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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.
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.
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.
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.
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.
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.
Mycobacterium pinnipedii , the known causative agent of tuberculosis (TB) in marine mammals, was only recognised as a member of the Mycobacterium tuberculosis complex in 2003 [1] and is believed to cause TB in several species, including non-marine mammals [2, 3] and even humans [4]. The assumption of zoonotic transmission has been strongly reinforced by a disruptive study published in 2014 by an archaeologists team from Tübingen [5]. Based on archaeological and genomic investigations on millennial human skeletons, the authors implicated sea mammals infected with M. pinnipedii as a source of New World human TB. Considering that this phenomenon dates several centuries before the human migrations to South America, they refuted the previous scientific hypothesis of tuberculosis driven by human contact [6]. Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal . It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article. Conflict of interest: Dr. Macedo has nothing to disclose. Conflict of interest: Dr. Isidro has nothing to disclose. Conflict of interest: Dr. Gomes has nothing to disclose. Conflict of interest: Dr. Botelho has nothing to disclose. Conflict of interest: Dr. Albuquerque has nothing to disclose. Conflict of interest: Dr. Sogorb has nothing to disclose. Conflict of interest: Dr. Bernardino has nothing to disclose. Conflict of interest: Dr. Fernandes has nothing to disclose. Conflict of interest: Dr. Mourato has nothing to disclose. Conflict of interest: Dr. Durval has nothing to disclose. Conflict of interest: Dr. Gomes has nothing to disclose.
Rita Macedo; Joana Isidro; Maria Conceição Gomes; Ana Botelho; Teresa Albuquerque; Arlete Sogorb; Rui Bernardino; Teresa Lobo Fernandes; Teresa Mourato; Mário Durval; João Paulo Gomes. Animal-to-human transmission of Mycobacterium pinnipedii. European Respiratory Journal 2020, 2000371 .
AMA StyleRita Macedo, Joana Isidro, Maria Conceição Gomes, Ana Botelho, Teresa Albuquerque, Arlete Sogorb, Rui Bernardino, Teresa Lobo Fernandes, Teresa Mourato, Mário Durval, João Paulo Gomes. Animal-to-human transmission of Mycobacterium pinnipedii. European Respiratory Journal. 2020; ():2000371.
Chicago/Turabian StyleRita Macedo; Joana Isidro; Maria Conceição Gomes; Ana Botelho; Teresa Albuquerque; Arlete Sogorb; Rui Bernardino; Teresa Lobo Fernandes; Teresa Mourato; Mário Durval; João Paulo Gomes. 2020. "Animal-to-human transmission of Mycobacterium pinnipedii." European Respiratory Journal , no. : 2000371.
Probiotics are living microorganisms used as nutritional additives that confer health benefits on the host. Their use in food products is very attractive, especially if they could also inhibit important foodborne pathogens. In this study, antimicrobial activity against several foodborne pathogens was screened for 280 lactic acid bacteria (LAB) isolated from different food products and the probiotic characteristics of bacteriocinogenic isolates were evaluated. Seven out of 280 LAB isolates were selected due to their bacteriocinogenic properties and identified by 16S rRNA gene sequence analysis as Pediococcus pentosaceus (n = 6) and Lactobacillus plantarum (n = 1). Virulence factors and antibiotic resistances were not detected for any of the isolates. Except for L. plantarum R23, all the isolates were able to survive through the simulated gastrointestinal tract conditions. Only P. pentosaceus CFF4 was able to adhere to Caco-2 cells after the simulated gastrointestinal tract passage. In conclusion, even though in vivo studies should be performed, P. pentosaceus CFF4, which was also able to inhibit the growth of foodborne pathogens in vitro, seems to be a potential probiotic to be used in the food industry.
Ana Pinto; Joana Barbosa; Helena Albano; Joana Isidro; Paula Teixeira. Screening of Bacteriocinogenic Lactic Acid Bacteria and Their Characterization as Potential Probiotics. Microorganisms 2020, 8, 393 .
AMA StyleAna Pinto, Joana Barbosa, Helena Albano, Joana Isidro, Paula Teixeira. Screening of Bacteriocinogenic Lactic Acid Bacteria and Their Characterization as Potential Probiotics. Microorganisms. 2020; 8 (3):393.
