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Al-Kadmy IMS, Abid SA, Aziz SN, Al-Kadmy Z, Suhail A, Al-Jubori SS, Naji EN, Alhomaidi E, Yahia R, Algammal AM, Batiha GES, Hetta HF. The secrets of environmental Pseudomonas aeruginosa in slaughterhouses: Antibiogram profile, virulence, and antibiotic resistance genes. Folia Microbiol (Praha) 2024; 69:805-822. [PMID: 38091178 DOI: 10.1007/s12223-023-01116-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/06/2023] [Indexed: 08/03/2024]
Abstract
Environmental pollution is a serious problem that can cause sicknesses, fatality, and biological contaminants such as bacteria, which can trigger allergic reactions and infectious illnesses. There is also evidence that environmental pollutants can have an impact on the gut microbiome and contribute to the development of various mental health and metabolic disorders. This study aimed to study the antibiotic resistance and virulence potential of environmental Pseudomonas aeruginosa (P. aeruginosa) isolates in slaughterhouses. A total of 100 samples were collected from different slaughterhouse tools. The samples were identified by cultural and biochemical tests and confirmed by the VITEK 2 system. P. aeruginosa isolates were further confirmed by CHROMagar™ Pseudomonas and genetically by rpsL gene analysis. Molecular screening of virulence genes (fimH, papC, lasB, rhlI, lasI, csgA, toxA, and hly) and antibiotic resistance genes (blaCTX-M, blaAmpC, blaSHV, blaNDM, IMP-1, aac(6')-Ib-, ant(4')IIb, mexY, TEM, tetA, and qnrB) by PCR and testing the antibiotic sensitivity, biofilm formation, and production of pigments, and hemolysin were carried out in all isolated strains. A total of 62 isolates were identified as P. aeruginosa. All P. aeruginosa isolates were multidrug-resistant and most of them have multiple resistant genes. blaCTX-M gene was detected in all strains; 23 (37.1%) strains have the ability for biofilm formation, 33 strains had virulence genes, and 26 isolates from them have more than one virulence genes. There should be probably 60 (96.8%) P. aeruginosa strains that produce pyocyanin pigment. Slaughterhouse tools are sources for multidrug-resistant and virulent pathogenic microorganisms which are a serious health problem. Low-hygienic slaughterhouses could be a reservoir for resistance and virulence genes which could then be transferred to other pathogens.
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Affiliation(s)
- Israa M S Al-Kadmy
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, POX 10244, Baghdad, Iraq.
| | - Suhad Abbas Abid
- Branch of Microbiology, Department of Biology, College of Science, Mustansiriyah University, POX 10244, Baghdad, Iraq
| | - Sarah Naji Aziz
- Branch of Microbiology, Department of Biology, College of Science, Mustansiriyah University, POX 10244, Baghdad, Iraq
| | - Zahraa Al-Kadmy
- Department of Dentistry, Al-Rasheed University College, Baghdad, Iraq
| | - Ahmed Suhail
- Departmentt of Physics, College of Science, University of Mosul, Mosul, Iraq
| | - Sawsan Sajid Al-Jubori
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, POX 10244, Baghdad, Iraq
| | - Eman Natiq Naji
- Branch of Microbiology, Department of Biology, College of Science, Mustansiriyah University, POX 10244, Baghdad, Iraq
| | - Eman Alhomaidi
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Ramadan Yahia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minya, Egypt
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicines, Damanhour University, Damanhour, 22511, Egypt
| | - Helal F Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
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Bouchali R, Mandon C, Danty-Berger E, Géloën A, Marjolet L, Youenou B, Pozzi ACM, Vareilles S, Galia W, Kouyi GL, Toussaint JY, Cournoyer B. Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns. Int J Hyg Environ Health 2024; 260:114391. [PMID: 38781750 DOI: 10.1016/j.ijheh.2024.114391] [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: 09/04/2023] [Revised: 03/15/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.
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Affiliation(s)
- Rayan Bouchali
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Claire Mandon
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Emmanuelle Danty-Berger
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Alain Géloën
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Laurence Marjolet
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Benjamin Youenou
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Adrien C M Pozzi
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Sophie Vareilles
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Wessam Galia
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | | | - Jean-Yves Toussaint
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Benoit Cournoyer
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France.
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Gatasheh MK, Murugan N, Krishnamoorthy R, Alshuniaber MA, Malathi J, Umashankar V, Ramalingam G, Veeraraghavan VP, Jayaraman S. Identification, prioritization, and evaluation of RlpA protein as a target against multidrug-resistant Pseudomonas aeruginosa. Acta Trop 2024; 255:107216. [PMID: 38636584 DOI: 10.1016/j.actatropica.2024.107216] [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: 12/20/2023] [Revised: 02/07/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024]
Abstract
According to the World Health Organization, infectious diseases, particularly those caused by multidrug-resistant bacteria (MDR), are projected to claim the lives of 15 million people by 2050. Septicemia carries a higher morbidity and mortality rate than infections caused by susceptible Pseudomonas aeruginosa, and MDR-mediated ocular infections can lead to impaired vision and blindness. To identify and develop a potential drug against MDR P. aeruginosa, we employed in silico reverse genetics-based target mining, drug prioritization, and evaluation. Rare Lipoprotein A (RlpA) was selected as the target protein, and its crystal structure was geometrically optimized. Molecular docking and virtual screening analyses revealed that RlpA exhibits strong binding affinity with 11 compounds. Among these, 3-chlorophthalic acid was evaluated, and subsequent in vitro assays demonstrated significant anti-Pseudomonas activity with negligible cytotoxicity. The compound was further evaluated against both drug-susceptible and MDR P. aeruginosa strains in vitro, with cytotoxicity assessed using an MTT assay. The study demonstrated that 3-chlorophthalic acid exhibits potent anti-Pseudomonas activity with minimal toxicity to host cells. Consequently, this compound emerges as a promising candidate against MDR P. aeruginosa, warranting further investigation.
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Affiliation(s)
- Mansour K Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O.Box 2455, Riyadh, 11451, Saudi Arabia
| | - Nandagopal Murugan
- Department of Microbiology, L & T Microbiology Research Centre, Vision Research Foundation, Sankara Nethralaya, Chennai, 6000 06, India
| | - Rajapandiyan Krishnamoorthy
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Mohammad A Alshuniaber
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Jambulingam Malathi
- Department of Microbiology, L & T Microbiology Research Centre, Vision Research Foundation, Sankara Nethralaya, Chennai, 6000 06, India
| | - Vetrivel Umashankar
- Centre for Bioinformatics, Vision Research Foundation, Sankara Nethralaya, Chennai 600 006, India
| | - Gopinath Ramalingam
- Department of Microbiology, Government Theni Medical College and Hospital, Theni, Tamil Na-du 625512, India
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, India
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, India.
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Elsen S, Simon V, Attrée I. Cross-regulation and cross-talk of conserved and accessory two-component regulatory systems orchestrate Pseudomonas copper resistance. PLoS Genet 2024; 20:e1011325. [PMID: 38861577 PMCID: PMC11195947 DOI: 10.1371/journal.pgen.1011325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/24/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
Bacteria use diverse strategies and molecular machinery to maintain copper homeostasis and to cope with its toxic effects. Some genetic elements providing copper resistance are acquired by horizontal gene transfer; however, little is known about how they are controlled and integrated into the central regulatory network. Here, we studied two copper-responsive systems in a clinical isolate of Pseudomonas paraeruginosa and deciphered the regulatory and cross-regulation mechanisms. To do so, we combined mutagenesis, transcriptional fusion analyses and copper sensitivity phenotypes. Our results showed that the accessory CusRS two-component system (TCS) responds to copper and activates both its own expression and that of the adjacent nine-gene operon (the pcoA2 operon) to provide resistance to elevated levels of extracellular copper. The same locus was also found to be regulated by two core-genome-encoded TCSs-the copper-responsive CopRS and the zinc-responsive CzcRS. Although the target palindromic sequence-ATTCATnnATGTAAT-is the same for the three response regulators, transcriptional outcomes differ. Thus, depending on the operon/regulator pair, binding can result in different activation levels (from none to high), with the systems demonstrating considerable plasticity. Unexpectedly, although the classical CusRS and the noncanonical CopRS TCSs rely on distinct signaling mechanisms (kinase-based vs. phosphatase-based), we discovered cross-talk in the absence of the cognate sensory kinases. This cross-talk occurred between the proteins of these two otherwise independent systems. The cusRS-pcoA2 locus is part of an Integrative and Conjugative Element and was found in other Pseudomonas strains where its expression could provide copper resistance under appropriate conditions. The results presented here illustrate how acquired genetic elements can become part of endogenous regulatory networks, providing a physiological advantage. They also highlight the potential for broader effects of accessory regulatory proteins through interference with core regulatory proteins.
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Affiliation(s)
- Sylvie Elsen
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Victor Simon
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Ina Attrée
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
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Aroca Molina KJ, Gutiérrez SJ, Benítez-Campo N, Correa A. Genomic Differences Associated with Resistance and Virulence in Pseudomonas aeruginosa Isolates from Clinical and Environmental Sites. Microorganisms 2024; 12:1116. [PMID: 38930498 PMCID: PMC11205572 DOI: 10.3390/microorganisms12061116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 06/28/2024] Open
Abstract
Pseudomonas aeruginosa is a pathogen that causes healthcare-associated infections (HAIs) worldwide. It is unclear whether P. aeruginosa isolated from the natural environment has the same pathogenicity and antimicrobial resistance potential as clinical strains. In this study, virulence- and resistance-associated genes were compared in 14 genomic sequences of clinical and environmental isolates of P. aeruginosa using the VFDB, PATRIC, and CARD databases. All isolates were found to share 62% of virulence genes related to adhesion, motility, secretion systems, and quorum sensing and 72.9% of resistance genes related to efflux pumps and membrane permeability. Our results indicate that both types of isolates possess conserved genetic information associated with virulence and resistance mechanisms regardless of the source. However, none of the environmental isolates were associated with high-risk clones (HRCs). These clones (ST235 and ST111) were found only in clinical isolates, which have an impact on human medical epidemiology due to their ability to spread and persist, indicating a correlation between the clinical environment and increased virulence. The genomic variation and antibiotic susceptibility of environmental isolates of P. aeruginosa suggest potential biotechnological applications if obtained from sources that are under surveillance and investigation to limit the emergence and spread of antibiotic resistant strains.
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Affiliation(s)
- Kelly J. Aroca Molina
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Sonia Jakeline Gutiérrez
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Neyla Benítez-Campo
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Adriana Correa
- Department of Basic Sciences, Universidad Santiago de Cali, Cali 760035, Colombia;
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Wu W, Huang J, Xu Z. Antibiotic influx and efflux in Pseudomonas aeruginosa: Regulation and therapeutic implications. Microb Biotechnol 2024; 17:e14487. [PMID: 38801351 PMCID: PMC11129675 DOI: 10.1111/1751-7915.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Pseudomonas aeruginosa is a notorious multidrug-resistant pathogen that poses a serious and growing threat to the worldwide public health. The expression of resistance determinants is exquisitely modulated by the abundant regulatory proteins and the intricate signal sensing and transduction systems in this pathogen. Downregulation of antibiotic influx porin proteins and upregulation of antibiotic efflux pump systems owing to mutational changes in their regulators or the presence of distinct inducing molecular signals represent two of the most efficient mechanisms that restrict intracellular antibiotic accumulation and enable P. aeruginosa to resist multiple antibiotics. Treatment of P. aeruginosa infections is extremely challenging due to the highly inducible mechanism of antibiotic resistance. This review comprehensively summarizes the regulatory networks of the major porin proteins (OprD and OprH) and efflux pumps (MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY) that play critical roles in antibiotic influx and efflux in P. aeruginosa. It also discusses promising therapeutic approaches using safe and efficient adjuvants to enhance the efficacy of conventional antibiotics to combat multidrug-resistant P. aeruginosa by controlling the expression levels of porins and efflux pumps. This review not only highlights the complexity of the regulatory network that induces antibiotic resistance in P. aeruginosa but also provides important therapeutic implications in targeting the inducible mechanism of resistance.
