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Background The SARS-CoV-2 Delta variant (B.1.617.2), initially identified in India, has become predominant in several countries, including Portugal. Few studies have compared the effectiveness of mRNA vaccines against Delta versus Alpha variant of concern (VOC) and estimated variant-specific viral loads in vaccine infection breakthroughs cases. In the context of Delta dominance, this information is critical to inform decision-makers regarding the planning of restrictions and vaccination roll-out. Methods We developed a case-case study to compare mRNA vaccines’ effectiveness against Delta (B.1.617.2) versus Alpha (B.1.1.7) variants. We used RT-PCR positive cases notified to the National Surveillance System between 17th of May and 4th of July 2021 (week 20 to 26) and information about demographics and vaccination status through the electronic vaccination register. Whole-genome sequencing (WGS) or spike (S) gene target failure (SGTF) data were used to classify SARS-CoV-2 variants. The odds of vaccinated individuals to become infected (odds of vaccine infection breakthrough) in Delta cases compared to Alpha SARS-CoV-2 cases was estimated by conditional logistic regression adjusted for age group, sex, and matched by the week of diagnosis. As a surrogate of viral load, mean RT-PCR Ct values were stratified and compared between vaccine status and VOC. Results Of the 2 097 SARS-CoV-2 RT-PCR positive cases included in the analysis, 966 (46.1%) were classified with WGS and 1131 (53.9%) with SGTF. Individuals infected with the Delta variant were more frequently vaccinated 162 (12%) than individuals infected with the Alpha variant 38 (5%). We report a statistically significant higher odds of vaccine infection breakthrough for partial (OR=1.70; CI95% 1.18 to 2.47) and complete vaccination (OR=1.96; CI95% 1.22 to 3.14) in the Delta cases when compared to the Alpha cases, suggesting lower mRNA vaccine effectiveness against Delta cases. On our secondary analysis, we observed lower mean Ct values for the Delta VOC cases versus Alpha, regardless the vaccination status. Additionally, the Delta variant cases revealed a Ct-value mean increase of 2.24 (CI95% 0.85 to 3.64) between unvaccinated and fully vaccinated breakthrough cases contrasting with 4.49 (CI95% 2.07 to 6.91) in the Alpha VOC, suggesting a lower impact of vaccine on viral load of Delta cases. Conclusions We found significantly higher odds of vaccine infection breakthrough in Delta cases when compared to Alpha cases, suggesting lower effectiveness of the mRNA vaccines in preventing infection with the Delta variant. Additionally, the vaccine breakthrough cases are estimated to be of higher mean Ct values, suggesting higher infectiousness with the Delta variant infection. These findings can help decision-makers weigh on the application or lifting of control measures and adjusting vaccine roll-out depending on the predominance of the Delta variant and the coverage of partial and complete mRNA vaccination.
Irina Kislaya; Eduardo Freire Rodrigues; Vítor Borges; João Paulo Gomes; Carlos Sousa; José Pedro Almeida; André Peralta-Santos; Baltazar Nunes. Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs. 2021, 1 .
AMA StyleIrina Kislaya, Eduardo Freire Rodrigues, Vítor Borges, João Paulo Gomes, Carlos Sousa, José Pedro Almeida, André Peralta-Santos, Baltazar Nunes. Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs. . 2021; ():1.
Chicago/Turabian StyleIrina Kislaya; Eduardo Freire Rodrigues; Vítor Borges; João Paulo Gomes; Carlos Sousa; José Pedro Almeida; André Peralta-Santos; Baltazar Nunes. 2021. "Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs." , no. : 1.
Tracking the within-patient evolution of SARS-CoV-2 is key to understanding how this pandemic virus shapes its genome toward immune evasion and survival. In the present study, by monitoring a long-term COVID-19 immunocompromised patient, we observed the concurrent emergence of mutations potentially associated with immune evasion and/or enhanced transmission, mostly targeting the SARS-CoV-2 key host-interacting protein and antigen.
Vítor Borges; Joana Isidro; Mário Cunha; Daniela Cochicho; Luís Martins; Luís Banha; Margarida Figueiredo; Leonor Rebelo; Maria Céu Trindade; Sílvia Duarte; Luís Vieira; Maria João Alves; Inês Costa; Raquel Guiomar; Madalena Santos; Rita Cortê-Real; André Dias; Diana Póvoas; João Cabo; Carlos Figueiredo; Maria José Manata; Fernando Maltez; Maria Gomes da Silva; João Paulo Gomes. Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. mSphere 2021, e0024421 .
AMA StyleVítor Borges, Joana Isidro, Mário Cunha, Daniela Cochicho, Luís Martins, Luís Banha, Margarida Figueiredo, Leonor Rebelo, Maria Céu Trindade, Sílvia Duarte, Luís Vieira, Maria João Alves, Inês Costa, Raquel Guiomar, Madalena Santos, Rita Cortê-Real, André Dias, Diana Póvoas, João Cabo, Carlos Figueiredo, Maria José Manata, Fernando Maltez, Maria Gomes da Silva, João Paulo Gomes. Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. mSphere. 2021; ():e0024421.
