Scientific publications

The dynamics of bla_TEM resistance genes in Salmonella Typhi
Nuanmuang et al. 2024

Salmonella Typhi (S. Typhi) is an important pathogen causing typhoid fever worldwide. The emergence of antibiotic resistance, including that of bla_TEM genes encoding to TEM
β-lactamases has been observed. This study aimed to investigate the dynamics of bla_TEM genes in S. Typhi by analyzing the phylogeny and flanking region patterns and phylogenetic associating them with metadata (year, country) and genomic data (genotypes, antibiotic resistance genes (ARGs), plasmids).

DOI:    https://doi.org/10.1038/s41598-024-74321-8    16-10-2024

Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark
Brinch et al. 2024

We report the discovery of a persistent presence of Vibrio cholerae at very low abundance in the inlet of a single wastewater treatment plant in Copenhagen, Denmark at least since 2015. Remarkably, no environmental or locally transmitted clinical case of V. cholerae has been reported in Denmark for more than 100 years.

DOI:   https://doi.org/10.1007/s00248-024-02419-7   31-07-2024

Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome
Martiny et al. 2024

The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is essential to identify which pairs of ARGs co-occur. Given the wealth of next-generation sequencing data available in public repositories, we have investigated the correlation between ARG abundances in a collection of 214,095 metagenomic data sets.

DOI:   https://doi.org/10.1128/spectrum.04108-23    04-06-2024

Complete genome sequences of Cytobacillus sp., Domibacillus sp., Enterobacter sp., Neisseria sp., Pseudomonas sp., and Streptococcus sp. strains from human clinical infections collected at diagnostic units in 2020
Szarvas et al. 2024

Members of Bacillota and Pseudomonadota phyla are frequently considered bacterial infectious agents in humans. As part of a large sequencing project of clinically relevant pathogens, we hybrid-assembled complete genomes of Cytobacillus, Domibacillus, Enterobacter, Neisseria, Pseudomonas, and Streptococcus species isolated from clinical specimens.

DOI:   https://doi.org/10.1128/mra.01040-23    29-05-2024

The European livestock resistome
Munk et al. 2024

Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves.

DOI:   https://doi.org/10.1128/msystems.01328-23   19-03-2024

ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
Martiny et al. 2024

Analyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs). However, there is a need for standardized and reproducible workflows to ensure the comparability of studies, as the current options involve various tools and reference databases, each designed with a specific purpose in mind.

DOI:   https://doi.org/10.1093/bioinformatics/btae086   20-02-2024

Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations
Bogri et al. 2023

Antimicrobial resistance (AMR) is a major global health concern, further complicated by its spread via the microbiome bacterial members. While mathematical models discuss AMR transmission through the symbiotic microbiome, experimental studies are scarce. Herein, we used a gregarious cockroach, Pycnoscelus surinamensis, as an in vivo animal model for AMR transmission investigations.

DOI:   https://doi.org/10.1128/msystems.01018-23   14-12-2023

Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis
Thorn et al. 2023

Analysis of flanking region sequences can be useful when comparing mobile prokaryotic sequences from different bacterial isolates or metagenomes. Here, we report a new bioinformatics tool, a pipeline called Flankophile, which can analyze flanking regions and sequence variants.

DOI:   https://doi.org/10.1128/spectrum.02413-23   12-12-2023

Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints
Apenteng et al. 2023

Current surveillance of antimicrobial resistance (AMR) is mostly based on testing indicator bacteria using minimum inhibitory concentration (MIC) panels. Metagenomics has the potential to identify all known antimicrobial resistant genes (ARGs) in complex samples and thereby detect changes in the occurrence earlier.

DOI:   https://doi.org/10.1038/s41598-023-47754-w    21-11-2023

Association of health, nutrition, and socioeconomic variables with global antimicrobial resistance: a modelling study
Njage et al. 2023

Although antimicrobial use is a key selector for antimicrobial resistance, recent studies have suggested that the ecological context in which antimicrobials are used might provide important factors for the prediction of the emergence and spread of antimicrobial resistance.

DOI:   https://doi.org/10.1016/S2542-5196(23)00213-9    06-11-2023

Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world
Johansson et al. 2023

We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide.

