Genetic variability of the 16S rRNA gene of Nocardia brasiliensis, the most common causative agent of actinomycetoma in Latin America and the Caribbean.

Mycetoma is a neglected tropical disease (NTD) declared by the World Health Organization (WHO) in 2016. It is characterized by the progressive growth of nodules and granulomatous lesions on the legs, arms, and trunk. It is potentially disfiguring and causes disability or amputations in working-age people from marginalized areas. The causative agents can be fungi (eumycetoma) or actinobacteria (actinomycetoma), the latter being the most common in America and Asia. Nocardia brasiliensis is the most important causal agent of actinomycetoma in the Americas. Taxonomic problems have been reported when identifying this species, so this study aimed to detect the 16S rRNA gene variations in N. brasiliensis strains using an in silico enzymatic restriction technique. The study included strains from clinical cases of actinomycetoma in Mexico, isolated from humans and previously identified as N. brasiliensis by traditional methods. The strains were characterized microscopically and macroscopically, then subjected to DNA extraction and amplification of the 16S rRNA gene by PCR. The amplification products were sequenced, and consensus sequences were constructed and used for genetic identification and in silico restriction enzyme analysis with the New England BioLabs® NEBcutter program. All study strains were molecularly identified as N. brasiliensis; however, in silico restriction analysis detected a diversity in the restriction patterns that were finally grouped and subclassified into 7 ribotypes. This finding confirms the existence of subgroups within N. brasiliensis. The results support the need to consider N. brasiliensis as a complex species.

Genetic variability of the 16S rRNA gene of Nocardia brasiliensis, the most common causative agent of actinomycetoma in Latin America and the Caribbean

ABSTRACT Mycetoma is a neglected tropical disease (NTD) declared by the World Health Organization (WHO) in 2016. It is characterized by the progressive growth of nodules and granulomatous lesions on the legs, arms, and trunk. It is potentially disfiguring and causes disability or amputations in working-age people from marginalized areas. The causative agents can be fungi (eumycetoma) or actinobacteria (actinomycetoma), the latter being the most common in America and Asia. Nocardia brasiliensis is the most important causal agent of actinomycetoma in the Americas. Taxonomic problems have been reported when identifying this species, so this study aimed to detect the 16S rRNA gene variations in N. brasiliensis strains using an in silico enzymatic restriction technique. The study included strains from clinical cases of actinomycetoma in Mexico, isolated from humans and previously identified as N. brasiliensis by traditional methods. The strains were characterized microscopically and macroscopically, then subjected to DNA extraction and amplification of the 16S rRNA gene by PCR. The amplification products were sequenced, and consensus sequences were constructed and used for genetic identification and in silico restriction enzyme analysis with the New England BioLabs® NEBcutter program. All study strains were molecularly identified as N. brasiliensis; however, in silico restriction analysis detected a diversity in the restriction patterns that were finally grouped and subclassified into 7 ribotypes. This finding confirms the existence of subgroups within N. brasiliensis. The results support the need to consider N. brasiliensis as a complex species.

Bacillus paralicheniformis isolated from a hypersaline sediment of Lake Texcoco, draft genome sequence of strain TXO7B-1SG6.

We present the draft genome sequence of the halotolerant strain Bacillus paralicheniformis TXO7B-1SG6.

Preliminary Identification of the Aerobic Cervicovaginal Microbiota in Mexican Women With Cervical Cancer as the First Step Towards Metagenomic Studies.

