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Mediati DG, Dan W, Lalaouna D, Dinh H, Pokhrel A, Rowell KN, Michie KA, Stinear TP, Cain AK, Tree JJ. The 3' UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions. Cell Rep 2024; 43:114082. [PMID: 38583155 DOI: 10.1016/j.celrep.2024.114082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 01/17/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024] Open
Abstract
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteremia, and treatment failure is often associated with vancomycin-intermediate S. aureus isolates. The regulatory 3' UTR of the vigR mRNA contributes to vancomycin tolerance and upregulates the autolysin IsaA. Using MS2-affinity purification coupled with RNA sequencing, we find that the vigR 3' UTR also regulates dapE, a succinyl-diaminopimelate desuccinylase required for lysine and peptidoglycan synthesis, suggesting a broader role in controlling cell wall metabolism and vancomycin tolerance. Deletion of the 3' UTR increased virulence, while the isaA mutant is completely attenuated in a wax moth larvae model. Sequence and structural analyses of vigR indicated that the 3' UTR has expanded through the acquisition of Staphylococcus aureus repeat insertions that contribute sequence for the isaA interaction seed and may functionalize the 3' UTR.
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Affiliation(s)
- Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia.
| | - William Dan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - David Lalaouna
- Université de Strasbourg, CNRS, ARN UPR 9002, Strasbourg, France
| | - Hue Dinh
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Alaska Pokhrel
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia; School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Keiran N Rowell
- Structural Biology Facility, University of New South Wales, Sydney, NSW, Australia
| | - Katharine A Michie
- Structural Biology Facility, University of New South Wales, Sydney, NSW, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Amy K Cain
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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2
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Zhuang S, Semenec L, Nagy SS, Cain AK, Inglis DW. High-precision screening and sorting of double emulsion droplets. Cytometry A 2024. [PMID: 38634684 DOI: 10.1002/cyto.a.24842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
Mounting evidence suggests that cell populations are extremely heterogeneous, with individual cells fulfilling different roles within the population. Flow cytometry (FC) is a high-throughput tool for single-cell analysis that works at high optical resolution. Sub-populations with unique properties can be screened, isolated and sorted through fluorescence-activated cell sorting (FACS), using intracellular fluorescent products or surface-tagged fluorescent products of interest. However, traditional FC and FACS methods cannot identify or isolate cells that secrete extracellular products of interest. Double emulsion (DE) droplets are an innovative approach to retaining these extracellular products so cells producing them can be identified and isolated with FC and FACS. The water-in-oil-in-water structure makes DE droplets compatible with the sheath flow of flow cytometry. Single cells can be encapsulated with other reagents into DEs, which act as pico-reactors. These droplets allow biological activities to take place while allowing for cell cultivation monitoring, rare mutant identification, and cellular events characterization. However, using DEs in FACS presents technical challenges, including rupture of DEs, poor accuracy and low sorting efficiency. This study presents high-performance sorting using fluorescent beads (as simulants for cells). This study aims to guide researchers in the use of DE-based flow cytometry, offering insights into how to resolve the technical difficulties associated with DE-based screening and sorting using FC.
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Affiliation(s)
- Siyuan Zhuang
- School of Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Lucie Semenec
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Stephanie S Nagy
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Amy K Cain
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - David W Inglis
- School of Engineering, Macquarie University, Sydney, New South Wales, Australia
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3
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Sullivan GJ, Barquist L, Cain AK. A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria. mSystems 2024; 9:e0066523. [PMID: 38470252 PMCID: PMC11019837 DOI: 10.1128/msystems.00665-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Functional genomics techniques, such as transposon insertion sequencing and RNA-sequencing, are key to studying relative differences in bacterial mutant fitness or gene expression under selective conditions. However, certain stress conditions, mutations, or antibiotics can directly interfere with DNA synthesis, resulting in systematic changes in local DNA copy numbers along the chromosome. This can lead to artifacts in sequencing-based functional genomics data when comparing antibiotic treatment to an unstressed control. Further, relative differences in gene-wise read counts may result from alterations in chromosomal replication dynamics, rather than selection or direct gene regulation. We term this artifact "chromosomal location bias" and implement a principled statistical approach to correct it by calculating local normalization factors along the chromosome. These normalization factors are then directly incorporated into statistical analyses using standard RNA-sequencing analysis methods without modifying the read counts themselves, preserving important information about the mean-variance relationship in the data. We illustrate the utility of this approach by generating and analyzing a ciprofloxacin-treated transposon insertion sequencing data set in Escherichia coli as a case study. We show that ciprofloxacin treatment generates chromosomal location bias in the resulting data, and we further demonstrate that failing to correct for this bias leads to false predictions of mutant drug sensitivity as measured by minimum inhibitory concentrations. We have developed an R package and user-friendly graphical Shiny application, ChromoCorrect, that detects and corrects for chromosomal bias in read count data, enabling the application of functional genomics technologies to the study of antibiotic stress.IMPORTANCEAltered gene dosage due to changes in DNA replication has been observed under a variety of stresses with a variety of experimental techniques. However, the implications of changes in gene dosage for sequencing-based functional genomics assays are rarely considered. We present a statistically principled approach to correcting for the effect of changes in gene dosage, enabling testing for differences in the fitness effects or regulation of individual genes in the presence of confounding differences in DNA copy number. We show that failing to correct for these effects can lead to incorrect predictions of resistance phenotype when applying functional genomics assays to investigate antibiotic stress, and we provide a user-friendly application to detect and correct for changes in DNA copy number.
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Affiliation(s)
- Geraldine J. Sullivan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Lars Barquist
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
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4
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Tobin LA, Cain AK, Djordjevic SP, Hamidian M. Transposons Carrying the aacC2e Aminoglycoside and blaTEM Beta-Lactam Resistance Genes in Acinetobacter. Microb Drug Resist 2024. [PMID: 38593463 DOI: 10.1089/mdr.2023.0299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
This study examines the genetic contexts and evolutionary steps responsible for the formation of the widely spread transposon Tn6925 carrying blaTEM and aacC2e, which confers resistance to beta-lactam and aminoglycoside antibiotics in Gram-negative bacteria. The blaTEM-1 and aacC2e genes were found in several transposons. They were first observed within an IS26 bounded 3.7 kb transposon (Tn6925) on several Acinetobacter baumannii plasmids located within a 4.7 kb dif module. Truncated and expanded variations of Tn6925 were found across other A. baumannii plasmids, as well as in other Gram-negative bacteria (including Vibrio cholerae). Moreover, blaTEM-1 and aacC2e were in much larger resistance-heavy transposons including the ISAba1-bounded 24.6 kb (here called Tn6927), found in an A. baumannii chromosome. A novel ISKpn12-bounded transposon was also observed to contain blaTEM and aacC2e which was found interrupting Tn5393 along with an IS26 pseudo-compound transposon to form a 24.9 kb resistance island in an Acinetobacter pittii plasmid. Multiple mobile genetic elements are involved in the formation of transposon structures that circulate blaTEM and aacC2e. Among these, IS26 and ISAba1 appear to have played a major role in the formation and spread of these elements in the Acinetobacter species.
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Affiliation(s)
- Liam A Tobin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
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5
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Li L, Short FL, Hassan KA, Naidu V, Pokhrel A, Nagy SS, Prity FT, Shah BS, Afrin N, Baker S, Parkhill J, Cain AK, Paulsen IT. Systematic analyses identify modes of action of ten clinically relevant biocides and antibiotic antagonism in Acinetobacter baumannii. Nat Microbiol 2023; 8:1995-2005. [PMID: 37814070 DOI: 10.1038/s41564-023-01474-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/11/2023] [Indexed: 10/11/2023]
Abstract
Concerns exist that widespread use of antiseptic or disinfectant biocides could contribute to the emergence and spread of multidrug-resistant bacteria. To investigate this, we performed transposon-directed insertion-site sequencing (TraDIS) on the multidrug-resistant pathogen, Acinetobacter baumannii, exposed to a panel of ten structurally diverse and clinically relevant biocides. Multiple gene targets encoding cell envelope or cytoplasmic proteins involved in processes including fatty acid biogenesis, multidrug efflux, the tricarboxylic acid cycle, cell respiration and cell division, were identified to have effects on bacterial fitness upon biocide exposure, suggesting that these compounds may have intracellular targets in addition to their known effects on the cell envelope. As cell respiration genes are required for A. baumannii fitness in biocides, we confirmed that sub-inhibitory concentrations of the biocides that dissipate membrane potential can promote A. baumannii tolerance to antibiotics that act intracellularly. Our results support the concern that residual biocides might promote antibiotic resistance in pathogenic bacteria.
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Affiliation(s)
- Liping Li
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Francesca L Short
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Karl A Hassan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Varsha Naidu
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Alaska Pokhrel
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- Australian Institute for Microbiology and Infection (AIMI), University of Technology, Sydney, New South Wales, Australia
| | - Stephanie S Nagy
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Farzana T Prity
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Bhumika S Shah
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Nusrat Afrin
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia.
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia.
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia.
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia.
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6
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van Niekerk A, Joseph MC, Kavanagh A, Dinh H, Swarts AJ, Mapolie SF, Zuegg J, Cain AK, Elliott AG, Blaskovich MAT, Frei A. The Antimicrobial Properties of Pd II - and Ru II -pyta Complexes. Chembiochem 2023; 24:e202300247. [PMID: 37593808 PMCID: PMC10947176 DOI: 10.1002/cbic.202300247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 08/19/2023]
Abstract
Infections associated with antimicrobial resistance (AMR) are poised to become the leading cause of death in the next few decades, a scenario that can be ascribed to two phenomena: antibiotic over-prescription and a lack of antibiotic drug development. The crowd-sourced initiative Community for Open Antimicrobial Drug Discovery (CO-ADD) has been testing research compounds contributed by researchers around the world to find new antimicrobials to combat AMR, and during this campaign has found that metallodrugs might be a promising, yet untapped source. To this end, we submitted 18 PdII - and RuII -pyridyl-1,2,3-triazolyl complexes that were developed as catalysts to assess their antimicrobial properties. It was found that the Pd complexes, especially Pd1, possessed potent antifungal activity with MICs between 0.06 and 0.125 μg mL-1 against Candida glabrata. The in-vitro studies were extended to in-vivo studies in Galleria mellonella larvae, where it was established that the compounds were nontoxic. Here, we effectively demonstrate the potential of PdII -pyta complexes as antifungal agents.