DOI:   https://doi.org/10.1371/journal.pone.0293169     19-10-2023

The resistomes of rural and urban pigs and poultry in Ghana
Jensen et al. 2023

There is limited knowledge on the bacteriome and resistome in livestock in Africa and the potential influence of the animal husbandry practices and scale has also been scantly explored. We quantified and characterized the antimicrobial resistance gene (ARG) pools (resistomes) and bacteriome in 30 pigs and 60 poultry samples (free-range: rural and urban, and industrialized) across Ghana using Resfinder and Silva databases and compared them to similar data from pigs and poultry from nine European countries.

DOI:   https://doi.org/10.1128/msystems.00629-23   22-09-2023

An Overview of Antimicrobial Resistance Profiles of Publicly Available Salmonella Genomes with Sufficient Quality and Metadata
Nuanmuang et al. 2023

Salmonella enterica (S. enterica) is a commensal organism or pathogen causing diseases in animals and humans, as well as widespread in the environment. Antimicrobial resistance (AMR) has increasingly affected both animal and human health and continues to raise public health concerns. A decade ago, it was estimated that the increased use of whole genome sequencing (WGS) combined with sharing of public data would drastically change and improve the surveillance and understanding of Salmonella epidemiology and AMR.

DOI:   https://doi.org/10.1089/fpd.2022.0080    04-09-2023

Distinctive hospital and community resistomes in Scottish urban wastewater: Metagenomics of a paired wastewater sampling design
Lepper et al. 2023

The wastewater microbiome contains a multitude of resistant bacteria of human origin, presenting an opportunity for surveillance of resistance in the general population. However, wastewater microbial communities are also influenced by clinical sources, such as hospitals.

DOI:   https://doi.org/10.1016/j.scitotenv.2023.165978    05-08-2023

Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering
Jespersen et al. 2023

Most investigations of geographical within-species differences are limited to focusing on a single species. Here, we investigate global differences for multiple bacterial species using a dataset of 757 metagenomics sewage samples from 101 countries worldwide. The within-species variations were determined by performing genome reconstructions, and the analyses were expanded by gene focused approaches.

DOI:   https://doi.org/10.1038/s42003-023-05083-8    08-07-2023

Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome
Ostenfeld et al. 2023

Microbial communities have huge impacts on their ecosystems and local environments spanning from marine and soil communities to the mammalian gut. Bacteriophages (phages) are important drivers of population control and diversity in the community, but our understanding of complex microbial communities is halted by biased detection techniques.

DOI:   https://doi.org/10.1371/journal.pone.0283676    30-03-2023

Interplay between strain fitness and transmission frequency determines prevalence of antimicrobial resistance
Bogri et al. 2023

The steep rise of infections caused by bacteria that are resistant to antimicrobial agents threatens global health. However, the association between antimicrobial use and the prevalence of resistance is not straightforward. Therefore, it is necessary to quantify the importance of additional factors that affect this relationship.

DOI:   https://doi.org/10.3389/fevo.2023.981377    15-03-2023

Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018
Duarte et al. 2023

Antimicrobial resistance (AMR) is a major global health threat. Multiple lines of evidence show that AMR bacteria emerge in livestock due to antimicrobial use (AMU), and that these AMR bacteria (or factors underlying their resistance capacity) might transmit from livestock to humans, including through food.

DOI:   https://doi.org/10.2807/1560-7917.ES.2023.28.20.2200678   14-03-2023

Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage
Ferreira et al. 2023

The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches.

DOI:   https://doi.org/10.1093/femsmc/xtad008   07-03-2023

Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Munk et al. 2022

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019.

DOI:   https://doi.org/10.1038/s41467-022-34312-7   01-12-2022

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies
Aytan-Aktug et al. 2022

High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages.

DOI:   https://doi.org/10.1128/spectrum.02641-22   15-11-2022

Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report
Wei et al. 2022

Fecal microbiota transplantation (FMT) effectively prevents the recurrence of Clostridioides difficile infection (CDI). Long-term engraftment of donor-specific microbial consortia may occur in the recipient, but potential further transfer to other sites, including the vertical transmission of donor-specific strains to future generations, has not been investigated. Here, we report, for the first time, the cross-generational transmission of specific bacterial strains from an FMT donor to a pregnant patient with CDI and further to her child, born at term, 26 weeks after the FMT treatment.

