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Background: Gram-negative bacilli are primarily responsible for the most common pediatric infections. Frequently, Escherichia fergusonii is identified as E. coli because of its close genetic proximity. Objectives: We aimed at the isolation and identification of multi-resistant strains of E. fergusonii, affecting children under two months of age. Methods: Strains were isolated from infectious processes and were identified phenotypically and molecularly. The microdilution method (MicroScan, autoSCAN-4) and the disk diffusion method (modified Kirby Bauer) were used to analyze antibiotic susceptibility. Results: Strains isolated were multi-resistant. Molecular identification provided the correct taxonomic assignment. Escherichia fergusonii strains were wrongly identified as E. coli with the phenotypic identification method. In addition, Pseudomonas aeruginosa and Klebsiella pneumoniae were identified. The best sensitivity results were obtained with Ceftazidime/avibactam and ceftolozane/tazobactam. Conclusions: We provided the first report of isolation and identification of multi-resistant E. fergusonii strains affecting children under two months of age in a neonatal intensive care unit.

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.

Currently for bacterial identification and classification the rrs gene encoding 16S rRNA is used as a reference method for the analysis of strains of the genus Nocardia. However, it does not have enough polymorphism to differentiate them at the species level. This fact makes it necessary to search for molecular targets that can provide better identification. The sodA gene (encoding the enzyme superoxide dismutase) has had good results in identifying species of other Actinomycetes. In this study the sodA gene is proposed for the identification and differentiation at the species level of the genus Nocardia. We used 41 type species of various collections; a 386 bp fragment of the sodA gene was amplified and sequenced, and a phylogenetic analysis was performed comparing the genes rrs (1171 bp), hsp65 (401 bp), secA1 (494 bp), gyrB (1195 bp) and rpoB (401 bp). The sequences were aligned using the Clustal X program. Evolutionary trees according to the neighbour-joining method were created with the programs Phylo_win and MEGA 6. The specific variability of the sodA genus of the genus Nocardia was analysed. A high phylogenetic resolution, significant genetic variability, and specificity and reliability were observed for the differentiation of the isolates at the species level. The polymorphism observed in the sodA gene sequence contains variable regions that allow the discrimination of closely related Nocardia species. The clear specificity, despite its small size, proves to be of great advantage for use in taxonomic studies and clinical diagnosis of the genus Nocardia.

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).

Mycobacteriumgenus causes a variety of zoonotic diseases. The best known example is the zoonotic tuberculosis due toM. 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 ofM. bovisin 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 asM. neoaurum(six strains),M. parafortuitum(four strains),M. moriokaense(two strains), andM. confluentis(one strain). ExceptM. parafortuitum, the other species identified are of public health and veterinary concern because they are pathogenic to humans, especially those with underlying medical conditions.

Background: The opportunistic pathogen Klebsiella pneumoniae is one of the main causes of pediatric bacterial blood stream infections (BSI), which is complicated with sepsis and high mortality. Objectives: To identify atypical Klebsiella species affecting a sample of infected neonates with low antimicrobial response. Methods: Multidrug resistant blood cultures for Klebsiella from a Neonatal Service, were submitted to molecular identification by sequencing analysis of 16S ribosomal RNA. Results: The mean age of the newborns was 14.7 ± 5.6 days. A total of 6 out of 8 cases were sepsis, 1 case of pneumonia, and 1 a catheter-related infection. The molecular identification showed 3 cases of K. pneumoniae subsp. ozaenae, 2 of K. pneumoniae and K. variicola, and 1 case of K. oxytoca. The highest antimicrobial resistance was against cephalosporins and Trimethoprim/sulfamethoxazole. Conclusions: Klebsiella pneumoniae subsp. ozaenae was responsible for multidrug resistant strains of Klebsiella even in 37.5% of cases. In our clinical setting, the use of Amikacin and carbapenems are still useful to treat neonatal infections by Klebsiella even against K. variicola, which is the most resistant.

Summary Objective The aim of our research was to update the situation concerning actinomycetoma in Mexico, to localize areas where it is frequently found and to identify the main strains from the isolates. Material and methods To localize cases of actinomycetoma, patients’ medical records from the dermatology departments of general and private hospitals were reviewed. Pathologic strains were looked for in general hospital patients and in reference institutes in Mexico City. The clinical strains were kept in Bennett agar and were subsequently identified using polyphasic approaches, including a partial sequence of 16S rDNA using species-specific primers designed to recognise Nocardia species. Results Eleven cases of actinomycetoma and five species of pathological strains were identified. Most cases were found in south-eastern Mexico and Nocardia brasiliensis was the most frequently isolated species. Conclusions This research confirmed the presence of actinomycetoma in Mexico as well as the zones of high incidence and the most frequent pathological strain.

Nocardia species are aerobic, Gram-positive bacteria with branched filaments reported as opportunistic microorganisms associated with infectious diseases of the skin. We report the isolation of N. wallacei in Mexico from a 43-year-old man, an HIV-positive construction worker who sought care for difficulty breathing and abundant sputum.

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 ofMycobacteriumspp. 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 10Pantoea agglomerans, 6Mycobacteriumspp., 6Pseudomonasspp. 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), andEnterobacter hormaechei(1).

Summary Background Mexico has the largest number of clinical cases of actinomycetoma in North and South America. Species originally identified by less specific methods have been recently reclassified as other known species or as new species. Objective To assess, by 16S rRNA gene sequencing and phenotypic methods, the species distribution of 18 human clinical isolates originally identified as N. brasiliensis , some of them isolated between 1947 and 1959 in Mexico City. Methods Clinical isolates came from the Hospital General, “Dr. Manuel Gea Gonzalez”, and Instituto Nacional de Diagnostico y Referencia Epidemiologica (INDRE) in Mexico, D.F. The strains used in this study included 15 clinical strains isolated between 1947 and 1959 that were originally identified as N. brasiliensis and three more strains obtained in 2007 identified as Nocardia spp. The isolates were identified genotypically by sequencing the 16S rRNA gene, and their phenotypic profiles were obtained with the API Coryne ® system. Antibiotic susceptibility patterns were tested according to the protocol of the Comite de l’antibiogramme de la Societe francaise de microbiologie [4] . Results According to 16S rRNA gene, sequencing were identified among 18 human clinical isolates as Nocardia farcinica ( n = 11) and Nocardia brasiliensis ( n = 7). A high number of the strains were susceptible to the majority of the antibiotics tested. The phenotypic profiles of the strains were quite uniform for N. farcinica and some variability was observed for N. brasiliensis strains. Conclusion N. farcinica was the most prevalent species identified. Modern methodologies should be applied in clinical laboratories to accurately identify etiological agents.