Molecular identification of Actinomadura madurae isolated from a patient originally from Algeria; observations from a case report

A Rare Strain Actinomadura geliboluensis Was First Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Pneumonia

Background

Actinomadura geliboluensis was first isolated in 2012 in Gelibolu, Canakkale, Turkey, and has not been reported to be isolated from humans until now. We have isolated it from the bronchoalveolar lavage fluid (BLF) of a patient with pneumonia and found its drug resistance. It is the first time that Actinomadura geliboluensis has been isolated from humans since its discovery and naming. This case may provide new ideas and methods for the clinical diagnosis and treatment of pulmonary actinomycosis.

Case Description

The patient was a 75-year-old male who was hospitalized in a township hospital and failed to improve after penicillin treatment. After admission to our hospital, the patient was treated with piperacillin/tazobactam according to clinical guidelines for 14 days. Actinomadura geliboluensis was isolated from the patient's BLF and was identified by 16S rRNA sequencing. This report shows the biological characteristics and in vitro drug susceptibility testing, as well as the genomics analysis based on next-generation sequencing (NGS). The results demonstrated that Actinomadura geliboluensis was easy to be mistakenly identified as Actinomyces dental caries by using the Merieux ANC identification card. Based on the MIC test, Actinomadura geliboluensis was susceptible to tetracyclines, quinolones and sulfonamides, but resistant to carbapenems, penicillins and cephalosporins. The K-B test results showed Actinomadura geliboluensis was highly sensitive to piperacillin/tazobactam. Genomic analysis based on NGS showed that the Actinomadura geliboluensis belongs to Planobispora rosea EF-Tu mutants conferring resistance to inhibitor GE2270A, AAC(3)-VIIa, vanRO, chrB, and mexY.

Conclusion

Actinomycetes is generally sensitive to Penicillin but Actinomadura geliboluensis is not. In vitro drug susceptibility test is needed to support individualized drug use to avoid delay in the disease.

A scoping review of mycetoma profile in Egypt: revisiting the global endemicity map

Mycetoma is a chronic infectious disease endemic in sub-Saharan Africa (SSA), India and parts of South and North America. The epidemiologic profile of the disease in Egypt, which neighbours SSA, has not been explored previously. Therefore we conducted a scoping review of the literature on mycetoma in Egypt. We searched the literature comprehensively on MEDLINE and Google Scholar using free-text words and Medical Subject Headings and terms. Both published and non-peer-reviewed (grey literature) articles were included. The initial search identified 133 reports. Of these, only eight were found to be relevant and were included in the study. The total number of mycetoma patients was 59, reported between 1949 and 2015. There was a predilection for eumycetoma (44 of 59) patients (75%), while actinomycetoma constituted 15 patients (25%). Six patients were female, 28 were male and 25 were unreported. Children and adolescents constituted 3 of 59 (5%), 52 (88%) were adults and age was not provided for 4 patients. Only four patients (7%) were non-autochthonous. The incidence of mycetoma in Egypt is higher than previously reported. Egypt is probably a low-endemic country. An accurate estimate of the prevalence and epidemiology of mycetoma necessitates further research collaboration.

specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data

BACKGROUND

Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3 ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.

RESULTS

We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.

CONCLUSIONS

specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.