Reclassification of Eubacterium combesii and discrepancies in the nomenclature of botulinum neurotoxin-producing clostridia: Challenging Opinion 69. Request for an Opinion.

To clarify the taxonomic position of Eubacterium combesii, the whole genome of its type strain, DSM 20696T, was sequenced. Comparison of this sequence with known sequences of other bacteria confirmed that E. combesii represented a member of the Clostridium sporogenes/Clostridium botulinum Group I clade. However, the results of phylogenetic analysis also demonstrated that the latter two species did not form the same genetic entity and that E. combesii was in the C. botulinum Group I subclade. Meanwhile, we showed that E. combesii DSM 20696T did not produce botulinum neurotoxins (BoNTs) and thus should be identified as a strain of C. sporogenes in accordance with the current nomenclature of BoNT-producing clostridia, which is based, in particular, on Opinion 69 issued by the Judicial Commission of the ICSB. However, review of the corresponding Request for an Opinion revealed that it had been based on an erroneous statement. Therefore, we request reconsideration of Opinion 69 and propose to reclassify Eubacterium combesii as a later synonym of Clostridium botulinum. The results of phylogenetic analysis of the other five groups of BoNT-producing clostridia indicated that all the groups were far distant from each other. However, the members of Groups IV-VI are classified as strains of different species, while all members of Groups I-III are designated C. botulinum. Meanwhile, similarly to Group I, Groups II and III are also polyphyletic and appear to consist of two and four species, respectively. These results demonstrate, once again, discrepancies in the nomenclature of BoNT-producing bacteria and corroborate our request for reconsideration of Opinion 69.

Clostridium tepidum sp. nov., a close relative of Clostridium sporogenes and Clostridium botulinum Group I.

Obligately anaerobic, Gram-stain-positive, spore-forming bacteria indistinguishable by pulsed-field gel electrophoresis were isolated from non-dairy protein shakes in bloated bottles. One of the isolates, strain IEH 97212T, was selected for further study. The strain was closely related to Clostridium sporogenes and Clostridium botulinum Group 1 based on 16S rRNA gene sequence similarities. Phylogenetic analysis also showed that strain IEH 97212T and strain PE (=DSM 18688), a bacterium isolated from solfataric mud, had identical 16S rRNA gene sequences. Strains IEH 97 212T and DSM 18 688 were relatively more thermophilic (temperature range for growth: 30-55 °C) and less halotolerant [growth range: 0-2.5 % (w/v) NaCl] than C. sporogenes and C. botulinum. They were negative for catalase, oxidase, urease and l-pyrrolidonyl-arylamidase and did not produce indole. The strains produced acid from d-glucose, maltose and trehalose, and hydrolysed gelatin, but did not hydrolyse aesculin. The end-products of growth included acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, isovaleric acid, isocaproic acid, phenylpropionic acid, 2-piperidinone, 2-pyrrolidinone and gas(es). The predominant fatty acids were C14 : 0, C16 : 0 and C18 : 1ω9c. The genomic DNA G+C content of strains IEH 97212T and DSM 18688 was 26.9 and 26.7 mol%, respectively. According to the digital DNA-DNA hybridization data, the relatedness of these strains was 98.4 %, while they showed only 35.7-36.0 % relatedness to C. sporogenes. Based on the results of this polyphasic study, these strains represent a novel species, for which the name Clostridium tepidum sp. nov. is proposed, with the type strain IEH 97212T (=NRRL B-65463T=DSM 104389T).

Reclassification of Paraburkholderia panaciterrae (Farh et al. 2015) Dobritsa & Samadpour 2016 as a later synonym of Paraburkholderia ginsengiterrae (Farh et al. 2015) Dobritsa & Samadpour 2016.

Whole-genome sequencing and PFGE analysis of Paraburkholderia ginsengiterrae DCY85T and Paraburkholderia panaciterrae DCY85-1T showed these strains are highly similar and may even be clones of the same strain. The PFGE patterns of XbaI-, AvaII-, and SpeI-digested genomic DNA of the two strains were indistinguishable. Based on the priority of valid publications of the species basonyms, Burkholderia ginsengiterrae and Burkholderia panaciterrae, it is proposed to reclassify P. panaciterrae as a later synonym of P. ginsengiterrae. The P. ginsengiterrae description was emended by replacing the DNA G+C content value of 66.0 mol%, which is higher than the 65 mol% considered the threshold for species of the genus Paraburkholderia, with the value of 62.4-62.5 mol%, calculated as the mean DNA G+C content of the draft genomes of strains DCY85-1T and DCY85T.

