An in vitro and in vivo approach for the isolation of Omicron variant from human clinical specimens

Due to failure of virus isolation of Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, we infected Syrian hamsters and then passage into Vero CCL-81 cells. The Omicron sequences were studied to assess if hamster could incorporate any mutation to changes its susceptibility. L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene and absence of V17I mutation in E gene was observed in sequences of hamster passage unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequence which suggests usefulness of these isolates in future studies.

Complete Genome Sequence of Rhodococcus sp. Strain W8901, a Human Clinical Specimen, Assembled Using MiSeq and MinION Sequence Data

Rhodococcus sp. strain W8901 is a Gram-positive, aerobic, mycolic acid-containing coccobacillus obtained from a patient with acute lymphocytic leukemia. Here, we report on the complete, circular genome sequence obtained using Illumina MiSeq and Oxford Nanopore Technologies MinION reads in order to better resolve the phylogeny of a rare pathogen.

First hybrid complete genome ofAeromonas veroniireveals chromosome-mediated novel structural variantmcr-3.19from human clinical specimen

BackgroundRecent findings substantiate the origin of plasmid-mediated colistin resistance genemcr-3from Aeromonads. The present study aimed to screen the plasmid-mediated colistin resistance among 30 clinical multidrug resistant (MDR)Aeromonas spp.ResultsThe presence ofmcr-1, mcr-2, mcr-3, and mcr-4were screened by PCR, which revealedmcr-3in a colistin susceptible isolate (FC951). All other isolates were negative formcrgenes. Sequencing of FC951 revealed thatmcr-3(mcr-3.19) identified was different from previously reported variants and had 95.62 and 95.28% nucleotide similarity withmcr-3.3andmcr-3.10gene. A hybrid assembly using IonTorrent and MinION reads revealed structural genetic information ofmcr-3.19with an insertion of ISAs18within the gene. Due to this,mcr-3.19was non-expressive which makes FC951 susceptible to colistin. Further,in silicosequence and protein structural analysis confirmed the new variant. To the best of our knowledge, this is the first report on novelmcr-3variant (mcr-3.19).ConclusionsThe significant role ofmcr-like genes in differentAeromonasspecies remains unknown and needs additional investigation to understand the insights on colistin resistance mechanism.

First Case Report of Campylobacter volucris Bacteremia in an Immunocompromised Patient

We report a case ofCampylobacter volucrisbacteremia in an immunocompromised patient with polycythemia vera and alcoholic liver cirrhosis. To our knowledge, this is the first case report in which this organism has been isolated from a human clinical specimen.

Dietzia aurantiaca sp. nov., isolated from a human clinical specimen

A Gram-positive, coccoid, non-endospore-forming actinobacterium (strain CCUG 35676T) was isolated from cerebrospinal fluid from a 24-year-old woman in Gothenborg, Sweden. Based on pairwise 16S rRNA gene sequence similarity studies, strain CCUG 35676T was shown to belong to the genus Dietzia and was most closely related to the type strains of Dietzia aerolata (99.3 %), Dietzia lutea (98.8 %), Dietzia schimae (98.5 %), Dietzia maris (98.5 %), Dietzia alimentaria (98.3 %) and Dietzia cercidiphylli (98.0 %). The major menaquinone was MK-8(H2). Major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid (APL1), an unidentified phospholipid (PL1) and unidentified glycolipids (GL1 and GL3). Numerous other lipids were also detected. The fatty acid profile, comprising C16 : 0, C17 : 0, C18 : 1ω9c and 10-methyl-C18 : 0 as major fatty acids, supported the affiliation of strain CCUG 35676T to the genus Dietzia. On the basis of the results of physiological and biochemical tests and DNA–DNA hybridizations, a clear phenotypic and genotypic differentiation of strain CCUG 35676T from the most closely related Dietzia species is possible. Strain CCUG 35676T represents a novel species, for which the name Dietzia aurantiaca sp. nov. is proposed, with CCUG 35676T ( = JCM 17645T) as the type strain.

Massilia oculi sp. nov., isolated from a human clinical specimen

A Gram-negative, rod-shaped, non-spore-forming bacterium (strain CCUG 43427AT) was isolated from a patient suffering from endophthalmitis and its taxonomic position was studied. 16S rRNA gene sequence analysis indicated that this strain was a member of the genus Massilia. Strain CCUG 43427AT was most closely related to the type strains of Massilia timonae (97.4 % 16S rRNA gene sequence similarity) and Massilia aurea (97.2 %); levels of similarity to the type strains of all other recognized Massilia species were below 97.0 %. Chemotaxonomic data [Q-8 as major ubiquinone; phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as major polar lipids; and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C12 : 0 and C10 : 0 3-OH as major fatty acids] supported the affiliation of the isolate to the genus Massilia. Levels of DNA–DNA relatedness of strain CCUG 43427AT with M. timonae CCUG 45783T and M. aurea AP13T were 60.6 % (reciprocal, 55.8 %) and 58.1 % (reciprocal, 34.0 %), respectively. Strain CCUG 43427AT could be differentiated from its closest phylogenetic neighbours based on a range of phenotypic characteristics. Strain CCUG 43427AT is therefore considered to represent a novel species of the genus Massilia, for which the name Massilia oculi sp. nov. is proposed. The type strain is CCUG 43427AT ( = CCM 7900T).