A model for pathogen population structure with cross-protection depending on the extent of overlap in antigenic variant repertoires

Population variability of Sclerotinia sclerotiorum, the causal organism of Sclerotinia stem rot of soybean, was determined by mycelial compatibility grouping (MCG) and isolate aggressiveness comparisons. MCG and aggressiveness of S. sclerotiorum isolates from diverse hosts and geographic locations (Diverse Set, 24 isolates), from a soybean field in Argentina (Argentine Set, 21 isolates), and from soybean fields in DeKalb and Watseka, Illinois (DeKalb Set, 124 isolates, and Watseka Set, 130 isolates) were assessed. Among 299 isolates tested, 42 MCGs were identified, and 61% were represented by single isolates observed at single locations. Within the Diverse Set, 17 MCGs were identified; 1 MCG consisted of six isolates, and 16 MCGs consisted of one isolate each. Nine MCGs were identified within the Argentine field with two MCGs composed of either five or six isolates, two MCGs composed of two isolates, and the remaining composed of one isolate each. Each Illinois field was a mosaic of MCGs, but MCG frequencies differed between the two fields. Common MCGs were identified among the Diverse, DeKalb, and Watseka Sets, but no MCGs within the Argentine Set were observed with other sets. MCG 8 was the most frequently sampled and widely dispersed MCG and occurred at a frequency of 29, 36, and 62% in the Diverse, DeKalb, and Watseka Sets, respectively. Variation in isolate aggressiveness was assessed using a limited-term, plug inoculation technique. Isolate aggressiveness varied (P = 0.001) within the Diverse, Argentine, DeKalb, and Watseka Sets. Within widely dispersed MCGs, isolate aggressiveness varied (P ≤ 0.10); however, within locally observed MCGs detected only in single fields, isolate aggressiveness did not vary. Additionally, individual MCGs within the DeKalb and Watseka Sets differed in isolate aggressiveness. Using six soybean cultivars and six S. sclerotiorum isolates, no cultivar-isolate interaction was detected, but resistant and susceptible cultivars performed similarly when inoculated with either less or highly aggressive isolates. Pathogen population structure and variability in isolate aggressiveness may be important considerations in disease management systems.

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Distribution of Surface Protein Variants among Hyperinvasive Meningococci: Implications for Vaccine Design

Infection and Immunity ◽

10.1128/iai.72.10.5955-5962.2004 ◽

2004 ◽

Vol 72 (10) ◽

pp. 5955-5962 ◽

Cited By ~ 149

Author(s):

Rachel Urwin ◽

Joanne E. Russell ◽

Emily A. L. Thompson ◽

Edward C. Holmes ◽

Ian M. Feavers ◽

...

Keyword(s):

Population Structure ◽

Immune Responses ◽

Outer Membrane Proteins ◽

Surface Protein ◽

Host Immunity ◽

Antigenic Variant ◽

Strong Positive Selection ◽

Antigenic Diversity ◽

Genetic Reassortment ◽

Protein Variants

ABSTRACT The bacterium Neisseria meningitidis is a major cause of meningitis and septicemia worldwide. Outer membrane proteins (OMPs) are candidates in the search for comprehensive meningococcal vaccines; however, the formulation of OMP vaccines is complicated by antigenic diversity, which is generated by high levels of genetic reassortment and strong positive selection in the meningococcal antigen genes. The genetic and antigenic diversity of three OMPs (FetA, PorA, and PorB) among a global collection of meningococcal isolates representative of the major hyperinvasive clonal complexes was determined. There was evidence for antigenic structuring among the three OMPs that could not be explained purely by descent. These observations violated the predictions of the clonal and epidemic clonal models of population structure but were in concordance with models of strain structure which propose that host immunity selects for nonoverlapping antigen combinations. The patterns of antigenic variant combinations suggested that an OMP-based vaccine with as few as six PorA and five FetA variant sequences could generate homologous immune responses against all 78 isolates examined.

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The host brain is permissive to colonization by Toxoplasma gondii

10.1101/2020.08.06.239822 ◽

2020 ◽

Author(s):

CJ. Wincott ◽

G. Sritharan ◽

M. Bunyan ◽

E. Alves ◽

HJ. Benns ◽

...

