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Asset Tag: Bacterial genome

April 21, 2020

Antimicrobial, plant growth-promoting and genomic properties of the peanut endophyte Bacillus velezensis LDO2.

Peanut suffer from a number of fungal and bacterial pathogens, while plant endophytes were considered excellent candidates as biocontrol agents. In this study, the peanut endophytic bacterium LDO2 was evaluated for the potential of peanut pathogens inhibition and growth-promotion, and the genetic mechanisms were explored by genome mining. Strain LDO2 significantly inhibited the growth of peanut pathogenic fungi and pathogenic bacteria, and specifically, it showed pronounced inhibition on mycelia growth of Aspergillus flavus mycelia and caused mycelial deformity. Gene clusters responsible for antifungal metabolites (fengycin, surfactin, bacilysin) and antibacterial metabolites (butirosin, bacillaene, difficidin, macrolactin, surfactin, bacilysin) were identified. Strain LDO2 also exhibited several growth-promoting related features including phosphate solubilization, siderophore production and growth promotion of peanut root. Genes associated with plant growth promotion were also identified and analyzed, as well as genes related to secreted proteins. These findings suggested that this peanut endophyte could be a potential biocontrol agent in peanut production and a source of antimicrobial compounds for further exploitation. Copyright © 2018 Elsevier GmbH. All rights reserved.

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April 21, 2020

Distribution and characterization of N-acylhomoserine lactone (AHL)-degrading activity and AHL lactonase gene (qsdS) in Sphingopyxis.

N-Acylhomoserine lactone (AHL)-degrading enzyme is identified from the various environments and applied for quorum-sensing inhibition. In this study, we isolated two AHL-degrading strains, Sphingopyxis sp. EG6 and FD7, from the industrial cooling water samples. When the eight Sphingopyxis type strains were checked for the AHL-degrading activity, two strains, Sphingopyxis alaskensis DSM 13593 and Sphingopyxis bauzanensis DSM 22271, showed high AHL-degrading activity. The complete genome sequences of EG6 and FD7 revealed the presence of gene homolog of qsdS, which encodes AHL-lactonase in Sphingomonas ursincola. The qsdS gene is seated between putative gene homologs involved in 3-isopropylmalate dehydratase large (leuC2) and small (leuD) subunits in the genome of EG6, FD7, DSM 13593, and DSM 22271, but completely disappeared between leuC2 and leuD in the genome sequences of Sphingopyxis type strains without AHL-degrading activity. Purified His-tagged QsdS showed high AHL-degrading activity and catalyzed AHL ring opening by hydrolyzing lactones. In addition, heterologous expression of qsdS in Pseudomonas aeruginosa resulted in reduction of biofilm formation. These results suggested that the AHL-degrading activity in Sphingopyxis is useful as an effective agent for biofilm inhibition.Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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April 21, 2020

Evolution and transmission of a conjugative plasmid encoding both ciprofloxacin and ceftriaxone resistance in Salmonella.

Ceftriaxone and ciprofloxacin are the drugs of choice in treatment of invasive Salmonella infections. This study discovered a novel type of plasmid, pSa44-CIP-CRO, which was recovered from a S. London strain isolated from meat product and comprised genetic determinants that encoded resistance to both ciprofloxacin and ceftriaxone. This plasmid could be resolved into two daughter plasmids and co-exist with such daughter plasmids in a dynamic form in Salmonella; yet it was only present as a single plasmid in Escherichia coli. One daughter plasmid, pSa44-CRO, was found to carry the blaCTX-M-130 gene, which encodes resistance to ceftriaxone, whereas the other plasmid, pSa44-CIP, carried multiple PMQR genes such as qnrB6-aac(6′)-Ib-cr, which mediated resistance to ciprofloxacin. These two daughter plasmids could be integrated into one single plasmid through ISPa40 mediated homologous recombination. Mouse infection and treatment experiments showed that carriage of plasmid, pSa44-CIP-CRO by S. typhimurium led to the impairment of treatment by ciprofloxacin or cefitiofur, a veterinary drug with similar properties as ceftriaxone. In conclusion, dissemination of such conjugative plasmids impairs current choices of treatment for life-threatening Salmonella infection and hence constitutes a serious public health threat.

