Biology subjects

Garcia-Contreras, R.

Publications and source records attributed to Garcia-Contreras, R..

8 recordsLinked to original sources

bioRxiv2026

Comparative genomics of clinical isolates of Pseudomonas aeruginosa from cystic fibrosis patients in Mexico

Pseudomonas aeruginosa (P. aeruginosa) is the primary pathogen responsible for morbidity and mortality in patients with cystic fibrosis (CF). Its genomic plasticity and constant selective pressure from antimicrobial treatments have favored the emergence of multidrug-resistant clones. This study conducted a comparative genomic analysis of 41 P. aeruginosa isolated from pediatric patients with CF in Mexico from 2015 to 2024, with the aim of characterizing their evolutionary dynamics, resistome, and virulome. Whole-genome sequencing (MGI, Illumina, and PacBio platforms) was used, with de novo assemblies performed using Unicycler v0.4.8 on the BV-BRC platform. The databases used for the resistome were CARD and NDARO, and for the virulome, VFDB. Phylogenetic reconstruction was based on core-genome alignments generated with Roary v3.13.0, with maximum likelihood reconstruction performed in IQ-TREE v2.1.2. The statistical significance of the segregation of resistance and virulence patterns was evaluated using PERMANOVA analysis. The results revealed a significant clonal prevalence of sequence types (ST) 307 and ST 167. Phylogenomic analysis grouped the isolates into three main clades; Clade 1 stood out for having the highest resistance gene load (mean of 75 genes/genome), establishing itself as the main reservoir of multidrug-resistant profiles. Genotype-phenotype concordance reached 65.5% overall, with high accuracy for aminoglycosides (87.8%) and fluoroquinolones (82.9%). Furthermore, virulome analysis identified 67 distinct patterns that were significantly segregated among the clades (PERMANOVA: R2=0.31, p=0.001). These findings demonstrate that the evolution of P. aeruginosa lineages in the pediatric clinical setting involves parallel and coordinated adaptations in both their resistance potential and their virulence arsenal. This study underscores the need to adopt a multidisciplinary approach to the clinical management of chronic P. aeruginosa infections in pediatric patients. The persistence of extensively drug-resistant (XDR) strains calls for the integration of genomic surveillance and functional diagnostics, as well as the search for therapeutic alternatives for the clinical management of patients with cystic fibrosis.

microbiology↗

bioRxiv2026

Enhancing Reverse Methanogenesis Using RNA-Guided Silencing

Utilizing methane and carbon dioxide before it can enter the upper atmosphere is beneficial for mitigating climate change as well as for producing valuable chemicals. Because anaerobic methanotrophic archaea (ANME) have not yet been cultured in isolation, we previously reversed methanogenesis by cloning the genes encoding methyl-coenzyme M reductase (Mcr) derived from Black Sea ANME-1 into the methanogen Methanosarcina acetivorans. The resulting engineered archaeal strain captures, rather than produces, methane and may be used to convert methane and carbon dioxide into electricity, acetate, L-lactate, and ethanol. However, the engineered M. acetivorans strain also contains a chromosomal locus encoding its native Mcr (McrM.a.), which produces methane from substrates such as methanol, whereas the heterologously expressed ANME-1 Mcr (McrANME-1) promotes methane oxidation. Therefore, we reasoned that McrM.a. may compete with McrANME-1-mediated reversal of methanogenesis. To enhance the reversal of methanogenesis, here we implemented an antisense RNA (asRNA) silencing approach to suppress McrM.a. during growth on methane while still allowing its expression during routine growth on methanol. We found that silencing McrM.a. during McrANME-1-mediated growth on methane increased ethanol and acetate production by more than an order of magnitude. These results were corroborated by both a more than 10-fold increase in methane utilization by McrANME-1 and a greater than 1,000-fold reduction in the McrM.a. mcrBGA transcript levels under methane-grown conditions. Therefore, asRNA-mediated silencing may be used to enhance methane capture by suppressing production of the host McrM.a. for biotechnological applications.