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Affiliation(s)
- Annick van Niekerk
- Department of Chemistry and Polymer ScienceUniversity of StellenboschStellenbosch, Private bag X1, Matieland7602South Africa
| | - M. Cassiem Joseph
- Molecular Science Institute, School of ChemistryUniversity of the WitwatersrandJohannesburg, PO Wits2050South Africa
| | - Angela Kavanagh
- Centre for Superbug Solutions Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Hue Dinh
- School of Natural Sciences ARC Centre of Excellence in Synthetic BiologyMacquarie UniversitySydneyNSW2109Australia
| | - Andrew J. Swarts
- Molecular Science Institute, School of ChemistryUniversity of the WitwatersrandJohannesburg, PO Wits2050South Africa
| | - Selwyn F. Mapolie
- Department of Chemistry and Polymer ScienceUniversity of StellenboschStellenbosch, Private bag X1, Matieland7602South Africa
| | - Johannes Zuegg
- Centre for Superbug Solutions Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Amy K. Cain
- School of Natural Sciences ARC Centre of Excellence in Synthetic BiologyMacquarie UniversitySydneyNSW2109Australia
| | - Alysha G. Elliott
- Centre for Superbug Solutions Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Mark A. T. Blaskovich
- Centre for Superbug Solutions Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Angelo Frei
- Dept. of Chemistry, Biochemistry & Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
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7
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Abstract
Antibiotic resistance is a growing global concern in the field of medicine as it renders bacterial infections difficult to treat and often more severe. Acinetobacter baumannii is a gram-negative bacterial pathogen causing a wide range of infections, including pneumonia, sepsis, urinary tract infections, and wound infections. A. baumannii has emerged as a significant healthcare-associated pathogen due to its high level of antibiotic resistance. The global spread of antibiotic-resistant strains of A. baumannii has resulted in limited treatment options, leading to increased morbidity and mortality rates, especially in vulnerable populations such as the elderly and immunocompromised individuals, as well as longer hospital stays and higher healthcare costs. Further complicating the situation, multi- and pan-drug-resistant strains of A. baumannii are becoming increasingly common, and these deadly strains are resistant to all or almost all available antibiotics. A. baumannii employs various clever strategies to develop antibiotic resistance, including horizontal transfer of resistance genes, overexpression of inherent efflux pumps that remove drugs from the cell, intrinsic mutations, combined with natural selection under antibiotic selective pressure leading to emergence of successful resistance clones. The typical multidrug resistance phenotype of A. baumannii is, therefore, an orchestrated collimation of all these mechanisms combined with the worldwide spread of "global clones," rendering infections caused by this pathogen challenging to control and treat. To address the escalating problem of antibiotic resistance in A. baumannii, there is a need for increased surveillance, strict infection control measures, and the development of new treatment strategies, requiring a concerted effort by healthcare professionals, researchers, and policymakers.
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Affiliation(s)
- Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mehrad Hamidian
- Australian Institute of Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
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8
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Prity FT, Tobin LA, Maharajan R, Paulsen IT, Cain AK, Hamidian M. The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate. Microb Genom 2023; 9. [PMID: 37171842 DOI: 10.1099/mgen.0.001010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Acinetobacter baumannii is an important opportunistic pathogen known for its high levels of resistance to many antibiotics, particularly those considered last resorts such as colistin and carbapenems. Plasmids of this organism are increasingly associated with the spread of clinically important antibiotic resistance genes. Although A. baumannii is a ubiquitous organism, to date, most of the focus has been on studying strains recovered from clinical samples ignoring those isolated in the environment (soil, water, food, etc.). Here, we analysed the genetic structures of eight novel plasmids carried by an environmental colistin-resistant A. baumannii (strain E-072658) recovered in a recycled fibre pulp in a paper mill in Finland. It was shown that E-072658 carries a new variant of the mcr-4 colistin resistance gene (mcr-4.7) in a novel Tn3-family transposon (called Tn6926) carried by a novel plasmid p8E072658. E-072658 is also resistant to sulphonamide compounds; consistent with this, the sul2 sulphonamide resistance gene was found in a pdif module. E-072658 also carries six additional plasmids with no antibiotic resistance genes, but they contained several pdif modules shared with plasmids carried by clinical strains. Detailed analysis of the genetic structure of all eight plasmids carried by E-072658 showed a complex evolutionary history revealing genetic exchange events within the genus Acinetobacter beyond the clinical or environmental origin of the strains. This work provides evidence that environmental strains might act as a source for some of the clinically significant antibiotic resistance genes.
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Affiliation(s)
- Farzana T Prity
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Liam A Tobin
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Ram Maharajan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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9
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Semenec L, Cain AK, Dawson CJ, Liu Q, Dinh H, Lott H, Penesyan A, Maharjan R, Short FL, Hassan KA, Paulsen IT. Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence. Nat Commun 2023; 14:702. [PMID: 36759602 PMCID: PMC9911699 DOI: 10.1038/s41467-023-36252-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
Acinetobacter baumannii and Klebsiella pneumoniae are opportunistic pathogens frequently co-isolated from polymicrobial infections. The infections where these pathogens co-exist can be more severe and recalcitrant to therapy than infections caused by either species alone, however there is a lack of knowledge on their potential synergistic interactions. In this study we characterise the genomes of A. baumannii and K. pneumoniae strains co-isolated from a single human lung infection. We examine various aspects of their interactions through transcriptomic, phenomic and phenotypic assays that form a basis for understanding their effects on antimicrobial resistance and virulence during co-infection. Using co-culturing and analyses of secreted metabolites, we discover the ability of K. pneumoniae to cross-feed A. baumannii by-products of sugar fermentation. Minimum inhibitory concentration testing of mono- and co-cultures reveals the ability for A. baumannii to cross-protect K. pneumoniae against the cephalosporin, cefotaxime. Our study demonstrates distinct syntrophic interactions occur between A. baumannii and K. pneumoniae, helping to elucidate the basis for their co-existence in polymicrobial infections.
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Affiliation(s)
- Lucie Semenec
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
| | - Catherine J Dawson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Qi Liu
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
| | - Hannah Lott
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
| | - Anahit Penesyan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
| | - Ram Maharjan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia
| | - Francesca L Short
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Karl A Hassan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia.
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia.
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia.
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2113, Australia.
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10
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Zhang T, Cain AK, Semenec L, Liu L, Hosokawa Y, Inglis DW, Yalikun Y, Li M. Microfluidic Separation and Enrichment of Escherichia coli by Size Using Viscoelastic Flows. Anal Chem 2023; 95:2561-2569. [PMID: 36656064 DOI: 10.1021/acs.analchem.2c05084] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Here, we achieve the separation and enrichment of Escherichia coli clusters from its singlets in a viscoelastic microfluidic device. E. coli, an important prokaryotic model organism and a widely used microbial factory, can aggregate in clusters, leading to biofilm development that can be detrimental to human health and industrial processes. The ability to obtain high-purity populations of E. coli clusters is of significance for biological, biomedical, and industrial applications. In this study, polystyrene particles of two different sizes, 1 and 4.8 μm, are used to mimic E. coli singlets and clusters, respectively. Experimental results show that particles migrate toward the channel center in a size-dependent manner, due to the combined effects of inertial and elastic forces; 4.8 and 1 μm particles are found to have lateral equilibrium positions closer to the channel centerline and sidewalls, respectively. The size-dependent separation performance of the microdevice is demonstrated to be affected by three main factors: channel length, the ratio of sheath to sample flow rate, and poly(ethylene oxide) (PEO) concentration. Further, the separation of E. coli singlets and clusters is achieved at the outlets, and the separation efficiency is evaluated in terms of purity and enrichment factor.
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Affiliation(s)
- Tianlong Zhang
- School of Engineering, Macquarie University, Sydney, NSW 2109, Australia.,Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Lucie Semenec
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ling Liu
- School of Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Yoichiroh Hosokawa
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - David W Inglis
- School of Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Yaxiaer Yalikun
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Ming Li
- School of Engineering, Macquarie University, Sydney, NSW 2109, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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11
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Pokhrel A, Dinh H, Li L, Hassan KA, Cain AK, Paulsen IT. Identification of a Novel LysR Family Transcriptional Regulator Controlling Acquisition of Sulfur Sources in Acinetobacter baumannii. Microb Physiol 2023; 33:27-35. [PMID: 36626888 DOI: 10.1159/000529038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023]
Abstract
l-cysteine biosynthesis from inorganic sulfur represents a major mechanism by which reduced sulfur is incorporated into organic compounds. Cysteine biosynthesis and regulation is well characterized in Escherichia coli. However, the regulation of sulfur metabolism in Acinetobacter baumannii is only partly understood, with the LysR-type regulator, GigC known to control some aspects of sulfur reduction. In this study, we have used transcriptomics and bioinformatic analyses to characterize a novel LysR-type transcriptional regulator encoded by ABUW_1016 (cbl), in a highly multidrug resistant and virulent isolate of A. baumannii. We have shown that Cbl is involved in controlling expression of the genes required for uptake and reduction of various sulfur sources in A. baumannii. Collectively, we have identified the global regulon of Cbl and proposed a model of cysteine biosynthesis and its regulation by Cbl and GigC in A. baumannii.
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Affiliation(s)
- Alaska Pokhrel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia,
| | - Hue Dinh
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Liping Li
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, New South Wales, Australia
| | - Amy K Cain
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
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12
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Frei A, Elliott AG, Kan A, Dinh H, Bräse S, Bruce AE, Bruce MR, Chen F, Humaidy D, Jung N, King AP, Lye PG, Maliszewska HK, Mansour AM, Matiadis D, Muñoz MP, Pai TY, Pokhrel S, Sadler PJ, Sagnou M, Taylor M, Wilson JJ, Woods D, Zuegg J, Meyer W, Cain AK, Cooper MA, Blaskovich MAT. Metal Complexes as Antifungals? From a Crowd-Sourced Compound Library to the First In Vivo Experiments. JACS Au 2022; 2:2277-2294. [PMID: 36311838 PMCID: PMC9597602 DOI: 10.1021/jacsau.2c00308] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
There are currently fewer than 10 antifungal drugs in clinical development, but new fungal strains that are resistant to most current antifungals are spreading rapidly across the world. To prevent a second resistance crisis, new classes of antifungal drugs are urgently needed. Metal complexes have proven to be promising candidates for novel antibiotics, but so far, few compounds have been explored for their potential application as antifungal agents. In this work, we report the evaluation of 1039 metal-containing compounds that were screened by the Community for Open Antimicrobial Drug Discovery (CO-ADD). We show that 20.9% of all metal compounds tested have antimicrobial activity against two representative Candida and Cryptococcus strains compared with only 1.1% of the >300,000 purely organic molecules tested through CO-ADD. We identified 90 metal compounds (8.7%) that show antifungal activity while not displaying any cytotoxicity against mammalian cell lines or hemolytic properties at similar concentrations. The structures of 21 metal complexes that display high antifungal activity (MIC ≤1.25 μM) are discussed and evaluated further against a broad panel of yeasts. Most of these have not been previously tested for antifungal activity. Eleven of these metal complexes were tested for toxicity in the Galleria mellonella moth larva model, revealing that only one compound showed signs of toxicity at the highest injected concentration. Lastly, we demonstrated that the organo-Pt(II) cyclooctadiene complex Pt1 significantly reduces fungal load in an in vivo G. mellonella infection model. These findings showcase that the structural and chemical diversity of metal-based compounds can be an invaluable tool in the development of new drugs against infectious diseases.