Keyword(s):

Population Structure ◽

Toxoplasma Gondii ◽

Cell Types ◽

Intervention Strategies ◽

Evolutionary Strategy ◽

Pathogen Population ◽

Persister Cells ◽

Host Blood ◽

Cellular Barcoding ◽

Host Brain

SummaryPathogenic infections and the diseases they cause are defined by invasion and colonization of distinct host cell types and tissue niches. In the case of viruses and bacteria, molecular and cellular barcoding has shaped our understanding of within-host pathogen population dynamics, and informed therapeutic intervention strategies. Host brain colonization is a clinically untreatable feature of persistent infection by the eukaryotic pathogen Toxoplasma gondii, and the process remains poorly understood. The host blood-brain barrier is expected to physically restrict parasite colonization of this tissue niche and force the infection through a selection bottleneck, however tools and technologies to test this hypothesis have not been available. Here, we have developed a simple CRISPR-based method to barcode Toxoplasma parasites, and then used complex libraries of barcoded parasites to define how the different phases of an infection shape the pathogen population structure. Unexpectedly, we have discovered that the murine host brain does not restrict parasite colonization, with the population structure predominantly shaped by a bottleneck experienced during the acute phase of infection. These data support an evolutionary strategy to maximize genetic diversity of parasite persister cells within the intermediate host brain for subsequent transmission into the definitive feline host.

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Vaccination can drive an increase in frequencies of antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1718712115 ◽

2018 ◽

Vol 115 (12) ◽

pp. 3102-3107 ◽

Cited By ~ 17

Author(s):

Uri Obolski ◽

José Lourenço ◽

Craig Thompson ◽

Robin Thompson ◽

Andrea Gori ◽

...

Keyword(s):

Public Health ◽

Antibiotic Resistance ◽

Population Structure ◽

Streptococcus Pneumoniae ◽

Bacterial Pathogen ◽

Epidemiological Studies ◽

Theoretical Framework ◽

Health Concern ◽

Public Health Concern ◽

Pathogen Population

The bacterial pathogen Streptococcus pneumoniae is a major public health concern, being responsible for more than 1.5 million deaths annually through pneumonia, meningitis, and septicemia. Available vaccines target only a subset of serotypes, so vaccination is often accompanied by a rise in the frequency of nonvaccine serotypes. Epidemiological studies suggest that such a change in serotype frequencies is often coupled with an increase of antibiotic resistance among nonvaccine serotypes. Building on previous multilocus models for bacterial pathogen population structure, we have developed a theoretical framework incorporating variation of serotype and antibiotic resistance to examine how their associations may be affected by vaccination. Using this framework, we find that vaccination can result in a rapid increase in the frequency of preexisting resistant variants of nonvaccine serotypes due to the removal of competition from vaccine serotypes.

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Severe outbreaks of Phytophthora infestans on potato in Turkey caused by recent changes in the pathogen population structure

Phytoparasitica ◽

10.1007/s12600-019-00768-5 ◽

2019 ◽

Vol 47 (5) ◽

pp. 693-709 ◽

Cited By ~ 1

Author(s):

Mehmet Erhan Göre ◽

Nedim Altın ◽

Tolga Yaman ◽

Kevin Myers ◽

Abdurrahman Çağlı ◽

...

Keyword(s):

Population Structure ◽

Phytophthora Infestans ◽

Pathogen Population

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Pathogen population structure and epidemiology are keys to wheat crown rot and Fusarium head blight management

Australasian Plant Pathology ◽

10.1071/ap06068 ◽

2006 ◽

Vol 35 (6) ◽

pp. 643 ◽

Cited By ~ 73

Author(s):

S. Chakraborty ◽

C. J. Liu ◽

V. Mitter ◽

J. B. Scott ◽

O. A. Akinsanmi ◽

...

