Application of laser capture microdissection and PCR sequencing in the diagnosis of Coccidioides spp. infection: A case report and literature review in China

Aspergillus flavus and aflatoxins control in long-term storage of food ingredients of Puerh tea, peanut and polished rice

Aflatoxins are a group of high toxic mycotoxins in food chain. Recent studies showed that aflatoxins might contaminate post-fermented tea, but the result remains controversial. Here, Aspgergillus flavus growth and aflatoxin production were characterized in Puerh tea, peanut and polished rice at different initial water activity (aw) values for long-term storage. As a result, food initial aw value was the critical factor for A. flavus growth and aflatoxin production, and A. flavus almost not grew on foods at aw value lower than 0.8. A. flavus grew best in peanut, followed by rice, but growth on Puerh tea was limited. A. flavus growth was inhibited significantly by adding tea to Potato Dextrose Agar (PDA). Accordingly, aflatoxins produced dramatically in peanut, followed by rice at the first 90 days storage. However, aflatoxin neither produced in Puerh tea nor on tea modified PDA, indicating tea components inhibited A. flavus growth and aflatoxins synthesis.

[Differential diagnosis of coccidioidomycosis manifested by peripheral pulmonary lesion]

We present this clinical case as a demonstration of difficulties in differential diagnosis of pulmonary coccidioidomycosis. Differential diagnostics of peripheral pulmonary lesion performed using bronchoscopy with BAL and TBCB and video-assisted thoracic surgery (VATS) biopsy. Diagnostic specimens were tested using microbiological (luminescent microscopy, culture for M. tuberculosis (BACTEC MGIT960 and Lowenstein-Jensen Medium), RT-PCR, cytological and morphological (hematoxylin-eosin, Ziehl-Neelsen, PAS, Grocott methenamine silver (GMS) stainings) examinations. A diagnosis was verified correctly In Russia the country is not endemic for coccidioidomycosis and patient was treated accordingly. Diagnostics of peripheral pulmonary lesions requires of multidisciplinary approaches. Morphological examination, based on detection of only granulomatous inflammation in lung biopsy cannot be used for finally DS and requires microbiological confirmation for TB or other infections, and dynamic monitoring of the patient with concordance their anamnesis vitae and morbi.

The first suspected disseminated Hormographiella aspergillata infection in China, diagnosed using metagenomic next-generation sequencing: a case report and literature review

Hormographiella aspergillata is a rare and emerging cause of invasive mould infections in patients with haematological malignancies, with a mortality rate of approximately 70%. Here, we present the first reported case of suspected disseminated H. aspergillata infection in China. The patient experienced a second relapse of acute myeloid leukaemia and developed neutropenia, fever, discrepant blood pressure between limbs, and cutaneous lesions limited to the left upper extremity. Since lung tissue biopsy was not feasible, metagenomic next-generation sequencing (mNGS) and panfungal polymerase chain reaction (PCR) analysis of bronchoalveolar lavage fluid and blood samples were performed, which indicated probable H. aspergillata pulmonary infection. Histopathology of cutaneous lesions revealed numerous fungal hyphae within dermal blood vessels. mNGS of a skin biopsy sample identified H. aspergillata sequences, and the fungi was subsequently recovered from fungal culture, proving cutaneous H. aspergillata infection. Despite combined antifungal therapy, the patient died owing to disease progression. Additionally, 22 previously reported cases of invasive H. aspergillata infection were reviewed in patients with haematological malignancies. Thus, mNGS is a powerful diagnostic tool for the early and effective detection of invasive H. aspergillata infections, with the advantage of sequencing all potential pathogens, and providing results within 24 h.

The use of combined PCR, fluorescence in situ hybridisation and immunohistochemical staining to diagnose mucormycosis from formalin-fixed paraffin-embedded tissues

OBJECTIVE

To develop a comprehensive diagnostic system for mucormycosis from formalin-fixed paraffin-embedded tissues, consisting of own-designed real-time polymerase chain reaction (PCR) assays, fluorescence in situ hybridisation, and immunohistochemical staining.

METHODS

We designed 11 primers and probes for specific real-time PCR assays based on genome sequences, and validated the specificity by Aspergillus, Fusarium, Scedosporium, Lomentospora, Cryptococcus and Candida species. Formalin-fixed paraffin-embedded (FFPE) tissues from forty-four mouse model infected by above fungi were collected and extracted DNA by laser capture microdissection (LCM) and direct extraction methods for real-time PCR assays. In addition, seventeen clinical specimens histopathologically proven for mucormycosis were included for specific detection with the new diagnostic system.

RESULTS

The real-time PCR assays allowed detection of a minimum of 10 CFU/ml equivalent gDNA of each species. No cross-reaction with gDNA among species was noted. From mouse model specimens, the sensitivity of real-time PCR in samples extracted with LCM versus direct extraction method was 100% versus 91.43% at Mucorales level and 80% versus 45.71% at species level, respectively. The specificity was 100%. From clinical samples, LCM combined with real-time PCR can test 88.24% (15/17) of Mucorales. Sensitivities of fluorescence in situ hybridisation (FISH) and immunohistochemical staining (IHC) were 70.59% and 41.18%, respectively. Combined LCM-RT-PCR, FISH and IHC yielded positive results in all samples.

CONCLUSIONS

The combination diagnostic system we developed is a culture-independent and robust method which enables rapid species identification from FFPE tissues for timely diagnosis of mucormycosis.

Laser Capture Proteomics: spatial tissue molecular profiling from the bench to personalized medicine

INTRODUCTION

Laser Capture Microdissection (LCM) uses a laser to isolate, or capture, specific cells of interest in a complex heterogeneous tissue section, under direct microscopic visualization. Recently, there has been a surge of publications using LCM for tissue spatial molecular profiling relevant to a wide range of research topics.

AREAS COVERED

We summarize the many advances in tissue Laser Capture Proteomics (LCP) using mass spectrometry for discovery, and protein arrays for signal pathway network mapping. This review emphasizes: a) transition of LCM phosphoproteomics from the lab to the clinic for individualized cancer therapy, and b) the emerging frontier of LCM single cell molecular analysis combining proteomics with genomic, and transcriptomic analysis. The search strategy was based on the combination of MeSH terms with expert refinement.

EXPERT OPINION

LCM is complemented by a rich set of instruments, methodology protocols, and analytical A.I. (artificial intelligence) software for basic and translational research. Resolution is advancing to the tissue single cell level. A vision for the future evolution of LCM is presented. Emerging LCM technology is combining digital and AI guided remote imaging with automation, and telepathology, to a achieve multi-omic profiling that was not previously possible.