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Affiliation(s)
- Weiyan Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Jiahui Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
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Janet-Maitre M, Job V, Bour M, Robert-Genthon M, Brugière S, Triponney P, Cobessi D, Couté Y, Jeannot K, Attrée I. Pseudomonas aeruginosa MipA-MipB envelope proteins act as new sensors of polymyxins. mBio 2024; 15:e0221123. [PMID: 38345374 PMCID: PMC10936184 DOI: 10.1128/mbio.02211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/09/2024] [Indexed: 03/14/2024] Open
Abstract
Due to the rising incidence of antibiotic-resistant infections, the last-line antibiotics, polymyxins, have resurged in the clinics in parallel with new bacterial strategies of escape. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa develops resistance to colistin/polymyxin B by distinct molecular mechanisms, mostly through modification of the lipid A component of the LPS by proteins encoded within the arnBCDATEF-ugd (arn) operon. In this work, we characterized a polymyxin-induced operon named mipBA, present in P. aeruginosa strains devoid of the arn operon. We showed that mipBA is activated by the ParR/ParS two-component regulatory system in response to polymyxins. Structural modeling revealed that MipA folds as an outer-membrane β-barrel, harboring an internal negatively charged channel, able to host a polymyxin molecule, while the lipoprotein MipB adopts a β-lactamase fold with two additional C-terminal domains. Experimental work confirmed that MipA and MipB localize to the bacterial envelope, and they co-purify in vitro. Nano differential scanning fluorimetry showed that polymyxins stabilized MipA in a specific and dose-dependent manner. Mass spectrometry-based quantitative proteomics on P. aeruginosa membranes demonstrated that ∆mipBA synthesized fourfold less MexXY-OprA proteins in response to polymyxin B compared to the wild-type strain. The decrease was a direct consequence of impaired transcriptional activation of the mex operon operated by ParR/ParS. We propose MipA/MipB to act as membrane (co)sensors working in concert to activate ParS histidine kinase and help the bacterium to cope with polymyxin-mediated envelope stress through synthesis of the efflux pump, MexXY-OprA.IMPORTANCEDue to the emergence of multidrug-resistant isolates, antibiotic options may be limited to polymyxins to eradicate Gram-negative infections. Pseudomonas aeruginosa, a leading opportunistic pathogen, has the ability to develop resistance to these cationic lipopeptides by modifying its lipopolysaccharide through proteins encoded within the arn operon. Herein, we describe a sub-group of P. aeruginosa strains lacking the arn operon yet exhibiting adaptability to polymyxins. Exposition to sub-lethal polymyxin concentrations induced the expression and production of two envelope-associated proteins. Among those, MipA, an outer-membrane barrel, is able to specifically bind polymyxins with an affinity in the 10-µM range. Using membrane proteomics and phenotypic assays, we showed that MipA and MipB participate in the adaptive response to polymyxins via ParR/ParS regulatory signaling. We propose a new model wherein the MipA-MipB module functions as a novel polymyxin sensing mechanism.
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Affiliation(s)
- Manon Janet-Maitre
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Viviana Job
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Maxime Bour
- UMR6249 Chrono-Environnement, UFR Santé, University of Franche-Comté, Besançon, France
- French National Reference Center for Antibiotic Resistance, Besançon, France
| | - Mylène Robert-Genthon
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Sabine Brugière
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, FranceGrenoble
| | - Pauline Triponney
- French National Reference Center for Antibiotic Resistance, Besançon, France
| | - David Cobessi
- University Grenoble Alpes, IBS, UMR5075, Team Synchrotron, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, FranceGrenoble
| | - Katy Jeannot
- UMR6249 Chrono-Environnement, UFR Santé, University of Franche-Comté, Besançon, France
- French National Reference Center for Antibiotic Resistance, Besançon, France
- Department of Bacteriology, Teaching Hospital of Besançon, Besançon, France
| | - Ina Attrée
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
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Trottier MC, de Oliveira Pereira T, Groleau MC, Hoffman LR, Dandekar AA, Déziel E. The end of the reign of a "master regulator''? A defect in function of the LasR quorum sensing regulator is a common feature of Pseudomonas aeruginosa isolates. mBio 2024; 15:e0237623. [PMID: 38315035 PMCID: PMC10936206 DOI: 10.1128/mbio.02376-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Pseudomonas aeruginosa, a bacterium causing infections in immunocompromised individuals, regulates several of its virulence functions using three interlinked quorum sensing (QS) systems (las, rhl, and pqs). Despite its presumed importance in regulating virulence, dysfunction of the las system regulator LasR occurs frequently in strains isolated from various environments, including clinical infections. This newfound abundance of LasR-defective strains calls into question existing hypotheses regarding their selection. Indeed, current assumptions concerning factors driving the emergence of LasR-deficient isolates and the role of LasR in the QS hierarchy must be reconsidered. Here, we propose that LasR is not the primary master regulator of QS in all P. aeruginosa genetic backgrounds, even though it remains ecologically significant. We also revisit and complement current knowledge on the ecology of LasR-dependent QS in P. aeruginosa, discuss the hypotheses explaining the putative adaptive benefits of selecting against LasR function, and consider the implications of this renewed understanding.
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Affiliation(s)
- Mylène C. Trottier
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Thays de Oliveira Pereira
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Lucas R. Hoffman
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, Washington, USA
| | - Ajai A. Dandekar
- Departments of Medicine and Microbiology, University of Washington, Seattle, Washington, USA
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
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Zhao Y, Xie L, Wang C, Zhou Q, Jelsbak L. Comparative whole-genome analysis of China and global epidemic Pseudomonas aeruginosa high-risk clones. J Glob Antimicrob Resist 2023; 35:149-158. [PMID: 37709140 DOI: 10.1016/j.jgar.2023.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVES The various sequence types (STs) of Pseudomonas aeruginosa (P. aeruginosa) high-risk clones (HiRiCs) have been sporadically reported in China, but the systematic analysis of genomes for these STs remains limited. This study aimed to address the evolutionary pathways underlying the emergence of HiRiCs and their routes of dissemination from Chinese and global perspectives. METHODS The phylogenetic analysis was performed based on 416 newly sequenced clinical P. aeruginosa strains from Guangdong (GD), published genome sequences of 282 Chinese isolates, and 868 HiRiCs isolates from other countries. The genomic comparison study of global HiRiC ST244 was conducted to detect the model of global dissemination and local separation driven by association regional-specific antibiotic resistance genes. Furthermore, the evolutionary route of the emerging, China-specific HiRiC ST1971 was explored using Most Recent Common Ancestor (MRCA) analysis. RESULTS Based on comparative genomics analysis, we found a clear geographical separation of ST244 isolates, yet with an association between ST244 isolates from GD and America. We identified a set of 38 AMR genes that contribute to the geographical separation in ST244, and we identified genetic determinants either positively (MexB) and negatively (opmD) associated with GD ST244. For the China-unique HiRiC ST1971, its evolutionary history across different continents before emerging as ST1971 in China was also deduced. CONCLUSION This study provides insight into the specific genetics underlying regional differences among globally disseminated P. aeruginosa HiRiCs (ST244) as well as new understanding of the dissemination and evolution of a regional HiRiC (ST1971). Understanding the genetics of these and other HiRiCs may assist in controlling their emergence and further spread.
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Affiliation(s)
- Yonggang Zhao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lu Xie
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, Guangdong Province, China
| | - Chongzhi Wang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Qian Zhou
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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10
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Quiroz-Morales SE, Muriel-Millán LF, Ponce-Soto GY, González-Valdez A, Castillo-Juárez I, Servín-González L, Soberón-Chávez G. Pseudomonas aeruginosa strains belonging to phylogroup 3 frequently exhibit an atypical quorum sensing response: the case of MAZ105, a tomato rhizosphere isolate. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001401. [PMID: 37819040 PMCID: PMC10634362 DOI: 10.1099/mic.0.001401] [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: 03/22/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Pseudomonas aeruginosa is a widespread γ-proteobacterium and an important opportunistic pathogen. The genetically diverse P. aeruginosa phylogroup 3 strains are characterized by producing the pore-forming ExlA toxin and by their lack of a type III secretion system. However, like all strains of this species, they produce several virulence-associated traits, such as elastase, rhamnolipids and pyocyanin, which are regulated by quorum sensing (QS). The P. aeruginosa QS response comprises three systems (Las, Rhl and Pqs, respectively) that hierarchically regulate these virulence factors. The Pqs QS system is composed of the PqsR transcriptional factor, which, coupled with the alkyl-quinolones HHQ or PQS, activates the transcription of the pqsABCDE operon. The products of the first four genes of this operon produce HHQ, which is then converted to PQS by PqsH, while PqsE forms a complex with RhlR and stabilizes it. In this study we report that mutations affecting the Pqs system are particularly common in phylogroup 3 strains. To better understand QS in phylogroup 3 strains we studied strain MAZ105 isolated from tomato rhizosphere and showed that it contains mutations in the central QS transcriptional regulator, LasR, and in the gene encoding the PqsA enzyme involved in the synthesis of PQS. However, it can still produce QS-regulated virulence factors and is virulent in Galleria mellonella and mildly pathogenic in the mouse abscess/necrosis model; our results show that this may be due to the expression of pqsE from a different PqsR-independent promoter than the pqsA promoter. Our results indicate that using anti-virulence therapy based on targeting the PQS system will not be effective against infections by P. aeruginosa phylogroup 3 strains.
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Affiliation(s)
- Sara E. Quiroz-Morales
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo, Postal 70228, C. P. 04510, CDMX, Mexico
| | - Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos CP 62210, Mexico
| | - Gabriel Y. Ponce-Soto
- Microbial Paleogenomics Unit, Department of Genomes and Genetics, Pasteur Institute, 75015 Paris, France
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo, Postal 70228, C. P. 04510, CDMX, Mexico
| | - Israel Castillo-Juárez
- Laboratorio de Investigación y Aplicación de Fitoquímicos Bioactivos, Colegio de Postgraduados, 56230, Campus Montecillo, Texcoco, Mexico
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo, Postal 70228, C. P. 04510, CDMX, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo, Postal 70228, C. P. 04510, CDMX, Mexico
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11
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Avakh A, Grant GD, Cheesman MJ, Kalkundri T, Hall S. The Art of War with Pseudomonas aeruginosa: Targeting Mex Efflux Pumps Directly to Strategically Enhance Antipseudomonal Drug Efficacy. Antibiotics (Basel) 2023; 12:1304. [PMID: 37627724 PMCID: PMC10451789 DOI: 10.3390/antibiotics12081304] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) poses a grave clinical challenge due to its multidrug resistance (MDR) phenotype, leading to severe and life-threatening infections. This bacterium exhibits both intrinsic resistance to various antipseudomonal agents and acquired resistance against nearly all available antibiotics, contributing to its MDR phenotype. Multiple mechanisms, including enzyme production, loss of outer membrane proteins, target mutations, and multidrug efflux systems, contribute to its antimicrobial resistance. The clinical importance of addressing MDR in P. aeruginosa is paramount, and one pivotal determinant is the resistance-nodulation-division (RND) family of drug/proton antiporters, notably the Mex efflux pumps. These pumps function as crucial defenders, reinforcing the emergence of extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains, which underscores the urgency of the situation. Overcoming this challenge necessitates the exploration and development of potent efflux pump inhibitors (EPIs) to restore the efficacy of existing antipseudomonal drugs. By effectively countering or bypassing efflux activities, EPIs hold tremendous potential for restoring the antibacterial activity against P. aeruginosa and other Gram-negative pathogens. This review focuses on concurrent MDR, highlighting the clinical significance of efflux pumps, particularly the Mex efflux pumps, in driving MDR. It explores promising EPIs and delves into the structural characteristics of the MexB subunit and its substrate binding sites.
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Affiliation(s)
| | | | | | | | - Susan Hall
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD 4222, Australia; (A.A.); (G.D.G.); (M.J.C.); (T.K.)
