioning

confidence: 99%

Genomic characterization of coxsackievirus type B3 strains associated with acute flaccid paralysis in south-western India

Laxmivandana

Cherian

Yergolkar

et al. 2016

Journal of General Virology

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“…There are only cells, tissues, organs, organisms, and populations. Likewise, there are no pathogens (34,68). There are only viruses, bacteria, fungi, or parasites, which are tremendously diverse, each being pathogenic in some individuals and not in others.…”

Section: Unconscious Trends?mentioning

confidence: 99%

Human genetic basis of interindividual variability in the course of infection

Casanova

2015

Proc. Natl. Acad. Sci. U.S.A.

161

111

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The key problem in human infectious diseases was posed at the turn of the 20th century: their pathogenesis. For almost any given virus, bacterium, fungus, or parasite, life-threatening clinical disease develops in only a small minority of infected individuals. Solving this infection enigma is important clinically, for diagnosis, prognosis, prevention, and treatment. Some microbes will inevitably remain refractory to, or escape vaccination, or chemotherapy, or both. The solution also is important biologically, because the emergence and evolution of eukaryotes alongside more rapidly evolving prokaryotes, archaea, and viruses posed immunological challenges of an ecological and evolutionary nature. We need to study these challenges in natural, as opposed to experimental, conditions, and also at the molecular and cellular levels. According to the human genetic theory of infectious diseases, inborn variants underlie life-threatening infectious diseases. Here I review the history of the field of human genetics of infectious diseases from the turn of the 19th century to the second half of the 20th century. This paper thus sets the scene, providing the background information required to understand and appreciate the more recently described monogenic forms of resistance or predisposition to specific infections discussed in a second paper in this issue.

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“…Our understanding of infectious diseases is changing with discoveries of how both host-and microbiome-associated factors affect the disease process. These conceptual advances suggest that a potential pathogen does not necessarily act on its own to cause impairment but may require certain conditions to manifest impairment (29). WPD may provide an interesting example of these issues.…”

Section: Discussionmentioning

confidence: 99%

Systematic Analysis of White Pox Disease in Acropora palmata of the Florida Keys and Role of Serratia marcescens

Joyner

Sutherland

Kemp

et al. 2015

Appl Environ Microbiol

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White pox disease (WPD) affects the threatened elkhorn coral, Acropora palmata. Owing in part to the lack of a rapid and simple diagnostic test, there have been few systematic assessments of the prevalence of acroporid serratiosis (caused specifically by Serratia marcescens) versus general WPD signs. Six reefs in the Florida Keys were surveyed between 2011 and 2013 to determine the disease status of A. palmata and the prevalence of S. marcescens. WPD was noted at four of the six reefs, with WPD lesions found on 8 to 40% of the colonies surveyed. S. marcescens was detected in 26.9% (7/26) of the WPD lesions and in mucus from apparently healthy colonies both during and outside of disease events (9%; 18/201). S. marcescens was detected with greater frequency in A. palmata than in the overlying water column, regardless of disease status (P ‫؍‬ 0.0177). S. marcescens could not be cultured from A. palmata but was isolated from healthy colonies of other coral species and was identified as pathogenic pulsedfield gel electrophoresis type PDR60. WPD lesions were frequently observed on the reef, but unlike in prior outbreaks, no wholecolony death was observed. Pathogenic S. marcescens was circulating on the reef but did not appear to be the primary pathogen in these recent WPD episodes, suggesting that other pathogens or stressors may contribute to signs of WPD. Results highlight the critical importance of diagnostics in coral disease investigations, especially given that field manifestation of disease may be similar, regardless of the etiological agent.T he combination of physical stress and disease has resulted in the decline of corals and coral reefs throughout the Caribbean (1, 2). In the Florida Keys and elsewhere, the iconic elkhorn coral (Acropora palmata) has experienced precipitous declines due in part to white pox disease (WPD) (3, 4). Following outbreaks of WPD in the late 1990s and early 2000s, the bacterium Serratia marcescens was isolated from diseased corals and subsequently identified as an etiological agent by fulfillment of Koch's postulates (4, 5). As originally proposed (4), to distinguish the disease caused by this bacterium from broader signs of WPD, it is referred to as acroporid serratiosis when, and only when, S. marcescens is confirmed from a lesion on an A. palmata colony.Between 1999 and 2006, two strains of S. marcescens were associated with large outbreaks of WPD (acroporid serratiosis) in the Florida Keys. The strain found in association with outbreaks in 2002 and 2003 was identical to a strain concurrently found in human sewage from the nearby islands that compose the Florida Keys archipelago (5, 6). Until recently, septic systems and cesspits were the primary mechanism of wastewater disposal (7-9). Inground disposal of waste led to sewage pollution in both nearshore and offshore waters of the Florida Keys (10-12).In recent studies in the Florida Keys and elsewhere in the Caribbean, researchers have reported that S. marcescens could not always be isolated from colonies displaying signs of WP...

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Microbiology: Ditch the term pathogen

Cited by 108 publications

References 6 publications

Genomic characterization of coxsackievirus type B3 strains associated with acute flaccid paralysis in south-western India

Genomic characterization of coxsackievirus type B3 strains associated with acute flaccid paralysis in south-western India

Human genetic basis of interindividual variability in the course of infection

Systematic Analysis of White Pox Disease in Acropora palmata of the Florida Keys and Role of Serratia marcescens

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