A spirit of scientific rigour: Koch's postulates in twentieth-century medicine

Polymicrobial consortia in the pathogenesis of biofilm vaginosis visualized by FISH. Historic review outlining the basic principles of the polymicrobial infection theory

The manuscript disputes the exclusive mono-infectious way of thinking, which presumes that for every infection only one pathogen is responsible and sufficient, when infectious vectors, close contact and reduced immunity meet. In situations involving heavily colonized anatomical sites such an approach often ends in insoluble contradictions. Upon critical reflection and evaluation of 20 years research on spatial organization of vaginal microbiota it is apparent, that in some situations, pathogens may act and operate in permanent, structurally organized consortia, whereas its individual components may be innocuous and innocent, failing to express any pathogenic effect. In these cases, consortia are the true pathogens responsible for many infectious conditions, which usually remain unrecognized as long as improperly diagnosed. The structure of such consortia can be unraveled using ribosomal fluorescence in situ hybridization (FISH). FISH methodology, that not only offers an ex vivo opportunity to recognize bacterial species, but provides unique physical insight into their specific role in the pathogenesis of polymicrobial infections. Ribosomal FISH technique applied to both, women with bacterial vaginosis (BV) and their male partners, has added significantly to our understanding of the pathogenesis of this condition and contributed to appreciating the mechanisms of polymicrobial, community-based infection, potentially leading to therapeutic advances.

Cercospora polygonatum, a New Species Causing Gray Leaf Spot Disease in Polygonatum cyrtonema

This study identified a new species (Cercospora polygonatum) that causes gray leaf spot (GLS) disease in cultivated Polygonatum cyrtonema. This fungal species was isolated from the affected region of GLS on P. cyrtonema leaves. Pathogenicity bioassays were conducted based on Koch's postulates. Morphology was examined based on the features of conidiomata, conidiogenous loci, conidia/conidiophores, and conidiogenous cells. The rDNA internal transcribed spacer region, calmodulin, translation elongation factor 1-alpha, and histone genes were subjected to phylogenetic analysis using the MrBayes tool in Phylosuite. Bootstrap support analysis for phylogenetic placement confirmed the new species, which was significantly different from the closely related species C. senecionis-walkeri and C. zeae-maydis. The morphological characteristics also supported this finding, with the conidiogenous cells of C. polygonatum being considerably shorter than those of C. senecionis-walkeri or C. zeae-maydis. In addition, C. polygonatum was distinguished by its cultural characteristics. As this fungus was isolated from P. cyrtonema, it was named C. polygonatum F.Q. Yin, M. Liu & W.L. Ma, sp. nov. The type specimen (H8-2) was preserved at the China General Microbiological Culture Collection Center. This is the first report of GLS caused by C. polygonatum on P. cyrtonema leaves in China. The current study enriches the knowledge regarding Cercospora sp., contributes to the identification of a species causing GLS in P. cyrtonema, and provides useful information for the effective management of this disease.

First report of black patch disease caused by Phyllosticta capitalensis on Litsea cubeba in China