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April 21, 2020

Bioinformatic analysis of the complete genome sequence of Pectobacterium carotovorum subsp. brasiliense BZA12 and candidate effector screening

AbstractPectobacterium carotovorum subsp. brasiliense (Pcb) is a gram-negative, plant pathogenic bacterium of the soft rot Enterobacteriaceae (SRE) family. We present the complete genome sequence of Pcb strain BZA12, which reveals that Pcb strain BZA12 carries a single 4,924,809 bp chromosome with 51.97% GC content and comprises 4508 predicted protein-coding genes.Geneannotationofthese genes utilizedGO, KEGG,and COG databases.Incomparison withthree closely related soft-rot pathogens, strain BZA12 has 3797 gene families, among which 3107 gene families are identified as orthologous with those of both P. carotovorum subsp. carotovorum PCC21 and P. carotovorum subsp. odoriferum BCS7, as well as 36 putative Unique Gene Families. We selected five putative effectors from the BZA12 genome and transiently expressed them in Nicotiana benthamiana. Candidate effector A12GL002483 was localized in the cell nucleus and induced cell death. This study provides a foundation for a better understanding of the genomic structure and function of Pcb, particularly in the discovery of potential pathogenic factors and for the development of more effective strategies against this pathogen.

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April 21, 2020

Whole genome sequencing used in an industrial context reveals a Salmonella laboratory cross-contamination.

In 2013, during a routine laboratory analysis performed on food samples, one finished product from a European factory was tested positive for Salmonella Hadar. At the same period, one environmental isolate in the same laboratory was serotyped Salmonella Hadar. Prior to this event, the laboratory performed a proficiency testing involving a sample spiked with NCTC 9877 Salmonella Hadar. The concomitance of Salmonella Hadar detection led to the suspicion of a laboratory cross-contamination between the Salmonella Hadar isolate used in the laboratory proficiency testing and the Salmonella Hadar isolate found on the finished product by the same laboratory. Since the classical phenotypic serotyping method is able to attribute a serotype to Salmonella isolates with a common antigenic formula, but cannot differentiate strains of the same serotype within the subspecies, whole genome sequencing was used to test the laboratory cross-contamination hypothesis. Additionally, 12 Salmonella Hadar from public databases, available until the time of the event, were included in the whole genome sequencing analysis to better understand the genomic diversity of this serotype in Europe. The outcome of the analysis showed a maximum of ten single nucleotide polymorphisms (SNPs) between the isolates coming from the laboratory and the finished product, and thus confirmed the laboratory cross-contamination. These results combined with all additional investigations done at the factory, allowed to release finished product batches produced and thus circumvented unnecessary food waste and economic losses for the factory. Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.

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April 21, 2020

Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces.

A Gram-stain-positive, obligately anaerobic, non-motile, nonspore-forming, and rod-shaped bacterial strain, designated KGMB01110T, was isolated from a faecal sample of a healthy male in South Korea. Phylogenetic analysis based on 16S rRNA gene showed that strain KGMB01110T belonged to Clostridium cluster XIVa and was most closely related to Mediterraneibacter glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB01110T based on its whole genome sequence was 44.1 mol%. The major cellular fatty acids (> 10%) of the isolate were C14:0 and C16:0. The strain KGMB01110T was positive for arginine dihydrolase, ß-galactosidase-6-phosphatase, and alkaline phosphatase. The strain KGMB01110T also produced acid from D-glucose and D-rhamnose, and hydrolyzed gelatin and aesculin. Furthermore, HPLC analysis and UV-tests of culture supernatant revealed that the strain KGMB01110T produced butyrate as the major end product of glucose fermentation. Based on the phylogenetic and phenotypic characteristics, strain KGMB01110T represent a novel species of the genus Mediterraneibacter in the family Lachnospiraceae. The type strain is KGMB01110T (= KCTC 15684T = CCUG 72830T).

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April 21, 2020

Novel trimethoprim resistance gene dfrA34 identified in Salmonella Heidelberg in the USA.

