Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge

Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater

Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species ( average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities.

IMPORTANCE

Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.

Horizontal transfer potential of antibiotic resistance genes in wastewater treatment plants unraveled by microfluidic-based mini-metagenomics

Wastewater treatment plants (WWTPs) are known to harbor antibiotic resistance genes (ARGs), which can potentially spread to the environment and human populations. However, the extent and mechanisms of ARG transfer in WWTPs are not well understood due to the high microbial diversity and limitations of molecular techniques. In this study, we used a microfluidic-based mini-metagenomics approach to investigate the transfer potential and mechanisms of ARGs in activated sludge from WWTPs. Our results show that while diverse ARGs are present in activated sludge, only a few highly similar ARGs are observed across different taxa, indicating limited transfer potential. We identified two ARGs, ermF and tla-1, which occur in a variety of bacterial taxa and may have high transfer potential facilitated by mobile genetic elements. Interestingly, genes that are highly similar to the sequences of these two ARGs, as identified in this study, display varying patterns of abundance across geographic regions. Genes similar to ermF found are widely found in Asia and the Americas, while genes resembling tla-1 are primarily detected in Asia. Genes similar to both genes are barely detected in European WWTPs. These findings shed light on the limited horizontal transfer potential of ARGs in WWTPs and highlight the importance of monitoring specific ARGs in different regions to mitigate the spread of antibiotic resistance.

Nanosensor Chemical Cytometry: Advances and Opportunities in Cellular Therapy and Precision Medicine

With the definition of therapeutics now encompassing transplanted or engineered cells and their molecular products, there is a growing scientific necessity for analytics to understand this new category of drugs. This Perspective highlights the recent development of new measurement science on label-free single cell analysis, nanosensor chemical cytometry (NCC), and their potential for cellular therapeutics and precision medicine. NCC is based on microfluidics integrated with fluorescent nanosensor arrays utilizing the optical lensing effect of a single cell to real-time extract molecular properties and correlate them with physical attributes of single cells. This new class of cytometry can quantify the heterogeneity of the multivariate physicochemical attributes of the cell populations in a completely label-free and nondestructive way and, thus, suggest the vein-to-vein conditions for the safe therapeutic applications. After the introduction of the NCC technology, we suggest the technological development roadmap for the maturation of the new field: from the sensor/chip design perspective to the system/software development level based on hardware automation and deep learning data analytics. The advancement of this new single cell sensing technology is anticipated to aid rich and multivariate single cell data setting and support safe and reliable cellular therapeutics. This new measurement science can lead to data-driven personalized precision medicine.

A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens

Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.

Application of flow cytometry for rapid, high-throughput, multiparametric analysis of environmental microbiomes

Quantification of the abundance and understanding of the dynamics of the microbial communities is essential to establish a basis for microbiome characterization. The conventional techniques used for the quantification of microbes are complicated and time-consuming. With scientific advancement, many techniques evolved and came into account. Among them, flow cytometry is a robust, high-throughput technique through which microbial dynamics, morphology, microbial distribution, physiological characteristics, and many more attributes can be studied in a high-throughput manner with comparatively less time and resources. Flow cytometry, when combined with other omics-based methods, offers a rapid and efficient platform to analyze and understand the composition of microbiome at the cellular level. The microbial diversity observed through flow cytometry will not be equivalent to that obtained by sequencing methods, but this integrated approach holds great potential for high throughput characterization of microbiomes. Flow cytometry is regarded as an established characterization tool in haematology, oncology, immunology, and medical microbiology research; however, its application in environmental microbiology is yet to be explored. This comprehensive review aims to delve into the diverse environmental applications of flow cytometry across various domains, including but not limited to bioremediation, landfills, anaerobic digestion, industrial bioprocesses, water quality regulation, and soil quality regulation. By conducting an in-depth analysis, this article seeks to shed light on the potential benefits and challenges associated with the utilization of flow cytometry in addressing environmental concerns.