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Steyaert S, Peeters C, Wieme AD, Muyldermans A, Vandoorslaer K, Spilker T, Wybo I, Piérard D, LiPuma JJ, Vandamme P. Novel Ralstonia species from human infections: improved matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification and analysis of antimicrobial resistance patterns. Microbiol Spectr 2024; 12:e0402123. [PMID: 38661349 PMCID: PMC11237764 DOI: 10.1128/spectrum.04021-23] [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: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
A collection of 161 Ralstonia isolates, including 90 isolates from persons with cystic fibrosis, 27 isolates from other human clinical samples, 8 isolates from the hospital environment, 7 isolates from industrial samples, and 19 environmental isolates, was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification and yielded confident species level identification scores for only 62 (39%) of the isolates, including four that proved misidentified subsequently. Whole-genome sequence analysis of 32 representative isolates for which no confident MALDI-TOF MS species level identification was obtained revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively, and provided the basis for updating an in-house MALDI-TOF MS database. A reanalysis of all mass spectra with the updated MALDI-TOF MS database increased the percentage of isolates with confident species level identification up to 77%. The antimicrobial susceptibility of 30 isolates mainly representing novel human clinical and environmental Ralstonia species was tested toward 17 antimicrobial agents and demonstrated that the novel Ralstonia species were generally multi-resistant, yet susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline. An analysis of genomic antimicrobial resistance genes in 32 novel and publicly available genome sequences revealed broadly distributed beta-lactam resistance determinants.IMPORTANCEThe present study demonstrated that a commercial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification database can be tailored to improve the identification of Ralstonia species. It also revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively. An analysis of minimum inhibitory concentration values demonstrated that the novel Ralstonia species were generally multi-resistant but susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline.
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Affiliation(s)
- Stephanie Steyaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
| | - Anneleen D. Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Astrid Muyldermans
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ingrid Wybo
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Denis Piérard
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - John J. LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
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Xiong K, Ao K, Wei W, Dong J, Li J, Yang Y, Tang B, Li Y. Periodontitis aggravates COPD through the activation of γδ T cell and M2 macrophage. mSystems 2024; 9:e0057223. [PMID: 38214520 PMCID: PMC10878042 DOI: 10.1128/msystems.00572-23] [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: 06/05/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic systemic inflammatory disease with high morbidity and mortality. Periodontitis exacerbates COPD progression; however, the immune mechanisms by which periodontitis affects COPD remain unclear. Here, by constructing periodontitis and COPD mouse models, we demonstrated that periodontitis and COPD could mutually aggravate disease progression. For the first time, we found that the progression was associated with the activation of γδ T cells and M2 macrophages, and M2 polarization of macrophages was affected by γδ T cells activation. In the lung tissues of COPD with periodontitis, the activation of γδ T cells finally led to the increase of IL 17 and IFN γ expression and M2 macrophage polarization. Furthermore, we found that the periodontitis-associated bacteria Porphyromonas gingivalis (P. gingivalis) promoted the activation of γδ T cells and M2 macrophages ex vivo. The data from clinical bronchoalveolar lavage fluid (BALF) samples were consistent with the in vivo and ex vivo experiments. For the first time, our results identified the crucial role of γδ T-M2 immune mechanism in mediating periodontitis-promoted COPD progression. Therefore, targeting at periodontitis treatment and the γδ T-M2 immune mechanism might provide a new practical strategy for COPD prevention or control.IMPORTANCEPeriodontitis exacerbates chronic obstructive pulmonary disease (COPD) progression. For the first time, the current study identified that the impact of periodontitis on COPD progression was associated with the activation of γδ T cells and M2 macrophages and that M2 polarization of macrophages was affected by γδ T cells activation. The results indicated that targeting at periodontitis treatment and the γδ T-M2 immune mechanism might provide a new practical strategy for COPD prevention or control.
