Micro RNAs (miRNAs) are short non-coding RNAs that act as post-transcriptional gene expression regulators. Genes regulated in vertebrates include those affecting growth and development or stress and ...immune response. Pikeperch (
) is a species that is increasingly being considered for farming in recirculation aquaculture systems. We characterized the pikeperch miRNA repertoire to increase the knowledge of the genomic mechanisms affecting performance and health traits by applying small RNA sequencing to different developmental stages and organs. There were 234 conserved and 8 novel miRNA genes belonging to 104 families. A total of 375 unique mature miRNAs were processed from these genes. Many mature miRNAs showed high relative abundances or were significantly more expressed at early developmental stages, like the miR-10 and miR-430 family, let-7, the miRNA clusters 106-25-93, and 17-19-92. Several miRNAs associated with immune responses (e.g., slu-mir-731-5p, slu-mir-2188-5p, and slu-mir-8159-5p) were enriched in the spleen. The mature miRNAs slu-mir-203a-3p and slu-mir-205-5p were enriched in gills. These miRNAs are similarly abundant in many vertebrates, indicating that they have shared regulatory functions. There was also a significantly increased expression of the disease-associated miR-462/miR-731 cluster in response to hypoxia stress. This first pikeperch miRNAome reference resource paves the way for future functional studies to identify miRNA-associated variations that can be utilized in marker-assisted breeding programs.
Abstract The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust ...pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing bacterial pathogen sequencing and data analysis capabilities for effective AMR surveillance and outbreak response. This study assesses the current landscape and challenges associated with pathogen next-generation sequencing (NGS) within EAC, explicitly focusing on World Health Organization (WHO) AMR-priority pathogens. The assessment adopts a comprehensive approach, integrating a questionnaire-based survey amongst National Public Health Laboratories (NPHLs) with an analysis of publicly available metadata on bacterial pathogens isolated in the EAC countries. In addition to the heavy reliance on third-party organizations for bacterial NGS, the findings reveal a significant disparity among EAC member States in leveraging bacterial pathogen sequencing and data analysis. Approximately 97% ( n = 4,462) of publicly available high-quality bacterial genome assemblies of samples collected in the EAC were processed and analyzed by external organizations, mainly in Europe and North America. Tanzania led in-country sequencing efforts, followed by Kenya and Uganda. The other EAC countries had no publicly available samples or had all their samples sequenced and analyzed outside the region. Insufficient local NGS sequencing facilities, limited bioinformatics expertise, lack of adequate computing resources, and inadequate data-sharing mechanisms are among the most pressing challenges that hinder the EAC’s NPHLs from effectively leveraging pathogen genomics data. These insights emphasized the need to strengthen microbial pathogen sequencing and data analysis capabilities within the EAC to empower these laboratories to conduct pathogen sequencing and data analysis independently. Substantial investments in equipment, technology, and capacity-building initiatives are crucial for supporting regional preparedness against infectious disease outbreaks and mitigating the impact of AMR burden. In addition, collaborative efforts should be developed to narrow the gap, remedy regional imbalances, and harmonize NGS data standards. Supporting regional collaboration, strengthening in-country genomics capabilities, and investing in long-term training programs will ultimately improve pathogen data generation and foster a robust NGS-driven AMR surveillance and outbreak response in the EAC, thereby supporting global health initiatives.
Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires ...advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. The sex-specific linkage maps spanned a total of 2985.16 cM in females and 2540.47 cM in males with an average inter-marker distance of 0.0030 and 0.0026 cM, respectively. The sex-averaged map spanned a total of 2725.53 cM with an average inter-marker distance of 0.0028 cM. Furthermore, the sex-averaged map was used for improving the contiguity and accuracy of the current pikeperch genome assembly. Based on 723,360 markers, 706 contigs were anchored and oriented into 24 pseudomolecules, covering a total of 896.48 Mb and accounting for 99.47% of the assembled genome size. The overall contiguity of the assembly improved with a scaffold N50 length of 41.06 Mb. Finally, an updated annotation of protein-coding genes and repetitive elements of the enhanced genome assembly is provided at NCBI.
