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Microbiology Spectrum Apr 2022The genus Nocardia includes ubiquitous environmental saprophytes and the most frequently isolated aerobic actinomycete human pathogen responsible for localized or...
The genus Nocardia includes ubiquitous environmental saprophytes and the most frequently isolated aerobic actinomycete human pathogen responsible for localized or disseminated infection. Herein, the species distribution and antimicrobial susceptibility profiles of 441 nonrepetitive Nocardia strains are reported, collected from 21 provinces/cities in China over 13 years (from 2009 to 2021). These isolates were identified to species level by mass spectrometry or targeted DNA sequencing. The susceptibility profiles of Nocardia species for 15 antibiotics were determined by the broth microdilution method. Among these Nocardia isolates, Nocardia farcinica was the most commonly isolated species (39.9%, 176 of 441), followed by Nocardia cyriacigeorgica (28.6%, 126), Nocardia abscessus (6.6%, 29), and Nocardia otitidiscaviarum (5.9%, 26). Furthermore, 361 Nocardia strains (81.9%) were collected from lower respiratory tract (sputum, lung tissue, and bronchoalveolar lavage fluid), 50 (11.3%) were collected from skin and soft tissues, 9 were collected from blood, 9 were collected from eye, 4 were collected from cerebrospinal fluid and brain abscesses, and 2 were collected from pleural effusion. All of the Nocardia strains were susceptible to linezolid, followed by amikacin (99.3%) and trimethoprim-sulfamethoxazole (TMP-SMX) (99.1%). The antibiotic resistance profiles of other antibiotics varied tremendously among different Nocardia species. This demonstrated that accurate species identification and/or antibiotic susceptibility testing should be performed before the usage of these antibiotics. In summary, this is the largest study on the species and antibiotic resistance profiles of the genus Nocardia circulating in China, and our data will contribute to a better understanding of clinical nocardiosis. The genus Nocardia has the potential to cause nocardiosis, which might be underrecognized and underdiagnosed. Herein, the demographical features of 441 nonrepetitive nocardiosis cases and species distribution of their Nocardia strains in China, 2009 to 2021, are summarized. The susceptibility profiles for 15 antibiotics against all of the above Nocardia strains were also determined by the broth microdilution method. To date, this is the largest study on the genus Nocardia contributing to nocardiosis in China. Our study will be helpful for understanding the species diversity of Nocardia isolates distributed in China and for decision-making in the context of nocardiosis diagnosis and treatment.
Topics: Anti-Bacterial Agents; Base Sequence; Drug Resistance, Bacterial; Humans; Nocardia; Nocardia Infections
PubMed: 35234511
DOI: 10.1128/spectrum.01560-21 -
Frontiers in Cellular and Infection... 2022has gradually become a common pathogen in clinical microbial infections. Identification of at the species level is essential to assess the susceptibility and...
has gradually become a common pathogen in clinical microbial infections. Identification of at the species level is essential to assess the susceptibility and pathogenicity of antimicrobials. However, there is no suitable method for rapid and accurate laboratory detection of . In this study, we combined PCR amplification with the CRISPR-Cas12a system to establish a novel detection platform, named CRISPR-PCR, and applied it to the detection of in clinical samples. The Cas12a protein exhibited collateral cleavage activity following CRISPR RNA binding to specific targets, then indiscriminately cleaved nearby single-stranded DNA, and this was evaluated for diagnostic nucleic acid detection by measuring the fluorescence signal using a fluorescence reader. The assay takes only 2 h, including DNA extraction for 20 min, nucleic acid pre-amplification for 70 min, and fluorescence detection for 20 min. The limit of detection for was 10 ng and the specificity was 100%. Thus, the CRISPR-PCR assay is a rapid and specific method for detecting , and the CRISPR-PCR fluorescence detection platform has great potential for detection of other pathogens.
Topics: CRISPR-Cas Systems; DNA, Single-Stranded; Nocardia; Nucleic Acid Amplification Techniques
PubMed: 35310854
DOI: 10.3389/fcimb.2022.835213 -
Journal of Medical Microbiology Dec 2020Accurate identification of species remains a challenge due to the complexities of taxonomy and insufficient discriminatory power of traditional techniques. We report...