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Affiliation(s)
- Angelo Frei
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
- Department
of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012Bern, Switzerland
| | - Alysha G. Elliott
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
| | - Alex Kan
- Molecular
Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology,
Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical
School, Sydney Institute for Infectious Diseases, Westmead Hospital-Research
and Education Network, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW2145, Australia
| | - Hue Dinh
- School
of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW2109, Australia
| | - Stefan Bräse
- Institute
of Organic Chemistry, Karlsruhe Institute
of Technology, Fritz-Haber-Weg 6, 76131Karlsruhe, Germany
- Institute
of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, 76344Eggenstein-Leopoldshafen, Germany
| | - Alice E. Bruce
- Department
of Chemistry, University of Maine, Orono, Maine04469, United States
| | - Mitchell R. Bruce
- Department
of Chemistry, University of Maine, Orono, Maine04469, United States
| | - Feng Chen
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CoventryCV4 7AL, U.K.
| | - Dhirgam Humaidy
- Department
of Chemistry, University of Maine, Orono, Maine04469, United States
| | - Nicole Jung
- Karlsruhe
Nano Micro Facility (KNMF), Karlsruhe Institute
of Technology, Hermann-von-Helmholtz-Platz 1, 76344Eggenstein-Leopoldshafen, Germany
- Institute
of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, 76344Eggenstein-Leopoldshafen, Germany
| | - A. Paden King
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York14853, United States
| | - Peter G. Lye
- School
of Science and Technology, University of
New England, Armidale, NSW2351, Australia
| | - Hanna K. Maliszewska
- School
of Chemistry, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, U.K.
| | - Ahmed M. Mansour
- Chemistry
Department, Faculty of Science, Cairo University, Giza12613, Egypt
| | - Dimitris Matiadis
- Institute
of Biosciences & Applications, National
Centre for Scientific Research “Demokritos”, 15310Athens, Greece
| | - María Paz Muñoz
- School
of Chemistry, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, U.K.
| | - Tsung-Yu Pai
- Molecular
Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology,
Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical
School, Sydney Institute for Infectious Diseases, Westmead Hospital-Research
and Education Network, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW2145, Australia
| | - Shyam Pokhrel
- Department
of Chemistry, University of Maine, Orono, Maine04469, United States
| | - Peter J. Sadler
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CoventryCV4 7AL, U.K.
| | - Marina Sagnou
- Institute
of Biosciences & Applications, National
Centre for Scientific Research “Demokritos”, 15310Athens, Greece
| | - Michelle Taylor
- School
of Science and Technology, University of
New England, Armidale, NSW2351, Australia
| | - Justin J. Wilson
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York14853, United States
| | - Dean Woods
- School
of Science and Technology, University of
New England, Armidale, NSW2351, Australia
| | - Johannes Zuegg
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
| | - Wieland Meyer
- Molecular
Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology,
Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical
School, Sydney Institute for Infectious Diseases, Westmead Hospital-Research
and Education Network, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW2145, Australia
| | - Amy K. Cain
- School
of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW2109, Australia
| | - Matthew A. Cooper
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
| | - Mark A. T. Blaskovich
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
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13
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Zhang T, Liu H, Okano K, Tang T, Inoue K, Yamazaki Y, Kamikubo H, Cain AK, Tanaka Y, Inglis DW, Hosokawa Y, Yaxiaer Y, Li M. Shape-based separation of drug-treated Escherichia coli using viscoelastic microfluidics. Lab Chip 2022; 22:2801-2809. [PMID: 35642562 DOI: 10.1039/d2lc00339b] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, we achieve shape-based separation of drug-treated Escherichia coli (E. coli) by viscoelastic microfluidics. Since shape is critical for modulating biological functions of E. coli, the ability to prepare homogeneous E. coli populations adopting uniform shape or sort bacterial sub-population based on their shape has significant implications for a broad range of biological, biomedical and environmental applications. A proportion of E. coli treated with 1 μg mL-1 of the antibiotic mecillinam were found to exhibit changes in shape from rod to sphere, and the heterogeneous E. coli populations after drug treatment with various aspect ratios (ARs) ranging from 1.0 to 5.5 were used for experiment. We demonstrate that E. coli with a lower AR, i.e., spherical E. coli (AR ≤ 1.5), are directed toward the middle outlet, while rod-shaped E. coli with a higher AR (AR > 1.5) are driven to the side outlets. Further, we demonstrate that the separation performance of the viscoelastic microfluidic device is influenced by two main factors: sheath-to-sample flow rate ratio and the concentration of poly-ethylene-oxide (PEO). To the best of our knowledge, this is the first report on shape-based separation of a single species of cells smaller than 4 μm by microfluidics.
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Affiliation(s)
- Tianlong Zhang
- School of Engineering, Macquarie University, Sydney 2122, NSW, Australia.
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Hangrui Liu
- School of Engineering, Macquarie University, Sydney 2122, NSW, Australia.
| | - Kazunori Okano
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Tao Tang
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Kazuki Inoue
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Yoichi Yamazaki
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney 2122, NSW, Australia
| | - Yo Tanaka
- Center for Biosystems Dynamics Research, RIKEN, Osaka 565-0871, Japan
| | - David W Inglis
- School of Engineering, Macquarie University, Sydney 2122, NSW, Australia.
| | - Yoichiroh Hosokawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Yalikun Yaxiaer
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Ming Li
- School of Engineering, Macquarie University, Sydney 2122, NSW, Australia.
- Biomolecular Discovery Research Centre, Macquarie University, Sydney 2122, NSW, Australia
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14
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Hamidian M, Maharjan RP, Farrugia DN, Delgado NN, Dinh H, Short FL, Kostoulias X, Peleg AY, Paulsen IT, Cain AK. Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity. Microb Genom 2022; 8. [PMID: 35166651 PMCID: PMC8942024 DOI: 10.1099/mgen.0.000765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Acinetobacter baumannii is a critically important pathogen known for its widespread antibiotic resistance and ability to persist in hospital-associated environments. Whilst the majority of A. baumannii infections are hospital-acquired, infections from outside the hospital have been reported with high mortality. Despite this, little is known about the natural environmental reservoir(s) of A. baumannii and the virulence potential underlying non-clinical strains. Here, we report the complete genome sequences of six diverse strains isolated from environments such as river, soil, and industrial sites around the world. Phylogenetic analyses showed that four of these strains were unrelated to representative nosocomial strains and do not share a monophyletic origin, whereas two had sequence types belonging to the global clone lineages GC1 and GC2. Further, the majority of these strains harboured genes linked to virulence and stress protection in nosocomial strains. These genotypic properties correlated well with in vitro virulence phenotypic assays testing resistance to abiotic stresses, serum survival, and capsule formation. Virulence potential was confirmed in vivo, with most environmental strains able to effectively kill Galleria mellonella greater wax moth larvae. Using phenomic arrays and antibiotic resistance profiling, environmental and nosocomial strains were shown to have similar substrate utilisation patterns although environmental strains were distinctly more sensitive to antibiotics. Taken together, these features of environmental A. baumannii strains suggest the existence of a strain-specific distinct gene pools for niche specific adaptation. Furthermore, environmental strains appear to be equally virulent as contemporary nosocomial strains but remain largely antibiotic sensitive.
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Affiliation(s)
- Mohammad Hamidian
- The iThree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ram P Maharjan
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Daniel N Farrugia
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Natasha N Delgado
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Francesca L Short
- Infection & Immunity Program Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Xenia Kostoulias
- Infection & Immunity Program Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Anton Y Peleg
- Infection & Immunity Program Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.,Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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15
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Liu P, Liu H, Semenec L, Yuan D, Yan S, Cain AK, Li M. Length-based separation of Bacillus subtilis bacterial populations by viscoelastic microfluidics. Microsyst Nanoeng 2022; 8:7. [PMID: 35127130 PMCID: PMC8766588 DOI: 10.1038/s41378-021-00333-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
In this study, we demonstrated the label-free continuous separation and enrichment of Bacillus subtilis populations based on length using viscoelastic microfluidics. B. subtilis, a gram-positive, rod-shaped bacterium, has been widely used as a model organism and an industrial workhorse. B. subtilis can be arranged in different morphological forms, such as single rods, chains, and clumps, which reflect differences in cell types, phases of growth, genetic variation, and changing environmental factors. The ability to prepare B. subtilis populations with a uniform length is important for basic biological studies and efficient industrial applications. Here, we systematically investigated how flow rate ratio, poly(ethylene oxide) (PEO) concentration, and channel length affected the length-based separation of B. subtilis cells. The lateral positions of B. subtilis cells with varying morphologies in a straight rectangular microchannel were found to be dependent on cell length under the co-flow of viscoelastic and Newtonian fluids. Finally, we evaluated the ability of the viscoelastic microfluidic device to separate the two groups of B. subtilis cells by length (i.e., 1-5 μm and >5 μm) in terms of extraction purity (EP), extraction yield (EY), and enrichment factor (EF) and confirmed that the device could separate heterogeneous populations of bacteria using elasto-inertial effects.
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Affiliation(s)
- Ping Liu
- Suqian University, Suqian, 223800 China
- School of Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University, Sydney, NSW 2109 Australia
| | - Lucie Semenec
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Science, Macquarie University, Sydney, NSW 2109 Australia
| | - Dan Yuan
- Centre for Regional and Rural Futures, Deakin University, Geelong, VIC 3216 Australia
| | - Sheng Yan
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Science, Macquarie University, Sydney, NSW 2109 Australia
| | - Ming Li
- School of Engineering, Macquarie University, Sydney, NSW 2109 Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109 Australia
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16
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Cornick J, Musicha P, Peno C, Seager E, Iroh Tam PY, Bilima S, Bennett A, Kennedy N, Feasey N, Heinz E, Cain AK. Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa. Microb Genom 2021; 7. [PMID: 34793293 PMCID: PMC8743538 DOI: 10.1099/mgen.0.000703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A special-care neonatal unit from a large public hospital in Malawi was noted as having more frequent, difficult-to-treat infections, and a suspected outbreak of multi-drug-resistant Klebsiella pneumoniae was investigated using genomic characterisation. All K. pneumoniae bloodstream infections (BSIs) from patients in the neonatal ward (n=62), and a subset of K. pneumoniae BSI isolates (n=38) from other paediatric wards in the hospital, collected over a 4 year period were studied. After whole genome sequencing, the strain sequence types (STs), plasmid types, virulence and resistance genes were identified. One ST340 clone, part of clonal complex 258 (CC258) and an ST that drives hospital outbreaks worldwide, harbouring numerous resistance genes and plasmids, was implicated as the likely cause of the outbreak. This study contributes molecular information necessary for tracking and characterizing this important hospital pathogen in sub-Saharan Africa.
