1
|
Paudel S, Zhao M, Stice SP, Dutta B, Kvitko BH. Thiosulfinate Tolerance Gene Clusters Are Common Features of Burkholderia Onion Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:507-519. [PMID: 38489400 DOI: 10.1094/mpmi-01-24-0005-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Burkholderia gladioli pv. alliicola, B. cepacia, and B. orbicola are common bacterial pathogens of onion. Onions produce organosulfur thiosulfinate defensive compounds after cellular decompartmentalization. Using whole-genome sequencing and in silico analysis, we identified putative thiosulfinate tolerance gene (TTG) clusters in multiple onion-associated Burkholderia species similar to those characterized in other Allium-associated bacterial endophytes and pathogens. Sequence analysis revealed the presence of three Burkholderia TTG cluster types, with both Type A and Type B being broadly distributed in B. gladioli, B. cepacia, and B. orbicola in both the chromosome and plasmids. Based on isolate natural variation and generation of isogenic strains, we determined the in vitro and in vivo contribution of TTG clusters in B. gladioli, B. cepacia, and B. orbicola. The Burkholderia TTG clusters contributed to enhanced allicin tolerance and improved growth in filtered onion extracts by all three species. TTG clusters also made clear contributions to B. gladioli foliar necrosis symptoms and bacterial populations. Surprisingly, the TTG cluster did not contribute to bacterial populations in onion bulb scales by these three species. Based on our findings, we hypothesize onion-associated Burkholderia may evade or inhibit the production of thiosulfinates in onion bulb tissues. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Sujan Paudel
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
| | - Mei Zhao
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shaun P Stice
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
| |
Collapse
|
2
|
Loeven NA, Reuven AD, McGee AP, Dabi C, Mwaura BW, Bliska JB. A Type VI Secretion System in Burkholderia Species cenocepacia and orbicola Triggers Distinct Macrophage Death Pathways Independent of the Pyrin Inflammasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.28.559184. [PMID: 38826213 PMCID: PMC11142134 DOI: 10.1101/2023.09.28.559184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Burkholderia cepacia complex contains opportunistic pathogens that cause chronic infections and inflammation in lungs of people with cystic fibrosis. Two closely related species within this complex are Burkholderia cenocepacia and the recently classified Burkholderia orbicola. B. cenocepacia and B. orbicola encode a type VI secretion system and the effector TecA, which is detected by the pyrin/caspase-1 inflammasome, and triggers macrophage inflammatory death. In our earlier study the pyrin inflammasome was dispensable for lung inflammation in mice infected with B. orbicola AU1054, indicating this species activates an alternative pathway of macrophage inflammatory death. Notably, B. cenocepacia J2315 and K56-2 can damage macrophage phagosomes and K56-2 triggers activation of the caspase-11 inflammasome, which detects cytosolic LPS. Here we investigated inflammatory cell death in pyrin-deficient ( Mefv -/- ) mouse macrophages infected with B. cenocepacia J2315 or K56-2 or B. orbicola AU1054 or PC184. Macrophage inflammatory death was measured by cleavage of gasdermin D protein, release of cytokines IL-1α and IL-1β and plasma membrane rupture. Findings suggest that J2315 and K56-2 are detected by the caspase-11 inflammasome in Mefv -/- macrophages, resulting in IL-1β release. In contrast, inflammasome activation is not detected in Mefv -/- macrophages infected with AU1054 or PC184. Instead, AU1054 triggers an alternative macrophage inflammatory death pathway that requires TecA and results in plasma membrane rupture and IL-1α release. Amino acid variation between TecA isoforms in B. cenocepacia and B. orbicola may explain how the latter species triggers a non-inflammasome macrophage death pathway.
