Xanthomonas bacteria are known phytopathogens difficult to control in the field, which cause great losses in many economically important crops. Genomic islands are fragments acquired by horizontal transference that are important for evolution and adaptation to diverse ecological niches. Virulence and pathogenicity islands (PAIs) enhance molecular mechanisms related to host adaptation. In this work, we have analyzed 81 genomes belonging to X. campestris, and a complex group of X. citri, X. axonopodis, and X. fuscans belonging to nine different pathovars and three subspecies, to analyze and compare their genomic contents. Xanthomonas pan-genome is open and has a massive accessory genome. Each genome showed between three and 15 exclusive PAIs, well conserved through strains of the same pathovar or subspecies. X. axonopodis pv. anacardii had higher general similarity to X. citri subsp. citri and X. fuscans subsp. aurantifolii, with which a few PAIs were shared. Genomic synteny was even for almost all strains, with few rearrangements found in X. axonopodis pv. anacardii. The prophage regions identified in the genomes were mostly questionable or incomplete, and PAI13 in X. campestris pv. campestris ATCC33913 matched a prophage region of 19 transposable elements. Finally, PAIs in Xanthomonas are pathovar-specific, requiring individual strategies of combat.

Understanding the genetic characteristics of Aeromonas jandaei in Brazilian aquaculture is crucial for developing effective control strategies against this fish pathogen. The present study conducted a genomic analysis of Brazilian A. jandaei strains with the objective of investigating their virulence potential and resistance profiles. Four Brazilian isolates were subjected to sequencing, and comparative genomic analyses were conducted in conjunction with 48 publicly available A. jandaei genomes. The methods employed included quality assessment, de novo assembly, annotation, and analyses of antimicrobial resistance and virulence factors. The results demonstrated the presence of fluoroquinolone resistance genes within the core genome. Notably, these antibiotics are not authorized for use in aquaculture in Brazil, suggesting that their resistance determinants may originate from other selective pressures or horizontal gene transfer unrelated to aquaculture practices. The analysis identified significant virulence mechanisms, including T2SS, T3SS, and notably T6SS (vgrG3 gene), which was more prevalent in Brazilian isolates. Additionally, genes associated with motility, adhesion, and heavy metal resistance were identified. These findings highlight the enhanced adaptability of Brazilian A. jandaei strains and raise concerns about antimicrobial resistance in aquaculture, emphasizing the need for improved regulatory oversight and control strategies.

Ralstonia solanacearum species complex (RSSC) cause several phytobacteriosis in many economically important crops around the globe, especially in the tropics. In Brazil, phylotypes I and II cause bacterial wilt (BW) and are indistinguishable by classical microbiological and phytopathological methods, while Moko disease is caused only by phylotype II strains. Type III effectors of RSSC (Rips) are key molecular actors regarding pathogenesis and are associated with specificity to some hosts. In this study, we sequenced and characterized 14 newly RSSC isolates from Brazil’s Northern and Northeastern regions, including BW and Moko ecotypes. Virulence and resistance sequences were annotated, and the Rips repertoire was predicted. Confirming previous studies, RSSC pangenome is open as $\mathsf{\alpha }\cong 0.77$. Genomic information regarding these isolates matches those for R. solanacearum in NCBI. All of them fit in phylotype II with a similarity above 96%, with five isolates in phylotype IIB and nine in phylotype IIA. Almost all R. solanacearum genomes in NCBI are actually from other species in RSSC. Rips repertoire of Moko IIB was more homogeneous, except for isolate B4, which presented ten non-shared Rips. Rips repertoire of phylotype IIA was more diverse in both Moko and BW, with 43 common shared Rips among all 14 isolates. New BW isolates shared more Rips with Moko IIA and Moko IIB than with other public BW genome isolates from Brazil. Rips not shared with other isolates might contribute to individual virulence, but commonly shared Rips are good avirulence candidates. The high number of Rips shared by new Moko and BW isolates suggests they are actually Moko isolates infecting solanaceous hosts. Finally, infection assays and Rips expression on different hosts are needed to better elucidate the association between Rips repertoire and host specificities.