Chicago/Turabian StyleAna Pinto; Joana Barbosa; Helena Albano; Joana Isidro; Paula Teixeira. 2020. "Screening of Bacteriocinogenic Lactic Acid Bacteria and Their Characterization as Potential Probiotics." Microorganisms 8, no. 3: 393.
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.
Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. 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 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%–18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8–29.7%, CI 95%; 3177–4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.
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. Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerging Microbes & Infections 2020, 9, 2488 -2496.
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. Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerging Microbes & Infections. 2020; 9 (1):2488-2496.
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. "Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal." Emerging Microbes & Infections 9, no. 1: 2488-2496.
Gastrointestinal infections caused by nontyphoidal Salmonella (NTS) remain one of the main causes of foodborne illness worldwide. Within the multiple existing Salmonella enterica serovars, the serovar Rissen is rarely reported, particularly as a cause of human salmonellosis. Between 2015 and 2017, the Portuguese National Reference Laboratory of Gastrointestinal Infections observed an increase in the number of clinical cases caused by multidrug-resistant (MDR) S. enterica serovar Rissen, particularly from the Azores archipelago. In the present study, we analyzed by whole genome sequencing (WGS) all clinical, animal, food, and environmental isolates received up to 2017 in the Portuguese Reference Laboratories. As such, through a wgMLST-based gene-by-gene analysis, we aimed to identify potential epidemiological clusters linking clinical and samples from multiple sources, while gaining insight into the genetic diversity of S. enterica serovar Rissen. We also investigated the genetic basis driving the observed multidrug resistance. By integrating 60 novel genomes with all publicly available serovar Rissen genomes, we observed a low degree of genetic diversity within this serovar. Nevertheless, the majority of Portuguese isolates showed high degree of genetic relatedness and a potential link to pork production. An in-depth analysis of these isolates revealed the existence of two major clusters from the Azores archipelago composed of MDR isolates, most of which were resistant to at least five antimicrobials. Considering the well-known spread of MDR between gastrointestinal bacteria, the identification of MDR circulating clones should constitute an alert to public health authorities. Finally, this study constitutes the starting point for the implementation of the “One Health” approach for Salmonella surveillance in Portugal.
Leonor Silveira; Miguel Pinto; Joana Isidro; Ângela Pista; Patrícia Themudo; Luís Vieira; Jorge Machado; João Paulo Gomes. Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal. International Journal of Genomics 2019, 2019, 1 -9.
AMA StyleLeonor Silveira, Miguel Pinto, Joana Isidro, Ângela Pista, Patrícia Themudo, Luís Vieira, Jorge Machado, João Paulo Gomes. Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal. International Journal of Genomics. 2019; 2019 ():1-9.
Chicago/Turabian StyleLeonor Silveira; Miguel Pinto; Joana Isidro; Ângela Pista; Patrícia Themudo; Luís Vieira; Jorge Machado; João Paulo Gomes. 2019. "Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal." International Journal of Genomics 2019, no. : 1-9.
Chlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.
Vítor Borges; Dora Cordeiro; Ana Isabel Salas; Zohra Lodhia; Cristina Correia; Joana Isidro; Cândida Fernandes; Ana Maria Rodrigues; Jacinta Azevedo; João Alves; João Roxo; Miguel Rocha; Rita Côrte-Real; Luís Vieira; Maria José Borrego; João Paulo Gomes. Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature. Microbial Genomics 2019, 5, e000313 .
AMA StyleVítor Borges, Dora Cordeiro, Ana Isabel Salas, Zohra Lodhia, Cristina Correia, Joana Isidro, Cândida Fernandes, Ana Maria Rodrigues, Jacinta Azevedo, João Alves, João Roxo, Miguel Rocha, Rita Côrte-Real, Luís Vieira, Maria José Borrego, João Paulo Gomes. Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature. Microbial Genomics. 2019; 5 (11):e000313.
Chicago/Turabian StyleVítor Borges; Dora Cordeiro; Ana Isabel Salas; Zohra Lodhia; Cristina Correia; Joana Isidro; Cândida Fernandes; Ana Maria Rodrigues; Jacinta Azevedo; João Alves; João Roxo; Miguel Rocha; Rita Côrte-Real; Luís Vieira; Maria José Borrego; João Paulo Gomes. 2019. "Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature." Microbial Genomics 5, no. 11: e000313.