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12
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Barp N, Marcacci M, Biagioni E, Serio L, Busani S, Ventura P, Franceschini E, Orlando G, Venturelli C, Menozzi I, Tambassi M, Scaltriti E, Pongolini S, Sarti M, Pietrangelo A, Girardis M, Mussini C, Meschiari M. A Fatal Case of Pseudomonas aeruginosa Community-Acquired Pneumonia in an Immunocompetent Patient: Clinical and Molecular Characterization and Literature Review. Microorganisms 2023; 11:1112. [PMID: 37317086 DOI: 10.3390/microorganisms11051112] [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: 03/16/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 06/16/2023] Open
Abstract
Rare cases of Pseudomonas aeruginosa community-acquired pneumonia (PA-CAP) were reported in non-immunocompromised patients. We describe a case of Pseudomonas aeruginosa (PA) necrotizing cavitary CAP with a fatal outcome in a 53-year-old man previously infected with SARS-CoV-2, who was admitted for dyspnea, fever, cough, hemoptysis, acute respiratory failure and a right upper lobe opacification. Six hours after admission, despite effective antibiotic therapy, he experienced multi-organ failure and died. Autopsy confirmed necrotizing pneumonia with alveolar hemorrhage. Blood and bronchoalveolar lavage cultures were positive for PA serotype O:9 belonging to ST1184. The strain shares the same virulence factor profile with reference genome PA01. With the aim to better investigate the clinical and molecular characteristics of PA-CAP, we considered the literature of the last 13 years concerning this topic. The prevalence of hospitalized PA-CAP is about 4% and has a mortality rate of 33-66%. Smoking, alcohol abuse and contaminated fluid exposure were the recognized risk factors; most cases presented the same symptoms described above and needed intensive care. Co-infection of PA-influenza A is described, which is possibly caused by influenza-inducing respiratory epithelial cell dysfunction: the same pathophysiological mechanism could be assumed with SARS-CoV-2 infection. Considering the high rate of fatal outcomes, additional studies are needed to identify sources of infections and new risk factors, along with genetic and immunological features. Current CAP guidelines should be revised in light of these results.
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Affiliation(s)
- Nicole Barp
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Matteo Marcacci
- Internal Medicine, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Emanuela Biagioni
- Intensive Care Unit, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Lucia Serio
- Intensive Care Unit, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Stefano Busani
- Intensive Care Unit, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Paolo Ventura
- Internal Medicine, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Erica Franceschini
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Gabriella Orlando
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Claudia Venturelli
- Microbiology, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Ilaria Menozzi
- Risk Analysis and Genomic Epidemiology Unit, Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna, 43126 Parma, Italy
| | - Martina Tambassi
- Risk Analysis and Genomic Epidemiology Unit, Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna, 43126 Parma, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna, 43126 Parma, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna, 43126 Parma, Italy
| | - Mario Sarti
- Microbiology, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Antonello Pietrangelo
- Internal Medicine, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Massimo Girardis
- Intensive Care Unit, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Cristina Mussini
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Marianna Meschiari
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
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13
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Castro-Velázquez V, Díaz-Cervantes E, Rodríguez-González V, Cortés-García CJ. In-silico assay of a dosing vehicle based on chitosan-TiO 2 and modified benzofuran-isatin molecules against Pseudomonas aeruginosa. PEERJ PHYSICAL CHEMISTRY 2023. [DOI: 10.7717/peerj-pchem.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
Abstract
A high priority of the World Health Organization (WHO) is the study of drugs against Pseudomonas aeruginosa, which has developed antibiotic resistance. In this order, recent research is analyzing biomaterials and metal oxide nanoparticles, such as chitosan (QT) and TiO2 (NT), which can transport molecules with biological activity against bacteria, to propose them as drug carrier candidates. In the present work, 10 modified benzofuran-isatin molecules were studied through computational simulation using density functional theory (DFT) and molecular docking assays against Hfq and LpxC (proteins of P. aeruginosa). The results show that the ligand efficiency of commercial drugs C-CP and C-AZI against Hfq is low compared with the best-designed molecule MOL-A. However, we highlight that the influence of NT promotes a better interaction of some molecules, where MOL-E generates a better interaction by 0.219 kcal/mol when NT is introduced in Hfq, forming the system Hfq-NT (Target-NT). Similar behavior is observed in the LpxC target, in which MOL-J is better at 0.072 kcal/mol. Finally, two pharmacophoric models for Hfq and LpxC implicate hydrophobic and aromatic-hydrophobic fragments.
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Affiliation(s)
- Verónica Castro-Velázquez
- División de Materiales Avanzados, Instituto Potosino de Investigación Científica y Tecnología, San Luis Potosí, San Luis Potosí, Mexico
- Departamento de Alimentos, Universidad de Guanajuato, Tierra Blanca, Guanajuato, Mexico
| | - Erik Díaz-Cervantes
- Departamento de Alimentos, Universidad de Guanajuato, Tierra Blanca, Guanajuato, Mexico
| | - Vicente Rodríguez-González
- División de Materiales Avanzados, Instituto Potosino de Investigación Científica y Tecnología, San Luis Potosí, San Luis Potosí, Mexico
| | - Carlos J. Cortés-García
- Laboratorio de Diseño Molecular/Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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14
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Botelho J, Tüffers L, Fuss J, Buchholz F, Utpatel C, Klockgether J, Niemann S, Tümmler B, Schulenburg H. Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa. EBioMedicine 2023; 90:104532. [PMID: 36958270 PMCID: PMC10053402 DOI: 10.1016/j.ebiom.2023.104532] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is an opportunistic pathogen consisting of three phylogroups (hereafter named A, B, and C). Here, we assessed phylogroup-specific evolutionary dynamics across available and also new P. aeruginosa genomes. METHODS In this genomic analysis, we first generated new genome assemblies for 18 strains of the major P. aeruginosa clone type (mPact) panel, comprising a phylogenetically diverse collection of clinical and environmental isolates for this species. Thereafter, we combined these new genomes with 1991 publicly available P. aeruginosa genomes for a phylogenomic and comparative analysis. We specifically explored to what extent antimicrobial resistance (AMR) genes, defence systems, and virulence genes vary in their distribution across regions of genome plasticity (RGPs) and "masked" (RGP-free) genomes, and to what extent this variation differs among the phylogroups. FINDINGS We found that members of phylogroup B possess larger genomes, contribute a comparatively larger number of pangenome families, and show lower abundance of CRISPR-Cas systems. Furthermore, AMR and defence systems are pervasive in RGPs and integrative and conjugative/mobilizable elements (ICEs/IMEs) from phylogroups A and B, and the abundance of these cargo genes is often significantly correlated. Moreover, inter- and intra-phylogroup interactions occur at the accessory genome level, suggesting frequent recombination events. Finally, we provide here the mPact panel of diverse P. aeruginosa strains that may serve as a valuable reference for functional analyses. INTERPRETATION Altogether, our results highlight distinct pangenome characteristics of the P. aeruginosa phylogroups, which are possibly influenced by variation in the abundance of CRISPR-Cas systems and are shaped by the differential distribution of other defence systems and AMR genes. FUNDING German Science Foundation, Max-Planck Society, Leibniz ScienceCampus Evolutionary Medicine of the Lung, BMBF program Medical Infection Genomics, Kiel Life Science Postdoc Award.
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Affiliation(s)
- João Botelho
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany; Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
| | - Leif Tüffers
- Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Florian Buchholz
- Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Hinrich Schulenburg
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany; Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
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15
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Wood SJ, Kuzel TM, Shafikhani SH. Pseudomonas aeruginosa: Infections, Animal Modeling, and Therapeutics. Cells 2023; 12:199. [PMID: 36611992 PMCID: PMC9818774 DOI: 10.3390/cells12010199] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas aeruginosa is an important Gram-negative opportunistic pathogen which causes many severe acute and chronic infections with high morbidity, and mortality rates as high as 40%. What makes P. aeruginosa a particularly challenging pathogen is its high intrinsic and acquired resistance to many of the available antibiotics. In this review, we review the important acute and chronic infections caused by this pathogen. We next discuss various animal models which have been developed to evaluate P. aeruginosa pathogenesis and assess therapeutics against this pathogen. Next, we review current treatments (antibiotics and vaccines) and provide an overview of their efficacies and their limitations. Finally, we highlight exciting literature on novel antibiotic-free strategies to control P. aeruginosa infections.
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Affiliation(s)
- Stephen J. Wood
- Department of Medicine, Division of Hematology, Oncology, & Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
| | - Timothy M. Kuzel
- Department of Medicine, Division of Hematology, Oncology, & Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA
- Cancer Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Sasha H. Shafikhani
- Department of Medicine, Division of Hematology, Oncology, & Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
- Cancer Center, Rush University Medical Center, Chicago, IL 60612, USA
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16
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Anbo M, Jelsbak L. A bittersweet fate: detection of serotype switching in Pseudomonas aeruginosa. Microb Genom 2023; 9:mgen000919. [PMID: 36748704 PMCID: PMC9973846 DOI: 10.1099/mgen.0.000919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
High-risk clone types in Pseudomonas aeruginosa are problematic global multidrug-resistant clones. However, apart from their ability to resist antimicrobial treatment, not much is known about what sets these clones apart from the multitude of other clones. In high-risk clone ST111, it has previously been shown that replacement of the native serotype biosynthetic gene cluster (O4) by a different gene cluster (O12) by horizontal gene transfer and recombination may have contributed to the global success of this clone. However, the extent to which isolates undergo this type of serotype switching has not been adequately explored in P. aeruginosa. In the present study, a bioinformatics tool has been developed and utilized to provide a first estimate of serotype switching in groups of multidrug resistant (MDR) clinical isolates. The tool detects serotype switching by analysis of core-genome phylogeny and in silico serotype. Analysis of a national survey of MDR isolates found a prevalence of 3.9 % of serotype-switched isolates in high-risk clone types ST111, ST244 and ST253. A global survey of MDR isolates was additionally analysed, and it was found that 2.3 % of isolates had undergone a serotype switch. To further understand this process, we determined the exact boundaries of the horizontally transferred serotype O12 island. We found that the size of the serotype island correlates with the clone type of the receiving isolate and additionally we found intra-clone type variations in size and boundaries. This suggests multiple serotype switch events. Moreover, we found that the housekeeping gene gyrA is co-transferred with the O12 serotype island, which prompted us to analyse this allele for all serotype O12 isolates. We found that 95 % of ST111 O12 isolates had a resistant gyrA allele and 86 % of all O12 isolates had a resistant gyrA allele. The rates of resistant gyrA alleles in isolates with other prevalent serotypes are all lower. Together, these results show that the transfer and acquisition of serotype O12 in high-risk clone ST111 has happened multiple times and may be facilitated by multiple donors, which clearly suggests a strong selection pressure for this process. However, gyrA-mediated antibiotic resistance may not be the only evolutionary driver.
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Affiliation(s)
- Mikkel Anbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
- *Correspondence: Lars Jelsbak,
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17
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Richter K, Wohlrab J. [Impact of preservatives in topicals on the cutaneous microbiota]. DERMATOLOGIE (HEIDELBERG, GERMANY) 2023; 74:171-181. [PMID: 36729161 PMCID: PMC9981539 DOI: 10.1007/s00105-023-05112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 02/03/2023]
Abstract
Preservatives are used to stabilize topical preparations and protect the user from the influence of pathogenic microbes. After the application of a topical preparation, the matrix undergoes a metamorphosis, and by proportional evaporation of the hydrophilic phase the preservative may accumulate on the skin surface. This is believed to lead to antiseptic effects and may influence the diversity of the cutaneous microbiota. The regulation of the cutaneous microbiome and the associated influencing factors is a complex system that results in highly individualized conditions. Therefore, investigations on the influence of defined interventions are methodologically difficult. In the present proof-of-concept study, potential antiseptic effects of preservatives were investigated in a combination of in vitro and in vivo methods using microbiological culture tests. In addition, the investigations served to develop a clinical study design to answer further questions and use of an extended range of methods. The results support the hypothesis of an antiseptic effect of the tested preservatives (methyl-4-hydroxybenzoate and propyl-4-hydroxybenzoate, potassium sorbate and propylene glycol) on prominent reference bacteria, which could also be observed in clinical settings.