Chicago/Turabian StyleVítor Borges; Joana Isidro; Mário Cunha; Daniela Cochicho; Luís Martins; Luís Banha; Margarida Figueiredo; Leonor Rebelo; Maria Céu Trindade; Sílvia Duarte; Luís Vieira; Maria João Alves; Inês Costa; Raquel Guiomar; Madalena Santos; Rita Cortê-Real; André Dias; Diana Póvoas; João Cabo; Carlos Figueiredo; Maria José Manata; Fernando Maltez; Maria Gomes da Silva; João Paulo Gomes. 2021. "Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma." mSphere , no. : e0024421.
Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211–04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203–05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(−), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(−) ST17 2211–04 and the DNase(+) ST19 1203–05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(−) 2211–04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(−) strain, which may suggest that these proteins might contribute to the lack of DNase activity. In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(−) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.
Inês Silvestre; Alexandra Nunes; Vítor Borges; Joana Isidro; Catarina Silva; Luís Vieira; João Paulo Gomes; Maria José Borrego. Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains. Infection, Genetics and Evolution 2021, 93, 104969 .
AMA StyleInês Silvestre, Alexandra Nunes, Vítor Borges, Joana Isidro, Catarina Silva, Luís Vieira, João Paulo Gomes, Maria José Borrego. Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains. Infection, Genetics and Evolution. 2021; 93 ():104969.
Chicago/Turabian StyleInês Silvestre; Alexandra Nunes; Vítor Borges; Joana Isidro; Catarina Silva; Luís Vieira; João Paulo Gomes; Maria José Borrego. 2021. "Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains." Infection, Genetics and Evolution 93, no. : 104969.
“How predictable is evolution?” is a key question in evolutionary biology. Experimental evolution has shown that the evolutionary path of microbes can be extraordinarily reproducible. Here, using experimental evolution in two circulating SARS-CoV-2, we estimate its mutation rate and demonstrate the repeatability of its evolution when facing a new cell type but no immune or drug pressures. We estimate a genomic mutation rate of 3.7×10-6 nt-1 cycle-1 for a lineage of SARS-CoV-2 with the originally described spike protein (CoV-2-D) and of 2.9×10-6 nt-1 cycle-1 for a lineage carrying the D614G mutation that has spread worldwide (CoV-2-G). We further show that mutation accumulation is heterogeneous along the genome, with the spike gene accumulating mutations at a mean rate 16×10-6 nt-1 per infection cycle across backgrounds, five-fold higher than the genomic average. We observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein. Despite strong bottlenecks, several de novo mutations spread to high frequencies by selection and considerable convergent evolution in spike occurs. These results demonstrate the high adaptive potential of SARS-CoV-2 during the first stages of cell infection in the absence of immune surveillance.
Vítor Borges; Maria João Alves; Massimo Amicone; Joana Isidro; Líbia Zé-Zé; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes; Isabel Gordo. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. 2021, 1 .
AMA StyleVítor Borges, Maria João Alves, Massimo Amicone, Joana Isidro, Líbia Zé-Zé, Sílvia Duarte, Luís Vieira, Raquel Guiomar, João Paulo Gomes, Isabel Gordo. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. . 2021; ():1.
Chicago/Turabian StyleVítor Borges; Maria João Alves; Massimo Amicone; Joana Isidro; Líbia Zé-Zé; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes; Isabel Gordo. 2021. "Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution." , no. : 1.
Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities.
Vítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; Judite Catarino; Liliana Ciobanu; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes. Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission. Viruses 2021, 13, 604 .
AMA StyleVítor Borges, Joana Isidro, Filipe Macedo, José Neves, Luís Silva, Mário Paiva, José Barata, Judite Catarino, Liliana Ciobanu, Sílvia Duarte, Luís Vieira, Raquel Guiomar, João Paulo Gomes. Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission. Viruses. 2021; 13 (4):604.
Chicago/Turabian StyleVítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; Judite Catarino; Liliana Ciobanu; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes. 2021. "Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission." Viruses 13, no. 4: 604.
We show that the SARS-CoV-2 B.1.1.7 lineage is highly disseminated in Portugal, with the odds of B.1.1.7 proportion increasing at an estimated 89% (95% confidence interval: 83–95%) per week until week 3 2021. RT-PCR spike gene target late detection (SGTL) can constitute a useful surrogate to track B.1.1.7 spread, besides the spike gene target failure (SGTF) proxy. SGTL/SGTF samples were associated with statistically significant higher viral loads, but not with substantial shift in age distribution compared to non-SGTF/SGTL cases.
Vítor Borges; Carlos Sousa; Luís Menezes; António Maia Gonçalves; Miguel Picão; José Pedro Almeida; Margarida Vieita; Rafael Santos; Ana Rita Silva; Mariana Costa; Luís Carneiro; Pedro Casaca; Pedro Pinto-Leite; André Peralta-Santos; Joana Isidro; Sílvia Duarte; Luís Vieira; Raquel Guiomar; Susana Silva; Baltazar Nunes; João P Gomes. Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021. Eurosurveillance 2021, 26, 2100131 .
AMA StyleVítor Borges, Carlos Sousa, Luís Menezes, António Maia Gonçalves, Miguel Picão, José Pedro Almeida, Margarida Vieita, Rafael Santos, Ana Rita Silva, Mariana Costa, Luís Carneiro, Pedro Casaca, Pedro Pinto-Leite, André Peralta-Santos, Joana Isidro, Sílvia Duarte, Luís Vieira, Raquel Guiomar, Susana Silva, Baltazar Nunes, João P Gomes. Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021. Eurosurveillance. 2021; 26 (10):2100131.