Accurate identification of species remains a challenge due to the complexities of taxonomy and insufficient discriminatory power of traditional techniques. We report the development of a molecular technique that utilizes real-time PCR-based high-resolution melting (HRM) analysis for differentiation of the most common species. Based on a novel intergenic region sequence, , and were clearly distinguished from one another by HRM analysis. The limit of detection of the HRM assay for purified spp. DNA was at least 10 fg. No false positives were observed for specificity testing of 20 non-target clinical samples. In comparison to established matrix-assisted laser desorption/ionization-time of flight MS, the HRM assay improved the identification of . Additionally, all the products of PCR were verified by direct sequencing. In conclusion, the developed molecular assay allows simultaneous detection and differentiation of , and with high sensitivity and specificity.
Topics: DNA, Bacterial; Genetic Loci; Molecular Typing; Nocardia; Nucleic Acid Denaturation; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 32478652
DOI: 10.1099/jmm.0.001205 -
The Brazilian Journal of Infectious... 2023Nocardiosis is a rare bacterial infection caused by Nocardia spp. However, an increasing incidence has been described whereby data about epidemiology and prognosis are... (Review)
Review
INTRODUCTION
Nocardiosis is a rare bacterial infection caused by Nocardia spp. However, an increasing incidence has been described whereby data about epidemiology and prognosis are essential.
METHODS
A retrospective descriptive study was conducted among patients with positive Nocardia spp. culture, from January 2019 to January 2023, at a Terciary Hospital in Portugal.
RESULTS
Nocardiosis was considered in 18 cases with a median age of 63.8-years-old. At least one immunosuppressive cause was identified in 70% of patients. Five patients had Disseminated Nocardiosis (DN). The lung was the most common site of clinical disease (77.8%) and Nocardia was most commonly identified in respiratory tract samples. The most frequently isolated species were Nocardia nova/africana (n = 7) followed by Nocardia cyriacigeorgica (n = 3) and Nocardia pseudobrasiliensis (n = 3). The majority of the patients (94.4%) received antibiotic therapy, of whom as many as 55.6% were treated with monotherapy. The most frequently prescribed antibiotic was trimethoprim-sulfamethoxazole. Selected antimicrobial agents were generally effective, with linezolid and cotrimoxazole (100% Susceptibility [S]) and amikacin (94% S) having the most activity against Nocardia species. The median (IQR) duration of treatment was 24.2 (1‒51.4) weeks for DN; The overall one-year case fatality was 33.3% (n = 6) and was higher in the DN (66.7%). No recurrence was observed.
CONCLUSION
Nocardiosis is an emerging infectious disease with a poor prognosis, particularly in DN. This review offers essential epidemiological insights and underscores the importance of gaining a better understanding of the microbiology of nocardiosis. Such knowledge can lead to the optimization of antimicrobial therapy and, when necessary, guide appropriate surgical interventions to prevent unfavorable outcomes.
Topics: Humans; Middle Aged; Retrospective Studies; Nocardia; Nocardia Infections; Anti-Bacterial Agents; Trimethoprim, Sulfamethoxazole Drug Combination; Anti-Infective Agents
PubMed: 37802128
DOI: 10.1016/j.bjid.2023.102806 -
BMC Infectious Diseases Dec 2022Nocardia cyriacigeorgica is one of the most common Nocardia species found in human infections, recently reclassified. Even though Nocardia may affect all organs by... (Review)
Review
BACKGROUND
Nocardia cyriacigeorgica is one of the most common Nocardia species found in human infections, recently reclassified. Even though Nocardia may affect all organs by hematogenous dissemination, bacteremia are uncommon. Among all possible dissemination sites, the involvement of the adrenal glands is particularly rare.
CASE PRESENTATION
We report here a rare case of Nocardia disseminated infection with notably bacteremia and adrenal gland abscess, in a 77-years-old immunocompetent man. Adrenal gland abscess diagnosis was made by imaging (computerized tomography, magnetic resonance and positron emission tomography scan). A complete regression of all lesions including the left adrenal gland was obtained after 6 months of antibiotics. A review of literature was also performed.
