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1.
An Acad Bras Cienc ; 93(3): e20190200, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33950134

RESUMEN

Listeria monocytogenes is an opportunistic pathogen that causes listeriosis, a foodborne disease with low incidence but with high mortality rate in humans. This microorganism has been recovered from several dairy products, especially those produced with raw milk. The objective of this work was to investigate the presence of virulence genes, and also to define the antimicrobial susceptibility profile of L. monocytogenes isolates recovered from serrano artisanal cheese produced in Southern region of Brazil. Nine strains of L. monocytogenes (serotypes 1/2b and 4b) were evaluated through PCR to detect the presence of the virulence genes hly, inlA, inlC, inlJ, actA, plcB and iap, while antimicrobial susceptibility profile was determined via disk diffusion method. All strains exhibited the presence of the genes hly and plcB, whereas the other genes (iap, actA, inlA, inlC and inlJ) were only detected in eight strains. We verified that all strains were resistant to at least one antimicrobial agent and three of them showed multidrug resistance. These findings demonstrated the serrano artisanal cheese offers risks to consumers' health and point to a need of adaptations and monitoring of manufacturing process of this food, in order to prevent the dissemination of L. monocytogenes.


Asunto(s)
Queso , Listeria monocytogenes , Listeriosis , Brasil , Humanos , Listeria monocytogenes/genética , Listeriosis/tratamiento farmacológico , Virulencia/genética
2.
BMC Plant Biol ; 21(1): 224, 2021 May 19.
Artículo en Inglés | MEDLINE | ID: mdl-34011295

RESUMEN

BACKGROUND: The pine wood nematode (PWN), Bursaphelenchus xylophilus, is a devastating pathogen of many Pinus species in China. The aim of this study was to understand the interactive molecular mechanism of PWN and its host by comparing differentially expressed genes and candidate effectors from three transcriptomes of B. xylophilus at different infection stages. RESULTS: In total, 62, 69 and 46 candidate effectors were identified in three transcriptomes (2.5 h postinfection, 6, 12 and 24 h postinoculation and 6 and 15 d postinfection, respectively). In addition to uncharacterized pioneers, other candidate effectors were involved in the degradation of host tissues, suppression of host defenses, targeting plant signaling pathways, feeding and detoxification, which helped B. xylophilus survive successfully in the host. Seven candidate effectors were identified in both our study and the B. xylophilus transcriptome at 2.5 h postinfection, and one candidate effector was identified in all three transcriptomes. These common candidate effectors were upregulated at infection stages, and one of them suppressed pathogen-associated molecular pattern (PAMP) PsXEG1-triggered cell death in Nicotiana benthamiana. CONCLUSIONS: The results indicated that B. xylophilus secreted various candidate effectors, and some of them continued to function throughout all infection stages. These various candidate effectors were important to B. xylophilus infection and survival, and they functioned in different ways (such as breaking down host cell walls, suppressing host defenses, promoting feeding efficiency, promoting detoxification and playing virulence functions). The present results provide valuable resources for in-depth research on the pathogenesis of B. xylophilus from the perspective of effectors.


Asunto(s)
Interacciones Huésped-Parásitos/genética , Infecciones/genética , Nematodos/genética , Nematodos/parasitología , Parásitos/genética , Pinus/parasitología , Virulencia/genética , Animales , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genes de Plantas
3.
Nat Commun ; 12(1): 2491, 2021 05 03.
Artículo en Inglés | MEDLINE | ID: mdl-33941780

RESUMEN

Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii's success and its ongoing adaptation to the human host.


Asunto(s)
Agua Potable/microbiología , Genoma Bacteriano/genética , Enfermedades Pulmonares/epidemiología , Infecciones por Mycobacterium no Tuberculosas/epidemiología , Mycobacterium kansasii/genética , Metabolismo Energético/genética , Variación Genética/genética , Genética de Población/métodos , Genómica , Humanos , Enfermedades Pulmonares/microbiología , Infecciones por Mycobacterium no Tuberculosas/microbiología , Mycobacterium kansasii/aislamiento & purificación , Virulencia/genética , Microbiología del Agua
4.
BMC Genomics ; 22(1): 382, 2021 May 25.
Artículo en Inglés | MEDLINE | ID: mdl-34034667

RESUMEN

BACKGROUND: The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised - ToxA, Tox1 and Tox3. RESULTS: A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions. CONCLUSIONS: We present an updated series of genomic resources for P. nodorum Sn15 - an important reference isolate and model necrotroph - with a comprehensive survey of its predicted pathogenicity content.


