Biology subjects

Perez-Cobas, A. E.

Publications and source records attributed to Perez-Cobas, A. E..

6 recordsLinked to original sources

bioRxiv2026

Spatiotemporal dynamics and stability of multi-kingdom microbial communities in hospital sinks acting as persistent pathogen reservoirs

Hospital sink drains act as persistent reservoirs for nosocomial pathogens, yet the structure and long-term stability of their associated microbial communities remain poorly known. Here, we present an extensive characterization integrating multi-kingdom meta-taxonomic profiling (16S rRNA, ITS, and 18S rRNA, n=93 samples) with culturomics (n>4000 isolates) and phenotypic resistance testing across 14 sinks from a former intensive care unit (ICU). Over a 17-month study period, we tracked community assembly and stability through the renovation and transition from an unpopulated baseline to active clinical use, encompassing both structural remodeling and functional conversion. We showed that former-ICU drains harbor a highly conserved multi-kingdom core that remains resilient despite significant structural changes and periods of inactivity. While a persistent core baseline exists, community composition changes along a continuous temporal gradient driven by structural and anthropogenic shifts. Furthermore, individual sinks assemble as unique microecosystems shaped by local environmental factors. Topological network modeling shows these communities are not random assemblages but integrated ecological units, with clinically relevant, multidrug-resistant WHO-priority pathogens deeply embedded in the network alongside often-overlooked fungi and protozoa. Together, these findings identify hospital sink drains as persistent and structured multi-kingdom microbial reservoirs that harbor clinically relevant multidrug-resistant organisms (MDROs). Their temporal stability and strong sink-specific signatures highlight the need to consider the broader microbial community when monitoring hospital environmental reservoirs and developing infection-control strategies.

microbiology↗

bioRxiv2026

Drinking water treatment drastically modifies multi-kingdom water communities, but clinically relevant opportunistic bacterial pathogens persist

Controlling pathogenic microorganisms during water treatment processes is a major public health concern. However, the impact of different water sources and treatment processes on the drinking water microbiome and opportunistic bacterial pathogens remains poorly understood. Here, we report the analyses of two water systems: a river and groundwater source, and their corresponding treated waters, sampled bi-weekly for 6 months. Microbial communities were analysed through a metabarcoding and dPCR workflow coupling universal prokaryotic and eukaryotic primers with genus-targeting primers for Legionella and Pseudomonas to achieve a deep taxonomic resolution. We show that microbial communities in groundwater were more diverse than those in river water and that water treatment affected -diversity. Water treatment had a stronger influence on community composition than water system or seasonal variation. Despite lower bacterial loads, the relative abundance of Legionella, Pseudomonas, and non-tuberculous Mycobacteria (NTM) remained stable or even increased after water treatment, suggesting that conventional treatment processes promote enrichment of specific taxa. Excitingly, the genus-targeting analyses revealed a remarkable and previously uncharacterized diversity of Legionella species. L.pneumophila, pathogenic Pseudomonas clades and P. aeruginosa were detected in all environments, emphasizing their ability to adapt to diverse ecological conditions. Analysis of the eukaryotic fraction emphasized the persistence and emergence of eukaryotic hosts associated with these waterborne opportunistic pathogens. Our findings offer important insights into how water source characteristics and treatment processes influence the composition of the drinking water microbiome, while the high taxonomic resolution achieved for waterborne opportunistic bacterial pathogens underscores their ecological adaptability.

microbiology↗

bioRxiv2025

The Antimicrobial Gut Resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialised populations, underscoring the robust-yet-fragile architecture of human gut microbiomes.

BackgroundMetagenomics enables detailed profiling of antimicrobial resistance genes, but most studies focus solely on antibiotic resistance genes (ARGs), use low-sensitivity methods, and rarely investigate populations with minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8,667 resistance genes to antibiotics (ARGs), metals (MRGs), and biocides (BRGs) (PMID: 29335005). Resistome profiles were compared with Europeans to assess population-level differences. ResultsARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + BRGs (BAC) gene richness was signifcantly higher in Wayampi (3,670 vs. 2,039). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for BAC), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed, followed by those for zinc, iron, cobalt, and, nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguised cohorts by ARG profiles (p < 0.001), but not MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs in both gut microbiomes. ConclusionsThe diverse and balanced Wayampi resistome reflect a less perturbed microbiome compared to industrialized populations, and reveals a background of core and shell acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient distribution of resistance genes reflects varying levels of conserved gene sharing highways probably shaped by long-term microbial-human evolution, and support a broader view of acquired antimicrobial resistance.

microbiology↗

bioRxiv2023

Long-term dynamics of the 'Serratia marcescens complex' in the hospital-built environment

Serratia marcescens is an opportunistic pathogen historically associated with abrupt, unpredictable, and severe outbreaks in hospital intensive care units (ICUs) and, more recently, with the spread of acquired genes encoding carbapenem resistance. However, the population biology and ecology of S. marcescens in the hospital ecosystem is still poorly understood. Here, we combine epidemiological information of 1417 Serratia isolates collected from the sinks of a large ICU ward that underwent significant demographic and operational changes (2019-2020) and 99 non-redundant outbreak/non-outbreak isolates from the same hospital (2003-2019), with genomic data of 165 isolates. We first report hospital sinks as reservoirs of heterogeneous and coexistent populations of the S. marcescens complex (SMC). A novel SMC clade congruent with the recently described Serratia nevei species is predominant, exhibiting chromosomal AmpC {beta}-lactamase with an unusual basal expression in contrast to one of the major features of S. marcescens. Persistent Serratia sink strains are identical to those involved in clonal and polyclonal outbreaks of VIM-1 and OXA-48 producers since at least 2017. The "source-sink" dynamics of SMC populations able to acquire the highly conserved plasmids such as IncL carrying blaVIM-1 or blaOXA-48 offer novel insights that might improve interventions to control outbreaks and treat Serratia infections in high-risk hospital areas.