Arcobacter butzleriis a food and waterborne bacteria and an emerging human pathogen, frequently displaying a multidrug resistant character. Still, no comprehensive genome-scale comparative analysis has been performed so far, which has limited our knowledge onA. butzleridiversification and pathogenicity. Here, we performed a deep genome analysis ofA. butzlerifocused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. In total, 49A. butzleristrains (collected from human, animal, food and environmental sources) were screened.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 core-genome with 1165 genes. The core-genome is highly diverse (≥55% of the core genes presenting at least 40/49 alleles), being enriched with genes associated with housekeeping functions. In contrast, the accessory genome presented a high proportion of loci with an unknown function, also being particularly overrepresented by genes associated with defence mechanisms.A. butzlerirevealed a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease clusterureD(AB)CEFG(phenotypically confirmed), the hypervariable hemagglutinin-encodinghecA, a putative type I secretion system (T1SS) harboring another agglutinin potentially related to adherence and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition,A. butzleriharbors a large repertoire of efflux pumps (EPs) (ten “core” and nine differentially present) and other antibiotic resistant determinants. We provide the first description of a genetic determinant of macrolides resistance inA. butzleri, by associating the inactivation of a TetR repressor (likely regulating an EP) with erythromycin resistance. Fluoroquinolones resistance correlated with the Thr-85-Ile substitution in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the porin- and adhesin-encoding main antigen PorA, this study strongly supports that this pathogen is able to exchangeporAas 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 detected potential phase-variable genes related to adaptation and host/environment interaction, such as lipopolysaccharide modification and motility/chemotaxis, suggesting that phase variation likely modulateA. butzlerikey adaptive functions.In summary, this study constitutes a turning point onA. butzlericomparative genomics revealing that this human gastrointestinal pathogen is equipped with vast virulence and antibiotic resistance arsenals, which, coupled with its remarkable core- and pan-genome diversity, opens a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.IMPACT STATEMENTDiarrhoeal diseases are the most common cause of human illness caused by foodborne hazards, but the surveillance of diarrhoeal diseases is biased towards the most commonly searched infectious agents (namelyCampylobacter jejuniandC. coli). In fact, other less studied pathogens are frequently found as the etiological agent when refined non-selective culture conditions are applied. A hallmark example is the diarrhoeal-causingArcobacter butzleriwhich, despite being also associated with extra-intestinal diseases, such as bacteremia in humans and mastitis in animals, and displaying high rates of antibiotic resistance, has not yet been profoundly investigated regarding its epidemiology, diversity and pathogenicity. To overcome the general lack of knowledge onA. butzlericomparative genomics, we provide the first comprehensive genome-scale analysis ofA. butzlerifocused on exploring the intraspecies virulome content and diversity, resistance determinants, as well as how this pathogen shapes its genome towards ecological adaptation and host invasion. The unveiled scenario ofA. butzlerirampant diversity and plasticity reinforces the pathogenic potential of this food and waterborne hazard, while opening multiple research lines that will certainly contribute to the future development of more robust species-oriented diagnostics and molecular surveillance ofA. butzleri.DATA SUMMARYA. butzleriraw sequence reads generated in the present study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441). The assembled contigs (.fasta and .gbk files), the nucleotide sequences of the predicted transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) are available athttp://doi.org/10.5281/zenodo.3434222. Detailed ENA accession numbers, as well as the draft genome statistics are described in Table S1.
Joana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. Virulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen. 2019, 775932 .
AMA StyleJoana Isidro, Susana Ferreira, Miguel Pinto, Fernanda Domingues, Mónica Oleastro, João Paulo Gomes, Vítor Borges. Virulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen. . 2019; ():775932.
Chicago/Turabian StyleJoana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. 2019. "Virulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen." , no. : 775932.
The increased popularity of raw milk consumption has created demand for relaxing legislation, despite the risk of contamination by pathogenic bacteria, notably STEC and C. jejuni . However, the epidemiology of these milk-borne pathogens on the herd level is still poorly understood, and data are lacking on the frequency of milk contamination on farms with cattle shedding these bacteria in their feces. This study suggests (i) that STEC contamination in milk can be reduced, but not prevented, by on-farm hygienic measures while fecal shedding is observable, (ii) that milk filters are more suitable sampling targets for monitoring than milk although pathogen detection from both sample matrices may be challenging, and (iii) that STEC and C. jejuni genotypes may persist in cattle herds for several months. The results can be utilized in developing and targeting pathogen monitoring and risk management on the farm level and contributed to the revision of Finnish legislation in 2017.