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Affiliation(s)
- Jennifer Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Patrick Musicha
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ezgi Seager
- Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Bordesley Green East, Birmingham, B9 5SS, UK
| | - Pui-Ying Iroh Tam
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sithembile Bilima
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Aisleen Bennett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute for Infection and Immunity, St George's, University of London, London, UK
| | - Neil Kennedy
- Centre for Medical Education, Queen's University Belfast, Belfast, Ireland.,Department of Paediatrics, College of Medicine, University of Malawi, Zomba, Malawi
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Eva Heinz
- Pathogen Genomics, Wellcome Sanger Institute, Cambridge, UK.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Amy K Cain
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Pathogen Genomics, Wellcome Sanger Institute, Cambridge, UK.,Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Liverpool School of Tropical Medicine, Liverpool, UK
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17
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Frei A, Ramu S, Lowe GJ, Dinh H, Semenec L, Elliott AG, Zuegg J, Deckers A, Jung N, Bräse S, Cain AK, Blaskovich MAT. Front Cover: Platinum Cyclooctadiene Complexes with Activity against Gram‐positive Bacteria (ChemMedChem /2021). ChemMedChem 2021. [DOI: 10.1002/cmdc.202100610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Angelo Frei
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - Soumya Ramu
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - Gabrielle J. Lowe
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic Biology Department of Molecular Sciences Macquarie University Sydney NSW Australia
| | - Lucie Semenec
- ARC Centre of Excellence in Synthetic Biology Department of Molecular Sciences Macquarie University Sydney NSW Australia
| | - Alysha G. Elliott
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - Johannes Zuegg
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - Anke Deckers
- Institute of Organic Chemistry Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Nicole Jung
- Institute of Organic Chemistry Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Stefan Bräse
- Institute of Organic Chemistry Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology Department of Molecular Sciences Macquarie University Sydney NSW Australia
| | - Mark A. T. Blaskovich
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
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18
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Frei A, Ramu S, Lowe GJ, Dinh H, Semenec L, Elliott AG, Zuegg J, Deckers A, Jung N, Bräse S, Cain AK, Blaskovich MAT. Platinum Cyclooctadiene Complexes with Activity against Gram-positive Bacteria. ChemMedChem 2021; 16:3165-3171. [PMID: 34018686 PMCID: PMC8596843 DOI: 10.1002/cmdc.202100157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Indexed: 11/17/2022]
Abstract
Antimicrobial resistance is a looming health crisis, and it is becoming increasingly clear that organic chemistry alone is not sufficient to continue to provide the world with novel and effective antibiotics. Recently there has been an increased number of reports describing promising antimicrobial properties of metal-containing compounds. Platinum complexes are well known in the field of inorganic medicinal chemistry for their tremendous success as anticancer agents. Here we report on the promising antibacterial properties of platinum cyclooctadiene (COD) complexes. Amongst the 15 compounds studied, the simplest compounds Pt(COD)X2 (X=Cl, I, Pt1 and Pt2) showed excellent activity against a panel of Gram-positive bacteria including vancomycin and methicillin resistant Staphylococcus aureus. Additionally, the lead compounds show no toxicity against mammalian cells or haemolytic properties at the highest tested concentrations, indicating that the observed activity is specific against bacteria. Finally, these compounds showed no toxicity against Galleria mellonella at the highest measured concentrations. However, preliminary efficacy studies in the same animal model found no decrease in bacterial load upon treatment with Pt1 and Pt2. Serum exchange studies suggest that these compounds exhibit high serum binding which reduces their bioavailability in vivo, mandating alternative administration routes such as e. g. topical application.
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Affiliation(s)
- Angelo Frei
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD 4072Australia
| | - Soumya Ramu
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD 4072Australia
| | - Gabrielle J. Lowe
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD 4072Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic BiologyDepartment of Molecular SciencesMacquarie UniversitySydneyNSWAustralia
| | - Lucie Semenec
- ARC Centre of Excellence in Synthetic BiologyDepartment of Molecular SciencesMacquarie UniversitySydneyNSWAustralia
| | - Alysha G. Elliott
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD 4072Australia
| | - Johannes Zuegg
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD 4072Australia
| | - Anke Deckers
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Nicole Jung
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Stefan Bräse
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Amy K. Cain
- ARC Centre of Excellence in Synthetic BiologyDepartment of Molecular SciencesMacquarie UniversitySydneyNSWAustralia
| | - Mark A. T. Blaskovich
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD 4072Australia
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19
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Affiliation(s)
- Amy K Cain
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Laura M Nolan
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jennifer Cornick
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
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20
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Nolan LM, Cain AK, Clamens T, Furniss RCD, Manoli E, Sainz-Polo MA, Dougan G, Albesa-Jové D, Parkhill J, Mavridou DA, Filloux A. Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells. Nat Microbiol 2021; 6:1199-1210. [PMID: 34413503 PMCID: PMC7611593 DOI: 10.1038/s41564-021-00950-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
The Type VI secretion system (T6SS) is a bacterial nanomachine that delivers toxic effectors to kill competitors or subvert some of their key functions. Here, we use transposon directed insertion-site sequencing to identify T6SS toxins associated with the H1-T6SS, one of the three T6SS machines found in Pseudomonas aeruginosa. This approach identified several putative toxin-immunity pairs, including Tse8-Tsi8. Full characterization of this protein pair demonstrated that Tse8 is delivered by the VgrG1a spike complex into prey cells where it targets the transamidosome, a multiprotein complex involved in protein synthesis in bacteria that lack either one, or both, of the asparagine and glutamine transfer RNA synthases. Biochemical characterization of the interactions between Tse8 and the transamidosome components GatA, GatB and GatC suggests that the presence of Tse8 alters the fine-tuned stoichiometry of the transamidosome complex, and in vivo assays demonstrate that Tse8 limits the ability of prey cells to synthesize proteins. These data expand the range of cellular components targeted by the T6SS by identifying a T6SS toxin affecting protein synthesis and validate the use of a transposon directed insertion site sequencing-based global genomics approach to expand the repertoire of T6SS toxins in T6SS-encoding bacteria.
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Affiliation(s)
- Laura M. Nolan
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Amy K. Cain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas Clamens
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - R. Christopher D. Furniss
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Eleni Manoli
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Maria A. Sainz-Polo
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David Albesa-Jové
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Despoina A.I. Mavridou
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom,Department of Molecular Biosciences, University of Texas at Austin, Austin, 78712, Texas, USA,Correspondence to Alain Filloux: ; Despoina Mavridou:
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom,Correspondence to Alain Filloux: ; Despoina Mavridou:
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21
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Adams FG, Pokhrel A, Brazel EB, Semenec L, Li L, Trappetti C, Paton JC, Cain AK, Paulsen IT, Eijkelkamp BA. Acinetobacter baumannii Fatty Acid Desaturases Facilitate Survival in Distinct Environments. ACS Infect Dis 2021; 7:2221-2228. [PMID: 34100578 DOI: 10.1021/acsinfecdis.1c00192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Maintaining optimal fluidity is essential to ensure adequate membrane structure and function under different environmental conditions. We apply integrated molecular approaches to characterize two desaturases (DesA and DesB) and define their specific roles in unsaturated fatty acid (UFA) production in Acinetobacter baumannii. Using a murine model, we reveal DesA to play a minor role in colonization of the respiratory tract, whereas DesB is important during invasive disease. Furthermore, using transcriptomic and bioinformatic analyses, a global regulator involved in fatty acid homeostasis and members of its regulon are characterized. Collectively, we show that DesA and DesB are primary contributors to UFA production in A. baumannii with infection studies illustrating that these distinct desaturases aid in the bacterium's ability to survive in multiple host niches. Hence, this study provides novel insights into the fundamentals of A. baumannii lipid biology, which contributes to the versatility of this critical bacterial pathogen.
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Affiliation(s)
- Felise G. Adams
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Alaska Pokhrel
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Erin B. Brazel
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Lucie Semenec
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Liping Li
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Claudia Trappetti
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - James C. Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Amy K. Cain
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Bart A. Eijkelkamp
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Bedford Park, South Australia 5042, Australia
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22
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Hogan AL, Grima N, Fifita JA, McCann EP, Heng B, Fat SCM, Wu S, Maharjan R, Cain AK, Henden L, Rayner S, Tarr I, Zhang KY, Zhao Q, Zhang ZH, Wright A, Lee A, Morsch M, Yang S, Williams KL, Blair IP. Splicing factor proline and glutamine rich intron retention, reduced expression and aggregate formation are pathological features of amyotrophic lateral sclerosis. Neuropathol Appl Neurobiol 2021; 47:990-1003. [PMID: 34288034 DOI: 10.1111/nan.12749] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
AIM Splicing factor proline and glutamine rich (SFPQ) is an RNA-DNA binding protein that is dysregulated in Alzheimer's disease and frontotemporal dementia. Dysregulation of SFPQ, specifically increased intron retention and nuclear depletion, has been linked to several genetic subtypes of amyotrophic lateral sclerosis (ALS), suggesting that SFPQ pathology may be a common feature of this heterogeneous disease. Our study aimed to investigate this hypothesis by providing the first comprehensive assessment of SFPQ pathology in large ALS case-control cohorts. METHODS We examined SFPQ at the RNA, protein and DNA levels. SFPQ RNA expression and intron retention were examined using RNA-sequencing and quantitative PCR. SFPQ protein expression was assessed by immunoblotting and immunofluorescent staining. At the DNA level, SFPQ was examined for genetic variation novel to ALS patients. RESULTS At the RNA level, retention of SFPQ intron nine was significantly increased in ALS patients' motor cortex. In addition, SFPQ RNA expression was significantly reduced in the central nervous system, but not blood, of patients. At the protein level, neither nuclear depletion nor reduced expression of SFPQ was found to be a consistent feature of spinal motor neurons. However, SFPQ-positive ubiquitinated protein aggregates were observed in patients' spinal motor neurons. At the DNA level, our genetic screen identified two novel and two rare SFPQ sequence variants not previously reported in the literature. CONCLUSIONS Our findings confirm dysregulation of SFPQ as a pathological feature of the central nervous system of ALS patients and indicate that investigation of the functional consequences of this pathology will provide insight into ALS biology.
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Affiliation(s)
- Alison L Hogan
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Natalie Grima
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jennifer A Fifita
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emily P McCann
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Benjamin Heng
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sandrine Chan Moi Fat
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sharlynn Wu
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ram Maharjan
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Lyndal Henden
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Stephanie Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ingrid Tarr
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Katharine Y Zhang
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Qiongyi Zhao
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Zong-Hong Zhang
- School of Medicine, IMPACT, Bioinformatics Core Research Facility, Deakin University, Geelong, Victoria, Australia
| | - Amanda Wright
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Marco Morsch
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Shu Yang
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
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23
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Frei A, King AP, Lowe GJ, Cain AK, Short FL, Dinh H, Elliott AG, Zuegg J, Wilson JJ, Blaskovich MAT. Nontoxic Cobalt(III) Schiff Base Complexes with Broad-Spectrum Antifungal Activity. Chemistry 2021; 27:2021-2029. [PMID: 33231906 PMCID: PMC7855930 DOI: 10.1002/chem.202003545] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Resistance to currently available antifungal drugs has quietly been on the rise but overshadowed by the alarming spread of antibacterial resistance. There is a striking lack of attention to the threat of drug-resistant fungal infections, with only a handful of new drugs currently in development. Given that metal complexes have proven to be useful new chemotypes in the fight against diseases such as cancer, malaria, and bacterial infections, it is reasonable to explore their possible utility in treating fungal infections. Herein we report a series of cobalt(III) Schiff base complexes with broad-spectrum antifungal activity. Some of these complexes show minimum inhibitory concentrations (MIC) in the low micro- to nanomolar range against a series of Candida and Cryptococcus yeasts. Additionally, we demonstrate that these compounds show no cytotoxicity against both bacterial and human cells. Finally, we report the first in vivo toxicity data on these compounds in Galleria mellonella, showing that doses as high as 266 mg kg-1 are tolerated without adverse effects, paving the way for further in vivo studies of these complexes.
