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Asset Tag: Bacteria

April 21, 2020

Emergence of an Escherichia coli strain co-harbouring mcr-1 and blaNDM-9 from a urinary tract infection in Taiwan.

Multidrug-resistant bacteria have become a serious threat worldwide. In particular, the coexistence of carbapenemase genes and mcr-1 leaves few available treatment options. Here we report a multidrug-resistant Escherichia coli isolate harbouring both mcr-1 and blaNDM-9 from a patient with a urinary tract infection.Antimicrobial susceptibility and resistance genes of the E. coli isolate were characterised. Furthermore, the assembled genome sequences of mcr-1- and blaNDM-9-carrying plasmids were determined and comparative genetic analysis with closely related plasmids was carried out.Three contigs were assembled comprising the E. coli chromosome and two plasmids harbouring mcr-1 (p5CRE51-MCR-1) and blaNDM-9 (p5CRE51-NDM-9), respectively. Whole-genome sequencing revealed that the two antimicrobial resistance genes are located on individual plasmids.The emergence of coexistence of carbapenemase genes and mcr-1 in Enterobacteriaceae highlights a serious threat to antimicrobial therapy.Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

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April 21, 2020

Comparative analysis of KPC-2-encoding chimera plasmids with multi-replicon IncR:IncpA1763-KPC:IncN1 or IncFIIpHN7A8:IncpA1763-KPC:IncN1.

IncR, IncFII, IncpA1763-KPC, and IncN1 plasmids have been increasingly found among Enterobacteriaceae species, but plasmids with hybrid structures derived from the above-mentioned incompatibility groups have not yet been described.Plasmids p721005-KPC, p504051-KPC, and pA3295-KPC were fully sequenced and compared with previously sequenced related plasmids pHN84KPC (IncR), pKPHS2 (IncFIIK), pKOX_NDM1 (IncFIIY), pHN7A8 (IncFIIpHN7A8), and R46 (IncN1).The backbone of p721005-KPC/p504051-KPC was a hybrid of the entire 10-kb IncR-type backbone from pHN84KPC, the entire 64.3-kb IncFIIK-type maintenance, and conjugal transfer regions from pKPHS2, a 15.5-kb IncFIIY-type maintenance region from pKOX_NDM1 and a 5.6-kb IncpA1763-KPC-type backbone region from pA1763-KPC, and it contained a primary IncR replicon and two auxiliary IncpA1763-KPC and IncN1 replicons. The backbone of pA3295-KPC was a hybrid of a 7.2-kb IncFIIpHN7A8-type backbone region from pHN7A8, the almost entire 33.3-kb IncN1-type maintenance and conjugal transfer regions highly similar to R46, a 26.2-kb IncFIIK-type maintenance regions from pKPHS2, the above 15.5-kb IncFIIY-type maintenance region, and the above 5.6-kb IncpA1763-KPC-type backbone region, and it contained a primary Inc-FIIpHN7A8 replicon and two auxiliary IncpA1763-KPC and IncN1 replicons. Each of p721005-KPC, p504051-KPC, and pA3295-KPC acquired a wealth of accessory modules, carrying a range of intact and residue mobile elements (such as insertion sequences, unit transposons, and integrons) and resistance markers (such as blaKPC, tetA, dfrA, and qnr).In each of p721005-KPC, p504051-KPC, and pA3295-KPC, multiple replicons in coordination with maintenance and conjugation regions of various origins would maintain a broad host range and a stable replication at a steady-state plasmid copy number.

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April 21, 2020

Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities.

