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Articles of Significant Interest Selected from This Issue by the Editors.
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Articles of Significant Interest Selected from This Issue by the Editors.

Appl Environ Microbiol. 2017 Apr 01;83(7):

Authors:

PMID: 28314737 [PubMed - in process]




Genome-wide single nucleotide polymorphism analysis identified clonal lineages of Erysipelothrix rhusiopathiae responsible for the recent increased incidence of acute swine erysipelas in Japan.
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Genome-wide single nucleotide polymorphism analysis identified clonal lineages of Erysipelothrix rhusiopathiae responsible for the recent increased incidence of acute swine erysipelas in Japan.

Appl Environ Microbiol. 2017 Mar 17;:

Authors: Ogawa Y, Shiraiwa K, Ogura Y, Ooka T, Nishikawa S, Eguchi M, Hayashi T, Shimoji Y

Abstract
Erysipelothrix rhusiopathiae causes swine erysipelas, an important infectious disease in the swine industry. In Japan, the incidence of acute swine erysipelas due to serovar 1a has recently increased markedly. To study the genetic relatedness of the strains from the recent cases, we analyzed 34 E. rhusiopathiae serovar 1a swine isolates collected between 1990 and 2011 and further investigated the possible association of the live Koganei 65-0.15 vaccine strain (serovar 1a) with the increase in cases. Pulsed-field gel electrophoresis analysis revealed no marked variation among the isolates; however, sequencing analysis of a hypervariable region in the surface protective antigen A (spaA) gene revealed that the strains isolated after 2007 exhibited the same spaA genotype and could be differentiated from older strains. Phylogenetic analysis based on genome-wide single nucleotide polymorphisms (SNPs) revealed that the Japanese strains examined were closely related, showing a relatively small number of SNPs among them. The strains were classified into four major lineages, with Koganei 65-0.15 (Lineage III) being phylogenetically separated from the other three lineages. The strains isolated after 2007 and the two older strains constituted one major lineage (Lineage IV) with a specific spaA genotype (M203/I257-SpaA), while the recent isolates were further divided into two geographic groups. The remaining older isolates belonged to either Lineage I with the I203/L257-SpaA-type or Lineage II with the I203/I257-SpaA-type. These results indicate that the recent increased incidence of acute swine erysipelas in Japan is associated with two sublineages of Lineage IV, which have independently evolved in two different geographic regions.Importance Using large-scale whole-genome sequence data from Erysipelothrix rhusiopathiae isolates from a wide range of hosts and geographic origins, a recent study clarified the existence of three distinct clades (Clades 1, 2, and 3) that are found across multiple continents and host species representing both livestock and wildlife, and an "intermediate" clade between Clade 2 and the dominant Clade 3 within the species. In this study, we found that the E. rhusiopathiae Japanese strains examined exhibited remarkably low levels of genetic diversity and confirmed that all of the Japanese and Chinese swine isolates examined in this study belong to clonal lineages within the intermediate clade. We report for the first time that spaA genotyping of E. rhusiopathiae strains is a practical alternative to whole-genome sequencing analysis of the E. rhusiopathiae isolates from eastern Asian countries.

PMID: 28314730 [PubMed - as supplied by publisher]




Efficacy of a Sonicating Swab for Removal and Capture of Listeria monocytogenes in Biofilm on Stainless Steel.
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Efficacy of a Sonicating Swab for Removal and Capture of Listeria monocytogenes in Biofilm on Stainless Steel.

Appl Environ Microbiol. 2017 Mar 17;:

