Ecological diversification reveals routes of pathogen emergence in endemic Vibrio vulnificus populations

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.

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EVOLUTION OF DNA SEQUENCING METHODS AND PROSPECTS FOR THEIR USE IN FORENSIC DNA EXAMINATION

Young Scientist ◽

10.32839/2304-5809/2020-11-87-27 ◽

2020 ◽

Vol 11 (87) ◽

Author(s):

Zhanna Bazyliuk ◽

Keyword(s):

Dna Sequencing ◽

Molecular Genetic ◽

Genetic Research ◽

Snp Markers ◽

Degraded Dna ◽

Phenotypic Traits ◽

Nucleotide Polymorphisms ◽

Biological Origin ◽

Genetic Traits ◽

Str Loci

The study of the human genome makes it possible to use genetic information to identify individual traits, diagnosis of diseases and forecasting and prevention of their development, promotes a personal approach when choosing treatment methods; population research, ethnogenesis and evolutionary processes. Introduction of DNA sequencing methods in domestic genetic fingerprinting will contribute to a more informative establishment of human genetic traits. The main purpose of molecular genetic research is to establish the genetic features of missing people, their relatives, to conduct paternity, to identify traces of biological origin and their identification. This article talks about the gradual development of DNA sequencing technology, which is conventionally divided into three types. The first type includes sequencing using capillary electrophoresis and pyrosequencing. The second type is high-throughput pyrosequencing, semiconductor, cyclic ligase, and the use of fluorescently labeled precursors, based on the sequencing of millions of DNA fragments simultaneously. The third stage includes methods that do not require prior sample preparation. These are methods of nanoporous sequencing, sequencing of one molecule, one-molecular sequencing. Today, each of the sequencing methods is aimed at performing different tasks. A number of methods are promising in the field of molecular-genetic examination. In world jurisprudence, sequencing is implemented mainly with the help of devices - Illumina’s, MiSeq FGx, Ion Torrent PGM from ThermoFisher and Ion S5. Research in forensic expertise of single nucleotide polymorphisms (SNP), sequencing of STR-loci and mitochondrial DNA, STR-loci and SNP-markers of the Y chromosome, will provide a high level of information, determination of human phenotypic traits, the possibility of establishing genetic traits from significantly degraded DNA. This article deals with modern problems of identification of human genetic traits and the prospect of introduction of the newest methods of sequencing for their qualitative and complete establishment.

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Exploring the Pathogenic Potential of Vibrio vulnificus Isolated from Seafood Harvested along the Mangaluru Coast, India

Microorganisms ◽

10.3390/microorganisms8070999 ◽

2020 ◽

Vol 8 (7) ◽

pp. 999

Author(s):

Caroline D’Souza ◽

Kattapuni Suresh Prithvisagar ◽

Vijay Kumar Deekshit ◽

Indrani Karunasagar ◽

Iddya Karunasagar ◽

...

Keyword(s):

Gene Sequence ◽

Virulence Genes ◽

Vibrio Vulnificus ◽

Disease Process ◽

Transcriptional Analysis ◽

Clinical Strain ◽

High Similarity ◽

Pathogenic Potential ◽

Fibronectin Binding Protein ◽

Fibronectin Binding

It has been observed that not all strains of Vibrio vulnificus are virulent. Determining the virulence of strains that are frequently present in seafood is of significance for ensuring seafood safety. This study is an attempt to predict the virulence of seafood-borne V. vulnificus isolated along the Mangaluru Coast, India. The isolates tested possessed a vcgC gene sequence with high similarity to that in the clinical strain. Transcriptional analysis of core virulence genes in seafood isolate E4010 showed the phenomenon of contact-mediated expression of rtxA1 which correlated well with the actin disintegration and cytotoxicity. These results suggest that the seafood isolates tested in this study possess a functional RtxA1 which could help in initiating the infection. However, other putative virulence genes such as vvpE encoding an extracellular protease, vvhA encoding hemolysin, flp encoding tad pilin and ompU encoding fibronectin-binding protein were also constitutively expressed. Virulence-associated attributes such as cytotoxicity and adherence matched the response of the clinical strain (p > 0.05). On the other hand, the environmental strains showed higher serum sensitivity compared with the clinical strain. These findings show that the part of virulence attributes required for the disease process might be intact in these isolates.