Trimethoprim/sulfamethoxazole is a synthetic antibiotic combination recommended for the treatment of complicated non-typhoidal Salmonella infections in humans. Resistance to trimethoprim/sulfamethoxazole is mediated by the acquisition of mobile genes, requiring both a dfr gene (trimethoprim resistance) and a sul gene (sulfamethoxazole resistance) for a clinical resistance phenotype (MIC =4/76?mg/L). In 2017, the CDC investigated a multistate outbreak caused by a Salmonella enterica serotype Heidelberg strain with trimethoprim/sulfamethoxazole resistance, in which sul genes but no known dfr genes were detected.To characterize and describe the molecular mechanism of trimethoprim resistance in a Salmonella Heidelberg outbreak isolate.Illumina sequencing data for one outbreak isolate revealed a 588?bp ORF encoding a putative dfr gene. This gene was cloned into Escherichia coli and resistance to trimethoprim was measured by broth dilution and Etest. Phylogenetic analysis of previously reported dfrA genes was performed using MEGA. Long-read sequencing was conducted to determine the context of the novel dfr gene.The novel dfr gene, named dfrA34, conferred trimethoprim resistance (MIC =32?mg/L) when cloned into E. coli. Based on predicted amino acid sequences, dfrA34 shares less than 50% identity with other known dfrA genes. The dfrA34 gene is located in a class 1 integron in a multiresistance region of an IncC plasmid, adjacent to a sul gene, thus conferring clinical trimethoprim/sulfamethoxazole resistance. Additionally, dfrA34 is associated with ISCR1, enabling easy transmission between other plasmids and bacterial strains.

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April 21, 2020

Intestinibaculum porci gen. nov., sp. nov., a new member of the family Erysipelotrichaceae isolated from the small intestine of a swine.

A strictly anaerobic, Gram-stain-positive, catalase-negative, non-motile, rod-shaped bacterium, designated SG0102T, was isolated from the small intestine of a swine. Optimal growth occurred at 37°C and pH 7.0. Furthermore, growth was observed in the presence of up to 3% (w/v) NaCl but not at salinity levels higher than 4%. The comparative analysis of 16S rRNA gene sequences showed that strain SG0102T was most closely related to Kandleria vitulina DSM 20405T (93.3%), followed by Catenibacterium mitsuokai KCTC 5053T (91.1%), Sharpea azabuensis KCTC 15217T (91.0%), and Eggerthia catenaformis DSM 5348T (89.6%). The average nucleotide identity values between strain SG0102T and related species, K. vitulina DSM 20405T, C. mitsuokai KCTC 5053T, S. azabuensis KCTC 15217T, and E. catenaformis DSM 5348T, were 71.0, 69.3, 70.0, and 69.2%, respectively. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SG0102T belonged to the family Erysipelotrichaceae in the class Erysipelotrichia. The DNA G + C content of the strain SG0102T was 39.5 mol%. The major cellular fatty acids (> 10%) of strain SG0102T were C16:0, C16:0 dimethyl acetal, and C18:2?9/12c. The cell wall peptidoglycan of strain SG0102T contained the meso-diaminopimelic acid. The strain SG0102T produced lactic acid as a major end product of fermentation. These distinct phenotypic and phylogenetic properties suggest that strain SG0102T represents a novel species in a novel genus of the family Erysipelotrichaceae, for which the name Intestinibaculum porci gen. nov. sp. nov. is proposed. The type strain is SG0102T (= KCTC 15725T = NBRC 113396T).

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April 21, 2020

Transcriptomic response of Escherichia coli O157 isolates on meat: Comparison between a typical Australian isolate from cattle and a pathogenic clinical isolate

The majority of foodborne illnesses associated with E. coli O157 are attributed to the consumption of foods of bovine origin. In this study, RNA-Seq experiments were undertaken with E. coli O157 to identify genes that may be associated with growth and survival on meat and the beef carcass at low temperature. In addition, the response of an E. coli O157 isolate representative of the general genetic ‘type’ found in Australia (E. coli O157:H- strain EC2422) was compared to that of a pathogenic clinical isolate (E. coli O157:H7 strain Sakai) not typically found in Australia. Both strains up-regulated genes involved in the acid stress response, cold shock response, quorum sensing, biofilm formation and Shiga toxin production. Differences were also observed, with E. coli O157:H7 Sakai up-regulating genes playing a critical role in the barrier function of the outer membrane, lipopolysaccharide biosynthesis, extracellular polysaccharide synthesis and curli production. In contrast, E. coli O157:H- EC2422 down-regulated genes involved in peptidoglycan biosynthesis and of the primary envelope stress response Cpx system. The unique gene expression profiles of the strains, indicate that these genotypes may differ in their ability to persist in the meat production environment and therefore also in their ability to cause disease.