Authors: Branck TA, Hurley MJ, Prata GN, Crivello CA, Marek PJ

Abstract
Listeria monocytogenes is of great concern in food processing facilities because it persists in biofilms, potentiating biotransfer. Stainless steel is commonly used for food contact surfaces and transport containers. L. monocytogenes biofilm on stainless steel served as a model system for surface sampling to test the performance of a sonicating swab in comparison to a standard cotton swab. Swab performance and consistency were determined using total viable counts. Stainless steel coupons sampled with both swabs were examined with SEM to visualize biofilms and surface structures (i.e. polishing grooves and scratches). LSCM was used to image and quantitate the percent area of remaining biofilm after sampling with each swab type. The total viable count was significantly higher (P ≤ 0.05) for the sonicating swab in comparison to the standard swab within each trial. The sonicating swab was more consistent in cell recovery than standard swab having lower CVs ranging from 8.9% to 12.3% and 7.1% to 37.6% respectively. SEM imaging showed biofilm remaining in the polished grooves of the coupons sampled with the standard swab but were noticeably absent for the sonicating swab. Percent area measurement of biofilm remaining on stainless steel coupons showed significantly (P ≤ 0.05) less biofilm remained when using the sonicating swab (median 1.1%) in comparison to the standard swab (median 70.4%). The sonicating swab provided a higher recovery of cells with more consistency than the standard swab and is the first swabbing device to employ: sonication, suction, and scrubbing.IMPORTANCE Inadequate surface sampling can result in food borne illness outbreaks from biotransfer since verification of sanitization protocols relies on surface sampling and recovery of microorganisms for detection and enumeration. Swabbing is a standard method for microbiological sampling of surfaces. Although swabbing offers portability and ease of use, there are limitations, such as high user variability and low recovery, which can be attributed to many different causes. This study demonstrates some benefits that a sonicating swab has over the performance of a standard swab for removal and collection of a microbiological sample from a surface to provide better verification of surface cleanliness and to help in lowering the potential for biotransfer of pathogens into foods.

PMID: 28314729 [PubMed - as supplied by publisher]




Competitive exclusion reduces transmission and excretion of extended-spectrum β-lactamase producing Escherichia coli in broilers.
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Competitive exclusion reduces transmission and excretion of extended-spectrum β-lactamase producing Escherichia coli in broilers.

Appl Environ Microbiol. 2017 Mar 17;:

Authors: Ceccarelli D, van Essen-Zandbergen A, Smid B, Veldman KT, Boender GJ, Fischer EA, Mevius DJ, van der Goot JA

Abstract
Extended-spectrum β-lactamases (ESBLs) and plasmid mediated AmpC β-lactamases (pAmpC) are enzymes able to hydrolyze a large variety of β-lactam antibiotics, including 3(rd) generation cephalosporins and monobactams. Broilers and broiler meat products can be highly contaminated with ESBL and pAmpC-producing Escherichia coli, also known as extended-spectrum cephalosporins (ESC)-resistant E. coli, and can be a source for human infections. As few data are available on interventions to reduce ESC-resistant E. coli presence in broilers, we used transmission experiments to examine the role of competitive exclusion (CE) on reducing transmission and excretion in broilers. A broiler model to study the transmission of ESC-resistant E. coli was set up. Day-old chickens were challenged with an ESBL-producing E. coli strain isolated from healthy broilers in the Netherlands. Challenged and not challenged chicks were housed together in pairs or in groups and ESBL-producing E. coli transmission was monitored via selective culturing of cloacal swabs. Statistically significant reduction compared to untreated controls was observed in both transmission and excretion of ESBL-producing E. coli when chicks were treated with probiotic flora before E. coli challenge. In conclusion, our results support the use of competitive exclusion as an intervention strategy to control ESC-resistant E. coli in the field.Importance Extended spectrum beta-lactamases (ESBL) and AmpC-plasmid mediated β-lactamases are a primary cause of resistance to beta-lactam antibiotics among members of the family Enterobacteriaceae in humans, animals and the environment. Food producing animals are not exempt from this, with high prevalence in broilers, and there is evidence pointing at a possible food-borne source for human contamination. We investigated the effect of administration of commercial probiotic product as intervention to reduce the amount of ESBL-producing Escherichia coli in broilers. Our results showed a substantial reduction in the colonization of broiler intestines by ESBL-producing E. coli after administration of a commercial probiotic product. The protective effect provided by these probiotics could be implemented on a larger scale in the poultry production. Reduction of ESBL-producing Enterobacteriaceae in the food chain would considerably benefit the public health.

PMID: 28314728 [PubMed - as supplied by publisher]




Transcriptomic Analyses Elucidate Adaptive Differences of Closely-Related Strains of P. aeruginosa in Fuel.
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Transcriptomic Analyses Elucidate Adaptive Differences of Closely-Related Strains of P. aeruginosa in Fuel.

