Wiedmann M

References (8)

Title : Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis - den Bakker_2014_Emerg.Infect.Dis_20_1306
Author(s) : den Bakker HC , Allard MW , Bopp D , Brown EW , Fontana J , Iqbal Z , Kinney A , Limberger R , Musser KA , Shudt M , Strain E , Wiedmann M , Wolfgang WJ
Ref : Emerg Infect Dis , 20 :1306 , 2014
Abstract : For Salmonella enterica serovar Enteritidis, 85% of isolates can be classified into 5 pulsed-field gel electrophoresis (PFGE) types. However, PFGE has limited discriminatory power for outbreak detection. Although whole-genome sequencing has been found to improve discrimination of outbreak clusters, whether this procedure can be used in real-time in a public health laboratory is not known. Therefore, we conducted a retrospective and prospective analysis. The retrospective study investigated isolates from 1 confirmed outbreak. Additional cases could be attributed to the outbreak strain on the basis of whole-genome data. The prospective study included 58 isolates obtained in 2012, including isolates from 1 epidemiologically defined outbreak. Whole-genome sequencing identified additional isolates that could be attributed to the outbreak, but which differed from the outbreak-associated PFGE type. Additional putative outbreak clusters were detected in the retrospective and prospective analyses. This study demonstrates the practicality of implementing this approach for outbreak surveillance in a state public health laboratory.
ESTHER : den Bakker_2014_Emerg.Infect.Dis_20_1306
PubMedSearch : den Bakker_2014_Emerg.Infect.Dis_20_1306
PubMedID: 25062035

Title : Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments - den Baker_2014_Int.J.Syst.Evol.Microbiol_64_1882
Author(s) : den Bakker HC , Warchocki S , Wright EM , Allred AF , Ahlstrom C , Manuel CS , Stasiewicz MJ , Burrell A , Roof S , Strawn LK , Fortes E , Nightingale KK , Kephart D , Wiedmann M
Ref : Int J Syst Evol Microbiol , 64 :1882 , 2014
Abstract : Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 Listeria-like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average BLAST nucleotide identity (ANIb) of less than 85% to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequences of 31 conserved loci showed the existence of four well-supported clades within the genus Listeria; (i) a clade representing Listeria monocytogenes, L. marthii, L. innocua, L. welshimeri, L. seeligeri and L. ivanovii, which we refer to as Listeria sensu stricto, (ii) a clade consisting of Listeria fleischmannii and two newly described species, Listeria aquatica sp. nov. (type strain FSL S10-1188(T) = DSM 26686(T) = LMG 28120(T) = BEI NR-42633(T)) and Listeria floridensis sp. nov. (type strain FSL S10-1187(T) = DSM 26687(T) = LMG 28121(T) = BEI NR-42632(T)), (iii) a clade consisting of Listeria rocourtiae, L. weihenstephanensis and three novel species, Listeria cornellensis sp. nov. (type strain TTU A1-0210(T) = FSL F6-0969(T) = DSM 26689(T) = LMG 28123(T) = BEI NR-42630(T)), Listeria grandensis sp. nov. (type strain TTU A1-0212(T) = FSL F6-0971(T) = DSM 26688(T) = LMG 28122(T) = BEI NR-42631(T)) and Listeria riparia sp. nov. (type strain FSL S10-1204(T) = DSM 26685(T) = LMG 28119(T) = BEI NR- 42634(T)) and (iv) a clade containing Listeria grayi. Genomic and phenotypic data suggest that the novel species are non-pathogenic.
ESTHER : den Baker_2014_Int.J.Syst.Evol.Microbiol_64_1882
PubMedSearch : den Baker_2014_Int.J.Syst.Evol.Microbiol_64_1882
PubMedID: 24599893
Gene_locus related to this paper: lismo-LMO2452 , 9list-w7b4a8 , 9list-w7dam8 , 9list-w7azc2 , 9list-a0a099wqa3 , 9list-m3gr61 , 9list-w7c0m4 , 9list-w7av97 , 9list-w7bx01 , 9list-w7cks9 , 9list-w7czu2 , 9list-w7dam4 , 9list-w7dnr4 , 9list-w7b7s0 , 9list-w7d2m6