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Phylogenetic Analysis ofStenotrophomonasspp. Isolates Contributes to the Identification of Nosocomial and Community-Acquired Infections

BioMed Research International ◽

10.1155/2014/151405 ◽

2014 ◽

Vol 2014 ◽

pp. 1-13 ◽

Cited By ~ 4

Author(s):

Vinicius Godoy Cerezer ◽

Silvia Yumi Bando ◽

Jacyr Pasternak ◽

Marcia Regina Franzolin ◽

Carlos Alberto Moreira-Filho

Keyword(s):

Phylogenetic Analysis ◽

Multidrug Resistance ◽

Phylogenetic Profile ◽

Opportunistic Pathogen ◽

Clinical Isolates ◽

Environmental Distribution ◽

Pathogenic Potential ◽

Clinical Strains ◽

Specific Fragment ◽

Clonal Variability

Stenotrophomonasssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species,S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromised patients. Therefore, it is relevant to conduct resistance profile and phylogenetic studies in clinical isolates for identifying infection origins and isolates with augmented pathogenic potential. Here, multilocus sequence typing was performed for phylogenetic analysis of nosocomial isolates ofStenotrophomonasspp. and, environmental and clinical strains ofS. maltophilia. Biochemical and multidrug resistance profiles of nosocomial and clinical strains were determined. The inferred phylogenetic profile showed high clonal variability, what correlates with the adaptability process ofStenotrophomonasto different habitats. Two clinical isolates subgroups ofS. maltophiliasharing high phylogenetic homogeneity presented intergroup recombination, thus indicating the high permittivity to horizontal gene transfer, a mechanism involved in the acquisition of antibiotic resistance and expression of virulence factors. For most of the clinical strains, phylogenetic inference was made using only partialppsA gene sequence. Therefore, the sequencing of just one specific fragment of this gene would allow, in many cases, determining whether the infection withS. maltophiliawas nosocomial or community-acquired.

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Molecular Typing of Environmental and Clinical Strains of Vibrio vulnificus Isolated in the Northeastern USA

PLoS ONE ◽

10.1371/journal.pone.0083357 ◽

2013 ◽

Vol 8 (12) ◽

pp. e83357 ◽

Cited By ~ 16

Author(s):

Yann Reynaud ◽

Steven Pitchford ◽

Sophie De Decker ◽

Gary H. Wikfors ◽

Christopher L. Brown

Keyword(s):

Molecular Typing ◽

Vibrio Vulnificus ◽

Clinical Strains ◽

Northeastern Usa

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Evaluation of the pathogenic potential, antimicrobial susceptibility, and genomic relations of Yersinia enterocolitica strains from food and human origin

Canadian Journal of Microbiology ◽

10.1139/cjm-2015-0391 ◽

2015 ◽

Vol 61 (11) ◽

pp. 851-860 ◽

Cited By ~ 3

Author(s):

Cecilia S.M. Lucero-Estrada ◽

José Miguel Soria ◽

Gabriela Isabel Favier ◽

María Esther Escudero

Keyword(s):

Yersinia Enterocolitica ◽

Antimicrobial Susceptibility ◽

Genomic Diversity ◽

Phenotypic Traits ◽

Pathogenic Potential ◽

Human Samples ◽

Virulence Markers ◽

San Luis ◽

Food Borne ◽

Genomic Relationships

Yersinia enterocolitica is a food-borne pathogen that causes gastroenteritis with occasional postinfection sequels. This study was aimed to determinate the pathogenic potential, antimicrobial susceptibility, and genomic relationships of Y. enterocolitica strains of different bioserotypes (B/O) isolated from foods and human samples in San Luis, Argentina. Strains obtained by culture were bioserotyped and characterized by phenotypic and genotypic virulence markers, antimicrobial susceptibility, and pulsed-field gel electrophoresis (PFGE). Yersinia enterocolitica was detected in 9.2% of 380 samples, with a distribution of 10.6% (30/284) for food products and 5.2% (5/96) for human samples. Regarding the pathogenic potential, B1A strains of different serotypes were virF– ail–, of which 72.0% (13/18) were ystB+ with virulence-related phenotypic characteristics. Among B2/O:9 isolates, 75.0% (9/12) exhibited the genotype virF+ ail+ ystB– along with phenotypic traits associated with virulence; the same genotype was observed in 80.0% (4/5) of B3/O:3 and B3/O:5 strains. By PFGE, it was possible to separate Y. enterocolitica biotypes into 4 clonal groups (A to D) with 23 genomic types, generating a discriminatory index of 0.96. All isolates were susceptible to antimicrobials used for clinical treatment. This study highlights the presence of pathogenic bioserotypes and the high genomic diversity of the Y. enterocolitica strains isolated in our region.

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Serogroup, Virulence, and Genetic Traits of Vibrio parahaemolyticus in the Estuarine Ecosystem of Bangladesh

Applied and Environmental Microbiology ◽

10.1128/aem.00266-09 ◽

2009 ◽

Vol 75 (19) ◽

pp. 6268-6274 ◽

Cited By ~ 20

Author(s):

Munirul Alam ◽

Wasimul B. Chowdhury ◽

N. A. Bhuiyan ◽

Atiqul Islam ◽

Nur A. Hasan ◽

...