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April 21, 2020

Characterization of a Novel Insecticidal Protein Cry9Cb1 from Bacillus thuringiensis.

In recent decades, there have been increasing reports of insect resistance in Bacillus thuringiensis (Bt) crops. Alternative use of Cry toxins, with high insecticidal activity and different mechanisms of action, may be an important strategy to manage this resistance. Cry9 protein, with high toxicity to the lepidopteran pests and no cross-resistance with commercial Cry1 proteins, is a valuable relevant resource. A novel insecticidal protein, MP1489, subsequently named as Cry9Cb1, with 88% amino acid sequence identity with Cry9Ca1, was identified from Bt strain SP663; it exhibited high insecticidal activity against Plutella xylostella, Ostrinia furnacalis, and Chilo suppressalis and no cross-resistance with Cry1Fa in Ostrinia furnacalis. Its minimal active fragments against Plutella xylostella and Ostrinia furnacalis were identified to be 72T-657V and 68D-655A, respectively; food-safety assessment showed no sequence homology with any known allergen and rapid degradation and inactivation by both heat and the gastrointestinal environment. Therefore, Cry9Cb1 is proposed to have a brilliant prospect as an insecticidal protein in agriculture.

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April 21, 2020

Nodule bacteria from the cultured legume Phaseolus dumosus (belonging to the Phaseolus vulgaris cross-inoculation group) with common tropici phenotypic characteristics and symbiovar but distinctive phylogenomic position and chromid.

Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI). CCGE531 and CCGE532 had common phenotypic characteristics with tropici type B rhizobial symbionts. Genome synteny analysis and ANI showed that P. dumosus isolates had different chromids and our analysis suggests that chromids have independently evolved in different lineages of the Rhizobium genus. Finally, we considered that P. dumosus and Phaseolus vulgaris plants belong to the same cross-inoculation group since they have conserved symbiotic affinites for rhizobia.Copyright © 2018 Elsevier GmbH. All rights reserved.

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April 21, 2020

Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation.

A strain of Nocardia isolated from crude oil-contaminated soils in the Qinghai-Tibetan Plateau degrades nearly all components of crude oil. This strain was identified as Nocardia soli Y48, and its growth conditions were determined. Complete genome sequencing showed that N. soli Y48 has a 7.3?Mb genome and many genes responsible for hydrocarbon degradation, biosurfactant synthesis, emulsification and other hydrocarbon degradation-related metabolisms. Analysis of the clusters of orthologous groups (COGs) and genomic islands (GIs) revealed that Y48 has undergone significant gene transfer events to adapt to changing environmental conditions (crude oil contamination). The structural features of the genome might provide a competitive edge for the survival of N. soli Y48 in oil-polluted environments and reflect the adaptation of coexisting bacteria to distinct nutritional niches.Copyright © 2018. Published by Elsevier Inc.

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April 21, 2020

Characterization of an NDM-19-producing Klebsiella pneumoniae strain harboring 2 resistance plasmids from China.

