Browsing by Author "Rocha, Jaqueline"
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- Antibiotic resistance in wastewater treatment plants: tackling the black boxPublication . Manaia, Célia M.; Rocha, Jaqueline; Scaccia, Nazareno; Marano, Roberto; Radu, Elena; Biancullo, Francesco; Cerqueira, Francisco; Fortunato, Gianuário; Iakovides, Iakovos C.; Zammit, Ian; Kampouris, Ioannis; Vaz-Moreira, Ivone; Nunes, Olga C.Wastewater is among the most important reservoirs of antibiotic resistance in urban environments. The abundance of carbon sources and other nutrients, a variety of possible electron acceptors such as oxygen or nitrate, the presence of particles onto which bacteria can adsorb, or a fairly stable pH and temperature are examples of conditions favouring the remarkable diversity of microorganisms in this peculiar habitat. The wastewater microbiome brings together bacteria of environmental, human and animal origins, many harbouring antibiotic resistance genes (ARGs). Although numerous factors contribute, mostly in a complex interplay, for shaping this microbiome, the effect of specific potential selective pressures such as antimicrobial residues or metals, is supposedly determinant to dictate the fate of antibiotic resistant bacteria (ARB) and ARGs during wastewater treatment. This paper aims to enrich the discussion on the ecology of ARB&ARGs in urban wastewater treatment plants (UWTPs), intending to serve as a guide for wastewater engineers or other professionals, who may be interested in studying or optimizing the wastewater treatment for the removal of ARB&ARGs. Fitting this aim, the paper overviews and discusses: i) aspects of the complexity of the wastewater system and/or treatment that may affect the fate of ARB&ARGs; ii) methods that can be used to explore the resistome, meaning the whole ARB&ARGs, in wastewater habitats; and iii) some frequently asked questions for which are proposed addressing modes. The paper aims at contributing to explore how ARB&ARGs behave in UWTPs having in mind that each plant is a unique system that will probably need a specific procedure to maximize ARB&ARGs removal.
- Antimicrobial resistance and clonal lineages of staphylococcus aureus from cattle: a cross-sectional study from the one health perspectivePublication . Silva, Vanessa; Correia, Susana; Rocha, Jaqueline; Manaia, Célia M.; Silva, Adriana; García-Díez, Juan; Pereira, José Eduardo; Semedo-Lemsaddek, Teresa; Igrejas, Gilberto; Poeta, PatríciaStaphylococcus aureus have been progressively identified in farm animals and in humans with direct contact with these animals showing that S. aureus may be a major zoonotic pathogen. Therefore, we aimed to isolate S. aureus from cows, their handlers, and their immediate surroundings, and to investigate the antimicrobial resistance and genetic lineages of the isolates. Mouth and nose swabs of 244 healthy cows (195 Maronesa, 11 Holstein-Friesians, and 28 crossbreeds), 82 farm workers, 53 water and 63 soil samples were collected. Identification of species was carried out by MALDI-TOF MS Biotyper. The presence of antimicrobial resistance genes and virulence factors was assessed based on gene search by PCR. All isolates were typed by multilocus sequence typing and spa-typing. From 442 samples, 33 (13.9%), 24 (29.3%), 1 (2%), and 1 (2%) S. aureus were recovered from cows, farm workers, water, and soil samples, respectively. Most of the isolates showed resistance only to penicillin. S. aureus isolates were ascribed to 17 sequence types (STs) and 26 spa-types. Some clonal lineages were common to both cows and farm workers such as ST30-t9413, ST72-t148, and ST45-t350. Through a One Health approach, this study revealed that there is a great diversity of clonal lineages of S. aureus in cows and their handlers. Furthermore, some S. aureus lineages are common to cows and handlers, which may suggest a possible transmission.
