Biology subjects

Castillo-Ramirez, S.

Publications and source records attributed to Castillo-Ramirez, S..

11 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↗

bioRxiv2026

Evidence of complete myofibril remodeling after severe damage in adult Drosophila.

Muscle function depends on the ability of myofibrils to withstand and repair mechanical damage, yet how adult muscles remodel damaged myofibrils remains poorly understood. Here, we establish a Drosophila model that allows the induction and longitudinal visualization of extensive myofibril damage and recovery in intact adult femur muscles. Sustained muscle depolarization caused extensive disruption of myofibrillar organization, with severe damage characterized by near-complete loss of Z-disc structures. Remarkably, myofibril architecture and muscle function were largely restored within days, revealing a substantial capacity for myofibril reconstruction in adult femur muscles. We identified two distinct states of myofibril damage, mild and severe, with mild damage appearing before severe damage during aging, suggesting a progressive process of myofibril deterioration and repair failure. We further show that filamins mechanosignaling is required for efficient myofibril remodeling. Following damage, wild-type filamin redistributes from the Z-disc and accumulates outside the myofibrils, whereas constitutively open filamin remains Z-disc-associated and constitutively closed filamin redistributes but results in increased damage and impaired recovery. These findings suggest that effective repair requires dynamic transitions between filamin conformational states and that filamin redistribution is an active component of the damage response rather than simply a consequence of muscle injury. During aging, filamin progressively redistributes from the Z-disc and muscle damage accumulates, with severe damage increasing after the appearance of mild damage. Together, our findings reveal a previously unappreciated capacity of adult muscle to reassemble damaged myofibrils and identify filamin mechanosignaling as a key component of this repair process, providing a framework for understanding how defective mechanosensing may contribute to age-related muscle decline and muscle disease.

cell biology↗

bioRxiv2026

Historical isolates provide insights into the evolution of Acinetobacter baumannii international clone 2 and its resistome

Acinetobacter baumannii remains a pervasive nosocomial pathogen, with international clone 2 (IC2) being the most successful lineage. IC2 is often discussed as a singular entity, and the genomic factors behind its success over other lineages are poorly characterised. This study aimed to track genomic changes occurring around the emergence of IC2 and further determine the within-clone population structure. A set of historical A. baumannii isolates from the 1970s to early 2000s were long-read sequenced and assembled into high-quality chromosomes. These were then used to supplement publicly available A. baumannii genomes, producing a dataset of 1,281 chromosomes derived from isolates collected across six continents. A recombination-free phylogeny was produced and combined with antimicrobial resistance gene (ARG) presence/absence data. Analysis showed that IC2 began to emerge as the dominant lineage around 2005, which coincides with the acquisition of oxa23 and AbGRI3. Further, IC2 can be split into at least four distinct groups. Groups 1, 2, and 3 represent incremental evolution of the A. baumannii chromosome over time, while group 4 represents a separate evolutionary path distinct from the main IC2 lineage, which has recently been isolated at higher frequency. Significance statementCharacterising the evolution and population structure of antimicrobial-resistant bacterial pathogens is of key importance both for epidemiological monitoring and developing approaches to combat infections and their spread. Here, we use a unique collection of historical isolates to show that the major international clone in the WHO priority pathogen Acinetobacter baumannii is comprised of different, independent groups with individual antimicrobial resistance gene compliments. This highlights new areas for research to understand the clinical impact of the different groups and the drivers underlying the evolution and spread of epidemic clones of antimicrobial-resistance bacterial pathogens.