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Affiliation(s)
- Angelo Frei
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD4072Australia
| | - A. Paden King
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNY14853USA
| | - Gabrielle J. Lowe
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD4072Australia
| | - Amy K. Cain
- Department of Molecular SciencesMacquarie UniversitySydneyNSW2109Australia
| | - Francesca L. Short
- Department of Molecular SciencesMacquarie UniversitySydneyNSW2109Australia
| | - Hue Dinh
- Department of Molecular SciencesMacquarie UniversitySydneyNSW2109Australia
- Department of Biological SciencesMacquarie UniversitySydneyNSW2109Australia
| | - Alysha G. Elliott
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD4072Australia
| | - Johannes Zuegg
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD4072Australia
| | - Justin J. Wilson
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNY14853USA
| | - Mark A. T. Blaskovich
- Centre for Superbug SolutionsInstitute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD4072Australia
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24
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Frei A, King AP, Lowe GJ, Cain AK, Short FL, Dinh H, Elliott AG, Zuegg J, Wilson JJ, Blaskovich MAT. Cover Feature: Nontoxic Cobalt(III) Schiff Base Complexes with Broad‐Spectrum Antifungal Activity (Chem. Eur. J. 6/2021). Chemistry 2021. [DOI: 10.1002/chem.202004912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Angelo Frei
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - A. Paden King
- Department of Chemistry and Chemical Biology Cornell University Ithaca NY 14853 USA
| | - Gabrielle J. Lowe
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - Amy K. Cain
- Department of Molecular Sciences Macquarie University Sydney NSW 2109 Australia
| | - Francesca L. Short
- Department of Molecular Sciences Macquarie University Sydney NSW 2109 Australia
| | - Hue Dinh
- Department of Molecular Sciences Macquarie University Sydney NSW 2109 Australia
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
| | - Alysha G. Elliott
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - Johannes Zuegg
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
| | - Justin J. Wilson
- Department of Chemistry and Chemical Biology Cornell University Ithaca NY 14853 USA
| | - Mark A. T. Blaskovich
- Centre for Superbug Solutions Institute for Molecular Bioscience The University of Queensland St. Lucia QLD 4072 Australia
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25
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Dinh H, Semenec L, Kumar SS, Short FL, Cain AK. Microbiology's next top model: Galleria in the molecular age. Pathog Dis 2021; 79:6105221. [PMID: 33476383 DOI: 10.1093/femspd/ftab006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Galleria mellonella has risen to fame as an invertebrate model organism given its ethical advantages, low maintenance costs, rapid reproduction time, short life cycle, high number of progeny, tolerance for human body temperatures, innate immune system and similarities to mammalian host models. It is increasingly being utilised to evaluate in vivo toxicity and efficacy of chemical compounds and antimicrobials, modelling microbial (bacterial, fungal and viral) pathogenicity and assessing host-pathogen interaction during infection. During this molecular age of genomic, transcriptomic, proteomic and genetic manipulation approaches, our understanding of microbial pathogenicity and host-pathogen interactions has deepened from high-throughput molecular studies performed in G. mellonella. In this review, we describe the use of G. mellonella in a broad range of studies involving omics, drug resistance, functional analysis and host-microbial community relationships. The future of G. mellonella in the molecular age is bright, with a multitude of new approaches and uses for this model from clinical to biotechnological on the horizon.
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Affiliation(s)
- Hue Dinh
- Macquarie University, ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, 4 Wally's Walk, NSW 2109, Australia.,Macquarie University, Department of Biological Sciences, 14 Eastern Road, NSW 2109, Australia
| | - Lucie Semenec
- Macquarie University, ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, 4 Wally's Walk, NSW 2109, Australia
| | - Sheemal S Kumar
- Macquarie University, ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, 4 Wally's Walk, NSW 2109, Australia.,Macquarie University, Applied BioSciences, 205B Culloden Road, NSW 2109, Australia
| | - Francesca L Short
- Macquarie University, ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, 4 Wally's Walk, NSW 2109, Australia.,Monash University, Department of Microbiology, 19 Innovation Walk, VIC 3800, Australia
| | - Amy K Cain
- Macquarie University, ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, 4 Wally's Walk, NSW 2109, Australia
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26
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Li L, Hassan KA, Tetu SG, Naidu V, Pokhrel A, Cain AK, Paulsen IT. The Transcriptomic Signature of Tigecycline in Acinetobacter baumannii. Front Microbiol 2020; 11:565438. [PMID: 33193153 PMCID: PMC7652931 DOI: 10.3389/fmicb.2020.565438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/08/2020] [Indexed: 11/14/2022] Open
Abstract
Tigecycline, a protein translation inhibitor, is a treatment of last resort for infections caused by the opportunistic multidrug resistance human pathogen Acinetobacter baumannii. However, strains resistant to tigecycline were reported not long after its clinical introduction. Translation inhibitor antibiotics perturb ribosome function and induce the reduction of (p)ppGpp, an alarmone involved in the stringent response that negatively modulates ribosome production. Through RNA sequencing, this study revealed a significant reduction in the transcription of genes in citric acid cycle and cell respiration, suggesting tigecycline inhibits or slows down bacterial growth. Our results indicated that the drug-induced reduction of (p)ppGpp level promoted the production but diminished the degradation of ribosomes, which mitigates the translational inhibition effect by tigecycline. The reduction of (p)ppGpp also led to a decrease of transcription coupled nucleotide excision repair which likely increases the chances of development of tigecycline resistant mutants. Increased expression of genes linked to horizontal gene transfer were also observed. The most upregulated gene, rtcB, involving in RNA repair, is either a direct tigecycline stress response or is in response to the transcription de-repression of a toxin-antitoxin system. The most down-regulated genes encode two β-lactamases, which is a possible by-product of tigecycline-induced reduction in transcription of genes associated with peptidoglycan biogenesis. This transcriptomics study provides a global genetic view of why A. baumannii is able to rapidly develop tigecycline resistance.
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Affiliation(s)
- Liping Li
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Varsha Naidu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Alaska Pokhrel
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Amy K Cain
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
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27
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Venturini E, Svensson SL, Maaß S, Gelhausen R, Eggenhofer F, Li L, Cain AK, Parkhill J, Becher D, Backofen R, Barquist L, Sharma CM, Westermann AJ, Vogel J. A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence. Microlife 2020; 1:uqaa002. [PMID: 37223003 PMCID: PMC10117436 DOI: 10.1093/femsml/uqaa002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/14/2020] [Indexed: 05/25/2023]
Abstract
Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of comprehensive characterization in microbes other than Escherichia coli. We have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (Transposon-directed insertion sequencing), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrate a virulence and motility defect of a Salmonella ΔmgrB mutant and reveal an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Our study highlights the power of interpreting available 'omics' datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.
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Affiliation(s)
- Elisa Venturini
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Sarah L Svensson
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080, Würzburg, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße, 17489, Greifswald, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee, 79110, Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee, 79110, Freiburg, Germany
| | - Lei Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Guangqiao Road, Guangming District, 518131, Shenzhen, China
| | - Amy K Cain
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, New South Wales, 2109, Sydney, Australia
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridge, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, Cambridge, UK
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße, 17489, Greifswald, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee, 79110, Freiburg, Germany
| | - Lars Barquist
- Corresponding author: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany. E-mail:
| | - Cynthia M Sharma
- Corresponding author: Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080, Würzburg, Germany. Tel: +49-9313182560; Fax: +49-9313182578; E-mail:
| | - Alexander J Westermann
- Corresponding author: Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany. Tel: +49 931 3182 575; E-mail:
| | - Jörg Vogel
- Corresponding author: Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany. Tel: +49 931 3182 575; E-mail:
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28
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Sullivan GJ, Delgado NN, Maharjan R, Cain AK. How antibiotics work together: molecular mechanisms behind combination therapy. Curr Opin Microbiol 2020; 57:31-40. [PMID: 32619833 DOI: 10.1016/j.mib.2020.05.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Antibiotics used in combination are an effective strategy for combatting numerous infectious diseases in clinical and veterinary settings, particularly as a last-line therapy for difficult-to-treat cases. Combination therapy can either increase or slow the rate of killing, broaden the antibiotic spectrum, reduce dosage and unwanted side-effects, and even control the emergence of resistance. The administration of antibiotics in combination has been used effectively against bacterial infections for >70 years, first used to treat tuberculosis. However, effective antibiotic combinations and their dosage regimes have been largely determined empirically in the clinic, and the molecular mechanisms underpinning how these combinations work remains surprisingly elusive. This review focuses on studies that have outlined the genetics and molecular mechanisms of action underlying antibiotic combinations, as well as those that examine how resistance develops. We highlight the need for further experimentation and genetic validation to fully realise the potential of combination therapy.
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Affiliation(s)
- Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, North Ryde, 2113, Australia
| | - Natasha N Delgado
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, North Ryde, 2113, Australia
| | - Ram Maharjan
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, North Ryde, 2113, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, North Ryde, 2113, Australia.
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29
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Elliott AG, Huang JX, Neve S, Zuegg J, Edwards IA, Cain AK, Boinett CJ, Barquist L, Lundberg CV, Steen J, Butler MS, Mobli M, Porter KM, Blaskovich MAT, Lociuro S, Strandh M, Cooper MA. An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria. Nat Commun 2020; 11:3184. [PMID: 32576824 PMCID: PMC7311426 DOI: 10.1038/s41467-020-16950-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/03/2020] [Indexed: 11/09/2022] Open
Abstract
Peptide antibiotics are an abundant and synthetically tractable source of molecular diversity, but they are often cationic and can be cytotoxic, nephrotoxic and/or ototoxic, which has limited their clinical development. Here we report structure-guided optimization of an amphipathic peptide, arenicin-3, originally isolated from the marine lugworm Arenicola marina. The peptide induces bacterial membrane permeability and ATP release, with serial passaging resulting in a mutation in mlaC, a phospholipid transport gene. Structure-based design led to AA139, an antibiotic with broad-spectrum in vitro activity against multidrug-resistant and extensively drug-resistant bacteria, including ESBL, carbapenem- and colistin-resistant clinical isolates. The antibiotic induces a 3–4 log reduction in bacterial burden in mouse models of peritonitis, pneumonia and urinary tract infection. Cytotoxicity and haemolysis of the progenitor peptide is ameliorated with AA139, and the ‘no observable adverse effect level’ (NOAEL) dose in mice is ~10-fold greater than the dose generally required for efficacy in the infection models. Peptide antibiotics often display a very narrow therapeutic index. Here, the authors present an optimized peptide antibiotic with broad-spectrum in vitro activities, in vivo efficacy in multiple disease models against multidrug-resistant Gram-negative infections, and reduced toxicity.
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Affiliation(s)
- Alysha G Elliott
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Johnny X Huang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia.,School of Life Science and Technology, Weifang Medical University, Weifang, 261053, China
| | - Søren Neve
- Orphazyme, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Johannes Zuegg
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Ingrid A Edwards
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Amy K Cain
- Wellcome Sanger Institute, Hinxton, UK.,Department of Molecular Sciences, Macquarie University, NSW, 2109, Australia
| | | | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | | | - Jason Steen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Queensland, Qld, Australia
| | - Mark S Butler
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, Queensland, Qld, Australia
| | - Kaela M Porter
- Adenium Biotech ApS, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Sergio Lociuro
- BioVersys AG, Hochbergerstrasse 60C, Technology Park, 4057, Basel, Switzerland
| | - Magnus Strandh
- Adenium Biotech ApS, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Matthew A Cooper
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia. .,Trinity College Dublin, Dublin, Ireland.