Litsea cubeba, an economical important tree species originally from China, produces fruit from which essential oils are extracted and extensively used in the chemical industry (Zhang et al. 2020). In August 2021, a large-scale outbreak of black patch disease was first observed on the leaves of Litsea cubeba in Huaihua (27°33'N; 109°57'E), Hunan province, China (disease incidence 78%). A second outbreak in 2022, in the same area, lasted from June to August. Symptoms consisted of irregular lesions that initially appeared as small black patches near the lateral veins. These lesions grew along the lateral veins and formed feathery patches until almost the entire lateral veins of the leaves were infected by the pathogen. The infected plants grew poorly and eventually the leaves desiccated and the tree defoliated. To identify the causal agent, the pathogen was isolated from nine symptomatic leaves from three trees. Symptomatic leaves were washed with distilled water three times. Leaves were cut into small pieces (11 cm), surface sterilized with 75% ethanol for 10s and 0.1% HgCl2 for 3 min, and then washed 3 times in sterile distilled water. Surface disinfected leaf pieces were placed onto potato dextrose agar (PDA) medium with cephalothin (0.2 mg/ml) and incubated at 28°C for 4-8 days (about 16h light, 8h dark). Seven morphologically identical isolates were obtained, from which five were selected for further morphological examination and three for molecular identification and pathogenicity test. Strains from grayish white colonies with a granular surface and grayish black wavy edges; bottom of the colonies turned black over time. Conidia were hyaline and nearly elliptical, unicellular. The sizes of conidia ranged from 8.59 to 15.06 μm (n=50) in length and 3.57 to 6.36 μm (n=50) in width. These morphological characteristics are consistent with the description of Phyllosticta capitalensis (Guarnaccia et al. 2017, Wikee et al. 2013). To further confirm the identity of this pathogen, genomic DNA of three isolates (phy1, phy2 and phy3) were extracted to amplify the internal transcribed spacer (ITS) region, the 18S rDNA region, the transcription elongation factor (TEF), and actin (ACT) gene with ITS1/ITS4 (Cheng et al. 2019), NS1/NS8 (Zhan et al. 2014), EF1-728F/EF1-986R (Druzhinina et al. 2005) and ACT-512F/ACT-783R (Wikee et al. 2013) primers, respectively. Sequence similarity indicated that these isolates were highly homologous to Phyllosticta capitalensis. The ITS (Genbank No. OP863032, ON714650 and OP863033), 18S rDNA (Genbank No. OP863038, ON778575 and OP863039), TEF (Genbank No. OP905580, OP905581 and OP905582) and ACT (Genbank No. OP897308, OP897309 and OP897310) sequences of isolates Phy1, Phy2 and Phy3 shared up to 99%, 99%, 100% and 100% similarities with their counterparts (Genbank No. OP163688, MH051003, ON246258 and KY855652) in Phyllosticta capitalensis, respectively. To further confirm their identity, a neighbor-joining phylogenetic tree was generated using MEGA7. Based on morphological characteristics and sequence analysis, the three strains were identified as P. capitalensis. To fulfill Koch's postulates, conidial suspension (1×105 conidia per mL) collected from three isolates were independently inoculated on artificially wounded detached leaves and leaves on trees of Litsea cubeba. Leaves were inoculated with sterile distilled water as negative controls. The experiment was repeated three times. All pathogen-inoculated wounds exhibited necrotic lesions within 5 days on detached leaves and 10 days on the leaves growing on trees after inoculation, whereas no symptoms were observed on the controls. The pathogen was exclusively re-isolated from the infected leaves and showed identical morphological characteristics to those of the original pathogens. P. capitalensis is a destructive plant pathogen that has been shown to cause leaf spots or black patch symptoms on variety of host plants around the world (Wikee et al. 2013), including oil palm (Elaeis guineensis Jacq.), tea plant (Camellia sinensis), Rubus chingii and castor (Ricinus communis L.). To our knowledge, this is the first report of black patch disease of Litsea cubeba caused by P. capitalensis in China. This disease causes severe leaf abscission in fruit development stage of Litsea cubeba and leads to a large amount of fruit drop.

First Report of Botrytis deweyae Causing Gray mold on Polygonatum cyrtonema in China