Natural product discovery from microorganisms provided important sources for antibiotics, anti-cancer agents, immune-modulators, anthelminthic agents, and insecticides during a span of 50 years starting in the 1940s, then became less productive because of rediscovery issues, low throughput, and lack of relevant new technologies to unveil less abundant or not easily detected drug-like natural products. In the early 2000s, it was observed from genome sequencing that Streptomyces species encode about ten times as many secondary metabolites as predicted from known secondary metabolomes. This gave rise to a new discovery approach-microbial genome mining. As the cost of genome sequencing dropped, the numbers of sequenced bacteria, fungi and archaea expanded dramatically, and bioinformatic methods were developed to rapidly scan whole genomes for the numbers, types, and novelty of secondary metabolite biosynthetic gene clusters. This methodology enabled the identification of microbial taxa gifted for the biosynthesis of drug-like secondary metabolites. As genome sequencing technology progressed, the realities relevant to drug discovery have emerged, the conjectures and misconceptions have been clarified, and opportunities to reinvigorate microbial drug discovery have crystallized. This perspective addresses these critical issues for drug discovery.

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April 21, 2020

Retrospective whole-genome sequencing analysis distinguished PFGE and drug-resistance-matched retail meat and clinical Salmonella isolates.

Non-typhoidal Salmonella is a leading cause of outbreak and sporadic-associated foodborne illnesses in the United States. These infections have been associated with a range of foods, including retail meats. Traditionally, pulsed-field gel electrophoresis (PFGE) and antibiotic susceptibility testing (AST) have been used to facilitate public health investigations of Salmonella infections. However, whole-genome sequencing (WGS) has emerged as an alternative tool that can be routinely implemented. To assess its potential in enhancing integrated surveillance in Pennsylvania, USA, WGS was used to directly compare the genetic characteristics of 7 retail meat and 43 clinical historic Salmonella isolates, subdivided into 3 subsets based on PFGE and AST results, to retrospectively resolve their genetic relatedness and identify antimicrobial resistance (AMR) determinants. Single nucleotide polymorphism (SNP) analyses revealed that the retail meat isolates within S. Heidelberg, S. Typhimurium var. O5- subset 1 and S. Typhimurium var. O5- subset 2 were separated from each primary PFGE pattern-matched clinical isolate by 6-12, 41-96 and 21-81 SNPs, respectively. Fifteen resistance genes were identified across all isolates, including fosA7, a gene only recently found in a limited number of Salmonella and a =95?%?phenotype to genotype correlation was observed for all tested antimicrobials. Moreover, AMR was primarily plasmid-mediated in S. Heidelberg and S. Typhimurium var. O5- subset 2, whereas AMR was chromosomally carried in S. Typhimurium var. O5- subset 1. Similar plasmids were identified in both the retail meat and clinical isolates. Collectively, these data highlight the utility of WGS in retrospective analyses and enhancing integrated surveillance for Salmonella from multiple sources.

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April 21, 2020

Genome Sequence of Bacillus Velezensis W1, A Strain with Strong Acaricidal Activity against Two-Spotted Spider Mite (Tetranychus Urticae)

Bacillus velezensis W1, isolated from two-spotted spider mites that had died naturally, is a patented strain with strong capability to cause mortality of the phytophagous mite Tetranychus urticae. The whole genome of W1 was completely sequenced with a combination of an Illumina Miseq platform (400-bp paired-end) with 2 × 250 bases and a Pacific Biosciences (PaBio) RS II Single Molecule Real Time (SMRT) sequencing platform using a 20 kb SMRTbellTM template library. Here, we report the complete genome sequence of B. velezensis W1, including one circular chromosome of 4,237,431 bp encoding 4,352 genes with GC content of 45.84%, providing insights into the genomic basis of its acaricidal activity and facilitating its application in red spider mite biocontrol.

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April 21, 2020

Multidrug-Resistant Bovine Salmonellosis Predisposing for Severe Human Clostridial Myonecrosis.

BACKGROUND The overuse of antibiotics in animals promotes the development of multidrug-resistance predisposing for severe polymicrobial human infections. CASE REPORT We describe a case of spontaneous clostridial myonecrosis due to ulcerative colonic infection with multidrug-resistant Salmonella enterica subsp. enterica, serotype 4,[5],12: i: -. Serotyping of the colonic Salmonella isolate in the index case and the bovine farm outbreak isolates from where the patient worked indicated they were both serotype I 4,[5],12: i: -, which is linked with a multitude of large reported disease outbreaks. Further analysis revealed that they are highly genetically related and antibiotic susceptibility testing indicated that they are phenotypically identical. CONCLUSIONS Enteritis due to human acquisition of multidrug-resistant Salmonella from cattle led to the invasion and dissemination of Clostridium septicum resulting in devastating myonecrotic disease. This highlights the ramifications of co-existence and evolution of pathogenic bacteria in animals and humans and lends support to reducing the use of antibiotics in animals.