- Assessment of full-scale tertiary wastewater treatment by UV-C based-AOPs: removal or persistence of antibiotics and antibiotic resistance genes?Publication . Rodríguez-Chueca, Jorge; Giustina, Saulo Varella della; Rocha, Jaqueline; Fernandes, Telma; Pablos, Cristina; Encinas, Ángel; Barceló, Damià; Rodríguez-Mozaz, Sara; Manaia, Célia M.; Marugána, JavierAOPs based on the photolytic decomposition of H2O2 and peroxymonosulfate tested at low dosages (0.05-0.5 mM) and with very low UV-C contact time (4-18 s) demonstrated to be more efficient than UV-C radiation alone on the removal of the analyzed ABs. PMS (0.5 mM) combined with UV-C (7 s contact time) was the most efficient treatment in terms of AB removal: 7 out of 10 ABs detected in the waste water were removed more efficiently than using the other oxidants. In terms of ARGs removal efficiency, UV-C alone seemed the most efficient treatment, although H2O2/UV-C, PMS/UV-C and PMS/Fe(II)/UV-C were supposed to generate higher concentrations of free radicals. The results show that treatments with the highest removal of ABs and ARGs did not coincide, which could be attributed to the competition between DNA and oxidants in the absorption of UV photons, reducing the direct photolysis of the DNA. Whereas the photolytic ABs removal is improved by the generation of hydroxyl and sulfate radicals, the opposite behavior occurs in the case of ARGs. These results suggest that a compromise between ABs and ARGs removal must be achieved in order to optimize wastewater treatment processes.
- Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance (Nature Communications, (2022), 13, 1, (7251), 10.1038/s41467-022-34312-7)Publication . Global Sewage Surveillance Consortium; Manaia, Celia; Rocha, JaquelineIn this article, the author name Antoinette Ngandjio was incorrectly written as Antoinette Ngandijo. In this article, the affiliation details for Author Sara Cuadros-Orellana were incorrectly given as ‘Centro de Biotecnologνa de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Talca, Chile’ but should have been ‘Universidad Catolica del Maule, Centro de Biotecnología de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Talca, Chile’. The original article has been corrected.
- Bacterial community and antibiotic resistance dynamics in a full-scale wastewater treatment plant with UV disinfectionPublication . Narciso-Da-Rocha, Carlos; Rocha, Jaqueline; Vaz-Moreira, Ivone; Lira, Felipe; Tamames, Javier; Henriques, Isabel; Martinez, José Luis; Manaia, Célia M.
- Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plantPublication . Narciso-da-Rocha, Carlos; Rocha, Jaqueline; Vaz-Moreira, Ivone; Lira, Felipe; Tamames, Javier; Henriques, Isabel; Martinez, Jose Luis; Manaia, Célia M.Urban wastewater treatment plants (UWTPs) are reservoirs of antibiotic resistance. Wastewater treatment changes the bacterial community and inevitably impacts the fate of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). Some bacterial groups are major carriers of ARGs and hence, their elimination during wastewater treatment may contribute to increasing resistance removal efficiency. This study, conducted at a full-scale UWTP, evaluated variations in the bacterial community and ARGs loads and explored possible associations among them. With that aim, the bacterial community composition (16S rRNA gene Illumina sequencing) and ARGs abundance (real-time PCR) were characterized in samples of raw wastewater (RWW), secondary effluent (sTWW), after UV disinfection (tTWW), and after a period of 3 days storage to monitoring possible bacterial regrowth (tTWW-RE). Culturable enterobacteria were also enumerated. Secondary treatment was associated with the most dramatic bacterial community variations and coincided with reductions of ~2 log-units in the ARGs abundance. In contrast, no significant changes in the bacterial community composition and ARGs abundance were observed after UV disinfection of sTWW. Nevertheless, after UV treatment, viability losses were indicated ~2 log-units reductions of culturable enterobacteria. The analysed ARGs (qnrS, blaCTX-M, blaOXA-A, blaTEM, blaSHV, sul1, sul2, and intI1) were strongly correlated with taxa more abundant in RWW than in the other types of water, and which associated with humans and animals, such as members of the families Campylobacteraceae, Comamonadaceae, Aeromonadaceae, Moraxellaceae and Bacteroidaceae. Further knowledge of the dynamics of the bacterial community during wastewater treatment and its relationship with ARGs variations may contribute with information useful for wastewater treatment optimization, aiming at a more effective resistance control.