Appl Environ Microbiol. 2017 Mar 17;:

Authors: Gunasekera TS, Bowen LL, Zhou CE, Howard-Byerly SC, Foley WS, Striebich RC, Dugan LC, Ruiz ON

Abstract
Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have varying degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons while strain PAO1, a human pathogen, is less-adapted and degrades jet fuel at a slower rate than does ATCC 33988. We investigated fuel specific transcriptomic differences between these strains in order to ascertain the underling mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat-shock response, membrane proteins, efflux pumps and several novel genes were upregulated in ATCC 33988. Overexpression of alk genes in PAO1 provided some improvement in growth, but not as robust as that of ATCC 33988, suggesting the role of other genes in adaptation. Expression of the function unknown gene PA5359 from ATCC 33988 in PAO1 increased the growth in fuel. Bioinformatic analysis revealed that PA5359 is a predicted lipoprotein with a conserved 'Yx(FWY)xxD' motif, which is shared among bacterial adhesins. Overexpression of the putative RND-efflux pump PA3521-PA3523 increased the growth of ATCC 33988 strain suggesting a possible role in fuel tolerance. Interestingly the PAO1 strain cannot utilize nC8 and nC10. Expression of GFP under the control of alkB promoters confirmed that alk gene promoter polymorphism affects the expression of alk genes. Promoter fusion assays further confirmed that regulation of alk genes was different in the two strains. Protein sequence analysis showed low amino acid differences for many of the upregulated genes, further supporting transcriptional control as the main mechanism for enhanced adaptation.IMPORTANCE These results support that specific signal transduction, gene regulation and coordination of multiple biological responses are required to improve survival, growth and metabolism of fuel in adapted strains. This study provides new insight into the mechanistic differences between strains and helpful information that may be applied in the improvement of bacterial strains for resistance to biotic and abiotic factors encountered during bioremediation and industrial biotechnological processes.

PMID: 28314727 [PubMed - as supplied by publisher]




Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3).
Related Articles Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). Appl Environ Microbiol. 2017 Mar 17;: Authors: Farag IF, Youssef NH, Elshahed MS Abstract We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic datasets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene datasets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of "Latescibacteria"-affiliated contigs in publicly available metagenomic datasets comprising 73,079 proteins. Metabolic reconstruction suggests a prevalent saprophytic lifestyle in all "Latescibacteria" orders, with marked capacities for the degradation of proteins, lipids, and polysaccharides predominant in plant, bacterial, fungal/crustacean, and eukaryotic algal cell walls. As well, extensive transport and central metabolic pathways for the metabolism of imported monomers were identified. Interestingly, genes and domains suggestive of the production of a cellulosome, e.g. protein-coding genes harboring dockerin I domains attached to a glycosyl hydrolase, and scaffoldin-encoding genes harboring cohesin I and CBM37 domains, were identified in orders PBSIII_9, GN03, and MSB-4E2 fragments recovered from four anoxic aquatic habitats; hence extending the cellulosomal production capabilities in Bacteria beyond the Gram-positive Firmicutes. In addition to fermentative pathways, a complete electron transport chain with terminal cytochrome C oxidases Caa3 (for operation under high oxygen tension), and Cbb3 (for operation under low oxygen tension) were identified in PBSIII_9, and GN03 fragments recovered from oxygenated, and partially/seasonally oxygenated aquatic habitats. Our metagenomic recruitment effort hence represents a comprehensive pangenomic view of this yet-uncultured phylum, and provides broader and complimentary insights to those gained from genome recovery initiatives focusing on a single or few sampled environments.Importance Our understanding of the phylogenetic diversity, metabolic capabilities, and ecological roles of yet-uncultured microorganisms is rapidly expanding. However, recent efforts mainly been focused on recovering genomes of novel microbial lineages from a specific sampling site, rather from a wide range of environmental habitats. To comprehensively evaluate the genomic landscape, putative metabolic capabilities, and ecological roles of yet-uncultured candidate phyla, efforts that focus on the recovery of genomic fragments from a wide range of habitats and that adequately sample the intra-phylum diversity within a specific target lineage are needed. Here, we investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria". Our results document the preference of specific "Latescibacteria" orders to specific habitats, the prevalence of plant polysaccharide degradation abilities within all "Latescibacteria" orders, the occurrence of all genes/domains necessary for the production of cellulosome within three "Latescibacteria" orders (GN03, PBSIII_9, and MSB-4E2) in datasets recovered from anaerobic locations, and the identification of the components of an aerobic respiratory chain, as well as occurrence of multiple O2 dependent metabolic reactions in "Latescibacteria" orders GN03 and PBSIII_9 recovered from oxygenated habitats. The results demonstrate the value of phylocentric pangenomic surveys for understanding the global ecological distribution and pan-metabolic abilities of yet-uncultured microbial lineages since they provide broader and complimentary in[...]