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a major cause of nosocomial infections and posed challenges on clinical treatments. The main objective of this study was to determinate the genetic characteristics of the NDM-19-producing CRKP strain SCM96. From 2015 to 2017, 18 CRKP strains were recovered from sputum samples of patients in respiratory medicine in 6 hospitals from 5 provinces and cities in China. Polymerase chain reaction results for carbapenem resistance genes detection showed strain SCM96 carried blaNDM-19. Three types of transconjugants harboring different plasmids were selected by conjugation experiment. The Whole Genome Sequencing (WGS) was performed using the PacBio RS platform. The genome size of SCM96 was 5,579,775?bp and composed of chromosomal DNA (5,398,745?bp) and 2 plasmids, IncFII type plasmid pSCM96-1 (134,869?bp) and IncX3 type plasmid pSCM96-2 (46,161?bp). SCM96 belonged to ST15 and K28. In addition to the 4 antibiotic resistance genes located in the chromosome, pSCM96-1 carried a complex resistance region containing 17 resistance genes and several mobile genetic elements (MGEs) like ?Tn6029, In4-like integron, and Tn3, and pSCM96-2 had only 1 blaNDM-19 gene. As far as we know, this was the first description of blaNDM-19 in K. pneumoniae. Up to 22 antibiotic resistance genes, several important MGEs, and transferable plasmids might increase the possibility of co-spreading of blaNDM-19 with other resistance genes.Copyright © 2018 Elsevier Inc. All rights reserved.

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April 21, 2020

Marinitoga lauensis sp. nov., a novel deep-sea hydrothermal vent thermophilic anaerobic heterotroph with a prophage.

A novel moderately thermophilic, heterotrophic anaerobe, designated strain LG1T, was isolated from the Mariner deep-sea hydrothermal vent field along the Eastern Lau Spreading Center and Valu Fa Ridge. Cells of strain LG1T were motile rods, occurring singly or in pairs, 0.6µm in width and 1.2µm in length. The strain LG1T grew between 40 and 70°C (optimum 50-55°C), at a pH between 5 and 8 (optimum pH 6.5) and with 7.5-50gL-1 NaCl (optimum 30gL-1). Sulfur, cystine and thiosulfate were reduced to sulfide, and cell yield was improved in the presence of cystine. Strain LG1T was an organotroph able to use a variety of organic compounds. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain LG1T was affiliated to the genus Marinitoga within the order Petrotogales. It shared 95.34-96.31% 16S rRNA gene sequence similarity with strains of other Marinitoga species, and is most closely related to Marinitoga okinawensis. Genome analysis revealed the presence of a prophage sharing high sequence homology with the viruses MPV1, MCV1 and MCV2 hosted by Marinitoga strains. Based on the data from the phylogenetic analyses and the physiological properties of the novel isolate, we propose that strain LG1T is a representative of a novel species, for which the name Marinitoga lauensis sp. nov. is proposed; the type strain is LG1T (=DSM 106824=JCM 32613).Copyright © 2019 Elsevier GmbH. All rights reserved.

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April 21, 2020

Genomic investigation of Staphylococcus aureus recovered from Gambian women and newborns following an oral dose of intra-partum azithromycin.

Oral azithromycin given during labour reduces carriage of bacteria responsible for neonatal sepsis, including Staphylococcus aureus. However, there is concern that this may promote drug resistance.Here, we combine genomic and epidemiological data on S. aureus isolated from mothers and babies in a randomized intra-partum azithromycin trial (PregnAnZI) to describe bacterial population dynamics and resistance mechanisms.Participants from both arms of the trial, who carried S. aureus in day 3 and day 28 samples post-intervention, were included. Sixty-six S. aureus isolates (from 7 mothers and 10 babies) underwent comparative genome analyses and the data were then combined with epidemiological data. Trial registration (main trial): ClinicalTrials.gov Identifier NCT01800942.Seven S. aureus STs were identified, with ST5 dominant (n?=?40, 61.0%), followed by ST15 (n?=?11, 17.0%). ST5 predominated in the placebo arm (73.0% versus 49.0%, P?=?0.039) and ST15 in the azithromycin arm (27.0% versus 6.0%, P?=?0.022). In azithromycin-resistant isolates, msr(A) was the main macrolide resistance gene (n?=?36, 80%). Ten study participants, from both trial arms, acquired azithromycin-resistant S. aureus after initially harbouring a susceptible isolate. In nine (90%) of these cases, the acquired clone was an msr(A)-containing ST5 S. aureus. Long-read sequencing demonstrated that in ST5, msr(A) was found on an MDR plasmid.Our data reveal in this Gambian population the presence of a dominant clone of S. aureus harbouring plasmid-encoded azithromycin resistance, which was acquired by participants in both arms of the study. Understanding these resistance dynamics is crucial to defining the public health drug resistance impacts of azithromycin prophylaxis given during labour in Africa. © The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

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