Biology subjects

Haraoui, L.-P.

Publications and source records attributed to Haraoui, L.-P..

9 recordsLinked to original sources

bioRxiv2026

Insights Into The Early Diversification of blaNDM-1 Genetic Contexts Following its Emergence in Acinetobacter species and Spread to Enterobacterales

Since its emergence, the New Delhi metallo-{beta}-lactamase (NDM) has become a major global antimicrobial resistance threat, enabling bacterial hosts to resist most {beta}-lactam antibiotics, including carbapenems, and spreading widely across bacterial species and geographic regions. Believed to have originated in Acinetobacter spp., blaNDM subsequently spread to Enterobacterales through mobile genetic elements, despite barriers to lateral gene transfer between these phylogenetically distant taxa. To investigate the genetic diversity and mechanisms underlying this interspecies transfer and subsequent global expansion, we sequenced and characterized 13 blaNDM-1-positive Gram-negative bacterial isolates collected in India in 2007, among the earliest known isolates harboring blaNDM-1. Clonal diversity was observed among both Escherichia coli and Klebsiella pneumoniae isolates. Comprehensive genomic analysis revealed that blaNDM-1 was consistently embedded within a conserved multidrug resistance region, often associated with mobile genetic elements involved in lateral gene transfer. Notably, the insertion sequence ISAba14 was identified in 6 of the 13 sequences, suggesting a potential role in the early dissemination of blaNDM-1 among diverse bacterial hosts. These findings contribute to our understanding of the evolutionary origins and early genetic context of blaNDM-1, highlighting the importance of continued genomic surveillance and functional studies to better understand the persistence and dissemination of carbapenem resistance.

molecular biology↗

bioRxiv2026

ARG-PASS v2.0 expands global resistome surveillance to reveal previously unrecognized antibiotic resistance genes reaching the human gut

Antimicrobial resistance (AMR) is a significant global public health threat, and antibiotic resistance genes (ARGs) that bacteria depend on to withstand treatment are its molecular basis. How ARGs move from environmental reservoirs into the human microbiome, and eventually into human pathogens, remains one of the most important unresolved questions in AMR research. Surveillance has largely targeted ARGs resembling those already clinically characterised. The environmental reservoir remains poorly described and the routes connecting it to human microbiomes are inferred rather than observed. Describing that reservoir requires computational methods able to recognise ARGs that share little similarity with known enzymes, yet retain accuracy after experimental validation to enable scalable applications. Dietary exposure through unprocessed ferments offers a tractable setting in which such a route can be observed directly. Here we introduce ARG-PASS v2.0 (ARG-prediction by PAirwise Sequence versus Structure v2.0) and first apply it to a lake metagenome from Kolkata, India, where 10 of 11 tested candidates across diverse ARG classes were functionally confirmed after expression in Escherichia coli. Given their clinical relevance, we then predicted 918 class B1 metallo-beta-lactamases (MBLs) from MGnify and the PLSDB, with most diverging from characterised enzymes, but as widely distributed. A number of globally widespread candidates track their hosts distribution, with some recovered only from human-associated biomes, yet most span a wider ecological range. Phylogenetic inference places clinically relevant class B1 MBLs within marine diversity and suggests a marine reservoir. Cross-referencing against the Unified Human Gastrointestinal Protein catalogue identified a carbapenemase, an ANT, and class A beta-lactamases from Bacillus sonorensis and Bacillus licheniformis, detected in South Korean fermented soybean paste (doenjang) as well as gut isolates of populations consuming these foods. Together, these results point to a largely chromosomal reservoir of undescribed ARG diversity that reaches the human gut through both resident and generalist hosts. Once in the human microbiome, treatment may be compromised directly if the host is an opportunistic pathogen, or after transfer to a clinical pathogen.

microbiology↗

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

Conserved protein sequence-structure signatures identify emerging antibiotic resistance genes from the human microbiome

Bacteria exhibiting antimicrobial resistance (AMR) is a problem that has grown to become a significant public health challenge worldwide. Antibiotic resistance genes (ARGs), determinants of AMR, mostly emerge from non-clinical settings. Identifying previously undetected ARGs in the human microbiome which confer resistance to clinical concentrations of antibiotics is a crucial component of addressing AMR, yet can be hindered by their low homology to existing ARGs. Here, we attempt to address this by focussing on functionally important protein regions. ARG-PASS (ARG-PAirwise Sequence vs Structure) represents a novel protein function prediction method which leverages a one-class support vector machine trained on pairwise primary and tertiary distributions of structurally conserved regions of proteins encoded by ARGs. ARG-PASS was applied to six reference strains of the Human Microbiome Project. Nine candidates were selected for experimental verification and all were functionally confirmed when expressed in E.coli, belonging to ARG classes: APH, dfr, class B and C {beta}-lactamases, and penicillin binding proteins. We also used ARG-PASS directly on protein structures within the AlphaFold database and predicted a phnP gene (metallo-{beta}-lactamase fold), which is highly divergent from existing {beta}-lactamases and had activity against ampicillin. In total, 80% of the tested genes confer resistance at CLSI resistant breakpoints and the remainder represent pre-resistance genes, with activity but not at clinically relevant minimum inhibitory concentrations. We suggest pre-resistance genes may preferentially evolve into clinically relevant resistance determinants. ARG-PASS represents a novel and precise method of identifying previously uncharacterized ARGs from DNA databases, contributing to resistance surveillance and antibiotic stewardship.

microbiology↗

bioRxiv2025

A niche construction-based perspective on chemical evolution before replication and reproduction