Escherichia coli O157:H7 Cluster Associated With Deer Harvested at a Single Wildlife Hunting Area, Oregon, 2017.

The Oregon Health Authority routinely investigates clusters of reportable enteric diseases identified by whole-genome sequencing. While investigating 2 cases of Escherichia coli O157:H7 in 2019, in which both patients were exposed to the same home-processed "jerky" and clinical isolates matched within 2 single nucleotide polymorphisms (SNPs), we discovered, by searching the National Library of Medicine's National Center for Biotechnology Information website, 3 other cases of E coli O157:H7 from 3 Oregon counties-Tillamook, Umatilla, and Douglas-whose clinical isolates were within 9 SNPs of the 2 initial matched cases. We analyzed interview data for 3 case patients and followed up with additional hypothesis-generating questions. Onset of illness for the Tillamook, Umatilla, and Douglas county cases were October 7, 2017, October 27, 2017, and April 30, 2018, respectively. The median age of the 5 case patients was 16 years. Parents of 2 of the 5 case patients, each from a different county, had harvested deer approximately 20 miles from each other in the same Douglas County wildlife hunting unit in late September 2017. The case from Umatilla County was lost to follow-up. Although it is well documented that deer are a viable and substantial reservoir of E coli O157:H7, to our knowledge, this is the first time that venison from a common wildlife hunting unit was found to be associated with a cluster of illnesses. This finding suggests a geographic nidus for E coli O157:H7. We recommend routinely asking about wildlife hunting units when developing exposure hypotheses involving potential venison-associated clusters.

Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319.

Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key species and of particular importance in understanding genome evolution, dynamics, and plasticity in the bacilli. B. megaterium is a commercially available, nonpathogenic host for the biotechnological production of several substances, including vitamin B(12), penicillin acylase, and amylases. Here, we report the analysis of the first complete genome sequences of two important B. megaterium strains, the plasmidless strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The 5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551 plasmids represent a combined 417 kb and 523 genes, one of the largest plasmid arrays sequenced in a single bacterial strain. We have documented extensive gene transfer between the plasmids and the chromosome. Each strain carries roughly 300 strain-specific chromosomal genes that account for differences in their experimentally confirmed phenotypes. B. megaterium is able to synthesize vitamin B(12) through an oxygen-independent adenosylcobalamin pathway, which together with other key energetic and metabolic pathways has now been fully reconstructed. Other novel genes include a second ftsZ gene, which may be responsible for the large cell size of members of this species, as well as genes for gas vesicles, a second ß-galactosidase gene, and most but not all of the genes needed for genetic competence. Comprehensive analyses of the global Bacillus gene pool showed that only an asymmetric region around the origin of replication was syntenic across the genus. This appears to be a characteristic feature of the Bacillus spp. genome architecture and may be key to their sporulating lifestyle.

New Delhi metallo-ß-lactamase-1 (NDM-1) Escherichia coli isolated from household vacuum cleaner-Oregon, 2013.

The first Oregon case of New Delhi metallo-ß-lactamase-1 (NDM-1)-producing Escherichia coli was reported during November 2013. Epidemiologic investigation revealed only local outpatient medical care and no travel outside Oregon for both the patient and his household contact. Environmental sampling discovered a matching isolate from the patient's household vacuum cleaner, suggesting environmental persistence.

Draft Genome Sequence of the Beer Spoilage Bacterium Megasphaera cerevisiae Strain PAT 1T.

The genus Megasphaera harbors important spoilage organisms that cause beer spoilage by producing off flavors, undesirable aroma, and turbidity. Megasphaera cerevisiae is mainly found in nonpasteurized low-alcohol beer. In this study, we report the draft genome of the type strain of the genus, M. cerevisiae strain PAT 1(T).

Draft Genome Sequence of blaNDM-1-Positive Escherichia coli O25b-ST131 Clone Isolated from an Environmental Sample.

A multidrug-resistant NDM-1 carbapenamase-producing Escherichia coli sequence type 131 (ST131) organism was obtained from vacuum cleaner dust collected from the home of a case patient. Here, we report the assembly and annotation of its genome.