Asunto(s)
Enfermedades de las Plantas , Proteoma , Ascomicetos , Australia , Cromosomas , Enfermedades de las Plantas/genética , Virulencia/genética
5.
BMC Genomics ; 22(1): 367, 2021 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-34016049

RESUMEN

BACKGROUND: Colonization of dairy cows by Staphylococcus aureus (S. aureus), especially those which are multi-drug resistant and toxin producing, is a concern for animal health and well-being as well as public health. The objective of this study was to investigate the prevalence, antibiotic resistance, gene content and virulence determinants of S. aureus in bulk tank milk samples (BTM) from U.S. dairy herds. RESULTS: BTM samples were collected, once in winter and once in summer, from 189 U.S. dairy herds. Of 365 BTM samples cultured, the sample and herd prevalence of S. aureus in BTM was 46.6% (170 of 365 samples) and 62.4% (118 of 189 herds), respectively. Among a subset of 138 S. aureus isolates that were stored for further analysis, 124 were genome sequenced after being confirmed as S. aureus using phenotypic tests. The most commonly identified antimicrobial resistance-associated gene was norA (99.2%) and mecA gene responsible for methicillin resistance (MRSA) was identified in one isolate (0.8%). The most frequently detected putative virulence genes were aur (100%), hlgB (100%), hlgA, hlgC, hlb (99.2%), lukE (95.9%) and lukD (94.3%). In the 53 staphylococcal enterotoxin positive isolates, sen (37.9%), sem (35.5%), sei (35.5%) and seg (33.1%) were the most frequently detected enterotoxin genes. Among the 14 sequence types (ST) and 18 spa types identified, the most common was ST2187 (20.9%) and t529 (28.2%), respectively. The most predominant clone was CC97 (47.6%) followed by CC unknown (36.3%). The single MRSA isolate belonged to ST72-CC8, spa type t126 and was negative for the tst gene but harbored all the other virulence genes investigated. CONCLUSION: Our findings indicated a high prevalence of S. aureus in BTM of U.S. dairy herds, with isolates showing little evidence of resistance to antibiotics commonly used to treat mastitis. However, isolates often carried genes for the various enterotoxins. This study identified predominant genetic clones. Despite lower prevalence, the presence of MRSA and multi-drug resistant strains in BTM poses a significant risk to animal and public health if their number were to increase in dairy environment. Therefore, it is necessary to continuously monitor the use of antibiotics in dairy cows.


Asunto(s)
Staphylococcus aureus Resistente a Meticilina , Infecciones Estafilocócicas , Animales , Antibacterianos/farmacología , Bovinos , Farmacorresistencia Microbiana , Femenino , Variación Genética , Staphylococcus aureus Resistente a Meticilina/genética , Pruebas de Sensibilidad Microbiana , Leche , Prevalencia , Infecciones Estafilocócicas/epidemiología , Infecciones Estafilocócicas/veterinaria , Staphylococcus aureus/genética , Virulencia/genética
6.
Nat Commun ; 12(1): 2790, 2021 05 13.
Artículo en Inglés | MEDLINE | ID: mdl-33986286

RESUMEN

SARS-CoV-2 is of zoonotic origin and contains a PRRA polybasic cleavage motif which is considered critical for efficient infection and transmission in humans. We previously reported on a panel of attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction of the spike protein. Here, we characterize pathogenicity, immunogenicity, and protective ability of a further cell-adapted SARS-CoV-2 variant, Ca-DelMut, in in vitro and in vivo systems. Ca-DelMut replicates more efficiently than wild type or parental virus in Vero E6 cells, but causes no apparent disease in hamsters, despite replicating in respiratory tissues. Unlike wild type virus, Ca-DelMut causes no obvious pathological changes and does not induce elevation of proinflammatory cytokines, but still triggers a strong neutralizing antibody and T cell response in hamsters and mice. Ca-DelMut immunized hamsters challenged with wild type SARS-CoV-2 are fully protected, with little sign of virus replication in the upper or lower respiratory tract, demonstrating sterilizing immunity.