Collapse
|
3
|
Badten AJ, Torres AG. Burkholderia pseudomallei Complex Subunit and Glycoconjugate Vaccines and Their Potential to Elicit Cross-Protection to Burkholderia cepacia Complex. Vaccines (Basel) 2024; 12:313. [PMID: 38543947 PMCID: PMC10975474 DOI: 10.3390/vaccines12030313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Burkholderia are a group of Gram-negative bacteria that can cause a variety of diseases in at-risk populations. B. pseudomallei and B. mallei, the etiological agents of melioidosis and glanders, respectively, are the two clinically relevant members of the B. pseudomallei complex (Bpc). The development of vaccines against Bpc species has been accelerated in recent years, resulting in numerous promising subunits and glycoconjugate vaccines incorporating a variety of antigens. However, a second group of pathogenic Burkholderia species exists known as the Burkholderia cepacia complex (Bcc), a group of opportunistic bacteria which tend to affect individuals with weakened immunity or cystic fibrosis. To date, there have been few attempts to develop vaccines to Bcc species. Therefore, the primary goal of this review is to provide a broad overview of the various subunit antigens that have been tested in Bpc species, their protective efficacy, study limitations, and known or suspected mechanisms of protection. Then, we assess the reviewed Bpc antigens for their amino acid sequence conservation to homologous proteins found in Bcc species. We propose that protective Bpc antigens with a high degree of Bpc-to-Bcc sequence conservation could serve as components of a pan-Burkholderia vaccine capable of protecting against both disease-causing groups.
Collapse
Affiliation(s)
- Alexander J. Badten
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alfredo G. Torres
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| |
Collapse
|
4
|
Kim B, Han SR, Lee H, Oh TJ. Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus. Front Microbiol 2024; 14:1302236. [PMID: 38293557 PMCID: PMC10826400 DOI: 10.3389/fmicb.2023.1302236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.
Collapse
Affiliation(s)
- Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
| | - Hyun Lee
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Division of Computer Science and Engineering, SunMoon University, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea
| |
Collapse
|
5
|
Tewkesbury DH, Pollard LR, Green HD, Horsley A, Kenna D, Jones AM. When is Burkholderia cepacia complex truly eradicated in adults with cystic fibrosis? A 20-year follow up study. J Cyst Fibros 2024; 23:87-90. [PMID: 37775444 DOI: 10.1016/j.jcf.2023.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023]
Abstract
BACKGROUND Burkholderia cepacia complex (BCC) infection in cystic fibrosis (CF) is associated with increased morbidity and mortality. Current UK guidance recommends segregation of people with CF according to infection status. To date there is no universally agreed consensus on the number of negative samples or time interval since last isolation of BCC for eradication to be deemed successful. METHODS All cases of new BCC isolation at Manchester Adult Cystic Fibrosis Centre were followed-up between May 2002-May 2022. The number of subsequent positive and negative sputum samples for BCC were recorded, as well as eradication treatment received. Eradication was deemed successful if there were ≥3 negative sputum samples and no further positive sputum samples for the same species and strain ≥12 months until the end of follow-up. RESULTS Of 46 new BCC isolation, 25 were successfully eradicated and 21 resulted in chronic infection. 5 (16.7%) cases with exclusively negative sputum samples 6-12 months after initial isolation had subsequent samples that were culture-positive for BCC and 3 (10.7%) cases with exclusively negative sputum samples after 12-24 months had subsequent culture-positive samples. Cases where BCC was eradicated had a greater median number of days of eradication treatment (42, IQR 21-63) compared to those in whom BCC isolation resulted in chronic infection (28, IQR 14-42), p = 0.04. CONCLUSIONS A cautious approach to segregation should be maintained after new isolation of BCC in CF, as some individuals with ≥3 negative samples 12-24 months after initial isolation had subsequent sputum samples culture-positive for BCC.