Conceptual analysis has, in the past decades, established that evolution by natural selection (ENS) can occur without reproduction (1-6). This theoretical advancement has significant imports for research on the origins of life that have yet to be explored. In this paper, we introduce and defend a niche construction-based account of evolution by natural selection without reproduction (ENSwR, pronounced like "answer"), which leads to three insights regarding Darwinian evolution at the origins of life. First, we show through ENSwR the plausibility of Darwinian evolution in the prebiotic world; second, ENSwR provides a novel explanatory framework that supports origins of life theories in which autocatalytic sets of chemical reactions play a central role; third, we argue that inorganic catalytic molecules (rather than autocatalytic sets (7-9)) are relevant units of selection to understand the origins of life prior to reproduction and replication. This third argument is especially important for the field, as it helps bridge the gap between chemical and biological evolution (10).

evolutionary biology↗

bioRxiv2024

Transcriptional landscape of the archaeal cell cycle is broadly conserved in eukaryotes

The cell cycle is a series of events that occur from the moment of cell birth to cell division. In eukaryotes, cell growth, genome replication, genome segregation, and cytokinesis are strictly coordinated, defining discrete cell cycle phases. In contrast, these key processes may occur concurrently in bacteria. Thermoacidophilic archaea in the genus Saccharolobus follow a defined cell cycle program, with the first pre-replicative growth (G1) phase, followed by the chromosome replication (S) phase, the second growth (G2) phase, and rapid genome segregation (M) and cytokinesis (D) phases. However, whether other processes, such as metabolism, catabolism, protein translation, and antiviral defense also occur at specific cell cycle phases, as in eukaryotes, or are active throughout the cell cycle, as in bacteria, remains unclear. To address this question, we synchronized cultures of S. islandicus and performed an in-depth transcriptomic analysis of samples enriched in cells undergoing the M-G1, S, and G2 phases. Differential gene expression and consensus gene co-expression network analyses provided a holistic view of the S. islandicus cell cycle. In addition to the core transcriptome network, which is expressed throughout the cell cycle, we show that diverse metabolic pathways, protein synthesis, cell motility and even antiviral defense systems, are expressed in a cell cycle dependent fashion. Our data also refines understanding of the processes previously known to be linked to the cell cycle, such as DNA replication. We show that most DNA replication genes are expressed prior to the S phase, during the M-G1, whereas expression of the major chromatin genes, and accordingly, chromatinization are concomitant with replication. A statistical model was used to define sets of signature genes characteristic of each of the analyzed cell cycle phases, emphasizing transcriptional stratification of the phases. Signature genes are more conserved across Thermoproteota than non-signature genes and their peak expression, especially for the M-G1 and G2 specific genes, matches that of homologs in yeast. Collectively, our data elucidate the complexity of the S. islandicus cell cycle and suggest that it more closely resembles the cell cycle of eukaryotes than previously appreciated.

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↗

bioRxiv2023

Earliest observation of the tetracycline destructase tet(X3)

Tigecycline is an antibiotic of last resort for infections with carbapenem-resistant Acinetobacter baumannii. Plasmids harboring variants of the tetracycline destructase tet(X) promote rising tigecycline resistance rates. We report the earliest observation of tet(X3) in a clinical strain predating tigecyclines commercialization, suggesting selective pressures other than tigecycline contributed to its emergence.

microbiology↗

bioRxiv2022

Molecular epidemiology of carbapenemase-producing Acinetobacter spp. from Israel, 2001-2006: earliest report of blaNDM predating the oldest known blaNDM-positive strains

BackgroundCarbapenem-resistant Acinetobacter baumannii (CRAb) is a WHO priority 1 critical pathogen. Despite early emergence of elevated CRAb rates in Israel, limited molecular data from this location are available. We searched for carbapenemases among 198 clinical Acinetobacter spp. from Israel between 2001 and 2006. MethodsStrains from 3 archives underwent whole-genome sequencing (Illumina NovaSeq on all, MinION on a subset) and computational analyses: assembly (Unicycler), annotation (prokka), identification (Kraken, rpoB similarity), search for carbapenemases (ResFinder, BLDB curation). FindingsA. baumannii (Ab) represented 179 (90{middle dot}4%) Acinetobacter spp. Eighty-four Ab (46{middle dot}9%) carried a carbapenemase: 38 (45{middle dot}2%) blaOXA-72 (blaOXA-24-like); 28 (33{middle dot}3%) blaOXA-23-like (20 blaOXA-23 and 8 blaOXA-225); 18 (21{middle dot}5%) blaOXA-58 (16 from 2001-2). Carbapenemase rates increased yearly from 2002 (32%) to 2006 (67%). Eight species of non-baumannii Acinetobacter (NbA) accounted for 19 isolates (9{middle dot}6%). Two of three A. junii contained blaOXA-58, one of which, Ajun-H1-3, isolated in January 2004, also possessed blaNDM-1. The pNDM-Ajun-H1-3 plasmid matched numerous NDM-positive plasmids reported from 2005 onwards in Acinetobacter spp. as well as Enterobacterales. InterpretationWe assessed carbapenemase diversity among Acinetobacter spp. in Israel from 2001-2006. Findings in Ab predate observations elsewhere: rapidly rising carbapenemase rates, driven by blaOXA-23-like and blaOXA-24-like genes replacing blaOXA-58. Among NbA, an A. junii isolated in 2004 carried blaNDM-1, making it the earliest NDM-positive isolate reported to date, preceding those from 2005 in India. Further research into blaNDMs emergence is warranted, in order to shed light on the evolution and spread of this and other antibiotic-resistance genes. FundingCentre de recherche Charles-Le Moyne; Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Universite de Sherbrooke; Fonds de recherche du Quebec - Sante; New Frontiers in Research Fund Grant NFRFE-2019-00444; CIFAR-Azrieli Global Scholars Program.

microbiology↗