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Affiliation(s)
- Kaixin Xiong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Keping Ao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Wei
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Jiajia Dong
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yutao Yang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Boyu Tang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Conservation Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yan Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Sun JX, Xia QD, Zhong XY, Liu Z, Wang SG. The bladder microbiome of NMIBC and MIBC patients revealed by 2bRAD-M. Front Cell Infect Microbiol 2023; 13:1182322. [PMID: 37351184 PMCID: PMC10282653 DOI: 10.3389/fcimb.2023.1182322] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/15/2023] [Indexed: 06/24/2023] Open
Abstract
Background Bladder cancer (BCa) is the most common malignancy of the urinary tract which can be divided into non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC), and their microbial differences are not fully understood. This study was conducted by performing 2bRAD sequencing for Microbiome (2bRAD-M) on NMIBC and MIBC tissue samples to investigate the microbiota differences between NMIBC and MIBC individuals. Methods A total of 22 patients with BCa, including 7 NMIBC and 15 MIBC, were recruited. Tumor tissues were surgically removed as samples and DNA was extracted. Type IIB restriction endonucleases were used to enzymatically cleave the microbial genome for each microbe's tag and map it to species-specific 2bRAD markers to enable qualitative and quantitative studies of microbes between MIBC and NMIBC tissues. Results A total of 527 species were detected. The microbial diversity of NMIBC tissues was significantly higher than that of MIBC tissues. Microbial composition of the two tumor tissues was similar, where Ralstonia_sp000620465 was the most dominant species. 4 species (Acinetobacter_guillouiae, Anoxybacillus_A_rupiensis, Brevibacillus_agri and Staphylococcus_lugdunensis) were enriched in NMIBC, while Ralstonia_mannitolilytica, Ralstonia_pickettii, and Ralstonia_sp000620465 were overrepresented in MIBC. 252 discriminatory character taxa were also revealed by linear discriminant analysis effect sizea (LEfSe). Species importance point plots identified Ralstonia_sp000620465, Cutibacterium_acnes and Ralstonia_pickettii as the three most important species between the two groups. Meanwhile, functional annotation analysis showed 3011 different COGs and 344 related signaling pathways between MIBC and NMIBC microbiome. Conclusion This first 2bRAD-M microbiome study on MIBC and NMIBC tissues revealed significant differences in the microbial environment between the two groups, which implies a potential association between tumor microbial dysbiosis and BCa, and provides a possible target and basis for subsequent studies on the mechanisms of BCa development and progression.
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Affiliation(s)
| | | | | | - Zheng Liu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shao-Gang Wang
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Sun X, Cai Y, Dai W, Jiang W, Tang W. The difference of gut microbiome in different biliary diseases in infant before operation and the changes after operation. BMC Pediatr 2022; 22:502. [PMID: 36002814 PMCID: PMC9404627 DOI: 10.1186/s12887-022-03570-1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/21/2022] [Indexed: 11/25/2022] Open
Abstract
Background Evidence supports an association between cholestatic liver disease and changes in microbiome composition. Nevertheless, the identification of this special type of biliary atresia from non-biliary atresia cholestasis is still a major clinical difficulty. The purpose of this study is to compare the differences in the composition of gut microbiome between infants with biliary atresia and infant with non-biliary atrestic cholestasis, to find new ways to identify and diagnose these two diseases early, to understand the influence of the presence or absence of bile on the composition of the gut microbiome in infants with cholestasis. Methods Using 16S rDNA gene sequencing technology to analyze the intestinal flora of the participants. Results In terms of diversity, there is an obvious structural separation in the intestinal microbiota of the BA group and the CD group, and this structural separation also exists in the comparison between the two groups before surgery. Taxonomic analysis demonstrated that the two groups showed an increase in Proteobacteria and Firmicutes before surgery, and the relative abundance of potential pathogens such as Shigella, Streptococcus, Klebsiella, etc. increased, potential probiotics such as Bifidobacteria and Lactobacillus decreased, but the relative abundance of each genus was different between groups. It was found that Enterococcus, Ralstonia, Nitriliruptoraceae, etc. were differentially enriched in the BA group, the CD group are mainly enriched in Veillonella, Clostridium_sensu_stricto_1 and Lactobacillus. Functional analysis of the groups showed that the BA group mainly focused on the processes of energy release processes, and the CD group mainly focused on the biosynthesis of amino-acids to consume energy. Conclusions The composition of intestinal flora is different between biliary atresia and non-biliary atretic cholestasis. Enterococcus, Ralstonia, etc. may become biomarkers for the identification and diagnosis of both.
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Affiliation(s)
- Xinhe Sun
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yaoyao Cai
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wenwen Dai
- Department of Pediatric Surgery, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Weiwei Jiang
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China.
| | - Weibing Tang
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China.
