Adaptation of IncX3 plasmid encoding blaNDM-4 within broad host range: A study from India

Abstract Different variants of blaNDM has been reported across Indian subcontinent within diverse host range of gram negative bacilli. Most of their transferability depends on types of plasmid that encodes resistance determinant. IncX type plasmid is more recently known for carrying carbapenem resistance and NDM-4 variant is considered to have better hydrolytic property. This study aims to investigate the maintenance and stability of blaNDM-4 within BHR and transcriptional response. E.coli of clinical origin that harbor blaNDM-4 within IncX3 plasmid were used. Six different hosts were selected for gene transfer experiment, two strains of E.coli, K.pneumoniae, P.mirabilis, A.baumannii and P.aeruginosa. All the transformants and parent isolate were subjected for stability within new host. IncX3 plasmid encoding blaNDM-4 was transferred in host when imipenem (0.5µg/ml) screen agar was used for selection of transformants which are coharbouring resistance for aminoglycosides and quinolone. Plasmid was successfully expanded within all the six recipients till 55th serial passages. Transcriptional expression with NDM gene was variable for parent isolates though for new hosts it was showing random increased pattern in Proteus, E.coli, and DH5α. This could highlight, external carbapenem pressure helps in maintenance and expression of blaNDM-4 within different host range and epidemiological significance and will help in tracking the genetic vehicle responsible for their transmission,restricting their spread.

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Adaptation of IncX3 plasmid encoding blaNDM-4 within broad host range: A study from India

10.21203/rs.3.rs-18649/v1 ◽

2020 ◽

Author(s):

Nargis Alom Choudhury ◽

Deepjyoti Paul ◽

Bhaskar Jyoti Das ◽

Debadatta Dhar ◽

Amitabha Bhattacharjee

Keyword(s):

Host Range ◽

Indian Subcontinent ◽

Transcriptional Response ◽

Carbapenem Resistance ◽

Broad Host Range ◽

Transcriptional Expression ◽

New Hosts ◽

Epidemiological Significance ◽

Selection Of ◽

Selection Of Transformants

Abstract Background: Different variants of blaNDM have been reported across Indian subcontinent within diverse host range of gram negative bacilli. Most of their transferability depends on types of plasmid that encodes resistance determinant. These plasmids with external sub-inhibitory stress of antibiotics facilitate their propagation and maintenance within broad host range. IncX type plasmid is more recently known for carrying carbapenem resistance and NDM-4 variant is considered to have better hydrolytic property than other variants. Both of these factors interferes with therapeutic outcome in clinical setting. The current study was aimed to investigate the maintenance and stability of blaNDM-4 within broad host range and transcriptional response.Results: IncX3 plasmid encoding blaNDM-4 was successfully transferred in six different host when imipenem (0.5µg/ml) screen agar was used for selection of transformants. It was also found to coharbour resistance for aminoglycosides and quinolone. When checked for stability, it was observed that the plasmid was successfully expanded within all the six recipients for 55th serial passages. Transcriptional expression with IncX3 was random but at consistent level for wild type and without concentration gradient stress of imipenem. Transcriptional expression with NDM gene was variable for parent isolates though for new hosts it was showing randomly increased pattern in proteus, E.coli, and DH5α Conclusion: the present study could highlight that external carbapenem pressure helps in maintenance and expression of blaNDM-4 within different host range. This study is of epidemiological significance and will help in tracking the genetic vehicle responsible for their transmission theirby restricting their spread.

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A large accessory genome, high recombination rates, and selection of secondary metabolite genes help maintain global distribution and broad host range of the fungal plant pathogen Claviceps purpurea

10.1101/2020.05.20.106880 ◽

2020 ◽

Author(s):

Stephen A. Wyka ◽

Stephen J. Mondo ◽

Miao Liu ◽

Vamsi Nalam ◽

Kirk D. Broders

Keyword(s):