Cervical cancer (CC) is considered a public health problem. Recent studies have evaluated the possible relationship between the cervicovaginal microbiome and gynecologic cancer but have not studied the relationship between aerobic bacterial communities and neoplasia. The study aimed to identify the cultivable aerobic bacterial microbiota in women with cervical cancer as a preliminary approach to the metagenomic study of the cervicovaginal microbiome associated with cervical cancer in Mexican women. An observational cross-sectional study was conducted, including 120 women aged 21-71 years, divided into two study groups, women with locally advanced CC (n=60) and women without CC (n=60). Sociodemographic, gynecological-obstetric, sexual, and habit data were collected. Cervicovaginal samples were collected by swabbing, from which standard microbiological methods obtained culturable bacteria. The strains were genetically characterized by PCR-RFLP of the 16S rRNA gene and subsequently identified by sequencing the same gene. Variables regularly reported as risk factors for the disease were found in women with CC. Differences were found in the prevalence and number of species isolated in each study group. Bacteria commonly reported in women with aerobic vaginitis were identified. There were 12 species in women with CC, mainly Corynebacterium spp. and Staphylococcus spp.; we found 13 bacterial species in the group without cancer, mainly Enterococcus spp. and Escherichia spp. The advanced stages presented a more significant number of isolates and species. This study provided a preliminary test for cervicovaginal metagenomic analysis, demonstrating the presence of aerobic cervicovaginal dysbiosis in women with CC and the need for more in-depth studies.

Changes in the diversity of local cervical bacteria in women with cervical cancer receiving antineoplastic treatment.

BACKGROUND: Some studies show changes in the microbiota in people undergoing antineoplastic treatment. Currently, there is not enough evidence of this effect in the treatment of cervical cancer (CC). The objective was to determine changes in the diversity of local cervical bacteria in women with CC receiving chemotherapy, radiotherapy, and brachytherapy. MATERIALS AND METHODS: A descriptive, longitudinal, and prospective study was conducted in 68 women with locally advanced CC with a treatment plan based on the administration of chemotherapy, external beam radiotherapy, and brachytherapy. Cervical-vaginal fluid samples were taken during antineoplastic treatment. The samples were used to isolate bacterial strains. The bacteria were identified at the molecular level by comparing sequences of the 16S ribosomal RNA gene. RESULTS: The bacteria identified belonged to three phyla: Firmicutes, Proteobacteria, and Actinobacteria. Nine genera and 25 species of bacteria were identified. The most frequent species were Staphylococcus epidermidis, Corynebacterium amycolatum, and Enterococcus faecalis. There were statistically significant differences when comparing bacterial diversity found in the different stages of treatment (≤0.05). Bacterial diversity decreased as antineoplastic treatment progressed and increased at the end of therapy. CONCLUSION: Antineoplastic treatments generate changes in the diversity of local cervical bacterial communities of women with CC.

Taxogenomic and Comparative Genomic Analysis of the Genus Saccharomonospora Focused on the Identification of Biosynthetic Clusters PKS and NRPS.

Actinobacteria are prokaryotes with a large biotechnological interest due to their ability to produce secondary metabolites, produced by two main biosynthetic gene clusters (BGCs): polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS). Most studies on bioactive products have been carried out on actinobacteria isolated from soil, freshwater or marine habitats, while very few have been focused on halophilic actinobacteria isolated from extreme environments. In this study we have carried out a comparative genomic analysis of the actinobacterial genus Saccharomonospora, which includes species isolated from soils, lake sediments, marine or hypersaline habitats. A total of 19 genome sequences of members of Saccharomonospora were retrieved and analyzed. We compared the 16S rRNA gene-based phylogeny of this genus with evolutionary relationships inferred using a phylogenomic approach obtaining almost identical topologies between both strategies. This method allowed us to unequivocally assign strains into species and to identify some taxonomic relationships that need to be revised. Our study supports a recent speciation event occurring between Saccharomonospora halophila and Saccharomonospora iraqiensis. Concerning the identification of BGCs, a total of 18 different types of BGCs were detected in the analyzed genomes of Saccharomonospora, including PKS, NRPS and hybrid clusters which might be able to synthetize 40 different putative products. In comparison to other genera of the Actinobacteria, members of the genus Saccharomonospora showed a high degree of novelty and diversity of BGCs.

