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Asset Tag: Bacterial genome

April 21, 2020

The Isolation and Characterization of Kronos, a Novel Caulobacter Rhizosphere Phage that is Similar to Lambdoid Phages.

Despite their ubiquity, relatively few bacteriophages have been characterized. Here, we set out to explore Caulobacter bacteriophages (caulophages) in the rhizosphere and characterized Kronos, the first caulophage isolated from the rhizosphere. Kronos is a member of the Siphoviridae family since it has a long flexible tail. In addition, an analysis of the Kronos genome indicated that many of the predicted proteins were distantly related to those of bacteriophages in the lambdoid family. Consistent with this observation, we were able to demonstrate the presence of cos sites that are similar to those found at the ends of lambdoid phage genomes. Moreover, Kronos displayed a relatively rare head and tail morphology compared to other caulophages but was similar to that of the lambdoid phages. Taken together, these data indicate that Kronos is distantly related to lambdoid phages and may represent a new Siphoviridae genus.

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April 21, 2020

Assembly of long, error-prone reads using repeat graphs.

Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers.

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April 21, 2020

Complete genome sequence of an IMP-8, CTX-M-14, CTX-M-3 and QnrS1 co-producing Enterobacter asburiae isolate from a patient with wound infection.

The aim of this study was to investigate the characteristics and complete genome sequence of an IMP-8, CTX-M-14, CTX-M-3 and QnrS1 co-producing multidrug-resistant Enterobacter asburiae isolate (EN3600) from a patient with wound infection.Species identification was confirmed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Carbapenemase genes were identified by PCR and Sanger sequencing. The complete genome sequence of E. asburiae EN3600 was obtained using a PacBio RS II platform. Genome annotation was done by Rapid Annotation using Subsystem Technology (RAST) server. Acquired antimicrobial resistance genes (ARGs) and plasmid replicons were detected using ResFinder 2.1 and PlasmidFinder 1.3, respectively.The genome of E. asburiae EN3600 consists of a 4.8-Mbp chromosome and five plasmids. The annotated genome contains various ARGs conferring resistance to aminoglycosides, ß-lactams, fluoroquinolones, fosfomycin, macrolides, phenicols, rifampicin and sulfonamides. In addition, plasmids of incompatibility (Inc) groups IncHI2A, IncFIB(pECLA), IncFIB(pQil) and IncP1 were identified. The genes blaIMP-8, blaCTX-M-14 and blaCTX-M-3 were located on different plasmids. The blaIMP-8 gene was carried by an 86-kb IncFIB(pQil) plasmid. The blaCTX-M-3 and qnrS1 genes were co-harboured by an IncP1 plasmid. In addition, blaCTX-M-14 was associated with blaTEM-1B, blaOXA-1, catB3 and sul1 genes in a 116-kb non-typeable plasmid.To our knowledge, this is the first complete genome sequence of an E. asburiae isolate co-producing IMP-8, CTX-M-14, CTX-M-3 and QnrS1. This genome may facilitate the understanding of the resistome, pathogenesis and genomic features of Enterobacter cloacae complex (ECC) and will provide valuable information for accurate identification of ECC.Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.

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April 21, 2020

Complete genome sequence of the novel agarolytic Catenovulum-like strain CCB-QB4

Members of the genus Catenovulum are recognized for their ability to degrade algal biomass. Here we report the complete genome of Cantenovulum–like strain CCB-QB4, an agarolytic bacterium isolated from the coastal area of Penang, Malaysia. The sequenced genome is composed of a 5,663,044?bp circular chromosome and a 208,085?bp circular plasmid. It contained 4409 protein coding and 83 RNA genes, including 62 tRNAs and 21 rRNAs. The genome of CCB-QB4 contains many agarases, which correlate with the high capacity of the strain to degrade agar. Genome sequencing of CCB-QB4 reveals gene candidates of potential interest in enzymatic industries or applications in the field of polysaccharides degradation.

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April 21, 2020

The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification.