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Abstract
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications. In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.
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Affiliation(s)
- Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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31
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Charbonneau ARL, Taylor E, Mitchell CJ, Robinson C, Cain AK, Leigh JA, Maskell DJ, Waller AS. Identification of genes required for the fitness of Streptococcus equi subsp. equi in whole equine blood and hydrogen peroxide. Microb Genom 2020; 6:e000362. [PMID: 32228801 PMCID: PMC7276704 DOI: 10.1099/mgen.0.000362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/12/2020] [Indexed: 12/25/2022] Open
Abstract
The availability of next-generation sequencing techniques provides an unprecedented opportunity for the assignment of gene function. Streptococcus equi subspecies equi is the causative agent of strangles in horses, one of the most prevalent and important diseases of equids worldwide. However, the live attenuated vaccines that are utilized to control this disease cause adverse reactions in some animals. Here, we employ transposon-directed insertion-site sequencing (TraDIS) to identify genes that are required for the fitness of S. equi in whole equine blood or in the presence of H2O2 to model selective pressures exerted by the equine immune response during infection. We report the fitness values of 1503 and 1471 genes, representing 94.5 and 92.5 % of non-essential genes in S. equi, following incubation in whole blood and in the presence of H2O2, respectively. Of these genes, 36 and 15 were identified as being important to the fitness of S. equi in whole blood or H2O2, respectively, with 14 genes being important in both conditions. Allelic replacement mutants were generated to validate the fitness results. Our data identify genes that are important for S. equi to resist aspects of the immune response in vitro, which can be exploited for the development of safer live attenuated vaccines to prevent strangles.
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Affiliation(s)
- Amelia R. L. Charbonneau
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Emma Taylor
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | | | - Carl Robinson
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Amy K. Cain
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - James A. Leigh
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Duncan J. Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- University of Melbourne, Victoria, Australia
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Alquethamy SF, Adams FG, Naidu V, Khorvash M, Pederick VG, Zang M, Paton JC, Paulsen IT, Hassan KA, Cain AK, McDevitt CA, Eijkelkamp BA. The Role of Zinc Efflux during Acinetobacter baumannii Infection. ACS Infect Dis 2020; 6:150-158. [PMID: 31658418 DOI: 10.1021/acsinfecdis.9b00351] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Acinetobacter baumannii is a ubiquitous Gram-negative bacterium, that is associated with significant disease in immunocompromised individuals. The success of A. baumannii is partly attributable to its high level of antibiotic resistance. Further, A. baumannii expresses a broad arsenal of putative zinc efflux systems that are likely to aid environmental persistence and host colonization, but detailed insights into how the bacterium deals with toxic concentrations of zinc are lacking. In this study we present the transcriptomic responses of A. baumannii to toxic zinc concentrations. Subsequent mutant analyses revealed a primary role for the resistance-nodulation-cell division heavy metal efflux system CzcCBA, and the cation diffusion facilitator transporter CzcD in zinc resistance. To examine the role of zinc at the host-pathogen interface we utilized a murine model of zinc deficiency and challenge with wild-type and czcA mutant strains, which identified highly site-specific roles for zinc during A. baumannii infection. Overall, we provide novel insight into the key zinc resistance mechanisms of A. baumannii and outline the role these systems play in enabling the bacterium to survive in diverse environments.
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Affiliation(s)
- Saleh F. Alquethamy
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Felise G. Adams
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia
| | - Varsha Naidu
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, New South Wales 2109, Australia
| | - Marjan Khorvash
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Victoria G. Pederick
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Maoge Zang
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - James C. Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, New South Wales 2109, Australia
| | - Karl A. Hassan
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, New South Wales 2308, Australia
| | - Amy K. Cain
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, New South Wales 2109, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Bart A. Eijkelkamp
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia
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33
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Cain AK, Nolan LM, Sullivan GJ, Whitchurch CB, Filloux A, Parkhill J. Complete Genome Sequence of Pseudomonas aeruginosa Reference Strain PAK. Microbiol Resour Announc 2019; 8:e00865-19. [PMID: 31601664 PMCID: PMC6787321 DOI: 10.1128/mra.00865-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/09/2019] [Indexed: 11/29/2022] Open
Abstract
We report the complete genome of Pseudomonas aeruginosa strain PAK, a strain which has been instrumental in the study of a range of P. aeruginosa virulence and pathogenesis factors and has been used for over 50 years as a laboratory reference strain.
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Affiliation(s)
- Amy K Cain
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Molecular Sciences, Macquarie University, North Ryde, Australia
| | - Laura M Nolan
- Imperial College London, MRC Centre for Molecular Bacteriology and Infection, South Kensington, London, United Kingdom
| | | | - Cynthia B Whitchurch
- The ithree institute, Faculty of Science, University of Technology Sydney, Ultimo, Australia
| | - Alain Filloux
- Imperial College London, MRC Centre for Molecular Bacteriology and Infection, South Kensington, London, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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34
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Ellington MJ, Heinz E, Wailan AM, Dorman MJ, de Goffau M, Cain AK, Henson SP, Gleadall N, Boinett CJ, Dougan G, Brown NM, Woodford N, Parkhill J, Török ME, Peacock SJ, Thomson NR. Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center. Genome Biol 2019; 20:184. [PMID: 31477167 PMCID: PMC6717969 DOI: 10.1186/s13059-019-1785-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 08/05/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing patterns of disease caused by these two pathogens is based on studies with limited timeframes that provide few insights into their population dynamics or the dynamics in AMR elements that they can carry. RESULTS We investigate the population dynamics of two priority AMR pathogens over 7 years between 2007 and 2012 in a major UK hospital, spanning changes made to UK national antimicrobial prescribing policy in 2007. Between 2006 and 2012, K. pneumoniae showed epidemiological cycles of multi-drug-resistant (MDR) lineages being replaced approximately every 2 years. This contrasted E. cloacae where there was no temporally changing pattern, but a continuous presence of the mixed population. CONCLUSIONS The differing patterns of clonal replacement and acquisition of mobile elements shows that the flux in the K. pneumoniae population was linked to the introduction of globally recognized MDR clones carrying drug resistance markers on mobile elements. However, E. cloacae carries a chromosomally encoded ampC conferring resistance to front-line treatments and shows that MDR plasmid acquisition in E. cloacae was not indicative of success in the hospital. This led to markedly different dynamics in the AMR populations of these two pathogens and shows that the mechanism of the resistance and its location in the genome or mobile elements is crucial to predict population dynamics of opportunistic pathogens in clinical settings.
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Affiliation(s)
- Matthew J Ellington
- Public Health England, National Infection Service, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK.
- Present address: National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK.
| | - Eva Heinz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Alexander M Wailan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Marcus de Goffau
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Amy K Cain
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, Australia
| | - Sonal P Henson
- KEMRI-Wellcome Trust Research Programme, CGMRC, Kilifi, Kenya
| | - Nicholas Gleadall
- Public Health England, National Infection Service, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, UK
| | - Christine J Boinett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Gordon Dougan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, UK
| | - Nicholas M Brown
- Public Health England, National Infection Service, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - M Estée Török
- Public Health England, National Infection Service, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - Sharon J Peacock
- Public Health England, National Infection Service, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, UK
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, Kallonen T, Khonga M, Denis B, Gray KJ, Heyderman RS, Thomson NR, Everett DB, Feasey NA. Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. J Antimicrob Chemother 2019; 74:1223-1232. [PMID: 30778540 PMCID: PMC6477993 DOI: 10.1093/jac/dkz032] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/27/2018] [Accepted: 01/08/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES ESBL-producing Klebsiella pneumoniae (KPN) pose a major threat to human health globally. We carried out a WGS study to understand the genetic background of ESBL-producing KPN in Malawi and place them in the context of other global isolates. METHODS We sequenced genomes of 72 invasive and carriage KPN isolates collected from patients admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi. We performed phylogenetic and population structure analyses on these and previously published genomes from Kenya (n = 66) and from outside sub-Saharan Africa (n = 67). We screened for presence of antimicrobial resistance (AMR) genetic determinants and carried out association analyses by genomic sequence cluster, AMR phenotype and time. RESULTS Malawian isolates fit within the global population structure of KPN, clustering into the major lineages of KpI, KpII and KpIII. KpI isolates from Malawi were more related to those from Kenya, with both collections exhibiting more clonality than isolates from the rest of the world. We identified multiple ESBL genes, including blaCTX-M-15, several blaSHV, blaTEM-63 and blaOXA-10, and other AMR genes, across diverse lineages of the KPN isolates from Malawi. No carbapenem resistance genes were detected; however, we detected IncFII and IncFIB plasmids that were similar to the carbapenem resistance-associated plasmid pNDM-mar. CONCLUSIONS There are multiple ESBL genes across diverse KPN lineages in Malawi and plasmids in circulation that are capable of carrying carbapenem resistance. Unless appropriate interventions are rapidly put in place, these may lead to a high burden of locally untreatable infection in vulnerable populations.
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Affiliation(s)
- Patrick Musicha
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Chrispin Chaguza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Amy K Cain
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | | | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Katherine J Gray
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, UK
| | - Nicholas R Thomson
- Quadram Institute Bioscience, Norwich, UK
- London School of Tropical Medicine, London, UK
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- University of Edinburgh, Edinburgh, UK
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
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36
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Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT, Thanh DP, Dordel J, Campbell JI, Lan NPH, Mayho M, Langridge GC, Hadfield J, Chau NVV, Thwaites GE, Parkhill J, Thomson NR, Holt KE, Baker S. Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. Microb Genom 2019; 5. [PMID: 30720421 PMCID: PMC6421349 DOI: 10.1099/mgen.0.000246] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The increasing incidence and emergence of multi-drug resistant (MDR) Acinetobacter baumannii has become a major global health concern. Colistin is a historic antimicrobial that has become commonly used as a treatment for MDR A. baumannii infections. The increase in colistin usage has been mirrored by an increase in colistin resistance. We aimed to identify the mechanisms associated with colistin resistance in A. baumannii using multiple high-throughput-sequencing technologies, including transposon-directed insertion site sequencing (TraDIS), RNA sequencing (RNAseq) and whole-genome sequencing (WGS) to investigate the genotypic changes of colistin resistance in A. baumannii. Using TraDIS, we found that genes involved in drug efflux (adeIJK), and phospholipid (mlaC, mlaF and mlaD) and lipooligosaccharide synthesis (lpxC and lpsO) were required for survival in sub-inhibitory concentrations of colistin. Transcriptomic (RNAseq) analysis revealed that expression of genes encoding efflux proteins (adeI, adeC, emrB, mexB and macAB) was enhanced in in vitro generated colistin-resistant strains. WGS of these organisms identified disruptions in genes involved in lipid A (lpxC) and phospholipid synthesis (mlaA), and in the baeS/R two-component system (TCS). We additionally found that mutations in the pmrB TCS genes were the primary colistin-resistance-associated mechanisms in three Vietnamese clinical colistin-resistant A. baumannii strains. Our results outline the entire range of mechanisms employed in A. baumannii for resistance against colistin, including drug extrusion and the loss of lipid A moieties by gene disruption or modification.