Chicago/Turabian StyleVítor Borges; Carlos Sousa; Luís Menezes; António Maia Gonçalves; Miguel Picão; José Pedro Almeida; Margarida Vieita; Rafael Santos; Ana Rita Silva; Mariana Costa; Luís Carneiro; Pedro Casaca; Pedro Pinto-Leite; André Peralta-Santos; Joana Isidro; Sílvia Duarte; Luís Vieira; Raquel Guiomar; Susana Silva; Baltazar Nunes; João P Gomes. 2021. "Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021." Eurosurveillance 26, no. 10: 2100131.
The search for antibacterial agents for the combat of nosocomial infections is a timely problem, as antibiotic-resistant bacteria continue to thrive. The effect of indoline substituents on the antibacterial properties of aminoalkylphenols was studied, leading to the development of a library of compounds with minimum inhibitory concentrations (MICs) as low as 1.18 µM. Two novel aminoalkylphenols were identified as particularly promising, after MIC and minimum bactericidal concentrations (MBC) determination against a panel of reference strain Gram-positive bacteria, and further confirmed against 40 clinical isolates (Staphylococcus aureus, S. epidermidis, Enterococcus faecalis, E. faecium, and Listeria monocytogenes). The same two aminoalkylphenols displayed low toxicity against two in vivo models (Artemia salina brine shrimp and Saccharomyces cerevisiae). The in vitro cytotoxicity evaluation (on human keratinocytes and human embryonic lung fibroblast cell lines) of the same compounds was also carried out. They demonstrated a particularly toxic effect on the fibroblast cell lines, with IC50 in the 1.7-5.1 mM range, thus narrowing their clinical use. The desired increase in the antibacterial properties of the alkylaminophenols, particularly indoline-derived phenolic Mannich bases, was reached by introducing an additional nitro group in the indolinyl substituent or by the replacement of a methyl by a bioisosteric trifluoromethyl substituent. Notably, the introduction of an additional nitro moiety did not confer added toxicity to the alkylaminophenols.
Tatu Rimpilainen; Alexandra Nunes; Rita Calado; Ana Fernandes; Joana Andrade; Epole Ngolle; Gabriella Spengler; Nikoletta Szemeredi; João Rodrigues; João Paulo Gomes; Patricia Rijo; Nuno Candeias. Increased Antibacterial Properties of Indoline-Derived Phenolic Mannich Bases. 2021, 1 .
AMA StyleTatu Rimpilainen, Alexandra Nunes, Rita Calado, Ana Fernandes, Joana Andrade, Epole Ngolle, Gabriella Spengler, Nikoletta Szemeredi, João Rodrigues, João Paulo Gomes, Patricia Rijo, Nuno Candeias. Increased Antibacterial Properties of Indoline-Derived Phenolic Mannich Bases. . 2021; ():1.
Chicago/Turabian StyleTatu Rimpilainen; Alexandra Nunes; Rita Calado; Ana Fernandes; Joana Andrade; Epole Ngolle; Gabriella Spengler; Nikoletta Szemeredi; João Rodrigues; João Paulo Gomes; Patricia Rijo; Nuno Candeias. 2021. "Increased Antibacterial Properties of Indoline-Derived Phenolic Mannich Bases." , no. : 1.
The search for antibacterial agents for the combat of nosocomial infections is a timely problem, as antibiotic-resistant bacteria continue to thrive. The effect of indoline substituents on the antibacterial properties of aminoalkylphenols was studied, leading to the development of a library of compounds with minimum inhibitory concentrations (MICs) as low as 1.18 µM. Two novel aminoalkylphenols were identified as particularly promising, after MIC and minimum bactericidal concentrations (MBC) determination against a panel of reference strain Gram-positive bacteria, and further confirmed against 40 clinical isolates (Staphylococcus aureus, S. epidermidis, Enterococcus faecalis, E. faecium, and Listeria monocytogenes). The same two aminoalkylphenols displayed low toxicity against two in vivo models (Artemia salina brine shrimp and Saccharomyces cerevisiae). The in vitro cytotoxicity evaluation (on human keratinocytes and human embryonic lung fibroblast cell lines) of the same compounds was also carried out. They demonstrated a particularly toxic effect on the fibroblast cell lines, with IC50 in the 1.7-5.1 mM range, thus narrowing their clinical use. The desired increase in the antibacterial properties of the alkylaminophenols, particularly indoline-derived phenolic Mannich bases, was reached by introducing an additional nitro group in the indolinyl substituent or by the replacement of a methyl by a bioisosteric trifluoromethyl substituent. Notably, the introduction of an additional nitro moiety did not confer added toxicity to the alkylaminophenols.
Tatu Rimpilainen; Alexandra Nunes; Rita Calado; Ana Fernandes; Joana Andrade; Epole Ngolle; Gabriella Spengler; Nikoletta Szemeredi; João Rodrigues; João Paulo Gomes; Patricia Rijo; Nuno Candeias. Increased Antibacterial Properties of Indoline-Derived Phenolic Mannich Bases. 2021, 1 .
AMA StyleTatu Rimpilainen, Alexandra Nunes, Rita Calado, Ana Fernandes, Joana Andrade, Epole Ngolle, Gabriella Spengler, Nikoletta Szemeredi, João Rodrigues, João Paulo Gomes, Patricia Rijo, Nuno Candeias. Increased Antibacterial Properties of Indoline-Derived Phenolic Mannich Bases. . 2021; ():1.