Polygonatum cyrtonema Hua., is one of the cultivated varieties of Polygonatum sibiricum Redouté., which also an important cash crop in China (Chen, J., et al. 2021). From 2021 to 2022, symptoms resembling gray mold were observed on P. cyrtonema leaves with 30 to 45% disease incidence in Wanzhou District (30°38'1″N, 108°42'27″E) of Chongqing. The symptoms started to occur from April to June and more than 39% of leaves were infected from July to September. Symptoms started as irregular brown spots and progressed to the leaf edges or tips and stems. In dry conditions, the infected tissue appeared dry and thin, light brown in color, and became dry and cracked in the later stages of disease development. When the relative humidity was high, infected leaves developed water-soaked decay with a brown stripe around the lesion, and a gray mold layer appeared. To identify the causal agent, 8 typical diseased leaves were collected, leaf tissues were chopped into small pieces (3×5 mm), surface sterilized for 1 min in 70% ethanol and 5 minutes in 3% sodium hypochlorite, rinsed three times using sterile water, placed onto potato dextrose agar (PDA) amended with streptomycin sulfate (50 μg/ml) and incubated at 25°C for 3 days in dark conditions. Then 6 colonies (3.5 to 4 cm diameter) with similar morphology were transferred onto new plates. In the initial stage of growth of isolates, all hyphal colonies were white, dense, and clustered, and dispersed in all directions. After 21 days, brown to black-colored sclerotia (2.3 to 5.8 mm diameter) were observed embedded on the bottom of the medium. The six colonies were confirmed to be Botrytis sp. based on the morphological characteristics. The conidia were attached in branches on the conidiophores in grape-like clusters. Conidiophores were straight and 150 to 500 μm in length, and the conidia were single-celled, long ellipsoidal, or oval-like, with no septa and 7.5 to 20 × 3.5 to 14 μm (n=50). For molecular identification, DNA was extracted from representative strains 4-2 and 1-5. The internal transcribed spacer (ITS) region and sequences from the RNA polymerase II second largest subunit (RPB2), and the heat-shock protein 60 (HSP60) genes were amplified using primers ITS1/ITS4, RPB2for/RPB2rev, and HSP60for/HSP60rev, respectively (White T.J., et al.1990; Staats, M., et al. 2005). The sequences were deposited in GenBank: 4-2 [ITS; OM655229: RPB2; OM960678: HSP60; OM960679] and 1-5 [ITS; OQ160236: RPB2; OQ164790: HSP60; OQ164791]. These sequences from isolates 4-2 and 1-5 had 100% similarity to the B. deweyae CBS 134649/ MK-2013 [ITS; HG799538.1: RPB2; HG799518.1: HSP60; HG799519.1] ex-type sequences, and phylogenetic analyses based on multi-locus alignment demonstrated strains 4-2 and 1-5 as B. deweyae. Isolate 4-2 was used to verify whether B. deweyae can cause gray mold on P. cyrtonema, by conducting Koch's postulates experiments (Gradmann, C., 2014). The leaves of P. cyrtonema planted in pots were washed with sterile water, and brushed with 10 mL of hyphal tissue in 55% glycerin. Leaves of another plant were brushed with 10 mL 55% glycerin as control, and Kochs' postulates experiments were conducted three times. Inoculated plants were kept in a chamber with 80% relative humidity at 20 ± 1°C. Seven days after inoculation, disease symptoms similar to those in the field were observed on leaves, whereas control plants remained asymptomatic. The fungus was reisolated from inoculated plants and identified as B. deweyae based on multi-locus phylogenetic analysis. To our knowledge, B. deweyae is mostly found on Hemerocallis, is likely to be an important contributor to the development of 'spring sickness' symptoms (Grant-Downton, R.T., et al. 2014.), and this is the first report of B. deweyae causing gray mold on P. cyrtonema in China. Although B. deweyae has a limited host range, it might also become a potential threat to P. cyrtonema. This work will provide a basis for the prevention and treatment of the disease in the future.

First report of leaf spot disease caused by Fusarium oxysporum on Litsea cubeba in China