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Affiliation(s)
- Christine J Boinett
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Amy K Cain
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,4Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Jane Hawkey
- 5Centre for Systems Genomics, University of Melbourne, Melbourne, Victoria, Australia.,6Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia.,7Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Nhu Tran Do Hoang
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhu Nguyen Thi Khanh
- 8School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Duy Pham Thanh
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Janina Dordel
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,9Department of Biology, Drexel University, Philadelphia 19104, PA, USA
| | - James I Campbell
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Nguyen Phu Huong Lan
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,10Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Matthew Mayho
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Gemma C Langridge
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,11Norwich Medical School, University of East Anglia, Norwich, UK
| | - James Hadfield
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - Guy E Thwaites
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Julian Parkhill
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nicholas R Thomson
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,12Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Kathryn E Holt
- 5Centre for Systems Genomics, University of Melbourne, Melbourne, Victoria, Australia.,6Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Baker
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,13Medicine, The University of Cambridge, Cambridge, UK.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
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Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J, Cain AK. A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa. Microb Genom 2018; 4. [PMID: 30383525 PMCID: PMC6321873 DOI: 10.1099/mgen.0.000229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is an extremely successful pathogen able to cause both acute and chronic infections in a range of hosts, utilizing a diverse arsenal of cell-associated and secreted virulence factors. A major cell-associated virulence factor, the Type IV pilus (T4P), is required for epithelial cell adherence and mediates a form of surface translocation termed twitching motility, which is necessary to establish a mature biofilm and actively expand these biofilms. P. aeruginosa twitching motility-mediated biofilm expansion is a coordinated, multicellular behaviour, allowing cells to rapidly colonize surfaces, including implanted medical devices. Although at least 44 proteins are known to be involved in the biogenesis, assembly and regulation of the T4P, with additional regulatory components and pathways implicated, it is unclear how these components and pathways interact to control these processes. In the current study, we used a global genomics-based random-mutagenesis technique, transposon directed insertion-site sequencing (TraDIS), coupled with a physical segregation approach, to identify all genes implicated in twitching motility-mediated biofilm expansion in P. aeruginosa. Our approach allowed identification of both known and novel genes, providing new insight into the complex molecular network that regulates this process in P. aeruginosa. Additionally, our data suggest that the flagellum-associated gene products have a differential effect on twitching motility, based on whether components are intra- or extracellular. Overall the success of our TraDIS approach supports the use of this global genomic technique for investigating virulence genes in bacterial pathogens.
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Affiliation(s)
- Laura M Nolan
- 1MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Cynthia B Whitchurch
- 2The ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Lars Barquist
- 3Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany.,4Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Marilyn Katrib
- 2The ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Christine J Boinett
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,†Present address: Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Matthew Mayho
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - David Goulding
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian G Charles
- 6Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Alain Filloux
- 1MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Julian Parkhill
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Amy K Cain
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,‡Present address: Chemical and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C, Cain AK. Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157. mBio 2018. [PMID: 30042196 DOI: 10.1128/mbio] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Experiments using bacteriophage (phage) to infect bacterial strains have helped define some basic genetic concepts in microbiology, but our understanding of the complexity of bacterium-phage interactions is still limited. As the global threat of antibiotic resistance continues to increase, phage therapy has reemerged as an attractive alternative or supplement to treating antibiotic-resistant bacterial infections. Further, the long-used method of phage typing to classify bacterial strains is being replaced by molecular genetic techniques. Thus, there is a growing need for a complete understanding of the precise molecular mechanisms underpinning phage-bacterium interactions to optimize phage therapy for the clinic as well as for retrospectively interpreting phage typing data on the molecular level. In this study, a genomics-based fitness assay (TraDIS) was used to identify all host genes involved in phage susceptibility and resistance for a T4 phage infecting Shiga-toxigenic Escherichia coli O157. The TraDIS results identified both established and previously unidentified genes involved in phage infection, and a subset were confirmed by site-directed mutagenesis and phenotypic testing of 14 T4 and 2 T7 phages. For the first time, the entire sap operon was implicated in phage susceptibility and, conversely, the stringent starvation protein A gene (sspA) was shown to provide phage resistance. Identifying genes involved in phage infection and replication should facilitate the selection of bespoke phage combinations to target specific bacterial pathogens.IMPORTANCE Antibiotic resistance has diminished treatment options for many common bacterial infections. Phage therapy is an alternative option that was once popularly used across Europe to kill bacteria within humans. Phage therapy acts by using highly specific viruses (called phages) that infect and lyse certain bacterial species to treat the infection. Whole-genome sequencing has allowed modernization of the investigations into phage-bacterium interactions. Here, using E. coli O157 and T4 bacteriophage as a model, we have exploited a genome-wide fitness assay to investigate all genes involved in defining phage resistance or susceptibility. This knowledge of the genetic determinants of phage resistance and susceptibility can be used to design bespoke phage combinations targeted to specific bacterial infections for successful infection eradication.
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Affiliation(s)
- Lauren A Cowley
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alison S Low
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Neil Perry
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - David L Gally
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C, Cain AK. Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157. mBio 2018; 9:e00705-18. [PMID: 30042196 PMCID: PMC6058288 DOI: 10.1128/mbio.00705-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/27/2018] [Indexed: 01/01/2023] Open
Abstract
Experiments using bacteriophage (phage) to infect bacterial strains have helped define some basic genetic concepts in microbiology, but our understanding of the complexity of bacterium-phage interactions is still limited. As the global threat of antibiotic resistance continues to increase, phage therapy has reemerged as an attractive alternative or supplement to treating antibiotic-resistant bacterial infections. Further, the long-used method of phage typing to classify bacterial strains is being replaced by molecular genetic techniques. Thus, there is a growing need for a complete understanding of the precise molecular mechanisms underpinning phage-bacterium interactions to optimize phage therapy for the clinic as well as for retrospectively interpreting phage typing data on the molecular level. In this study, a genomics-based fitness assay (TraDIS) was used to identify all host genes involved in phage susceptibility and resistance for a T4 phage infecting Shiga-toxigenic Escherichia coli O157. The TraDIS results identified both established and previously unidentified genes involved in phage infection, and a subset were confirmed by site-directed mutagenesis and phenotypic testing of 14 T4 and 2 T7 phages. For the first time, the entire sap operon was implicated in phage susceptibility and, conversely, the stringent starvation protein A gene (sspA) was shown to provide phage resistance. Identifying genes involved in phage infection and replication should facilitate the selection of bespoke phage combinations to target specific bacterial pathogens.IMPORTANCE Antibiotic resistance has diminished treatment options for many common bacterial infections. Phage therapy is an alternative option that was once popularly used across Europe to kill bacteria within humans. Phage therapy acts by using highly specific viruses (called phages) that infect and lyse certain bacterial species to treat the infection. Whole-genome sequencing has allowed modernization of the investigations into phage-bacterium interactions. Here, using E. coli O157 and T4 bacteriophage as a model, we have exploited a genome-wide fitness assay to investigate all genes involved in defining phage resistance or susceptibility. This knowledge of the genetic determinants of phage resistance and susceptibility can be used to design bespoke phage combinations targeted to specific bacterial infections for successful infection eradication.
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Affiliation(s)
- Lauren A Cowley
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alison S Low
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Neil Perry
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - David L Gally
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, Holt KE, Parkhill J, Thomson NR. Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. Sci Rep 2018; 8:9868. [PMID: 29959380 PMCID: PMC6026146 DOI: 10.1038/s41598-018-28199-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 06/08/2018] [Indexed: 11/09/2022] Open
Abstract
Colistin remains one of the few antibiotics effective against multi-drug resistant (MDR) hospital pathogens, such as Klebsiella pneumoniae. Yet resistance to this last-line drug is rapidly increasing. Characterized mechanisms of colR in K. pneumoniae are largely due to chromosomal mutations in two-component regulators, although a plasmid-mediated colR mechanism has recently been uncovered. However, the effects of intrinsic colistin resistance are yet to be characterized on a whole-genome level. Here, we used a genomics-based approach to understand the mechanisms of adaptive colR acquisition in K. pneumoniae. In controlled directed-evolution experiments we observed two distinct paths to colistin resistance acquisition. Whole genome sequencing identified mutations in two colistin resistance genes: in the known colR regulator phoQ which became fixed in the population and resulted in a single amino acid change, and unstable minority variants in the recently described two-component sensor crrB. Through RNAseq and microscopy, we reveal the broad range of effects that colistin exposure has on the cell. This study is the first to use genomics to identify a population of minority variants with mutations in a colR gene in K. pneumoniae.
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Affiliation(s)
- Amy K Cain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Würzburg, D-97080, Germany
| | - Janina Dordel
- Department of Biology, Drexel University, Philadelphia, 19104, PA, USA
| | - Maria Fookes
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - David Goulding
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ryan R Wick
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Musicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C, Peno C, Khonga M, Thompson S, Gray KJ, Mather AE, Heyderman RS, Everett DB, Thomson NR, Msefula CL. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. J Antimicrob Chemother 2017; 72:1602-1609. [PMID: 28333330 PMCID: PMC5437524 DOI: 10.1093/jac/dkx058] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/01/2017] [Indexed: 12/24/2022] Open
Abstract
Objectives Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Methods Ninety-four E. coli isolates from patients admitted to Queen's Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Results Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was bla CTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. Conclusions This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.
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Affiliation(s)
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Amy K Cain
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Teemu Kallonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chrispin Chaguza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Margaret Khonga
- Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Sarah Thompson
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Katherine J Gray
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Division of Infection and Immunity, University College London, London, UK
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
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Ruiz L, Bottacini F, Boinett CJ, Cain AK, O'Connell-Motherway M, Lawley TD, van Sinderen D. The essential genomic landscape of the commensal Bifidobacterium breve UCC2003. Sci Rep 2017; 7:5648. [PMID: 28717159 PMCID: PMC5514069 DOI: 10.1038/s41598-017-05795-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the Bifidobacterium and B. breve core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.
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Affiliation(s)
- Lorena Ruiz
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.,Department of Nutrition, Bromatology and Food Technology, Complutense University, Avda Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Francesca Bottacini
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mary O'Connell-Motherway
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.
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Charbonneau ARL, Forman OP, Cain AK, Newland G, Robinson C, Boursnell M, Parkhill J, Leigh JA, Maskell DJ, Waller AS. Defining the ABC of gene essentiality in streptococci. BMC Genomics 2017; 18:426. [PMID: 28569133 PMCID: PMC5452409 DOI: 10.1186/s12864-017-3794-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp. equi, the causative agent of strangles in horses, for the first time. The gene essentiality data for this group C Streptococcus was compared to that of group A and B streptococci. RESULTS Six barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries containing between 33,000-66,000 unique mutants. TraDIS was performed on DNA extracted from each library and data were analysed separately and as a combined master pool. Gene essentiality determined that 19.5% of the S. equi genome was essential. Gene essentialities were compared to those of group A and group B streptococci, identifying concordances of 90.2% and 89.4%, respectively and an overall concordance of 83.7% between the three species. CONCLUSIONS The use of barcoded pGh9:ISS1 to generate mutant libraries provides a highly useful tool for the assignment of gene function in S. equi and other streptococci. The shared essential gene set of group A, B and C streptococci provides further evidence of the close genetic relationships between these important pathogenic bacteria. Therefore, the ABC of gene essentiality reported here provides a solid foundation towards reporting the functional genome of streptococci.