Title : Genomic comparison of sporeforming bacilli isolated from milk - Moreno_2014_BMC.Genomics_15_26
Author(s) : Moreno Switt AI , Andrus AD , Ranieri ML , Orsi RH , Ivy R , den Bakker HC , Martin NH , Wiedmann M , Boor KJ
Ref : BMC Genomics , 15 :26 , 2014
Abstract : BACKGROUND: Sporeformers in the order Bacillales are important contributors to spoilage of pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6 degrees C, the majority of Paenibacillus isolated from pasteurized fluid milk can grow under these conditions. To gain a better understanding of genomic features of these important spoilage organisms and to identify candidate genomic features that may facilitate cold growth in milk, we performed a comparative genomic analysis of selected dairy associated sporeformers representing isolates that can and cannot grow in milk at 6 degrees C.
RESULTS: The genomes for seven Paenibacillus spp., two Bacillus spp., and one Viridibacillus sp. isolates were sequenced. Across the genomes sequenced, we identified numerous genes encoding antimicrobial resistance mechanisms, bacteriocins, and pathways for synthesis of non-ribosomal peptide antibiotics. Phylogenetic analysis placed genomes representing Bacillus, Paenibacillus and Viridibacillus into three distinct well supported clades and further classified the Paenibacillus strains characterized here into three distinct clades, including (i) clade I, which contains one strain able to grow at 6 degrees C in skim milk broth and one strain not able to grow under these conditions, (ii) clade II, which contains three strains able to grow at 6 degrees C in skim milk broth, and (iii) clade III, which contains two strains unable to grow under these conditions. While all Paenibacillus genomes were found to include multiple copies of genes encoding beta-galactosidases, clade II strains showed significantly higher numbers of genes encoding these enzymes as compared to clade III strains. Genome comparison of strains able to grow at 6 degrees C and strains unable to grow at this temperature identified numerous genes encoding features that might facilitate the growth of Paenibacillus in milk at 6 degrees C, including peptidases with cold-adapted features (flexibility and disorder regions in the protein structure) and cold-adaptation related proteins (DEAD-box helicases, chaperone DnaJ).
CONCLUSIONS: Through a comparative genomics approach we identified a number of genomic features that may relate to the ability of selected Paenibacillus strains to cause spoilage of refrigerated fluid milk. With additional experimental evidence, these data will facilitate identification of targets to detect and control Gram positive spore formers in fluid milk.
ESTHER : Moreno_2014_BMC.Genomics_15_26
PubMedSearch : Moreno_2014_BMC.Genomics_15_26
PubMedID: 24422886
Gene_locus related to this paper: bacce-c2zyv1 , bacce-BC2337 , bacce-BC5130 , geos4-d3ed06 , geos4-d3edx2 , 9bacl-w4bas9 , 9bacl-w4drs0 , 9bacl-w4bws1 , 9bacl-w4b6j5 , 9bacl-w4f050 , 9bacl-w4c3j8 , 9bacl-w4b844 , 9bacl-w4cb60 , 9bacl-w4bk58 , 9bacl-w4dle8 , 9bacl-w4avh4 , 9bacl-w4bpv3 , 9bacl-w4cbt0 , 9bacl-w4eid3 , 9bacl-w4en52 , 9bacl-w4els5 , 9bacl-w4ej46 , 9bacl-w4eqh1 , 9bacl-a0a089mve8 , 9bacl-w4e0c1 , 9bacl-w4ah68 , 9bacl-w4ccg0 , 9bacl-w4eha7 , 9bacl-w4ag71