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Affiliation(s)
- Kathrin Richter
- Universitätsklinik und Poliklinik für Dermatologie und Venerologie, Martin-Luther-Universität Halle-Wittenberg, Ernst-Grube-Straße 40, 06114 Halle (Saale), Deutschland
| | - Johannes Wohlrab
- Universitätsklinik und Poliklinik für Dermatologie und Venerologie, Martin-Luther-Universität Halle-Wittenberg, Ernst-Grube-Straße 40, 06114, Halle (Saale), Deutschland. .,An-Institut für angewandte Dermatopharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Deutschland.
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18
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Kiel A, Creutz I, Rückert C, Kaltschmidt BP, Hütten A, Niehaus K, Busche T, Kaltschmidt B, Kaltschmidt C. Genome-Based Analysis of Virulence Factors and Biofilm Formation in Novel P. aeruginosa Strains Isolated from Household Appliances. Microorganisms 2022; 10:microorganisms10122508. [PMID: 36557761 PMCID: PMC9781345 DOI: 10.3390/microorganisms10122508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In household washing machines, opportunistic pathogens such as Pseudomonas aeruginosa are present, which represent the household as a possible reservoir for clinical pathogens. Here, four novel P. aeruginosa strains, isolated from different sites of household appliances, were investigated regarding their biofilm formation. Only two isolates showed strong surface-adhered biofilm formation. In consequence of these phenotypic differences, we performed whole genome sequencing using Oxford Nanopore Technology together with Illumina MiSeq. Whole genome data were screened for the prevalence of 285 virulence- and biofilm-associated genes as well as for prophages. Linking biofilm phenotypes and parallelly appearing gene compositions, we assume a relevancy of the las quorum sensing system and the phage-encoded bacteriophage control infection gene bci, which was found on integrated phi297 DNA in all biofilm-forming isolates. Additionally, only the isolates revealing strong biofilm formation harbored the ϕCTX-like prophage Dobby, implicating a role of this prophage on biofilm formation. Investigations on clinically relevant pathogens within household appliances emphasize their adaptability to harsh environments, with high concentrations of detergents, providing greater insights into pathogenicity and underlying mechanisms. This in turn opens the possibility to map and characterize potentially relevant strains even before they appear as pathogens in society.
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Affiliation(s)
- Annika Kiel
- Department of Cell Biology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Correspondence:
| | - Ines Creutz
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Bernhard Peter Kaltschmidt
- Department of Thin Films and Physics of Nanostructures, Center of Spinelectronic Materials and Devices, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Andreas Hütten
- Department of Thin Films and Physics of Nanostructures, Center of Spinelectronic Materials and Devices, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Barbara Kaltschmidt
- Department of Cell Biology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Christian Kaltschmidt
- Department of Cell Biology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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19
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Lorusso AB, Carrara JA, Barroso CDN, Tuon FF, Faoro H. Role of Efflux Pumps on Antimicrobial Resistance in Pseudomonas aeruginosa. Int J Mol Sci 2022; 23:15779. [PMID: 36555423 PMCID: PMC9779380 DOI: 10.3390/ijms232415779] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance is an old and silent pandemic. Resistant organisms emerge in parallel with new antibiotics, leading to a major global public health crisis over time. Antibiotic resistance may be due to different mechanisms and against different classes of drugs. These mechanisms are usually found in the same organism, giving rise to multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacteria. One resistance mechanism that is closely associated with the emergence of MDR and XDR bacteria is the efflux of drugs since the same pump can transport different classes of drugs. In Gram-negative bacteria, efflux pumps are present in two configurations: a transmembrane protein anchored in the inner membrane and a complex formed by three proteins. The tripartite complex has a transmembrane protein present in the inner membrane, a periplasmic protein, and a porin associated with the outer membrane. In Pseudomonas aeruginosa, one of the main pathogens associated with respiratory tract infections, four main sets of efflux pumps have been associated with antibiotic resistance: MexAB-OprM, MexXY, MexCD-OprJ, and MexEF-OprN. In this review, the function, structure, and regulation of these efflux pumps in P. aeruginosa and their actions as resistance mechanisms are discussed. Finally, a brief discussion on the potential of efflux pumps in P. aeruginosa as a target for new drugs is presented.
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Affiliation(s)
- Andre Bittencourt Lorusso
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz, Curitiba 81350-010, Brazil
- School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil
| | - João Antônio Carrara
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz, Curitiba 81350-010, Brazil
| | | | - Felipe Francisco Tuon
- Laboratory of Emerging Infectious Diseases, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz, Curitiba 81350-010, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
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20
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Abstract
Bacteria commonly live in surface-associated communities where steep gradients of antibiotics and other chemical compounds can occur. While many bacterial species move on surfaces, we know surprisingly little about how such antibiotic gradients affect cell motility. Here, we study the behaviour of the opportunistic pathogen Pseudomonas aeruginosa in stable spatial gradients of several antibiotics by tracking thousands of cells in microfluidic devices as they form biofilms. Unexpectedly, these experiments reveal that bacteria use pili-based ('twitching') motility to navigate towards antibiotics. Our analyses suggest that this behaviour is driven by a general response to the effects of antibiotics on cells. Migrating bacteria reach antibiotic concentrations hundreds of times higher than their minimum inhibitory concentration within hours and remain highly motile. However, isolating cells - using fluid-walled microfluidic devices - reveals that these bacteria are terminal and unable to reproduce. Despite moving towards their death, migrating cells are capable of entering a suicidal program to release bacteriocins that kill other bacteria. This behaviour suggests that the cells are responding to antibiotics as if they come from a competing colony growing nearby, inducing them to invade and attack. As a result, clinical antibiotics have the potential to lure bacteria to their death.
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21
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Rudra B, Duncan L, Shah AJ, Shah HN, Gupta RS. Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36355412 DOI: 10.1099/ijsem.0.005542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The strains of
Pseudomonas aeruginosa
exhibit considerable differences in their genotypic and pathogenic properties. To clarify their evolutionary/taxonomic relationships, comprehensive phylogenomic and comparative genomic studies were conducted on the genome sequences of 212
P
.
aeruginosa
strains covering their genetic diversity. In a phylogenomic tree based on 118 conserved proteins, the analysed strains formed two distinct clades. One of these clades, Clade-1, encompassing >70 % of the strains including the type strain DSM 50071T, represents the species P. aeruginosa sensu stricto. Clade-2, referred to in earlier work as the outlier group, with NCTC 13628T as its type strain, constitutes a novel species level lineage. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the strains from Clade-1 and Clade-2 are in the range of 93.4–93.7, 95.1–95.3 and 52–53 %, respectively. The 16S rRNA gene of
P. aeruginosa
DSM 50071T also shows 98.3 % similarity to that of NCTC 13628T. These values are lower than the suggested cut-off values for species distinction, indicating that the Clade-2 strains (NCTC 13628T) constitute a new species. We also report the identification of 12 conserved signature indels in different proteins and 24 conserved signature proteins that are exclusively found in either Clade-1 or Clade-2, providing a reliable means for distinguishing these clades. Additionally, in contrast to swimming motility, twitching motility is only present in Clade-1 strains. Based on earlier work, the strains from these two clades also differ in their pathogenic mechanisms (presence/absence of Type III secretion system), production of biosurfactants, phenazines and siderophores, and several other genomic characteristics. Based on the evidence from different studies, we propose that the Clade-2 strains constitute a novel species for which the name Pseudomonas paraeruginosa is proposed. The type strain is NCTC 13628T (=PA7T=ATCC 9027T). The description of
Pseudomonas aeruginosa
is also emended to include information for different molecular markers specific for this species.
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Affiliation(s)
- Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Canada
| | - Louise Duncan
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 9NH, UK
| | - Ajit J Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Haroun N Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Canada
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22
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Chagas MDS, Medeiros F, dos Santos MT, de Menezes MA, Carvalho-Assef APD, da Silva FAB. An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851. Mem Inst Oswaldo Cruz 2022; 117:e220111. [PMID: 36259790 PMCID: PMC9565603 DOI: 10.1590/0074-02760220111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/09/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Healthcare-associated infections due to multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa are significant public health issues worldwide. A system biology approach can help understand bacterial behaviour and provide novel ways to identify potential therapeutic targets and develop new drugs. Gene regulatory networks (GRN) are examples of in silico representation of interaction between regulatory genes and their targets. OBJECTIVES In this work, we update the MDR P. aeruginosa CCBH4851 GRN reconstruction and analyse and discuss its structural properties. METHODS We based this study on the gene orthology inference methodology using the reciprocal best hit method. The P. aeruginosa CCBH4851 genome and GRN, published in 2019, and the P. aeruginosa PAO1 GRN, published in 2020, were used for this update reconstruction process. FINDINGS Our result is a GRN with a greater number of regulatory genes, target genes, and interactions compared to the previous networks, and its structural properties are consistent with the complexity of biological networks and the biological features of P. aeruginosa. MAIN CONCLUSIONS Here, we present the largest and most complete version of P. aeruginosa GRN published to this date, to the best of our knowledge.
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Affiliation(s)
- Márcia da Silva Chagas
- Fundação Oswaldo Cruz-Fiocruz, Programa de Computação Científica, Rio de Janeiro, RJ, Brasil,+ Corresponding authors: /
| | - Fernando Medeiros
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia, Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Rio de Janeiro, RJ, Brasil
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23
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Lin S, Chen S, Li L, Cao H, Li T, Hu M, Liao L, Zhang LH, Xu Z. Genome characterization of a uropathogenic Pseudomonas aeruginosa isolate PA_HN002 with cyclic di-GMP-dependent hyper-biofilm production. Front Cell Infect Microbiol 2022; 12:956445. [PMID: 36004331 PMCID: PMC9394441 DOI: 10.3389/fcimb.2022.956445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa can cause various types of infections and is one of the most ubiquitous antibiotic-resistant pathogens found in healthcare settings. It is capable of adapting to adverse conditions by transforming its motile lifestyle to a sessile biofilm lifestyle, which induces a steady state of chronic infection. However, mechanisms triggering the lifestyle transition of P. aeruginosa strains with clinical significance are not very clear. In this study, we reported a recently isolated uropathogenic hyper-biofilm producer PA_HN002 and characterized its genome to explore genetic factors that may promote its transition into the biofilm lifestyle. We first showed that high intracellular c-di-GMP content in PA_HN002 gave rise to its attenuated motilities and extraordinary strong biofilm. Reducing the intracellular c-di-GMP content by overexpressing phosphodiesterases (PDEs) such as BifA or W909_14950 converted the biofilm and motility phenotypes. Whole genome sequencing and comprehensive analysis of all the c-di-GMP metabolizing enzymes led to the identification of multiple mutations within PDEs. Gene expression assays further indicated that the shifted expression profile of c-di-GMP metabolizing enzymes in PA_HN002 might mainly contribute to its elevated production of intracellular c-di-GMP and enhanced biofilm formation. Moreover, mobile genetic elements which might interfere the endogenous regulatory network of c-di-GMP metabolism in PA_HN002 were analyzed. This study showed a reprogrammed expression profile of c-di-GMP metabolizing enzymes which may promote the pathoadaption of clinical P. aeruginosa into biofilm producers.