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Affiliation(s)
- Amelia R L Charbonneau
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK. .,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | | | - Amy K Cain
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Graham Newland
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Carl Robinson
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Mike Boursnell
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James A Leigh
- The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, Nottingham, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Paulsen IT, Cain AK, Hassan KA. Physical enrichment of transposon mutants from saturation mutant libraries using the TraDISort approach. Mob Genet Elements 2017; 7:1-7. [PMID: 28580195 DOI: 10.1080/2159256x.2017.1313805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 03/27/2017] [Indexed: 12/21/2022] Open
Abstract
Transposon-insertion sequencing methods are finding their way into the molecular toolbox of many fields of microbiology. These methods can identify the genomic locations and density of transposon insertions in saturated transposon mutant libraries and can be used to make inferences on gene function. For example, where no insertions or very few insertions are identified within a gene in a mutant library grown under permissive conditions, the gene may be essential. Furthermore, where mutations are enriched or lost in a gene after passaging the library through a selective process, the gene is likely to be involved in phenotypes linked to the process. Typically, a fitness based selection such as a stress condition is used in these experiments and the processed sequencing data are used to identify genes required for fitness under the selection. Our research team recently expanded the utility of the transposon directed insertion sequencing (TraDIS) method by applying a physical separation of a transposon mutant library mediated by fluorescence activated cell sorting, rather than a fitness-based selection. This approach, which we have named "TraDISort" is significant because it allows the study of phenotypes that are not linked to cell survival. The TraDISort approach has a broad range of future applications, in drug development, metabolic engineering and in studies of basic bacterial cell physiology.
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Affiliation(s)
- Ian T Paulsen
- Department of Chemistry and Biomolecular Science, Macquarie University, North Ryde, NSW, Australia
| | - Amy K Cain
- Department of Chemistry and Biomolecular Science, Macquarie University, North Ryde, NSW, Australia.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Liverpool School Tropical Medicine, Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Karl A Hassan
- Department of Chemistry and Biomolecular Science, Macquarie University, North Ryde, NSW, Australia.,School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA, Parkhill J. The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. Bioinformatics 2016; 32:1109-11. [PMID: 26794317 PMCID: PMC4896371 DOI: 10.1093/bioinformatics/btw022] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/13/2016] [Indexed: 12/05/2022] Open
Abstract
Summary: Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR amplification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology. Availability and implementation: The optimized sequencing protocol is included as supplementary information. The Bio-Tradis analysis pipeline is available under a GPL license at https://github.com/sanger-pathogens/Bio-Tradis Contact:parkhill@sanger.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Carla Cummins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | | | - Andrew J Page
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Gemma C Langridge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | | | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
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Abstract
A report on the seventh annual Infectious Disease Genomics Conference, held in Hinxton, Cambridge, UK, 14–16 October 2015.
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Affiliation(s)
- Amy K Cain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - John A Lees
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK, Ellington M, Baker KS, Dongol S, Thompson C, Harris SR, Jombart T, Le Thi Phuong T, Tran Do Hoang N, Ha Thanh T, Shretha S, Joshi S, Basnyat B, Thwaites G, Thomson NR, Rabaa MA, Baker S. A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. EMBO Mol Med 2015; 7:227-39. [PMID: 25712531 PMCID: PMC4364942 DOI: 10.15252/emmm.201404767] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multidrug-resistant (MDR) Klebsiella pneumoniae has become a leading cause of nosocomial infections worldwide. Despite its prominence, little is known about the genetic diversity of K. pneumoniae in resource-poor hospital settings. Through whole-genome sequencing (WGS), we reconstructed an outbreak of MDR K. pneumoniae occurring on high-dependency wards in a hospital in Kathmandu during 2012 with a case-fatality rate of 75%. The WGS analysis permitted the identification of two MDR K. pneumoniae lineages causing distinct outbreaks within the complex endemic K. pneumoniae. Using phylogenetic reconstruction and lineage-specific PCR, our data predicted a scenario in which K. pneumoniae, circulating for 6 months before the outbreak, underwent a series of ward-specific clonal expansions after the acquisition of genes facilitating virulence and MDR. We suggest that the early detection of a specific NDM-1 containing lineage in 2011 would have alerted the high-dependency ward staff to intervene. We argue that some form of real-time genetic characterisation, alongside clade-specific PCR during an outbreak, should be factored into future healthcare infection control practices in both high- and low-income settings.
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Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Abhilasha Karkey
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Amy K Cain
- The Wellcome Trust Sanger Institute, Hinxton Cambridge, UK
| | - Matthew Ellington
- The Wellcome Trust Sanger Institute, Hinxton Cambridge, UK Addenbrooke's Hospital, Cambridge, UK
| | - Kate S Baker
- The Wellcome Trust Sanger Institute, Hinxton Cambridge, UK
| | - Sabina Dongol
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Corinne Thompson
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Simon R Harris
- The Wellcome Trust Sanger Institute, Hinxton Cambridge, UK
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, UK
| | - Tu Le Thi Phuong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhu Tran Do Hoang
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Shrijana Shretha
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Suchita Joshi
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Buddha Basnyat
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Guy Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Nicholas R Thomson
- The Wellcome Trust Sanger Institute, Hinxton Cambridge, UK The London School of Hygiene and Tropical Medicine, London, UK
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK The London School of Hygiene and Tropical Medicine, London, UK
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Baker KS, Burnett E, McGregor H, Deheer-Graham A, Boinett C, Langridge GC, Wailan AM, Cain AK, Thomson NR, Russell JE, Parkhill J. The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource. Genome Med 2015; 7:97. [PMID: 26411565 PMCID: PMC4584482 DOI: 10.1186/s13073-015-0222-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Studies of historical isolates inform on the evolution and emergence of important pathogens and phenotypes, including antimicrobial resistance. Crucial to studying antimicrobial resistance are isolates that predate the widespread clinical use of antimicrobials. The Murray collection of several hundred bacterial strains of pre-antibiotic era Enterobacteriaceae is an invaluable resource of historical strains from important pathogen groups. Studies performed on the Collection to date merely exemplify its potential, which will only be realised through the continued effort of many scientific groups. To enable that aim, we announce the public availability of the Murray collection through the National Collection of Type Cultures, and present associated metadata with whole genome sequence data for over half of the strains. Using this information we verify the metadata for the collection with regard to subgroup designations, equivalence groupings and plasmid content. We also present genomic analyses of population structure and determinants of mobilisable antimicrobial resistance to aid strain selection in future studies. This represents an invaluable public resource for the study of these important pathogen groups and the emergence and evolution of antimicrobial resistance.
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Affiliation(s)
- Kate S Baker
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Edward Burnett
- National Collection of Type Cultures, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Hannah McGregor
- National Collection of Type Cultures, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Ana Deheer-Graham
- National Collection of Type Cultures, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | | | | | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Pathogen Molecular Biology, the London School of Hygiene and Tropical Medicine, London, UK
| | - Julie E Russell
- National Collection of Type Cultures, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
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49
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Feasey NA, Cain AK, Msefula CL, Pickard D, Alaerts M, Aslett M, Everett DB, Allain TJ, Dougan G, Gordon MA, Heyderman RS, Kingsley RA. Drug resistance in Salmonella enterica ser. Typhimurium bloodstream infection, Malawi. Emerg Infect Dis 2015; 20:1957-9. [PMID: 25340988 PMCID: PMC4214322 DOI: 10.3201/eid2011.141175] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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50
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Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ, Feasey NA, Kingsley RA, Thomson NR, Keane JA, Weill FX, Edwards DJ, Hawkey J, Harris SR, Mather AE, Cain AK, Hadfield J, Hart PJ, Thieu NTV, Klemm EJ, Glinos DA, Breiman RF, Watson CH, Kariuki S, Gordon MA, Heyderman RS, Okoro C, Jacobs J, Lunguya O, Edmunds WJ, Msefula C, Chabalgoity JA, Kama M, Jenkins K, Dutta S, Marks F, Campos J, Thompson C, Obaro S, MacLennan CA, Dolecek C, Keddy KH, Smith AM, Parry CM, Karkey A, Mulholland EK, Campbell JI, Dongol S, Basnyat B, Dufour M, Bandaranayake D, Naseri TT, Singh SP, Hatta M, Newton P, Onsare RS, Isaia L, Dance D, Davong V, Thwaites G, Wijedoru L, Crump JA, De Pinna E, Nair S, Nilles EJ, Thanh DP, Turner P, Soeng S, Valcanis M, Powling J, Dimovski K, Hogg G, Farrar J, Holt KE, Dougan G. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nat Genet 2015; 47:632-9. [PMID: 25961941 PMCID: PMC4921243 DOI: 10.1038/ng.3281] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/23/2015] [Indexed: 11/09/2022]
Abstract
The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.
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Affiliation(s)
- Vanessa K Wong
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Microbiology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK
| | - Stephen Baker
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | | | | | - Robert A Kingsley
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Nicholas R Thomson
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Hawkey
- 1] Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia. [2] Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Peter J Hart
- Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nga Tran Vu Thieu
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Robert F Breiman
- 1] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya. [2] Centers for Disease Control and Prevention, Atlanta, Georgia, USA. [3] Emory Global Health Institute, Atlanta, Georgia, USA
| | - Conall H Watson
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Samuel Kariuki
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Melita A Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Robert S Heyderman
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Jan Jacobs
- 1] Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. [2] Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium
| | - Octavie Lunguya
- 1] National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo. [2] University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Chisomo Msefula
- 1] Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi. [2] Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Jose A Chabalgoity
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay
| | | | | | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Florian Marks
- International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea
| | - Josefina Campos
- Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina
| | - Corinne Thompson
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Stephen Obaro
- 1] Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA. [2] University of Abuja Teaching Hospital, Abuja, Nigeria. [3] Bingham University, Karu, Nigeria
| | - Calman A MacLennan
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK. [3] Novartis Vaccines Institute for Global Health, Siena, Italy
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher M Parry
- 1] Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK. [2] Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Abhilasha Karkey
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - E Kim Mulholland
- 1] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. [2] Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - James I Campbell
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Sabina Dongol
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Buddha Basnyat
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Muriel Dufour
- Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand
| | - Don Bandaranayake
- National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand
| | | | - Shalini Pravin Singh
- National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji
| | - Mochammad Hatta
- Department of Microbiology, Hasanuddin University, Makassar, Indonesia
| | - Paul Newton
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | | | | | - David Dance
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Guy Thwaites
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Lalith Wijedoru
- 1] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [2] Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK
| | - John A Crump
- Centre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Elizabeth De Pinna
- Salmonella Reference Service, Public Health England, Colindale, London, UK
| | - Satheesh Nair
- Salmonella Reference Service, Public Health England, Colindale, London, UK
| | - Eric J Nilles
- Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji
| | - Duy Pham Thanh
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Turner
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [3] Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sona Soeng
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Mary Valcanis
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Joan Powling
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Karolina Dimovski
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Geoff Hogg
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jeremy Farrar
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
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