Anniina Jaakkonen; Hanna Castro; Saija Hallanvuo; Jukka Ranta; Mirko Rossi; Joana Isidro; Miia Lindström; Marjaana Hakkinen. Longitudinal Study of Shiga Toxin-Producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk. Applied and Environmental Microbiology 2019, 85, 1 .
AMA StyleAnniina Jaakkonen, Hanna Castro, Saija Hallanvuo, Jukka Ranta, Mirko Rossi, Joana Isidro, Miia Lindström, Marjaana Hakkinen. Longitudinal Study of Shiga Toxin-Producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk. Applied and Environmental Microbiology. 2019; 85 (7):1.
Chicago/Turabian StyleAnniina Jaakkonen; Hanna Castro; Saija Hallanvuo; Jukka Ranta; Mirko Rossi; Joana Isidro; Miia Lindström; Marjaana Hakkinen. 2019. "Longitudinal Study of Shiga Toxin-Producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk." Applied and Environmental Microbiology 85, no. 7: 1.
Background: Clostridium difficile infection (CDI) is prevalent in healthcare settings. The emergence of hypervirulent and antibiotic resistant strains has led to an increase in CDI incidence and frequent outbreaks. While the main virulence factors are the TcdA and TcdB toxins, antibiotic resistance is thought to play a key role in the infection by and dissemination of C. difficile. Methods: A CDI outbreak involving 12 patients was detected in a tertiary care hospital, in Lisbon, which extended from January to July, with a peak in February, in 2016. The C. difficile isolates, obtained from anaerobic culture of stool samples, were subjected to antimicrobial susceptibility testing with Etest®strips against 11 antibiotics, determination of toxin genes profile, PCR-ribotyping, multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). Results: Of the 12 CDI cases detected, 11 isolates from 11 patients were characterized. All isolates were tcdA-/tcdB+ and belonged to ribotype 017, and showed high level resistance to clindamycin, erythromycin, gentamicin, imipenem, moxifloxacin, rifampicin and tetracycline. The isolates belonged to four genetically related MLVA types, with six isolates forming a clonal cluster. Three outbreak isolates, each from a different MLVA type, were selected for WGS. Bioinformatics analysis showed the presence of several antibiotic resistance determinants, including the Thr82Ile substitution in gyrA, conferring moxifloxacin resistance, the substitutions His502Asn and Arg505Lys in rpoB for rifampicin resistance, the tetM gene, associated with tetracycline resistance, and two genes encoding putative aminoglycoside-modifying enzymes, aadE and aac(6′)-aph(2″). Furthermore, a not previously described 61.3 kb putative mobile element was identified, presenting a mosaic structure and containing the genes ermG, mefA/msrD and vat, associated with macrolide, lincosamide and streptogramins resistance. A substitution found in a class B penicillin-binding protein, Cys721Ser, is thought to contribute to imipenem resistance. Conclusion: We describe an epidemic, tcdA-/tcdB+, multidrug resistant clone of C. difficile from ribotype 017 associated with a hospital outbreak, providing further evidence that the lack of TcdA does not impair the infectious potential of these strains. We identified several determinants of antimicrobial resistance, including new ones located in mobile elements, highlighting the importance of horizontal gene transfer in the pathogenicity and epidemiological success of C. difficile.
Joana Isidro; Juliana Menezes; Mónica Serrano; Vítor Borges; Pedro Paixão; Margarida Mimoso; Filomena Martins; Cristina Toscano; Andrea Santos; Adriano O. Henriques; Mónica Oleastro. Genomic Study of a Clostridium difficile Multidrug Resistant Outbreak-Related Clone Reveals Novel Determinants of Resistance. Frontiers in Microbiology 2018, 9, 2994 .
AMA StyleJoana Isidro, Juliana Menezes, Mónica Serrano, Vítor Borges, Pedro Paixão, Margarida Mimoso, Filomena Martins, Cristina Toscano, Andrea Santos, Adriano O. Henriques, Mónica Oleastro. Genomic Study of a Clostridium difficile Multidrug Resistant Outbreak-Related Clone Reveals Novel Determinants of Resistance. Frontiers in Microbiology. 2018; 9 ():2994.