Litsea cubeba, an important industrial plant species that originated in China, produces fruit essential oil extensively applied in the chemical industry (Xiang et al. 2020). In July 2020, a large-scale outbreak of leaf spot disease on Litsea cubeba was first observed and then monitored over time in Yueyang (29°37'N; 113°13'E) and Changsha (28°06'N; 113°02'E), Hunan province, China. Symptoms of this disease consisted of round-shaped lesions that initially appeared as small light-brown spots. With the increase in number, these small spots coalesced into larger, dark-brown lesions leading to yellowing and abscission of the leaves. To identify the causal agent this disease, the pathogen was isolated with a tissue separation method (Gao et al. 2020). The infected leaf tissues surface-disinfected with 75% ethanol and 0.1% HgCl were aseptically cut into small pieces (11 cm) and then placed onto potato dextrose agar (PDA) medium with cephalothin (0.2 mg/ml) and incubated at 28°C for 3-5 days. The purified colonies on PDA exhibited fluffy white hyphae, secreted a dark red pigment that had been observed in previous studies (Xiao et al. 2015) and produced microconidia and macroconidia. The microconidia were single-celled, non-septate, ovoid, and ranged from 3.08 to 13.89 μm long and 2.17 to 3.62 μm wide (n=50). Macroconidia were three to five-septate, slightly curved, and ranged from 11.77 to 26.85 μm long and 3.31 to 4.50 μm wide (n=50). These morphological features suggested that theisolates were most likely Fusarium oxysporum (Savian et al. 2021). To further confirm the identity of this pathogen (designated as Fox-1), the TEF-1a gene (Genbank accession No. OM281065) and rDNA ITS region (Genbank accession No. OM250084) were cloned and then sequenced (Cui et al, 2021). Sequence alignments indicated that the ITS and TEF-1a sequences shared 99.8% (504/505) and 99.7% (665/667) similarities with that of F. oxysporum (Genbank accession No. MF667966, KT230848), respectively. Both of the morphological characteristics and molecular data were used to identify this pathogen as F. oxysporum Schltdl.: Fr. 1824. To further verify whether these isolates of F. oxysporum can cause leaf spot disease, Koch's postulates were tested (Gradmann 2014). The purified pathogens were inoculated on artificial wounds of detached Litsea cubeba leaves and the leaves on the field plants of Litsea cubeba, respectively. The wounds of leaves were inoculated with sterile distilled water as negative controls. The experiment was performed independently three times, each with three leaves and three inoculated wounds on each leaf. All pathogen-inoculated wounds developed dark brown or black lesions on detached leaves within 3 days and on leaves on plants within 9 days, whereas the controls showed no symptoms. Re-isolations from infected leaves confirmed that the re-isolated pathogens possessed identical morphological characteristics to those of the original pathogens. To our knowledge, this is the first report of leaf spot infection of Litsea cubeba caused by F. oxysporum in China. This disease severely delays plant development and significantly decreases the yield of essential oil of Litsea cubeba. Our results laid a foundation for the subsequent research into pathogenic mechanisms drug sensitivity tests, which will contribute to the prevention and cure of leaf spot disease of Litsea cubeba. References: Cui, L. X., et al. 2021. Plant Dis. 105:7. Gao, W., et al. 2020. Plant Dis. 105:501. Gradmann. 2014. J. Microbes Infect. 16:885-892. Savian, L. G., et al. 2021. Plant Dis. 104:1870. Xiang, Y. J., et al. 2020. J. Chin. Cereals Oils Assco. 35:186-195. Xiao, J. L., et al. 2015. Hunan Agric. Sci. 4:105-108.

Next-generation microbiology: from comparative genomics to gene function

Microbiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have been imagined by pioneers such as Pasteur, Escherich and Koch. This data cascade brings enormous potential to improve our understanding of individual bacterial cells and the genetic basis of phenotype variation. However, this revolution in data science cannot replace established microbiology practices, presenting the challenge of how to integrate these new techniques. Contrasting comparative and functional genomic approaches, we evoke molecular microbiology theory and established practice to present a conceptual framework and practical roadmap for next-generation microbiology.

