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July 7, 2019  |  

Complete genome sequence of an avian native NDM-1-producing Salmonella enterica subsp. enterica serovar Corvallis strain.

Carbapenems are an important class of ß-lactams and one of the last options for treating severe human infections. We present here the complete genome sequence of avian native carbapenemase-producing Salmonella enterica subsp. enterica serovar Corvallis strain 12-01738, harboring a blaNDM-1-carrying IncA/C2 plasmid, isolated in 2012 from a wild bird (Milvus migrans) in Germany. Copyright © 2018 Hadziabdic et al.


July 7, 2019  |  

DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection

Genes prot6E and sefA are used as targets for detection of Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella ser. Enteritidis). We investigated variations in these genes across 64 different Salmonella ser. Enteritidis strains isolated from egg and chicken samples, then used Whole Genome Sequence (WGS) data to model the structures of their protein products. Isolates were sequenced using Illumina technologies. Based on the resulting phylogenetic tree, our isolates clustered in 2 distinct clades. All isolates carried prot6E and sefA. Comparative genomic analyses indicated two non-synonymous mutations (Glycine ? Serine and Valine ? Isoleucine) of prot6E in 11 isolates (9 egg samples, 2 chicken samples). However, SWISS-MODEL was unable to clearly model the protein structure of these two mutations. We identified one non-synonymous mutation (Valine ? Glutamic Acid) in the sefA gene in 4 isolates from egg samples. The model for the protein structure of this mutant gene was clearly different from that of the other isolates studied herein. Circular maps of plasmid genomes from two PacBio platform-sequenced Salmonella ser. Enteritidis isolates revealed prot6E gene was located on the tail of the plasmid. Based on the biosynthesis of amino acids – Reference pathway in the KEGG pathway Database, the transition of amino acid from sefA Var. was a transversion from essential amino acid to non-essential amino acid, while that of prot6E Var.1 happened between the conditionally non-essential amino acid, and prot6E Var. 2 occurred between essential amino acids. Properties of these mutated amino acids, such as side-chain polarity or charge, may contribute to the occurrence and rate of mutations in prot6E and sefA. These insights can be used to improve detection methods for Salmonella ser. Enteritidis.


July 7, 2019  |  

Complete genome sequence of Salmonella enterica subsp. enterica serotype Derby, associated with the pork sector in France.

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.


July 7, 2019  |  

Closed genome sequences and antibiograms of 16 Pasteurella multocida isolates from bovine respiratory disease complex cases and apparently healthy controls.

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.


July 7, 2019  |  

New variant of multidrug-resistant Salmonella enterica serovar Typhimurium associated with invasive disease in immunocompromised patients in Vietnam.

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.


July 7, 2019  |  

Complete genome sequence of the Arcobacter molluscorum type strain LMG 25693.

As components of freshwater and marine microflora, Arcobacter spp. are often recovered from shellfish, such as mussels, clams, and oysters. Arcobacter mol- luscorum was isolated from mussels from the Ebro Delta in Catalonia, Spain. This ar- ticle describes the whole-genome sequence of the A. molluscorum strain LMG 25693T(= F98-3T= CECT 7696T).


July 7, 2019  |  

Complete genome sequence of the Arcobacter suis type strain LMG 26152.

Arcobacter species are prevalent in pigs, and strains have been isolated from pig feces and pork meat; some Arcobacter strains may be porcine abortifacients. Arcobacter suis was recovered from pork meat in Spain. This study describes the whole-genome sequence of the A. suis type strain LMG 26152 (=F41T =CECT 7833T).


July 7, 2019  |  

Overview of the germline and expressed repertoires of the TRB genes in Sus scrofa.

The a/ß T cell receptor (TR) is a complex heterodimer that recognizes antigenic peptides and binds to major histocompatibility complex (MH) molecules. Both a and ß chains are encoded by different genes localized on two distinct chromosomal loci: TRA and TRB. The present study employed the recent release of the swine genome assembly to define the genomic organization of the TRB locus. According to the sequencing data, the pig TRB locus spans approximately 400 kb of genomic DNA and consists of 38 TRBV genes belonging to 24 subgroups located upstream of three in tandem TRBD-J-C clusters, which are followed by a TRBV gene in an inverted transcriptional orientation. Comparative analysis confirms that the general organization of the TRB locus is similar among mammalian species, but the number of germline TRBV genes varies greatly even between species belonging to the same order, determining the diversity and specificity of the immune response. However, sequence analysis of the TRB locus also suggests the presence of blocks of conserved homology in the genomic region across mammals. Furthermore, by analysing a public cDNA collection, we identified the usage pattern of the TRBV, TRBD, and TRBJ genes in the adult pig TRB repertoire, and we noted that the expressed TRBV repertoire seems to be broader and more diverse than the germline repertoire, in line with the presence of a high level of TRBV gene polymorphisms. Because the nucleotide differences seems to be principally concentrated in the CDR2 region, it is reasonable to presume that most T cell ß-chain diversity can be related to polymorphisms in pig MH molecules. Domestic pigs represent a valuable animal model as they are even more anatomically, genetically and physiologically similar to humans than are mice. Therefore, present knowledge on the genomic organization of the pig TRB locus allows the collection of increased information on the basic aspects of the porcine immune system and contributes to filling the gaps left by rodent models.


July 7, 2019  |  

Complete genome sequence of Streptacidiphilus sp. strain 15-057A, obtained from bronchial lavage fluid.

Streptacidiphilus sp. strain 15-057A was isolated from a bronchial lavage sample and represents the only member of the genus not isolated from acidic soils. A single circular chromosome of 7.01?Mb was obtained by combining Illumina and PacBio sequencing data. Bioinformatic analysis detected 63 putative secondary biosynthetic gene clusters and recognized 43 transposons.


July 7, 2019  |  

CTX-M-65 extended-spectrum ß-lactamase-producing Salmonella enterica serotype infantis, United States.

Extended-spectrum ß-lactamases (ESBLs) confer resistance to clinically important third-generation cephalosporins, which are often used to treat invasive salmonellosis. In the United States, ESBLs are rarely found in Salmonella. However, in 2014, the US Food and Drug Administration found blaCTX-M-65 ESBL-producing Salmonella enterica serotype Infantis in retail chicken meat. The isolate had a rare pulsed-field gel electrophoresis pattern. To clarify the sources and potential effects on human health, we examined isolates with this pattern obtained from human surveillance and associated metadata. Using broth microdilution for antimicrobial susceptibility testing and whole-genome sequencing, we characterized the isolates. Of 34 isolates, 29 carried the blaCTX-M-65 gene with <9 additional resistance genes on 1 plasmid. Of 19 patients with travel information available, 12 (63%) reported recent travel to South America. Genetically, isolates from travelers, nontravelers, and retail chicken meat were similar. Expanded surveillance is needed to determine domestic sources and potentially prevent spread of this ESBL-containing plasmid.


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