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

Molecular surveillance and antimicrobial susceptibility profile of bacterial contamination in pastries of Iranian confectioneries: a public health concern

Introduction

Microbial contamination in food products such as pastries, poses a significant public health concern due to the potential risks of foodborne infection and outbreak, Therefore, to prevent these infections, it is essential to investigate the frequency and extent of microbial contamination as well as the level of drug resistance in pastries. Due to this issue, our study aimed to assess the microbial diversity and the drug susceptibility patterns of microbial pollutants in pastry shops in Markazi province, Iran.

Methods

The study involved collecting 120 pastry samples from 30 pastry shops in Markazi province, Iran. The isolates were identified using a series of biochemical, phenotypic, and molecular assays, including specific PCR and 16S rRNA gene sequencing. Drug susceptibility testing (AST) was performed by using the Kirby-Bauer method according to the CLSI 2023 guidelines.

Results and discussion

A total of 56 isolates (46.66%) were recovered from 120 pastries samples, The most prevalent species isolated in the current study were S. aureus 12 isolates (21.43%), M. luteus 7 isolates (12.5%), E. coli 7 isolates (12.5%), S. warneri 6 isolates (11.12%), 6 isolates of S. succinus (11.12%), B. cereus 5 isolates (10.7%), Nocardia 4 isolates (7.15%), K. pneumoniae 3 isolates (5.35%), S. epidermidis 3 isolates (5.35%), and E. faecium 3 isolates (5.35%). The isolates showed the most sensitivity to imipenem and trimethoprim-sulfamethoxazole and the least sensitivity to erythromycin and tetracycline. The AST showed that 7 isolates of S. aureus were MRSA, 3 isolates of E. coli and, 2 isolates of K. pneumoniae were identified as ESBL. In conclusion, the results of the current study showed that the microbial contamination of pastries produced in confectionaries of Markazi province was not in standard ranges. These problems may be related to fecal contamination of pastries or lack of hygiene by handlers and it is urgent to develop the standards of hygiene of food handling techniques and aseptic pastry production in confectioneries.

Fifteen years of phenotypic and genotypic surveillance and antibiotic susceptibility pattern of Actinomycetes (Mycobacterium, Nocardia, Rhodococcus, etc.) in clinical and environmental samples of Iran

Actinomycetes, ubiquitous in the natural world, have been known to inflict infections upon both immunocompromised and healthy individuals. Interestingly enough, these species are oftentimes found residing within the microbiota of humans and animals alike. Unfortunately, these infections are frequently misdiagnosed as more sinister ailments such as malignancy or tuberculosis. Due to this issue, this review deals with 15 years of study on clinical and environmental samples to determine Actinomycetes' prevalence, isolation, identification, and antibiotic susceptibility pattern in Iran by Davood Azadi et al. According to the Davood Azadi framework, we searched the following databases: PubMed/MEDLINE, Embase, Scopus, Web of Science, SID, and Google Scholar in the period from 2007 to 2023. This review aimed to provide an overview of the most recent techniques for collecting environmental samples, cultivating them, and identifying the Actinomycetes group's members. The isolation of Actinomycetes from clinical and ecological sources is becoming more prevalent and should be a concern for health authorities in developing countries. Health centers should take action to increase awareness of diagnostic criteria and management guidelines for actinomycete diseases. Improvements in national and regional reference laboratories may also aid in accurately diagnosing these diseases.

Updated Review on Nocardia Species: 2006-2021

This review serves as an update to the previous Nocardia review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.

Disseminated life threatening Nocardia otitidiscaviarum infection in a young female with newly diagnosed systemic lupus erythematosus, case report and review of literature

Infection due to Nocardia is reported mainly in immunocompromised patients. It usually presents as a pulmonary or disseminated disease with a predilection for the brain. Infections are a rare etiology of intracranial vascular aneurysms. Herein we report a case of disseminated Nocardia otitidiscaviarum (N. otitidiscaviarum) in a young female newly diagnosed with systemic lupus erythematosus (SLE) complicated by the development of an infectious intracranial aneurysm. To the best of our knowledge this is the fourth case of nocardial infection-related intracranial aneurysm and the second case of N. otitidiscaviarum infection to be reported in a patient with systemic lupus erythematosus. Features of previously reported N. otitidiscaviarum related intracranial aneurysm are reviewed.