Asunto(s)
/diagnóstico , Mutación , Glicoproteína de la Espiga del Coronavirus/genética , Replicación Viral/genética , Animales , /virología , Línea Celular Tumoral , Chlorocebus aethiops , Cricetinae , Citocinas/inmunología , Citocinas/metabolismo , Femenino , Interacciones Huésped-Patógeno , Humanos , Masculino , Mesocricetus , Ratones Endogámicos BALB C , /patogenicidad , Linfocitos T/inmunología , Linfocitos T/metabolismo , Células Vero , Virulencia/genética , Virulencia/inmunología
7.
BMC Genomics ; 22(1): 393, 2021 May 27.
Artículo en Inglés | MEDLINE | ID: mdl-34044766

RESUMEN

BACKGROUND: Plant pathogens cause substantial crop losses in agriculture production and threaten food security. Plants evolved the ability to recognize virulence factors and pathogens have repeatedly escaped recognition due rapid evolutionary change at pathogen virulence loci (i.e. effector genes). The presence of transposable elements (TEs) in close physical proximity of effector genes can have important consequences for gene regulation and sequence evolution. Species-wide investigations of effector gene loci remain rare hindering our ability to predict pathogen evolvability. RESULTS: Here, we performed genome-wide association studies (GWAS) on a highly polymorphic mapping population of 120 isolates of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe. We identified a major locus underlying significant variation in reproductive success of the pathogen and damage caused on the wheat cultivar Claro. The most strongly associated locus is intergenic and flanked by genes encoding a predicted effector and a serine-type endopeptidase. The center of the locus contained a highly dynamic region consisting of multiple families of TEs. Based on a large global collection of assembled genomes, we show that the virulence locus has undergone substantial recent sequence evolution. Large insertion and deletion events generated length variation between the flanking genes by a factor of seven (5-35 kb). The locus showed also strong signatures of genomic defenses against TEs (i.e. RIP) contributing to the rapid diversification of the locus. CONCLUSIONS: In conjunction, our work highlights the power of combining GWAS and population-scale genome analyses to investigate major effect loci in pathogens.


Asunto(s)
Elementos Transponibles de ADN , Genoma Fúngico , Ascomicetos , Elementos Transponibles de ADN/genética , Europa (Continente) , Evolución Molecular , Estudio de Asociación del Genoma Completo , Enfermedades de las Plantas/genética , Virulencia/genética
8.
Int J Mol Sci ; 22(5)2021 Mar 02.
Artículo en Inglés | MEDLINE | ID: mdl-33801529

RESUMEN

During the infection of a host, plant pathogenic fungi secrete small proteins called effectors, which then modulate the defence response of the host. In the Fusarium oxysporum species complex (FOSC), the secreted in xylem (SIX) gene effectors are important for host-specific pathogenicity, and are also useful markers for identifying the various host-specific lineages. While the presence and diversity of the SIX genes has been explored in many of the pathogenic lineages of F. oxysporum, there is a limited understanding of these genes in non-pathogenic, endophytic isolates of F. oxysporum. In this study, universal primers for each of the known SIX genes are designed and used to screen a panel of endophytically-associated Fusarium species isolated from healthy, asymptomatic banana tissue. SIX gene orthologues are identified in the majority of the Fusarium isolates screened in this study. Furthermore, the SIX gene profiles of these endophytic isolates do not overlap with the SIX genes present in the pathogenic lineages of F. oxysporum that are assessed in this study. SIX gene orthologues have not been commonly identified in Fusarium species outside of the FOSC nor in non-pathogenic isolates of F. oxysporum. The results of this study indicate that the SIX gene effectors may be more broadly distributed throughout the Fusarium genus than previously thought. This has important implications for understanding the evolution of pathogenicity in the FOSC.