Positive Selection ◽

Host Range ◽

Global Distribution ◽

Broad Host Range ◽

Claviceps Purpurea ◽

Recombination Rates ◽

Factors Affecting ◽

Accessory Genome ◽

Genomic Analyses ◽

Selection Of

AbstractPangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms, which is often governed by variable gene content. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome of Claviceps purpurea from 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed that C. purpurea has a relatively large accessory genome (∼ 38%) that is likely maintained by high recombination rates (ρ = 0.044) and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion is likely controlled by these high recombination rates, which may additionally be influencing the overall trend of purifying selection across the genome. Despite this trend, we observed a strong positive selection pressure on secondary metabolite genes, particularly within the ergoline biosynthetic cluster where we also revealed that the lpsA1 and lpsA2 genes were the result of a recombination event. These results indicate that secondary metabolites are primary factors affecting the diversification of the species into new ecological niches and help maintain its global distribution and broad host range. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism.Author SummaryThe use of genomic data to better understand the lifestyle of a pathogen and its relationship with its host has expanded our ability to investigate the evolutionary history of these organisms. This in turn has allowed us to decipher and understand the ambiguity surrounding the true nature of the fungal plant pathogen Claviceps purpurea. By combining three different types of broad genomic analyses we identified primary factors affecting the evolution and adaptive potential of this pathogen; particularly a large accessory genome, high recombination rates, and positive selection of genes associated with stress tolerance. These factors likely contribute to the pathogen’s global distribution and broad host range. Furthermore, these findings will influence the direction of future research into optimal control methods.

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Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00004-08 ◽

2008 ◽

Vol 72 (3) ◽

pp. 457-470 ◽

Cited By ~ 386

Author(s):

Colin R. Parrish ◽

Edward C. Holmes ◽

David M. Morens ◽

Eun-Chung Park ◽

Donald S. Burke ◽

...

Keyword(s):

Host Range ◽

Virus Transmission ◽

Host Population ◽

Evolutionary Mechanisms ◽

New Host ◽

Transmission Cycle ◽

Host Interactions ◽

Natural Hosts ◽

New Hosts ◽

Host Infection

SUMMARY Host range is a viral property reflecting natural hosts that are infected either as part of a principal transmission cycle or, less commonly, as “spillover” infections into alternative hosts. Rarely, viruses gain the ability to spread efficiently within a new host that was not previously exposed or susceptible. These transfers involve either increased exposure or the acquisition of variations that allow them to overcome barriers to infection of the new hosts. In these cases, devastating outbreaks can result. Steps involved in transfers of viruses to new hosts include contact between the virus and the host, infection of an initial individual leading to amplification and an outbreak, and the generation within the original or new host of viral variants that have the ability to spread efficiently between individuals in populations of the new host. Here we review what is known about host switching leading to viral emergence from known examples, considering the evolutionary mechanisms, virus-host interactions, host range barriers to infection, and processes that allow efficient host-to-host transmission in the new host population.

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A broad-host-range event detector: expanding and quantifying performance between Escherichia coli and Pseudomonas species

Synthetic Biology ◽

10.1093/synbio/ysaa002 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 1

Author(s):

Nymul Khan ◽

Enoch Yeung ◽

Yuliya Farris ◽

Sarah J Fansler ◽

Hans C Bernstein

Keyword(s):

Escherichia Coli ◽

Host Range ◽

Memory Device ◽

Broad Host Range ◽

Complex Environments ◽

New Host ◽

E Coli ◽

Pseudomonas Fluorescens Sbw25 ◽

The Common ◽

New Applications

Abstract Modern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains of Escherichia coli. It is clear that new applications such as chemical sensing and event logging in complex environments will benefit from new host chassis. This study quantitatively compared how the same chemical event logger performed across four strains and three different microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads—Pseudomonas fluorescens SBW25 and Pseudomonas putida DSM 291. Quantitative comparisons were made between these two non-traditional hosts and two benchmark E. coli chassis including the probiotic Nissle 1917 and common cloning strain DH5α. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and downstream recombinant region and via data-driven kinetic models. The Pseudomonads proved to be acceptable chassis for the operation of this event logger, which outperformed the common E. coli DH5α in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.

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Uromyces ciceris-arietini, the Cause of Chickpea Rust: New Hosts in the Trifolieae, Fabaceae

Plant Disease ◽

10.1094/pdis-94-3-0293 ◽

2010 ◽

Vol 94 (3) ◽

pp. 293-297 ◽

Cited By ~ 3

Author(s):

D. L. Stuteville ◽

W. L. Graves ◽

L. J. Dixon ◽

L. A. Castlebury ◽

A. M. Minnis

Keyword(s):