DOI:   https://doi.org/10.1186/s40168-022-01394-w     10-11-2022

The Role of the Environment in Dynamics of Antibiotic Resistance in Humans and Animals: A Modelling Study
Lepper et al. 2022

Antibiotic resistance is transmitted between animals and humans either directly or indirectly, through transmission via the environment. However, little is known about the contribution of the environment to resistance epidemiology. Here, we use a mathematical model to study the effect of the environment on human resistance levels and the impact of interventions to reduce antibiotic consumption in animals. We developed a model of resistance transmission with human, animal, and environmental compartments.

DOI:   https://doi.org/10.3390/antibiotics11101361   05-10-2022

Global Distribution and Diversity of Prevalent Sewage Water Plasmidomes
Teudt et al. 2022

Sewage water from around the world contains an abundance of short plasmids, several of which harbor antimicrobial resistance genes (ARGs). The global dynamics of plasmid-derived antimicrobial resistance and functions are only starting to be unveiled. Here, we utilized a previously created data set of 159,332 assumed small plasmids from 24 different global sewage samples.

DOI:   https://doi.org/10.1128/msystems.00191-22    07-09-2022

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome
Martiny et al. 2022

The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods, as well as a deeper understanding of how antimicrobial resistance genes (ARGs) have been transmitted around the world. The large pool of sequencing data available in public repositories provides an excellent resource for monitoring the temporal and spatial dissemination of AMR in different ecological settings.

DOI:   https://doi.org/10.1371/journal.pbio.3001792   06-09-2022

One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings
Rebelo et al. 2022

Antimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make them an attractive alternative.

DOI:   https://doi.org/10.3389/fmicb.2022.804627    10-06-2022

Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study
Janes et al. 2022

Semi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy and speed by sequencing the microbiota and resistome directly from urine. We aimed to compare metagenomics to culture for semi-quantitative pathogen and resistome detection from urine.

DOI:   https://doi.org/10.1016/S2666-5247(22)00088-X    07-06-2022

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest
Aytan-Aktug et al. 2022

Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved using automated pattern detection methods compared to homology-based methods due to the diversity and genetic plasticity of plasmids. In this study, we developed a method for predicting the host range of plasmids using machine learning—specifically, random forests.

DOI:   https://doi.org/10.1128/msystems.01180-21   06-04-2022

Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes
Poulsen et al. 2022

Metagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common steps in sample preparation include sample collection, storage, DNA isolation, library preparation, and DNA sequencing.

DOI:   https://doi.org/10.1128/spectrum.00090-22    15-03-2022

Genome binning of viral entities from bulk metagenomics data
Johansen et al. 2022

Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data.

DOI:   https://doi.org/10.1038/s41467-022-28581-5   18-02-2022

One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods
Rebelo et al. 2022

Implementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark.

DOI:  https://doi.org/10.1371/journal.pone.0261999   11-02-2022

ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes
Florensa et al. 2022

Antimicrobial resistance (AMR) is one of the most important health threats globally. The ability to accurately identify resistant bacterial isolates and the individual antimicrobial resistance genes (ARGs) is essential for understanding the evolution and emergence of AMR and to provide appropriate treatment. The rapid developments in next-generation sequencing technologies have made this technology available to researchers and microbiologists at routine laboratories around the world. However, tools available for those with limited experience with bioinformatics are lacking, especially to enable researchers and microbiologists in low- and middle-income countries (LMICs) to perform their own studies. The CGE-tools (Center for Genomic Epidemiology) including ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/) was developed to provide freely available easy to use online bioinformatic tools allowing inexperienced researchers and microbiologists to perform simple bioinformatic analyses. The main purpose was and is to provide these solutions for people involved in frontline diagnosis especially in LMICs. Since its original publication in 2012, ResFinder has undergone a number of improvements including improvement of the code and databases, inclusion of point mutations for selected bacterial species and predictions of phenotypes also for selected species.