Keyword(s):

Vibrio Parahaemolyticus ◽

Marker Gene ◽

Human Health Risk ◽

Geographic Origin ◽

Virulence Gene ◽

Estuarine Ecosystem ◽

Genetic Traits ◽

Clinical Strains ◽

Pandemic Strains ◽

And Cluster Analysis

ABSTRACT Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes tox R and tlh were confirmed by PCR in all but two strains, which also lacked tox R. A total of 18 (41%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., “clonal cluster,” as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.

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Sub-Specific Populations of Verticillium dahliae and their Roles in Vascular Wilt Pathogsystems

10.32747/1996.7574343.bard ◽

1996 ◽

Author(s):

Randall C. Rowe ◽

Jaacov Katan ◽

Talma Katan ◽

Leah Tsror

Keyword(s):

Host Plant ◽

Plant Species ◽

Verticillium Dahliae ◽

Severe Disease ◽

Vegetative Compatibility ◽

Phenotypic Traits ◽

Potato Seed ◽

Vascular Wilt ◽

Large Collection ◽

Pathogenic Potential

Verticillium dahliae is an economically important pathogen causing vascular wilt on over 160 plant species. In North America, potato early dying is a significant disease of potato, especially in the midwest and Pacific northwest states. This disease is caused by the fungus Verticillium dahliae and in some cases involves a synergistic interaction with root-lesion nematodes, primarily Pratylenchus penetrans. In Israel, Verticillium wilt occurs in many regions and inflicts serious losses in potato, cotton, and other crops. Objectives of this project were to establish a large collection of isolates of Verticillium dahliae from potato (USA) and several host plants (Israel) and to characterize and compare the isolates with regard to morphology, vegetative compatibility group (VCG), and pathogenic capabilities on several hosts. Isolations were made from 224 commercial lots of certified potato seed tubers from across N. America and 87 potato fields located in the Columbia Basin of Oregon and Washington. A large collection of isolates from central U.S. states already existed. In Israel, 47 field sites were sampled and isolates of Verticillium dahliae were recovered from 13 host plant species and from soil. Potato isolates from N. America were tested for vegetative compatibility and all found to be in VCG 4 with about 2/3 in VCG 4A and the rest in VCG 4B. VCG 4A isolates were significantly more aggressive on potato than VCG 4B isolates and were more likely to interact synergistically with P. penetrans. The Israeli isolates fell into three vegetative compatibility groups. Nearly all (> 90%) VCG2B and VCG 4B isolates were recovered from the northern and southern parts of Israel, respectively, with some overlap in central areas. Several pathotypes were defined in cotton, using cotton and eggplant together as differentials. All VCG 2B isolates from cotton caused severe disease in cotton, while VCG 2A and VCG 4B isolates from several crops were much less aggressive to cotton. When Israeli isolates of VCGs 2A, 2B and 4B were inoculated to potato and tomato, VCG 4B isolates caused much more severe disease on potato and VCG 2A isolates caused much more severe disease in tomato. Differential patterns of pathogenicity and aggressiveness of these VCGs on potato and tomato were consistent regardless of the host plant of origin. Isolates of the same VCG resembled one another more than isolates from different VCGs based on colony and microsclerotial morphology, temperature responses and, partially, in pathogenicity. Vegetative compatibility grouping of V. dahliae in Israel appears closely associated with specific pathogenicity and other phenotypic traits. The absence of VCG 4A in Israel is significant. VCG patterns among Verficillium populations are useful to predict relatedness and pathogenic potential in both countries.

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PHENOTYPICAL CHARACTERISTICS OF THE BIOLOGICAL PROPERTIES OF STAPHYLOCOCCI WITHDRAWN FROM PATIENTS WITH ALLERGIC DERMATITIS

EUREKA Health Sciences ◽

10.21303/2504-5679.2020.001125 ◽

2020 ◽

Vol 1 ◽

pp. 15-21 ◽

Cited By ~ 1

Author(s):

Svetlana Dzhoraeva ◽

Nataliya Sobol ◽

Helen Ivantsova

Keyword(s):