Host Range ◽

Cicer Arietinum ◽

Dna Sequences ◽

San Diego ◽

Medicago Polymorpha ◽

New Host ◽

New Hosts

Uromyces ciceris-arietini has been reported on Cicer arietinum (chickpea) and Medicago polyceratia. Plants of Medicago polymorpha in Riverside and San Diego, CA were collected with severe rust caused by U. ciceris-arietini. To confirm the identification and potential new host range, a monouredinial isolate of U. ciceris-arietini from M. polymorpha was inoculated on eight accessions each of C. arietinum and M. polyceratia. All plants showed symptoms of the disease. Consequently, a range of fabaceous hosts were evaluated for their reaction to U. ciceris-arietini. New hosts for U. ciceris-arietini included 29 species of Medicago, specifically M. arabica, M. blancheana, M. ciliaris, M. constricta, M. coronata, M. doliata, M. granadensis, M. intertexta, M. italica, M. laciniata, M. lanigera, M. lesinsii, M. lupulina, M. minima, M. murex, M. muricoleptis, M. orbicularis, M. praecox, M. radiata, M. rigidula, M. rotata, M. rugosa, M. sativa, M. sauvagei, M. scutellata, M. soleirolii, M. tenoreana, M. truncatula, and M. varia, and three species of Melilotus, specifically M. italicus, M. speciosus, and M. spicatus. This isolate of U. ciceris-arietini produced no symptoms on plants in the 33 accessions tested in the genera Anthyllis, Astragalus, Lotus, and Lupinus. DNA sequences are provided to aid in the identification of this pathogen.

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A broad-host-range event detector: expanding and quantifying performance across bacterial species

10.1101/369967 ◽

2018 ◽

Author(s):

Nymul Khan ◽

Enoch Yeung ◽

Yuliya Farris ◽

Sarah J. Fansler ◽

Hans C. Bernstein

Keyword(s):

Escherichia Coli ◽

Host Range ◽

Bacterial Species ◽

Memory Device ◽

Bench Mark ◽

Broad Host Range ◽

Complex Environments ◽

New Host ◽

E Coli ◽

New Applications

ABSTRACTModern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains ofEscherichia coli. It is clear that new applications – such as chemical sensing and event logging in complex environments – will benefit from new host chassis. This study quantitatively compared how a chemical event logger performed across multiple microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads –Pseudomonas fluorescensSBW25 andPseudomonas putidaDSM 291. Quantitative comparisons were made between these two non-traditional hosts and two bench-markEscherichia colichassis including the probiotic Nissle 1917 and common cloning strain DH5α. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and down-stream recombinant region and via data-driven kinetic models. ThePseudomonadsproved to be acceptable chassis for the operation of this event logger, which outperformed the commonE. coliDH5α in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.

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Emergence of plasmid-mediated oxazolidinone resistance gene poxtA from CC17 Enterococcus faecium of pig origin

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkz250 ◽

2019 ◽

Vol 74 (9) ◽

pp. 2524-2530 ◽

Cited By ~ 8

Author(s):

Jinhu Huang ◽

Mengli Wang ◽

Yi Gao ◽

Li Chen ◽

Liping Wang

Keyword(s):

Host Range ◽

Resistance Gene ◽

Enterococcus Faecium ◽

Susceptibility Testing ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Broad Host Range ◽

Broad Host Range Plasmids ◽

Genetic Context ◽

Selection Of

AbstractObjectivesTo characterize the oxazolidinone resistance gene poxtA on broad-host-range Inc18 plasmids from CC17 Enterococcus faecium of pig origin.MethodsOxazolidinone-resistant E. faecium isolates were screened for the presence of poxtA. The poxtA-carrying isolates were characterized by antimicrobial susceptibility testing, conjugation, S1-PFGE and hybridization. The poxtA-carrying plasmids were completely sequenced and their instability was verified.ResultsTwo individual CC17 E. faecium strains were positive for poxtA. S1-PFGE and hybridization revealed the presence of a poxtA-carrying plasmid of ∼62 kb in both WZ27-2 and the transconjugant, while poxtA-carrying plasmids of different sizes were observed in QF25-1 and the transconjugant. The two poxtA-carrying plasmids, pC25-1 and pC27-2, belonged to the broad-host-range plasmids of the Inc18 family and carried dfrG, aadE, Δsat4, aph(3′)-III, erm(B), tet(M), tet(L) and fexB. Plasmid pC27-2 was virtually identical to pC25-1, with minor differences. The calculated transfer frequency was ∼0.87 × 10−8 and ∼1.03 × 10−7 per recipient to plasmids pC25-1 and pC27-2, respectively. Instability assays of the region with four adjacent IS1216Es, which forms three IS1216E translocatable units, revealed the formation of a series of mosaic circular intermediates.ConclusionsWe report the emergence of the plasmid-mediated oxazolidinone resistance gene poxtA in E. faecium from different farms in China. Comparison of the poxtA genetic context suggests that IS1216E elements play an important role in the dissemination of poxtA. The co-occurrence of poxtA with other antimicrobial and heavy metal resistance genes on the broad-host-range plasmids of the Inc18 family may lead to the co-selection of poxtA, contributing to its persistence and accelerating its dissemination.