DOI:   http://dx.doi.org/10.1099/mgen.0.000748    24-01-2022

Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life Years for 29 Cancer Groups From 2010 to 2019
A Systematic Analysis for the Global Burden of Disease Study 2019
Global Burden of Disease 2019 Cancer Collaboration

Question: What was the burden of cancer globally and across Sociodemographic Index (SDI) groupings in 2019, and how has incidence, morbidity, and mortality changed since 2010?
Findings: In this systematic analysis, there were 23.6 million new global cancer cases in 2019 (17.2 million when excluding those with nonmelanoma skin cancer), 10.0 million cancer deaths, and an estimated 250 million disability-adjusted life years estimated to be due to cancer; since 2010, these represent increases of 26.3%, 20.9%, and 16.0%, respectively. Absolute cancer burden increased in all SDI quintiles since 2010, but the largest percentage increases occurred in the low and low-middle SDI quintiles.
Meanings: The study results suggest that increased cancer prevention and control efforts are needed to equitably address the evolving and increasing burden of cancer across the SDI spectrum.

DOI:   http://dx.doi.org/10.1001/jamaoncol.2021.6987   30-12-2021

The global burden of adolescent and young adult cancer in 2019: a systematic analysis for the Global Burden of Disease Study 2019
GBD 2019 Adolescent Young Adult Cancer Collaborators

In estimating the global burden of cancer, adolescents and young adults with cancer are often overlooked, despite being a distinct subgroup with unique epidemiology, clinical care needs, and societal impact. Comprehensive estimates of the global cancer burden in adolescents and young adults (aged 15–39 years) are lacking. To address this gap, we analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, with a focus on the outcome of disability-adjusted life-years (DALYs), to inform global cancer control measures in adolescents and young adults.

DOI:  https://doi.org/10.1016/S1470-2045(21)00581-7   03-12-2021

Danish Whole-Genome-Sequenced Candida albicans and Candida glabrata Samples Fit into Globally Prevalent Clades
Szarvas et al. 2021

Candida albicans and Candida glabrata are opportunistic fungal pathogens with increasing incidence worldwide and higher-than-expected prevalence in Denmark. We whole-genome sequenced yeast isolates collected from Danish Clinical Microbiology Laboratories to obtain an overview of the Candida population in the country. The majority of the 30 C. albicans isolates were found to belong to three globally prevalent clades, and, with one exception, the remaining isolates were also predicted to cluster with samples from other geographical locations. Similarly, most of the eight C. glabrata isolates were predicted to be prevalent subtypes. Antifungal susceptibility testing proved all C. albicans isolates to be susceptible to both azoles and echinocandins. Two C. glabrata isolates presented azole-resistant phenotypes, yet all were susceptible to echinocandins. There is no indication of causality between population structure and resistance phenotypes for either species.

DOI:   https://doi.org/10.3390/jof7110962    12-11-2021

Pandemics– One Health preparedness for the next
Frank M. Aarestrup, Marc Bonten, Marion Koopmans

The majority of emerging infectious diseases originate in animals. Current routine surveillance is focused on known diseases and clinical syndromes, but the increasing likelihood of emerging disease outbreaks shows the critical importance of early detection of unusual illness or circulation of pathogens - prior to human disease manifestation. In this Viewpoint, we focus on one key pillar of preparedness—the need for early warning surveillance at the human, animal, environmental interface. The COVID-19 pandemic has revolutionized the scale of sequencing of pathogen genomes, and the current investments in global genomic surveillance offer great potential for a novel, truly integrated Disease X (with epidemic or pandemic potential) surveillance arm provided we do not make the mistake of developing them solely for the case at hand.

DOI:   https://doi.org/10.1016/j.lanepe.2021.100210   07-10-2021

Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns
Poulsen et al. 2021

Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer, −80°C; freezer, −20°C; refrigerator, 5°C; room temperature, 22°C) and storage times (immediate sample processing, 0 h; next day, 16 h; over weekend, 64 h; longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes.

DOI:   https://doi.org/10.1128/Spectrum.01387-21   06-10-2021

Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family
Perry et al. 2021

Background: Hospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances in hospital wastewater.
Conclusion: We found that the relationship between hospital wastewater ARGs and antimicrobial usage or clinical isolate resistance varies by specific antimicrobial and bacterial family studied. One explanation, we consider is that relationships observed from multiple departments within a single hospital site will be detectable only for ARGs against parenteral antimicrobials uniquely used in the hospital setting. Our work highlights that using metagenomics to identify the full range of ARGs in hospital wastewater is a useful surveillance tool to monitor hospital ARG carriage and outflow and guide environmental policy on AMR.