- Cell-based internal standard for qPCR determinations of antibiotic resistance indicators in environmental water samplesPublication . Rocha, Jaqueline; Manaia, Célia M.Quantitative PCR (qPCR) has been used to quantify antibiotic resistance genes (ARGs) in water, wastewater, soil, sediment and tissue samples. Concerns regarding the comparability of data obtained in different laboratories has been a major bottleneck to incentivize the compilation of publicly available of ARGs quantifications gathered from different reports. In this study, the influence of the DNA extraction kits (NZY Tissue gDNA Isolation kit or DNeasy PowerWater kit) and of the operator on the DNA extraction yield and on qPCR genes quantification was assessed. Since in wastewater and water samples the matrix effect can affect the DNA recovery and, therefore, gene quantification, an internal standard, consisting in a cloned gene not found in environmental samples, was tested. The aim was to assess how qPCR determinations in wastewater and water samples can be affected by the matrix effect. The results show that the DNA extraction operator did not significantly influence DNA yield. The use of distinct kits resulted in qPCR gene quantifications that did not differ in more than 1 log-unit mL−1. The matrix effect, assessed based on the use of an internal standard, was associated with an underestimation that ranged 0.1–0.9 log gene copy number mL−1 of sample, irrespective of the water type. The reliability on the use of a DNA extraction kit that costs about 3 times less than the most commonly used can be an incentive for the use of DNA based analyses of ARGs in environmental waters. Moreover, the fact that both the DNA extraction operator and the reduced matrix effect have little influence on the final results, are good news, encouraging the compilation of data produced in distinct laboratories. Nevertheless, harmonization efforts are still necessary to minimize bias that may be due associated with other conditions, such as equipment.
- 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.
- Comparative genomics insights into clinical or environmental methicillin resistant staphylococcus aureusPublication . Rocha, Jaqueline; Silva, Vanessa; Poeta, Patrícia; Manaia, Célia M.
- Comparison of culture- and quantitative PCR-Based indicators of antibiotic resistance in wastewater, recycled water, and tap waterPublication . Rocha, Jaqueline; Fernandes, Telma; Riquelme, Maria V.; Zhu, Ni; Pruden, Amy; Manaia, Célia M.Standardized methods are needed to support monitoring of antibiotic resistance in environmental samples. Culture-based methods target species of human-health relevance, while the direct quantification of antibiotic resistance genes (ARGs) measures the antibiotic resistance potential in the microbial community. This study compared measurements of tetracycline-, sulphonamide-, and cefotaxime-resistant presumptive total and fecal coliforms and presumptive enterococci versus a suite of ARGs quantified by quantitative polymerase chain reaction (qPCR) across waste-, recycled-, tap-, and freshwater. Cross-laboratory comparison of results involved measurements on samples collected and analysed in the US and Portugal. The same DNA extracts analysed in the US and Portugal produced comparable qPCR results (variation <28%), except for blaOXA-1 gene (0%–57%). Presumptive total and fecal coliforms and cefotaxime-resistant total coliforms strongly correlated with blaCTX-M and intI1 (0.725 ≤ R2 ≤ 0.762; p < 0.0001). Further, presumptive total and fecal coliforms correlated with the Escherichia coli-specific biomarkers, gadAB, and uidA, suggesting that both methods captured fecal-sourced bacteria. The genes encoding resistance to sulphonamides (sul1 and sul2) were the most abundant, followed by genes encoding resistance to tetracyclines (tet(A) and tet(O)) and β-lactams (blaOXA-1 and, blaCTX-M), which was in agreement with the culture-based enumerations. The findings can help inform future application of methods being considered for international antibiotic resistance surveillance in the environment.
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