Avian pathogenic Escherichia coli (APEC) is the causative agent of colibacil- losis, a disease that affects poultry production worldwide and leads to multimillion-dollar losses annually. Here, we report the genome sequence of APEC O2-211, a sequence type 117 (ST117) strain isolated from a diseased chicken.
Neonatal meningitis Escherichia coli (NMEC) is the second leading cause of neonatal bacterial meningitis worldwide. We report the genome sequence of the multidrug-resistant NMEC serotype O75:H5:K1 strain mcjchv-1, which resulted in an infant’s death. The O75 serogroup is rare among NMEC isolates; therefore, this strain is considered an emergent pathogen.
In the European Union, Salmonella enterica subsp. enterica serovar Derby is the most abundant serotype isolated from pork. Recent studies have shown that this serotype is polyphyletic. However, one main genomic lineage, characterized by sequence type 40 (ST40), the presence of the Salmonella pathogenicity island 23, and showing resistance to streptomycin, sulphonamides, and tetracycline (STR-SSS- TET), is pork associated. Here, we describe the complete genome sequence of a strain from this lineage isolated in France.
We report here the complete closed genome sequence of Moraxella bo- vis strain Epp-63 (300) (Epp63). This strain was isolated from an infectious bovine keratoconjunctivitis (IBK) case in 1963. Since then, Epp63 has been used extensively for IBK research. Consequently, the genome sequence of Epp63 should help eluci- date IBK host-pathogen interactions.
Enterococcus gilvus CR1, isolated from raw cow’s milk, can produce carotenoids. The complete genome sequence of this strain was determined using the PacBio RS II platform. The assembly was found to contain a circular chromosome, including carotenoid biosynthesis genes, and comprises 2,863,043 bp, with a GC content of 41.86% and three plasmids.
Pasteurella multocida is an animal-associated Gram-negative member of the Pasteurellaceae family. It is an opportunistic pathogen and is one of the principal bacterial species contributing to bovine respiratory disease complex (BRDC) in feedlot cattle. We present 16 closed genome sequences and antibiograms of isolates cultured from calves exhibiting clinical signs of BRDC and from control calves not showing signs of BRDC.
Marinobacterium aestuarii ST58-10Twas identified as a benzene-degrading aerobic bacterium isolated from estuarine sediment in the Republic of Korea. The ge- nome of strain ST58-10Twas found to be composed of a single circular chromosome (5,191,608bp) with a G+C content of 58.78% and harboring 4,473 protein-coding genes. The assembled sequence data will help elucidate potential metabolic pathways and mechanisms responsible for the hydrocarbon-degrading ability of M. aestuarii ST58-10T.
Sphingosinicella microcystinivorans strain B-9 has the ability to degrade cyanobacterial hepatotoxic cyclic peptides, microcystins, and nodularins. This is the first report of the complete genome sequence of the microcystin-degrading bacterium.
Herpes simplex virus 2, or human herpesvirus 2, is a ubiquitous human pathogen that causes genital ulcerations and establishes latency in sacral root ganglia. We fully sequenced and manually curated the viral genome sequence of herpes simplex virus 2, strain 333 using Pacific Biosciences and Illumina sequencing technologies.
Clostridioides (Clostridium) difficile is a spore-forming anaerobic bacte- rium that causes severe intestinal diseases in humans. Here, we report the complete genome sequence of the first C. difficile foodborne type strain (PCR ribotype 078) isolated from food animals in Canada in 2004, which has 100% similarity to the ge- nome sequence of the historic human clinical strain M120.
Based on a combination of next-generation sequencing and single-molecule sequencing, we obtained the whole-genome sequence of Bacillus megaterium strain TG1-E1, which is a highly salt-tolerant rhizobacterium that enhances plant tolerance to drought stress. The complete genome is estimated to be approximately 5.48 Mb containing a total of 5,858 predicted protein-coding DNA sequences.
Here, we report the complete genome sequence of Weissella cibaria M2, a potential probiotic strain isolated from the feces of a giant panda (Ailuropoda melanoleuca). The genome consists of one chromosome of 2.56 Mb and two plas- mids. The genome contains 2,420 genes which make up 86.17% of genome.
The complete genome sequence of Caulobacter vibrioides strain CB1 consists of a chromosome of 4,137,285 bp, with a GC content of 67.2% and 3,990 coding DNA sequences. This strain contains the typical genome rearrangement that is characteristic of the Caulobacter strains that are currently sequenced. However, this strain is so closely related to sequenced strain NA1000 that rearrangements were minimal. This will allow further clarification of the causes of rearrangements in the species.
We report the complete genome sequences of two strains of the Alphaproteobacteria genus Rhodobacter, Rhodobacter blasticus 28/5, the source of the commercially available enzyme RsaI, and a new isolate of Rhodobacter sphaeroides 2.4.1. Both strains contain multiple restriction-modification systems, and their DNA methylation motifs are included in this report.
Nontyphoidal Salmonella (NTS), particularly Salmonella enterica serovar Typhimurium, is among the leading etiologic agents of bacterial enterocolitis globally and a well-characterized cause of invasive disease (iNTS) in sub-Saharan Africa. In contrast, S Typhimurium is poorly defined in Southeast Asia, a known hot spot for zoonotic disease with a recently described burden of iNTS disease. Here, we aimed to add insight into the epidemiology and potential impact of zoonotic transfer and antimicrobial resistance (AMR) in S Typhimurium associated with iNTS and enterocolitis in Vietnam. We performed whole-genome sequencing and phylogenetic reconstruction on 85 human (enterocolitis, carriage, and iNTS) and 113 animal S Typhimurium isolates isolated in Vietnam. We found limited evidence for the zoonotic transmission of S Typhimurium. However, we describe a chain of events where a pandemic monophasic variant of S Typhimurium (serovar I:4,[5],12:i:- sequence type 34 [ST34]) has been introduced into Vietnam, reacquired a phase 2 flagellum, and acquired an IncHI2 multidrug-resistant plasmid. Notably, these novel biphasic ST34 S Typhimurium variants were significantly associated with iNTS in Vietnamese HIV-infected patients. Our study represents the first characterization of novel iNTS organisms isolated outside sub-Saharan Africa and outlines a new pathway for the emergence of alternative Salmonella variants into susceptible human populations.IMPORTANCESalmonella Typhimurium is a major diarrheal pathogen and associated with invasive nontyphoid Salmonella (iNTS) disease in vulnerable populations. We present the first characterization of iNTS organisms in Southeast Asia and describe a different evolutionary trajectory from that of organisms causing iNTS in sub-Saharan Africa. In Vietnam, the globally distributed monophasic variant of Salmonella Typhimurium, the serovar I:4,[5],12:i:- ST34 clone, has reacquired a phase 2 flagellum and gained a multidrug-resistant plasmid to become associated with iNTS disease in HIV-infected patients. We document distinct communities of S Typhimurium and I:4,[5],12:i:- in animals and humans in Vietnam, despite the greater mixing of these host populations here. These data highlight the importance of whole-genome sequencing surveillance in a One Health context in understanding the evolution and spread of resistant bacterial infections. Copyright © 2018 Mather et al.
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