Chicago/Turabian StyleTatu Rimpilainen; Alexandra Nunes; Rita Calado; Ana Fernandes; Joana Andrade; Epole Ngolle; Gabriella Spengler; Nikoletta Szemeredi; João Rodrigues; João Paulo Gomes; Patricia Rijo; Nuno Candeias. 2021. "Increased Antibacterial Properties of Indoline-Derived Phenolic Mannich Bases." , no. : 1.
Background Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Methods We conducted an investigation of a cluster of SARS-CoV-2 positive cases detected in a “non-COVID-19” hospital ward during Summer 2020. The magnitude of the nosocomial outbreak was disclosed by massive testing, challenging the retrospective reconstruction of the introduction and transmission events. An in-depth contact tracing investigation was carried out to identify the contacts network during the 15-day period before the screening. In parallel, positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Results Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among the vulnerable patient group reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain, thus confirming a single origin behind this nosocomial outbreak. By combining vast epidemiological and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination within the hospital ward, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to a more timely detection and containment of novel nosocomial outbreaks. Conclusions The present study shows the benefit of combining genomic and epidemiological data for the investigation of complex nosocomial outbreaks, and provides valuable data to minimize the risk of transmission of COVID-19 in healthcare facilities. Short summary SARS-CoV-2 nosocomial outbreaks are of utmost public health concern. Here, we performed an in-depth investigation of a high-fatality rate nosocomial outbreak by combining vast genomic and epidemiological data, providing valuable information to understand cryptic transmission of SARS-CoV-2 within healthcare institutions.
Vítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; Judite Catarino; Liliana Ciobanu; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes. Nosocomial outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward: virus genome sequencing as a key tool to understand cryptic transmission. 2021, 1 .
AMA StyleVítor Borges, Joana Isidro, Filipe Macedo, José Neves, Luís Silva, Mário Paiva, José Barata, Judite Catarino, Liliana Ciobanu, Sílvia Duarte, Luís Vieira, Raquel Guiomar, João Paulo Gomes. Nosocomial outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward: virus genome sequencing as a key tool to understand cryptic transmission. . 2021; ():1.
Chicago/Turabian StyleVítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; Judite Catarino; Liliana Ciobanu; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes. 2021. "Nosocomial outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward: virus genome sequencing as a key tool to understand cryptic transmission." , no. : 1.
Background Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. This unprecedented collaborative effort culminated in the generation of 1275 SARS-CoV-2 genome sequences, which represent 15.5% of all confirmed cases in March 2020, making Portugal one of the countries generating the highest volumes of SARS-CoV-2 genomic data during early COVID-19 pandemic. Methods We reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal using recent phylodynamic models that allow integration of individual-based travel history, in order to obtain a more realistic reconstruction of the viral dynamics. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy and Switzerland), which was broadly consistent with the available travel history data, as well as with the countries with most frequent connectivity and/or with the highest number of Portuguese immigrants. Although most introductions were estimated to have occurred during the last week of February and the first week of March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal several weeks before the first confirmed local cases on March 2, 2020. Discussion and Conclusion While the implemented preventive and early control measures seem to have been successful in mitigating community transmission from most independent introductions, our results suggest that their earlier implementation could have largely minimized the number of introductions and subsequent virus expansion. Here we lay the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlight the need for systematic, continuous and geographically-representative genomic surveillance to guide national and international public health authorities toward the characterization and control of SARS-CoV-2 circulating diversity.
V Borges; J Isidro; Ns Trovão; S Duarte; H Cortes-Martins; H Martiniano; I Gordo; R Leite; L Vieira; Portuguese network for SARS-CoV-2 genomics (Consortium); R Guiomar; Jp Gomes. The early dynamics of the SARS-CoV-2 epidemic in Portugal. 2021, 1 .
AMA StyleV Borges, J Isidro, Ns Trovão, S Duarte, H Cortes-Martins, H Martiniano, I Gordo, R Leite, L Vieira, Portuguese network for SARS-CoV-2 genomics (Consortium), R Guiomar, Jp Gomes. The early dynamics of the SARS-CoV-2 epidemic in Portugal. . 2021; ():1.
Chicago/Turabian StyleV Borges; J Isidro; Ns Trovão; S Duarte; H Cortes-Martins; H Martiniano; I Gordo; R Leite; L Vieira; Portuguese network for SARS-CoV-2 genomics (Consortium); R Guiomar; Jp Gomes. 2021. "The early dynamics of the SARS-CoV-2 epidemic in Portugal." , no. : 1.