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April 21, 2020

Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208.

Marine Streptomyces sp. CC0208 isolated from the Bohai Bay showed high efficiency of cellulose degradation under optimized fermentation parameters. Also, as one of the bioinformatics-based approaches for the discovery of novel natural product and enzyme effectively, genome mining has been developed and applied widely. Herein, we reported the complete genome sequence of Streptomyces sp. CC0208.Whole-genome sequencing analysis revealed a genome size of 9,325,981?bp with a linear chromosome, GC content of 70.59% and 8487 protein-coding genes. Abundant genes have predicted functions in antibiotic metabolism and enzymes. A 20 enzymes closely associated with cellulose degradation were discovered. A total of 25 biosynthetic gene clusters (BGCs) of secondary metabolites were identified, including diverse classes of natural products. The availability of genome sequence of Streptomyces sp. CC0208 not only will assist in cracking the mechanism of cellulose degradation but also will provide the insights into the significant secondary metabolic potentials for the production of diverse compound classes based on rational strategies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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April 21, 2020

Carbohydrate catabolic capability of a Flavobacteriia bacterium isolated from hadal water.

Flavobacteriia are abundant in many marine environments including hadal waters, as demonstrated recently. However, it is unclear how this flavobacterial population adapts to hadal conditions. In this study, extensive comparative genomic analyses were performed for the flavobacterial strain Euzebyella marina RN62 isolated from the Mariana Trench hadal water in low abundance. The complete genome of RN62 possessed a considerable number of carbohydrate-active enzymes with a different composition. There was a predominance of GH family 13 proteins compared to closely related relatives, suggesting that RN62 has preserved a certain capacity for carbohydrate utilization and that the hadal ocean may hold an organic matter reservoir distinct from the surface ocean. Additionally, RN62 possessed potential intracellular cycling of the glycogen/starch pathway, which may serve as a strategy for carbon storage and consumption in response to nutrient pulse and starvation. Moreover, the discovery of higher glycoside hydrolase dissimilarities among Flavobacteriia, compared to peptidases and transporters, suggested variation in polysaccharide utilization related traits as an important ecophysiological factor in response to environmental alterations, such as decreased labile organic carbon in hadal waters. The presence of abundant toxin exporting, transcription and signal transduction related genes in RN62 may further help to survive in hadal conditions, including high pressure/low temperature.Copyright © 2019 Elsevier GmbH. All rights reserved.

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April 21, 2020

Evolution of Goat’s Rue Rhizobia (Neorhizobium galegae): Analysis of Polymorphism of the Nitrogen Fixation and Nodule Formation Genes

The goat’s rue rhizobia (Neorhizobium galegae) represent a convenient model to study the evolution and speciation of symbiotic bacteria. This rhizobial species is composed of two biovars (bv. orientalis and bv. officinalis), which form N2-fixing nodules with certain species of goat’s rue (Galega orientalis and G. officinalis). The cross-inoculation between them results in the formation of nodules unable to fix nitrogen. On the basis of the data on the whole-genome sequencing, we studied the nucleotide polymorphism of 11 N. galegae strains isolated from the North Caucasus ecosystems, where G. orientalis has higher diversity than G. officinalis. The low level of differences in the polymorphism within the group of the sym genes in comparison with the nonsymbiotic genes can be associated with the active participation of host plants in the evolution of rhizobia. The intragenic polymorphism of bv. orientalis proved to be significantly higher than that of bv. officinalis. The level of polymorphism of nonsymbiotic genes was lower than that of the symbiotic genes, which are functionally more homogeneous. The divergence of the nitrogen fixation genes (nif/fix) is more pronounced than that of the nodule formation genes (nod) in the N. galegae biovars. These facts indicate the leading role of the host-specific nitrogen fixation in the evolution of the studied rizhobial species.