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↗

bioRxiv2024

Lipidomics and colistin resistance in non-human isolates of Acinetobacter seifertii

Acinetobacter baumannii is most well known for its role as a human pathogen and as a member of the Acinetobacter calcoaceticus-baumannii (ACB) complex. However, lesser characterised members of the ACB complex, have also been implicated in hospital-acquired infections. Once mainly considered opportunistic pathogens, many A. baumannii and non-baumannii strains are being isolated from agricultural, water and food sources. The surveillance and tracking of Acinetobacter spp. have been recently suggested to be part of the One Health consortium, to understand and prevent the spread of antimicrobial resistance. Here, we isolated four Acinetobacter strains from tank milk in Bogor, Indonesia and using ANI and dDDH techniques have identified them as Acinetobacter seifertii. MLST methods assigned these A. seifertii strains to a novel Sequence Types (ST), highlighting the diversity not only within the ACB complex but also in non-human Acinetobacter spp. These four A. seifertii strains are colistin-resistant and while they do not harbour any known mechanism of colistin resistance, they do share amino acid substitutions in regulatory proteins, AdeS, PmrAB, H-NS, and the membrane associated proteins, LpxACD, MlaD, PldA, LpsB and EptA that may contribute to this phenotype. Furthermore, down-regulation of the RND efflux pump AdeAB, may also be a key factor in colistin resistance in these non-human A. seifertii strains. Lipidomics revealed an acyl-homoserine lactone (AHL) molecule, and lyso-phosphatidylethanolamine (lyso-PE) in significant abundance compared to colistin-sensitive A. baumannii ATCC17978 revealing lipidomic differences between species. Finally, these four tank milk A. seifertii strains are avirulent in an insect model of virulence. It is possible that A. seifertii strains are intrinsically resistant to colistin and require further study. By investigating these less understood Acinetobacter spp. from non-human sources, our study supports the One Health approach to combatting antibiotic resistance.

microbiology↗

bioRxiv2023

Phylogenomic and phenotypic analyses highlight the diversity of antibiotic resistance and virulence in both human and non-human Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative opportunistic pathogen causing infections of the immunocompromised. With a high incidence of muti-drug resistance, carbapenem-resistant A. baumannii is as a priority 1 pathogen designated by the WHO. The current literature has expertly characterized clinical isolates of A. baumannii. As the challenge of these infections has recently been classified as a One Health issue, we set out to explore the diversity of isolates from human and non-clinical sources such as agricultural surface water, urban streams, various effluents from wastewater-treatment plants and tank milk; and, importantly, these isolates came from a wide geographic distribution. Phylogenomic analysis considering almost 200 isolates showed that our diverse set is well-differentiated from the main international clones of A. baumannii. We discovered novel sequence types in both hospital and non-clinical settings, and five strains that overexpress the RND efflux pump adeIJK without changes in susceptibility. Further, we detected a blaADC-79 in a non-human isolate despite its sensitivity to all antibiotics. There was no significant differentiation between the virulence profiles of clinical and non-clinical isolates in the Galleria mellonella insect model of virulence suggesting that virulence is neither dependent on geographic origin nor isolation source. Detection of antibiotic resistance and virulence genes in non-human strains suggests that these isolates may act as a genetic reservoir for clinical strains. This endorses the notion that in order to combat multi-drug resistant infection caused by A. baumannii, a One Health approach is required, and a deeper understanding of non-clinical strains must be achieved. ImportanceThe global crisis of antibiotic resistance is a silent one. More and more bacteria are becoming resistant to all antibiotics available for treatment, leaving no options remaining. This includes Acinetobacter baumannii. This Gram-negative opportunistic pathogen shows a high frequency of multi-drug resistance, and many strains are resistant to last-resort drugs carbapenem and colistin. Research has focused on strains of clinical origin, but there is a knowledge gap regarding virulence traits, particularly, how A. baumannii become the notorious pathogen of today. Antibiotic resistance and virulence genes have been detected in strains from animals, and environmental locations such as grass and soil. As such, A. baumannii is a One Health concern which includes the health of humans, animals and the environment. Thus, in order to truly combat the antibiotic resistance crisis, we need to understand antibiotic resistance and virulence gene reservoirs of this pathogen under the One Health continuum. RepositoriesNCBI GenBank Accession numbers: Bioproject PRJNA819071, Biosamples SAMN26898552 - SAMN26898587.