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Construction of broad-host-range vectors for the selection of divergent promoters

Gene ◽

10.1016/0378-1119(90)90451-v ◽

1990 ◽

Vol 90 (1) ◽

pp. 145-148 ◽

Cited By ~ 18

Author(s):

S.L. Ronald ◽

A.M. Kropinski ◽

M.A. Farinha

Keyword(s):

Host Range ◽

Broad Host Range ◽

Divergent Promoters ◽

Selection Of

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Direct Selection of IS903 Transposon Insertions by Use of a Broad-Host-Range Vector: Isolation of Catalase-Deficient Mutants of Actinobacillus actinomycetemcomitans

Journal of Bacteriology ◽

10.1128/jb.181.23.7298-7307.1999 ◽

1999 ◽

Vol 181 (23) ◽

pp. 7298-7307 ◽

Cited By ~ 58

Author(s):

Valeri J. Thomson ◽

Mrinal K. Bhattacharjee ◽

Daniel H. Fine ◽

Keith M. Derbyshire ◽

David H. Figurski

Keyword(s):

Host Range ◽

Transposon Mutagenesis ◽

Actinobacillus Actinomycetemcomitans ◽

Direct Selection ◽

Nucleotide Sequence Analysis ◽

Broad Host Range ◽

Dna Uptake ◽

Transposase Gene ◽

Insertion Mutants ◽

Selection Of

ABSTRACT Transposon mutagenesis in bacteria generally requires efficient delivery of a transposon suicide vector to allow the selection of relatively infrequent transposition events. We have developed an IS903-based transposon mutagenesis system for diverse gram-negative bacteria that is not limited by transfer efficiency. The transposon, IS903φkan, carries a cryptic kangene, which can be expressed only after successful transposition. This allows the stable introduction of the transposon delivery vector into the host. Generation of insertion mutants is then limited only by the frequency of transposition. IS903φkan was placed on an IncQ plasmid vector with the transposase gene located outside the transposon and expressed from isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible promoters. After transposase induction, IS903φkaninsertion mutants were readily selected in Escherichia coliby their resistance to kanamycin. We used IS903φkan to isolate three catalase-deficient mutants of the periodontal pathogenActinobacillus actinomycetemcomitans from a library of random insertions. The mutants display increased sensitivity to hydrogen peroxide, and all have IS903φkan insertions within an open reading frame whose predicted product is closely related to other bacterial catalases. Nucleotide sequence analysis of the catalase gene (designated katA) and flanking intergenic regions also revealed several occurrences of an 11-bp sequence that is closely related to the core DNA uptake signal sequence for natural transformation of Haemophilus influenzae. Our results demonstrate the utility of the IS903φkan mutagenesis system for the study of A. actinomycetemcomitans. Because IS903φkan is carried on a mobilizable, broad-host-range IncQ plasmid, this system is potentially useful in a variety of bacterial species.

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Transcriptional response to host chemical cues underpins expansion of host range in a fungal plant pathogen lineage

10.1101/2020.10.29.360412 ◽

2020 ◽

Author(s):

Stefan Kusch ◽

Justine Larrouy ◽

Heba M. M. Ibrahim ◽

Noémie Gasset ◽

Olivier Navaud ◽

...

Keyword(s):

Host Range ◽

Plant Pathogen ◽

Transcriptional Response ◽

Gene Clusters ◽

Wild Plants ◽

Adaptive Plasticity ◽

Close Relative ◽

Broad Host Range ◽

Narrow Host Range ◽

Life Styles

AbstractThe host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic. The fungus Sclerotinia sclerotiorum parasitizes more than 400 plant species from diverse eudicot families while its close relative, S. trifoliorum, is restricted to plants from the Fabaceae family. We analyzed S. sclerotiorum global transcriptome reprogramming on hosts from six botanical families and reveal a flexible, host-specific transcriptional program driven by core and host-response co-expression (SPREx) gene clusters. We generated a chromosome-level genome assembly for S. trifoliorum and found near-complete gene space conservation in broad and narrow host range Sclerotinia species. However, S. trifoliorum showed increased sensitivity to the Brassicaceae defense compound camalexin. Inter-specific transcriptome analyses revealed a lack of transcriptional response to camalexin in S. trifoliorum and provide evidence that cis-regulatory variation associates with the genetic accommodation of Brassicaceae in the Sclerotinia host range. Our work demonstrates adaptive plasticity of a broad host range pathogen with specific responses to different host plants and demonstrates the co-existence of signatures for generalist and polyspecialist life styles in the genome of a plant pathogen. We reason that this mechanism enables the emergence of new disease with no or limited gene flow between strains and species, and could underlie the emergence of new epidemics originating from wild plants in agricultural settings.

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