Asunto(s)
Proteínas Fúngicas/metabolismo , Fusarium/genética , Regulación Fúngica de la Expresión Génica , Especificidad del Huésped , Musa/microbiología , Enfermedades de las Plantas/microbiología , Transcriptoma , Proteínas Fúngicas/genética , Fusarium/patogenicidad , Perfilación de la Expresión Génica , Interacciones Huésped-Patógeno , Filogenia , Virulencia/genética
9.
Int J Mol Sci ; 22(6)2021 Mar 10.
Artículo en Inglés | MEDLINE | ID: mdl-33801996

RESUMEN

Viroids are tiny single-stranded circular RNA pathogens that infect plants. Viroids do not encode any proteins, yet cause an assortment of symptoms. The following review describes viroid classification, molecular biology and spread. The review also discusses viroid pathogenesis, host interactions and detection. The review concludes with a description of future prospects in viroid research.


Asunto(s)
ARN Circular/genética , ARN Viral/genética , Viroides/genética , Replicación Viral/genética , Resistencia a la Enfermedad/genética , Interacciones Huésped-Patógeno , Modelos Genéticos , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/virología , Plantas/genética , Plantas/virología , Viroides/clasificación , Viroides/patogenicidad , Virulencia/genética
10.
BMC Infect Dis ; 21(1): 370, 2021 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-33879083

RESUMEN

BACKGROUND: Native valves infective endocarditis due to Escherichia coli is still a rare disease and a particular virulence of some E.coli isolate may be suspected. CASE PRESENTATION: A 79-year-old woman presented during the post-operative period of an orthopedic surgery a urinary tract infection following obstructive ureteral lithiasis. E. coli was isolated from a pure culture of urine and blood sampled simultaneously. After evidence of sustained E.coli septicemia, further investigations revealed acute cholecystitis with the same micro-organism in biliary drainage and a native valve mitral endocarditis. E.coli was identified as O2:K7:H6, phylogenetic group B2, ST141, and presented several putative and proven virulence genes. The present isolate can be classified as both extra-intestinal pathogenic E.coli (ExPECJJ) and uropathogenic E. coli (UPECHM). CONCLUSIONS: The relationship between the virulent factors present in ExPEC strains and some serotypes of E. coli that could facilitate the adherence to cardiac valves warrants further investigation.


Asunto(s)
Endocarditis/diagnóstico , Escherichia coli Patógena Extraintestinal/aislamiento & purificación , Anciano , Animales , Endocarditis/microbiología , Escherichia coli Patógena Extraintestinal/clasificación , Escherichia coli Patógena Extraintestinal/patogenicidad , Femenino , Humanos , Procedimientos Ortopédicos/efectos adversos , Filogenia , Periodo Posoperatorio , Infecciones Urinarias/microbiología , Infecciones Urinarias/patología , Urolitiasis/cirugía , Virulencia/genética
11.
Int J Mol Sci ; 22(5)2021 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-33800857

RESUMEN

Fusarium wilt of flax is an aggressive disease caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini. It is a challenging pathogen presenting a constant threat to flax production industry worldwide. Previously, we reported chromosome-level assemblies of 5 highly pathogenic F. oxysporum f. sp. lini strains. We sought to characterize the genomic architecture of the fungus and outline evolutionary mechanisms shaping the pathogen genome. Here, we reveal the complex multi-compartmentalized genome organization and uncover its diverse evolutionary dynamics, which boosts genetic diversity and facilitates host adaptation. In addition, our results suggest that host of functions implicated in the life cycle of mobile genetic elements are main contributors to dissimilarity between proteomes of different Fusaria. Finally, our experiments demonstrate that mobile genetics elements are expressed in planta upon infection, alluding to their role in pathogenicity. On the whole, these results pave the way for further in-depth studies of evolutionary forces shaping the host-pathogen interaction.


Asunto(s)
Lino/microbiología , Fusarium/genética , Genoma Fúngico , Enfermedades de las Plantas/microbiología , Cromosomas Fúngicos/genética , Evolución Molecular , Proteínas Fúngicas/genética , Interacciones Huésped-Patógeno/genética , Redes y Vías Metabólicas/genética , Anotación de Secuencia Molecular , Filogenia , Proteoma , Especificidad de la Especie , Virulencia/genética
12.
BMC Infect Dis ; 21(1): 361, 2021 Apr 17.
Artículo en Inglés | MEDLINE | ID: mdl-33865334

