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- Acinetobacter rudis sp. nov., isolated from raw milk and raw wastewaterPublication . Vaz-Moreira, Ivone; Novo, Ana; Hantsis-Zacharov, Elionora; Lopes, Ana Rita; Gomila, Margarita; Nunes, Olga C.; Manaia, Célia M.; Halpern, MalkaTwo bacterial strains, G30T and A1PC16, isolated respectively from raw milk and raw wastewater, were characterized using a polyphasic approach. Chemotaxonomic characterization supported the inclusion of these strains in the genus Acinetobacter, with Q-8 and Q-9 as the major respiratory quinones, genomic DNA G+C contents within the range observed for this genus(38–47 mol%) and C16 : 0, C18 : 1v9c and C16 : 1v7c/iso-C15 : 0 2-OH as the predominant fatty acids. The observation of 16S rRNA gene sequence similarity lower than 97% with other Acinetobacter species with validly published names led to the hypothesis that these isolates could represent a novel species. This hypothesis was supported by comparative analysis of partial sequences of the genes rpoB and gyrB, which showed that strains G30T and A1PC16 did not cluster with any species with validly published names, forming a distinct lineage. DNA–DNA hybridizations confirmed that the two strains were members of the same species, which could be distinguished from their congeners by several phenotypic characteristics. On the basis of these arguments, it is proposed that strains G30T and A1PC16 represent a novel species, for which the name Acinetobacter rudis sp. nov. is proposed. The type strain is strain G30T (5LMG 26107T 5CCUG 57889T 5DSM 24031T 5CECT 7818T).
- Applications of optical DNA mapping in microbiologyPublication . Bogas, Diana; Nyberg, Lena; Pacheco, Rui; Azevedo, Nuno F.; Beech, Jason P.; Gomila, Margarita; Lalucat, Jorge; Manaia, Célia M.; Nunes, Olga C.; Tegenfeldt, Jonas O.; Westerlund, FredrikOptical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.
- Common and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settingsPublication . Rocha, Jaqueline; Henriques, Isabel; Gomila, Margarita; Manaia, Célia M.The Klebsiella pneumoniae complex is comprised of ubiquitous bacteria that can be found in soils, plants or water, and as humans’ opportunistic pathogens. This study aimed at inferring common and distinctive features in clinical and environmental K. pneumoniae. Whole genome sequences of members of the K. pneumoniae complex (including K. variicola, n = 6; and K. quasipneumoniae, n = 7), of clinical (n = 78) and environmental (n = 61) origin from 21 countries were accessed from the GenBank. These genomes were compared based on phylogeny, pangenome and selected clinically relevant traits. Phylogenetic analysis based on 2704 genes of the core genome showed close relatedness between clinical and environmental strains, in agreement with the multi-locus sequence typing. Eight out of the 62 sequence types (STs) identified, included both clinical and environmental genomes (ST11, ST14, ST15, ST37, ST45, ST147, ST348, ST437). Pangenome-wide association studies did not evidence significant differences between clinical and environmental genomes. However, the genomes of clinical isolates presented significantly more exclusive genes related to antibiotic resistance/plasmids, while the environmental isolates yielded significantly higher allelic diversity of genes related with functions such as efflux or oxidative stress. The study suggests that K. pneumoniae can circulate among the natural environment and clinical settings, probably under distinct adaptation pressures.
- Do Klebsiella pneumoniae environmental strains maintain clinically relevant genomic and phenotypic traits?Publication . Rocha, Jaqueline; Ferreira, Catarina; Mil-Homens, Dalila; Brito, Margarida; Lameiras, Catarina; Fialho, Arsénio; Henriques, Isabel; Gomila, Margarita; Manaia, Célia M.
- Third generation cephalosporin-resistant Klebsiella pneumoniae thriving in patients and in wastewater: what do they have in common?Publication . Rocha, Jaqueline; Ferreira, Catarina; Mil-Homens, Dalila; Busquets, Antonio; Fialho, Arsénio M.; Henriques, Isabel; Gomila, Margarita; Manaia, Célia M.Background Klebsiella pneumoniae are ubiquitous bacteria and recognized multidrug-resistant opportunistic pathogens that can be released into the environment, mainly through sewage, where they can survive even after wastewater treatment. A major question is if once released into wastewater, the selection of lineages missing clinically-relevant traits may occur. Wastewater (n = 25) and clinical (n = 34) 3(rd) generation cephalosporin-resistant K. pneumoniae isolates were compared based on phenotypic, genotypic and genomic analyses. Results Clinical and wastewater isolates were indistinguishable based on phenotypic and genotypic characterization. The analysis of whole genome sequences of 22 isolates showed that antibiotic and metal resistance or virulence genes, were associated with mobile genetic elements, mostly transposons, insertion sequences or integrative and conjugative elements. These features were variable among isolates, according to the respective genetic lineage rather than the origin. Conclusions It is suggested that once acquired, clinically relevant features of K. pneumoniae may be preserved in wastewater, even after treatment. This evidence highlights the high capacity of K. pneumoniae for spreading through wastewater, enhancing the risks of transmission back to humans.