Keyword(s):

Population Structure ◽

Fusarium Head Blight ◽

Crown Rot ◽

Head Blight ◽

Pathogen Population

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Downy Mildew: A Serious Disease Threat to Rose Health Worldwide

Plant Disease ◽

10.1094/pdis-12-17-1968-fe ◽

2018 ◽

Vol 102 (10) ◽

pp. 1873-1882 ◽

Cited By ~ 7

Author(s):

Catalina Salgado-Salazar ◽

Nina Shiskoff ◽

Margery Daughtrey ◽

Cristi L. Palmer ◽

Jo Anne Crouch

Keyword(s):

Population Structure ◽

Downy Mildew ◽

Genetic Relatedness ◽

Herbarium Specimens ◽

Pathogen Population ◽

Significant Research ◽

Nursery Production ◽

Natural Movement ◽

Serious Disease ◽

Basic Comprehension

Peronospora sparsa is a downy mildew-causing oomycete that can infect roses, blackberries, and other members of the rose family. During the last 70 years, this disease has become a serious problem for rose growers in the U.S. and worldwide. While much is known about the disease and its treatment, including significant research on molecular identification methods, as well as environmental conditions conducive to disease and the fungicides used to prevent it, significant knowledge gaps remain in our basic comprehension of the pathogen’s biology. For example, the degree of genetic relatedness of pathogen isolates collected from rose, caneberries, and cherry laurel has never been examined, and the natural movement of genotypes from host to host is not known. Further work could be done to determine the differences in pathogen population structure over time (using herbarium specimens and fresh collections) or differences in pathogen population structure and pathogen environmental adaptation for specimens from different geographic regions. The oospore stage of the organism is poorly understood, both as to how it forms and whether it serves as an overwintering structure in nurseries and landscapes. In production greenhouses, the detection of the pathogen using infrared thermographic imaging and possible inhibition by ultraviolet light needs to be explored. Further work needs to be done on breeding using wild roses as new sources for resistance and using new methods such as marker assisted selection and RNAi technologies. As roses are one of the most economically important ornamental crops worldwide, a proper understanding of the disease cycle could allow for better use of cultural and chemical controls to manage rose downy mildew in landscapes and in greenhouse and nursery production areas.

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Environmental Heterogeneity Drives Within-Host Diversification and Evolution of Pseudomonas aeruginosa

mBio ◽

10.1128/mbio.01592-14 ◽

2014 ◽

Vol 5 (5) ◽

Cited By ~ 98

Author(s):

Trine Markussen ◽

Rasmus Lykke Marvig ◽

María Gómez-Lozano ◽

Kasper Aanæs ◽

Alexandra E. Burleigh ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Population Structure ◽

Infected Individual ◽

Host Population ◽

Population Diversity ◽

Pathogen Population ◽

Content Type ◽

Airway Infections

ABSTRACTMicrobial population polymorphisms are commonly observed in natural environments, including long-term infected hosts. However, the underlying processes promoting and stabilizing diversity are difficult to unravel and are not well understood. Here, we use chronic infection of cystic fibrosis airways by the opportunistic pathogenPseudomonas aeruginosaas a system for investigating bacterial diversification processes during the course of infection. We analyze clonal bacterial isolates sampled during a 32-year period and map temporal and spatial variations in population diversity to different infection sites within the infected host. We show that the ancestral infecting strain diverged into distinct sublineages, each with their own functional and genomic signatures and rates of adaptation, immediately after initial colonization. The sublineages coexisted in the host for decades, suggesting rapid evolution of stable population polymorphisms. Critically, the observed generation and maintenance of population diversity was the result of partitioning of the sublineages into physically separated niches in the CF airway. The results reveal a complex within-host population structure not previously realized and provide evidence that the heterogeneity of the highly structured and complex host environment promotes the evolution and long-term stability of pathogen population diversity during infection.IMPORTANCEWithin-host pathogen evolution and diversification during the course of chronic infections is of importance in relation to therapeutic intervention strategies, yet our understanding of these processes is limited. Here, we investigate intraclonal population diversity inP. aeruginosaduring chronic airway infections in cystic fibrosis patients. We show the evolution of a diverse population structure immediately after initial colonization, with divergence into multiple distinct sublineages that coexisted for decades and occupied distinct niches. Our results suggest that the spatial heterogeneity in CF airways plays a major role in relation to the generation and maintenance of population diversity and emphasize that a single isolate in sputum may not represent the entire pathogen population in the infected individual. A more complete understanding of the evolution of distinct clonal variants and their distribution in different niches could have positive implications for efficient therapy.

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