Browsing by Author "Ugalde, Juan A."

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    A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp longum SC596
    (2016) Garrido, Daniel; Ruiz-Moyano, Santiago; Kirmiz, Nina; Davis, Jasmine C.; Totten, Sarah M.; Lemay, Danielle G.; Ugalde, Juan A.; German, J. Bruce; Lebrilla, Carlito B.; Mills, David A.
    The infant intestinal microbiota is often colonized by two subspecies of Bifidobacterium longum: subsp. infantis (B. infantis) and subsp. longum (B. longum). Competitive growth of B. infantis in the neonate intestine has been linked to the utilization of human milk oligosaccharides (HMO). However, little is known how B. longum consumes HMO. In this study, infant-borne B. longum strains exhibited varying HMO growth phenotypes. While all strains efficiently utilized lacto-N-tetraose, certain strains additionally metabolized fucosylated HMO. B. longum SC596 grew vigorously on HMO, and glycoprofiling revealed a preference for consumption of fucosylated HMO. Transcriptomes of SC596 during early-stage growth on HMO were more similar to growth on fucosyllactose, transiting later to a pattern similar to growth on neutral HMO. B. longum SC596 contains a novel gene cluster devoted to the utilization of fucosylated HMO, including genes for import of fucosylated molecules, fucose metabolism and two alpha-fucosidases. This cluster showed a modular induction during early growth on HMO and fucosyllactose. This work clarifies the genomic and physiological variation of infant-borne B. longum to HMO consumption, which resembles B. infantis. The capability to preferentially consume fucosylated HMO suggests a competitive advantage for these unique B. longum strains in the breast-fed infant gut.
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    Ceftazidime/avibactam resistance is associated with PER-3-producing ST309 lineage in Chilean clinical isolates of non-carbapenemase producing Pseudomonas aeruginosa
    (2024) Soto, Katherine D.; Alcalde-Rico, Manuel; Ugalde, Juan A.; Olivares-Pacheco, Jorge; Quiroz, Valeria; Brito, Barbara; Rivas, Lina M.; Munita, Jose M.; Garcia, Patricia C.; Wozniak, Aniela
    Introduction Ceftazidime/avibactam (CZA) is indicated against multidrug-resistant Pseudomonas aeruginosa, particularly those that are carbapenem resistant. CZA resistance in P. aeruginosa producing PER, a class A extended-spectrum beta-lactamase, has been well documented in vitro. However, data regarding clinical isolates are scarce. Our aim was to analyze the contribution of PER to CZA resistance in non-carbapenemase-producing P. aeruginosa clinical isolates that were ceftazidime and/or carbapenem non-susceptible. Methods Antimicrobial susceptibility was determined through agar dilution and broth microdilution, while bla(PER) gene was screened through PCR. All PER-positive isolates and five PER-negative isolates were analyzed through Whole Genome Sequencing. The mutational resistome associated to CZA resistance was determined through sequence analysis of genes coding for PBPs 1b, 3 and 4, MexAB-OprM regulators MexZ, MexR, NalC and NalD, AmpC regulators AmpD and AmpR, and OprD porin. Loss of bla(PER-3) gene was induced in a PER-positive isolate by successive passages at 43 degrees C without antibiotics. Results Twenty-six of 287 isolates studied (9.1%) were CZA-resistant. Thirteen of 26 CZA-resistant isolates (50%) carried bla(PER). One isolate carried bla(PER) but was CZA-susceptible. PER-producing isolates had significantly higher MICs for CZA, amikacin, gentamicin, ceftazidime, meropenem and ciprofloxacin than non-PER-producing isolates. All PER-producing isolates were ST309 and their bla(PER-3) gene was associated to ISCR1, an insertion sequence known to mobilize adjacent DNA. PER-negative isolates were classified as ST41, ST235 (two isolates), ST395 and ST253. PER-negative isolates carried genes for narrow-spectrum beta-lactamases and the mutational resistome showed that all isolates had one major alteration in at least one of the genes analyzed. Loss of bla(PER-3) gene restored susceptibility to CZA, ceftolozane/tazobactam and other beta-lactamsin the in vitro evolved isolate. Discussion PER-3-producing ST309 P. aeruginosa is a successful multidrug-resistant clone with bla(PER-3) gene implicated in resistance to CZA and other beta-lactams.