Neisseria gonorrhoeae , the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing N. gonorrhoeae infections demands effective preventive measures, antibiotic treatment and epidemiological surveillance. The latter two are progressively being supported by the generation of whole-genome sequencing (WGS) data on behalf of national and international surveillance programmes. In this context, this study aims to perform N. gonorrhoeae clustering into genogroups based on WGS data, for enhanced prospective laboratory surveillance. Particularly, it aims to identify the major circulating WGS-genogroups in Europe and to establish a relationship between these and AMR. Ultimately, it enriches public databases by contributing with WGS data from Portuguese isolates spanning 15 years of surveillance. A total of 3791 carefully inspected N. gonorrhoeae genomes from isolates collected across Europe were analysed using a gene-by-gene approach (i.e. using cgMLST). Analysis of cluster composition and stability allowed the classification of isolates into a two-step hierarchical genogroup level determined by two allelic distance thresholds revealing cluster stability. Genogroup clustering in general agreed with available N. gonorrhoeae typing methods [i.e. MLST (multilocus sequence typing), NG-MAST ( N. gonorrhoeae multi-antigen sequence typing) and PubMLST core-genome groups], highlighting the predominant genogroups circulating in Europe, and revealed that the vast majority of the genogroups present a dominant AMR profile. Additionally, a non-static gene-by-gene approach combined with a more discriminatory threshold for potential epidemiological linkage enabled us to match data with previous reports on outbreaks or transmission chains. In conclusion, this genogroup assignment allows a comprehensive analysis of N. gonorrhoeae genetic diversity and the identification of the WGS-based genogroups circulating in Europe, while facilitating the assessment (and continuous monitoring) of their frequency, geographical dispersion and potential association with specific AMR signatures. This strategy may benefit public-health actions through the prioritization of genogroups to be controlled, the identification of emerging resistance carriage, and the potential facilitation of data sharing and communication.
Miguel Pinto; Vítor Borges; Joana Isidro; João Carlos Rodrigues; Luís Vieira; Maria José Borrego; João Paulo Gomes. Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance. Microbial Genomics 2021, 7, 000481 .
AMA StyleMiguel Pinto, Vítor Borges, Joana Isidro, João Carlos Rodrigues, Luís Vieira, Maria José Borrego, João Paulo Gomes. Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance. Microbial Genomics. 2021; 7 (2):000481.
Chicago/Turabian StyleMiguel Pinto; Vítor Borges; Joana Isidro; João Carlos Rodrigues; Luís Vieira; Maria José Borrego; João Paulo Gomes. 2021. "Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance." Microbial Genomics 7, no. 2: 000481.
Previously, we identified a Chlamydia trachomatis lymphogranuloma venereum (LGV) recombinant strain possessing a non-LGV ompA genotype. Here, culture-independent genome sequencing confirms its circulation in Europe, Middle East, and North America, and unveils emergence of antibiotic resistance. Broad surveillance is needed.
Vítor Borges; Joana Isidro; Cristina Correia; Dora Cordeiro; Luís Vieira; Zohra Lodhia; Cândida Fernandes; Ana Maria Rodrigues; Jacinta Azevedo; João Alves; João Roxo; Miguel Rocha; Rita Côrte-Real; Cristina Toscano; Maria Ana Pessanha; Israel Nissan; Shlomo Pilo; Efrat Rorman; Zeev Dveyrin; Yossi Paitan; Haim Paran; Gal Wagner-Kolasko; Jennifer Beirnes; Suzanne Gibbons; Alberto Severini; Maria José Borrego; João Paulo Gomes. Transcontinental Dissemination of the L2b/D-Da Recombinant Chlamydia trachomatis Lymphogranuloma venereum (LGV) Strain: Need of Broad Multi-Country Molecular Surveillance. Clinical Infectious Diseases 2021, 1 .
AMA StyleVítor Borges, Joana Isidro, Cristina Correia, Dora Cordeiro, Luís Vieira, Zohra Lodhia, Cândida Fernandes, Ana Maria Rodrigues, Jacinta Azevedo, João Alves, João Roxo, Miguel Rocha, Rita Côrte-Real, Cristina Toscano, Maria Ana Pessanha, Israel Nissan, Shlomo Pilo, Efrat Rorman, Zeev Dveyrin, Yossi Paitan, Haim Paran, Gal Wagner-Kolasko, Jennifer Beirnes, Suzanne Gibbons, Alberto Severini, Maria José Borrego, João Paulo Gomes. Transcontinental Dissemination of the L2b/D-Da Recombinant Chlamydia trachomatis Lymphogranuloma venereum (LGV) Strain: Need of Broad Multi-Country Molecular Surveillance. Clinical Infectious Diseases. 2021; ():1.
Chicago/Turabian StyleVítor Borges; Joana Isidro; Cristina Correia; Dora Cordeiro; Luís Vieira; Zohra Lodhia; Cândida Fernandes; Ana Maria Rodrigues; Jacinta Azevedo; João Alves; João Roxo; Miguel Rocha; Rita Côrte-Real; Cristina Toscano; Maria Ana Pessanha; Israel Nissan; Shlomo Pilo; Efrat Rorman; Zeev Dveyrin; Yossi Paitan; Haim Paran; Gal Wagner-Kolasko; Jennifer Beirnes; Suzanne Gibbons; Alberto Severini; Maria José Borrego; João Paulo Gomes. 2021. "Transcontinental Dissemination of the L2b/D-Da Recombinant Chlamydia trachomatis Lymphogranuloma venereum (LGV) Strain: Need of Broad Multi-Country Molecular Surveillance." Clinical Infectious Diseases , no. : 1.
Salmonella enterica serovars Heidelberg and Minnesota frequently display several genetic mobile elements making them potential spreaders of resistance genes. Here, we phenotypically determined the antibiotic resistance profile and subsequently performed whole-genome sequencing on 36 isolates recovered from samples of fresh poultry meat, within the Portuguese Official Inspection Plan for Imported Foodstuffs. Several isolates of both serovars showed high genetic relatedness either with isolates from raw poultry meat imported to the Netherlands from Brazil or with isolates from samples from the broiler production chain in Brazil. The multidrug-resistant (MDR) character was common to the vast majority (94.4%) of isolates from both serovars, and several isolates carried the plasmid IncA/C2 containing the β-lactamase gene blaCMY-2 and IncX1 containing a type IV secretion system. These results somehow mirror the scenario observed in the Netherlands, showing the introduction, through fresh imported poultry meat in compliance with European legislation, of MDR Salmonella enterica serovars Heidelberg and Minnesota in Europe, with the potential spread of resistance markers. These data suggest the need to revise the hygiene criteria for foodstuffs monitoring before its placement on the market, with the determination of the resistome being an invaluable contribute to limit the dissemination of resistance markers.
