1
|
Varda Brkić D, Babel J, Budimir A, Butić I, Gužvinec M, Jurić D, Ferenčak I, Bošnjak S, Mareković I. Disseminated Infection Caused by Nocardia cyriacigeorgica in Immunocompromised Patient Confirmed by Whole Genome Sequencing. Chemotherapy 2024:1-8. [PMID: 39128464 DOI: 10.1159/000539977] [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: 03/25/2024] [Accepted: 06/19/2024] [Indexed: 08/13/2024]
Abstract
INTRODUCTION Nocardia spp. is an opportunistic pathogen capable of causing localized and disseminated infections in immunocompromised hosts. It is critical for serious infections to have an early and accurate identification of this pathogen in order to enable timely and focused combination antimicrobial treatment. CASE PRESENTATION We describe the case of an 87-year-old patient previously treated for myasthenia gravis with corticosteroids and azathioprine. Patient was admitted at the emergency department with clinical signs of sepsis with cellulitis of right hand associated with injury acquired after gardening and trimming roses and did not respond to empirical antimicrobial treatment. Computerized tomography revealed pulmonary infiltrates with inflammatory etiology. Nocardia cyriacigeorgica was cultivated from blood culture, skin swab, abscess aspirate, and endotracheal aspirate and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), 16S rRNA sequencing, and whole genome sequencing (WGS). Susceptibility testing was performed with E-test (bioMerieux, Marcy-l'Étoile, France), and corresponding resistance genes were detected by WGS. Resistance to amoxicillin-clavulanate, azithromycin, ciprofloxacin, and vancomycin was detected by both methods. Despite all interventions and the patient receiving antimicrobial treatment including imipenem-cilastatin, amikacin, and trimethoprim-sulfamethoxazole, the course and outcome of infection were unfavorable. CONCLUSION We would like to emphasize the need to consider the possibility of disseminated Nocardia infection in immunocompromised patients, especially in patients receiving long-term corticosteroid treatment with skin infections and/or cavitary lung lesions, especially if these do not improve with standard antimicrobial treatment. Precise species identity provides a critical guide for physicians in the choice of targeted treatment. Thanks to MALDI-TOF MS, Nocardia spp. identification is now available in routine lab work. WGS is still inevitable for the identification of uncommon and novel species due to the high sequence similarities between closely related species and the genetic diversity of that genus.
Collapse
Affiliation(s)
- Dijana Varda Brkić
- Clinical Department of Clinical Microbiology, Infection Prevention and Control, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Jakša Babel
- Department of Intensive Care Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ana Budimir
- Clinical Department of Clinical Microbiology, Infection Prevention and Control, University Hospital Centre Zagreb, Zagreb, Croatia
- Department of Medical Microbiology and Parasitology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Iva Butić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia
| | - Marija Gužvinec
- Department of Clinical Microbiology, University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia
| | - Dragan Jurić
- Department of Microbiology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Ivana Ferenčak
- Department of Microbiology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Selma Bošnjak
- Department of Microbiology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Ivana Mareković
- Clinical Department of Clinical Microbiology, Infection Prevention and Control, University Hospital Centre Zagreb, Zagreb, Croatia
- Department of Medical Microbiology and Parasitology, University of Zagreb School of Medicine, Zagreb, Croatia
| |
Collapse
|
2
|
Alotaibi F, Lee SJ, Lahrach Z, St-Arnaud M, Hijri M. Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil. Microorganisms 2023; 11:2972. [PMID: 38138115 PMCID: PMC10745995 DOI: 10.3390/microorganisms11122972] [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: 10/24/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
The bacterial strain WB46 was isolated from the rhizosphere of willow plants (Salix purpurea L.) growing in soil contaminated with petroleum hydrocarbons. The strain was subjected to whole-genome shotgun sequencing using Illumina HiSeq. Its draft genome is 7.15 Mb, with a 69.55% GC content, containing 6387 protein-coding genes and 51 tRNA and 15 rRNA sequences. The quality and reliability of the genome were assessed using CheckM, attaining an estimated genome completeness of 98.75% and an estimated contamination of 1.68%. These results indicate a high-quality genome (>95%) and low contamination (<5%). Many of these genes are responsible for petroleum hydrocarbon degradation, such as alkane 1-monooxygenase (alkB) and naphthalene dioxygenase (ndo). 16S rRNA gene analysis, including in silico DNA-DNA hybridization (DDH) and average nucleotide identity (ANI), showed that strain WB46 belongs to the genus Nocardia, and the most closely related species is Nocardia asteroides. The strain WB46 showed a distance of 63.4% and sequence identity of 88.63%, respectively. These values fall below the threshold levels of 70% and 95%, respectively, suggesting that the strain WB46 is a new species. We propose the name of Nocardia canadensis sp. nov. for this new species. Interestingly, the sequence divergence of the 16S rRNA gene showed that the divergence only occurred in the V2 region. Therefore, the conventional V3-V4, V5-V7, or V8-V9 targeting metabarcoding, among others, would not be able to assess the diversity related to this new species.