microbiology↗

bioRxiv2023

Emergence of Acinetobacter baumannii International Clone 10 predominantly found in the Middle East

Acinetobacter baumannii is a globally distributed human pathogen. Infections caused by carbapenem-resistant isolates of A. baumannii (CRAB) are of great concern, as treatment options are very limited. Despite having among the highest rates reported worldwide, there exists limited genomic data from CRAB strains isolated in the Middle East. Here we report epidemiological, phenotypic, and genome sequencing data (short reads and long reads) on a set of 60 A. baumannii isolates belonging to Sequence Type ST158 (Pasteur MLST scheme). They represent a novel international clone (IC), designated IC10, with limited geographic spread beyond the Middle East. Specific antibiotic-resistance genes associated with this clone were identified and data on the plasmid content associated with this lineage are presented.

microbiology↗

bioRxiv2022

Acinetobacter baumannii sampled from cattle and pigs represent novel clones

Acinetobacter baumannii is a very important human pathogen. Nonetheless, we know very little about non-human isolates of A. baumannii. Here we determine the genomic identity of 15 cattle and pig isolates, as well their antibiotic and virulence genetic determinants, and compare them to the main human clinical international clones.

microbiology↗

bioRxiv2021

Mining of thousands of prokaryotic genomes reveals high abundance of prophage signals

Phages and prophages are one of the principal modulators of microbial populations. However, much of their diversity is still poorly understood. Here, we extracted 33,624 prophages from 13,713 complete prokaryotic genomes in order to explore the prophage diversity and their relationships with their host. Our results reveal that prophages were present in 75% of the genomes studied. In addition, Enterobacterales were significantly enriched in prophages. We also found that pathogens are a significant reservoir of prophages. Finally, we determined that the prophage relatedness and the range of genomic hosts were delimited by the evolutionary relationships of their hosts. On a broader level, we got insights into the prophage population, identified in thousands of publicly available prokaryotic genomes, by comparing the prophage distribution and relatedness between them and their hosts.

bioinformatics↗

bioRxiv2021

Accessory genomic epidemiology of co-circulating Acinetobacter baumannii clones

A. baumannii has become one of the most important multidrug resistant nosocomial pathogens all over the world. Nonetheless, very little is known about the diversity of A. baumannii lineages co-existing in hospital settings. Here, using whole-genome sequencing, epidemiological data and antimicrobial susceptibility tests, we uncover the transmission dynamics of extensive and multidrug resistant A. baumannii in a tertiary hospital for a decade. Our core genome phylogeny of almost 300 genomes suggests that there were several introductions of lineages from international clone 2 into the hospital. The molecular dating analysis shows that these introductions happened between 2004 and 2015. Furthermore, using the accessory genome, we show that these lineages were extensively disseminated across many wards in the hospital. Our results demonstrate that accessory genome variation can be a very powerful tool for conducting genomic epidemiology. We anticipate future studies employing the accessory genome as a phylogenomic marker over very short microevolutionary scales.

microbiology↗

bioRxiv2021

The promiscuous and highly mobile resistome of a superbug.

Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the resistome of Acinetobacter baumannii, a very important nosocomial pathogen. Here we analyze 1450+ genomes (covering > 40 countries and > 4 decades) to infer the global population dynamics of the resistome of this species. We show that gene flow and horizontal transfer have driven the dissemination of AR genes in A. baumannii. We found considerable variation in AR gene content across lineages. Although the individual AR gene histories have been affected by recombination, the AR gene content has been shaped by the phylogeny. Furthermore, many AR genes have been transferred to other well-known pathogens, such as Pseudomonas aeruginosa or Klebsiella pneumoniae. Finally, despite using this massive data set, we were not able to sample the whole diversity of AR genes, which suggests that this species has an open resistome. Ours results highlight the high mobilization risk of AR genes between important pathogens. On a broader perspective, this study gives a framework for an emerging perspective (resistome-centric) on the genome epidemiology (and surveillance) of bacterial pathogens.

microbiology↗