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Affiliation(s)
- Siying Lin
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Li Li
- Women and Children’s Health Institute, Guangdong Women and Children Hospital, Guangzhou, China
- *Correspondence: Li Li, ; Zeling Xu,
| | - Huiluo Cao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ting Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Ming Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lisheng Liao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- *Correspondence: Li Li, ; Zeling Xu,
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24
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Afzal M, Vijay AK, Stapleton F, Willcox MDP. Genomics of Staphylococcus aureus Strains Isolated from Infectious and Non-Infectious Ocular Conditions. Antibiotics (Basel) 2022; 11:1011. [PMID: 36009880 PMCID: PMC9405196 DOI: 10.3390/antibiotics11081011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 01/08/2023] Open
Abstract
Staphylococcus aureus is a major cause of ocular infectious (corneal infection or microbial keratitis (MK) and conjunctivitis) and non-infectious corneal infiltrative events (niCIE). Despite the significant morbidity associated with these conditions, there is very little data about specific virulence factors associated with the pathogenicity of ocular isolates. A set of 25 S. aureus infectious and niCIEs strains isolated from USA and Australia were selected for whole genome sequencing. Sequence types and clonal complexes of S. aureus strains were identified by using multi-locus sequence type (MLST). The presence or absence of 128 virulence genes was determined by using the virulence finder database (VFDB). Differences between infectious (MK + conjunctivitis) and niCIE isolates from USA and Australia for possession of virulence genes were assessed using the chi-square test. The most common sequence types found among ocular isolates were ST5, ST8 while the clonal complexes were CC30 and CC1. Virulence genes involved in adhesion (ebh, clfA, clfB, cna, sdrD, sdrE), immune evasion (chp, esaD, esaE, esxB, esxC, esxD), and serine protease enzymes (splA, splD, splE, splF) were more commonly observed in infectious strains (MK + conjunctivitis) than niCIE strains (p = 0.004). Toxin genes were present in half of infectious (49%, 25/51) and niCIE (51%, 26/51) strains. USA infectious isolates were significantly more likely to possess splC, yent1, set9, set11, set36, set38, set40, lukF-PV, and lukS-PV (p < 0.05) than Australian infectious isolates. MK USA strains were more likely to possesses yent1, set9, set11 than USA conjunctivitis strains (p = 0.04). Conversely USA conjunctivitis strains were more likely to possess set36 set38, set40, lukF-PV, lukS-PV (p = 0.03) than MK USA strains. The ocular strain set was then compared to 10 fully sequenced non-ocular S. aureus strains to identify differences between ocular and non-ocular isolates. Ocular isolates were significantly more likely to possess cna (p = 0.03), icaR (p = 0.01), sea (p = 0.001), set16 (p = 0.01), and set19 (p = 0.03). In contrast non-ocular isolates were more likely to possess icaD (p = 0.007), lukF-PV, lukS-PV (p = 0.01), selq (p = 0.01), set30 (p = 0.01), set32 (p = 0.02), and set36 (p = 0.02). The clones ST5, ST8, CC30, and CC1 among ocular isolates generally reflect circulating non-ocular pathogenic S. aureus strains. The higher rates of genes in infectious and ocular isolates suggest a potential role of these virulence factors in ocular diseases.
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Affiliation(s)
- Madeeha Afzal
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
| | | | - Fiona Stapleton
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
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25
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Reig S, Le Gouellec A, Bleves S. What Is New in the Anti–Pseudomonas aeruginosa Clinical Development Pipeline Since the 2017 WHO Alert? Front Cell Infect Microbiol 2022; 12:909731. [PMID: 35880080 PMCID: PMC9308001 DOI: 10.3389/fcimb.2022.909731] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
The spread of antibiotic-resistant bacteria poses a substantial threat to morbidity and mortality worldwide. Carbapenem-resistant Pseudomonas aeruginosa (CRPA) are considered “critical-priority” bacteria by the World Health Organization (WHO) since 2017 taking into account criteria such as patient mortality, global burden disease, and worldwide trend of multi-drug resistance (MDR). Indeed P. aeruginosa can be particularly difficult to eliminate from patients due to its combinatory antibiotic resistance, multifactorial virulence, and ability to over-adapt in a dynamic way. Research is active, but the course to a validated efficacy of a new treatment is still long and uncertain. What is new in the anti–P. aeruginosa clinical development pipeline since the 2017 WHO alert? This review focuses on new solutions for P. aeruginosa infections that are in active clinical development, i.e., currently being tested in humans and may be approved for patients in the coming years. Among 18 drugs of interest in December 2021 anti–P. aeruginosa development pipeline described here, only one new combination of β-lactam/β-lactamase inhibitor is in phase III trial. Derivatives of existing antibiotics considered as “traditional agents” are over-represented. Diverse “non-traditional agents” including bacteriophages, iron mimetic/chelator, and anti-virulence factors are significantly represented but unfortunately still in early clinical stages. Despite decade of efforts, there is no vaccine currently in clinical development to prevent P. aeruginosa infections. Studying pipeline anti–P. aeruginosa since 2017 up to now shows how to provide a new treatment for patients can be a difficult task. Given the process duration, the clinical pipeline remains unsatisfactory leading best case to the approval of new antibacterial drugs that treat CRPA in several years. Beyond investment needed to build a robust pipeline, the Community needs to reinvent medicine with new strategies of development to avoid the disaster. Among “non-traditional agents”, anti-virulence strategy may have the potential through novel and non-killing modes of action to reduce the selective pressure responsible of MDR.
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Affiliation(s)
- Sébastien Reig
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université-CNRS, UMR7255, Marseille, France
- *Correspondence: Sébastien Reig, ; Sophie Bleves,
| | - Audrey Le Gouellec
- Laboratoire Techniques de l’Ingénierie Médicale et de la Complexité (UMR5525), Centre National de la Recherche Scientifique, Université Grenoble Alpes, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, Grenoble, France
| | - Sophie Bleves
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université-CNRS, UMR7255, Marseille, France
- *Correspondence: Sébastien Reig, ; Sophie Bleves,
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26
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Thacharodi A, Lamont IL. Aminoglycoside-Modifying Enzymes Are Sufficient to Make Pseudomonas aeruginosa Clinically Resistant to Key Antibiotics. Antibiotics (Basel) 2022; 11:884. [PMID: 35884138 PMCID: PMC9312099 DOI: 10.3390/antibiotics11070884] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
Aminoglycosides are widely used to treat infections of Pseudomonas aeruginosa. Genes encoding aminoglycoside-modifying enzymes (AMEs), acquired by horizontal gene transfer, are commonly associated with aminoglycoside resistance, but their effects have not been quantified. The aim of this research was to determine the extent to which AMEs increase the antibiotic tolerance of P. aeruginosa. Bioinformatics analysis identified AME-encoding genes in 48 out of 619 clinical isolates of P. aeruginosa, with ant(2')-Ia and aac(6')-Ib3, which are associated with tobramcyin and gentamicin resistance, being the most common. These genes and aph(3')-VIa (amikacin resistance) were deleted from antibiotic-resistant strains. Antibiotic minimum inhibitory concentrations (MICs) were reduced by up to 64-fold, making the mutated bacteria antibiotic-sensitive in several cases. Introduction of the same genes into four antibiotic-susceptible P. aeruginosa strains increased the MIC by up to 128-fold, making the bacteria antibiotic-resistant in all cases. The cloned genes also increased the MIC in mutants lacking the MexXY-OprM efflux pump, which is an important contributor to aminoglycoside resistance, demonstrating that AMEs and this efflux pump act independently in determining levels of aminoglycoside tolerance. Quantification of the effects of AMEs on antibiotic susceptibility demonstrates the large effect that these enzymes have on antibiotic resistance.
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Affiliation(s)
| | - Iain L. Lamont
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand;
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27
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Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance. mSystems 2022; 7:e0138421. [PMID: 35695507 PMCID: PMC9238379 DOI: 10.1128/msystems.01384-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here, we describe the diversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of bacterial isolate genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 groups of related species. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal-component analysis of accessory genes (PCA-A). Core genome genetic distances and rates of evolution varied among species, which has practical implications for defining shared ancestry during outbreaks and for our broader understanding of the origins of bacterial strains and species. Finally, antimicrobial resistance genes and putative mobile genetic elements were frequently observed, and our systematic analysis revealed patterns of occurrence across the different species sampled from our hospital. Overall, this study shows how understanding the population structure of diverse pathogens circulating in a single health care setting can improve the discriminatory power of genomic epidemiology studies and can help define the processes leading to strain and species differentiation. IMPORTANCE Hospitalized patients are at increased risk of becoming infected with antibiotic-resistant organisms. We used whole-genome sequencing to survey and compare over 3,000 clinical bacterial isolates collected from hospitalized patients at a large medical center over a 2-year period. We identified nearly 100 different bacterial species, which we divided into 14 different groups of related species. When we examined how genetic relatedness differed between species, we found that different species were likely evolving at different rates within our hospital. This is significant because the identification of bacterial outbreaks in the hospital currently relies on genetic similarity cutoffs, which are often applied uniformly across organisms. Finally, we found that antibiotic resistance genes and mobile genetic elements were abundant and were shared among the bacterial isolates we sampled. Overall, this study provides an in-depth view of the genomic diversity and evolutionary processes of bacteria sampled from hospitalized patients, as well as genetic similarity estimates that can inform hospital outbreak detection and prevention efforts.
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28
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Huber P. ExlA: A New Contributor to Pseudomonas aeruginosa Virulence. Front Cell Infect Microbiol 2022; 12:929150. [PMID: 35811671 PMCID: PMC9260685 DOI: 10.3389/fcimb.2022.929150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
ExlA (also called exolysin) is a recently discovered virulence factor secreted by a subset of Pseudomonas aeruginosa strains in which a type 3 secretion system is lacking. exlA-positive strains were identified worldwide in the clinic, causing several types of infectious diseases, and were detected in various locations in the environment. ExlA possesses pore-forming activity and is cytolytic for most human cell types. It belongs to a class of poorly characterized bacterial toxins, sharing a similar protein domain organization and a common secretion pathway. This review summarizes the recent findings regarding ExlA synthesis, its secretion pathway, and its toxic behavior for host cells.
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29
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Nichols WW, Bradford PA, Lahiri SD, Stone GG. The primary pharmacology of ceftazidime/avibactam: in vitro translational biology. J Antimicrob Chemother 2022; 77:2321-2340. [PMID: 35665807 DOI: 10.1093/jac/dkac171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Previous reviews of ceftazidime/avibactam have focused on in vitro molecular enzymology and microbiology or the clinically associated properties of the combination. Here we take a different approach. We initiate a series of linked reviews that analyse research on the combination that built the primary pharmacology data required to support the clinical and business risk decisions to perform randomized controlled Phase 3 clinical trials, and the additional microbiological research that was added to the above, and the safety and chemical manufacturing and controls data, that constituted successful regulatory licensing applications for ceftazidime/avibactam in multiple countries, including the USA and the EU. The aim of the series is to provide both a source of reference for clinicians and microbiologists to be able to use ceftazidime/avibactam to its best advantage for patients, but also a case study of bringing a novel β-lactamase inhibitor (in combination with an established β-lactam) through the microbiological aspects of clinical development and regulatory applications, updated finally with a review of resistance occurring in patients under treatment. This first article reviews the biochemistry, structural biology and basic microbiology of the combination, showing that avibactam inhibits the great majority of serine-dependent β-lactamases in Enterobacterales and Pseudomonas aeruginosa to restore the in vitro antibacterial activity of ceftazidime. Translation to efficacy against infections in vivo is reviewed in the second co-published article, Nichols et al. (J Antimicrob Chemother 2022; dkac172).
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30
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Veetilvalappil VV, Manuel A, Aranjani JM, Tawale R, Koteshwara A. Pathogenic arsenal of Pseudomonas aeruginosa: an update on virulence factors. Future Microbiol 2022; 17:465-481. [PMID: 35289684 DOI: 10.2217/fmb-2021-0158] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The emergence of Pseudomonas aeruginosa as a potential threat in persistent infections can be attributed to the plethora of virulence factors expressed by it. This review discusses the various virulence factors that help this pathogen to establish an infection and regulatory systems controlling these virulence factors. Cell-associated virulence factors such as flagella, type IV pili and non-pilus adhesins have been reviewed. Extracellular virulence factors have also been explained. Quorum-sensing systems present in P. aeruginosa play a cardinal role in regulating the expression of virulence factors. The identification of novel virulence factors in hypervirulent strains indicate that the expression of virulence is dynamic and constantly evolving. An understanding of this is critical for the better clinical management of infections.