Collapse
Affiliation(s)
- Fahad Alotaibi
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
- Department of Soil Science, King Saud University, Riyadh 11564, Saudi Arabia
| | - Soon-Jae Lee
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
| | - Zakaria Lahrach
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir 43150, Morocco
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir 43150, Morocco
| |
Collapse
|
3
|
Sarkar B, Gupta AM, Mandal S. Insights from the comparative genome analysis of natural rubber degrading Nocardia species. Bioinformation 2021; 17:880-890. [PMID: 35574501 PMCID: PMC9070631 DOI: 10.6026/97320630017880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 11/23/2022] Open
Abstract
Nocardia are known to be a facultative human pathogen and can cause infection in immune compromised patients. Though the details research on the virulence factors of Nocardia are scanty but numerous genes that code such factors were reported from different species of Nocardia. Despite of the presence of several virulence factors, species of this genus have been shown to have role in remediation of many toxic and hazardous materials from the environment. In this study, genome sequences of rubber degrading Nocardia sp. BSTN01 and N.nova SH22a have been analyzed to locate the potential virulence genes. Also, the genomes of facultative pathogenic Nocardia like, N.africana, N. brasiliensis, N. kruczakiae, N. transvalensis and N. veterana have been analyzed to find the gene encoding latex clearing protein (Lcp), a rubber oxygenase enzyme of Gram-positive action bacteria. The study provides an insight about the potentiality of rubberdegrading Nocardia species to emerge as future human pathogens and also the probability of a serious concern if the studied facultative pathogens of Nocardia like N. africana, N. brasiliensis, N. kruczakiae, N. transvalensis and N. veterana are capable of degrading rubber, a regularly used material in clinics. Moreover, use of such possible pathogenic strains for their known role in bioremediation of rubber waste from the environment might be deleterious.
Collapse
Affiliation(s)
- Biraj Sarkar
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Aayatti Mallick Gupta
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata-700 106, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| |
Collapse
|
4
|
Microbial risk assessment of Nocardia cyriacigeorgica in polluted environments, case of urban rainfall water. Comput Struct Biotechnol J 2020; 19:384-400. [PMID: 33489008 PMCID: PMC7787915 DOI: 10.1016/j.csbj.2020.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 12/29/2022] Open
Abstract
Urban infiltration basins are a reservoir of a high diversity of Nocardia encompassing both pathogenic and not-pathogenic species. Relative abundance of pathogenic Nocardia species presents a positive correlation with metal trace elements. High infraspecific variability within N. cyriacigeorgica, forming three phylogroups. Environmental N. cyriacigeorgica strains may be as virulent as clinical GUH-2 strain. hsp65 marker can be used by metabarcoding approach for assessment of environmental Nocardia biodiversity.