There are still numerous difficulties in the successful farming of pikeperch in the anthropogenic environment of various aquaculture systems, especially during early developmental steps in the ...hatchery. To investigate the physiological processes involved on the molecular level, we determined the basal expression patterns of 21 genes involved in stress and immune responses and early ontogenesis of pikeperch between 0 and 175 days post hatch (dph). Their transcription patterns most likely reflect the challenges of growth and feed conversion. The gene coding for apolipoprotein A (
APOE
) was strongly expressed at 0 dph, indicating its importance for yolk sac utilization. Genes encoding bone morphogenetic proteins 4 and 7 (
BMP4
,
BMP7
), creatine kinase M (
CKM
), and SRY-box transcription factor 9 (
SOX9
) were highly abundant during the peak phases of morphological changes and acclimatization processes at 4–18 dph. The high expression of genes coding for peroxisome proliferator-activated receptors alpha and delta (
PPARA
,
PPARD
) at 121 and 175 dph, respectively, suggests their importance during this strong growth phase of juvenile stages. As an alternative experimental model to replace further in vivo investigations of ontogenetically important processes, we initiated the first approach towards a long-lasting primary cell culture from whole pikeperch embryos. The present study provides a set of possible biomarkers to support the monitoring of pikeperch farming and provides a first basis for the establishment of a suitable cell model of this emerging aquaculture species.
The emergence of extended-spectrum beta-lactamase-producing
(ESBL-E) is causing increased morbidity and mortality around the world as a result of therapeutic failures. ESBL-E are priority pathogens ...due to their multidrug resistance (MDR). In Northern Cameroon, ESBL-producing bacteria, particularly in urinary tract infections (UTIs), are being increasingly isolated. This study aimed to retrospectively determine the prevalence of multi-drug resistant ESBL strains isolated from UTIs in Northern Cameroon and to evaluate the effectiveness of the ATB UR Gallery of BioMérieux in diagnosing ESBL-E in clinical settings.
Standard microbiology protocols and statistical tools were utilized to identify ESBL-producing bacteria and characterize their phenotypic susceptibility and resistance profiles in the study population.
Out of the 144 enterobacteria isolates successfully cultured, 59 (41%) were identified as MDR strains. The ATB UR EU gallery identified 33 (23%) multi-drug resistant ESBL-producing strains, while the double synergy test identified 35 strains without disc reconciliation and 38 strains after reconciliation. The most prevalent ESBL-E isolate was Escherichia coli, accounting for 77.1% of the isolates, followed by
(20%) and
(2.9%). Additionally, the study revealed the emergence of Imipenem resistance (5.7%), a critical last-resort antibiotic. However, all ESBL strains were sensitive to Fosfomycin (FSF/FOS), demonstrating its potential as an effective therapeutic option. Moreover, 37% of the ESBL producers exhibited co-resistance to over 20 different antibiotics.
This study provides valuable insights into the prevalence and susceptibility patterns of ESBL-E associated with UTIs in Northern Cameroon. These insights emphasizes the importance of implementing appropriate treatment guidelines and antimicrobial stewardship measures to mitigate the spread and impact of MDR ESBL-producing strains on public health.
Fish farming in Recirculating Aquaculture Systems (RAS) is a sustainable and efficient practice to produce fish. Knowledge of microbial communities, particularly harmful pathogens on fish, is ...required to better understand microbiological processes occurring at different RAS compartments and to optimize the overall RAS management. In this study, we assessed the influence of different
Clarias gariepinus
stocking densities in RAS on the water microbiome composition. Molecular targeting the V3-V4 16S rRNA hypervariable region was used to infer Amplicon Sequence Variants (ASV), identify microbes, and assess their abundance and diversity. We identified bacterial pathogens in the rearing environment associated with common fish farming practices. Our findings show that microbiomes differ across all systems (high, medium and low stocking densities) and within sampling points (water inflow, outflow and sedimentation tank). The medium-density system had the most fish biomass, resulting in high ASVs cumulative abundance. In water samples from high- and low-density systems, we discovered a wide range of phyla, with
Mycobacterium
sp. being the most common potentially pathogenic group. We discuss the effects of fish biomass and water physicochemical properties on the microbiome.