Molecular Detection of Selected Pathogens with Zoonotic Potential in Deer Keds (Lipoptena fortisetosa)

Deer keds are obligatory hematophagous ectoparasites of birds and mammals. Cervids serve as specific hosts for these insects. However, ked infestations have been observed in non-specific hosts, including humans, companion animals, and livestock. Lipoptena fortisetosa is a weakly studied ectoparasite, but there is evidence to indicate that it continues to spread across Europe. The existing knowledge on deer keds' impact on wildlife is superficial, and their veterinary importance is enigmatic. Lipoptena fortisetosa is a species with vectorial capacity, but potential pathogen transmission has not been assessed. The objective of this study was to evaluate the prevalence of selected pathogens in L. fortisetosa collected from cervids and host-seeking individuals in the environment. Out of 500 acquired samples, 307 (61.4%) had genetic material from at least one tested pathogen. Our research suggests that L. fortisetosa may be a potential vector of several pathogens, including A. phagocytophilum, Babesia spp., Bartonella spp., Borellia spp., Coxiella-like endosymbionts, Francisiella tularensis, Mycoplasma spp., Rickettsia spp., and Theileria spp.; however, further, more extensive investigations are required to confirm this. The results of the study indicate that keds can be used as biological markers for investigating the prevalence of vector-borne diseases in the population of free-ranging cervids.

The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection

Infectious diseases are major threats to human health and lead to a serious public health burden. The emergence of new pathogens and the mutation of known pathogens challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology exhibited versatile applications in pathogenic microorganism detection due to its flexible data throughput. This review article introduced the applications of nanopore sequencing in clinical microbiology and infectious diseases management, including the monitoring of emerging infectious diseases outbreak, identification of pathogen drug resistance, and disease-related microbial communities characterization.

'Birth, life, and death of infectious diseases': Charles Nicolle (1866-1936) and the invention of medical ecology in France

In teasing out the diverse origins of our "modern, ecological understanding of epidemic disease" (Mendelsohn, in: Lawrence and Weisz (eds) Greater than the parts: holism in biomedicine, 1920-1950, Oxford University Press, Oxford, 1998), historians have downplayed the importance of parasitology in the development of a natural history perspective on disease. The present article reassesses the significance of parasitology for the "invention" of medical ecology in post-war France. Focussing on the works of microbiologist Charles Nicolle (1866-1936) and on that of physician and zoologist Hervé Harant (1901-1986), I argue that French "medical ecology" was not professionally (or cognitively) insulated from some major trends in parasitology, especially in Tunis where disciplinary borders in the medical sciences collapsed. This argument supports the claim that ecological perspectives of disease developed in colonial context (Anderson in Osiris 19: 39-61, 2004) but I show that parasitologists such as Harant built on the works of medical geographers who had called attention to the dynamic and complex biological relations between health and environment in fashioning the field of medical ecology in the mid-1950s. As the network of scientists who contributed to the global emergence of "disease ecology" is widening, both medical geography and parasitology stand out as relevant sites of inquiries for a broader historical understanding of the multiple "ecological visions" in twentieth-century biomedical sciences.

No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases

Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.

Detection of tilapia lake virus (TiLV) infection by PCR in farmed and wild Nile tilapia (Oreochromis niloticus) from Lake Victoria

Tilapia lake virus disease (TiLVD) has emerged to be an important viral disease of farmed Nile tilapia (Oreochromis niloticus) having the potential to impede expansion of aquaculture production. There is a need for rapid diagnostic tools to identify infected fish to limit the spread in individual farms. We report the first detection of TiLV infection by PCR in farmed and wild Nile tilapia from Lake Victoria. There was no difference in prevalence between farmed and wild fish samples (p = .65), and of the 442 samples examined from 191 fish, 28 were positive for TiLV by PCR. In terms of tissue distribution, the head kidney (7.69%, N = 65) and spleen (10.99%, N = 191), samples had the highest prevalence (p < .0028) followed by heart samples (3.45%, N = 29). Conversely, the prevalence was low in the liver (0.71%, N = 140) and absent in brain samples (0.0%, N = 17), which have previously been shown to be target organs during acute infections. Phylogenetic analysis showed homology between our sequences and those from recent outbreaks in Israel and Thailand. Given that these findings were based on nucleic acid detection by PCR, future studies should seek to isolate the virus from fish in Lake Victoria and show its ability to cause disease and virulence in susceptible fish.

Petri dish versus Winogradsky column: a longue durée perspective on purity and diversity in microbiology, 1880s-1980s

Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology's current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch's bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by tools such as the "clean" Petri dish versus the "dirty" Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered.