Draft Genome Sequence of Saccharomonospora piscinae KCTC 19743T, an Actinobacterium Containing Secondary Metabolite Biosynthetic Gene Clusters.

The draft genome sequence of Saccharomonospora piscinae KCTC 19743T, with a size of 4,897,614 bp, was assembled into 11 scaffolds containing 4,561 open reading frames and a G+C content of 71.0 mol%. Polyketide synthase and nonribosomal peptide synthetase gene clusters, which are responsible for the biosynthesis of several biomolecules, were identified and located in different regions in the genome.

Molecular Identification of Mycobacterium Species of Public Health and Veterinary Importance from Cattle in the South State of México.

Mycobacterium genus causes a variety of zoonotic diseases. The best known example is the zoonotic tuberculosis due to M. bovis. Much less is known about "nontuberculous mycobacteria (NTM)," which are also associated with infections in humans. The Mexican standard NOM-ZOO-031-1995 regulates the presence of M. bovis in cattle; however, no regulation exists for the NTM species. The objective of this study was to isolate and identify nontuberculous mycobacteria species from cattle of local herds in the south region of the State of Mexico through the identification and detection of the 100 bp molecular marker in the 23S rRNA gene with subsequent sequencing of the 16S rRNA gene. Milk samples (35) and nasal exudate samples (68) were collected. From the 108 strains isolated, 39 were selected for identification. Thirteen strains isolated from nasal exudates amplified the 100 bp molecular marker and were identified as M. neoaurum (six strains), M. parafortuitum (four strains), M. moriokaense (two strains), and M. confluentis (one strain). Except M. parafortuitum, the other species identified are of public health and veterinary concern because they are pathogenic to humans, especially those with underlying medical conditions.

Pelvic Actinomycosis.

INTRODUCTION: Actinomycosis is a chronic bacterial infection caused by Actinomyces, Gram-positive anaerobic bacteria. Its symptomatology imitates some malignant pelvic tumours, tuberculosis, or nocardiosis, causing abscesses and fistulas. Actinomycoses are opportunistic infections and require normal mucous barriers to be altered. No epidemiological studies have been conducted to determine prevalence or incidence of such infections. OBJECTIVE: To analyse the clinical cases of pelvic actinomycosis reported worldwide, to update the information about the disease. METHODS: A systematic review of worldwide pelvic actinomycosis cases between 1980 and 2014 was performed, utilising the PubMed, Scopus, and Google Scholar databases. The following information was analysed: year, country, type of study, number of cases, use of intrauterine device (IUD), final and initial diagnosis, and method of diagnosis. RESULTS: 63 articles met the search criteria, of which 55 reported clinical cases and 8 reported cross-sectional studies. CONCLUSIONS: Pelvic actinomycosis is confusing to diagnose and should be considered in the differential diagnosis of pelvic chronic inflammatory lesions. It is commonly diagnosed through a histological report, obtained after a surgery subsequent to an erroneous initial diagnosis. A bacterial culture in anaerobic medium could be useful for the diagnosis but requires a controlled technique and should be performed using specialised equipment.

Detection of Actinomyces spp. in cervical exudates from women with cervical intraepithelial neoplasia or cervical cancer.

