Biology subjects

Morgado, S.

Publications and source records attributed to Morgado, S..

9 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

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

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↗

bioRxiv2022

Global genomic epidemiology, resistome, virulome and plasmidome of the Extraintestinal Pathogenic Escherichia coli (ExPEC) ST38 lineage

Most of the extraintestinal human infections worldwide are determined by some specific Extraintestinal Pathogenic Escherichia coli (ExPEC) lineages, which also present a zoonotic character. One of these lineages belongs to ST38, which is considered a uropathogenic/enteroaggregative E. coli hybrid and a high-risk globally disseminated ExPEC. To get insights on the aspects of ST38 epidemiology and evolution as a multidrug resistant and pathogenic lineage, this study performed a global comparative genomic analysis on ST38 genomes. A total of 376 genomes recovered from environments, humans, livestock, wild and domestic animals in all continents throughout three decades were analyzed considering the ST38 phylogenomics, resistome, plasmidome, and virulome. In general, our analyses revealed that, independently of host sources and geographic origin, these genomes were distributed in two clusters comprising clonal and non-clonal genomes. Moreover, the ST38 accessory genome was not strictly associated with clusters and sub-clusters. Interestingly, the High Pathogenicity Island (HPI) prevailed in the major cluster (cluster 2), which comprised most of the genomes from human origin recovered worldwide (2000 to 2020). In addition, the ExPEC ST38 harbors a huge and diverse plasmidome that might contribute to the evolution of this lineage, reflecting in ST38 ability to live in a diversity of niches as a commensal or pathogenic organism.

genomics↗

bioRxiv2021

Conjugative transfer of naturally occurring plasmids in Mycolicibacterium sp.

Conjugation is considered the main horizontal gene transfer (HGT) mechanism in bacterial adaptation and evolution. In the Mycobacteriaceae family, Mycolicibacterium smegmatis has been used as the model organism for the conjugative transfer of hybrid plasmids. However, the natural conjugation process in any bacteria would involve the transfer of naturally occurring plasmids. Currently, there is a gap in this regard in relation to this abundant environmental genus of Mycobacteriaceae. Here, we performed conjugation experiments between wild Mycolicibacterium sp. strains involving naturally occurring plasmids (sizes of 21 and 274 kb), and interestingly, evidence of conjugative transfer was obtained. Thus, it is likely that conjugation occurs in Mycolicibacterium in the natural environment, representing a source of diversification and evolution in this genus of bacteria.

microbiology↗

bioRxiv2021

Emergence of XDR high-risk Pseudomonas aeruginosa ST309 in South America: a global comparative genomic analysis

Pseudomonas aeruginosa has been considered one of the major nosocomial pathogens associated with elevated morbidity and mortality worldwide. Outbreaks have been associated with few high-risk pandemic P. aeruginosa lineages, presenting a remarkable antimicrobial resistance. However, the biological features involved with the persistence and spread of such lineages among clinical settings remain to be unravel. This study reports the emergence of the ST309 P. aeruginosa lineage in South America/Brazil, more precisely, in the Amazon region. Global genomic analyses were performed with the Brazilian strain (PA834) and more 41 complete and draft ST309 genomes publicly available, giving insights about ST309 epidemiology and its resistome and mobilome. Antimicrobial susceptibility tests revealed that the Brazilian PA834 strain presented the XDR phenotype, which was mainly due to intrinsic resistance mechanisms. Genomic analyses revealed a heterogeneous distribution of acquired antimicrobial resistance genes among ST309 genomes, which included blaVIM-2, blaIMP-15 and qnrVC1, all of them associated with class 1 integrons. The mobilome mining showed the presence of Integrative and Conjugative Elements, transposons and genomic islands harbouring a huge arsenal of hevy metal resistance genes. Moreover, these elements also carried genes involved with virulence and adaptive traits. Therefore, the presence of such genes in ST309 lineage possibly accounted for the global spread and persistence of this emerging clone, and for its establishment as a pandemic lineage of clinical importance.

genomics↗

bioRxiv2018

Exploring tRNA gene cluster in archaea

Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organization of tRNA genes as clusters, but this trait has not been explored in archaea domain. Here, based on analyses of complete and draft archaeal genomes, we demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene cluster was identified at least in three Archaea class, Halobacteria, Methanobacteria and Methanomicrobia from Euryarchaeota supergroup. Genomic analyses also revealed evidence of tRNA gene cluster associated with mobile genetic elements and horizontal gene transfer inter/intra-domain. The presence of tRNA gene clusters in the three domain of life suggests a role of this type of tRNA gene organization in the biology of the living organisms.

genomics↗