Fingerlings (0.23 g) and juveniles (267.04 g) of African catfish (Clarias gariepinus) were reared for 32 days under experimental aquarium conditions and were exposed to either 0.75 mg/L or 3.0 mg/L ...diethylenetriaminepentaacetic acid-iron(II) (Fe-DTPA) and 3.0 mg/L or 12.0 mg/L Fe-DTPA in the water, respectively. These treatment groups were compared to a control group without additional Fe-DTPA. The growth, mortality, ethological indicators (activity, agonistic interactions, air-breathing), leukocyte distribution, histopathological changes in liver and gills, and genetic biomarkers were evaluated for each group. While the growth, mortality, and behavior were not significantly different between the groups, the lymphocyte count in the fish’s blood increased significantly in all groups during the course of the experiment, but independently from the treatments. A similar trend (p > 0.05) was observed in monocytes. The number of granulocytes decreased significantly, but independently from the treatments. These changes indicated the possibility of an ongoing immune response in the fish from all treatments that might be caused by the increasing aggressive behavior of the fish. However, the Fe-DTPA treatments did not cause a notable suppression or enhancement of the immune reactions. Fe3+ accumulations in liver tissues were detected at the tested concentrations, and further changes occurred in the cells of the gills. Gene-expression biochips were used to simultaneously quantify the transcript levels of 34 genes associated with iron metabolism and stress physiology in head kidney samples. The obtained gene-expression profiles did not reveal any significant differences across either the different treatments or the time points. The results indicate that Fe-DTPA supplementation in the tested concentrations can be considered relatively harmless for the health and welfare of African catfish.
Promising efforts are ongoing to extend genomics resources for pikeperch (
), a species of high interest for the sustainable European aquaculture sector. Although previous work, including reference ...genome assembly, transcriptome sequence, and single-nucleotide polymorphism genotyping, added a great wealth of genomic tools, a comprehensive characterization of gene expression across major tissues in pikeperch still remains an unmet research need. Here, we used deep RNA-Sequencing of ten vital tissues collected in eight animals to build a high-confident and annotated trancriptome atlas, to detect the tissue-specificity of gene expression and co-expression network modules, and to investigate genome-wide selective signatures in the Percidae fish family. Pathway enrichment and protein-protein interaction network analyses were performed to characterize the unique biological functions of tissue-specific genes and co-expression modules. We detected strong functional correlations and similarities of tissues with respect to their expression patterns-but also significant differences in the complexity and composition of their transcriptomes. Moreover, functional analyses revealed that tissue-specific genes essentially play key roles in the specific physiological functions of the respective tissues. Identified network modules were also functionally coherent with tissues' main physiological functions. Although tissue specificity was not associated with positive selection, several genes under selection were found to be involved in hypoxia, immunity, and gene regulation processes, that are crucial for fish adaption and welfare. Overall, these new resources and insights will not only enhance the understanding of mechanisms of organ biology in pikeperch, but also complement the amount of genomic resources for this commercial species.
The pikeperch (
) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in ...Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of
. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the
genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
Fingerlings (0.23 g) and juveniles (267.04 g) of African catfish (Clarias gariepinus) were reared for 32 days under experimental aquarium conditions and were exposed to either 0.75 mg/L or 3.0 mg/L ...diethylenetriaminepentaacetic acid-iron(II) (Fe-DTPA) and 3.0 mg/L or 12.0 mg/L Fe-DTPA in the water, respectively. These treatment groups were compared to a control group without additional Fe-DTPA. The growth, mortality, ethological indicators (activity, agonistic interactions, air-breathing), leukocyte distribution, histopathological changes in liver and gills, and genetic biomarkers were evaluated for each group. While the growth, mortality, and behavior were not significantly different between the groups, the lymphocyte count in the fish’s blood increased significantly in all groups during the course of the experiment, but independently from the treatments. A similar trend (p > 0.05) was observed in monocytes. The number of granulocytes decreased significantly, but independently from the treatments. These changes indicated the possibility of an ongoing immune response in the fish from all treatments that might be caused by the increasing aggressive behavior of the fish. However, the Fe-DTPA treatments did not cause a notable suppression or enhancement of the immune reactions. Fesup.3+ accumulations in liver tissues were detected at the tested concentrations, and further changes occurred in the cells of the gills. Gene-expression biochips were used to simultaneously quantify the transcript levels of 34 genes associated with iron metabolism and stress physiology in head kidney samples. The obtained gene-expression profiles did not reveal any significant differences across either the different treatments or the time points. The results indicate that Fe-DTPA supplementation in the tested concentrations can be considered relatively harmless for the health and welfare of African catfish.
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