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions

Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions.

Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions. Data from the Parasite Microbiome Project will help identify the mechanisms driving microbiome variation in parasites and infected hosts and how that variation is associated with the ecology and evolution of parasites and their disease outcomes. This is a call to arms to prevent fragmented research endeavors, encourage best practices in experimental approaches, and allow reliable comparative analyses across model systems. It is also an invitation to foundations and national funding agencies to propel the field of parasitology into the microbiome/metagenomic era.

Old and new models for studying host-microbe interactions in health and disease: C. difficile as an example

There has been an explosion of interest in studying the indigenous microbiota, which plays an important role in human health and disease. Traditionally, the study of microbes in relationship to human health involved consideration of individual microbial species that caused classical infectious diseases. With the interest in the human microbiome, an appreciation of the influence that complex communities of microbes can have on their environment has developed. When considering either individual pathogenic microbes or a symbiotic microbial community, researchers have employed a variety of model systems with which they can study the host-microbe interaction. With the use of studies of infections with the toxin-producing bacterium Clostridium difficile as a model for both a pathogen and beneficial bacterial communities as an example, this review will summarize and compare various model systems that can be used to gain insight into the host-microbe interaction.

Commensal or pathogen - a challenge to fulfil Koch's Postulates

1. Infectious diseases have a large impact on poultry health and economics. Elucidating the pathogenesis of a certain disease is crucial to implement control strategies.

2. Multiplication of a pathogen and its characterisation in vitro are basic requirements to perform experimental studies. However, passaging of the pathogen in vitro can influence the pathogenicity, a process targeted for live vaccine development, but limits the reproduction of clinical signs.

3. Numerous factors can influence the outcome of experimental infections with some importance on the pathogen, application route and host as exemplarily outlined for Histomonas meleagridis, Gallibacterium anatis and fowl aviadenoviruses (FAdVs).

4. In future, more comprehensive and detailed settings are needed to obtain as much information as possible from animal experiments. Processing of samples with modern diagnostic tools provides the option to closely monitor the host–pathogen interaction.

Emerging Concepts and Technologies for the Discovery of Microorganisms Involved in Human Disease

Established infectious agents continue to be a major cause of human morbidity and mortality worldwide. However, the causative agent remains unknown for a wide range of diseases; many of these are suspected to be attributable to yet undiscovered microorganisms. The advent of unbiased high-throughput sequencing and bioinformatics has enabled rapid identification and molecular characterization of known and novel infectious agents in human disease. An exciting era of microbe discovery, now under way, holds great promise for the improvement of global health via the development of antimicrobial therapies, vaccination strategies, targeted public health measures, and probiotic-based preventions and therapies. Here, we review the history of pathogen discovery, discuss improvements and clinical applications for the detection of microbially associated diseases, and explore the challenges and strategies for establishing causation in human disease.

Writing the history of virology in the twentieth century: Discovery, disciplines, and conceptual change

Concerned with the study of viruses and the diseases they cause, virology is now a well-established scientific discipline. Whereas aspects of its history from the late nineteenth to the mid-twentieth century have often been recounted through a number of detailed case studies, few general discussions of the historiography of virology have been offered. Looking at the ways in which the history of virology has been told, this article examines a number of debates among scientists and historians of biology and show how they are based on a different understanding of notions such as "discipline", of processes such as "scientific discovery" as well as on distinct views about what the history of science is and how it should be written (the opposition between "longue durée" and "micro-history" or between history of "concepts" versus "experimental methods"). The analysis provided here also suggests that a richer historiography of virology will require looking at the variations over time of the relations between conceptual, technological, and institutional factors that fostered its development at the intersection of several other scientific fields in the life sciences.

