Tracking the establishment of local endemic populations of an emergent enteric pathogen.
Ontology highlight
ABSTRACT:
SUBMITTER: Holt KE
PROVIDER: S-EPMC3808646 | biostudies-literature | 2013 Oct
REPOSITORIES: biostudies-literature
Publications
Tracking the establishment of local endemic populations of an emergent enteric pathogen.
Holt Kathryn E KE Thieu Nga Tran Vu TV Thanh Duy Pham DP Vinh Ha H Kim Dong Wook DW Vu Tra My Phan MP Campbell James I JI Hoang Nguyen Van Minh NV Vinh Nguyen Thanh NT Minh Pham Van PV Thuy Cao Thu CT Nga Tran Thi Thu TT Thompson Corinne C Dung Tran Thi Ngoc TT Nhu Nguyen Thi Khanh NT Vinh Phat Voong PV Tuyet Pham Thi Ngoc PT Phuc Hoang Le HL Lien Nguyen Thi Nam NT Phu Bui Duc BD Ai Nguyen Thi Thuy NT Tien Nguyen Manh NM Dong Nguyen N Parry Christopher M CM Hien Tran Tinh TT Farrar Jeremy J JJ Parkhill Julian J Dougan Gordon G Thomson Nicholas R NR Baker Stephen S
Proceedings of the National Academy of Sciences of the United States of America 20130930 43
Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and converg ...[more]
Similar Datasets
Project description:Pathogen emergence is a complex phenomenon that, despite its public health relevance, remains poorly understood. Vibrio vulnificus, an emergent human pathogen, can cause a deadly septicaemia with over 50% mortality rate. To date, the ecological drivers that lead to the emergence of clinical strains and the unique genetic traits that allow these clones to colonize the human host remain mostly unknown. We recently surveyed a large estuary in eastern Florida, where outbreaks of the disease frequently occur, and found endemic populations of the bacterium. We established two sampling sites and observed strong correlations between location and pathogenic potential. One site is significantly enriched with strains that belong to one phylogenomic cluster (C1) in which the majority of clinical strains belong. Interestingly, strains isolated from this site exhibit phenotypic traits associated with clinical outcomes, whereas strains from the second site belong to a cluster that rarely causes disease in humans (C2). Analyses of C1 genomes indicate unique genetic markers in the form of clinical-associated alleles with a potential role in virulence. Finally, metagenomic and physicochemical analyses of the sampling sites indicate that this marked cluster distribution and genetic traits are strongly associated with distinct biotic and abiotic factors (e.g., salinity, nutrients, or biodiversity), revealing how ecosystems generate selective pressures that facilitate the emergence of specific strains with pathogenic potential in a population. This knowledge can be applied to assess the risk of pathogen emergence from environmental sources and integrated toward the development of novel strategies for the prevention of future outbreaks.
| S-EPMC8501797 | biostudies-literature
Project description:BackgroundPrevention of Chagas disease depends mainly on control of the insect vectors that transmit infection. Unfortunately, the vectors have been resurgent in some areas. It is important to understand the dynamics of reinfestation where it occurs. Here we show how continuous- and discrete-time models fitted to patch-level infestation states can elucidate different aspects of re-establishment. Triatoma infestans, the main vector of Chagas disease, reinfested sites in three villages in northwest Argentina after community-wide insecticide spraying in October 1992.Methodology/principal findingsDifferent methods of estimating the probabilities of bug establishment on each site were compared. The results confirmed previous results showing a 6-month time lag between detection of a new infestation and dispersal events. The analysis showed that more new bug populations become established from May to November than from November to May. This seasonal increase in bug establishment coincides with a seasonal increase in dispersal distance. In the fitted models, the probability of new bug establishment increases with increasing time since last detected infestation.Conclusions/significanceThese effects of season and previous infestation on bug establishment challenge our current understanding of T. infestans ecology and highlight important gaps in knowledge. Experiments necessary to close these gaps are discussed.