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Siddiqui T, Patel SS, Sinha R, Ghoshal U, Sahu C. Ralstonia mannitolilytica: an emerging multidrug-resistant opportunistic pathogen in a tertiary care hospital setting. Access Microbiol 2022; 4:acmi000367. [PMID: 36003352 PMCID: PMC9394538 DOI: 10.1099/acmi.0.000367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/06/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction. Ralstonia mannitolilytica is a rare opportunistic pathogen capable of causing a serious infection in immunocompromised patients. Our objective was to describe all cases of R. mannitolilytica bloodstream infection identified within 2 years at our tertiary care centre, focusing on clinical characteristics, risk factors, antibiotic sensitivity patterns, management and outcomes. Case Series. We compiled a descriptive case series including 14 non-duplicate R. mannitolilytica isolates obtained from bloodstream infection samples from the microbiology laboratory of a tertiary care centre from June 2019 to June 2021. All isolates were initially identified based on their morphological properties and biochemical reactions, and then underwent matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) examination for confirmation of identity. Antibiotic susceptibility testing was performed using the Kirby–Bauer disc diffusion method and Vitek 2. All 14 patients presented with symptoms of fever and/or chills, and a positive blood culture for R. mannitolilytica. After 48 h of incubation, no Ralstonia growth was reported from any of the current environmental or pharmaceutical water samples. Chemotherapy (9/14), mechanical ventilation (4/14), steroid use (2/14) and diabetes mellitus (1/14) were associated risk factors in our patients. The antibiotic sensitivity panel showed maximum resistance to aminoglycosides (64.3%) and no resistance to cefoperazone/sulbactum. Patients received treatment with cefoperazone/sulbactum and meropenem or ceftazidime. Thirteen patients recovered with antibiotic therapy and one patient succumbed to his illness. Conclusion. R. mannitolilytica can cause bloodstream infections in immunocompromised patients. It is likely to be missed or underreported due to lack of clinical awareness. MALDI-TOF MS is helpful in rapid identification. R. mannitolilytica is resistant to many routinely used antibiotics, including carbapenems.
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Affiliation(s)
- Tasneem Siddiqui
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Sangram Singh Patel
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Richa Sinha
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Ujjala Ghoshal
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Chinmoy Sahu
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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Papagrigorakis E, Vavourakis M, Vlachos C, Zachariou D, Galanis A, Marougklianis V, Polyzois V, Pneumaticos S. Osteomyelitis Caused by Ralstonia mannitolilytica, a Rare Opportunistic Pathogen. Cureus 2022; 14:e24151. [PMID: 35586345 PMCID: PMC9109608 DOI: 10.7759/cureus.24151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 11/11/2022] Open
Abstract
Ralstonia spp. are non-fermenting aerobic gram-negative rods found in humid environments, whose role as opportunistic human pathogens has lately been recognized. Ralstonia mannitolilytica is one of the three members of the Ralstonia genus (together with Ralstonia pickettii and Ralstonia insidiosa). Bone infections by Ralstonia spp. are very rare. We report a case of femoral osteomyelitis caused by R. mannitolilytica. Among literature search, only eight cases of bone infection due to the Ralstonia genus have been described, in all of which the causative agent was identified as R. pickettii. To our knowledge, this is the first reported case of osteomyelitis attributed to R. mannitolilytica. Despite its low virulence, Ralstonia has specific characteristics that promote its spread and shows high antibiotic resistance, partly due to its ability to create a biofilm. Identification of Ralstonia spp. poses unique difficulties as the distinction between the species of the genus is not straightforward. Additionally, the bacteria may be misidentified as other closely related species. Recent data suggests that modern spectrometry and gene sequencing techniques are essential to avoid these pitfalls. Susceptibility data about the genus is limited and based on a small number of case reports, therefore there is no standardized antibiotic susceptibility testing and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints exist. The report aims is to provide useful information on the antibiotic selection and treatment suggestions to be followed for bone infections caused by the Ralstonia genus, along with a review on the literature of this emerging opportunistic pathogen.
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Batarilo I, Maravic-Vlahovicek G, Bedenic B, Kazazic S, Bingulac Popovic J, Slade Vitkovic M, Katic S, Jukic I. Oxacillinases and antimicrobial susceptibility of Ralstonia pickettii from pharmaceutical water systems in Croatia. Lett Appl Microbiol 2022; 75:103-113. [PMID: 35352370 DOI: 10.1111/lam.13711] [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: 12/02/2021] [Revised: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 11/30/2022]
Abstract
This study evaluated antibiotic susceptibility and presence of blaOXA22 and blaOXA60 genes in 81 isolates of Ralstonia pickettii obtained from different purified and ultra-pure water systems in two different geographical areas of Croatia. E-test and disk diffusion test were performed to determine antibiotic susceptibility. Polymerase Chain Reaction was applied to detect genes encoding OXA-22 and OXA-60, oxacillinases previously identified in R. pickettii. The isolates were genotyped by pulsed-field gel electrophoresis. The results revealed variable susceptibility/resistance profiles. Our isolates exhibited high susceptibility rates to ceftriaxone, cefotaxime, piperacillin-tazobactam, ciprofloxacin, imipenem, cefepime and in lesser extent to ceftazidime. High rates of susceptibility were also observed for sulfamethoxazole-trimethoprim and piperacillin. High resistance rates were noticed for ticarcillin-clavulanate, aztreonam and meropenem, as well as for all aminoglycosides tested. Modified Hodge test was positive in 51,9% strains, indicating production of carbapenemases. blaOXA22 and blaOXA60 genes were detected in 37.0% and 80.3% strains, respectively. Pulsed-field gel electrophoresis identified three major clusters containing subclusters. R. pickettii should be taken seriously as a possible cause of nosocomial infections to ensure adequate therapy, to prevent the development of resistant strains and to try to reduce the possibility of R. pickettii surviving in clean and ultra clean water systems.