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Affiliation(s)
- Vimal V Veetilvalappil
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Atulya Manuel
- Central Frozen Semen Production and Training Institute, Bengaluru, Karnataka, 560088, India
| | - Jesil M Aranjani
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Roshan Tawale
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Ananthamurthy Koteshwara
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
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31
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Trouillon J, Han K, Attrée I, Lory S. The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages. Nat Commun 2022; 13:1258. [PMID: 35273147 PMCID: PMC8913705 DOI: 10.1038/s41467-022-28849-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 02/14/2022] [Indexed: 01/16/2023] Open
Abstract
The major RNA-binding protein Hfq interacts with mRNAs, either alone or together with regulatory small noncoding RNAs (sRNAs), affecting mRNA translation and degradation in bacteria. However, studies tend to focus on single reference strains and assume that the findings may apply to the entire species, despite the important intra-species genetic diversity known to exist. Here, we use RIP-seq to identify Hfq-interacting RNAs in three strains representing the major phylogenetic lineages of Pseudomonas aeruginosa. We find that most interactions are in fact not conserved among the different strains. We identify growth phase-specific and strain-specific Hfq targets, including previously undescribed sRNAs. Strain-specific interactions are due to different accessory gene sets, RNA abundances, or potential context- or sequence- dependent regulatory mechanisms. The accessory Hfq interactome includes most mRNAs encoding Type III Secretion System (T3SS) components and secreted toxins in two strains, as well as a cluster of CRISPR guide RNAs in one strain. Conserved Hfq targets include the global virulence regulator Vfr and metabolic pathways involved in the transition from fast to slow growth. Furthermore, we use rGRIL-seq to show that RhlS, a quorum sensing sRNA, activates Vfr translation, thus revealing a link between quorum sensing and virulence regulation. Overall, our work highlights the important intra-species diversity in post-transcriptional regulatory networks in Pseudomonas aeruginosa.
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Affiliation(s)
- Julian Trouillon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Kook Han
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Ina Attrée
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Stephen Lory
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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Marcoleta AE, Arros P, Varas MA, Costa J, Rojas-Salgado J, Berríos-Pastén C, Tapia-Fuentes S, Silva D, Fierro J, Canales N, Chávez FP, Gaete A, González M, Allende ML, Lagos R. The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152003. [PMID: 34856283 DOI: 10.1016/j.scitotenv.2021.152003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. This work demonstrated that the Antarctic Peninsula soils host a remarkable microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. We observed resistance to a wide array of antibiotics among isolates, including Pseudomonas resisting ten or more different compounds, with an overall increased resistance in bacteria from non-intervened areas. In addition, genome analysis of selected isolates showed several genes encoding efflux pumps, as well as a lack of known resistance genes for some of the resisted antibiotics, including colistin, suggesting novel uncharacterized mechanisms. By combining metagenomic approaches based on analyzing raw reads, assembled contigs, and metagenome-assembled genomes, we found hundreds of widely distributed genes potentially conferring resistance to different antibiotics (including an outstanding variety of inactivation enzymes), metals, and biocides, hosted mainly by Polaromonas, Pseudomonas, Streptomyces, Variovorax, and Burkholderia. Furthermore, a proportion of these genes were found inside predicted plasmids and other mobile elements, including a putative OXA-like carbapenemase from Polaromonas harboring conserved key residues and predicted structural features. All this evidence indicates that the Antarctic Peninsula soil microbiota has a broad natural resistome, part of which could be transferred horizontally to pathogenic bacteria, acting as a potential source of novel resistance genes.
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Affiliation(s)
- Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena A Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José Costa
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Johanna Rojas-Salgado
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sofía Tapia-Fuentes
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Daniel Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José Fierro
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nicolás Canales
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile; FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Kin selection for cooperation in natural bacterial populations. Proc Natl Acad Sci U S A 2022; 119:2119070119. [PMID: 35193981 PMCID: PMC8892524 DOI: 10.1073/pnas.2119070119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 01/03/2023] Open
Abstract
Bacteria secrete many molecules outside the cell, where they provide benefits to other cells. One potential reason for producing these “public goods” is that they benefit closely related cells that share the gene for cooperation (kin selection). While many laboratory studies have supported this hypothesis, there is a lack of evidence that kin selection favors cooperation in natural populations. We examined bacterial genomes from the environment and used population genetics theory to analyze the DNA sequences. Our analyses suggest that public goods cooperation has indeed been favored by kin selection in natural populations. Bacteria produce a range of molecules that are secreted from the cell and can provide a benefit to the local population of cells. Laboratory experiments have suggested that these “public goods” molecules represent a form of cooperation, favored because they benefit closely related cells (kin selection). However, there is a relative lack of data demonstrating kin selection for cooperation in natural populations of bacteria. We used molecular population genetics to test for signatures of kin selection at the genomic level in natural populations of the opportunistic pathogen Pseudomonas aeruginosa. We found consistent evidence from multiple traits that genes controlling putatively cooperative traits have higher polymorphism and greater divergence and are more likely to harbor deleterious mutations relative to genes controlling putatively private traits, which are expressed at similar rates. These patterns suggest that cooperative traits are controlled by kin selection, and we estimate that the relatedness for social interactions in P. aeruginosa is r = 0.84. More generally, our results demonstrate how molecular population genetics can be used to study the evolution of cooperation in natural populations.
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Overview on Glycosylated Lipids Produced by Bacteria and Fungi: Rhamno-, Sophoro-, Mannosylerythritol and Cellobiose Lipids. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 181:73-122. [DOI: 10.1007/10_2021_200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:3-28. [DOI: 10.1007/978-3-031-08491-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Lebreton F, Snesrud E, Hall L, Mills E, Galac M, Stam J, Ong A, Maybank R, Kwak YI, Johnson S, Julius M, Ly M, Swierczewski B, Waterman PE, Hinkle M, Jones A, Lesho E, Bennett JW, McGann P. A panel of diverse Pseudomonas aeruginosa clinical isolates for research and development. JAC Antimicrob Resist 2021; 3:dlab179. [PMID: 34909689 DOI: 10.1093/jacamr/dlab179] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/05/2021] [Indexed: 11/15/2022] Open
Abstract
Objectives Pseudomonas aeruginosa is a leading cause of community- and hospital-acquired infections. Successful treatment is hampered by its remarkable ability to rapidly develop resistance to antimicrobial agents, primarily through mutation. In response, WHO listed carbapenem-resistant P. aeruginosa as a Priority 1 (Critical) pathogen for research and development of new treatments. A key resource in developing effective countermeasures is access to diverse and clinically relevant strains for testing. Herein we describe a panel of 100 diverse P. aeruginosa strains to support this endeavour. Methods WGS was performed on 3785 P. aeruginosa isolates in our repository. Isolates were cultured from clinical samples collected from healthcare facilities around the world between 2003 and 2017. Core-genome MLST and high-resolution SNP-based phylogenetic analyses were used to select a panel of 100 strains that captured the genetic diversity of this collection. Antibiotic susceptibility testing was also performed using 14 clinically relevant antibiotics. Results This 100-strain diversity panel contained representative strains from 91 different STs, including genetically distinct strains from major epidemic clones ST-111, ST-235, ST-244 and ST-253. Seventy-one distinct antibiotic susceptibility profiles were identified ranging from pan-susceptible to pan-resistant. Known resistance alleles as well as the most prevalent mutations underlying the antibiotic susceptibilities were characterized for all isolates. Conclusions This panel provides a diverse and comprehensive set of P. aeruginosa strains for use in developing solutions to antibiotic resistance. The isolates and available metadata, including genome sequences, are available to industry, academia, federal and other laboratories at no additional cost.
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Affiliation(s)
- Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Erik Snesrud
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lindsey Hall
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Emma Mills
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Madeline Galac
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jason Stam
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ana Ong
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Yoon I Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sheila Johnson
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael Julius
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Melissa Ly
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Brett Swierczewski
- Bacterial Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Mary Hinkle
- Infectious Diseases Unit, Rochester General Hospital, Rochester, NY, USA
| | - Anthony Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Emil Lesho
- Infectious Diseases Unit, Rochester General Hospital, Rochester, NY, USA
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Patrick McGann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Irum S, Naz K, Ullah N, Mustafa Z, Ali A, Arslan M, Khalid K, Andleeb S. Antimicrobial Resistance and Genomic Characterization of Six New Sequence Types in Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates from Pakistan. Antibiotics (Basel) 2021; 10:antibiotics10111386. [PMID: 34827324 PMCID: PMC8615273 DOI: 10.3390/antibiotics10111386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 01/13/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a major bacterial pathogen associated with a variety of infections with high mortality rates. Most of the clinical P. aeruginosa isolates belong to a limited number of genetic subgroups characterized by multiple housekeeping genes’ sequences (usually 5–7) through the Multi-Locus Sequence Typing (MLST) scheme. The emergence and dissemination of novel multidrug-resistant (MDR) sequence types (ST) in P. aeruginosa pose serious clinical concerns. We performed whole-genome sequencing on a cohort (n = 160) of MDR P. aeruginosa isolates collected from a tertiary care hospital lab in Pakistan and found six isolates belonging to six unique MLST allelic profiles. The genomes were submitted to the PubMLST database and new ST numbers (ST3493, ST3494, ST3472, ST3489, ST3491, and ST3492) were assigned to the respective allele combinations. MLST and core-genome-based phylogenetic analysis confirmed the divergence of these isolates and positioned them in separate branches. Analysis of the resistome of the new STs isolates revealed the presence of genes blaOXA-50, blaPAO, blaPDC, blaVIM-2, aph(3′)-IIb, aac(6′)-II, aac(3)-Id, fosA, catB7, dfrB2, crpP, merP and a number of missense and frame-shift mutations in chromosomal genes conferring resistance to various antipseudomonal antibiotics. The exoS, exoT, pvdE, rhlI, rhlR, lasA, lasB, lasI, and lasR genes were the most prevalent virulence-related genes among the new ST isolates. The different genotypic features revealed the adaptation of these new clones to a variety of infections by various mutations in genes affecting antimicrobial resistance, quorum sensing and biofilm formation. Close monitoring of these antibiotic-resistant pathogens and surveillance mechanisms needs to be adopted to reduce their spread to the healthcare facilities of Pakistan. We believe that these strains can be used as reference strains for future comparative analysis of isolates belonging to the same STs.
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Affiliation(s)
- Sidra Irum
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Kanwal Naz
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Nimat Ullah
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Zeeshan Mustafa
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Muhammad Arslan
- Pakistan Institute of Medical Sciences (PIMS), Islamabad 44000, Pakistan;
| | - Kashaf Khalid
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Saadia Andleeb
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
- Correspondence: or
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Deruelle V, Berry A, Bouillot S, Job V, Maillard AP, Elsen S, Huber P. ExlA Pore-Forming Toxin: Localization at the Bacterial Membrane, Regulation of Secretion by Cyclic-Di-GMP, and Detection In Vivo. Toxins (Basel) 2021; 13:toxins13090645. [PMID: 34564649 PMCID: PMC8472254 DOI: 10.3390/toxins13090645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
ExlA is a highly virulent pore-forming toxin that has been recently discovered in outlier strains from Pseudomonas aeruginosa. ExlA is part of a two-partner secretion system, in which ExlA is the secreted passenger protein and ExlB the transporter embedded in the bacterial outer membrane. In previous work, we observed that ExlA toxicity in a host cell was contact-dependent. Here, we show that ExlA accumulates at specific points of the outer membrane, is likely entrapped within ExlB pore, and is pointing outside. We further demonstrate that ExlA is maintained at the membrane in conditions where the intracellular content of second messenger cyclic-di-GMP is high; lowering c-di-GMP levels enhances ExlB-dependent ExlA secretion. In addition, we set up an ELISA to detect ExlA, and we show that ExlA is poorly secreted in liquid culture, while it is highly detectable in broncho-alveolar lavage fluids of mice infected with an exlA+ strain. We conclude that ExlA translocation is halted at mid-length in the outer membrane and its secretion is regulated by c-di-GMP. In addition, we developed an immunological test able to quantify ExlA in biological samples.