| S-EPMC2709728 | biostudies-literature
Project description:1. Prevention of Chagas disease is mainly dependent on control of the insect vectors that transmit infection. Unfortunately, this control is not wholly successful and the vectors have been resurgent in some areas. Where re-infestation has occurred, it is important to understand the dynamics of the process. We investigated how a metapopulation framework can elucidate key aspects of re-infestation and thereby contribute to more efficient disease control.2.Triatoma infestans, the main vector of Chagas disease, re-infested sites in three villages in north-west Argentina after community-wide insecticide spraying in October 1992. Ten surveys were carried out at 6-monthly intervals from November 1994 to May 1999.3. Comparisons were made of different methods of estimating the sources of dispersal and the number of sites in which bug infestations became established.4. The results indicated that (i) the number of dispersing Triatoma infestans from a given site was proportional to the number of bugs found at the site; (ii) there was a 6-month time lag between detection of a new infestation and dispersal events; (iii) the relationship between infestations and new establishments varied by season.5. Three of 156 sites at which bugs were found were estimated to be the source of more than 50% of establishment events. These three sites were the only ones with large, persistent bug populations.6.Synthesis and applications. To reduce the risk of human Chagas disease, identifying those few sites infested with large, persistent bug populations and targeting control measures at those sites should greatly improve the efficiency of vector control. The appropriate seasonal timing of vector control could also greatly increase its efficiency. Specific recommendations for the timing of insecticide spraying require further research to establish how the observed temporal pattern of bug establishment is associated with the seasonality of bug dispersal.
| S-EPMC1948873 | biostudies-literature
Project description:Despite significant progress in recent decades toward ameliorating the excess burden of diarrheal disease globally, childhood diarrhea remains a leading cause of morbidity and mortality in low-and-middle-income countries (LMICs). Recent large-scale studies of diarrhea etiology in these populations have revealed widespread co-infection with multiple enteric pathogens, in both acute and asymptomatic stool specimens. We applied methods from network science and ecology to better understand the underlying structure of enteric co-infection among infants in two large longitudinal birth cohorts in Bangladesh. We used a configuration model to establish distributions of expected random co-occurrence, based on individual pathogen prevalence alone, for every pathogen pair among 30 enteropathogens detected by qRT-PCR in both diarrheal and asymptomatic stool specimens. We found two pairs, Enterotoxigenic E. coli (ETEC) with Enteropathogenic E. coli (EPEC), and ETEC with Campylobacter spp., co-infected significantly more than expected at random (both pairs co-occurring almost 4 standard deviations above what one could expect due to chance alone). Furthermore, we found a general pattern that bacteria-bacteria pairs appear together more frequently than expected at random, while virus-bacteria pairs tend to appear less frequently than expected based on model predictions. Finally, infants co-infected with leading bacteria-bacteria pairs had more days of diarrhea in the first year of life compared to infants without co-infection (p-value <0.0001). Our methods and results help us understand the structure of enteric co-infection which can guide further work to identify and eliminate common sources of infection or determine biologic mechanisms that promote co-infection.
| S-EPMC10664872 | biostudies-literature
Project description:BackgroundCosts of adaptation play an important role in host-parasite coevolution. For parasites, evolving the ability to circumvent host resistance may trade off with subsequent growth or transmission. Such costs of virulence (sensu plant pathology) limit the spread of all-infectious genotypes and thus facilitate the maintenance of genetic polymorphism in both host and parasite. We investigated costs of three virulence factors in Puccinia striiformis f.sp.tritici, a fungal pathogen of wheat (Triticum aestivum).ResultsIn pairwise competition experiments, we compared the fitness of near-isogenic genotypes that differed by a single virulence factor. Two virulence factors (vir4, vir6) imposed substantial fitness costs in the absence of the corresponding resistance genes. In contrast, the vir9 virulence factor conferred a strong competitive advantage to several isolates, and this for different host cultivars and growing seasons. In part, the experimentally derived fitness costs and benefits are consistent with frequency changes of these virulence factors in the French pathogen population.ConclusionOur results illustrate the variation in the evolutionary trajectories of virulence mutations and the potential role of compensatory mutations. Anticipation of such variable evolutionary outcomes represents a major challenge for plant breeding strategies. More generally, we believe that agro-patho-systems can provide valuable insight in (co)evolutionary processes in host-parasite systems.
| S-EPMC2660305 | biostudies-literature
Project description:Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world's new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Conclusions: Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.