synthetic biology↗

bioRxiv2025

Persister Cells Form Based on Low Ribosome Content

Persister cells survive any severe stress including antibiotics, starvation, heat, oxidative conditions, and phage attack, by entering a dormant physiological state. They arise without genetic change and can resume growth once the stress is removed and nutrients are available. Critically, upon resuscitation, persister cells can reconstitute infections. Although it is known that persister cells resuscitate in proportion to their ribosome content, it has remained unclear whether ribosome levels also influence the formation of persister cells. Here, we used fluorescence-activated cell sorting (FACS) to fractionate exponentially growing cells into four populations spanning low to high ribosome levels and demonstrated that cells with low ribosome content form persister cells approximately 80-fold more frequently than cells with population-average ribosome levels. These findings show that persister cell formation is inversely proportional to ribosome abundance. Cells with low ribosome levels are less metabolically-active and therefore less capable of initiating a stress response like most cells; instead, they become dormant.

microbiology↗

bioRxiv2024

Effect of curcumin and 5-bromoindole-3-carboxyaldehyde on the inhibition of Quorum sensig-dependent virulence factors in Pseudomonas aeruginosa

Curcumin and 5-bromoindole-3-carboxaldehyde were tested for their ability to inhibit quorum sensing-dependent virulence factors in Pseudomonas aeruginosa strains Pa01, Pa14, and ATCC 27853. The compounds were evaluated at curcumin (1, 5 g/ml) and 5-bromoindole-3-carboxaldehyde (30, 50, 100 g/ml). Virulence factors--exoprotease, elastase, pyocyanin, and alginate --were measured. Chemoinformatics properties were analyzed using Molinspiration, Molsoft, Osiris Property Explorer, pkCSM, and SwissADME. Results showed 5-bromoindole-3-carboxaldehyde significantly reduced pyocyanin in Pa01 (92.5% at 100 g/ml), elastase (79.85% at 100 g/ml), exoprotease (92.8% at 50 g/ml), and alginate in ATCC 27853 (76.16% at 100 g/ml). Curcumin effectively inhibited pyocyanin in ATCC 27853 (100% at 5 g/ml), elastase in Pa14 (56.19% at 5 g/ml), exoprotease in Pa01 (87.04% at 5 g/ml), and alginate (48.26% at 5 g/ml). Both compounds demonstrated strong inhibition of virulence factors, suggesting their potential as anti-virulence agents against P. aeruginosa, a highly resistant bacterium prevalent in nosocomial infections.

microbiology↗

bioRxiv2023

Phages Produce Persisters

Bacteria primarily encounter stress, and, arguably, their greatest threats are phages. It is often assumed that those bacteria that escape phage attack have mutated; however, another possibility is that a subpopulation forms the dormant persister state, in a manner similar to that demonstrated for bacterial cells undergoing nutritive, oxidative, and antibiotic stress. Persister cells do not undergo mutation and survive lethal conditions by ceasing growth transiently. Slower growth and dormancy play a key physiological role as they allow host phage defense systems more time to clear the phage infection. Here we investigated how bacteria survive lytic phage infection by isolating surviving cells from the plaques of T2, T4, and lambda (cI mutant) virulent phages. We found that bacteria in plaques can escape phage attack both by mutation (i.e., become resistant) and without mutation (i.e., become persistent). Specifically, whereas T4-resistant and lambda-resistant bacteria with over a 100,000-fold less sensitivity were isolated from plaques with obvious genetic mutations (e.g., causing mucoidy), cells were also found after T2 infection that undergo no significant mutation, retain wild-type phage sensitivity, and survive lethal doses of antibiotics. Corroborating this, adding T2 phage to persister cells resulted in 137,000-fold more survival compared to that of addition to exponentially-growing cells. Phage treatments with Klebsiella pneumonia and Pseudomonas aeruginosa also generated persister cells. Hence, along with resistant strains, bacteria also form persister cells during phage infection.

microbiology↗

bioRxiv2023

Single-Cell Analysis Reveals Cryptic Prophage Protease LfgB Protects Escherichia coli During Oxidative Stress by Cleaving Antitoxin MqsA

