Comparison of restriction enzyme pattern analysis and full gene sequencing of 16S rRNA gene for Nocardia species identification, the first report of Nocardia transvalensis isolated of sputum from Iran, and review of the literature

Loop-mediated Isothermal Amplification Test for Rapid Identification of Clinical Nocardia Isolates

Background: Nocardia is a Gram-positive and partially acid-fast bacterium. The species are widely distributed in the environment and cause severe human infections. Nocardiosis is not easily identifiable due to the lack of pathognomonic clinical signs. Objectives: The present study was designed to develop and evaluate a simple and quick method based on a loop-mediated isothermal amplification (LAMP) assay for detecting Nocardia spp isolated from bronchoalveolar lavage (BAL) samples. Methods: In this cross-sectional study, 357 BAL samples were collected from two teaching hospitals. The polymerase chain reaction (PCR) was performed using a set of species-specific primers for the 16S rRNA gene. Kinyoun acid-fast staining and culture were done on the Sabouraud dextrose plate. The optimal LAMP reaction condition was set at 65°C for 45 min, with the recognition limit as 1 pg DNA/tube and 100 CFU/reaction. In addition to calcein and manganous ions, agarose gel electrophoresis was used to visualize the amplified LAMP products. Results: Out of 357 BAL samples, 0 (0.0%), 4 (1.1%), 9 (2.5%), and 10 (2.8%) Nocardia strains were identified by direct staining of partial acid-fast, streak culture plate, PCR, and LAMP methods, respectively. Conclusions: We developed a new LAMP technique for the recognition of Nocardia, which is fast, very precise, simple, and low-cost. According to our knowledge, this is the first report of the LAMP method to detect Nocardia in clinical samples.

Effect of β - hydroxy - γ -aminophosphonate (β - HPC) on the hydrolytic activity of Nocardia brasiliensis as determined by FT-IR spectrometry

The use of immunomodulatory and metabolic modulating drugs has been considered a better strategy to improve the efficacy of conventional treatments against pathogens and metabolic diseases. L-carnitine is relevant in fatty acid metabolism and energy production by β-oxidation, but it also has a beneficial therapeutic immunomodulatory effect. The β-hydroxy-γ-aminophosphonate (β-HPC) was developed, synthesized and studied in different pathologies as a more soluble and stable analog than L-carnitine, which has been studied in bacterial physiology and metabolism; therefore, we set out to investigate the direct effect of β-HPC on the metabolism of N. brasiliensis, which causes actinomycetoma in Mexico and is underdiagnosed. To analyze the effect of β-HPC on the metabolic capacity of the bacterium for the hydrolysis of substrate casein, L-tyrosine, egg yolk, and tween 80, Fourier transform infrared spectroscopy (FT-IR) was employed. It was found that β-HPC increases the metabolic activity of N. brasiliensis associated with increased growth and increased hydrolysis of the substrates tested. By the effect of β-HPC, it was observed that, in the hydrolysis of L-tyrosine, the aromatic ring and functional groups were degraded. At 1515 cm^-1, any distinctive signal or peak for this amino acid was missing, almost disappearing at 839, 720, 647, and 550 cm^-1. In casein, hydrolysis is enhanced in the substrate, which is evident by the presence of NH, OH, amide, and CO. In casein, hydrolysis is enhanced in the substrate, which is evident by the presence of NH, OH, amide, COO, and P = O signals, characteristic of amino acids, in addition to the increase of the amide I and II bands. In Tween 80 the H-C = and C = C signals disappear and the ether signals are concentrated, it was distinguished by the intense band at 1100 cm^-1. Egg yolk showed a large accumulation of phosphate groups at 1071 cm^-1, where phosvitin is located. FT-IR has served to demonstrate that β-HPC is a hydrolysis enhancer. Furthermore, by obtaining the spectrum of N. brasiliensis, we intend to use it as a quick comparison tool with other spectra related to actinobacteria. Eventually, FT-IR may serve as a species identification option.

Genotypic and phenotypic prevalence of Nocardia species in Iran: First systematic review and meta-analysis of data accumulated over years 1992-2021

Background

Nocardia species belong to the aerobic actinomycetes group of bacteria which are gram-positive and partially acid-fast Bacilli. These bacteria may sometimes be associated with nosocomial infections. Nocardia diseases are not required to be reported to public health authorities in Iran. Hence, the present study was designed to determine the prevalence of human Nocardia spp. in Iran by using a systematic review and meta-analysis according to the preferred reporting items for systematic reviews and meta-Analyses statement.