Towards Predicting Protective Vaccine Responses in the Very Young

Infectious diseases remain a major cause of death in infancy. Vaccination is a proven-effective strategy to reduce the risk of infectious diseases. However, important gaps remain in our understanding of vaccine responses in early life. Systems vaccinology has provided new insight into mechanisms and predictors of vaccine responses. However, systems vaccinology has not yet been systematically applied to infants younger than 12 months of age. Here, we review the knowledge gained from systems vaccinology studies of vaccines that are licensed for administration to infants. We propose that systems vaccinology should be applied to age-specific studies focused on protection, to derive the necessary insight for optimal design of vaccines for the very young.

Bacterial Transformation and the Origins of Epidemics in the Interwar Period: The Epidemiological Significance of Fred Griffith's "Transforming Experiment"

Frederick Griffith (1879-1941) was an English bacteriologist at the Pathological Laboratory of the Ministry of Health in London who believed that progress in the epidemiology and control of infectious diseases would come only with more precise knowledge of the identity of the causative microorganisms. Over the years, Griffith developed and expanded a serological technique for identifying pathogenic microorganisms, which allowed the tracing of the sources of infectious disease outbreaks: slide agglutination. Yet Griffith is not remembered for his contributions to the biology and epidemiology of infectious diseases so much as for discovering the phenomenon known as 'transformation'. Griffith's discovery, for many, was a pure case of serendipity whose biological relevance had also largely escaped him. In this paper, I argue that the key to understanding the significance of bacterial transformation - and the scientific legacy of Fred Griffith - rests not only on it initiating a cascade of events leading to molecular genetics but also on its implications for epidemiology based on the biology of host-parasite interactions. Looking at Griffith's entire career, instead of focusing only on the transformation study, we can better appreciate the place of the latter within Griffith's overall contributions. Presented in this way, Griffith's experiment on bacterial transformation also ceases to appear as an anomaly, which in turn leads us to rethink some of the most prevalent historical conceptions about his work.

The role of infectious agents, antibiotics, and antiviral therapy in the treatment of extranodal marginal zone lymphoma and other low-grade lymphomas

OPINION STATEMENT

There is strong evidence to corroborate the association with Helicobacter pylori (Hp) to gastric extranodal marginal zone lymphoma (ENMZL) and hepatitis C virus (HCV) to splenic/nodal marginal zone lymphoma. Koch's postulates generally hold for these two associations and eradication of the infectious agent is well supported. Hp eradication (HPE) is recommended as front-line therapy for early stage gastric ENMZL regardless of Hp status. Complete response (CR) rate for Hp-negative patients is not as high as for Hp-positive patients; however, the benign nature of HPE and high rates of salvage allow this strategy to be safe while sparing some Hp-negative patients from systemic therapy or radiation. Similarly for HCV-seropositive patients, treatment with antivirals should be strongly considered as first-line for those who do not require immediate cytoreductive therapy or at some point even after completing chemoimmunotherapy. The controversy regarding the role for antibiotics is greatest for primary ocular adnexal lymphoma (POAL). Considering the low incidence of Chlamydia psittaci (Cp) infection with OAL and the challenges to reliably identifying Cp, we typically do not consider doxycycline in POAL treatment. Involved-field radiotherapy (IFRT) remains the treatment of choice for most with unilateral POAL. However, if reliable detection of Cp is available and Cp is identified, patients with unilateral low tumor stage POAL who do not require immediate radiotherapy could be considered for doxycycline as front-line treatment. Other infectious associations to indolent lymphomas have been made, including Borrelia borgdorferi (Bb) in cutaneous lymphoma and Campylobacter in immunoproliferative small intestinal disease (IPSID), but these associations are not as strong and primary treatment targeting the infectious agents is not recommended.