When choosing antibiotics to treat bacterial infections, it is assumed that the susceptibility of the target bacteria to an antibiotic is reflected by laboratory estimates of the minimum inhibitory concentration (MIC) needed to prevent bacterial growth. A caveat of using MIC data for this purpose is heteroresistance, the presence of a resistant subpopulation in a main population of susceptible cells. We investigated the prevalence and mechanisms of heteroresistance in 41 clinical isolates of the pathogens Escherichia coli, Salmonella enterica, Klebsiella pneumoniae and Acinetobacter baumannii against 28 different antibiotics. For the 766 bacteria-antibiotic combinations tested, as much as 27.4% of the total was heteroresistant. Genetic analysis demonstrated that a majority of heteroresistance cases were unstable, with an increased resistance of the subpopulations resulting from spontaneous tandem amplifications, typically including known resistance genes. Using mathematical modelling, we show how heteroresistance in the parameter range estimated in this study can result in the failure of antibiotic treatment of infections with bacteria that are classified as antibiotic susceptible. The high prevalence of heteroresistance with the potential for treatment failure highlights the limitations of MIC as the sole criterion for susceptibility determinations. These results call for the development of facile and rapid protocols to identify heteroresistance in pathogens.

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April 21, 2020

Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis.

Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K.?pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K.?pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K.?pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.

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April 21, 2020

Complete genome sequence of Pseudomonas frederiksbergensis ERDD5:01 revealed genetic bases for survivability at high altitude ecosystem and bioprospection potential.

Pseudomonas frederiksbergensis ERDD5:01 is a psychrotrophic bacteria isolated from the glacial stream flowing from East Rathong glacier in Sikkim Himalaya. The strain showed survivability at high altitude stress conditions like freezing, frequent freeze-thaw cycles, and UV-C radiations. The complete genome of 5,746,824?bp circular chromosome and a plasmid of 371,027?bp was sequenced to understand the genetic basis of its survival strategy. Multiple copies of cold-associated genes encoding cold active chaperons, general stress response, osmotic stress, oxidative stress, membrane/cell wall alteration, carbon storage/starvation and, DNA repair mechanisms supported its survivability at extreme cold and radiations corroborating with the bacterial physiological findings. The molecular cold adaptation analysis in comparison with the genome of 15 mesophilic Pseudomonas species revealed functional insight into the strategies of cold adaptation. The genomic data also revealed the presence of industrially important enzymes.Copyright © 2018 Elsevier Inc. All rights reserved.

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April 21, 2020

Phylogenetic relationships and regional spread of meningococcal strains in the meningitis belt, 2011-2016.

Historically, the major cause of meningococcal epidemics in the meningitis belt of sub-Saharan Africa has been Neisseria meningitidis serogroup A (NmA), but the incidence has been substantially reduced since the introduction of a serogroup A conjugate vaccine starting in 2010. We performed whole-genome sequencing on isolates collected post-2010 to assess their phylogenetic relationships and inter-country transmission.A total of 716 invasive meningococcal isolates collected between 2011 and 2016 from 11 meningitis belt countries were whole-genome sequenced for molecular characterization by the three WHO Collaborating Centers for Meningitis.We identified three previously-reported clonal complexes (CC): CC11 (n?=?434), CC181 (n?=?62) and CC5 (n?=?90) primarily associated with NmW, NmX, and NmA, respectively, and an emerging CC10217 (n?=?126) associated with NmC. CC11 expanded throughout the meningitis belt independent of the 2000 Hajj outbreak strain, with isolates from Central African countries forming a distinct sub-lineage within this expansion. Two major sub-lineages were identified for CC181 isolates, one mainly expanding in West African countries and the other found in Chad. CC10217 isolates from the large outbreaks in Nigeria and Niger were more closely related than those from the few cases in Mali and Burkina Faso.Whole-genome based phylogenies revealed geographically distinct strain circulation as well as inter-country transmission events. Our results stress the importance of continued meningococcal molecular surveillance in the region, as well as the development of an affordable vaccine targeting these strains. FUND: Meningitis Research Foundation; CDC’s Office of Advanced Molecular Detection; GAVI, the Vaccine Alliance. Copyright © 2019. Published by Elsevier B.V.

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April 21, 2020

Complete genome sequence of Paracoccus denitrificans ATCC 19367 and its denitrification characteristics.