DOI:   https://doi.org/10.3389/fmicb.2021.703560  10-09-2021

Global, regional, and national burden of stroke and its risk factors, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019
GBD 2019 Stroke Collaborators

Regularly updated data on stroke and its pathological types, including data on their incidence, prevalence, mortality, disability, risk factors, and epidemiological trends, are important for evidence-based stroke care planning and resource allocation. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) aims to provide a standardised and comprehensive measurement of these metrics at global, regional, and national levels.

DOI:   https://doi.org/10.1016/S1474-4422(21)00252-0    03-09-2021

Genomic evolution of antimicrobial resistance in Escherichia coli
Leekitcharoenphon et al. 2021

The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms.

DOI:   http://dx.doi.org/10.1038/s41598-021-93970-7   23-07-2021

Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria
Jaffe et al. 2021

Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth’s ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions among these habitats remain unclear. Here, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain Saccharibacteria have broad bacterial host ranges and constrain possible host relationships for Absconditabacteria and Gracilibacteria.

DOI:  https://doi.org/10.1128/mBio.00521-21   13-07-2021

Predicting Antimicrobial Resistance Using Partial Genome Alignments
Aytan-Aktug et al. 2021

Antimicrobial resistance (AMR) is an important global health threat that impacts millions of people worldwide each year. Developing methods that can detect and predict AMR phenotypes can help to mitigate the spread of AMR by informing clinical decision making and appropriate mitigation strategies. Many bioinformatic methods have been developed for predicting AMR phenotypes from whole-genome sequences and AMR genes, but recent studies have indicated that predictions can be made from incomplete genome sequence data. In order to more systematically understand this, we built random forest-based machine learning classifiers for predicting susceptible and resistant phenotypes for Klebsiella pneumoniae (1,640 strains), Mycobacterium tuberculosis (2,497 strains), and Salmonella enterica (1,981 strains).

DOI:  https://doi.org/10.1128/mSystems.00185-21   15-06-2021

A Peek into the Plasmidome of Global Sewage
Kirstahler et al. 2021

Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impact the ecology and evolution of bacteria and can significantly influence the burden of infectious diseases. Insight about the identity and functions encoded on plasmids on the global scale are largely lacking. Here, we investigate the plasmidome of 24 samples (22 countries, 5 continents) from the global sewage surveillance project. We obtained 105-Gbp Oxford Nanopore and 167-Gbp Illumina NextSeq DNA sequences from plasmid DNA preparations and assembled 165,302 contigs (159,322 circular). Of these, 58,429 carried genes encoding for plasmid-related and 11,222 for virus/phage-related proteins. About 90% of the circular DNA elements did not have any similarity to known plasmids.

DOI:   https://doi.org/10.1128/mSystems.00283-21   26-05-2021

Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage
Strange et al. 2021

Bacteriophages, or phages, are ubiquitous bacterial and archaeal viruses with an estimated total global population of 1031. It is well-known that wherever there are bacteria, their phage counterparts will be found, aiding in shaping the bacterial population. The present study used metagenomic data from global influent sewage in 79 cities in 60 countries to identify phages associated with bacteria and to explore their potential role in antimicrobial resistance gene (ARG) dissemination.

DOI:  https://doi.org/10.1038/s41598-021-80990-6    15-01-2021

Risk factors for carbapenemase-producing organisms among inpatients in Scotland: A national matched case–control study
Zhao et al. 2020

To determine risk factors for carbapenemase-producing organisms (CPOs) and to determine the prognostic impact of CPOs.
A history of (prolonged) hospitalization, prolonged ICU or HDU stay; ENM diseases; and being immunocompromised increased risk for CPO. CPO infection was not associated with increased mortality but was associated with prolonged hospital stay.

DOI:  http://dx.doi.org/10.1017/ice.2020.1351    22-12-2020

Extended-spectrum beta-lactamase-producing Escherichia coli and antimicrobial resistance in municipal and hospital wastewaters in Czech Republic: Culture-based and metagenomic approaches
Kutilova et al. 2020

Wastewaters serve as important hot spots for antimicrobial resistance and monitoring can be used to analyse the abundance and diversity of antimicrobial resistance genes at the level of large bacterial and human populations. In this study, whole genome sequencing of beta-lactamase-producing Escherichia coli and metagenomic analysis of whole-community DNA were used to characterize the occurrence of antimicrobial resistance in hospital, municipal and river waters in the city of Brno (Czech Republic).