CONCLUSION
Nocardia bacteremia is a rare event but blood cultures may help to improve detection of Nocardia spp. in a non-invasive way. Adrenal abscess due to Nocardia spp. is very rare with only fourteen cases reported in the literature, but it is a true cause of adrenal masses. Our report suggests that clinician should be aware of this rare location and prioritize a non-invasive diagnosis strategy.
Topics: Male; Humans; Aged; Abscess; Nocardia Infections; Nocardia; Adrenal Glands; Bacteremia; Anti-Bacterial Agents
PubMed: 36581805
DOI: 10.1186/s12879-022-07839-9 -
MSystems Jun 2022Nocardia cyriacigeorgica is a common etiological agent of nocardiosis that has increasingly been implicated in serious pulmonary infections, especially in...
Nocardia cyriacigeorgica is a common etiological agent of nocardiosis that has increasingly been implicated in serious pulmonary infections, especially in immunocompromised individuals. However, the evolution, diversity, and pathogenesis of have remained unclear. Here, we performed a comparative genomic analysis using 91 strains, 45 of which were newly sequenced in this study. Phylogenetic and average nucleotide identity (ANI) analyses revealed that contained five species-level clades (8.6 to 14.6% interclade genetic divergence), namely, the complex (NCC). Further pan-genome analysis revealed extensive differences among the five clades in nine functional categories, such as energy production, lipid metabolism, secondary metabolites, and signal transduction mechanisms. All 2,935 single-copy core genes undergoing purifying selection were highly conserved across NCC. However, clades D and E exhibited reduced selective constraints, compared to clades A to C. Horizontal gene transfer (HGT) and mobile genetic elements contributed to genomic plasticity, and clades A and B had experienced a higher level of HGT events than other clades. A total of 129 virulence factors were ubiquitous across NCC, such as the operon, hemolysin, and type VII secretion system (T7SS). However, different distributions of three toxin-coding genes and two new types of operons were detected, which might contribute to pathogenicity differences among the members of the NCC. Overall, our study provides comprehensive insights into the evolution, genetic diversity, and pathogenicity of NCC, facilitating the prevention of infections. species are opportunistic bacterial pathogens that can affect all organ systems, primarily the skin, lungs, and brain. is the most prevalent species within the genus, exhibits clinical significance, and can cause severe infections when disseminated throughout the body. However, the evolution, diversity, and pathogenicity of remain unclear. Here, we have conducted a comparative genomic analysis of 91 strains and revealed that is not a single species but is composed of five closely related species. In addition, we discovered that these five species differ in many ways, involving selection pressure, horizontal gene transfer, functional capacity, pathogenicity, and antibiotic resistance. Overall, our work provides important clues in dissecting the evolution, genetic diversity, and pathogenicity of NCC, thereby advancing prevention measures against these infections.
Topics: Humans; Virulence; Phylogeny; Nocardia; Virulence Factors
PubMed: 35430877
DOI: 10.1128/msystems.01406-21 -
Antimicrobial Agents and Chemotherapy Jul 2018spp. are Gram-positive opportunistic pathogens that affect largely immunocompromised patients, leading to serious pulmonary or systemic infections. Combination therapy...
spp. are Gram-positive opportunistic pathogens that affect largely immunocompromised patients, leading to serious pulmonary or systemic infections. Combination therapy using the folate biosynthesis pathway inhibitors trimethoprim (TMP) and sulfamethoxazole (SMX) is commonly used as an antimicrobial therapy. Not surprisingly, as antibiotic therapies for nocardiosis can extend for many months, resistance to TMP-SMX has emerged. Using experimental evolution, we surveyed the genetic basis of adaptation to TMP-SMX across 8 strains of and 2 strains of By employing both continuous experimental evolution to provide longitudinal information on the order of changes and characterization of resistant endpoint isolates, we observe changes that are consistent with modifications of two enzymes of the folate biosynthesis pathway: dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) (FolP), with the mutations often being clustered near the active site of the enzymes. While changes to DHFR and DHPS might be expected, we also noted that mutations in a previously undescribed homolog of DHPS (DHPS2 or FolP2) that was annotated as being "nonfunctional" were also sufficient to generate TMP-SMX resistance, which serves as a cautionary tale for the use of automated annotation by investigators and for the future discovery of drugs against this genus. Additionally, overlapped glucosyl-3-phosphoglycerate synthase. Remarkably, an adaptive frameshift mutation within the overlapping region resulted in a new in-frame fusion to the downstream gene to produce a potentially new bifunctional enzyme. How a single potentially bifunctional DHPS2 enzyme might confer resistance is unclear. However, it highlights the unexpected ways in which adaptive evolution finds novel solutions for selection.