Leonor Silveira; Alexandra Nunes; Angela Pista; Joana Isidro; Cristina Belo Correia; Margarida Saraiva; Rita Batista; Isabel Castanheira; Jorge Machado; João Paulo Gomes. Characterization of Multidrug-Resistant Isolates of Salmonella enterica Serovars Heidelberg and Minnesota from Fresh Poultry Meat Imported to Portugal. Microbial Drug Resistance 2021, 27, 87 -98.
AMA StyleLeonor Silveira, Alexandra Nunes, Angela Pista, Joana Isidro, Cristina Belo Correia, Margarida Saraiva, Rita Batista, Isabel Castanheira, Jorge Machado, João Paulo Gomes. Characterization of Multidrug-Resistant Isolates of Salmonella enterica Serovars Heidelberg and Minnesota from Fresh Poultry Meat Imported to Portugal. Microbial Drug Resistance. 2021; 27 (1):87-98.
Chicago/Turabian StyleLeonor Silveira; Alexandra Nunes; Angela Pista; Joana Isidro; Cristina Belo Correia; Margarida Saraiva; Rita Batista; Isabel Castanheira; Jorge Machado; João Paulo Gomes. 2021. "Characterization of Multidrug-Resistant Isolates of Salmonella enterica Serovars Heidelberg and Minnesota from Fresh Poultry Meat Imported to Portugal." Microbial Drug Resistance 27, no. 1: 87-98.
Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity. In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.
Inês Silvestre; Alexandra Nunes; Vítor Borges; Joana Isidro; Catarina Silva; Luís Vieira; João Paulo Gomes; Maria José Borrego. Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains. 2020, 1 .
AMA StyleInês Silvestre, Alexandra Nunes, Vítor Borges, Joana Isidro, Catarina Silva, Luís Vieira, João Paulo Gomes, Maria José Borrego. Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains. . 2020; ():1.
Chicago/Turabian StyleInês Silvestre; Alexandra Nunes; Vítor Borges; Joana Isidro; Catarina Silva; Luís Vieira; João Paulo Gomes; Maria José Borrego. 2020. "Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains." , no. : 1.
Streptococcus agalactiae is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. One of the first S. agalactiae isolates to be subjected to whole genome sequencing was NEM316, a strain responsible for a fatal case of septicemia that has been widely used as reference strain for in vitro assays. Whole transcriptome analyses may provide an essential contribute to the understanding of the molecular mechanisms responsible for bacteria adaptation and pathogenicity, still, so far, very few studies were dedicated to the analysis of global gene expression of S. agalactiae. Here, we applied RNA-sequencing to perform a comparative overview of the global gene expression levels of the S. agalactiae reference strain NEM316 at the exponential growth phase. Genes were ranked by expression level and grouped by functional category and 46% of the top-100 expressed genes encode proteins involved in “Translation, ribosomal structure and biogenesis”. Among the group of highly expressed genes were also represented genes with no assigned functional category. Although this result warrants further investigation, most of them might be implicated in stress response. As very little is known about the molecular mechanisms behind the release of DNase’s in vitro and in vivo, we also performed preliminary assays to understand whether direct DNA exposure affects the gene expression of strain NEM316 at the exponential growth phase. No differentially expressed genes were detected, which indicates that follow-up studies are needed to disclose the complex molecular pathways (and stimuli) triggering the release of DNase’s. In general, we provide data on the global expression levels of NEM316 at exponential growth phase that may contribute to better understand S. agalactiae adaptation and virulence.
Inês Silvestre; Vítor Borges; Sílvia Duarte; Alexandra Nunes; Rita Sobral; Luís Vieira; João Paulo Gomes; Maria José Borrego. Global gene expression analysis of Streptococcus agalactiae at exponential growth phase. 2020, 1 .
AMA StyleInês Silvestre, Vítor Borges, Sílvia Duarte, Alexandra Nunes, Rita Sobral, Luís Vieira, João Paulo Gomes, Maria José Borrego. Global gene expression analysis of Streptococcus agalactiae at exponential growth phase. . 2020; ():1.
Chicago/Turabian StyleInês Silvestre; Vítor Borges; Sílvia Duarte; Alexandra Nunes; Rita Sobral; Luís Vieira; João Paulo Gomes; Maria José Borrego. 2020. "Global gene expression analysis of Streptococcus agalactiae at exponential growth phase." , no. : 1.
Mutations in the Spike motif predicted to correspond to the fusion peptide are considered of interest as this domain is a potential target for anti-viral drug development that plays a pivotal role in inserting SARS-CoV-2 into human cell membranes. We tracked the temporal and geographical spread of a SARS-CoV-2 variant with the Spike D839Y mutation in the fusion peptide, which was detected early during the COVID-19 epidemic in Portugal. We show that this variant was most likely imported from Italy in mid-late February 2020, becoming prevalent in the Northern and Central regions of Portugal, where represented 22% and 59% of the sampled genomes, respectively, until the end of April 2020. Based on our high sequencing sampling during the early epidemics [15,5% (1275/8251) and 6,0% (1500/24987) of all confirmed cases until the end of March and April, respectively)], we estimate that, between March 14th and April 9th (covering the exponential phase of the epidemic), the relative frequency of Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) at every three days, being potentially associated with one in each four (20.8-29.7%, CI 95%) COVID-19 cases in Portugal during the same period. This observation places the Spike Y839 variant in the origin of the largest SARS-CoV-2 transmission chain during the first month of the COVID-19 epidemic in Portugal. We hypothesize that population/epidemiological effects (founder effects) and enhanced selective advantage might have concomitantly contributed to the increasing frequency trajectory of the Spike Y839 variant. Screening of the D839Y mutation globally confirmed its detection in 12 additional countries, even though the huge differences in genome sampling between countries hampers any accurate estimate of D839Y global frequency. In summary, our data points out that SARS-CoV-2 Spike Y839 variants, namely the descendent variant of the globally spread G614 variant detected in Portugal, need continuous and close surveillance.
Vítor Borges; Joana Isidro; Helena Cortes-Martins; Sílvia Duarte; Luís Vieira; Ricardo Leite; Isabel Gordo; Constantino P. Caetano; Baltazar Nunes; Regina Sá; Ana Oliveira; Raquel Guiomar; João Paulo Gomes. On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: emergence and geotemporal spread of a highly prevalent variant in Portugal. 2020, 1 .
AMA StyleVítor Borges, Joana Isidro, Helena Cortes-Martins, Sílvia Duarte, Luís Vieira, Ricardo Leite, Isabel Gordo, Constantino P. Caetano, Baltazar Nunes, Regina Sá, Ana Oliveira, Raquel Guiomar, João Paulo Gomes. On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: emergence and geotemporal spread of a highly prevalent variant in Portugal. . 2020; ():1.
Chicago/Turabian StyleVítor Borges; Joana Isidro; Helena Cortes-Martins; Sílvia Duarte; Luís Vieira; Ricardo Leite; Isabel Gordo; Constantino P. Caetano; Baltazar Nunes; Regina Sá; Ana Oliveira; Raquel Guiomar; João Paulo Gomes. 2020. "On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: emergence and geotemporal spread of a highly prevalent variant in Portugal." , no. : 1.
To report the first case of a lung abscess caused by Neisseria meningitidis (Nm) and to genetically characterize the rare underlying capsule switching event. The strain (PT NmX) was subjected to whole genome sequencing, and a comparative gene-by-gene analysis was performed based on 1605 N. meningitidis core loci that constitute the MLST core-genome scheme (cgMLST) V1.0. All ~ 9,600 genomes available on Neisseria PubMLST (until 30th November 2019) from all serogroups were used to better identify the genome make-up of the PT NmX strain. This strain was found to be highly divergent from other NmX reported worldwide and to belong to a new sequence type (ST-14273), with the finetype X: P1.19,15-1:F5-2. Moreover, it revealed a closer genetic proximity to strains from serogroup B than to other serogroups, suggesting a genome backbone associated with serogroup B, while it presents a capsule synthesis region derived from a NmX strain. We describe a new hybrid NmB/X isolate from a noninvasive meningococcal infection, causing lung abscess. Despite capsular switching events involving serogroup X are rare, it may lead to the emergence of pathogenic potential. Studies should continue to better understand the molecular basis underlying Neisseria strains’ ability to spread to body compartments other than the tissues for which their tropism is already known.
Célia Bettencourt; Alexandra Nunes; Ana Maria Correia; João Paulo Gomes; Maria João Simões. Lung abscess due to Neisseria meningitidis serogroup X—unexpected virulence of a commensal resulting from putative serogroup B capsular switching. European Journal of Clinical Microbiology & Infectious Diseases 2020, 39, 2327 -2334.
AMA StyleCélia Bettencourt, Alexandra Nunes, Ana Maria Correia, João Paulo Gomes, Maria João Simões. Lung abscess due to Neisseria meningitidis serogroup X—unexpected virulence of a commensal resulting from putative serogroup B capsular switching. European Journal of Clinical Microbiology & Infectious Diseases. 2020; 39 (12):2327-2334.
Chicago/Turabian StyleCélia Bettencourt; Alexandra Nunes; Ana Maria Correia; João Paulo Gomes; Maria João Simões. 2020. "Lung abscess due to Neisseria meningitidis serogroup X—unexpected virulence of a commensal resulting from putative serogroup B capsular switching." European Journal of Clinical Microbiology & Infectious Diseases 39, no. 12: 2327-2334.