| S-EPMC7921886 | biostudies-literature
Project description:Delftia tsuruhatensis, which was first isolated in environmental samples, was rarely associated with human infections. We report on pneumonia caused by D. tsuruhatensis in an infant who underwent cardiac surgery. Retrospective analyses detected 9 other isolates from 8 patients. D. tsuruhatensis is an emergent pathogen, at least for immunocompromised patients.
| S-EPMC5823324 | biostudies-literature
Project description:Coherent vortical motion has been reported in a wide variety of populations including living organisms (bacteria, fishes, human crowds) and synthetic active matter (shaken grains, mixtures of biopolymers), yet a unified description of the formation and structure of this pattern remains lacking. Here we report the self-organization of motile colloids into a macroscopic steadily rotating vortex. Combining physical experiments and numerical simulations, we elucidate this collective behaviour. We demonstrate that the emergent-vortex structure lives on the verge of a phase separation, and single out the very constituents responsible for this state of polar active matter. Building on this observation, we establish a continuum theory and lay out a strong foundation for the description of vortical collective motion in a broad class of motile populations constrained by geometrical boundaries.
| S-EPMC4557359 | biostudies-literature
Project description:UnlabelledBovine parvovirus (BPV), the causative agent of respiratory and gastrointestinal disease in cows, is the type member of the Bocaparvovirus genus of the Parvoviridae family. Toward efforts to obtain a template for the development of vaccines and small-molecule inhibitors for this pathogen, the structure of the BPV capsid, assembled from the major capsid viral protein 2 (VP2), was determined using X-ray crystallography as well as cryo-electron microscopy and three-dimensional image reconstruction (cryo-reconstruction) to 3.2- and 8.8-Å resolutions, respectively. The VP2 region ordered in the crystal structure, from residues 39 to 536, conserves the parvoviral eight-stranded jellyroll motif and an αA helix. The BPV capsid displays common parvovirus features: a channel at and depressions surrounding the 5-fold axes and protrusions surrounding the 3-fold axes. However, rather than a depression centered at the 2-fold axes, a raised surface loop divides this feature in BPV. Additional observed density in the capsid interior in the cryo-reconstructed map, compared to the crystal structure, is interpreted as 10 additional N-terminal residues, residues 29 to 38, that radially extend the channel under the 5-fold axis, as observed for human bocavirus 1 (HBoV1). Surface loops of various lengths and conformations extend from the core jellyroll motif of VP2. These loops confer the unique surface topology of the BPV capsid, making it strikingly different from HBoV1 as well as the type members of other Parvovirinae genera for which structures have been determined. For the type members, regions structurally analogous to those decorating the BPV capsid surface serve as determinants of receptor recognition, tissue and host tropism, pathogenicity, and antigenicity.ImportanceBovine parvovirus (BPV), identified in the 1960s in diarrheic calves, is the type member of the Bocaparvovirus genus of the nonenveloped, single-stranded DNA (ssDNA) Parvoviridae family. The recent isolation of human bocaparvoviruses from children with severe respiratory and gastrointestinal infections has generated interest in understanding the life cycle and pathogenesis of these emerging viruses. We have determined the high-resolution structure of the BPV capsid assembled from its predominant capsid protein VP2, known to be involved in a myriad of functions during host cell entry, pathogenesis, and antigenicity for other members of the Parvovirinae. Our results show the conservation of the core secondary structural elements and the location of the N-terminal residues for the known bocaparvovirus capsid structures. However, surface loops with high variability in sequence and conformation give BPV a unique capsid surface topology. Similar analogous regions in other Parvovirinae type members are important as determinants of receptor recognition, tissue and host tropism, pathogenicity, and antigenicity.
| S-EPMC4325758 | biostudies-literature
Project description:Swine enteric coronavirus (SeCoV) causes acute gastroenteritis and high mortality in newborn piglets. Since the last century, porcine transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) have swept farms all over the world and caused substantial economic losses. In recent years, porcine delta coronavirus (PDCoV) and swine acute diarrhea syndrome coronavirus (SADS-CoV) have been emerging SeCoVs. Some of them even spread across species, which made the epidemic situation of SeCoV more complex and changeable. Recent studies have begun to reveal the complex SeCoV-host interaction mechanism in detail. This review summarizes the current advances in autophagy, apoptosis, and innate immunity induced by SeCoV infection. These complex interactions may be directly involved in viral replication or the alteration of some signal pathways.
| S-EPMC8999375 | biostudies-literature