Topics: Amino Acid Sequence; Anti-Bacterial Agents; Base Sequence; Dihydropteroate Synthase; Drug Resistance, Multiple, Bacterial; Frameshift Mutation; Glucosyltransferases; High-Throughput Nucleotide Sequencing; Humans; Longitudinal Studies; Microbial Sensitivity Tests; Nocardia; Nocardia Infections; Tetrahydrofolate Dehydrogenase; Trimethoprim Resistance; Trimethoprim, Sulfamethoxazole Drug Combination
PubMed: 29686152
DOI: 10.1128/AAC.00364-18 -
Microbiology Resource Announcements Aug 2019We report four draft genome sequences of spp. The strains are the DSM 44484 pathogenic type strain; two environmental isolates, EML446 and EML1456; and the ATCC...
We report four draft genome sequences of spp. The strains are the DSM 44484 pathogenic type strain; two environmental isolates, EML446 and EML1456; and the ATCC 19247 nonpathogenic type strain, with estimated genome sizes of 6.3 to 6.8 Mb. The study of these isolates will provide insight into physiology, evolution, and pathogenicity of spp.
PubMed: 31416867
DOI: 10.1128/MRA.00600-19 -
Cureus Nov 2021species are difficult to identify, saprophytic, aerobic actinomycetes that are associated with high mortality rates and primarily affect immunocompromised...
species are difficult to identify, saprophytic, aerobic actinomycetes that are associated with high mortality rates and primarily affect immunocompromised hosts. Recently, the number ofdiagnoses of has grown in the United States, yet complicated clinical diagnosis and costly identification methods presume an underestimation of its presence in patients. We describe a case of brain abscess secondary to a pulmonary infection in an elderly, diabetic, Afghani man with an extensive history of chewing tobacco use.
PubMed: 34786274
DOI: 10.7759/cureus.19373 -
BMC Infectious Diseases Jul 2022Nocardia cyriacigeorgica was first described in 2001. It is an emerging pathogen that mainly affects immunocompromised patients. A brain abscess caused by N.... (Review)
Review
BACKGROUND
Nocardia cyriacigeorgica was first described in 2001. It is an emerging pathogen that mainly affects immunocompromised patients. A brain abscess caused by N. cyriacigeorgica has been reported only in immunocompromised hosts. We present a rare case of brain abscess caused by N. cyriacigeorgica in an adult male receiving low dose steroids.
CASE PRESENTATION
A 75-year-old male weekend gardener without an immunocompromising condition presented with neurological complaints that were initially attributed to an ischemic stroke. Due to the unusual presentation and rapid progression, his condition was thought to be caused by a cerebral space-occupying lesion. He underwent an emergent right-sided parietal craniotomy and the histopathological report of the specimen was an abscess caused by N. cyriacigeorgica. The patient received appropriate antibiotic treatment and completely recovered without sequelae.
CONCLUSIONS
Nocardia species are a rare cause of brain abscess in immunocompetent patients. Their clinical presentation can mimic other more common cerebral diseases, such as brain tumors (primary and secondary) and stroke. The possibility of an abscess caused by N. cyriacigeorgica should also be considered in the differential diagnosis in an immunocompetent patient.
Topics: Adult; Aged; Anti-Bacterial Agents; Brain Abscess; Humans; Male; Nocardia; Nocardia Infections; Steroids
PubMed: 35864454
DOI: 10.1186/s12879-022-07612-y