A genome survey and postharvest transcriptome analysis in Lentinula edodes.
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A genome survey and postharvest transcriptome analysis in Lentinula edodes.

Appl Environ Microbiol. 2017 Mar 17;:

Authors: Sakamoto Y, Nakade K, Sato S, Yoshida K, Miyazaki K, Natsume S, Konno N

Abstract
Lentinula edodes is a popular cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction of Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and long reads by PacBio, resulting in a contig number of 1951 and an N50 of 1 Mb. Further, we predicted genes by Augustus using RNA-seq data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes. This analysis revealed that Lentinula edodes lacks lignin peroxidase. To reveal genes involved in Lentinula edodes postharvest fruiting body quality loss, transcriptome analysis was carried out using Super-SAGE. This analysis revealed that many cell wall-related enzymes are upregulated after harvest, such as β-1,3-1,6-glucan-degrading enzymes in glycoside hydrolase (GH) families 5, 16, 30, 55, 128, and thaumatin-like proteins. In addition, we found several chitin-related genes are upregulated, such as putative chitinases in GH family18, exo-chitinases in GH 20, and a putative chitosanase in GH 75. The results suggest that cell wall-degrading enzymes synergistically cooperate for rapid fruiting body autolysis. Many putative transcription factor genes were upregulated postharvest, such as genes containing high mobility group (HMG) domains and zinc finger domains. Several cell death-related proteins were also upregulated postharvest.Importance Our data collectively suggest that there is a rapid fruiting body autolysis system in Lentinula edodes The genes for postharvest quality loss newly found in this research will be targets for future breeding of strains that can keep freshness longer than present strains. De novo Lentinula edodes genome assembly data will be used for construction of the complete Lentinula edodes chromosome map for the future breeding.

PMID: 28314725 [PubMed - as supplied by publisher]




Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment.
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Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment.

Appl Environ Microbiol. 2017 Mar 17;:

Authors: Lipsewers YA, Vasquez-Cardenas D, Seitaj D, Schauer R, Hidalgo Martinez S, Sinninghe Damsté JS, Meysman FJ, Villanueva L, Boschker HT

Abstract
Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyze these reoxidation reactions, is rarely studied. Here we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria (Thiotrichales) and Epsilonproteobacteria (Campylobacterales) were prevalent during spring, whereas Deltaproteobacteria (Desulfobacterales) related to sulfate reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring compared to summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae. The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment probably driven by the availability of reduced sulfur compounds (H2S, S(0), S2O3(-2)) and electron acceptors (O2, NO3(-)) regulated by seasonal hypoxia.IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors like oxygen and nitrate that diffuse from the overlying water. Seasonal hypoxia however drastically changes the availability of these electron acceptors in the bottom water, and hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A multidisciplinary investigation of the sediments in a seasonally hypoxic coastal basin confirms this hypothesis. Our data show that bacterial community structure and the chemolithoautotrophic activity varied with the seasonal depletion of oxygen. Unexpectedly, the dark carbon fixation was also dependent on the dominant microbial pathway of sulfur oxidation occurring in the sediment (i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae). These results suggest that a complex niche partitioning within the sulfur-oxidizing bacterial community additionally affects the chemolithoautotrophic community of seasonally hypoxic sediments.

PMID: 28314724 [PubMed - as supplied by publisher]