Marseilleviruses: An Update in 2021.

The family Marseilleviridae was the second family of giant viruses that was described in 2013, after the family Mimiviridae. Marseillevirus marseillevirus, isolated in 2007 by coculture on Acanthamoeba polyphaga, is the prototype member of this family. Afterward, the worldwide distribution of marseilleviruses was revealed through their isolation from samples of various types and sources. Thus, 62 were isolated from environmental water, one from soil, one from a dipteran, one from mussels, and two from asymptomatic humans, which led to the description of 67 marseillevirus isolates, including 21 by the IHU Méditerranée Infection in France. Recently, five marseillevirus genomes were assembled from deep sea sediment in Norway. Isolated marseilleviruses have ≈250 nm long icosahedral capsids and 348-404 kilobase long mosaic genomes that encode 386-545 predicted proteins. Comparative genomic analyses indicate that the family Marseilleviridae includes five lineages and possesses a pangenome composed of 3,082 clusters of genes. The detection of marseilleviruses in both symptomatic and asymptomatic humans in stool, blood, and lymph nodes, and an up-to-30-day persistence of marseillevirus in rats and mice, raise questions concerning their possible clinical significance that are still under investigation.

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus.

Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics.IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.

Comparative Genomics Unveils Regionalized Evolution of the Faustovirus Genomes.

Faustovirus is a recently discovered genus of large DNA virus infecting the amoeba Vermamoeba vermiformis, which is phylogenetically related to Asfarviridae. To better understand the diversity and evolution of this viral group, we sequenced six novel Faustovirus strains, mined published metagenomic datasets and performed a comparative genomic analysis. Genomic sequences revealed three consistent phylogenetic groups, within which genetic diversity was moderate. The comparison of the major capsid protein (MCP) genes unveiled between 13 and 18 type-I introns that likely evolved through a still-active birth and death process mediated by intron-encoded homing endonucleases that began before the Faustovirus radiation. Genome-wide alignments indicated that despite genomes retaining high levels of gene collinearity, the central region containing the MCP gene together with the extremities of the chromosomes evolved at a faster rate due to increased indel accumulation and local rearrangements. The fluctuation of the nucleotide composition along the Faustovirus (FV) genomes is mostly imprinted by the consistent nucleotide bias of coding sequences and provided no evidence for a single DNA replication origin like in circular bacterial genomes.

Molecular drivers of emerging multidrug resistance in Proteus mirabilis clinical isolates from Algeria.

OBJECTIVES: The aim of this study was to characterise the molecular drivers of multidrug resistance in Proteus mirabilis isolated from Algerian community and hospital patients. METHODS: A total of 166 P. mirabilis isolates were collected from two hospitals and eight private laboratories from four cities (Khemis Miliana, Aïn Defla, Oran and Chlef) located in northwestern Algeria. All isolates were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antimicrobial susceptibility testing was performed by the disk diffusion and Etest methods. Genes encoding AmpC ß-lactamases, extended-spectrum ß-lactamases (ESBLs), quinolone resistance and aminoglycoside-modifying enzymes (AMEs) as well as plasmid replicon typing were characterised by PCR. Clonal relationships were also determined by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) typing and were compared with MALDI-TOF/MS proteomic typing. RESULTS: Of the 166 P. mirabilis isolates, 14 (8.4%) exhibited resistance to important antibiotics, including amoxicillin, amoxicillin/clavulanic acid, cefotaxime, gentamicin and ciprofloxacin, of which 4/14 (28.6%) had an ESBL genotype (blaCTX-M-2) and 10 (71.4%) had an AmpC/ESBL genotype (blaCMY-2/blaTEM-1). AME genes were detected in all isolates, including ant(2'')-I, aac(3)-I, aac(6')-Ib-cr and aac(3)-IV. The qnrA gene was identified in 13 isolates (7.8%). ERIC-PCR showed one predominant clone, with eight blaCMY-2-producing isolates from UHC Oran belonging to profile A clustering together in the MALDI-TOF/MS dendrogram. CONCLUSION: Here we report the first description of AME and plasmid-mediated quinolone resistance genes among ESBL- and/or AmpC ß-lactamase-producing P. mirabilis isolates from community- and hospital-acquired infections in northwestern Algeria.