Biology subjects

Aguilar-Vera, A.

Publications and source records attributed to Aguilar-Vera, A..

3 recordsLinked to original sources

bioRxiv2026

Leveraging genomes and metagenome-assembled genomes unveils novel diversity and transmission between public transport and clinical settings in Acinetobacter

The molecular epidemiology of Acinetobacter, which is almost exclusively culture-dependent, has centered mainly on clinical isolates of A. baumannii. Yet, this overlooks sources not amenable to microbial culture and many non-A. baumannii species. Here, by analysing metagenomic projects from public transport systems worldwide, we show that metagenome-assembled genomes (MAGs) are highly relevant for assessing the unrecognized diversity of Acinetobacter. We recovered 839 Acinetobacter MAGs, with 269 being high-quality MAGs. The high-quality MAGs were across more than 20 well-defined Acinetobacter species; however, five species (A. nosocomilalis, A. ursingii, A. radioresistens, A. schindleri, and A. variabilis) had the most MAGs. Pangenome and phylogenetic diversity analyses of 685 genomes plus the 269 high-quality MAGs from those 5 species showed that MAGs are an important source of both lineage and gene diversity. Also, FST analyses and genome phylogenies show that for some species there is no genetic differentiation between MAGs and clinical isolates, implying transmission between hospitals and public transport settings. In addition to finding the antibiotic resistance genes (ARGs) in MAGs, we implemented an ad hoc strategy (leveraging the use of genomes) to recover considerably more ARGs. PCoA and PERMANOVA analyses show that, whereas in A. nosocomialis and A. ursingii, the ARG profiles of MAGs and clinical genomes are different, in A. radioresistens and A. schindleri, the ARG profiles are not different. Finally, some clinically important ARGs, such as sul1 and sul2, aadA, and blaOXA23, were found in all or some of the 5 species. Our study shows how combining MAGs and regular genomes is a powerful strategy for better appraising the genomic diversity (including the resistome) of Acinetobacter. On a broader level, our study showcases the importance of MAGs for genomic surveillance of man-made environments with clear public health implications.

microbiology↗

bioRxiv2025

Genomic epidemiology reveals antibiotic resistance transfer and polyclonal dissemination of Acinetobacter baumannii in a Paraguayan hospital

Acinetobacter baumannii is a major nosocomial pathogen worldwide and, specifically, in Latin America. Genomic epidemiology has been instrumental in determining the transmission dynamics of A. baumannii in many countries of the world, yet some Latin American countries have conducted no genomic epidemiology studies. Here, we conduct the first genomic epidemiology study about this pathogen in Paraguay. We sequenced 43 isolates from a big tertiary hospital in Paraguay collected from different wards in 2021 and 2022. Our genomic epidemiology analyses, including almost 200 genomes and considering the main international clones (ICs), show that IC1, IC2, IC4, IC5 and IC7 were found in the hospital. We found novel genetic variation (3 novel Sequence Types as per the Oxford MLST scheme and one as per the Pasteur scheme) within IC7. Antibiotic susceptibility tests show that all but one of the Paraguayan isolates were resistant to carbapenems. Notably, 98% were classified as multidrug-resistant. We detected plasmids in almost all the Paraguayan isolates. Furthermore, we detected cases of recent horizontal transfer of important antibiotic-resistance genes between different ICs. On a general note, our findings highlight polyclonal spreading across different hospital wards and horizontal transfer of clinically relevant antibiotic-resistance genes among the different clones. On a more local note, this is the first genomic epidemiology study of A. baumannii in Paraguay and will be a reference point for future studies in the country and the region.

microbiology↗

bioRxiv2023

Engineering of Robust Host Strains: Enhancing Escherichia coli Abiotic Stress Resistance through Ornithine Lipid Formation

Escherichia coli is a common host for biotechnology and synthetic biology applications. During growth and fermentation, the microbes are often exposed to stress conditions, such as variations in pH or solvent concentrations. Bacterial membranes play a key role in response to abiotic stresses. Ornithine lipids (OLs) are a group of membrane lipids whose presence and synthesis have been related to stress resistance in bacteria. We wondered if this stress resistance could be transferred to bacteria not encoding the capacity to form OLs in their genome, such as E. coli. In this study, we engineered different E. coli strains to produce unmodified OLs and hydroxylated OLs by expressing the synthetic operon olsFC. Our results showed that OL formation improved pH resistance and increased biomass under phosphate limitation. Transcriptome analysis revealed that OL-forming strains differentially expressed stress- and membrane-related genes. OL-producing strains also showed better growth in the presence of the ionophore carbonyl cyanide 3-chlorophenylhydrazone (CCCP), suggesting reduced proton leakiness in OL-producing strains. Furthermore, our engineered strains showed improved heterologous violacein production at phosphate limitation and also at low pH. Overall, this study demonstrates the potential of engineering the E. coli membrane composition for constructing robust hosts with an increased abiotic stress resistance for biotechnology and synthetic biology applications. KeypointsO_LIThe E. coli membrane composition was engineered by producing ornithine lipids C_LIO_LIOrnithine lipid production increase biomass yield under phosphate limitation C_LIO_LIEngineered strains show enhanced production phenotype under low pH stress C_LIO_LITranscriptome analysis and CCCP experiments revealed reduced proton leakage C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/544863v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1e261ecorg.highwire.dtl.DTLVardef@18ae062org.highwire.dtl.DTLVardef@915b57org.highwire.dtl.DTLVardef@103b74d_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