Although toxin/antitoxin (TA) systems are ubiquitous, beyond phage inhibition and mobile element stabilization, their role in host metabolism is obscure. One of the best-characterized TA systems is MqsR/MqsA of Escherichia coli, which has been linked previously to protecting this gastrointestinal species during the stress it encounters from the bile salt deoxycholate as it colonizes humans. However, some recent whole-population studies have challenged the role of toxins such as MqsR in bacterial physiology, since the mqsRA locus is induced over a hundred-fold during stress, but a phenotype was not found upon its deletion. Here, we investigate further the role MqsR/MqsA by utilizing single cells and demonstrate that upon oxidative stress, the TA system MqsR/MqsA has a heterogeneous effect on the transcriptome of single cells. Furthermore, we discovered that MqsR activation leads to induction of the poorly-characterized yfjXY ypjJ yfjZF operon of cryptic prophage CP4-57. Moreover, deletion of yfjY makes the cells sensitive to H2O2, acid, and heat stress, and this phenotype was complemented. Hence, we recommend yfjY be renamed to lfgB (less fatality gene B). Critically, MqsA represses lfgB by binding the operon promoter, and LfgB is a protease that degrades MqsA to derepress rpoS and facilitate the stress response. Therefore, the MqsR/MqsA TA system facilitates the stress response through cryptic phage protease LfgB.

molecular biology↗

bioRxiv2020

Quinolone resistance in different uropathogens isolated from urine cultures in patients with urinary tract infection

ObjectiveTo identify patterns of resistance against quinolones in various uropathogens in urinary tract infections in the population of the Toluca valley, Mexico IntroductionQuinolones are antibiotics with a spectrum of activity for both gram-positives and gram-negatives and are antibiotics used for the empirical treatment of urinary tract infections. Recently, a high index of resistance to quinolones has been reported due to different mechanisms on the part of bacteria, however the one that has taken the greatest importance is the presence of extended spectrum beta-lactamases Methods155 samples were collected from patients with suspected urinary tract infection without exclusion criteria such as age or gender. Automated equipment was used for the identification of the etiological agent and sensitivity tests to quinolones. ResultsThe results positives were divided to evaluate which of the two antibiotics studied had greater resistance. For ciprofloxacin there are 27 resistant strains 37%, 1 strain with intermediate resistance 1% and 45 susceptible strains 62%. For levofloxacin 26 strains are resistant 36%, 41 strains are sensitive 56% and 6 strains show intermediate sensitivity 8%. ConclusionDifferent microorganisms, both gram-positive and gram-negative, were isolated and it can be observed that gram-negative strains are the ones with the greatest resistance against quinolones, mainly Escherichia coli, which produces extended-spectrum beta-lactamases, in the case of gram-positive resistance patterns are variable with a tendency towards sensitivity.

microbiology↗

bioRxiv2020

Iron limitation by transferrin promotes simultaneous cheating of pyoverdine and exoprotease in Pseudomonas aeruginosa

Pseudomonas aeruginosa is the main bacterial model to study cooperative behaviors, since it yields exoproducts such as exoproteases and siderophores that act as public goods and can be exploited by selfish non-producers that behave as social cheaters. Non-producers of the siderophore pyoverdine are typically isolated in media with low free iron, mainly casamino acids medium supplemented with transferrin. Nevertheless, using a protein as the iron chelator could additionally select mutants unable to produce exoproteases that degrade the transferrin to facilitate iron release. Here, we investigated the dynamics of pyoverdine and exoprotease production in media in which iron was limited by using either transferrin or a cation chelating resin. Our experiments show that concomitant loss of pyoverdine and exoprotease production readily develops in media with transferrin whereas only lack of pyoverdine emerges in medium treated with the resin. Genomic characterization of the exoprotease- and pyoverdine-less mutants revealed large deletions (13 to 33 Kb) including Quorum Sensing (lasR, rsal and lasl) and flagellar genes. Complementation experiments, PCR and motility tests confirmed the deletions. Our work shows that using transferrin as an iron chelator imposes simultaneous selective pressure for the loss of pyoverdine and exoprotease production. The unintended effect of transferrin observed in our experiment settings can help revisiting or informing the design of similar studies.

microbiology↗