Title : Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch - den Bakker_2013_Int.J.Syst.Evol.Microbiol_63_3257
Author(s) : den Bakker HC , Manuel CS , Fortes ED , Wiedmann M , Nightingale KK
Ref : Int J Syst Evol Microbiol , 63 :3257 , 2013
Abstract : Twenty Listeria-like isolates were obtained from environmental samples collected on a cattle ranch in northern Colorado; all of these isolates were found to share an identical partial sigB sequence, suggesting close relatedness. The isolates were similar to members of the genus Listeria in that they were Gram-stain-positive, short rods, oxidase-negative and catalase-positive; the isolates were similar to Listeria fleischmannii because they were non-motile at 25 degrees C. 16S rRNA gene sequencing for representative isolates and whole genome sequencing for one isolate was performed. The genome of the type strain of Listeria fleischmannii (strain LU2006-1(T)) was also sequenced. The draft genomes were very similar in size and the average MUMmer nucleotide identity across 91% of the genomes was 95.16%. Genome sequence data were used to design primers for a six-gene multi-locus sequence analysis (MLSA) scheme. Phylogenies based on (i) the near-complete 16S rRNA gene, (ii) 31 core genes and (iii) six housekeeping genes illustrated the close relationship of these Listeria-like isolates to Listeria fleischmannii LU2006-1(T). Sufficient genetic divergence of the Listeria-like isolates from the type strain of Listeria fleischmannii and differing phenotypic characteristics warrant these isolates to be classified as members of a distinct infraspecific taxon, for which the name Listeria fleischmannii subsp. coloradonensis subsp. nov. is proposed. The type strain is TTU M1-001(T) ( =BAA-2414(T) =DSM 25391(T)). The isolates of Listeria fleischmannii subsp. coloradonensis subsp. nov. differ from the nominate subspecies by the inability to utilize melezitose, turanose and sucrose, and the ability to utilize inositol. The results also demonstrate the utility of whole genome sequencing to facilitate identification of novel taxa within a well-described genus. The genomes of both subspecies of Listeria fleischmannii contained putative enhancin genes; the Listeria fleischmannii subsp. coloradonensis subsp. nov. genome also encoded a putative mosquitocidal toxin. The presence of these genes suggests possible adaptation to an insect host, and further studies are needed to probe niche adaptation of Listeria fleischmannii.
ESTHER : den Bakker_2013_Int.J.Syst.Evol.Microbiol_63_3257
PubMedSearch : den Bakker_2013_Int.J.Syst.Evol.Microbiol_63_3257
PubMedID: 23524352
Gene_locus related to this paper: 9list-m3igw0 , 9list-m3gr61 , 9list-m3hv56

Title : Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43\/6\/78(T.) - Lin_2013_Genome.Announc_1_E00215
Author(s) : Lin C , den Bakker HC , Suzuki H , Lefebure T , Ponnala L , Sun Q , Stanhope MJ , Wiedmann M , Duhamel GE
Ref : Genome Announc , 1 :E00215 , 2013
Abstract : Reported herein is the complete genome sequence of Brachyspira pilosicoli strain P43/6/78T, isolated from a pig with clinical disease. This sequence will aid in the study of genome-wide comparison among Brachyspira species.
ESTHER : Lin_2013_Genome.Announc_1_E00215
PubMedSearch : Lin_2013_Genome.Announc_1_E00215
PubMedID: 23469345
Gene_locus related to this paper: brap9-d8ife9

Title : FSL J1-208, a virulent uncommon phylogenetic lineage IV Listeria monocytogenes strain with a small chromosome size and a putative virulence plasmid carrying internalin-like genes - den Bakker_2012_Appl.Environ.Microbiol_78_1876
Author(s) : den Bakker HC , Bowen BM , Rodriguez-Rivera LD , Wiedmann M
Ref : Applied Environmental Microbiology , 78 :1876 , 2012
Abstract : The bacterial genus Listeria contains both saprotrophic and facultative pathogenic species. A small genome size has been suggested to be associated with the loss of pathogenic potential of L. welshimeri and L. seeligeri. In this paper we present data on the genome of L. monocytogenes strain FSL J1-208, a representative of phylogenetic lineage IV. Although this strain was isolated from a clinical case in a caprine host and has no decreased invasiveness in human intestinal epithelial cells, our analyses show that this strain has one of the smallest Listeria chromosomes reported to date (2.78 Mb). The chromosome contains 2,772 protein-coding genes, including well-characterized virulence-associated genes, such as inlA, inlB, and inlC and the full prfA gene cluster. The small genome size is mainly caused by the absence of prophages in the genome of L. monocytogenes FSL J1-208, and further analyses showed that the total size of prophage-related regions is highly correlated to chromosome size in the genus Listeria. L. monocytogenes FSL J1-208 carries a unique type of plasmid of approximately 80 kbp that does not carry genes annotated as being involved in resistance to antibiotics or heavy metals. The accessory genes in this plasmid belong to the internalin family, a family of virulence-associated proteins, and therefore this is the first report of a potential virulence plasmid in the genus Listeria.
ESTHER : den Bakker_2012_Appl.Environ.Microbiol_78_1876
PubMedSearch : den Bakker_2012_Appl.Environ.Microbiol_78_1876
PubMedID: 22247147
Gene_locus related to this paper: lismo-LMO1674