A Dormant Microbial Component in the Development of Preeclampsia

Preeclampsia (PE) is a complex, multisystem disorder that remains a leading cause of morbidity and mortality in pregnancy. Four main classes of dysregulation accompany PE and are widely considered to contribute to its severity. These are abnormal trophoblast invasion of the placenta, anti-angiogenic responses, oxidative stress, and inflammation. What is lacking, however, is an explanation of how these themselves are caused. We here develop the unifying idea, and the considerable evidence for it, that the originating cause of PE (and of the four classes of dysregulation) is, in fact, microbial infection, that most such microbes are dormant and hence resist detection by conventional (replication-dependent) microbiology, and that by occasional resuscitation and growth it is they that are responsible for all the observable sequelae, including the continuing, chronic inflammation. In particular, bacterial products such as lipopolysaccharide (LPS), also known as endotoxin, are well known as highly inflammagenic and stimulate an innate (and possibly trained) immune response that exacerbates the inflammation further. The known need of microbes for free iron can explain the iron dysregulation that accompanies PE. We describe the main routes of infection (gut, oral, and urinary tract infection) and the regularly observed presence of microbes in placental and other tissues in PE. Every known proteomic biomarker of "preeclampsia" that we assessed has, in fact, also been shown to be raised in response to infection. An infectious component to PE fulfills the Bradford Hill criteria for ascribing a disease to an environmental cause and suggests a number of treatments, some of which have, in fact, been shown to be successful. PE was classically referred to as endotoxemia or toxemia of pregnancy, and it is ironic that it seems that LPS and other microbial endotoxins really are involved. Overall, the recognition of an infectious component in the etiology of PE mirrors that for ulcers and other diseases that were previously considered to lack one.

Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly

A recent paper in this journal argued that reported expression levels, k_cat and K_m for drug transporters could be used to estimate the likelihood that drug fluxes through Caco-2 cells could be accounted for solely by protein transporters. It was in fact concluded that if five such transporters contributed ‘randomly’ they could account for the flux of the most permeable drug tested (verapamil) 35% of the time. However, the values of permeability cited for verapamil were unusually high; this and other drugs have much lower permeabilities. Even for the claimed permeabilities, we found that a single ‘random’ transporter could account for the flux 42% of the time, and that two transporters can achieve 10 · 10⁻⁶ cm·s⁻¹ 90% of the time. Parameter optimisation methods show that even a single transporter can account for Caco-2 drug uptake of the most permeable drug. Overall, the proposal that ‘phospholipid bilayer diffusion (of drugs) is negligible’ is not disproved by the calculations of ‘likely’ transporter-based fluxes.

There has been recent debate as to the relative extents to which cellular transmembrane drug transports occur through any phospholipid bilayer region or is transporter-mediated only.

Much recent evidence suggests (perhaps surprisingly) that phospholipid bilayer diffusion is negligible.

A recent article in this journal suggested that the expression profile and kinetics of known transporters might not be adequate to explain the most active drug fluxes (of verapamil and propranolol) in Caco-2 cells via transporters only.

We show with our own simulations that this is not in fact the case, especially when evolutionary selection is taken into account, and that the Haldane relation accounts straightforwardly for directional differences, even for equilibrative transporters.

Typical protein transporters alone can easily account for measured drug fluxes in Caco-2 cells.

Activation and resolution of periodontal inflammation and its systemic impact

Inflammation is a highly organized event impacting upon organs, tissues and biological systems. Periodontal diseases are characterized by dysregulation or dysfunction of resolution pathways of inflammation that results in failure to heal and in a dominant chronic, progressive, destructive and predominantly unresolved inflammation. The biological consequences of inflammatory processes may be independent of the etiological agents, such as trauma, microbial organisms and stress. The impact of the inflammatory pathological process depends upon the tissues or organ system affected. Whilst mediators are similar, there is tissue specificity for the inflammatory events. It is plausible that inflammatory processes in one organ could directly lead to pathologies in another organ or tissue. Communication between distant parts of the body and their inflammatory status is also mediated by common signaling mechanisms mediated via cells and soluble mediators. This review focuses on periodontal inflammation, its systemic associations and advances in therapeutic approaches based on mediators acting through orchestration of natural pathways to resolution of inflammation. We also discuss a new treatment concept in which natural pathways of resolution of periodontal inflammation can be used to limit systemic inflammation and promote healing and regeneration.

Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as 'persisters'. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one's bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit.

Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as 'persisters'. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one's bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit.