Biology subjects

Vicente, A. C. P.

Publications and source records attributed to Vicente, A. C. P..

11 recordsLinked to original sources

bioRxiv2025

Unmasking Vibrio paracholerae: Genomic Reclassification and Epidemiology

The genus Vibrio encompasses globally relevant pathogens, of which Vibrio cholerae is the best known due to its role in cholera. Closely related species within the Cholerae clade--Vibrio paracholerae, Vibrio metoecus, and Vibrio tarriae--were long misclassified as non-O1/O139 V. cholerae. The objective of this study was to analyze all 13,000+ available V. cholerae genomes in GenBank to determine the presence of species from the Cholerae clade. Genome-wide analyses using Mash, Whole-genome based Average Nucleotide Identity (gANI), and digital DNA-DNA hybridization (dDDH) reclassified 193 unique genomes as V. paracholerae, while V. metoecus and V. tarriae were not identified. Phylogenomic analyses revealed that V. paracholerae forms distinct but relatively homogeneous lineages, spanning clinical, environmental, and animal sources over a period of more than a century. Virulence profiling revealed the absence of CTX and TCP; however, most genomes exhibited other virulence factors, including hemolysins, RTX toxins, colix toxin, and a conserved type VI secretion system. Resistome analysis revealed several antibiotic resistance genes, many of which were incorporated into superintegrons, highlighting the role of V. paracholerae as a reservoir of resistance determinants. Importantly, two genomic markers exhibited high discriminatory power for species identification, providing robust tools for epidemiological surveillance. These findings underscore the relevance of V. paracholerae for clinical and epidemiological monitoring.

genomics↗

bioRxiv2024

Vibrio mimicus carrying the Type III Secretion System 2 (T3SS2) and TDH toxin of Vibrio parahaemolyticus in an integrative conjugative element context

ObjectivesIdentify possible virulence factors in the genomes of Vibrio mimicus that may be determinants of diarrheal cases/outbreaks. MethodsAll V. mimicus genomes from Genbank were retrieved and the virulome was searched with Abricate using the VFDB database. Genomic islands (GIs) and integrative conjugative elements (ICEs) were identified using IslandViewer and ICEberg, respectively. ResultsFive ctx-negative V. mimicus genomes carrying the Type III Secretion System 2 (T3SS2) and the TDH/TRH toxin from Vibrio parahaemolyticus were identified. The T3SS-positive genomes presented the phylotypes T3SS2 and T3SS2{beta} and formed two clusters and one singleton throughout the V. mimicus phylogeny. Genomes carrying T3SS2 and T3SS2{beta} were associated with the tdh and trh genes, respectively. Furthermore, genomic analyses characterized an integrative conjugative element (ICE) with a size of [~]150 kb carrying both V. parahaemolyticus virulence determinants. ConclusionsIn addition to looking for cholera toxin genes in V. mimicus cases/outbreaks, it is important to consider V. parahaemolyticus toxins such as TDH and TRH. Furthermore, an ICE was identified and characterized in V. mimicus, being associated with T3SS2 and the TDH toxin, which is worrying, as it can disseminate these virulence factors among Vibrio spp.

genomics↗

bioRxiv2024

Expression pattern of the ST heat-stable enterotoxin gene cassettes in Vibrios superintegrons

BACKGROUNDVibrio mimicus has been associated with a cholera-like diarrhea and other gastroenteritis due to the presence of virulence factors such as the heat-stable ST enterotoxin. In spite of its relevant role in Vibrio pathogenesis, there is still a lack of information concerning ST expression dynamics and associated genomic context. OBJECTIVEthis study aimed to determine the prevalence, genomic context, and expression of the st gene found in V. cholerae and V. mimicus strains. METHODSgenome sequencing, in silico analyses of st promoter region and genomic context, and relative quantification pf st expression by real time RT-PCR were applied. FINDINGSThe st gene was found within the SI of both Vibrio species, presenting variations in their amino acid sequences. The in silico analysis of the st 5UTR identified different promoter versions among them. Significant differences were observed in the st expression level, which varied from 10X to 640X-fold, correlating with the differences found in the promoter versions. MAIN CONCLUSIONSTherefore, the present study highlighted the link between the ST toxin gene and the superintegron, not only for V. cholerae, but also for V. mimicus. The differential st expression revealed that it is detrimental to the cognate promoter version, which would impact the toxin production and strain virulence.

genomics↗

bioRxiv2024

Genomic insights on the potential role of the accessory genome in the emergence of a novel geographically restricted K. pneumoniae lineage as a high-risk clone

Klebsiella pneumoniae causes life-threatening nosocomial infections and is featured by a remarkable propensity for multidrug resistance acquisition. Infections caused by multidrug- (MDR) and extensively drug-resistant (XDR) strains lead to a limitation of therapeutic options and an increase in persistent infections, and they are usually represented by high-risk lineages. Based on these features and their relevance to global public health, most of the studies focused on such high-risk clones, and little is known about the epidemiological and evolutionary dynamics of new/geographically restricted lineages. This study aimed to unveil the antimicrobial resistance and virulence genetic repertoire of a clinical XDR K. pneumoniae (Kp199) strain belonging to geographically-restricted ST, not linked to any known clonal complex. Its intrinsic (gyrA, parC, ramR, soxR and soxS mutations) and acquired resistome agreed with the observed XDR phenotype. An extensive arsenal of both antibiotic and heavy metal resistance genes was observed, as well as genes involved with resistance to several antiseptics currently used in clinical settings. The co-occurrence of blaKPC-2 and blaNDM-1 carbapenemase genes in Kp199 was an alarming finding since it could contribute to increased carbapenem resistance. Kp199 virulome was associated with bacterial survival and replication during infections. This study raises concern about a novel, geographically restricted K. pneumoniae lineage harbouring a huge resistome and virulome, which may strongly contribute to its successful establishment as an epidemic lineage. Therefore, our findings underscore the importance of vigilant surveillance and control measures to mitigate the threat posed by the potential emergence of new high-risk pandemic clones.

microbiology↗

bioRxiv2023

In-depth analysis of Klebsiella aerogenes resistome, virulome and mobilome worldwide

Klebsiella aerogenes is an emergent pathogen associated with outbreaks of carbapenem-resistant strains. To date, studies focusing on K. aerogenes have been small-scale and/or geographically restricted. Here, we analyzed the epidemiology, resistome, virulome, and mobilome of this species based on 561 genomes, spanning all continents. Furthermore, we sequenced four new strains from Brazil (mostly from the Amazon region). Dozens of STs occur worldwide, but the pandemic clones ST93 and ST4 have prevailed in several countries. Almost all genomes were clinical, however, most of them did not carry ESBL or carbapenemases, instead, they carried chromosomal alterations (omp36, ampD, ampG, ampR) associated with resistance to {beta}-lactams. Integrons were also identified, presenting gene cassettes not yet reported in this species (blaIMP, blaVIM, blaGES). Considering the virulence loci, the yersiniabactin and colibactin operons were found in the ICEKp10 element, which is disseminated in genomes of several STs, as well as an incomplete salmochelin cluster. In contrast, the aerobactin hypervirulence trait was observed only in one ST432 genome. Plasmids were common, mainly from the ColRNAI replicon, with some carrying resistance genes (mcr, blaTEM, blaNDM, blaIMP, blaKPC, blaVIM) and virulence genes (EAST1, senB). Interestingly, plasmids containing the colicin gene occurred in hundreds of genomes of different STs.

genomics↗

bioRxiv2023

Revealing Heavy Metal Resistances in the Yanomami Microbiome

BACKGROUNDThe Amazon hosts invaluable and unique biodiversity as well as mineral resources. As a consequence, there are large illegal and artisanal gold mining areas in indigenous territories. Mercury has been used in gold mining, and some are released into the environment and atmosphere, primarily affecting indigenous as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region. OBJECTIVEInvestigation of the Yanomami gut microbiome focusing on metal resistance. METHODSMetagenomic data from the Yanomami gut microbiome were assembled into contigs, and their putative proteins were matched to a database of metal resistance proteins. FINDINGSMost identified proteins have the potential to confer resistance to multiple metals (two or more), followed by mercury, copper, zinc, chromium, arsenic, and others. Operons with potential resistance to mercury, arsenic, chromium, nickel, zinc, copper, copper/silver, and cobalt/nickel were identified. Mercury resistance operon was the most abundant, even though a diversity of operons in the Yanomami microbiome was observed to have the potential to confer resistance to various metals CONCLUSIONThe Yanomami gut microbiome gene composition shows that these people have been exposed directly or indirectly to mercury and other heavy metals. SponsorshipsThis study was partly financed by the Fundacao de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ); and PAEF (IOC-023-FIO-18-2-47).

microbiology↗

bioRxiv2023

Genomic characterization of a pandrug-resistant Klebsiella pneumoniae belonging to the high-risk ST11 in the Brazilian Amazon region

Pandrug-resistant (PDR) K. pneumoniae has been reported sporadically in many countries and remains rare in Brazil. The lack of genomic studies limits the comprehension of the determinants mostly involved with the PDR emergence in K. pneumoniae. This study aimed to unravel the main genetic determinants involved with the PDR background of a clinical ST11 K. pneumoniae recovered in the Brazilian Amazon region. The carbapenem-resistant Kp196 was submitted to WGS and its intrinsic and acquired resistome was assessed by CARD and comparison with wild-type genes. Kp196 resistome was composed of acquired resistance determinants and mutations in chromosomal genes. Among the formers, blaCTX-M-15 and blaNDM-1, blaOXA-9, blaOXA-1, aadA1, aacA4, strAB, aph(3)-VI, aac(3)-IId, qnrS1, qnrB1, oqxAB, dfrA14, sul2, catB3 were found in the vicinity of mobile genetic elements, which could contribute to their spread. Kp196 colistin resistance was multifactorial and attributed to modifications in ArnT (M114L/V117I/R372K), PhoQ (D150G), and the mgrB disruption by ISKpn25. Besides the presence of qnr and oqxAB genes, Kp196 also presented altered GyrA (S83I) and ParC (S80I). An in-block deletion in the repressor RamR, contributing to acrAB overexpression, and the presence of an enhanced-function AcrB variant (S966A), probably led to the Kp196 multidrug and tigecycline resistance. Insertions, in-block deletion, and missense mutations were involved with ompK35-36-37 inactivation, also accounting for the Kp196 multidrug resistance, including carbapenems. The Kp196 PDR profile, especially the carbapenem resistance, was due to the accumulation of different mechanisms, in which modifications in housekeeping genes accounted for a more stable resistome.

genomics↗

bioRxiv2021

A Plasmid Network from the Gut Microbiome of Semi-isolated Human Groups Reveals Unique and Shared Metabolic and Virulence Traits

The plasmidome, the set of plasmids in gut microbiomes, has the potential to contribute to the microbiome assembly, as well as human health and physiology. Nevertheless, this niche remains poorly explored, likely due to the difficulties attributed to mining mobile elements from complex environments such as microbiomes. In general, most microbiome studies focus on urban-industrialized groups, but here, we studied semi-isolated groups, which represent a link between the ancestral and modern human groups. Based on metagenomic data, we characterized their plasmidome, including the set of accessory genes and functions from the gut microbiome of the Hadza, Matses, Tunapuco, and Yanomami. In silico analyzes revealed unique plasmid clusters and gene functions for each human group related to their diet and lifestyle. In addition, network analysis revealed a dozen plasmid clusters shared by these distinct groups but that are also circulating in other niches worldwide. Moreover, in these microbiomes, there are novel and unique plasmids associated with their resistome and virulome. A resistome encompassing six antibiotic classes and multiple metals, and a virulome with type VI secretion systems were identified. Functional analysis revealed pathways associated with urban-industrialized groups, such as lipopolysaccharide biosynthesis that was characterized in the Hadza plasmidome. These results demonstrate the richness of features in the semi-isolated human groups plasmidome and provide a snapshot of the forces that are acting in their gut microbiome. Their plasmidomes also represent an important source of information with biotechnological and/or pharmaceutical potential.

microbiology↗

bioRxiv2019

Gut Microbiome Functional and Taxonomic Diversity within an Amazonian semi-nomadic hunter-gatherer group

BackgroundHuman gut microbiome profiles have been associated with human health and disease. These profiles have been defined based on microbes taxonomy and more recently, on their functionality. Human groups that still maintain traditional modes of subsistence (hunter-gatherers and rural agriculturalists) represent the groups non-impacted by urban-industrialized lifestyles, and therefore study them provide the basis for understanding the human microbiome evolution. The Yanomami is the largest semi-nomadic hunter-gatherer group of the Americas, exploring different niches of the Amazon rainforest in Brazil and Venezuela. In order to extend the analysis of this unique and diverse group, we focused on the gut microbiome of the Yanomami from Brazil and compared with those from Venezuela, and also with other traditional groups from the Amazon, considering taxonomic and functional profiles. ResultsA diversity of taxonomic biomarkers were identified to each South American traditional group studied, including the two Yanomami groups, despite their overall similarity in the taxonomic gut microbiome profiles. Broader levels of functional categories poorly discriminated traditional and urban-industrialized groups. Interestingly, a diversity was observed with the stratification of these categories, clearly segregating those groups. The Yanomami/Brazil gut microbiome presented unique functional features, such as a higher abundance of gene families involved in regulation/cell signaling, motility/chemotaxis, and virulence, contrasting with the microbiomes from the Yanomami/Venezuela and other groups. ConclusionsOur study revealed biomarkers, taxonomic and functional differences between the gut microbiome of Yanomami/Brazil and Yanomami/Venezuela individuals. This intra-Yanomami group diversity was accessed due to the increase number of individuals and group studied. These differences may reflect their semi-nomadic behavior, as well as, the local and seasonal diversity of the vast rainforest niche they explore, despite their shared cultural and genetic background. Overall, their microbiome profiles are shared with South American and African traditional groups, probably due to their lifestyle. The unique features identified within the Yanomami highlight the bias imposed by underrepresented sampling, and factors such as variations over space and time (seasonality) that impact, mainly, the hunter-gatherers. Therefore, to reach knowledge about human microbiome variations and their implications in human health, it is essential to enlarge data concerning the number of individuals, as well as the groups representing different lifestyles.

microbiology↗

bioRxiv2019

Distinct YFV lineages co-circulated in the Central-Western and Southeastern Brazilian regions from 2015 to 2018

The current outbreak of yellow fever virus (YFV) that is afflicting Brazil since the end of 2016 probably originated from a re-introduction of YFV from endemic areas into the non-endemic Southeastern Brazil. However, the lack of genomic sequences from endemic regions hinders the tracking of YFVs dissemination routes. We assessed the origin and spread of the ongoing YFV Brazilian outbreak analyzing a new set of YFV strains infecting humans, non-human primates (NHP) and mosquitoes sampled across five Brazilian states from endemic and non-endemic regions between 2015 and 2018. We found two YFV sub-clade 1E lineages circulating in NHP from Goias state (GO), resulting from independent viral introductions into the Araguaia tributary river basin: while the strain from 2017 clustered intermingled with Venezuelan YFV strains from 2000, the YFV strain sampled in 2015 clustered with sequences of the current YFV outbreak in the Brazilian Southeastern region (named YFV2015-2018 lineage), displaying the same molecular signature associated to the current YFV outbreak. After its introduction in GO at around mid-2014, the YFV2015-2018 lineage followed two paths of dissemination outside GO, originating two major YFV sub-lineages: 1) the YFVMG/ES/RJ sub-lineage spread sequentially from the eastern area of Minas Gerais state to Espirito Santo and then to Rio de Janeiro states, following the Southeast Atlantic basin; 2) the YFVMG/SP sub-lineage spread from the southwestern area of Minas Gerais to the metropolitan region of Sao Paulo state, following the Parana basin. These results indicate the ongoing YFV outbreak in Southeastern Brazil originated from a dissemination event from GO almost two years before its recognition at the end of 2016. From GO this lineage was introduced in Minas Gerais state at least two times, originating two sub-lineages that followed different routes towards densely populated areas. The spread of YFV outside endemic regions for at least four years stresses the imperative importance of the continuous monitoring of YFV to aid decision-making for effective control policies aiming the increase of vaccination coverage to avoid the YFV transmission in densely populated urban centers.

epidemiology↗

bioRxiv2017

Genomic and structural features of the Yellow Fever virus from the 2016-2017 Brazilian outbreak

Brazil has been suffering a severe sylvatic epidemic of yellow fever virus (YFV) since late 2016. Analysis of full-length YFV genomes from all hosts involved in the Brazilian 2017 outbreak reveals that they belong to sub-lineage 1E within modern-lineage, but display several unique amino acid substitutions in highly conserved positions at NS3 and NS5 viral proteins. Evolutionary analyses indicate that YFV carrying that set of amino acid substitution circulates in the Southern Brazilian region for several months before being detected in December 2016. Structural and selection analyses support that some of these substitutions were under positive selection and could impact enzyme structure and function. Altogether, this evidence demonstrated that the current Brazilian YFV carries unique amino acid signatures in the non-structural proteins and support the hypothesis that those substitutions may be affecting the viral fitness and transmissibility.

microbiology↗