Microbiome reservoirs of antimicrobial resistance

Doctoral thesis (2022)

Antimicrobial resistance (AMR) presents a global threat to public health due to the inability to comprehensively treat bacterial infections. Emerging resistant bacteria residing within human, animal and ... [more ▼]

Antimicrobial resistance (AMR) presents a global threat to public health due to the inability to comprehensively treat bacterial infections. Emerging resistant bacteria residing within human, animal and environmental reservoirs may spread from one to the other, at both local and global levels. Consequently, AMR has the potential to rapidly become pandemic whereby it is no longer constrained by either geographical or human-animal borders. Therefore, to enhance our understanding on the dissemination of AMR we systematically resolved different reservoirs of antimicrobial resistance, leveraging animal, environmental and human samples, to provide a One Health perspective. To identify antimicrobial resistance genes (ARGs) and compare their identity and prevalence across different microbial reservoirs, we developed the PathoFact pipeline which also contextualizes ARG localization on mobile genetic elements (MGEs). This methodology was applied to several metagenomic datasets covering microbiomes of infants, laboratory mice, a wastewater treatment plant (WWTP) and biofilms from glacier-fed streams (GFS). Investigating the infant gut resistome we found that the abundance of ARGs against (semi)-synthetic agents were increased in infants born via caesarian section compared to those born via vaginal delivery. Additionally, we identified mobile genetic elements (MGEs) encoding ARGs such as glycopeptide, diaminopyrimidine and multidrug resistance at an early age. MGEs are often pivotal in the accumulation and dissemination of AMR within a microbial population. Therefore, we assessed the effect of selective pressure on the evolution and consecutive dissemination of AMR within the commensal gut microbiome, utilizing a mouse model. While plasmids and phages were found to contribute to the spread of AMR, we found that integrons represented the primary factors mediating AMR in the antibiotic-treated mice. In addition to the above-described studies, we investigated the environmental resistome, comprising both the urban environment, i.e., the WWTP, and a natural environment, GFS biofilms. Utilizing a multi-omics approach we investigated the WWTP resistome over a 1.5 years timeseries and found that a core group of fifteen AMR categories were always present. Additionally, we found a significant difference in AMR categories encoded on phages versus plasmids indicating that the MGEs contributed differentially to the dissemination of AMR. On the other hand, the GFS biofilms represent pristine environments with limited anthropogenic influences. Therein, we found that eukaryotes, as well as prokaryotes, may serve as AMR reservoirs owing to their potential for encoding ARGs. In addition to our identification of biosynthetic gene clusters encoding antibacterial secondary metabolites, our findings highlight the constant intra- and inter-domain competition and the underlying mechanisms influencing microbial survival in GFS epilithic biofilms. In general, we observed that the overall AMR abundances were highest in human and animal microbial reservoirs whilst environmental reservoirs demonstrated a higher diversity of ARG subtypes. Additionally, we identified human-associated, MGE-derived ARGs in all three components of the One Health triad, indicating possible transmission routes for AMR dissemination. In summary, this work provides a comprehensive assessment of the prevalence of antimicrobial resistance and its dissemination mechanisms in human, animal, and environmental mechanisms. [less ▲]

Functional meta-omics provide critical insights into long- and short-read assemblies

in Briefings in Bioinformatics (2021)

Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only ... [more ▼]

Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only and hybrid assembly approaches on four different metagenomic samples of varying complexity. We demonstrate how different assembly approaches affect gene and protein inference, which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic and metaproteomic data to assess the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions. We propose a reference-independent solution, which exploits the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data. [less ▲]

Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life

in ISME Communications (2021)

Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether ... [more ▼]

Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-α) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation. [less ▲]

Mobilome-driven segregation of the resistome in biological wastewater treatment 2021.11.15.468621

E-print/Working paper (2021)

Biological wastewater treatment plants (BWWTP) are considered to be hotspots of evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization ... [more ▼]

Biological wastewater treatment plants (BWWTP) are considered to be hotspots of evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of fifteen AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS, sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both MGEs. Subsequent expression- and protein-level analyses further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. Longitudinal assessment further underlined these findings whereby the log2-fold changes of aminoglycoside, bacitracin and sulfonamide resistance genes were increased in plasmids, while fosfomycin and peptide resistance showed similar trends in phages. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, for which MGEs also contributed differentially to the dissemination of ARGs. Collectively our findings pave the way towards understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.Competing Interest StatementThe authors have declared no competing interest. [less ▲]

Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams 2021.10.07.463499

E-print/Working paper (2021)

Microorganisms dominate life in cryospheric ecosystems. In glacier-fed streams (GFSs), ecological windows of opportunities allow complex microbial biofilms to develop and transiently form the basis of the ... [more ▼]

Microorganisms dominate life in cryospheric ecosystems. In glacier-fed streams (GFSs), ecological windows of opportunities allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Here, using high-resolution metagenomics, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We found a diverse microbiome spanning the entire tree of life and including a rich virome. Various and co-existing energy acquisition pathways point to diverse niches and the simultaneous exploitation of available resources, likely fostering the establishment of complex biofilms in GFSs during windows of opportunity. The wide occurrence of rhodopsins across metagenome-assembled genomes (MAGs), besides chlorophyll, highlights the role of solar energy capture in these biofilms. Concomitantly, internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by the high oligotrophy in GFSs. MAGs also revealed mechanisms potentially protecting bacteria against low temperatures and high UV-radiation. The selective pressure of the GFS environment is further highlighted by the phylogenomic analysis, differentiating the representatives of the genus Polaromonas, an important component of the GFS microbiome, from those found in other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits that contribute to the success of complex biofilms to exploit environmental opportunities in GFSs, now rapidly changing owing to global warming.Competing Interest StatementThe authors have declared no competing interest. [less ▲]