Phenotypic Expression ◽

Skin Surface ◽

Biological Properties ◽

Phenotypic Traits ◽

Pathogenic Potential ◽

Allergic Dermatitis ◽

Host Protection ◽

Protection Mechanisms ◽

Biochemical Identification ◽

Diagnosis Criterion

Atopic dermatitis, eczema, allergic dermatitis occupy the main place among dermatoses, where the allergic component is leading in the onset and development of the disease. The most common complication of allergic dermatitis is the attachment of a secondary pyococcus infection, which is associated with a decrease in the antimicrobial resistance of the skin surface. Therapy of infectious lesions is complicated by the increasing resistance of the main pathogens of pyoderma - Staphylococcus aureus and Staphylococcus epidermidis - to widely used antibiotics. The aim of the research: to determine the phenotypic features of staphylococci extracted from patients with allergic dermatitis to assess their pathogenic potential. Materials and methods. The object of the study was 369 staphylococcus isolates removed from affected and intact skin sections of patients with allergic dermatitis, as well as from representative skin sections of healthy individuals undergoing inpatient treatment at the Department of Dermatology of “Institute of Dermatology and Venereology of NAMS of Ukraine”. Biochemical identification and biological properties of staphylococci were determined using methods of classical bacteriology. Results. As a result of the conducted researches, it is established that the complex of phenotypic traits of the removed staphylococcus cultures indicates the presence in the pathogen of factors related to the resistance of the host protection mechanisms and determines the intensity of the alterative action of the infectant in relation to the host organism, the phenotypic manifestation of the studied factors was higher in the staphylococcus isolates removed from the affected skin areas of patients with allergic dermatitis. Conclusions. The level and frequency of phenotypic expression of pathogenicity factors are more pronounced in microorganisms obtained from patients from affected and intact areas compared to controls, which confirms their pathogenetic role in the burden of the disease, which in turn can be used as an auxiliary differential diagnosis criterion.

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Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

10.21203/rs.2.20033/v1 ◽

2020 ◽

Author(s):

Archile Eric paguem ◽

Babette Abanda ◽

Mbunkah Daniel Achukwi ◽

Praveen Baskaran ◽

Stefan Czemmel ◽

...

Keyword(s):

Bos Taurus ◽

Bos Indicus ◽

Cattle Breed ◽

Phenotypic Traits ◽

Zebu Cattle ◽

Whole Genome ◽

Genetic Traits ◽

Cattle Breeds ◽

Taurine Breed ◽

Taurine Cattle

Abstract BackgroundWest African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with a number of factors, amongst others small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their populations size rendering them vulnerable to extinction. The Namchi (Doayo) taurine cattle breed has documented resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced for the first time the genomes of five cattle breeds from Cameroon: the Namchi (Doayo), an endangered trypanotolerant taurine breed, the Kapsiki, an indigenous trypanosusceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.ResultsApproximately 167 Giga bases of raw sequencing data were generated and mapped to the cattle reference genome UMD3.1. The coverage was 22 to 30-fold. The single nucleotide polymorphisms (SNPs) were compared with reference genomes of European Bos taurus Holstein and of Asian Bos indicus Brahman and the African trypanotolerant N’Dama breeds.Of a total of 50 million SNPs identified, 3.43 million were breed-specific ranging from 0.37 to 0.47 million SNPs in the domestic Cameroonian breeds and approximately 0.58 million constituted of small insertions and deletions. We identified breed specific-non-synonymous variants as genetic traits that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi (Doayo) breed, heat tolerance in the Kapsiki breed, and growth, metabolism and meat quality in the Gudali breeds. Phylogenetic comparison grouped Namchi (Doayo) to the African Zebu clade indicating a hybrid status of the selected animal with a Zebu breed, albeit it showed the Namchi breed’s phenotype.ConclusionsThe findings provide the first comprehensive set of full genome variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

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Vermamoeba vermiformis - A Free-Living Amoeba with Public Health and Environmental Health Significance

The Open Parasitology Journal ◽

10.2174/1874421401907010040 ◽

2019 ◽

Vol 7 (1) ◽

pp. 40-47 ◽

Cited By ~ 2

Author(s):

Patrick L. Scheid

Keyword(s):

Public Health ◽

Environmental Health ◽

Case Reports ◽

Human Pathogens ◽

Free Living ◽

Pathogenic Potential ◽

Vermamoeba Vermiformis ◽

Wide Range ◽

Health Significance ◽

Health Relevance

Many case reports emphasize the fact that Free-Living Amoebae (FLA) can relatively easily get in contact with humans or animals. The presence of several facultative parasitic FLA in habitats related to human activities supports their public health relevance. While some strains of Acanthamoeba,Naegleria fowleri,Balamuthia mandrillarisand several other FLA have been described as facultative human pathogens, it remains controversial whetherVermamoeba vermiformisstrains may have a pathogenic potential, or whether this FLA is just an incidental contaminant in a range of human cases. However, several cases support its role as a human parasite, either as the only etiological agent, or in combination with other pathogens. Additionally, a wide range of FLA is known as vectors of microorganisms (endocytobionts), hereby emphasizing their environmental significance. Among those FLA serving as hosts for and vectors of (pathogenic) endocytobionts, there are also descriptions ofV. vermiformisas a vehicle and a reservoir of those endocytobionts. The involvement in animal and human health, the role as vector of pathogenic microorganisms and the pathogenicity in cell cultures, led to the assumption thatV. vermiformisshould be considered relevant in terms of public health and environmental health.

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