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View article: Mosquito bacterial communities show stage-specific patterns relevant for vector ecology and AMR surveillance
Mosquito bacterial communities show stage-specific patterns relevant for vector ecology and AMR surveillance Open
Mosquito-associated microbiota are influenced by a number of factors, e.g., geography, host species, and developmental stage. Understanding these microbiotas is crucial for assessing their role as vectors and in pathogen dissemination and …
View article: Serological evidence of clade Ib Mpox transmission by sex workers and within household in South Kivu, DRC
Serological evidence of clade Ib Mpox transmission by sex workers and within household in South Kivu, DRC Open
View article: Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms
Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms Open
Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of…
View article: Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing
Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing Open
The effects of sample multiplexing on the detection sensitivity of antimicrobial resistance genes (ARGs) and pathogenic bacteria in metagenomic sequencing remain underexplored in newer sequencing technologies such as Oxford Nanopore Techno…
View article: Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC
Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC Open
Mpox is an emerging zoonotic disease that caused two public health emergencies of international concern within two years. Less is known about the interplay of microbial organisms in mpox lesions which could result in superinfections that e…
View article: Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens
Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens Open
The expansion of intensive poultry farming has led to a substantial increase in antibiotic use, which in turn has promoted the accumulation of antibiotic resistance genes (ARGs). The chicken gut serves as a reservoir for these genes and pr…
View article: Effect of large-scale population-based dietary change to vegetarianism on antimicrobial resistance and bacterial composition of sewage in Thailand
Effect of large-scale population-based dietary change to vegetarianism on antimicrobial resistance and bacterial composition of sewage in Thailand Open
Antimicrobial resistance (AMR) is on one of the global priority challenges. This study explored the impact of diet alteration on AMR bacteria through metagenomic analysis during the annual vegetarian festival in Thailand in October 2019. T…
View article: Serological evidence supports the transmission of clade Ib mpox virus by professional sex workers and spread within households in South Kivu, DRC
Serological evidence supports the transmission of clade Ib mpox virus by professional sex workers and spread within households in South Kivu, DRC Open
Understanding secondary attack rates is a key knowledge gap in the ongoing clade Ib mpox virus (MPXV) outbreak in the Democratic Republic of the Congo. Here, we report the first serological study to investigate the extent of local MPXV cla…
View article: Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations
Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations Open
In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza …
View article: Draft genomic sequences of <i>Vibrio cholerae</i> strains linked to the cholera outbreak in Kamituga, South Kivu, DRC
Draft genomic sequences of <i>Vibrio cholerae</i> strains linked to the cholera outbreak in Kamituga, South Kivu, DRC Open
Vibrio cholerae is responsible for outbreaks in Africa, but the cause of the outbreaks remains poorly understood. Here, we report the draft genomes of four Vibrio cholerae strains isolated from individuals affected by an outbreak in Kamitu…
View article: ListPred: A predictive ML tool for virulence potential and disinfectant tolerance in Listeria monocytogenes
ListPred: A predictive ML tool for virulence potential and disinfectant tolerance in Listeria monocytogenes Open
Despite current surveillance and sanitation strategies, foodborne pathogens continue to threaten the food industry and public health. Whole genome sequencing (WGS) has reached an unprecedented resolution to analyse and compare pathogenic b…
View article: Mosquito-borne bacterial communities are shaped by their insect host species, geography and developmental stage
Mosquito-borne bacterial communities are shaped by their insect host species, geography and developmental stage Open
Mosquitoes harbour diverse bacterial communities that are influenced by a number of factors, e.g., geography, host species, and developmental stage. Understanding these microbiotas is crucial for assessing their role as vectors and in path…
View article: Epidemiological and genomic evolution of the ongoing outbreak of clade Ib mpox virus in the eastern Democratic Republic of the Congo
Epidemiological and genomic evolution of the ongoing outbreak of clade Ib mpox virus in the eastern Democratic Republic of the Congo Open
View article: Using genomics to explore the epidemiology of vancomycin resistance in a sewage system
Using genomics to explore the epidemiology of vancomycin resistance in a sewage system Open
VanHAX -mediated glycopeptide resistance has been consistently high in one of the three main sewer systems in Copenhagen, Lynetten, for +20 years. To explore this for other glycopeptide resistance genes, and whether the colonization has re…