RESUMEN

BACKGROUND: Urinary Tract Infection (UTI) is one of the most common bacterial infectious diseases which causes considerable morbidity and costly health problems. Uropathogenic Escherichia coli (UPEC), the most common pathogen causing UTI, is a highly heterogeneous group of extraintestinal pathogenic E. coli (ExPEC) which may carry a variety of virulence factors and belonging to different phylogenetic backgrounds. The current study aimed to investigate the frequency and association between various virulence factors (VFs) and phylogenetic groups of UPEC and commensal isolates. METHODS: UPEC and commensal E. coli strains isolated from UTI and feces of healthy humans were compared for the presence of VFs and phylogenetic groups. Association between virulence genes was investigated and cluster analysis was employed. RESULTS: According to the results, among a 30 virulence markers tested, the pathogenicity-associated island (PAI), papAH, papEF, fimH, fyuA, and traT genes prevalence were statistically significant in UPEC isolates. A strong association was found between the B2 and D phylogenetic groups and clinical isolates of UPEC; while, commensal isolates were mostly associated with phylogenetic group A. The aggregated VFs scores were more than twice higher in the UPEC isolates in comparison with the commensal isolates. Interestingly, the B2 group in both UPEC and commensal isolates had the highest VF scores. A strong positive association was found between several virulence genes. The clustering results demonstrated that UPEC or commensal E. coli isolates were highly heterogeneous due to different composition of their virulence gene pool and pathogenicity islands. CONCLUSION: Genetic structure and VFs of UPEC strains vary from region to region; therefore, to control the UTI, the epidemiological aspects and characterization of the UPEC isolates need to be investigated in different regions. Since UPEC isolates are generally originate from the commensal strains, it may be feasible to reduce the UTI burden by interfering the intestinal colonization, particularly in the highly pathogenic clonal lineages such as B2.


Asunto(s)
Infecciones por Escherichia coli/microbiología , Infecciones Urinarias/microbiología , Escherichia coli Uropatógena , Factores de Virulencia/genética , Virulencia/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Casos y Controles , Niño , Preescolar , Infecciones por Escherichia coli/epidemiología , Proteínas de Escherichia coli/genética , Escherichia coli Patógena Extraintestinal/genética , Escherichia coli Patógena Extraintestinal/aislamiento & purificación , Escherichia coli Patógena Extraintestinal/patogenicidad , Femenino , Islas Genómicas/genética , Humanos , Lactante , Recién Nacido , Irán/epidemiología , Masculino , Persona de Mediana Edad , Filogenia , Prevalencia , Infecciones Urinarias/epidemiología , Escherichia coli Uropatógena/clasificación , Escherichia coli Uropatógena/genética , Escherichia coli Uropatógena/aislamiento & purificación , Escherichia coli Uropatógena/patogenicidad , Adulto Joven
13.
J Med Microbiol ; 70(4)2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33830911

RESUMEN

Introduction. Antipathogenic or antivirulence strategy is to target a virulence pathway that is dispensable for growth, in the hope to mitigate the selection for drug resistance.Hypothesis/Gap Statment. Peroxide stress responses are one of the conserved virulence pathways in bacterial pathogens and thus good targets for antipathogenic strategy.Aim. This study aims to identify a new chemical compound that targets OxyR, the peroxide sensor required for the full virulence of the opportunistic human pathogen, Pseudomonas aeruginosa.Methodology. Computer-based virtual screening under consideration of the 'eNTRy' rules and molecular docking were conducted on the reduced form of the OxyR regulatory domain (RD). Selected hits were validated by their ability to phenocopy the oxyR null mutant and modulate the redox cycle of OxyR.Results. We first isolated three robust chemical hits that inhibit OxyR without affecting prototrophic growth or viability. One (compound 1) of those affected the redox cycle of OxyR in response to H2O2 treatment, in a way to impair its function. Compound 1 displayed selective antibacterial efficacy against P. aeruginosa in Drosophila infection model, without antibacterial activity against Staphylococcus aureus.Conclusion. These results suggest that compound 1 could be an antipathogenic hit inhibiting the P. aeruginosa OxyR. More importantly, our study provides an insight into the computer-based discovery of new-paradigm selective antibacterials to treat Gram-negative bacterial infections presumably with few concerns of drug resistance.


Asunto(s)
Antibacterianos/farmacología , Pseudomonas aeruginosa/efectos de los fármacos , Pseudomonas aeruginosa/patogenicidad , Transactivadores/antagonistas & inhibidores , Animales , Drosophila , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Peróxido de Hidrógeno/farmacología , Simulación del Acoplamiento Molecular , Mutación , Oxidación-Reducción , Estrés Oxidativo/efectos de los fármacos , Infecciones por Pseudomonas/tratamiento farmacológico , Infecciones por Pseudomonas/mortalidad , Pseudomonas aeruginosa/genética , Tasa de Supervivencia , Transactivadores/química , Transactivadores/genética , Transactivadores/metabolismo , Virulencia/efectos de los fármacos , Virulencia/genética
14.
BMC Genomics ; 22(1): 302, 2021 Apr 26.
Artículo en Inglés | MEDLINE | ID: mdl-33902447

RESUMEN

BACKGROUND: Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops. There is currently a lack of a high-quality reference genome for this species despite several attempts that have been made towards sequencing its genome. The lack of a good quality genome sequence has been a setback for various genetic and genomic research to be done on this species. As a consequence, little is known regarding its genome characteristics and how these contribute to its pathogenicity and invasiveness. RESULTS: In this work we generated a high-quality genome sequence and annotation for P. cinnamomi using a combination of Oxford Nanopore and Illumina sequencing technologies. The annotation was done using RNA-Seq data as supporting gene evidence. The final assembly consisted of 133 scaffolds, with an estimated genome size of 109.7 Mb, N50 of 1.18 Mb, and BUSCO completeness score of 97.5%. Genome partitioning analysis revealed that P. cinnamomi has a two-speed genome characteristic, similar to that of other oomycetes and fungal plant pathogens. In planta gene expression analysis revealed up-regulation of pathogenicity-related genes, suggesting their important roles during infection and host degradation. CONCLUSION: This study has provided a high-quality reference genome and annotation for P. cinnamomi. This is among the best assembled genomes for any Phytophthora species assembled to date and thus resulted in improved identification and characterization of pathogenicity-related genes, some of which were undetected in previous versions of genome assemblies. Phytophthora cinnamomi harbours a large number of effector genes which are located in the gene-poor regions of the genome. This unique genomic partitioning provides P. cinnamomi with a high level of adaptability and could contribute to its success as a highly invasive species. Finally, the genome sequence, its annotation and the pathogenicity effectors identified in this study will serve as an important resource that will enable future studies to better understand and mitigate the impact of this important pathogen.


Asunto(s)
Phytophthora , Ecosistema , Genómica , Phytophthora/genética , Enfermedades de las Plantas , Virulencia/genética
15.
Science ; 372(6541)2021 04 30.
Artículo en Inglés | MEDLINE | ID: mdl-33926925

RESUMEN

Although almost all mycobacterial species are saprophytic environmental organisms, a few, such as Mycobacterium tuberculosis, have evolved to cause transmissible human infection. By analyzing the recent emergence and spread of the environmental organism M. abscessus through the global cystic fibrosis population, we have defined key, generalizable steps involved in the pathogenic evolution of mycobacteria. We show that epigenetic modifiers, acquired through horizontal gene transfer, cause saltational increases in the pathogenic potential of specific environmental clones. Allopatric parallel evolution during chronic lung infection then promotes rapid increases in virulence through mutations in a discrete gene network; these mutations enhance growth within macrophages but impair fomite survival. As a consequence, we observe constrained pathogenic evolution while person-to-person transmission remains indirect, but postulate accelerated pathogenic adaptation once direct transmission is possible, as observed for M. tuberculosis Our findings indicate how key interventions, such as early treatment and cross-infection control, might restrict the spread of existing mycobacterial pathogens and prevent new, emergent ones.