Molecular identification and antibiotic resistance pattern of actinomycetes isolates among immunocompromised patients in Iran, emerging of new infections

Recent advancements in DNA-based approaches have led to the identification of uncommon and rare bacterial pathogens. In this study, by utilizing a DNA-based approach, a total of 1043 clinical specimens were processed for the identification of actinobacteria targeting the 16S rRNA and gyrB genes. Drug susceptibility testing was also conducted using micro-broth dilution and PCR. Two isolates of Nocardia flavorosea and Rhodococcus erythropolis were reported for the first time in Iran. Also, Nocardiopsis dassonvillei, Streptomyces olivaceus, and Streptomyces griseus were reported for the first time in Asia. Infections caused by Nocardia caishijiensis and Prauserella muralis have also been reported in this study. The first Asian case of pulmonary infection caused by Nocardia ignorata and the first global case of brain abscess caused by Nocardia ninae and Nocardia neocaledoniensis have been reported in this study. Overall 30 isolates belonging to 6 genera (Nocardia, Streptomyces, Rodoccoccus, Nocardiopsis, Rothia, and Prauserella) were detected in 30 patients. All 30 isolates were susceptible to amikacin and linezolid. Three isolates including Nocardia otitidiscaviarum (n = 2) and Nocardia flavorosea (n = 1) were resistant to trimethoprim-sulfamethoxazole which were the first trimethoprim-sulfamethoxazole resistant clinical actinomycetes in Iran. Isolation of rare species of actinomycetes particularly Nocardia spp. requires urgent action before they spread clinically particularly among immunocompromised patients.

Pulmonary Nocardiosis in Pemphigus Vulgaris Patients from Tehran, Iran

OBJECTIVE

Nocardiosis is an opportunistic infection in individuals who had organ transplants and in patients with immunosuppressive diseases such as pemphigus Vulgaris (PV), diabetes mellitus, and HIV. Nocardiosis rate has not been assessed in Iranian PV patients, and this was the first study to estimate nocardiosis rate in these patients.

METHODS

In this study, 103 patients with PV were examined. BAL samples were obtained and direct smear was prepared and visualized by microscopy after PAS staining. Samples were cultured on antibiotic-containing blood and chocolate agar media. DNA extraction and PCR were performed on positive cultures, and final identification was done by 16S rRNA gene sequencing. Drug susceptibility testing was done by microbroth dilution method.

RESULTS

Four positive cultures (3.88%) were found in the samples (n = 103). According to sequence analysis, 2 isolates were identified as Nocardia cyriacigeorgica and 2 as Nocardia otitidiscaviarum and Nocardia cerradoensis. Nocardia cerradoensis was isolated from an invasive brain infection. Isolated bacteria were susceptible to majority of the tested antibiotics, except for 2 strains of Nocardia cyriacigeorgica and Nocardia cerradoensis. This was the first isolation of Nocardia cerradoensis of human infection in Asia. Patients with PV are susceptible to nocardiosis, similar to other immunocompromised patients.

CONCLUSION

Pemphigus Vulgaris is a severe autoimmune disease which is treated by a high dosage of corticosteroids. Opportunistic infections are one of the greatest challenges of these patients. One of the neglected agents of opportunistic infection in this disorder is Nocardiosis which can cause a high mortality rate in PV patients.

Production and Characterization of Biosurfactant by Nocardia Species Isolated Form Soil Samples in Tehran

In this work, we report the Nocardia species were initially screened and then tested for their ability to produce biosurfactant. The biosurfactant production from the Nocardia species was determined by qualitative standard methods. The selected bacterial strain had better oil spreading and emulsifying activity and surface tension reduction. The biosurfactant producer strain was identified by 16S rRNA gene sequencing method. Using Fourier transform infrared spectroscopy and comparative analysis, the biosurfactant structure could be detected. Oil spreading tests and blue agar plate tests confirmed the presence of biosurfactant and extracellular anionic glycolipids. The E24% assay using olive oil showed strong emulsifying characteristic of extracted biosurfactant with a 100%. The stability of the biosurfactant produced in different conditions was significant. Nocardia coubleae was identified by biochemical methods and molecular methods.

Biodegradation of polycyclic aromatic hydrocarbons, phenol and sodium sulfate by Nocardia species isolated and characterized from Iranian ecosystems

Anthropogenic pollutants are known to have adverse effect on ecosystem, biodiversity and human health. Bioremediation is an option that has been widely used to remediate organic contaminants and reduce the risk of these hazardous materials. Microorganisms are readily available to screen and can be rapidly characterized to be applied in many extreme environmental conditions. Actinomycetes have a great potential for the production of bioactive secondary metabolites which have biodegradation activity. This study aimed to screen and characterize Nocardia species with biodegradation potential from diverse Iranian ecosystems. The isolates were screened from 90 collected environmental samples, identified and characterized using conventional and molecular microbiological methods including the PCR amplification and sequencing analysis of 16S rRNA and rpoB genetic markers. Growth rate in presence of pollutants, chromatography, Gibbs and turbidometric methods were used to determine bioremediation ability. A total of 19 Nocardia isolates were recovered from the cultured samples (21.1%) that belonged to 10 various species. The most prevalent Nocardia species was N. farcinica; 4 isolates (21%), followed by N. cyriacigeorgica and N. cashijiensis like; 3 isolates each (15.7%) and N. asteroides and N. kroppenstedtii; 2 isolates each (10.5%). Our results showed that various Nocardia species have great potential for bioremediation purposes, although they have not received much attention of the scholars for such significant usage.