Title : Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica - den Bakker_2011_BMC.Genomics_12_425
Author(s) : den Bakker HC , Moreno Switt AI , Govoni G , Cummings CA , Ranieri ML , Degoricija L , Hoelzer K , Rodriguez-Rivera LD , Brown S , Bolchacova E , Furtado MR , Wiedmann M
Ref : BMC Genomics , 12 :425 , 2011
Abstract : BACKGROUND: Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization.
RESULTS: Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a beta-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of beta-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment.
CONCLUSIONS: S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.
ESTHER : den Bakker_2011_BMC.Genomics_12_425
PubMedSearch : den Bakker_2011_BMC.Genomics_12_425
PubMedID: 21859443
Gene_locus related to this paper: salty-STY1441 , salty-YFBB

Title : Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss - den Bakker_2010_BMC.Genomics_11_688
Author(s) : den Bakker HC , Cummings CA , Ferreira V , Vatta P , Orsi RH , Degoricija L , Barker M , Petrauskene O , Furtado MR , Wiedmann M
Ref : BMC Genomics , 11 :688 , 2010
Abstract : BACKGROUND: The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA cluster and clusters of internalin genes. Initial evidence for multiple deletions of the prfA cluster during the evolution of Listeria indicates that this genus provides an interesting model for studying the evolution of virulence and also presents practical challenges with regard to definition of pathogenic strains.
RESULTS: To better understand genome evolution and evolution of virulence characteristics in Listeria, we used a next generation sequencing approach to generate draft genomes for seven strains representing Listeria species or clades for which genome sequences were not available. Comparative analyses of these draft genomes and six publicly available genomes, which together represent the main Listeria species, showed evidence for (i) a pangenome with 2,032 core and 2,918 accessory genes identified to date, (ii) a critical role of gene loss events in transition of Listeria species from facultative pathogen to saprotroph, even though a consistent pattern of gene loss seemed to be absent, and a number of isolates representing non-pathogenic species still carried some virulence associated genes, and (iii) divergence of modern pathogenic and non-pathogenic Listeria species and strains, most likely circa 47 million years ago, from a pathogenic common ancestor that contained key virulence genes.
CONCLUSIONS: Genome evolution in Listeria involved limited gene loss and acquisition as supported by (i) a relatively high coverage of the predicted pan-genome by the observed pan-genome, (ii) conserved genome size (between 2.8 and 3.2 Mb), and (iii) a highly syntenic genome. Limited gene loss in Listeria did include loss of virulence associated genes, likely associated with multiple transitions to a saprotrophic lifestyle. The genus Listeria thus provides an example of a group of bacteria that appears to evolve through a loss of virulence rather than acquisition of virulence characteristics. While Listeria includes a number of species-like clades, many of these putative species include clades or strains with atypical virulence associated characteristics. This information will allow for the development of genetic and genomic criteria for pathogenic strains, including development of assays that specifically detect pathogenic Listeria strains.
ESTHER : den Bakker_2010_BMC.Genomics_11_688
PubMedSearch : den Bakker_2010_BMC.Genomics_11_688
PubMedID: 21126366
Gene_locus related to this paper: 9list-e3yqw9 , lisin-LIN0589 , lisin-LIN0850 , lisin-LIN0949 , lisin-LIN0950 , lisin-LIN2544 , lisin-LIN2722 , lisiv-e3zgw7 , lismc-c1l0d9 , lismo-e3ygy8 , lismo-LMO0110 , lismo-LMO0493 , lismo-LMO0857 , lismo-LMO0951 , lismo-LMO1258 , lismo-LMO2089 , lismo-LMO2433 , lismo-LMO2452 , lismo-LMO2755 , lismo-metx , lisse-e3zni8 , lisse-e3zr75