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Affiliation(s)
- Vincent Deruelle
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, CNRS UMR 3528, Institut Pasteur, 75015 Paris, France
| | - Alice Berry
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
| | - Stéphanie Bouillot
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Institut de Biologie Structurale (IBS), Université Grenoble-Alpes, CNRS, CEA, 38044 Grenoble, France
| | - Viviana Job
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Institut de Biologie Structurale (IBS), Université Grenoble-Alpes, CNRS, CEA, 38044 Grenoble, France
| | - Antoine P. Maillard
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Institut de Biologie Structurale (IBS), Université Grenoble-Alpes, CNRS, CEA, 38044 Grenoble, France
| | - Sylvie Elsen
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Institut de Biologie Structurale (IBS), Université Grenoble-Alpes, CNRS, CEA, 38044 Grenoble, France
| | - Philippe Huber
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, 92265 Fontenay-aux-Roses, France
- Correspondence:
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García-Reyes S, Moustafa DA, Attrée I, Goldberg JB, Quiroz-Morales SE, Soberón-Chávez G. Vfr or CyaB promote the expression of the pore-forming toxin exlBA operon in Pseudomonas aeruginosa ATCC 9027 without increasing its virulence in mice. MICROBIOLOGY-SGM 2021; 167. [PMID: 34424157 DOI: 10.1099/mic.0.001083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pseudomonas aeruginosa is a wide-spread γ-proteobacterium that produces the biosurfactant rhamnolipid that has a great commercial value due to excellent properties of low toxicity and high biodegradability. However, this bacterium is an opportunist pathogen that constitutes an important health hazard due to its production of virulence-associated traits and its high antibiotic resistance. Thus, it is highly desirable to have a non-virulent P. aeruginosa strain for rhamnolipid production. It has been reported that strain ATCC 9027 is avirulent in mouse models of infection, and it is still able to produce rhamnolipid. Thus, it has been proposed to be suitable for it industrial production, since it encodes a defective LasR quorum sensing (QS) transcriptional regulator that is the head of this regulatory network. However, the restoration of virulence factor production by overexpression of rhlR (the gene encoding a QS-transcriptional regulator which is under the transcriptional control of LasR) is not sufficient to restore its virulence in mice. It is desirable to obtain a deeper understanding of ATCC 9027 attenuated-virulence phenotype and to assess the safety of this strain to be used at an industrial scale. In this work we determined whether increasing the expression of the pore-forming toxin encoded by the exlBA operon in strain ATCC 9027 had an impact on its virulence using Galleria mellonella and mouse models of infections. We increased the expression of the exlBA operon by overexpressing from a plasmid its transcriptional activator Vfr or of the Vfr ligand cyclic AMP produced by CyaB. We found that in G. mellonella ATCC 9027/pUCP24-vfr and ATCC 9027/pUCP24-cyaB gained a virulent phenotype, but these strains remained avirulent in murine models of P. aeruginosa infection. These results reinforce the possibility of using ATCC 9027 for industrial biosurfactants production.
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Affiliation(s)
- Selene García-Reyes
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Dina A Moustafa
- Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA.,Emory Children's Centre for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ina Attrée
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, Grenoble, France
| | - Joanna B Goldberg
- Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA.,Emory Children's Centre for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sara E Quiroz-Morales
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
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García-Reyes S, Cocotl-Yañez M, Soto-Aceves MP, González-Valdez A, Servín-González L, Soberón-Chávez G. PqsR-independent quorum-sensing response of Pseudomonas aeruginosa ATCC 9027 outlier-strain reveals new insights on the PqsE effect on RhlR activity. Mol Microbiol 2021; 116:1113-1123. [PMID: 34418194 DOI: 10.1111/mmi.14797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an opportunistic pathogen that represents an important health hazard. The quorum-sensing response regulates the expression of several virulence factors and involves three regulons: Las, Rhl, and Pqs. The P. aeruginosa ATCC 9027 strain, which belongs to the genetically diverse PA7 clade, contains a frame-shift mutation in the pqsR gene that encodes a transcriptional activator necessary for pyocyanin (PYO) synthesis in type strains PAO1 and PA14. Here we characterize the PqsE-dependent production of PYO in strain ATCC 9027. We show that this strain expresses pqsE independently of PqsR and in the absence of quinolone production, and that PqsE promotes the RhlR-dependent production of PYO, yet this production is not strictly dependent on PqsE. In addition, we show that in both strains ATCC 9027 and PAO1, PqsE overexpression causes an increased concentration of RhlR and enhances PYO production but does not affect rhamnolipids (RL) production in the same way. These results suggest that PqsE interaction with RhlR preferentially modifies its ability to activate transcription of genes involved in PYO production and provide new evidence about PqsE-dependent RhlR activation, highlighting the variability of the QS response among different P. aeruginosa clades and strains. HIGHLIGHTS: Pseudomonas aeruginosa ATCC 9027 is able to produce pyocyanin in phosphate limiting conditions, even in the absence of a functional PqsR. This strain does not produce alkyl quinolones like PQS and HHQ, but expresses pqsE. Synthesis of pyocyanin by ATCC 9027 is only partially dependent on pqsE. The overexpression of pqsE in the ATCC 9027 and PAO1 strains causes pyocyanin overproduction. The overexpression of pqsE in these strains causes an increased RhlR concentration without affecting rhlR transcription or translation. Rhamnolipids production is not affected to the same extent as pyocyanin by overexpression of pqsE in these strains.
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Affiliation(s)
- Selene García-Reyes
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico, Mexico
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico, Mexico
| | - Martín Paolo Soto-Aceves
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico, Mexico
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico, Mexico
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico, Mexico
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Espinosa-Camacho LF, Delgado G, Cravioto A, Morales-Espinosa R. Diversity in the composition of the accessory genome of Mexican Pseudomonas aeruginosa strains. Genes Genomics 2021; 44:53-77. [PMID: 34410625 DOI: 10.1007/s13258-021-01155-3] [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: 03/05/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is an important opportunistic pathogen especially in nosocomial infections due to its easy adaptation to different environments; this characteristic is due to the great genetic diversity that presents its genome. In addition, it is considered a pathogen of critical priority due to the high antimicrobial resistance. OBJECTIVES The aim of this study was to characterize the mobile genetic elements present in the chromosome of six Mexican P. aeruginosa strains isolated from adults with pneumonia and children with bacteremia. METHODS The genomic DNA of six P. aeruginosa strains were isolated and sequenced using PacBio RS-II platform. They were annotated using Prokaryotic Genome Annotation Pipeline and manually curated and analyzed for the presence of mobile genetic elements, antibiotic resistances genes, efflux pumps and virulence factors using several bioinformatics programs and databases. RESULTS The global analysis of the strains chromosomes showed a novel chromosomal rearrangement in two strains, possibly mediated by subsequent recombination and inversion events. They have a high content of mobile genetic elements: 21 genomic islands, four new islets, four different integrative conjugative elements, 28 different prophages, one CRISPR-Cas arrangements, and one class 1 integron. The acquisition of antimicrobials resistance genes into these elements are in concordance with their phenotype of multi-drug resistance. CONCLUSION The accessory genome increased the ability of the strains to adapt or survive to the hospital environment, promote genomic plasticity and chromosomal rearrangements, which may affect the expression or functionality of the gene and might influence the clinical outcome, having an impact on the treatment.
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Affiliation(s)
- Luis F Espinosa-Camacho
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Gabriela Delgado
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Alejandro Cravioto
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico.
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42
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Evolution of Subfamily I.1 Lipases in Pseudomonas aeruginosa. Curr Microbiol 2021; 78:3494-3504. [PMID: 34279672 DOI: 10.1007/s00284-021-02589-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/21/2021] [Indexed: 10/20/2022]
Abstract
The gram-negative Pseudomonas aeruginosa is an opportunistic human pathogen that contains two different types of strains: the "classical" and the "outlier". In the "classical" strain, its bacterial subfamily I.1 lipases, such as LipA and LipC in P. aeruginosa PAO1, play critical roles in its pathogenicity. However, less is known about the subfamily I.1 lipases in the "outlier" strain, nor the evolution paths of those lipases in both types of P. aeruginosa strains. Our genome-scale investigation on I.1 lipases across different bacterial strains demonstrates the presence of one LipA-like and one new type of I.1 lipase (LipC2) in those "outlier" strains. The related genomic islands analyses further suggest that the LipC counterpart gene in the "outlier" strain was lost by gene truncation. In addition, the evolutionary analyses also indicates the horizontal LipC2 gene transfer from other gammaproteobacterial species, as well as the horizontal LipA gene transfer between two different phyla, both suggesting that the gene transfer of bacterial I.1 lipases might occur in different taxonomical levels. Our results not only provide an evidence to understand the pathogenicity among different P. aeruginosa strains, but add to the knowledge of I.1 lipase evolution in bacteria.
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García-Reyes S, Soto-Aceves MP, Cocotl-Yañez M, González-Valdez A, Servín-González L, Chávez GS. The outlier Pseudomonas aeruginosa strain ATCC 9027 harbors a defective LasR quorum-sensing transcriptional regulator. FEMS Microbiol Lett 2021; 367:5874253. [PMID: 32691823 DOI: 10.1093/femsle/fnaa122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas aeruginosa infections represent an important health problem that has been recognized by the World Health Organization as a research priority. A complex regulatory network called the quorum sensing (QS) regulates several P. aeruginosa virulence-related traits, including production of elastase, rhamnolipids and pyocyanin. The avirulent P. aeruginosa strain ATCC 9027 belongs to clade 3, which is the more distant phylogroup in relationship to the other four clades of this species. This strain does not produce QS-regulated virulence factors such as elastase and rhamnolipids when cultured in rich LB medium. We report here that ATCC 9027 harbors a defective LasR protein, presumably due to the presence of an aspartic acid in position 196 instead of a glutamic acid which is the amino acid present in this position in functional LasR proteins of the type strains PAO1 (clade 1) and PA7 (also belonging to clade 3), among others. In addition, we report that ATCC 9027 and PA7 strains present differences compared to the PAO1 strain in lasB which encodes elastase, and in the rhlR regulatory sequences that modify las-boxes, and that these mutations have a little effect in the expression of these genes by a functional LasR transcriptional regulator.
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Affiliation(s)
- Selene García-Reyes
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Martín P Soto-Aceves
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México. C.P. 04510
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Gloria Soberón Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
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Callens M, Scornavacca C, Bedhomme S. Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution. Microb Genom 2021; 7:000587. [PMID: 34165421 PMCID: PMC8461475 DOI: 10.1099/mgen.0.000587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/19/2021] [Indexed: 12/18/2022] Open
Abstract
Prokaryote genome evolution is characterized by the frequent gain of genes through horizontal gene transfer (HGT). For a gene, being horizontally transferred can represent a strong change in its genomic and physiological context. If the codon usage of a transferred gene deviates from that of the receiving organism, the fitness benefits it provides can be reduced due to a mismatch with the expression machinery. Consequently, transferred genes with a deviating codon usage can be selected against or elicit evolutionary responses that enhance their integration, such as gene amelioration and compensatory evolution. Within bacterial species, the extent and relative importance of these different mechanisms has never been considered altogether. In this study, a phylogeny-based method was used to investigate the occurrence of these different evolutionary responses in Pseudomonas aeruginosa. Selection on codon usage of genes acquired through HGT was observed over evolutionary time, with the overall codon usage converging towards that of the core genome. Gene amelioration, through the accumulation of synonymous mutations after HGT, did not seem to systematically affect transferred genes. This pattern therefore seemed to be mainly driven by selective retention of transferred genes with an initial codon usage similar to that of the core genes. Additionally, variation in the copy number of tRNA genes was often associated with the acquisition of genes for which the observed variation could enhance their expression. This provides evidence that compensatory evolution might be an important mechanism for the integration of horizontally transferred genes.
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Affiliation(s)
- Martijn Callens
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Stéphanie Bedhomme
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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Overexpression of the MexXY Multidrug Efflux System Correlates with Deficient Pyoverdine Production in Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10060658. [PMID: 34073068 PMCID: PMC8226967 DOI: 10.3390/antibiotics10060658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 12/02/2022] Open
Abstract
Multidrug-resistant Pseudomonas aeruginosa poses a serious problem due to hospital- and healthcare-associated infections. A major drug resistance mechanism of P. aeruginosa involves active efflux via resistance nodulation cell division (RND)-type multidrug efflux pumps of which MexXY is increasingly recognized as a primary determinant of aminoglycoside resistance in P. aeruginosa. MexXY overexpression is often observed in drug-resistant P. aeruginosa clinical isolates. MexXY deficiency increased pyoverdine production in all four P. aeruginosa strains we tested. MexXY-overproducing multidrug-resistant P. aeruginosa PA7 exhibited the greatest effect among the strains. Complementation with a MexXY-expressing plasmid restored low-level pyoverdine production in a MexXY-deficient P. aeruginosa mutant from PA7, indicating that MexXY expression decreases pyoverdine production. Because P. aeruginosa produces pyoverdine to acquire iron, MexXY-deficient mutants might be more susceptible to iron deficiency than MexXY-producing strains or might require extra iron. High-risk clones of multidrug-resistant P. aeruginosa reportedly tend to be MexXY overproducers but defective pyoverdine producers. This study suggests that P. aeruginosa reduces production of a virulence factor after acquiring a drug resistance factor.