View article: Monkeypox Clade Ib virus introduction into Burundi: first findings, July to mid-August 2024
Monkeypox Clade Ib virus introduction into Burundi: first findings, July to mid-August 2024 Open
We describe cases with monkeypox virus (MPXV) Clade Ib in Burundi from their first detection in July until 20 August 2024. Testing 442 people with vesicular lesions confirmed 170 cases (98 male; 72 female), 82 (48%) being < 15 years old. D…
View article: Author Correction: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance
Author Correction: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance Open
View article: Improved ability to utilize lactose and grow in milk as a potential explanation for emergence of the novel bovine Staphylococcus aureus ST5477
Improved ability to utilize lactose and grow in milk as a potential explanation for emergence of the novel bovine Staphylococcus aureus ST5477 Open
Staphyloccous aureus belonging to sequence type 5477 have recently been identified as a predominant clone causing bovine mastitis in Rwanda and Tanzania. We compared nine S. aureus ST5477 to 17 isolates belonging to other sequence types by…
View article: Analysis of genetic signatures of virulence and resistance in foodborne Staphylococcus aureus isolates from Algeria
Analysis of genetic signatures of virulence and resistance in foodborne Staphylococcus aureus isolates from Algeria Open
View article: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance
Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance Open
View article: Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark
Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark Open
View article: Discovery of Vibrio cholerae in urban sewage in Copenhagen, Denmark
Discovery of Vibrio cholerae in urban sewage in Copenhagen, Denmark Open
We report the unexpected 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 tr…
View article: Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance
Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance Open
Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve …
View article: Complete genome sequences of <i>Cytobacillus</i> sp., <i>Domibacillus</i> sp., <i>Enterobacter</i> sp., <i>Neisseria</i> sp., <i>Pseudomonas</i> sp., and <i>Streptococcus</i> sp. strains from human clinical infections collected at diagnostic units in 2020
Complete genome sequences of <i>Cytobacillus</i> sp., <i>Domibacillus</i> sp., <i>Enterobacter</i> sp., <i>Neisseria</i> sp., <i>Pseudomonas</i> sp., and <i>Streptococcus</i> sp. strains from human clinical infections collected at diagnostic units in 2020 Open
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 , D…
View article: Azithromycin resistance in <i>Escherichia coli</i> and <i>Salmonella</i> from food-producing animals and meat in Europe
Azithromycin resistance in <i>Escherichia coli</i> and <i>Salmonella</i> from food-producing animals and meat in Europe Open
Objectives To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014–18 and the Danish AMR surveillance …
View article: Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes
Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes Open
Metagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount o…
View article: Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024
Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024 Open
Since the beginning of 2023, the number of people with suspected monkeypox virus (MPXV) infection have sharply increased in the Democratic Republic of the Congo (DRC). We report near-to-complete MPXV genome sequences derived from six cases…
View article: A novel metagenomic approach uncovers phage genes as markers for increased disinfectant tolerance in mixed Listeria monocytogenes communities
A novel metagenomic approach uncovers phage genes as markers for increased disinfectant tolerance in mixed Listeria monocytogenes communities Open
View article: ListPred: A predictive ML tool for virulence potential and disinfectant tolerance in<i>Listeria monocytogenes</i>
ListPred: A predictive ML tool for virulence potential and disinfectant tolerance in<i>Listeria monocytogenes</i> Open
Despite current surveillance and sanitation strategies, foodborne pathogens continue to threaten the food industry and public health. Whole genome sequencing (WGS) has reached an unprecedented resolution to analyse and compare pathogenic b…
View article: The first complete genome sequence of <i>Staphylococcus aureus</i> ST5477
The first complete genome sequence of <i>Staphylococcus aureus</i> ST5477 Open
This study presents the first complete genome of Staphylococcus aureus ST5477, one of the most common sequence types (ST) from bovine in eastern Africa. The genome consists of a 2,723,132-bp circular chromosome and a 3,044-bp plasmi…
View article: Foodborne Pathogen Dynamics in Meat and Meat Analogues Analysed Using Traditional Microbiology and Metagenomic Sequencing
Foodborne Pathogen Dynamics in Meat and Meat Analogues Analysed Using Traditional Microbiology and Metagenomic Sequencing Open
Meat analogues play an increasing role in meeting global nutritional needs. However, while it is well known that meat possesses inherent characteristics that create favourable conditions for the growth of various pathogenic bacteria, much …