PURPOSE: Under certain circumstances, Actinomyces behaves as an opportunistic microorganism and can cause actinomycosis, a chronic and inflammatory granulomatous infection. The purpose of this project was to detect the presence of Actinomyces in cervical exudates from women with cervical intraepithelial neoplasia (CIN) and women with cervical cancer. METHODOLOGY: Cervical samples from 92 women were divided into three groups: CIN, cervical cancer and healthy women. Metagenomic DNA extraction was performed following the Qiagen QIAamp Mini Kit protocol. A specific fragment (675 bp) was amplified by PCR in order to detect the presence of Actinomycetales. Samples in which Actinomycetales was detected were subjected to separate amplification reactions with primer pairs for A. israelii, A. viscosus, A. meyeri and A. odontolyticus. Amplified products were observed by 2 % agarose gel electrophoresis. RESULTS: Actinomyces were found in 10 % of women with CIN, 36.6 % of women with cervical cancer and 9 % of healthy women. The species identified in this study were A. meyeri in 14/92 samples (15.2 %), A. viscosus in 10/92 samples (10.8 %), A. odontolyticus in 4/92 samples (4.3 %) and A. israelii in 6/92 samples (6.5 %). CONCLUSION: Patients with cervical cancer had a higher prevalence of the presence of Actinomyces compared to the CIN and control groups. This is the first study in which a deliberate search of this genus has been performed in women with cervical pathologies. The use of specific primers for each species facilitated their detection in comparison with traditional isolation methods. More information is necessary to understand the molecular mechanisms involved in the complex role that bacterial communities may play in the development of cancer (and vice versa).

Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide Synthase and Nonribosomal Peptide Synthetase Systems.

The draft genome sequence of Saccharomonospora sp. strain LRS4.154, a moderately halophilic actinobacterium, has been determined. The genome has 4,860,108 bp, a G+C content of 71.0%, and 4,525 open reading frames (ORFs). The clusters of PKS and NRPS genes, responsible for the biosynthesis of a large number of biomolecules, were identified in the genome.

Pantoea agglomerans in immunodeficient patients with different respiratory symptoms.

The aim of this paper was to determine in 32 patients from 4 different Mexican hospitals the frequency of opportunistic bacteria in the 2010 to 2011 time period. The patients were divided in 4 groups. Group 1 included 21 HIV positive patients with acute respiratory syndrome. Four HIV positive patients with tuberculosis symptoms were included in Group 2; two patients with tuberculosis symptoms and one asymptomatic person formed Group 3. Reference Group 4 included 4 patients from whom 4 strains of Mycobacterium spp. had been reported. The strains were isolated and identified by 16S rRNA gene amplification, API 20E and 50CH, biochemical test, and antibiotic sensitivity. The strains found were 10 Pantoea agglomerans, 6 Mycobacterium spp., 6 Pseudomonas spp. and 10 strains of normal floral species: Thermoactinomycetes bacterium (1), Enterococcus faecium (2), Bacillus licheniformis (1), Lactobacillus rhamnosus (2), Streptococcus oralis (2), Streptococcus anginosus (1), and Enterobacter hormaechei (1).

[Composition of fat acids in three Mexican populations of Artemia franciscana from epicontinental waters]. / Composici6n del contenido de ácidos grasos en tres poblaciones mexicanas de Artemia franciscana de aguas epicontinentales.

In this paper is presented the percentage of fatty acids composition of three Artemia franciscana Mexican populations of epicontinentals waters; two are from natural environments (Coahuila and San Luis Potosf) and one (Texcoco) is a culture fed with Spirulina. Determination of fatty acids composition in each population, was performed by extraction of total lipid by the soxhlet method and the fatty acids methyl esters were determined by gas chromatography. The results show that Artemia of Texcoco contains the six fatty acids recommended for the culture of fish and crustaceans (16:0; 16:1; 18:1; 18:2w6; 18:3w3 and 20:5w3); Artemia from San Luis Potosi showed the poorest content in these acids and Artemia from Coahuila, although it showed a wide profile, it lacks the linolenic acid. When comparing results among the three populations with ecological data that have been published, it can be pointed out that the environment is decisive for this crustacean; Artemia from Texcoco fed with Spirulina showed the largest variety of fatty acids; the other two populations are wild, and lives in different habitats, Artemia of Coahuila is found in waters that are rich in sulfates and Artemia of San Luis Potosf lives in evaporation saltern ponds, built with stone blocks and therefore with scarce phytoplankton growth. Both Artemia populations showed deficiencies in essential fatty acids, mainly the last one.