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    Comparative transcriptome assembly and genome-guided profiling for Brettanomyces bruxellensis LAMAP2480 during p-coumaric acid stress
    (2016) Godoy, Liliana; Vera Wolf, Patricia.; Martínez, Claudio.; Ugalde, Juan A.; Ganga, María Angélica.
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    Distinctive archaeal composition of an artisanal crystallizer pond and functional insights into salt-saturated hypersaline environment adaptation
    (2018) Plominsky, Alvaro M.; Henríquez Castillo, Carlos Andrés; Delherbe, Nathalie; Podell, Sheila; Ramirez Flandes, Salvador; Ugalde, Juan A.; Santibañez, Juan F.|Van den Engh, Ger; Hanselmann, Kurt; De la Iglesia Cabezas, Rodrigo Alonso; Ulloa, Osvaldo; Allen, Eric E.; Trefault Carrillo, Nicole Natalie
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    Genome sequence of Vibrio VPAP30, isolated from an episode of massive mortality of reared larvae of scallop Argopecten purpuratus
    (2015) Rojas Ávila, Rodrigo; Miranda, Claudio D.; Romero, Jaime; Asenjo, Freddy; Valderrama, Katherinne; Segovia, Cristopher; Ugalde, Juan A.; Santander, Javier
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    Human metapneumovirus respiratory infection affects both innate and adaptive intestinal immunity
    (2024) Sepulveda-Alfaro, Javiera; Catalan, Eduardo A.; Vallejos, Omar P.; Ramos-Tapia, Ignacio; Madrid-Munoz, Cristobal; Mendoza-Leon, Maria J.; Suazo, Isidora D.; Rivera-Asin, Elizabeth; Silva, Pedro H.; Alvarez-Mardones, Oscar; Castillo-Godoy, Daniela P.; Riedel, Claudia A.; Schinnerling, Katina; Ugalde, Juan A.; Soto, Jorge A.; Bueno, Susan M.; Kalergis, Alexis M.; Melo-Gonzalez, Felipe
    Introduction Respiratory infections are one of the leading causes of morbidity and mortality worldwide, mainly in children, immunocompromised people, and the elderly. Several respiratory viruses can induce intestinal inflammation and alterations in intestinal microbiota composition. Human metapneumovirus (HMPV) is one of the major respiratory viruses contributing to infant mortality in children under 5 years of age worldwide, and the effect of this infection at the gut level has not been studied.Methods Here, we evaluated the distal effects of HMPV infection on intestinal microbiota and inflammation in a murine model, analyzing several post-infection times (days 1, 3, and 5). Six to eight-week-old C57BL/6 mice were infected intranasally with HMPV, and mice inoculated with a non-infectious supernatant (Mock) were used as a control group.Results We did not detect HMPV viral load in the intestine, but we observed significant changes in the transcription of IFN-gamma in the colon, analyzed by qPCR, at day 1 post-infection as compared to the control group. Furthermore, we analyzed the frequencies of different innate and adaptive immune cells in the colonic lamina propria, using flow cytometry. The frequency of monocyte populations was altered in the colon of HMPV -infected mice at days 1 and 3, with no significant difference from control mice at day 5 post-infection. Moreover, colonic CD8+ T cells and memory precursor effector CD8+ T cells were significantly increased in HMPV-infected mice at day 5, suggesting that HMPV may also alter intestinal adaptive immunity. Additionally, we did not find alterations in antimicrobial peptide expression, the frequency of colonic IgA+ plasma cells, and levels of fecal IgA. Some minor alterations in the fecal microbiota composition of HMPV -infected mice were detected using 16s rRNA sequencing. However, no significant differences were found in beta-diversity and relative abundance at the genus level.Discussion To our knowledge, this is the first report describing the alterations in intestinal immunity following respiratory infection with HMPV infection. These effects do not seem to be mediated by direct viral infection in the intestinal tract. Our results indicate that HMPV can affect colonic innate and adaptive immunity but does not significantly alter the microbiota composition, and further research is required to understand the mechanisms inducing these distal effects in the intestine.