Studies show that Paracoccus denitrificans can denitrify nitrogen sources under aerobic conditions. However, the lack of data on its genome sequence has restricted molecular studies and practical applications. In this study, the complete genome of P. denitrificans ATCC 19367 was sequenced and its nitrogen metabolism properties were characterized. The size of the whole genome is 5?242?327 bp, with two chromosomes and one plasmid. The average G + C content is 66.8%, and it contains 5308 protein-coding genes, 54 tRNA genes, and nine rRNA operons. Among the protein-coding genes, 71.35% could be assigned to the Gene Ontology (GO) pathway, 86.66% to the Clusters of Orthologous Groups (COG) pathway, and 50.57% to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Comparative genome analysis between P. denitrificans ATCC 19367 and P. denitrificans PD1222 revealed that there are 428 genes specific to ATCC 19367 and 4738 core genes. Furthermore, the expression of genes related to denitrification, biofilm formation, and nitrogen metabolism (nar, nir, and nor) by P. denitrificans ATCC 19367 under aerobic conditions was affected by incubation time and shaking speed. This study elucidates the genomic background of P. denitrificans ATCC 19367 and suggests the possibility of controlling nitrogen pollution in the environment by using this bacterium.

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April 21, 2020

Complete Genome Sequence of Lactic Acid Bacterium Pediococcus acidilactici Strain ATCC 8042, an Autolytic Anti-bacterial Peptidoglycan Hydrolase Producer

Pediococcus acidilactici is a probiotic bacterium that is industrially utilized in the food industry and antibiotics development. Here, we determine the complete nucleotide sequence of the genome of Pediococcus acidilactici ATCC 8042. The genome was sequenced by the PacBio RSII to generate a single contig consisting of circular chromosome sequence. Illumina MiniSeq sequencing platform and Sanger sequencing method were additionally utilized to correct errors resulting from the long-read sequencing platform. The sequence consists of 2,009,598 bp with a G + C content of 42.1% and contains 1,865 protein-coding sequences. Based on the sequence information, we could confirm and predict the presence of four peptidoglycan hydrolases by HyPe software. This work, therefore, provides the complete genomic information of P. acidilactici ATCC 8042 with a profitable potential of genome-scale comprehension of anti-pathogenic activity, which can be applied in nutraceutical and pharmaceutical biotechnology field.

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April 21, 2020

Genetic Analysis of p17S-208 Plasmid Encoding the Colistin Resistance mcr-3 Gene in Escherichia coli Isolated from Swine in South Korea.

We screened, for the first time, plasmid-mediated colistin resistance mcr-3 genes among 636 Escherichia coli isolates collected from swine in South Korea. Whole-genome sequencing showed that the E. coli strain harbored the mcr-3 gene in a p17S-208 plasmid with an IncHI2-ST3 plasmid type and a size of 260,399 base pairs. The deduced amino acid sequences revealed that persistent evolution in the bacterial genome has resulted in mcr gene variants. There is a need for extensive surveillance to prevent the dissemination of colistin resistance mcr genes from animal to human.

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April 21, 2020

Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.

The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.

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April 21, 2020

Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp.

Plant-beneficial Pseudomonas spp. competitively colonize the rhizosphere and display plant-growth promotion and/or disease-suppression activities. Some strains within the P. fluorescens species complex produce phenazine derivatives, such as phenazine-1-carboxylic acid. These antimicrobial compounds are broadly inhibitory to numerous soil-dwelling plant pathogens and play a role in the ecological competence of phenazine-producing Pseudomonas spp. We assembled a collection encompassing 63 strains representative of the worldwide diversity of plant-beneficial phenazine-producing Pseudomonas spp. In this study, we report the sequencing of 58 complete genomes using PacBio RS II sequencing technology. Distributed among four subgroups within the P. fluorescens species complex, the diversity of our collection is reflected by the large pangenome which accounts for 25 413 protein-coding genes. We identified genes and clusters encoding for numerous phytobeneficial traits, including antibiotics, siderophores and cyclic lipopeptides biosynthesis, some of which were previously unknown in these microorganisms. Finally, we gained insight into the evolutionary history of the phenazine biosynthetic operon. Given its diverse genomic context, it is likely that this operon was relocated several times during Pseudomonas evolution. Our findings acknowledge the tremendous diversity of plant-beneficial phenazine-producing Pseudomonas spp., paving the way for comparative analyses to identify new genetic determinants involved in biocontrol, plant-growth promotion and rhizosphere competence. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

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April 21, 2020

Identification and pathogenicity of an XDR Streptococcus suis isolate that harbours the phenicol-oxazolidinone resistance genes optrA and cfr, and the bacitracin resistance locus bcrABDR.