Collapse
Affiliation(s)
- Daniel H Tewkesbury
- Manchester University NHS Foundation Trust, Manchester, United Kingdom; University of Manchester, Manchester, United Kingdom
| | | | - Heather D Green
- Manchester University NHS Foundation Trust, Manchester, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Alexander Horsley
- Manchester University NHS Foundation Trust, Manchester, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Dervla Kenna
- UK Health Security Agency, Colindale, United Kingdom
| | - Andrew M Jones
- Manchester University NHS Foundation Trust, Manchester, United Kingdom; University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
6
|
Munson E, Carella A, Carroll KC. Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022. J Clin Microbiol 2023; 61:e0083823. [PMID: 37889007 PMCID: PMC10662342 DOI: 10.1128/jcm.00838-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
Although some nomenclature changes have caused consternation among clinical microbiologists, the discovery of novel taxa and improving classification of existing groups of organisms is exciting and adds to our understanding of microbial pathogenesis. In this mini-review, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2022. Henceforth, these bacteriology taxonomic summaries will appear annually. Several of the novel Gram-positive organisms have been associated with disease, namely, the Corynebacterium kroppenstedtii-like organisms Corynebacterium parakroppenstedtii sp. nov. and Corynebacterium pseudokroppenstedtii sp. nov. A newly described Streptococcus species, Streptococcus toyakuensis sp. nov., is noteworthy for exhibiting multi-drug resistance. Among the novel Gram-negative pathogens, Vibrio paracholerae sp. nov. stands out as an organism associated with diarrhea and sepsis and has probably been co-circulating with pandemic Vibrio cholerae for decades. Many new anaerobic organisms have been described in this past year largely from genetic assessments of gastrointestinal microbiome collections. With respect to revised taxa, as discussed in previous reviews, the genus Bacillus continues to undergo further division into additional genera and reassignment of existing species into them. Reassignment of two subspecies of Fusobacterium nucleatum to species designations (Fusobacterium animalis sp. nov. and Fusobacterium vincentii sp. nov.) is also noteworthy. As was typical of previous reviews, literature updates for selected clinically relevant organisms discovered between 2017 and 2021 have been included.
Collapse
Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Arianna Carella
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C. Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
7
|
Karthikeyan R, Agri H, Yadav A, Jayakumar V, Kiranmayee B, Karikalan M, Chandra M, Lyngdoh V, Ghatak S, Sinha DK, Singh BR. A study on the occurrence of Burkholderia cepacia complex in ultrasound gels used in different veterinary clinical settings in India. Vet Res Commun 2023; 47:1413-1425. [PMID: 36914918 DOI: 10.1007/s11259-023-10091-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
Burkholderia cepacia complex (Bcc) organisms are emerging multidrug-resistant pathogens. They are opportunistic and cause severe diseases in humans that may result in fatal outcomes. They are mainly reported as nosocomial pathogens, and transmission often occurs through contaminated pharmaceutical products. From 1993 to 2019, 14 Bcc outbreaks caused by contaminated ultrasound gels (USGs) have been reported in several countries, including India. We screened a total of 63 samples of USGs from various veterinary and human clinical care centers across 17 states of India and isolated 32 Bcc strains of Burkholderia cenocepacia (46.8%), B. cepacia (31.3%), B. pseudomultivorans (18.8%) and B. contaminans (3.1%) species. Some isolates were co-existent in a single ultrasound gel sample. The isolation from unopened gel bottles revealed the intrinsic contamination from manufacturing sites. The MALDI-TOF analysis to identify the Bcc at the species level was supported by the partial sequencing of the recA gene for accurate species identification. The phylogenetic analysis revealed that isolates shared clades with human clinical isolates, which is an important situation because of the possible infections of Bcc by USGs both in humans and animals. The pulsed field gel electrophoresis (PFGE) typing identified the genetic variation among the Bcc isolates present in the USGs. The findings indicated USGs as the potential source of Bcc species.
