Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples.

Viruses are an abundant and crucial component of the human microbiome, but accurately discovering them via metagenomics is still challenging. Currently, the available viral reference genomes poorly represent the diversity in microbiome samples, and expanding such a set of viral references is difficult. As a result, many viruses are still undetectable through metagenomics even when considering the power of metagenomic assembly and binning, as viruses lack universal markers.

Has Data Quality of an Antimicrobial Resistance Surveillance System in a Province of Nepal Improved between 2019 and 2022?

An operational research study was conducted in 2019 to assess the quality of data submitted by antimicrobial resistance (AMR) surveillance sites in the Bagmati Province of Nepal to the National Public Health Laboratory for Global Antimicrobial Resistance and Use Surveillance System (GLASS). Measures were implemented to enhance the quality of AMR surveillance by strengthening capacity, improving infrastructure, implementing data sharing guidelines, and supervision. The current study examined reports submitted by surveillance sites in the same province in 2022 to assess whether the data quality had improved since 2019.

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.

Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome.

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.

Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.

The person-to-person transmission landscape of the gut and oral microbiomes.

The human microbiome is an integral component of the human body and a co-determinant of several health conditions. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns.

Recent advances of machine learning applications in human gut microbiota study: from observational analysis toward causal inference and clinical intervention.

Statistical methods, especially machine learning, learning(ML), are pivotal for the analyses of large data generated by multiomics human gut microbiota study. These analyses lead to the discovery of microbe-disease associations. Furthermore, recent efforts for more data transparency and accessible analytical tools improved data availability and study reproducibility.

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data.

The identification of the protospacer adjacent motif (PAM) sequences of Cas9 nucleases is crucial for their exploitation in genome editing. Here we develop a computational pipeline that was used to interrogate a massively expanded dataset of metagenome and virome assemblies for accurate and comprehensive PAM predictions. This procedure allows the identification and isolation of sequence-tailored Cas9 nucleases by using the target sequence as bait.

Antibiotic-Resistant Bacteria in Drinking Water from the Greater Accra Region, Ghana: A Cross-Sectional Study, December 2021-March 2022.

With safely managed water accessible to only 19% of the population in Ghana, the majority of its residents are at risk of drinking contaminated water. Furthermore, this water could be a potential vehicle for the transmission of antimicrobial-resistant bacteria. This study assessed the presence of bacteria and the antibiotic resistance profile of and in drinking-water sources using membrane filtration and Kirby-Bauer disc diffusion methods.

Snakebite case management: a cohort study in Northwest Ethiopia, 2012-2020.

Introduction: Timely and appropriate management of snakebites in the tropics is a lifesaver. Many snakebite patients are being bitten in remote rural areas and do not manage to get in due time to healthcare facilities. This study assessed the clinical features and the risk factors associated with treatment outcomes of snakebite patients admitted at two hospitals in the Northwest of Ethiopia.

Distribution of snake species and snakebites in hotspots of Ethiopia.

Introduction: In Sub-Saharan Africa, snakebites are a public health problem. In Ethiopia, clinical cases have been described, but little information exists on snakebites burden and its geographical distribution. The aim of this study was to document the spatial distribution of venomous snakes and snakebites in Ethiopia.

Surgical output within the Fast Track Initiative against trachoma in Amhara region, Ethiopia.

Introduction: Trachomatous trichiasis (TT) is the advanced stage of trachoma where lashes touch the globe of the eye causing permanent damage. Without eyelid surgery, TT can lead to irreversible blindness. In 2015 the Ethiopian Ministry of Health launched the Fast Track Initiative with the aim of enhancing the provision of surgical services for TT.

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly.

Background: Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A.

Veterinary Healthcare Provision and Quality of Reported Data on Antimicrobial Use in the Treatment of Livestock in Sierra Leone, 2016-2019.

Antimicrobials help in the prevention and treatment of infections and are crucial for animal production, but overuse can result in antimicrobial resistance. Hence, understanding data quality on livestock antimicrobial use is essential. We assessed frequency of reporting, completeness, and concordance of reported data and availability of human resources and infrastructure in 14 districts in Sierra Leone.

Infection Prevention and Control at Lira University Hospital, Uganda: More Needs to Be Done.

Globally, 5-15% of hospitalized patients acquire infections (often caused by antimicrobial-resistant microbes) due to inadequate infection prevention and control (IPC) measures. We used the World Health Organization's (WHO) 'Infection Prevention and Control Assessment Framework' (IPCAF) tool to assess the IPC compliance at Lira University hospital (LUH), a teaching hospital in Uganda. We also characterized challenges in completing the tool.

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available.

Quality Assessment of an Antimicrobial Resistance Surveillance System in a Province of Nepal.

Antimicrobial resistance (AMR) is a global problem, and Nepal is no exception. Countries are expected to report annually to the World Health Organization on their AMR surveillance progress through a Global Antimicrobial Resistance Surveillance System, in which Nepal enrolled in 2017. We assessed the quality of AMR surveillance data during 2019-2020 at nine surveillance sites in Province 3 of Nepal for completeness, consistency, and timeliness and examined barriers for non-reporting sites.

Towards the trachoma elimination target in the Southern region of Ethiopia: How well is the SAFE strategy being implemented?

Introduction: Trachoma is one of the 20 neglected tropical diseases and a serious public health problem in Ethiopia. To reach the WHO elimination target by 2020, SAFE (Surgery, Antibiotics, Facial cleanliness, Environmental improvement) strategy has been implemented in the Southern Nations, Nationalities, and Peoples' Region (SNNPRs), Ethiopia. Scarce evidence exists regarding recent progress in achieving elimination of active trachoma (< 5%) and how well the SAFE strategy implemented.

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and sensitive from closely related strains to divergent phyla. We present PhyloPhlAn 3.