Disseminated Nocardia infection with a lesion occupying the intracranial space complicated with coma: a case report

Background

Disseminated Nocardia infection is a disease that is easily overlooked in patients with lesions occupying the intracranial space complicated with coma. Early diagnosis and treatment are crucial.

Case presentation

A 65-year-old man was admitted to the First Affiliated Hospital of Zhejiang University in October 2018 with weakness in the right limbs for 3 days and altered consciousness for 1 day. Five months earlier, he had been diagnosed with membranous kidney disease and had received cyclophosphamide and prednisone. At admission, the white blood cell count was 1.37 × 10¹⁰/L (with 86.4% neutrophils), and C-reactive protein was 115.60 mg/L. Imaging examinations revealed a lesion occupying the intracranial space, lung infection, and multiple abscesses in the rhomboid muscle. The abscesses were drained. Pus culture confirmed Nocardia cyriacigeorgica infection. With antibiotics and vacuum-sealed drainage of the back wound, the patient improved and was discharged from the hospital.

Conclusions

This case report shows that infection should be considered during the differential diagnosis of lesions in the intracranial space, especially in patients receiving immunosuppressive treatment. In patients with disseminated N. cyriacigeorgica infection, combination antibiotic therapy and surgical drainage of localised abscesses can be effective.

Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases

Strains 335427^T and 234509^T, isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427^T and 234509^T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129^T and Nocardia abscessus NBRC 100374^T were 99.5% and 100%, respectively. Digital DNA-DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427^T and 234509^T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427^T has C_16:0, C_18:1 ω₉c, C_18:0 and C_18:0 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52-54 carbon atoms. However, only C_18:1 ω₉c was detected for isolate 234509^T, which had mycolic acids with 44-56 carbon. Based on phenotypic and genetic data, strains 335427^T (DSM 109819^T = CECT 9924^T) and 234509^T (DSM 111366^T = CECT 30129^T) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis, including experimentally verified virulence genes in humans related to tuberculosis. The narGHIJ (nitrate reduction pathway) and gvpAFGOJLMK (gas vesicles) genetic maps of strains 335427^T, 234509^T, NBRC 100129^T and NBRC 100374^T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp.

Pulmonary Nocardia ignorata Infection in Gardener, Iran, 2017

Nocardia ignorata, which was first described in 2001, is a rare human pathogen. We report a case of pulmonary nocardiosis caused by this bacterium in a 55-year-old man from Iran. The patient, a gardener, had frequent exposure to soil and may have acquired the infection from that source.

First case of fatal bacteremia due to Nocardia neocaledoniensis

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First case of bacteremia due to N.neocaledoniensis in an immunocompromised patient.

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Mass spectrometry is a discriminant technique to identify rapidly N.neocaledoniensis.

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Incubating culture media for a longer time helps to obtain definitive diagnosis and adapt antibiotics.

Nocardia neocaledoniensis is an uncommon cause of human-infections. Few cases are reported in the literature. We describe the first case of bacteremia caused by N. neocaledoniensis. This article underlines the importance of mass spectrometry for easy and rapid identification of such bacterium.

Detection of Nocardia, Streptomyces and Rhodococcus from bronchoalveolar lavage specimens of patients with HIV by Multiplex PCR Assay

BACKGROUND

Nocardia, Streptomyces and Rhodococcus are life threatening opportunistic pathogens under immunodeficiency conditions, particularly among patients infected with HIV. Rapid and accurate detection of these infections can improve immune health quality, patient management and appropriate treatment. The aim of this study was to design a novel multiplex-PCR assay for rapid diagnosis of these three organisms directly from bronchoalveolar lavage (BAL) specimens of patients infected with HIV.

METHODS

The genus specific primers were designed for direct-detection of Nocardia, Streptomyces and Rhodococcus in a single tube multiplex PCR. This PCR specifically amplified the target genes from pure cultures. It subsequently was applied on BAL specimens of 29 HIV positive patients that had previously been culture negative for actinomycete bacteria, of which Nocardia, Streptomyces and Rhodococcus are members.

RESULTS

Of 29 respiratory clinical specimens, there were positive for Nocardia spp. and one was positive for Streptomyces spp using the multiplex PCR assay. The sequencing of the PCR products identified the species as Nocardia cyriacigeorgica (n=2), Nocardia farcinica and Streptomyces albus.