Collapse
Affiliation(s)
- Ravichandran Karthikeyan
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Himani Agri
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Akanksha Yadav
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Varsha Jayakumar
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Bhimavarapu Kiranmayee
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Mathesh Karikalan
- Center for wildlife Conservation Management and Disease Surveillance, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Mudit Chandra
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Vanita Lyngdoh
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - Sandeep Ghatak
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - Dharmendra K Sinha
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Bhoj R Singh
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
| |
Collapse
|
8
|
Parfitt KM, Green AE, Connor TR, Neill DR, Mahenthiralingam E. Identification of two distinct phylogenomic lineages and model strains for the understudied cystic fibrosis lung pathogen Burkholderia multivorans. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001366. [PMID: 37526960 PMCID: PMC10482378 DOI: 10.1099/mic.0.001366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023]
Abstract
Burkholderia multivorans is the dominant Burkholderia pathogen recovered from lung infection in people with cystic fibrosis. However, as an understudied pathogen there are knowledge gaps in relation to its population biology, phenotypic traits and useful model strains. A phylogenomic study of B. multivorans was undertaken using a total of 283 genomes, of which 73 were sequenced and 49 phenotypically characterized as part of this study. Average nucleotide identity analysis (ANI) and phylogenetic alignment of core genes demonstrated that the B. multivorans population separated into two distinct evolutionary clades, defined as lineage 1 (n=58 genomes) and lineage 2 (n=221 genomes). To examine the population biology of B. multivorans, a representative subgroup of 77 B. multivorans genomes (28 from the reference databases and the 49 novel short-read genome sequences) were selected based on multilocus sequence typing (MLST), isolation source and phylogenetic placement criteria. Comparative genomics was used to identify B. multivorans lineage-specific genes - ghrB_1 in lineage 1 and glnM_2 in lineage 2 - and diagnostic PCRs targeting them were successfully developed. Phenotypic analysis of 49 representative B. multivorans strains showed considerable inter-strain variance, but the majority of the isolates tested were motile and capable of biofilm formation. A striking absence of B. multivorans protease activity in vitro was observed, but no lineage-specific phenotypic differences were demonstrated. Using phylogenomic and phenotypic criteria, three model B. multivorans CF strains were identified, BCC0084 (lineage 1), BCC1272 (lineage 2a) and BCC0033 lineage 2b, and their complete genome sequences determined. B. multivorans CF strains BCC0033 and BCC0084, and the environmental reference strain, ATCC 17616, were all capable of short-term survival within a murine lung infection model. By mapping the population biology, identifying lineage-specific PCRs and model strains, we provide much needed baseline resources for future studies of B. multivorans.
Collapse
Affiliation(s)
- Kasia M. Parfitt
- Cardiff University, Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, CF10 3AX, UK
- Present address: Department of Biology, Big Data Institute, Nuffield Department of Population Health, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Angharad E. Green
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Thomas R. Connor
- Cardiff University, Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, CF10 3AX, UK
| | - Daniel R. Neill
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- Present address: Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH UK, UK
| | - Eshwar Mahenthiralingam
- Cardiff University, Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, CF10 3AX, UK
| |
Collapse
|
9
|
Hubert L, Barton TE, Leighton HJ, Richards B. Preclinical testing of antimicrobials for cystic fibrosis lung infections: current needs and future priorities. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001361. [PMID: 37428539 PMCID: PMC10433426 DOI: 10.1099/mic.0.001361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
A workshop was held by the PIPE-CF strategic research centre to consider preclinical testing of antimicrobials for cystic fibrosis (CF). The workshop brought together groups of people from the CF community to discuss current challenges and identify priorities when developing CF therapeutics. This paper summarizes the key points from the workshop from the different sessions, including talks given by presenters on the day and round table discussions. Currently, it is felt that there is a large disconnect throughout the community, with communication between patients, clinicians and researchers being the main issue. This leads to little consideration being given to factors such as treatment regimes, routes of administration and side effects when developing new therapies, that could alter the day-to-day lifestyles of people living with CF. Translation of numerical data that are obtained in the laboratory to successful outcomes of clinical trials is also a key challenge facing researchers today. Laboratory assays in preclinical testing involve basing results on bacterial clearance and decrease in viable cells, when these are not factors that are considered when determining the success of a treatment in the clinic. However, there are several models currently in development that seek to tackle some of these issues, such as the organ-on-a-chip technology and adaptation of a hollow-fibre model, as well as the development of media that aim to mimic the niche environments of a CF respiratory tract. It is hoped that by summarizing these opinions and discussing current research, the communication gap between groups can begin to close.