DOI:   https://doi.org/10.1016/j.envres.2020.110487  21-11-2020

Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder
Johansson et al. 2020

Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community.

DOI:   https://doi.org/10.1093/jac/dkaa390   03-10-2020

Setting a baseline for global urban virome surveillance in sewage
Nieuwenhuijse et al. 2020

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

DOI:   https://doi.org/10.1038/s41598-020-69869-0    13-08-2020

ResFinder 4.0 for predictions of phenotypes from genotypes
Bortolaia et al. 2020

WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output.

The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n= 584),Salmonella spp. (n= 1081),Campylobacter jejuni (n= 239), Enterococcus faecium (n= 106), Enterococcus faecalis (n= 50) and Staphylococcus aureus (n= 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins.

DOI:  https://doi.org/10.1093/jac/dkaa345  11-08-2020

The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children
Osakunor et al. 2020

Helminth parasites have been shown to have systemic effects in the host. Using shotgun metagenomic sequencing, we characterise the gut microbiome and resistome of 113 Zimbabwean preschool-aged children (1–5 years). We test the hypothesis that infection with the human helminth parasite, Schistosoma haematobium, is associated with changes in gut microbial and antimicrobial resistance gene abundance/diversity. Here, we show that bacteria phyla Bacteroidetes, Firmicutes, Proteobacteria, and fungi phyla Ascomycota, Microsporidia, Zoopagomycota dominate the microbiome. The abundance of Proteobacteria, Ascomycota, and Basidiomycota differ between schistosome-infected versus uninfected children. Specifically, infection is associated with increases in Pseudomonas, Stenotrophomonas, Derxia, Thalassospira, Aspergillus, Tricholoma, and Periglandula, with a decrease in Azospirillum. We find 262 AMR genes, from 12 functional drug classes, but no association with individual-specific data. To our knowledge, we describe a novel metagenomic dataset of Zimbabwean preschool-aged children, indicating an association between urogenital schistosome infection and changes in the gut microbiome.

DOI:   https://doi.org/10.1038/s42003-020-0859-7     02-04-2020

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering
Ahrenfeldt et al. 2020

Knowledge about the difference in the global distribution of pathogens and non-pathogens is limited. Here, we investigate it using a multi-sample metagenomics phylogeny approach based on short-read metagenomic sequencing of sewage from 79 sites around the world. For each metagenomic sample, bacterial template genomes were identified in a non-redundant database of whole genome sequences. Reads were mapped to the templates identified in each sample. Phylogenetic trees were constructed for each template identified in multiple samples.

DOI:  https://doi.org/10.1038/s41598-020-59292-w     20-02-2020

Clades of huge phages from across Earth’s ecosystems
Basem Al-Shayeb et al. 2020

Bacteriophages typically have small genomes and depend on their bacterial hosts for replication. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins.

DOI:   https://doi.org/10.1038/s41586-020-2007-4   12-02-2020

Using sewage for surveillance of antimicrobial resistance
Frank M. Aarestrup and Mark E. J. Woolhouse

Antimicrobial resistance (AMR), a cross-cutting and increasing threat to global health, is a complex problem with multiple and interconnected drivers. Reliable surveillance data that accurately describe and characterize the global occurrence and distribution of AMR are essential for tracking changes in resistance over time, setting national and global priorities, assessing the impacts of interventions, identifying new kinds of resistance, and supporting investigation of (international) outbreaks of resistant pathogens. AMR surveillance data can also inform development of treatment guidelines. Yet it has proven difficult to achieve these objectives on a global scale, and especially in low- and middle-income countries (LMICs), largely because current surveillance systems deliver data that are extremely variable in quality and quantity and highly heterogeneous in terms of which population is sampled (usually a category of hospital patients) and what drug-bug combinations are included. Here, we outline a plan for a global AMR surveillance system based on applying next-generation sequencing (NGS) to human sewage that will be especially helpful for community AMR surveillance, which is difficult to achieve in other ways, and will provide an affordable surveillance option in resource-poor settings.