One hundred and seven Streptococcus suis isolates were collected from healthy pigs or asymptomatic carriers in Jiangsu, China in 2016-2017. Thirty-eight percent of the isolates were linezolid-resistant and all carried the optrA gene. Among them, one isolate, SFJ44, was resistant to all 20 of the antibiotics tested, except for ceftiofur, and thus exhibited an extensively-drug-resistant phenotype. This isolate carried the optrA gene and the bacitracin resistance locus bcrABDR on an antibiotic-resistance-associated genomic island (ARGI1), and harboured the resistance genes cfr, aadE, sat4, spw-like, aphA3, mef(A), msr(D), erm(A)-like, erm(B), tetAB(P)’, tet(M) and catQ on ARGI2~4. The IS1216E-bcrABDR-ISEnfa1 segment showed >99.9% sequence identity to corresponding sequences from other species. The cfr gene was located on ARGI4, and two IS6 family insertion sequences, IS1216E and ISTeha2, were found upstream and downstream of cfr-?ISEnfa5, respectively. A circular intermediate of bcrABDR-ISEnfa1 was detected, suggesting the role of ISEnfa1 in dissemination of bcrABDR. Other antibiotic resistance genes might be acquired from different Gram-positive pathogens. Infection of zebrafish showed that SFJ44 exhibited a virulence level comparable to serotype 2 hypervirulent strain SC070731, highlighting the need for surveillance of the pathogenicity of multi-drug-resistant S. suis isolates. This is the first report of the co-existence of optrA and cfr, and of the bcrABDR locus in streptococci. As it has been suggested that S. suis may act as an antibiotic resistance reservoir contributing to the spread of resistance genes to major streptococcal pathogens, the potential dissemination of these resistance genes among Gram-positive bacteria is of concern and routine surveillance should be strengthened.Copyright © 2019 Elsevier Ltd. All rights reserved.

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April 21, 2020

Genome mining and metabolic profiling illuminate the chemistry driving diverse biological activities of Bacillus siamensis SCSIO 05746.

Bacillus spp. are important producers of bioactive natural products with potential applications in medicine and agriculture. Bacillus sp. SCSIO 05476 from a deep-sea sediment exhibits broad-spectrum antimicrobial activities and strong cytotoxic activity. Here, an integrative approach combining genome mining and metabolic profiling has been applied to decipher the chemical origins of this strain’s varied and significant biological activities. First, genome mining revealed 19 candidate gene clusters encoding the biosynthesis of diverse secondary metabolites. Then, a series of bacillibactins, fengycins, bacillomycins, surfactins, bacillaenes, macrolactins, and related species were found by LC-DAD-MS. Finally, three new linear bacillibactins, linbacillibactins A-C (1-3), along with 11 known secondary metabolites, bacillibactin (4), normal-C13 Val7 surfactin (5), anteiso-C13 Leu7 surfactin (6), iso-C14 Leu7 surfactin (7), normal-C14 Leu7 surfactin (8), anteiso-C14 Leu7 surfactin (9), macrolactin D (10), normal-C14 bacillomycin D (11), iso-C16 bacillomycin D (12), normal-C17 bacillomycin D (13), and iso-C17 bacillomycin D (14), were obtained and elucidated by bioactivity and structure-guided isolation from the fermentation of strain SCSIO 05746. Among them, new compounds 1-3 show significant siderophore activities comparable to that of bacillibactin (4), compounds 13 and 14 exhibit strong cytotoxic activity. At the same time, the strain classification status was confirmed by genomic analyses, and the complete genome sequence of Bacillus siamensis was presented firstly. This study provides a foundation for understanding the mechanisms driving SCSIO 05746’s multiple bioactivities and demonstrates a successful way of discovering bioactive metabolites using a combination of genome mining and metabolic profiling methods.

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