Urban Infiltration Basins (UIBs) are used to manage urban runoff transfers and feed aquifers. These UIBs can accumulate urban pollutants and favor the growth of potentially pathogenic biological agents as Nocardia. Objectives To assess the spatio-temporal dynamics of pathogenic Nocardia in UIBs and to stablish phylogenetic relationships between clinical and UIB N. cyriacigeorgica strains. To assess pathogenicity associated with environmental N. cyriacigeorgica using an animal model, and to identify genetic elements that may be associated to its virulence. Methods A well-characterized UIB in terms of chemical pollutants from Lyon area was used in this study during a whole year. Cultural and Next-Generation-Sequencing methods were used for Nocardia detection and typing. Clinical and environmental isolates phylogenetic relationships and virulences were compared with Multilocus-Sequence-Analysis study together with a murine model. Results In autumn, N. cyriacigeorgica and N. nova were the pathogenic most prevalent species in the UIB. The complex N. abscessus/asiatica was also detected together with some other non-pathogenic species. The presence of pathogenic Nocardia was positively correlated to metallic trace elements. Up to 1.0 × 103 CFU/g sediment of N. cyriacigeorgica and 6 OTUs splited in two different phylogroups were retrieved and were close to clinical strains. The EML446 tested UIB isolate showed significant infectivity in mice with pulmonary damages similar to clinical clone (GUH-2). Conclusion Hsp65 marker-based metabarcoding approach allowed detecting N. cyriacigeogica as the most abundant Nocardia pathogenic species in a UIB. Metal trace elements-polluted environments can be reservoirs of pathogenic Nocardia which may have a similar virulence to clinical strains.
Collapse
|
5
|
Lafont E, Conan PL, Rodriguez-Nava V, Lebeaux D. Invasive Nocardiosis: Disease Presentation, Diagnosis and Treatment - Old Questions, New Answers? Infect Drug Resist 2020; 13:4601-4613. [PMID: 33376366 PMCID: PMC7764858 DOI: 10.2147/idr.s249761] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Abstract
Nocardia spp. is an environmental filamentous Gram-positive bacterium that may cause infections in humans and, despite recent progress, many challenges remain regarding the management of nocardiosis. This review aims at describing most recently published data regarding the diagnosis, treatment and follow-up of patients with invasive nocardiosis. As nocardiosis mainly affects patients with cell-mediated immunity defects, a comprehensive workup is mandatory in case of invasive nocardiosis occurring in ”apparently healthy patients”. Indeed, invasive nocardiosis might reveal an unknown primary immunodeficiency or the presence of anti-GM-CSF autoantibodies. Even if the diagnosis of nocardiosis mostly relies on direct examination and bacterial culture, a genus-specific PCR may be used for the detection of Nocardia, when directly performed on a clinical sample. Brain imaging should always be performed, even in the absence of neurological symptoms. Cotrimoxazole (trimethoprim/sulfamethoxazole), linezolid, parenteral cephalosporins, carbapenems and amikacin may be used as initial antibiotics to treat nocardiosis. Cotrimoxazole or linezolid can be used as monotherapy in selected patients without brain involvement. Although treatment duration has historically been set to at least 6 months in the absence of central nervous system involvement, shorter durations (<120 days) seem to be associated with a favourable outcome.
Collapse
Affiliation(s)
- Emmanuel Lafont
- Department of Infectious Diseases and Tropical Medicine, Université de Paris, Necker-Enfants Malades University Hospital, Centre d'Infectiologie Necker-Pasteur, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Pierre-Louis Conan
- Service de Maladies Infectieuses et Tropicales, Hôpital d'Instruction des Armées Bégin, Saint-Mandé, France
| | - Véronica Rodriguez-Nava
- Research Group on Bacterial Opportunistic Pathogens and Environment UMR5557 Écologie Microbienne, French Observatory of Nocardiosis, Université de Lyon 1, CNRS, VetAgro Sup, Lyon, France
| | - David Lebeaux
- Université de Paris, Paris 75006, France.,Service de Microbiologie, Unité Mobile d'Infectiologie, Hôpital Européen Georges Pompidou, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris 75015, France
| |
Collapse
|
6
|
Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans. Microorganisms 2020; 8:microorganisms8060900. [PMID: 32549367 PMCID: PMC7355893 DOI: 10.3390/microorganisms8060900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).
Collapse
|