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Hao M, Ma W, Dong X, Li X, Cheng F, Wang Y. Comparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms. BMC Microbiol 2021; 21:133. [PMID: 33932986 PMCID: PMC8088628 DOI: 10.1186/s12866-021-02203-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The prevalence of clinical multidrug-resistant (MDR) Pseudomonas aeruginosa has been increasing rapidly worldwide over the years and responsible for a wide range of acute and chronic infections with high mortalities. Although hundreds of complete genomes of clinical P. aeruginosa isolates have been sequenced, only a few complete genomes of mucoid strains are available, limiting a comprehensive understanding of this important group of opportunistic pathogens. Herein, the complete genome of a clinically isolated mucoid strain P. aeruginosa JNQH-PA57 was sequenced and assembled using Illumina and Oxford nanopore sequencing technologies. Genomic features, phylogenetic relationships, and comparative genomics of this pathogen were comprehensively analyzed using various bioinformatics tools. A series of phenotypic and molecular-genetic tests were conducted to investigate the mechanisms of carbapenem resistance in this strain. RESULTS Several genomic features of MDR P. aeruginosa JNQH-PA57 were identified based on the whole-genome sequencing. We found that the accessory genome of JNQH-PA57 including several prophages, genomic islands, as well as a PAPI-1 family integrative and conjugative element (ICE), mainly contributed to the larger genome of this strain (6,747,067 bp) compared to other popular P. aeruginosa strains (with an average genome size of 6,445,223 bp) listed in Pseudomonas Genome Database. Colony morphology analysis and biofilm crystal staining assay respectively demonstrated an enhanced alginate production and a thicker biofilm formation capability of JNQH-PA57. A deleted mutation at nt 424 presented in mucA gene, resulted in the upregulated expression of a sigma-factor AlgU and a GDP mannose dehydrogenase AlgD, which might explain the mucoid phenotype of this strain. As for the carbapenem resistance mechanisms, our results revealed that the interplay between impaired OprD porin, chromosomal β-lactamase OXA-488 expression, MexAB-OprM and MexXY-OprM efflux pumps overexpression, synergistically with the alginates-overproducing protective biofilm, conferred the high carbapenem resistance to P. aeruginosa JNQH-PA57. CONCLUSION Based on the genome analysis, we could demonstrate that the upregulated expression of algU and algD, which due to the truncation variant of MucA, might account for the mucoid phenotype of JNQH-PA57. Moreover, the resistance to carbapenem in P. aeruginosa JNQH-PA57 is multifactorial. The dataset presented in this study provided an essential genetic basis for the comprehensive cognition of the physiology, pathogenicity, and carbapenem resistance mechanisms of this clinical mucoid strain.
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Affiliation(s)
- Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Xiaofeng Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Fang Cheng
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Yujiao Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China.
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China.
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Antimicrobial susceptibility of multidrug-resistant Pseudomonas aeruginosa isolated from drinking water and hospitalized patients in Jordan. Acta Trop 2021; 217:105859. [PMID: 33582141 DOI: 10.1016/j.actatropica.2021.105859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/28/2022]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is an important environmental, opportunistic and nosocomial pathogen with a significant threat to public health. The objectives of this study were to determine the in vitro antimicrobial susceptibility patterns of, and antibiotic drug combinations with synergistic effects against P. aeruginosa isolated from drinking water and hospitalized patients in Jordan. A total of 16 P. aeruginosa isolates were obtained from hospitalized patients and 15 were isolated from bottled drinking water were used in the study. Bacterial isolation and identification was performed using routine microbiological methods and confirmed using PCR technique targeting the 16S rDNA gene. The antimicrobial susceptibility patterns were determined by measuring the minimum inhibitory concentration (MIC) using the 2-fold microdilution method. Synergy interaction between various antimicrobials was determined using the checkerboard method and fractional inhibitory concentration index (FICI). The majority of water isolates were sensitive to gentamicin (93.3%), ticarcillin (86.7%) and ciprofloxacin, levofloxacin, amikacin, colistin, piperacillin, azlocillin, aztreonam, ceftazidime and imipenem (100% each). All water isolates (100%) were resistant to amoxicillin, oxytetracycline and doxycycline (93.3% and 86.7, respectively). For the clinical isolates, all (100%) were sensitive to ceftazidime, 81.3% were sensitive to aztreonam, while 62.5% were sensitive to ciprofloxacin, levofloxacin, gentamicin, amikacin, colistin, piperacillin, ticracillin, azlocillin, and imipenem. All clinical isolates (100%) were resistant to oxytetracycline, doxycycline and amoxicillin. Analysis of the checkerboard synergy assay of multi-drug resistant isolates (n=26) showed significant synergism (P ≤ 0.05) when ciprofloxacin or gentamicin were included in the combination. There were no significant differences in synergistic activity between ciprofloxacin and levofloxacin when combined with other antimicrobial agents of the beta-lactams or aminoglycosides classes. There were no significant differences in the synergistic activities between beta lactams - aminoglycoside and beta lactams - fluoroquinolone combinations. Results of this study indicate an alarming widespread presence of multidrug-resistant P. aeruginosa associated with chronic suppurative infections in hospitalized patients and apparently clean drinking water in Jordan. Treatment of clinical suppurative lesions must be based on culture and in vitro susceptibility testing using potent antimicrobial combinations to avoid emergence of resistant strains and to improve the clinical outcome of treated patients.
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Díaz-Ríos C, Hernández M, Abad D, Álvarez-Montes L, Varsaki A, Iturbe D, Calvo J, Ocampo-Sosa AA. New Sequence Type ST3449 in Multidrug-Resistant Pseudomonas aeruginosa Isolates from a Cystic Fibrosis Patient. Antibiotics (Basel) 2021; 10:antibiotics10050491. [PMID: 33922748 PMCID: PMC8146123 DOI: 10.3390/antibiotics10050491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most critical bacterial pathogens associated with chronic infections in cystic fibrosis patients. Here we show the phenotypic and genotypic characterization of five consecutive multidrug-resistant isolates of P. aeruginosa collected during a month from a CF patient with end-stage lung disease and fatal outcome. The isolates exhibited distinct colony morphologies and pigmentation and differences in their capacity to produce biofilm and virulence potential evaluated in larvae of Galleria mellonella. Whole genome-sequencing showed that isolates belonged to a novel sequence type ST3449 and serotype O6. Analysis of their resistome demonstrated the presence of genes blaOXA-396, blaPAO, aph(3')-IIb, catB, crpP and fosA and new mutations in chromosomal genes conferring resistance to different antipseudomonal antibiotics. Genes exoS, exoT, exoY, toxA, lasI, rhlI and tse1 were among the 220 virulence genes detected. The different phenotypic and genotypic features found reveal the adaptation of clone ST3449 to the CF lung environment by a number of mutations affecting genes related with biofilm formation, quorum sensing and antimicrobial resistance. Most of these mutations are commonly found in CF isolates, which may give us important clues for future development of new drug targets to combat P. aeruginosa chronic infections.
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Affiliation(s)
- Catalina Díaz-Ríos
- Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain; (C.D.-R.); (L.Á.-M.)
| | - Marta Hernández
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), 47071 Valladolid, Spain; (M.H.); (D.A.)
| | - David Abad
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), 47071 Valladolid, Spain; (M.H.); (D.A.)
| | - Laura Álvarez-Montes
- Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain; (C.D.-R.); (L.Á.-M.)
| | - Athanasia Varsaki
- Centro de Investigación y Formación Agraria (CIFA), 39600 Muriedas, Spain;
| | - David Iturbe
- Servicio de Neumología, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain;
| | - Jorge Calvo
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain;
| | - Alain A. Ocampo-Sosa
- Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain; (C.D.-R.); (L.Á.-M.)
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain;
- Correspondence:
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Moore MP, Lamont IL, Williams D, Paterson S, Kukavica-Ibrulj I, Tucker NP, Kenna DTD, Turton JF, Jeukens J, Freschi L, Wee BA, Loman NJ, Holden S, Manzoor S, Hawkey P, Southern KW, Walshaw MJ, Levesque RC, Fothergill JL, Winstanley C. Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain. Microb Genom 2021; 7:mgen000511. [PMID: 33720817 PMCID: PMC8190615 DOI: 10.1099/mgen.0.000511] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
The Liverpool epidemic strain (LES) is an important transmissible clonal lineage of Pseudomonas aeruginosa that chronically infects the lungs of people with cystic fibrosis (CF). Previous studies have focused on the genomics of the LES in a limited number of isolates, mostly from one CF centre in the UK, and from studies highlighting identification of the LES in Canada. Here we significantly extend the current LES genome database by genome sequencing 91 isolates from multiple CF centres across the UK, and we describe the comparative genomics of this large collection of LES isolates from the UK and Canada. Phylogenetic analysis revealed that the 145 LES genomes analysed formed a distinct clonal lineage when compared with the wider P. aeruginosa population. Notably, the isolates formed two clades: one associated with isolates from Canada, and the other associated with UK isolates. Further analysis of the UK LES isolates revealed clustering by clinic geography. Where isolates clustered closely together, the association was often supported by clinical data linking isolates or patients. When compared with the earliest known isolate, LESB58 (from 1988), many UK LES isolates shared common loss-of-function mutations, such as in genes gltR and fleR. Other loss-of-function mutations identified in previous studies as common adaptations during CF chronic lung infections were also identified in multiple LES isolates. Analysis of the LES accessory genome (including genomic islands and prophages) revealed variations in the carriage of large genomic regions, with some evidence for shared genomic island/prophage complement according to clinic location. Our study reveals divergence and adaptation during the spread of the LES, within the UK and between continents.
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Affiliation(s)
- Matthew P. Moore
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
- Present address: Nuffield Department of Health, University of Oxford, UK
| | - Iain L. Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - David Williams
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Irena Kukavica-Ibrulj
- Institute for Integrative and Systems Biology, Université Laval, Quebec City, QC, Canada
| | - Nicholas P. Tucker
- Strathclyde Institute of Pharmacy & Biomedical Sciences. University of Strathclyde, Glasgow, UK
| | | | - Jane F. Turton
- National Infection Service, Public Health England, London, UK
| | - Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval, Quebec City, QC, Canada
| | - Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval, Quebec City, QC, Canada
- Present address: Harvard Medical School, Boston, MA, USA
| | - Bryan A. Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Present address: Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Nicholas J. Loman
- Institute for Microbiology & Infection, University of Birmingham, Birmingham, UK
| | - Stephen Holden
- Nottingham University Hospitals NHS Trust, Nottingham, UK
- Present address: MSD Research Laboratories, Two Pancras Square, London, UK
| | - Susan Manzoor
- University Hospitals Birmingham, Heartlands Hospital, Bordesley Green East, Birmingham, UK
| | - Peter Hawkey
- Institute for Microbiology & Infection, University of Birmingham, Birmingham, UK
- Present address: University of Birmingham Microbiome Treatment Centre, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | | | - Roger C. Levesque
- Institute for Integrative and Systems Biology, Université Laval, Quebec City, QC, Canada
| | - Joanne L. Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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Berger C, Rückert C, Blom J, Rabaey K, Kalinowski J, Rosenbaum MA. Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. Sci Rep 2021; 11:1370. [PMID: 33446769 PMCID: PMC7809047 DOI: 10.1038/s41598-020-80592-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/21/2020] [Indexed: 12/31/2022] Open
Abstract
The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.
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Affiliation(s)
- Carola Berger
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Rückert
- Center for Biotechnology - CeBiTec, University of Bielefeld, Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Giessen, Germany
| | - Korneel Rabaey
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, University of Bielefeld, Bielefeld, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
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