Collapse
Affiliation(s)
- Lucile Hubert
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Park Place, Cardiff, UK
| | - Thomas E. Barton
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK
| | - Hollie J. Leighton
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK
| | - Brogan Richards
- School of Life Sciences, University of Nottingham, Nottingham, UK
| |
Collapse
|
10
|
Stanton CR, Batinovic S, Petrovski S. Burkholderia contaminans Bacteriophage CSP3 Requires O-Antigen Polysaccharides for Infection. Microbiol Spectr 2023; 11:e0533222. [PMID: 37199610 PMCID: PMC10269572 DOI: 10.1128/spectrum.05332-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
The Burkholderia cepacia complex is a group of opportunistic pathogens that cause both severe acute and chronic respiratory infections. Due to their large genomes containing multiple intrinsic and acquired antimicrobial resistance mechanisms, treatment is often difficult and prolonged. One alternative to traditional antibiotics for treatment of bacterial infections is bacteriophages. Therefore, the characterization of bacteriophages infective for the Burkholderia cepacia complex is critical to determine their suitability for any future use. Here, we describe the isolation and characterization of novel phage, CSP3, infective against a clinical isolate of Burkholderia contaminans. CSP3 is a new member of the Lessievirus genus that targets various Burkholderia cepacia complex organisms. Single nucleotide polymorphism (SNP) analysis of CSP3-resistant B. contaminans showed that mutations to the O-antigen ligase gene, waaL, consequently inhibited CSP3 infection. This mutant phenotype is predicted to result in the loss of cell surface O-antigen, contrary to a related phage that requires the inner core of the lipopolysaccharide for infection. Additionally, liquid infection assays showed that CSP3 provides suppression of B. contaminans growth for up to 14 h. Despite the inclusion of genes that are typical of the phage lysogenic life cycle, we saw no evidence of CSP3's ability to lysogenize. Continuation of phage isolation and characterization is crucial in developing large and diverse phage banks for global usage in cases of antibiotic-resistant bacterial infections. IMPORTANCE Amid the global antibiotic resistance crisis, novel antimicrobials are needed to treat problematic bacterial infections, including those from the Burkholderia cepacia complex. One such alternative is the use of bacteriophages; however, a lot is still unknown about their biology. Bacteriophage characterization studies are of high importance for building phage banks, as future work in developing treatments such as phage cocktails should require well-characterized phages. Here, we report the isolation and characterization of a novel Burkholderia contaminans phage that requires the O-antigen for infection, a distinct phenotype seen among other related phages. Our findings presented in this article expand on the ever-evolving phage biology field, uncovering unique phage-host relationships and mechanisms of infection.