Aedes albopictus, along with Ae. aegypti, are key arbovirus vectors that have been expanding their geographic range over the last decades. In 2017, Ae. albopictus was detected for the first time at two distinct locations in Portugal. In order to understand how the Ae. albopictus populations recently introduced in Portugal are genetically related and which is their likely route of invasion, we performed an integrative cytochrome C oxidase I gene (COI)- and mitogenome-based phylogeographic analysis of mosquitoes samples collected in Portugal in 2017 and 2018 in the context of the global Ae. albopictus diversity. COI-based analysis (31 partial sequences obtained from 83 mosquitoes) revealed five haplotypes (1 to 5), with haplotype 1 (which is widely distributed in temperate areas worldwide) being detected in both locations. Haplotypes 2 and 3 were exclusively found in Southern region (Algarve), while haplotype 4 and 5 were only detected in the North of Portugal (Penafiel, Oporto region). Subsequent high discriminatory analyses based on Ae. albopictus mitogenome (17 novel sequences) not only confirmed a high degree of genetic variability within and between populations at both geographic locations (compatible with the Ae. albopictus mosquito populations circulating in Europe), but also revealed two mitogenome mutational signatures not previously reported at worldwide level. While our results generally sustain the occurrence of multiple introduction events, fine mitogenome sequence inspection further indicates a possible Ae. albopictus migration within the country, from the Northern introduction locality to the Southern region. In summary, the observed scenario of high Ae. albopictus genetic diversity in Portugal, together with the detection of mosquitoes in successive years since 2017 in Algarve and Penafiel, points that both Ae. albopictus populations seem to be already locally establish, as its presence has been reported for three consecutive years, raising the public health awareness for future mosquito-borne diseases outbreaks.Author SummaryIn 2017, Aedes albopictus was reported for the first time in Portugal at two distinct locations, in the premises of a tyre company in Penafiel, in the North, and nearby a golf course in Algarve, a tourism destination in the southernmost country region. The geographical spread of this species is boosted by larvae and desiccation-resistant eggs transport in aquatic trade goods, as tires and aquatic plants, and adult anthropophilic behavior that favors passive land transportation. In Portugal, especially in the Southern region, temperate climate conditions are adequate for adult mosquitoes survival most of the year. In a way to understand the genetic variability of Ae. albopictus populations introduced in Portugal, we analyzed 31 cytochrome C oxidase I gene (COI) partial sequences and 17 mitogenome sequences, integrating them in the context of the global Ae. albopictus phylogeographic diversity (i.e., 183 COI and 26 mitogenome sequences previously reported at worldwide level). Although COI haplotype 1 predominated, four additional haplotypes (2 to 5) were detected in Portugal. Subsequent in-depth mitogenome analysis revealed considerable genetic diversity, including not only sequences relating to mitogenomes reported mainly from Italy, Japan and China, but also two novel mitogenome mutational signatures.Our study indicate that Ae. albopictus is locally established in Portugal and intra-country dispersal may have already happened, highlighting the challenges for vector surveillance and control programs aiming at restraining arbovirus disease burden in the future.
Libia Ze-Ze; Vitor Borges; Hugo Costa Osório; Jorge Machado; Joao Paulo Gomes; Maria Joao Alves. Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal. 2020, 1 .
AMA StyleLibia Ze-Ze, Vitor Borges, Hugo Costa Osório, Jorge Machado, Joao Paulo Gomes, Maria Joao Alves. Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal. . 2020; ():1.
Chicago/Turabian StyleLibia Ze-Ze; Vitor Borges; Hugo Costa Osório; Jorge Machado; Joao Paulo Gomes; Maria Joao Alves. 2020. "Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal." , no. : 1.
Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities.
Luís Pinto; Carmen Torres; Concha Gil; Hugo Santos; José Luís Capelo; Vítor Borges; João Paulo Gomes; Catarina Silva; Luís Vieira; Patrícia Poeta; Gilberto Igrejas. Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-ResistantEnterococcus faecalisClinical Strain. OMICS: A Journal of Integrative Biology 2020, 24, 81 -95.
AMA StyleLuís Pinto, Carmen Torres, Concha Gil, Hugo Santos, José Luís Capelo, Vítor Borges, João Paulo Gomes, Catarina Silva, Luís Vieira, Patrícia Poeta, Gilberto Igrejas. Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-ResistantEnterococcus faecalisClinical Strain. OMICS: A Journal of Integrative Biology. 2020; 24 (2):81-95.
Chicago/Turabian StyleLuís Pinto; Carmen Torres; Concha Gil; Hugo Santos; José Luís Capelo; Vítor Borges; João Paulo Gomes; Catarina Silva; Luís Vieira; Patrícia Poeta; Gilberto Igrejas. 2020. "Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-ResistantEnterococcus faecalisClinical Strain." OMICS: A Journal of Integrative Biology 24, no. 2: 81-95.
Arcobacter butzleri is a foodborne emerging human pathogen, frequently displaying a multidrug resistant character. Still, the lack of comprehensive genome-scale comparative analysis has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. A. butzleri (genome size 2.07–2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small but diverse core-genome with 1165 genes. It presents a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a type I secretion system (T1SS) harboring another agglutinin and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) and other antibiotic resistant determinants. We unprecedentedly describe a genetic mechanism of A. butzleri macrolides resistance, (inactivation of a TetR repressor likely regulating an EP). Fluoroquinolones resistance correlated with Thr-85-Ile in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the main antigen PorA, we show that A. butzleri is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats indicates that phase variation likely modulates A. butzleri key adaptive functions. In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast and diverse virulence and antibiotic resistance arsenals that open a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.
Joana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen. Infection, Genetics and Evolution 2020, 80, 104213 .
AMA StyleJoana Isidro, Susana Ferreira, Miguel Pinto, Fernanda Domingues, Mónica Oleastro, João Paulo Gomes, Vítor Borges. Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen. Infection, Genetics and Evolution. 2020; 80 ():104213.
Chicago/Turabian StyleJoana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. 2020. "Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen." Infection, Genetics and Evolution 80, no. : 104213.