CONCLUSION

This novel multiplex PCR assay yielded reliable results for accurate identification of Nocardia, Streptomyces and Rhodococcus from BAL while the results of bacterial culture were negative.

Correlation between biofilm formation and carbapenem resistance among clinical isolates of Klebsiella pneumoniae

BACKGROUND

Klebsiella pneumoniae is a Gram-negative enteric bacterium that causes nosocomial infections; this bacterium has survived from harsh condition using biofilm formation in hospital equipment and cause severe infection. In the other hand, the emergence and extension of carbapenem resistance burden among K. pneumonia producing biofilm is the current concern of public health services. There are controversial findings about this subject. The aim of this study was to evaluate the correlation between biofilm formation and resistance to carbapenem among clinical isolates of K. pneumoniae.

METHODS

A total of 160 K. pneumoniae isolates were collected from various infections of hospitalized patients. The Carba NP test and molecular methods were used for detection of carbapenem resistance isolates of K. pneumonia. Subsequently, the ability for biofilm production was performed from all isolates. Finally, Correlation of biofilm formation among carbapenem resistant isolates was calculated using χ2 and Fisher's exact tests.

RESULTS

Among K. pneumoniae isolates 42.5% have carbapenemase activity by Carba NP test, while carbapenemase genes were detected in 35.6% of isolates in amplification assay. Moreover, there are 52.5% (n= 84) of all isolates were formed a strong biofilm, while 38.1% (n= 61) and 9.3% (n= 15) of isolates were middle and weak biofilm producer, respectively. Among carbapenem resistant cases (n= 68), there are 77.9% (n= 53) and 22% (n= 15) of isolates were reported as strong and middle biofilm producer, respectively. We see a significant correlation was seen between biofilm formation ability and carbapenem resistant isolates (p-value < 0.00001).

CONCLUSION

The increase of carbapenem resistance burden in biofilm producing isolates of K. pneumoniae is considered as serious alert and the basic measures to combat this phenomenon is imperative.

Endocarditis with Aeromonas salmonicida

Aeromonas salmonicida (A. salmonicida) is a facultative Gram-negative bacillus, inhabiting in water. It is a common source of furunculosis and septicemia in fish. Report on the human infection with this organism is rare. A male farmer referred with weakness and intermittent fever. He had cardiac valves' regurgitation due to fever with rheumatic heart disease. He had a history of swimming in well water. Transthoracic echocardiography (TTE) revealed a mobile mass of 1.3 × 0.9 cm attached to the mitral valve chordae, suggestive of a vegetation. Aeromonas salmonicida was isolated from the blood. After cardiac surgery and taking ceftriaxone for 4 weeks, he was discharged in good general condition. Five previous case reports of human infection with this organism were found. The patient was the sixth human case, and the first endocarditis, reported with this organism. A. salmonicida is a rare agent for human infection. Contact with water is a risk factor for this type of infection. It seems that the use of modern diagnostic methods has been effective in identifying the microorganism.

Screening, isolation and molecular identification of biodegrading mycobacteria from Iranian ecosystems and analysis of their biodegradation activity

Anthropogenic origin pollutants including pesticides, heavy metals, pharmaceuticals and industry chemicals impose many risks to human health and environment and bioremediation has been considered the strategy of choice to reduce the risk of hazardous chemicals. In the current study, we aimed to screen and characterize mycobacteria from the diverse range of Iranian aquatic and terrestrial ecosystems with harsh and unfavorable environmental conditions that can be utilized for biodegradation of target pollutants. Mycobacteria were isolated from a collection of 90 environmental samples and identified to the species level using conventional microbiological and molecular methods including the PCR amplification of hsp65 and sequence analysis of, 16S rRNA genetic markers. The growth rate of the isolates in presence of pollutants, chromatography, Gibbs and turbidometric methods were used to assess their biodegradation activity. A total of 39 mycobacterial isolates (43.3%) were recovered from 90 samples that belonged to 21 various species consisting of M. fortuitum; 6 isolates, M. flavescens and M. paragordonae; 4 isolates each, M. monacense, M. fredriksbergense and M. aurum; 2 isolates each, 7 single isolates of M. conceptionense, M. porcinum, M. simiae, M. celeriflavum, M. novocastrense, M. neoaurum, M. obuense and 12 isolates that belonged to 8 unknown potentially novel mycobacterial species. The isolates were categorized in three groups based on their bioremediation activity, i.e., 5 (12.8%) organisms without biodegradation activity, 20 (51.2%) organisms with previously reported biodegradation activity, and 14 (35.9%) organisms that showed biodegradation activity but not previously reported. Our results showed that the Iranian ecosystems harbor a good reservoir of diverse mycobacterial species with biodegrading potentiality for neutralizing environmental chemical pollutants.