Collapse
Affiliation(s)
- Cassandra R. Stanton
- Department of Microbiology, Anatomy, Physiology & Pharmacology, La Trobe University, Bundoora, Australia
| | - Steven Batinovic
- Department of Microbiology, Anatomy, Physiology & Pharmacology, La Trobe University, Bundoora, Australia
- Division of Materials Science and Chemical Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology & Pharmacology, La Trobe University, Bundoora, Australia
| |
Collapse
|
11
|
Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria. Minutes of the closed annual meeting: videoconference on 11 October 2022 followed by online discussion until 31 December 2022. Int J Syst Evol Microbiol 2023; 73. [PMID: 37115621 DOI: 10.1099/ijsem.0.005856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Affiliation(s)
- Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| |
Collapse
|
12
|
Velez LS, Aburjaile FF, Farias ARG, Baia ADB, Oliveira WJ, Silva AMF, Benko-Iseppon AM, Azevedo V, Brenig B, Ham JH, Souza EB, Gama MAS. Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin. Syst Appl Microbiol 2023; 46:126415. [PMID: 36933352 DOI: 10.1016/j.syapm.2023.126415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Two putative novel Burkholderia cenocepacia lineages found in the semi-arid region of north-east Brazil causing onion sour skin were studied using genomic approaches to determine their taxonomic position. Four strains belonging to one novel lineage (CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171) and one strain (CCRMBC51) belonging to another novel lineage had their whole genome sequenced to carry out taxogenomic analyses. The phylogenomic tree built using the type (strain) genome server (TYGS) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 into the same clade, while grouped the strain CCRMBC51 separately. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analysis showed values above 99.21 % and 93.2 %, respectively, among the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171, while ANI and dDDH values between these strains and the strain CCRMBC51 were below 94.49 % and 56.6 %, respectively. All these strains showed ANI and dDDH values below 94.78 % and 58.8 % concerning type strains of the B. cepacia complex (Bcc) species. The phylogenetic maximum likelihood tree constructed based on the multilocus sequence analysis of core genes (cMLSA) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 and the strain CCRMBC51 in two exclusive clades, which did not cluster with any known species of the Bcc. Therefore, combined data from TYGS, ANI, dDDH, and cMLSA demonstrated that the strains represent two novel species of the Bcc, which we classified as Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., and proposed the strains CCRMBC74T (=IBSBF 3371 T = CBAS 905 T) and CCRMBC51T (=IBSBF3370T = CBAS 904 T) as type strains, respectively.
Collapse
Affiliation(s)
- Leandro S Velez
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Flávia F Aburjaile
- Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Antonio R G Farias
- Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Ana D B Baia
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Willams J Oliveira
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Adriano M F Silva
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Ana M Benko-Iseppon
- Department of Genetics, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Bertram Brenig
- Department of Molecular Biology of Livestock, Institute of Veterinary Medicine, Georg August University Göttingen, 37077 Göttingen, Germany
| | - Jong H Ham
- Department Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, United States
| | - Elineide B Souza
- Department of Biology, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Marco A S Gama
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil.
| |
Collapse
|
13
|
Compilation of the Antimicrobial Compounds Produced by Burkholderia Sensu Stricto. Molecules 2023; 28:molecules28041646. [PMID: 36838633 PMCID: PMC9958762 DOI: 10.3390/molecules28041646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Due to the increase in multidrug-resistant microorganisms, the investigation of novel or more efficient antimicrobial compounds is essential. The World Health Organization issued a list of priority multidrug-resistant bacteria whose eradication will require new antibiotics. Among them, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae are in the "critical" (most urgent) category. As a result, major investigations are ongoing worldwide to discover new antimicrobial compounds. Burkholderia, specifically Burkholderia sensu stricto, is recognized as an antimicrobial-producing group of species. Highly dissimilar compounds are among the molecules produced by this genus, such as those that are unique to a particular strain (like compound CF66I produced by Burkholderia cepacia CF-66) or antimicrobials found in a number of species, e.g., phenazines or ornibactins. The compounds produced by Burkholderia include N-containing heterocycles, volatile organic compounds, polyenes, polyynes, siderophores, macrolides, bacteriocins, quinolones, and other not classified antimicrobials. Some of them might be candidates not only for antimicrobials for both bacteria and fungi, but also as anticancer or antitumor agents. Therefore, in this review, the wide range of antimicrobial compounds produced by Burkholderia is explored, focusing especially on those compounds that were tested in vitro for antimicrobial activity. In addition, information was gathered regarding novel compounds discovered by genome-guided approaches.
Collapse
|
14
|
Oren A, Garrity GM. Validation List no. 206. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005422] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|