Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil

Background: Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states. Methods: We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG, originally identified as Acinetobacter baumannii, Rhizobium radiobacter, Pantoea sp. or Enterobacteriaceae using molecular methods. Results: The first two bacterial species were confirmed while the third group of species could not be identified using standard identification protocols. These isolates were subsequently identified by Multi-Locus Sequence Analysis as Phytobacter diazotrophicus, a species related to strains from similar outbreaks in the United States in the 1970’s. Within each species, TPN and blood isolates proved to be clonal, whereas the R. radiobacter isolates retrieved from CG were found to be unrelated. Conclusion: This is the first report of a three-species outbreak caused by TPN contaminated with A. baumannii, R. radiobacter and P. diazotrophicus. The concomitant presence of clonal A. baumannii and P. diazotrophicus isolates in several TPN and blood samples, as well as the case of one patient, where all three different species were isolated simultaneously, suggest that the outbreak may be ascribed to a discrete contamination of TPN. In addition, this study highlights the clinical relevance of P. diazotrophicus, which has been involved in outbreaks in the past, but was often misidentified as P. agglomerans

Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil

Background: Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states. Methods: We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG, originally identified as Acinetobacter baumannii, Rhizobium radiobacter, Pantoea sp. or Enterobacteriaceae using molecular methods. Results: The first two bacterial species were confirmed while the third group of species could not be identified using standard identification protocols. These isolates were subsequently identified by Multi-Locus Sequence Analysis as Phytobacter diazotrophicus, a species related to strains from similar outbreaks in the United States in the 1970’s. Within each species, TPN and blood isolates proved to be clonal, whereas the R. radiobacter isolates retrieved from CG were found to be unrelated. Conclusion: This is the first report of a three-species outbreak caused by TPN contaminated with A. baumannii, R. radiobacter and P. diazotrophicus. The concomitant presence of clonal A. baumannii and P. diazotrophicus isolates in several TPN and blood samples, as well as the case of one patient, where all three different species were isolated simultaneously, suggest that the outbreak may be ascribed to a discrete contamination of TPN. In addition, this study highlights the clinical relevance of P. diazotrophicus, which has been involved in outbreaks in the past, but was often misidentified as P. agglomerans

Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974 T (ATCC 19319 T)

Jaenicke S, Bunk B, Wibberg D, et al. Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974 T (ATCC 19319 T). Genome Announcements. 2016;4(6): e01334-16.We report here the complete 4.7-Mb genome sequence of Xanthomonas translucens pv. translucens DSM 18974T, which causes black chaff disease on barley (Hordeum vulgare). Genome data of this X. translucens type strain will improve our understanding of this bacterial species

Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

Abstract Background Xanthomonas translucens pathovars differ in their individual host ranges among Poaceae. As the causal agent of bacterial wilt in Italian ryegrass ( Lolium multiflorum Lam.), X. translucens pv. graminis ( Xtg ) is one of the most important bacterial pathogens in temperate grassland regions. The genomes of six Xtg strains from Switzerland, Norway, and New Zealand were sequenced in order to gain insight into conserved genomic traits from organisms covering a wide geographical range. Subsequent comparative analysis with previously published genome data of seven non- graminis X. translucens strains including the pathovars arrhenatheri , poae , phlei , cerealis , undulosa , and translucens was conducted to identify candidate genes linked to the host adaptation of Xtg to Italian ryegrass. Results Phylogenetic analysis revealed a tight clustering of Xtg strains, which were found to share a large core genome. Conserved genomic traits included a non-canonical type III secretion system (T3SS) and a type IV pilus (T4P), which both revealed distinct primary structures of the pilins when compared to the non- graminis X. translucens strains. Xtg -specific traits that had no homologues in the other X. translucens strains were further found to comprise several hypothetical proteins, a TonB-dependent receptor, transporters, and effector proteins as well as toxin-antitoxin systems and DNA methyltransferases. While a nearly complete flagellar gene cluster was identified in one of the sequenced Xtg strains, phenotypic analysis pointed to swimming-deficiency as a common trait of the pathovar graminis . Conclusion Our study suggests that host adaptation of X. translucens pv. graminis may be conferred by a combination of pathovar-specific effector proteins, regulatory mechanisms, and adapted nutrient acquisition. Sequence deviations of pathogen-associated molecular patterns (PAMPs), as observed for the pilins of the T4P and T3SS, are moreover likely to impede perception by the plant defense machinery and thus facilitate successful host colonization of Italian ryegrass

The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection

Wichmann F, Vorhölter F-J, Hersemann L, et al. The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection. Molecular plant pathology. 2013;14(6):576-588

Additional file 4: Figure S2. of Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

Number of strain-specific CDS predicted for seven Xtg strains. The data reflect the amount of predicted hypothetical proteins (blue), CDS with annotated functions (green) as well as detected transposases (grey). (PDF 171ย�kb

Additional file 7: Figure S3. of Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

Percentage identity matrix of the minor type IV pilus pilins PilE, PilX, PilW, PilV, and FimT as well as the T4P adhesin PilY1 across X. translucens strains (i.e. X. t. pv. graminis Xtg29, X. t. pv. arrhenatheri LMG 727, X. t. pv. poae LMG 728, X. t. pv. phlei LMG 730, X. t. pv. cerealis CFBP 2541, X. t. pv undulosa Xtu4699, X. t. pv. translucens DSM 18974, and X. t. DAR61454) including pathotype strains (PT) and the X. translucens type strain (T). Class III signal peptides identified for the minor pilins are indicated. For PilW homologues in X. t. pv. translucens DSM 18974 and X. t. DAR61454 no corresponding class III signal peptide was found. (PDF 386ย�kb

Additional file 8: Figure S4. of Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

wxc gene cluster comparison of four X. translucens pathovars represented by X. t. pv. graminis Xtg2 and the pathotype strains X. t. pv. arrhenatheri LMG 727PT, X. t. pv. poae LMG 728PT, and X. t. pv. phlei LMG 730PT. The strain Xtg2 was chosen as a representative of the pv. graminis. Intra-pathovar differences of Xtg strains, i.e. CDS with gene separation events due to non-sense mutations as observed for Xtg29, ICMP 6431, and NCPPB 3709, are indicated by red borders. Inter-pathovar gene cluster comparison revealed a highly variable region highlighted by a grey background, while the flanking regions were largely conserved. (PDF 202ย�kb