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Affiliation(s)
- I Batarilo
- Croatian Institute for Transfusion Medicine, Zagreb, Croatia
| | | | - B Bedenic
- School of Medicine, University of Zagreb, Croatia.,University Hospital Center Zagreb, Croatia
| | - S Kazazic
- Ruđer Bošković Institute, Zagreb, Croatia
| | | | | | - S Katic
- School of Medicine, University of Zagreb, Croatia
| | - I Jukic
- Croatian Institute for Transfusion Medicine, Zagreb, Croatia.,Josip Juraj Strossmayer University of Osijek, Croatia
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Zhou S, Tang D, Wei S, Hu Z, Wang X, Luo D. Ralstonia mannitolilytica sepsis after elective cesarean delivery: a case report. BMC Pregnancy Childbirth 2021; 21:737. [PMID: 34717569 PMCID: PMC8556946 DOI: 10.1186/s12884-021-04214-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022] Open
Abstract
Background Ralstonia mannitolilytica, a newly emerging opportunistic pathogen worldwide, has been reported to be responsible for human pneumonia, septicemia and meningitis. This is the first report of a case of Ralstonia mannitolilytica sepsis after elective cesarean delivery. Case presentation A 25-year-old woman, gravida 1 para 0, was scheduled for an elective cesarean delivery at 39+ 1 weeks of gestation. Sudden high fever and decreased blood pressure occurred a short time after the operation. Ralstonia mannitolilytica was identified in her blood culture 5 days after the operation. Based on the presence of sepsis and septic shock, massive fluid replacement, blood transfusion, vasoactive agents, imipenem/cilastatin and cefoperazone sulbactam sodium were applied. She was discharged after intensive care without complications. Conclusions Although the incidence of sepsis due to Ralstonia mannitolilytica is relatively low, once infection occurs in a puerpera, severe symptoms develop abruptly. Thus, prompt diagnosis and appropriate treatment are key to the cure.
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Affiliation(s)
- Shenglan Zhou
- Department of Critical Obstetrics, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Dongmei Tang
- Department of Critical Obstetrics, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Sumei Wei
- Department of Critical Obstetrics, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Zhengchang Hu
- Department of Intensive Care Unit, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Xuemei Wang
- Department of Clinical Laboratory, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Dan Luo
- Department of Critical Obstetrics, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China.
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Characterization of clinical Ralstonia strains and their taxonomic position. Antonie van Leeuwenhoek 2021; 114:1721-1733. [PMID: 34463860 PMCID: PMC8448721 DOI: 10.1007/s10482-021-01637-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/03/2021] [Indexed: 12/03/2022]
Abstract
To improve understanding of the role of Ralstonia in cystic fibrosis (CF), whole genomes of 18 strains from clinical samples were sequenced using Illumina technology. Sequences were analysed by core genome Multi-Locus Sequence Typing, Average Nucleotide Identity based on BLAST (ANIb), RAST annotation, and by ResFinder. Phylogenetic analysis was performed for the 16S rRNA gene, and the OXA-22 and OXA-60 ß-lactamase families. The minimal inhibitory concentrations (MICs) were determined using broth microdilution. ANIb data for the 18 isolates and 54 strains from GenBank, supported by phylogenetic analysis, showed that 8 groups of clusters (A-H), as well as subgroups that should be considered as species or subspecies. Groups A-C contain strains previously identified as Ralstonia solanacearum and Ralstonia pseudosolanacearum. We propose that group A is a novel species. Group B and C are Ralstonia syzygii, Ralstonia solanacearum, respectively. Group D is composed of Ralstonia mannitolilytica and Group E of Ralstonia pickettii. Group F and G should be considered novel species. Group H strains belong to R. insidiosa. OXA-22 and OXA-60 family ß-lactamases were encoded by all strains. Co-trimoxazole generally showed high activity with low MICs (≤1 mg/l) as did ciprofloxacin (≤0.12 mg/l). MICs against the other antibiotics were more variable, but generally high. RAST annotation revealed limited differences between the strains, and virulence factors were not identified. The taxonomy of the genus Ralstonia is in need of revision, but sequencing additional isolates is needed. Antibiotic resistance levels are high. Annotation did not identify potential virulence factors.