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    Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection
    (NATURE PORTFOLIO, 2023) Ruiz-Tagle Seguel, Cinthya Grace; Ugalde, Juan A.; Naves Pichuante, Rodrigo Antonio; Araos, Rafael; Garcia Canete, Patricia Del Carmen; Balcells Marty, Maria Elvira
    The upper respiratory tract is an obliged pathway for respiratory pathogens and a healthy microbiota may support the host's mucosal immunity preventing infection. We analyzed the nasopharyngeal microbiome in tuberculosis household contacts (HHCs) and its association with latent tuberculosis infection (TBI). A prospective cohort of HHCs was established and latent TBI status was assessed by serial interferon-& gamma; release assay (IGRA). Nasopharyngeal swabs collected at baseline were processed for 16S rRNA gene sequencing. The 82 participants included in the analysis were classified as: (a) non-TBI [IGRA negative at baseline and follow-up, no active TB (n = 31)], (b) pre-TBI [IGRA negative at baseline but converted to IGRA positive or developed active TB at follow-up (n = 16)], and (c) TBI [IGRA positive at enrollment (n = 35)]. Predominant phyla were Actinobacteriota, Proteobacteria, Firmicutes and Bacteroidota. TBI group had a lower alpha diversity compared to non-TBI (p(adj) = 0.04) and pre-TBI (p(adj) = 0.04). Only TBI and non-TBI had beta diversity differences (p(adj) = 0.035). Core microbiomes' had unique genera, and genus showed differential abundance among groups. HHCs with established latent TBI showed reduced nasopharyngeal microbial diversity with distinctive taxonomical composition. Whether a pre-existing microbiome feature favors, are a consequence, or protects against Mycobacterium tuberculosis needs further investigation.
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    Role of the multi-drug efflux systems on the baseline susceptibility to ceftazidime/avibactam and ceftolozane/tazobactam in clinical isolates of non-carbapenemase-producing carbapenem-resistant Pseudomonas aeruginosa
    (2022) Jose Contreras-Gomez, Maria; Martinez, Jose R. W.; Rivas, Lina; Riquelme-Neira, Roberto; Ugalde, Juan A.; Wozniak, Aniela; Garcia, Patricia; Munita, Jose M.; Olivares-Pacheco, Jorge; Alcalde-Rico, Manuel
    Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is one of the pathogens that urgently needs new drugs and new alternatives for its control. The primary strategy to combat this bacterium is combining treatments of beta-lactam with a beta-lactamase inhibitor. The most used combinations against P. aeruginosa are ceftazidime/avibactam (CZA) and ceftolozane/tazobactam (C/T). Although mechanisms leading to CZA and C/T resistance have already been described, among which are the resistance-nodulation-division (RND) efflux pumps, the role that these extrusion systems may play in CZA, and C/T baseline susceptibility of clinical isolates remains unknown. For this purpose, 161 isolates of non-carbapenemase-producing (Non-CP) CRPA were selected, and susceptibility tests to CZA and C/T were performed in the presence and absence of the RND efflux pumps inhibitor, Phenylalanine-arginine beta-naphthylamide (PA beta N). In the absence of PA beta N, C/T showed markedly higher activity against Non-CP-CRPA isolates than observed for CZA. These results were even more evident in isolates classified as extremely-drug resistant (XDR) or with difficult-to-treat resistance (DTR), where CZA decreased its activity up to 55.2% and 20.0%, respectively, whereas C/T did it up to 82.8% (XDR), and 73.3% (DTR). The presence of PA beta N showed an increase in both CZA (37.6%) and C/T (44.6%) activity, and 25.5% of Non-CP-CRPA isolates increased their susceptibility to these two combined antibiotics. However, statistical analysis showed that only the C/T susceptibility of Non-CP-CRPA isolates was significantly increased. Although the contribution of RND activity to CZA and C/T baseline susceptibility was generally low (two-fold decrease of minimal inhibitory concentrations [MIC]), a more evident contribution was observed in a non-minor proportion of the Non-CP-CRPA isolates affected by PA beta N [CZA: 25.4% (15/59); C/T: 30% (21/70)]. These isolates presented significantly higher MIC values for C/T. Therefore, we conclude that RND efflux pumps are participating in the phenomenon of baseline susceptibility to CZA and, even more, to C/T. However, the genomic diversity of clinical isolates is so great that deeper analyzes are necessary to determine which elements are directly involved in this phenomenon.