microbiology↗

bioRxiv2019

Legionella pneumophila infection and antibiotic treatment engenders a highly disturbed pulmonary microbiome with decreased microbial diversity

BackgroundLung microbiome analyses have shown that the healthy lung is not sterile but it is colonized like other body sites by bacteria, fungi and viruses. However, little is known about the microbial composition of the lung microbiome during infectious diseases such as pneumonia and how it evolves during antibiotic therapy. To better understand the impact of the composition of the pulmonary microbiome on severity and outcome of pneumonia we analysed the composition and evolution of the human lung microbiome during pneumonia caused by the bacterium Legionella pneumophila.\n\nResultsWe collected 10 bronchoalveolar lavage (BAL) samples from three patients during long-term hospitalisation due to severe pneumonia and performed a longitudinal in-depth study of the composition of their lung microbiome by high-throughput Illumina sequencing of the 16S rRNA gene (bacteria and archaea), ITS region (fungi) and 18S rRNA gene (eukaryotes). We found that the composition of the bacterial lung microbiome during pneumonia is hugely disturbed containing a very high percentage of the pathogen, a very low bacterial diversity, and an increased presence of opportunistic microorganisms such as species belonging to Staphylococcaceae and Streptococcaceae. The microbiome of antibiotic treated patients cured from pneumonia represented a different perturbation state with a higher abundance of resistant bacteria (mainly Firmicutes) and a significantly different bacterial composition as that found in healthy individuals. In contrast, the mycobiome remains more stable during pneumonia and antimicrobial therapy. Interestingly we identified possible cooperation within and between both communities. Furthermore, archaea (Methanobrevibacter) and protozoa (Acanthamoeba and Trichomonas) were detected.\n\nConclusionsBacterial pneumonia leads to a collapse of the healthy microbiome and a strongly disturbed bacterial composition of the pulmonary microbiome that is dominated by the pathogen. Antibiotic treatment allows some bacteria to regrow or recolonize the lungs but the restoration of a healthy lung microbiome composition is only regained a certain time after the antibiotic treatment. Archaea and protozoa should also be considered, as they might be important but yet overseen members of the lung microbiome. Interactions between the micro- and the mycobiome might play a role in the restoration of the microbiome and the clinical evolution of the disease.

microbiology↗

bioRxiv2018

More than 16,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells

SignificanceLegionella pneumophila is a bacterial pathogen causing outbreaks of a lethal pneumonia. The genus Legionella comprises 65 species for which aquatic amoebae are the natural reservoirs. Using functional and comparative genomics to deconstruct the entire bacterial genus we reveal the surprising parallel evolutionary trajectories that have led to the emergence of human pathogenic Legionella. An unexpectedly large and unique repository of secreted proteins (>16,000) containing eukaryotic-like proteins acquired from all domains of life (plant, animal, fungal, archaea) is contrasting with a highly conserved type 4 secretion system. This study reveals an unprecedented environmental reservoir of bacterial virulence factors, and provides a new understanding of how reshuffling and gene-acquisition from environmental eukaryotic hosts, may allow for the emergence of human pathogens.\n\nAbstractThe bacterial genus Legionella comprises 65 species among, which Legionella pneumophila is a human pathogen causing severe pneumonia. To understand the evolution of an environmental to an accidental human pathogen, we have functionally analyzed 80 Legionella genomes spanning 58 species. Uniquely, an immense repository of 16,000 secreted proteins encoding 137 different eukaryotic-like domains and more than 200 eukaryotic-like proteins is paired with a highly conserved T4SS. Specifically, we show that eukaryotic Rho and Rab GTPase domains are found nearly exclusively in eukaryotes and Legionella species. Translocation assays for selected Rab-GTPase proteins revealed that they are indeed T4SS secreted substrates. Furthermore, F/U-box and SET domains were present in >70% of all species suggesting that manipulation of host signal transduction, protein turnover and chromatin modification pathways, respectively are fundamental intracellular replication strategies for Legionellae. In contrast, the Sec-7 domain was restricted to L. pneumophila and seven other species, indicating effector repertoire tailoring within different amoebae. Functional screening of 47 species revealed 60% were competent for intracellular replication in THP-1 cells, but interestingly this phenotype was associated with diverse effector assemblages. These data, combined with evolutionary analysis indicate that the capacity to infect eukaryotic cells has been acquired independently many times within the genus and that a highly conserved yet versatile T4SS secretes an exceptional number of different proteins shaped by inter-domain gene transfer. Furthermore we revealed the surprising extent to which legionellae have co-opted genes and thus cellular functions from their eukaryotic hosts and provides a new understanding of how dynamic reshuffling and gene-acquisition has led to the emergence of major human pathogens.

genomics↗