Asunto(s)
Enfermedades Transmisibles Emergentes/microbiología , Evolución Molecular , Aptitud Genética , Pulmón/microbiología , Infecciones por Mycobacterium no Tuberculosas/microbiología , Mycobacterium abscessus/genética , Mycobacterium abscessus/patogenicidad , Neumonía Bacteriana/microbiología , Enfermedades Transmisibles Emergentes/transmisión , Conjuntos de Datos como Asunto , Epigénesis Genética , Transferencia de Gen Horizontal , Genoma Bacteriano , Humanos , Mutación , Infecciones por Mycobacterium no Tuberculosas/transmisión , Neumonía Bacteriana/transmisión , Virulencia/genética
16.
Epidemiol Infect ; 149: e110, 2021 04 30.
Artículo en Inglés | MEDLINE | ID: mdl-33928885

RESUMEN

The outbreak of pneumonia-like respiratory disorder at China and its rapid transmission world-wide resulted in public health emergency, which brought lineage B betacoronaviridae SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) into spotlight. The fairly high mutation rate, frequent recombination and interspecies transmission in betacoronaviridae are largely responsible for their temporal changes in infectivity and virulence. Investigation of global SARS-CoV-2 genotypes revealed considerable mutations in structural, non-structural, accessory proteins as well as untranslated regions. Among the various types of mutations, single-nucleotide substitutions are the predominant ones. In addition, insertion, deletion and frame-shift mutations are also reported, albeit at a lower frequency. Among the structural proteins, spike glycoprotein and nucleocapsid phosphoprotein accumulated a larger number of mutations whereas envelope and membrane proteins are mostly conserved. Spike protein and RNA-dependent RNA polymerase variants, D614G and P323L in combination became dominant world-wide. Divergent genetic variants created serious challenge towards the development of therapeutics and vaccines. This review will consolidate mutations in different SARS-CoV-2 proteins and their implications on viral fitness.


Asunto(s)
/virología , Genoma Viral/fisiología , Mutación , /genética , Animales , Genoma Viral/genética , Humanos , Familia de Multigenes , Fosfoproteínas/genética , Glicoproteína de la Espiga del Coronavirus/genética , Proteínas Reguladoras y Accesorias Virales/genética , Virulencia/genética
18.
Gene ; 787: 145646, 2021 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-33848574

RESUMEN

Salmonella spp. is one of the major agents of foodborne disease worldwide, and its virulence genes are responsible for the main pathogenic mechanisms of this micro-organism. The whole-genome sequencing (WGS) of pathogens has become a lower-cost and more accessible genotyping tool providing many gene analysis possibilities. This study provided an in silico investigation of 129 virulence genes, including plasmidial and bacteriophage genes from Brazilian strains' public Salmonella genomes. The frequency analysis of the four most sequenced serovars and a temporal analysis over the past four decades was also performed. The NCBI sequence reads archive (SRA) database comprised 1077 Salmonella public whole-genome sequences of strains isolated in Brazil between 1968 and 2018. Among the 1077 genomes, 775 passed in Salmonella in silico Typing (SISTR) quality control, which also identified 41 different serovars in which the four most prevalent were S. Enteritidis, S. Typhimurium, S. Dublin, and S. Heidelberg. Among these, S. Heidelberg presented the most distinct virulence profile, besides presenting Yersinia High Pathogenicity Island (HPI), rare and first reported in Salmonella from Brazil. The genes mgtC, csgC, ssaI and ssaS were the most prevalent within the 775 genomes with more than 99% prevalence. On the other hand, the less frequent genes were astA, iucBCD, tptC and shdA, with less than 1% frequency. All of the plasmids and bacteriophages virulence genes presented a decreasing trend between the 2000 s and 2010 s decades, except for the phage gene grvA, which increased in this period. This study provides insights into Salmonella virulence genes distribution in Brazil using freely available bioinformatics tools. This approach could guide in vivo and in vitro studies besides being an interesting method for the investigation and surveillance of Salmonella virulence. Moreover, here we propose the genes mgtC, csgC, ssaI and ssaS as additional targets for PCR identification of Salmonella in Brazil due to their very high frequency in the studied genomes.


