Browsing by Author "Cabrera-Soregui, Milagros"

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Draft genome of the multidrug-resistant Citrobacter freundii strain CAPA023 isolated from Arapaima gigas in Peru: Is it a reservoir of resistance and virulence genes?
(Elsevier BV, 2025-05) García-Candela, Jose Luis Enrique; Mondragón-Martínez, Aarón Maguín; Noceda-Rodríguez, Manuel; Mesias-Valle, Fernando Daniel; Cabrera-Soregui, Milagros; Valverde-Vera, Verónica; Benito-García, Maria; Romayna-Ríos, Romina; Verástegui-Tello, Miriam; Dubey, Saurabh; Munang'Andu, Hetron M.; Yunis-Aguinaga, Jefferson
Objectives: The purpose of this study was to analyze the genome of the multidrug-resistant Citrobacter freundii strain CAPA023, which was obtained from diseased Arapaima gigas fry. The study focused on determining mobile genetic elements and genetic factors that contribute to antibiotic resistance and pathogenicity. Methods: Genomic DNA was sequenced using Illumina NovaSeq (2 × 150 bp) and assembled de novo using Shovill v1.1.0. Resistance genes, virulence factors, plasmids, and mobile elements were identified using ResFinder, CARD, PlasmidFinder, MobileFinder, PathogenFinder, and VFDB. Results: The 5,059,550 bp draft genome (60 contigs, 51.5% GC) revealed resistance genes for various antibiotic classes, efflux pumps, IncFIB(K) and Col440I plasmids, insertion sequences, and multiple virulence genes. Conclusion: Considering that this bacterium was found in diseased fish, it is possible that C. freundii plays an important role in the spread of virulence factors and antibiotic resistance in aquaculture environments. This highlights the importance of genomic surveillance in Amazonian aquaculture. © 2025 Elsevier B. V., All rights reserved.
Histological lesions by monogeneans in gills of Piaractus brachypomus farmed in semi-intensive systems from Peru
(Brazilian Journal of Veterinary Pathology, 2024) Torres-Lozano, Karel Gelina; Cabrera-Soregui, Milagros; García-Candela, Jose Luis Enrique; Cuadros-Cuya, Martín; Cubas-Rengifo, Andrés; Puicón-Niño-De-Guzmán, Víctor Humberto; Mesias-Valle, Fernando Daniel
Piaractus brachypomus Cuvier, 1818, is Peru’s most produced Amazonian fish; however, little is known about histological lesions that monogeneans produce in their gills. When examining 40 juveniles of P. brachypomus from two commercial fish farms, Anacanthorus penilabiatus (Boeger et al., 1995) and Mymarothecium viatorum (Boeger et al., 2002) were found, with a total monogenean prevalence of 100%, with a mean intensity and mean abundance of 225.5 parasites/fish for both species. At the level of the gill tissue, lesions identified were dilation and congestion of the central vein and hyperplasia of the secondary lamella with eosinophilic and lymphocytic infiltration. The histopathological alterations caused by infection of A. penilabiatus and M. viatorum are reported for the first timein cultured P. brachypomus in the Peruvian Amazon. These findings indicate the need to improve good practices and biosafety in producing this fish to prevent or control the impact of these monogeneans.