DOI:  10.1126/science.aba3432     07-02-2020

Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks
Aytan-Aktug et al. 2020

Machine learning has proven to be a powerful method to predict antimicrobial resistance (AMR) without using prior knowledge for selected bacterial species-antimicrobial combinations. To date, only species-specific machine learning models have been developed, and to the best of our knowledge, the inclusion of information from multiple species has not been attempted. The aim of this study was to determine the feasibility of including information from multiple bacterial species to predict AMR for an individual species, since this may make it easier to train and update resistance predictions for multiple species and may lead to improved predictions.

DOI:  https://doi.org/10.1128/mSystems.00774-19  21-01-2020

Using Genomics to Track Global Antimicrobial Resistance
Hendriksen et al. 2019

The recent advancements in rapid and affordable DNA sequencing technologies have revolutionized diagnostic microbiology and microbial surveillance. The availability of bioinformatics tools and online accessible databases has been a prerequisite for this. We conducted a scientific literature review and here we present a description of examples of available tools and databases for antimicrobial resistance (AMR) detection and provide future perspectives and recommendations. At least 47 freely accessible bioinformatics resources for detection of AMR determinants in DNA or amino acid sequence data have been developed to date. These include, among others but not limited to, ARG-ANNOT, CARD, SRST2, MEGARes, Genefinder, ARIBA, KmerResistance, AMRFinder, and ResFinder.

DOI:  https://doi.org/10.3389/fpubh.2019.00242   04-09-2019

Worldwide human mitochondrial haplogroup distribution from urban sewage
Pipek et al. 2019

Community level genetic information can be essential to direct health measures and study demographic tendencies but is subject to considerable ethical and legal challenges. These concerns become less pronounced when analyzing urban sewage samples, which are ab ovo anonymous by their pooled nature. We were able to detect traces of the human mitochondrial DNA (mtDNA) in urban sewage samples and to estimate the distribution of human mtDNA haplogroups. An expectation maximization approach was used to determine mtDNA haplogroup mixture proportions for samples collected at each different geographic location. Our results show reasonable agreement with both previous studies of ancient evolution or migration and current US census data; and are also readily reproducible and highly robust. Our approach presents a promising alternative for sample collection in studies focusing on the ethnic and genetic composition of populations or diseases associated with different mtDNA haplogroups and genotypes.

DOI:   https://doi.org/10.1038/s41598-019-48093-5     12-08-2019

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Edwards et al. 2019

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals.

DOI:   https://doi.org/10.1038/s41564-019-0494-6   08-07-2019

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
Hendriksen et al. 2019

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR.

DOI:  https://doi.org/10.1038/s41467-019-08853-3   08-03-2019

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Munk et al. 2018

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.

DOI:    https://doi.org/10.1038/s41564-018-0192-9      23-07-2018

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
Petersen et al. 2015

Human populations worldwide are increasingly confronted with infectious diseases and antimicrobial resistance spreading faster and appearing more frequently. Knowledge regarding their occurrence and worldwide transmission is important to control outbreaks and prevent epidemics. Here, we performed shotgun sequencing of toilet waste from 18 international airplanes arriving in Copenhagen, Denmark, from nine cities in three world regions. An average of 18.6 Gb (14.8 to 25.7 Gb) of raw Illumina paired end sequence data was generated, cleaned, trimmed and mapped against reference sequence databases for bacteria and antimicrobial resistance genes. An average of 106,839 (0.06%) reads were assigned to resistance genes with genes encoding resistance to tetracycline, macrolide and beta-lactam resistance genes as the most abundant in all samples. We found significantly higher abundance and diversity of genes encoding antimicrobial resistance, including critical important resistance (e.g. blaCTX-M) carried on airplanes from South Asia compared to North America. Presence of Salmonella enterica and norovirus were also detected in higher amounts from South Asia, whereas Clostridium difficile was most abundant in samples from North America. Our study provides a first step towards a potential novel strategy for global surveillance enabling simultaneous detection of multiple human health threatening genetic elements, infectious agents and resistance genes.

DOI:  https://doi.org/10.1038/srep11444       10-07-2015