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de Almeida OGG, Capizzani CPDC, Tonani L, Grizante Barião PH, da Cunha AF, De Martinis ECP, Torres LAGMM, von Zeska Kress MR. The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi. Front Cell Infect Microbiol 2020; 10:598938. [PMID: 33262957 PMCID: PMC7686462 DOI: 10.3389/fcimb.2020.598938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/09/2020] [Indexed: 12/29/2022] Open
Abstract
Microbial communities infiltrate the respiratory tract of cystic fibrosis patients, where chronic colonization and infection lead to clinical decline. This report aims to provide an overview of the diversity of bacterial and fungal species from the airway secretion of three young CF patients with severe pulmonary disease. The bacterial and fungal microbiomes were investigated by culture isolation, metataxonomics, and metagenomics shotgun. Virulence factors and antibiotic resistance genes were also explored. A. fumigatus was isolated from cultures and identified in high incidence from patient sputum samples. Candida albicans, Penicillium sp., Hanseniaspora sp., Torulaspora delbrueckii, and Talaromyces amestolkiae were isolated sporadically. Metataxonomics and metagenomics detected fungal reads (Saccharomyces cerevisiae, A. fumigatus, and Schizophyllum sp.) in one sputum sample. The main pathogenic bacteria identified were Staphylococcus aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, and Achromobacter xylosoxidans. The canonical core CF microbiome is composed of species from the genera Streptococcus, Neisseria, Rothia, Prevotella, and Haemophilus. Thus, the airways of the three young CF patients presented dominant bacterial genera and interindividual variability in microbial community composition and diversity. Additionally, a wide diversity of virulence factors and antibiotic resistance genes were identified in the CF lung microbiomes, which may be linked to the clinical condition of the CF patients. Understanding the microbial community is crucial to improve therapy because it may have the opposite effect, restructuring the pathogenic microbiota. Future studies focusing on the influence of fungi on bacterial diversity and microbial interactions in CF microbiomes will be welcome to fulfill this huge gap of fungal influence on CF physiopathology.
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Affiliation(s)
- Otávio Guilherme Gonçalves de Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Carolina Paulino da Costa Capizzani
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ludmilla Tonani
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Patrícia Helena Grizante Barião
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Anderson Ferreira da Cunha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Elaine Cristina Pereira De Martinis
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - Marcia Regina von Zeska Kress
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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Basso M, Venditti C, Raponi G, Navazio AS, Alessandri F, Giombini E, Nisii C, Di Caro A, Venditti M. A case of persistent bacteraemia by Ralstonia mannitolilytica and Ralstonia pickettii in an intensive care unit. Infect Drug Resist 2019; 12:2391-2395. [PMID: 31447567 PMCID: PMC6686741 DOI: 10.2147/idr.s206492] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022] Open
Abstract
The Ralstonia spp. genus is a group of non-fermentative, Gram-negative bacteria often resistant to many antibiotics, which are emerging as opportunistic pathogens frequently associated with infections in hospital settings. We present herein a case of combined R. pickettii and R. mannitolilytica persisting and relapsing bacteraemia, possibly caused by a septic arterial thrombosis secondary to the rupture of an internal carotid artery aneurysm. Microbiology studies showed that both Ralstonia isolates produced biofilm and carried class D oxacillinase genes. When confronted with infections caused by members of the Ralstonia genus, identification to the species level is crucial for correct clinical management, as the two species show different antibiotic susceptibility patterns.
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Affiliation(s)
- Monica Basso
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Carolina Venditti
- Laboratory of Microbiology, L. Spallanzani National Institute for Infectious Diseases, Rome, Italy
| | - Giammarco Raponi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome Italy
| | - Anna Sara Navazio
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome Italy
| | - Francesco Alessandri
- Department of Anesthesia and Intensive Care Medicine, Sapienza University of Rome, Rome, Italy
| | - Emanuela Giombini
- Laboratory of Microbiology, L. Spallanzani National Institute for Infectious Diseases, Rome, Italy
| | - Carla Nisii
- Laboratory of Microbiology, L. Spallanzani National Institute for Infectious Diseases, Rome, Italy
| | - Antonino Di Caro
- Laboratory of Microbiology, L. Spallanzani National Institute for Infectious Diseases, Rome, Italy
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome Italy
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