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April 21, 2020

A new variant of mcr-1 identified from an extended-spectrum ß lactamase-producing Escherichia coli.

Plasmid-mediated colistin resistance gene, mcr-1, has been widely reported almost all over the world. The product of the gene, MCR-1, is one of the members of the phosphoethanolamine transferase enzyme family, which can add phosphoethanolamine to lipid A, thus reducing affinity to polymyxins. Isolates carrying mcr-1 gene are often multidrug resistant (MDR), including co-production of MCR-1 and extended spectrum B lactamases (ESBLs) or carbapenemases, resulting in great clinical concerns.

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April 21, 2020

Genetic characterization and potential molecular dissemination mechanism of tet(31) gene in Aeromonas caviae from an oxytetracycline wastewater treatment system.

Recently, the rarely reported tet(31) tetracycline resistance determinant was commonly found in Aeromonas salmonicida, Gallibacterium anatis, and Oblitimonas alkaliphila isolated from farming animals and related environment. However, its distribution in other bacteria and potential molecular dissemination mechanism in environment are still unknown. The purpose of this study was to investigate the potential mechanism underlying dissemination of tet(31) by analysing the tet(31)-carrying fragments in A. caviae strains isolated from an aerobic biofilm reactor treating oxytetracycline bearing wastewater. Twenty-three A. caviae strains were screened for the tet(31) gene by polymerase chain reaction (PCR). Three strains (two harbouring tet(31), one not) were subjected to whole genome sequencing using the PacBio RSII platform. Seventeen A. caviae strains carried the tet(31) gene and exhibited high resistance levels to oxytetracycline with minimum inhibitory concentrations (MICs) ranging from 256 to 512?mg/L. tet(31) was comprised of the transposon Tn6432 on the chromosome of A. caviae, and Tn6432 was also found in 15 additional tet(31)-positive A. caviae isolates by PCR. More important, Tn6432 was located on an integrative conjugative element (ICE)-like element, which could mediate the dissemination of the tet(31)-carrying transposon Tn6432 between bacteria. Comparative analysis demonstrated that Tn6432 homologs with the structure ISCR2-?phzF-tetR(31)-tet(31)-?glmM-sul2 were also carried by A. salmonicida, G. anatis, and O. alkaliphila, suggesting that this transposon can be transferred between species and even genera. This work provides the first report on the identification of the tet(31) gene in A. caviae, and will be helpful in exploring the dissemination mechanisms of tet(31) in water environment.Copyright © 2018. Published by Elsevier B.V.

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April 21, 2020

Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida.

Pasteurella multocida causes respiratory infectious diseases in a multitude of birds and mammals. A number of virulence-associated genes were reported across different strains of P. multocida, including those involved in the iron transport and metabolism. Comparative iron-associated genes of P. multocida among different animal hosts towards their interaction networks have not been fully revealed. Therefore, this study aimed to identify the iron-associated genes from core- and pan-genomes of fourteen P. multocida strains and to construct iron-associated protein interaction networks using genome-scale network analysis which might be associated with the virulence. Results showed that these fourteen strains had 1587 genes in the core-genome and 3400 genes constituting their pan-genome. Out of these, 2651 genes associated with iron transport and metabolism were selected to construct the protein interaction networks and 361 genes were incorporated into the iron-associated protein interaction network (iPIN) consisting of nine different iron-associated functional modules. After comparing with the virulence factor database (VFDB), 21 virulence-associated proteins were determined and 11 of these belonged to the heme biosynthesis module. From this study, the core heme biosynthesis module and the core outer membrane hemoglobin receptor HgbA were proposed as candidate targets to design novel antibiotics and vaccines for preventing pasteurellosis across the serotypes or animal hosts for enhanced precision agriculture to ensure sustainability in food security. Copyright © 2018. Published by Elsevier Ltd.