Asunto(s)
Genes Bacterianos , Islas Genómicas , Salmonella/patogenicidad , Brasil , Simulación por Computador , Genoma Bacteriano , Salmonella/clasificación , Salmonella/genética , Serotipificación , Virulencia/genética , Secuenciación Completa del Genoma , Yersinia/genética
19.
Curr Microbiol ; 78(5): 2001-2014, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33860841

RESUMEN

Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious superbug which poses serious health threats to humanity. The severity of the infections depends on the prevalence of virulence factors and antibiotic resistance. In this study, attempts have been made to nominate the two most virulent and multidrug-resistant MRSA isolates demonstrating the preliminary features of intestinal adhesion for the futuristic applications of probiotics and postbiotics as antagonists to combat MRSA infections. In this context, six clinical isolates of MRSA were polyphasically characterized for their identity, multidrug resistance, and few selected virulence determinates such as hemolytic activity and production of coagulase, nuclease, and capsule. The gut colonizing ability of MRSA isolates was assessed by mucoadhesion, auto-aggregation, and cell surface hydrophobicity. An antibiogram of MRSA isolates suggested the resistance towards several antibiotics with multiple antibiotic resistance (MAR) index >0.5 (12/241, 12/206, and 5/255) as well as their genome portraying mecA mediated methicillin resistance. Besides exhibiting strong biofilm formation ability, all the isolates exhibited positive responses towards tested virulence assays coupled with their genome displaying Coa, NucA, and CapE genes. On the other hand, isolates exhibited different levels of auto-aggregation (37.90 ± 1.8 to 51.53 ± 3.1%) and mucin adhesion ability (68.93 ± 0.61% to 86.62 ± 1.96%) with a significant (P ≤ 0.05) variation in adhesion to different hydrocarbons. Finally, multivariate Principal Component Analysis and Hierarchical Cluster Analysis (HCA) heatmap using Euclidean distance measurement indicated MRSA 12/206 and 5/255 as most resistant and virulent isolates with the potential to adhere to the hydrophobic gut niche.


Asunto(s)
Staphylococcus aureus Resistente a Meticilina , Infecciones Estafilocócicas , Antibacterianos/farmacología , Humanos , Resistencia a la Meticilina , Staphylococcus aureus Resistente a Meticilina/genética , Pruebas de Sensibilidad Microbiana , Virulencia/genética , Factores de Virulencia/genética
20.
Int J Food Microbiol ; 347: 109197, 2021 Jun 02.
Artículo en Inglés | MEDLINE | ID: mdl-33895597

RESUMEN

Shiga toxin-producing Escherichia coli (STEC) can cause severe human illness, which are frequently linked to the consumption of contaminated beef or dairy products. However, recent outbreaks associated with contaminated flour and undercooked dough in the United States and Canada, highlight the potential of plant based food as transmission routes for STEC. In Germany STEC has been isolated from flour, but no cases of illness have been linked to flour. In this study, we characterized 123 STEC strains isolated from flour and flour products collected between 2015 and 2019 across Germany. In addition to determination of serotype and Shiga toxin subtype, whole genome sequencing (WGS) was used for isolates collected in 2018 to determine phylogenetic relationships, sequence type (ST), and virulence-associated genes (VAGs). We found a high diversity of serotypes including those frequently associated with human illness and outbreaks, such as O157:H7 (stx2c/d, eae), O145:H28 (stx2a, eae), O146:H28 (stx2b), and O103:H2 (stx1a, eae). Serotypes O187:H28 (ST200, stx2g) and O154:H31 (ST1892, stx1d) were most prevalent, but are rarely linked to human cases. However, WGS analysis revealed that these strains, as well as, O156:H25 (ST300, stx1a) harbour high numbers of VAGs, including eae, nleB and est1a/sta1. Although STEC-contaminated flour products have yet not been epidemiologically linked to human clinical cases in Germany, this study revealed that flour can serve as a vector for STEC strains with a high pathogenic potential. Further investigation is needed to determine the sources of STEC contamination in flour and flour products particularly in regards to these rare serotypes.


Asunto(s)
Escherichia coli O157/genética , Escherichia coli O157/aislamiento & purificación , Harina/microbiología , Contaminación de Alimentos/análisis , Toxina Shiga/genética , Animales , Canadá , Bovinos , Brotes de Enfermedades , Infecciones por Escherichia coli/transmisión , Escherichia coli O157/patogenicidad , Proteínas de Escherichia coli/genética , Microbiología de Alimentos , Variación Genética/genética , Genoma Bacteriano/genética , Alemania , Humanos , Filogenia , Virulencia/genética , Factores de Virulencia/genética , Secuenciación Completa del Genoma
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