Methods

The data of the prevalence of Nocardia species were collected from databases such as Embase, PubMed/MEDLINE via Ovid, Web of Science, Scopus and Google Scholar as well as national Iranian databases, including SID, Magiran. Analyses were conducted by STATA 14.0.

Results

The meta-analyses showed that the proportion of Nocardia spp. in Iranian studies varied from 1.71(1.17, 2.24) to 0.46(0.09, 0.83). N. asteroides (21% [95% CI 1.17, 2.24]), N. cyriacigeorgica (17% [95% CI 0.99, 1.77]), N. facanica (10% [95% CI 0.75, 1.00]) were considered to be common causative agents.

Conclusions

Our study presents that despite the fact that Nocardia spp. are normally are saprophytic organisms, are currently accounts as emerging pathogens due to an increase in immunocompromised patients among Iranian populations. Considering our results, the establishment of advanced diagnostic facilities for the rapid detection of Nocardia infections are required for optimal therapeutic strategies of Nocardia spp. in Iran. Our findings could help the programmatic management of the disease within the context of Nocardia control programs.

Comment on a Primary Cutaneous Nocardiosis of the Hand

Nocardia spp. are gram-positive, partially acid-fast bacteria which are lives in environmental sources and cause of various infection that called nocardiosis in animals and humans. Identification of this group of bacteria was important due to accurate diagnosis, patient management and prevention of antibiotic resistant among of bacteria. Molecular methods including PCR-RFLP and sequencing using housekeeping genes such as 16S rRNA, hsp65, rpoB and gyrB are recommended to accurate and reliable identification of nocardiosis.

Nocardiosis from 1888 to 2017

The genus Nocardia is an aerobic bacterium, Gram-positive and catalase positive that is in Nocardiaceae family. This bacterium first described by Edmond Nocard in 1888 and is not in human commensal bacteria. To date, nocardiosis incidence is increasing due to increase population growth rate, increase in patients with immune disorder diseases and immunocompromised patients. We surveyed taxonomic position, isolation methods, phenotypic and molecular identification at the genus and species levels, antibiogram, treatment and epidemiology in the world from 1888 to 2017.

The cytopathology of Actinomyces, Nocardia, and their mimickers

Nocardia species and Actinomyces species are 2 of the most commonly diagnosed filamentous bacteria in routine cytopathology practice. These genera share many overlapping cytomorphologic features, including their thin, beaded, branching, Gram-positive, GMS-positive filamentous structures that fragment at their peripheries into bacillary- and coccoid-appearing forms. Features that help distinguish between these 2 microorganisms include the width of their filamentous structures, the angles at which they branch, and their ability or lack thereof to retain a modified acid-fast stain. In addition to cytomorphologic overlap, overlap in clinical presentation is frequent with pulmonary and mucocutaneous presentations seen in both. Differentiating between Nocardia and Actinomyces is essential because patients with these infections require different approaches to medical management. Both antibiotic susceptibilities and the need for early surgical intervention as part of the treatment plan vary greatly among these 2 groups. This review focuses on the clinical presentation, cytomorphology and staining characteristics that can be useful in identifying and distinguishing between Nocardia and Actinomyces infections, as well as their mimickers.

Molecular analysis and species diversity of Nocardia in the hospital environment in a developing country, a potential health hazard

PURPOSE

Despite hundreds of reports on the isolation of Nocardia from clinical samples, the presence and diversity of Nocardia species that are capable of survival in a harsh and adverse condition, such as a hospital environment, have not been comprehensively studied. The aim of this study was to assess Nocardia species diversity in a hospital environment to provide a better insight into their potential threat as a reservoir for the development of nosocomial infections.

METHODOLOGY

A total of 90 samples of hospital water, dust and soil, collected from 30 hospitals, were analysed for the presence of Nocardia using standard protocols for isolation and characterization of the isolates. Conventional tests were used for preliminary identification, and PCR amplification of the 596 bp amplicon of the 16S rRNA and sequence analysis of 16S rRNA were performed for genus and species identification.

RESULTS

A total of 25 Nocardia isolates (27.7 %) from 10 species were recovered from 90 samples. The three most prevalent species were N. cyriacigeorgica, 24 %, N. asteroides, 16 % and N. kroppenstedtii, 12 %, followed by N. salmonicida-like, 8 % and single isolates of N.otitidiscaviarum, N. flavorozea-like, N. neocaledoniensis-like and N. sungurluensis-like. Thirteen out of twenty five isolates showed characteristics of six novel species.

CONCLUSION

Our study showed that the hospital environment is a potential reservoir of a diverse range of Nocardia species, due to the remarkable survival capability of these bacteria in an adverse hospital environment, which carries a threat to the health of patients.