Molecular identification of Mymarothecium viatorum and Anacanthorus penilabiatus in extensive native fish farming systems of the Peruvian Amazon
(Elsevier BV, 2024-09) Cabrera-Soregui, Milagros; Torres-Lozano, Karel Gelina; García-Candela, Jose Luis Enrique; Mesias-Valle, Fernando Daniel; Martínez-Rojas, Rosa; Cruz-Neyra, Lidia; Mondragón-Martínez, Aarón Maguín; Bertholdi-Ebert, Mariana; Da-Silva, Reinaldo José; Cala-Delgado, Daniel Leonardo
Piaractus brachypomus (Pacú) is the main native fish species cultivated in Peru and holds great potential for growth in aquaculture from the Peruvian Amazon. Between October 2021 and January 2022 in two fish producing farms in the Amazon region of San Martín in Peru, P. brachypomus individuals were examined for parasite evaluation. A total of 6366 monogeneans were isolated from the gills of 30 fish, revealing a prevalence of 100%, with an abundance and mean intensity of 212 parasites per fish. Monogeneans were morphologically identified as Mymarothecium viatorum and Anacanthorus penilabiatus. The genetic divergence in the 28S rDNA gene found among A. penilabiatus sequences was 0.1% and among Anacanthorus spp. it ranged from 0.9% to 7.5%. The genetic divergence found among the M. viatorum sequences was 0.3%. These finding represents the first molecular data of M. viatorum and A. penilabiatus in Peru using the 28S rDNA gene of these monogeneans. The new sequences obtained will contribute to future studies on the phylogenetic relationships among dactylogyrids. However, further research with a broader range of host-parasite samples and additional genetic markers is needed to clarify these relationships and provide stronger support for the phylogenetic positions. © 2024 Elsevier B. V., All rights reserved.
Phylogenomic and comparative genomic analyses of Aeromonas spp. from South American aquatic systems reveal extensive genomic diversity, antimicrobial resistance, and predicted human pathogenicity
(Frontiers Media SA, 2026-06-16) García-Candela, Jose Luis Enrique; Mondragón-Martínez, Aarón Maguín; Moreno-Morales, Gerald; Cabrera-Soregui, Milagros; Puicón-Niño-De-Guzmán, Víctor Humberto; Ramos-Gorbeña, Juan Carlos; Santa-Cruz, Alcides Guerra; Cruz-Neyra, Lidia; Solis-Sarmiento, Julio
Introduction – Aquaculture systems function as dynamic ecological interfaces facilitating the circulation of opportunistic pathogens and antimicrobial resistance (AMR) determinants across environmental, animal, and human compartments. Aeromonas spp. are ubiquitous freshwater bacteria and emerging human opportunistic pathogens, yet genomic data from tropical South American aquaculture remain scarce. Methods – Nine Aeromonas isolates from Amazonian aquaculture facilities in Peru were subjected to whole-genome sequencing. Species identification was performed using Average Nucleotide Identity and phylogenomic reconstruction within a dataset of 112 genomes. Ribosomal MLST, comparative gene content analysis, virulence and resistome profiling, human pathogenicity prediction, and quinolone resistance-determining region (QRDR) screening were conducted. Phenotypic antimicrobial susceptibility testing was performed against five antibiotics. Results – Phylogenomic analysis revealed substantial genetic diversity among the analyzed isolates, encompassing Aeromonas hydrophila, Aeromonas caviae, and Aeromonas veronii, with no clustering by host species or production site. Ribosomal MLST assigned 8 distinct rSTs across the 9 isolates. Comparative genomic analysis identified 19, 486 gene clusters, of which a subset was shared across all genomes, while the majority were variably distributed, indicating extensive genomic diversity across Aeromonas spp. All isolates shared conserved colonizationand secretion-associated determinants, whereas major cytotoxic toxin genes were absent. PathogenFinder v2 predicted high probabilities of human pathogenicity (0.93–0.96) across all genomes. Resistome analysis identified genes associated with tetracycline, quinolone, sulfonamide, and β-lactam resistance, including intrinsic blaOXA and cphA, while QRDR screening identified mutations potentially associated with quinolone resistance. Genomic findings were broadly consistent with phenotypic susceptibility profiles. Conclusion – Amazonian aquaculture systems harbor genetically diverse Aeromonas lineages with conserved opportunistic virulence traits and clinically relevant AMR determinants. These findings highlight the role of aquaculture environments as reservoirs and potential transmission interfaces of antimicrobial resistance and opportunistic pathogens, underscoring the importance of genomic surveillance within a One Health context.