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April 21, 2020

Integration of two pKPX-2-derived antibiotic resistance islands in the genome of an ESBL-producing Klebsiella pneumoniae ST3483 from Lebanon.

Contamination of fresh water with clinically important Gram-negative bacteria in Lebanon is being investigated in-depth, especially with evidence of dissemination into clinical settings. This study aimed to report the draft genome sequence of a Klebsiella pneumoniae strain with an integrated plasmid segment harbouring two antibiotic resistance islands (ARI). It is believed that this is the first report of plasmid antibiotic resistance islands integration in the genome of K. pneumoniae.Whole genome sequencing of the isolate was performed using Sequel platform. The genome was assembled using HGAP4. Analysis was conducted by uploading the sequence to the online databases from the Center for Genomic Epidemiology.The strain had a newly assigned ST 3483 with a genome size of 5385844 bp. The investigation of the antibiotic resistance islands suggested integration of two DNA segments from a previously identified IncFIA plasmid. The results revealed that the integration could have been accomplished either as a single-step integration event, with the two segments being integrated as a whole transposon mediated by the flanking IS26, or through two separate integration events involving the two segments, but independently.The sequenced genome revealed interesting aspects related to antibiotic resistance dissemination. The ARI are more stable in the genome and the chance of losing it is less probable, with the possibility of the described transposon to re-integrate in other plasmids, facilitating the dissemination of such resistance determinants.Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.

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April 21, 2020

Genome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551.

Sphingobium fuliginis ATCC 27551, previously classified as Flavobacterium sp. ATCC 27551, degrades neurotoxic organophosphate insecticides and nerve agents through the activity of a membrane-associated organophosphate hydrolase. This study was designed to determine the complete genome sequence of S. fuliginis ATCC 27551 to unravel its degradative potential and adaptability to harsh environments. The 5,414,624?bp genome with a GC content of 64.4% is distributed between two chromosomes and four plasmids and encodes 5,557 proteins. Of the four plasmids, designated as pSF1, pSF2, pSF3, and pSF4, only two (pSF1 and pSF2) are self-transmissible and contained the complete genetic repertoire for a T4SS. The other two plasmids (pSF3 and pSF4) are mobilizable and both showed the presence of an oriT and relaxase-encoding sequences. The sequence of plasmid pSF3 coincided with the previously determined sequence of pPDL2 and included an opd gene encoding organophosphate hydrolase as a part of the mobile element. About 15,455 orthologous clusters were identified from among the cumulatively annotated genes of 49 Sphingobium species. Phylogenetic analysis done using the core genome consisting of 802 orthologous clusters revealed a close relationship between S. fuliginis ATCC 27551 and bacteria capable of degradation of polyaromatic hydrocarbon compounds. Genes coding for transposases, efflux pumps conferring resistance to heavy metals, and TonR-type outer membrane receptors are selectively enriched in the genome of S. fuliginis ATCC 27551 and appear to contribute to the adaptive potential of the organism to challenging and harsh environments. © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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April 21, 2020

Thermosynechococcus as a thermophilic photosynthetic microbial cell factory for CO2 utilisation.

Thermophilic unicellular cyanobacterium Thermosynechococcus elongatus PKUAC-SCTE542, has been developed as a thermophilic photosynthetic microbial cell factory for CO2 utilisation. The strain exhibits its highest growth rate around 55?°C, can withstand up to 15% CO2, and up to 0.5?M concentration of sodium bicarbonate. The strain is also capable of resisting a 200?ppm concentration of NO and SO2 in simulated flue gasses, and these compounds have a positive effect on its growth. Whole genome sequencing of the strain revealed the presence of numerous forms of active transport of nutrients and additional chaperones acting as the predominant mechanism of strain adaptation to high temperatures. Based on the sequenced genome, two neutral gene insertion sites have been identified and engineered using modular vectors. Site-specific knock-ins and knock-outs have been performed using the spectinomycin resistance gene and proved functional, enabling future application of the strain to produce biofuels and biochemicals from waste CO2. Copyright © 2019 Elsevier Ltd. All rights reserved.

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