Chicago/Turabian StyleJoana Isidro; Juliana Menezes; Mónica Serrano; Vítor Borges; Pedro Paixão; Margarida Mimoso; Filomena Martins; Cristina Toscano; Andrea Santos; Adriano O. Henriques; Mónica Oleastro. 2018. "Genomic Study of a Clostridium difficile Multidrug Resistant Outbreak-Related Clone Reveals Novel Determinants of Resistance." Frontiers in Microbiology 9, no. : 2994.
In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole‐genome sequencing in surveillance and outbreak investigation of food‐borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross‐sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user‐centered design strategy involving the end‐users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand‐alone, portable, open‐source, end‐to‐end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species‐specific protocols that can be run using a user‐friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species‐specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene‐by‐gene methodology; quality control measures from raw reads to allele calling; reporting system; a built‐in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof‐of‐concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web‐sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open‐source software in genomic epidemiology.
Ann‐Katrin Llarena; Bruno Filipe Ribeiro‐Gonçalves; Diogo Nuno Silva; Jani Halkilahti; Miguel Paulo Machado; Mickael Santos Da Silva; Anniina Jaakkonen; Joana Isidro; Crista Hämäläinen; Jasmin Joenperä; Vítor Borges; Luís Vieira; João Paulo Gomes; Cristina Correia; Janne Lunden; Riikka Laukkanen‐Ninios; Maria Fredriksson-Ahomaa; Joseba Bikandi; Rosario San Millan; Ilargi Martinez‐Ballesteros; Lorena Laorden; Mihael Mäesaar; Lelde Grantina‐Ievina; Friederike Hilbert; Javier Garaizar; Mónica Oleastro; Mari Nevas; Saara Salmenlinna; Marjaana Hakkinen; João André Carriço; Mirko Rossi. INNUENDO: A cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens. EFSA Supporting Publications 2018, 15, 1 .
AMA StyleAnn‐Katrin Llarena, Bruno Filipe Ribeiro‐Gonçalves, Diogo Nuno Silva, Jani Halkilahti, Miguel Paulo Machado, Mickael Santos Da Silva, Anniina Jaakkonen, Joana Isidro, Crista Hämäläinen, Jasmin Joenperä, Vítor Borges, Luís Vieira, João Paulo Gomes, Cristina Correia, Janne Lunden, Riikka Laukkanen‐Ninios, Maria Fredriksson-Ahomaa, Joseba Bikandi, Rosario San Millan, Ilargi Martinez‐Ballesteros, Lorena Laorden, Mihael Mäesaar, Lelde Grantina‐Ievina, Friederike Hilbert, Javier Garaizar, Mónica Oleastro, Mari Nevas, Saara Salmenlinna, Marjaana Hakkinen, João André Carriço, Mirko Rossi. INNUENDO: A cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens. EFSA Supporting Publications. 2018; 15 (11):1.
Chicago/Turabian StyleAnn‐Katrin Llarena; Bruno Filipe Ribeiro‐Gonçalves; Diogo Nuno Silva; Jani Halkilahti; Miguel Paulo Machado; Mickael Santos Da Silva; Anniina Jaakkonen; Joana Isidro; Crista Hämäläinen; Jasmin Joenperä; Vítor Borges; Luís Vieira; João Paulo Gomes; Cristina Correia; Janne Lunden; Riikka Laukkanen‐Ninios; Maria Fredriksson-Ahomaa; Joseba Bikandi; Rosario San Millan; Ilargi Martinez‐Ballesteros; Lorena Laorden; Mihael Mäesaar; Lelde Grantina‐Ievina; Friederike Hilbert; Javier Garaizar; Mónica Oleastro; Mari Nevas; Saara Salmenlinna; Marjaana Hakkinen; João André Carriço; Mirko Rossi. 2018. "INNUENDO: A cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens." EFSA Supporting Publications 15, no. 11: 1.
We describe imipenem-resistant and imipenem-susceptible clinical isolates of Clostridium difficile ribotype 017 in Portugal. All ribotype 017 isolates carried an extra penicillin-binding protein gene, pbp5, and the imipenem-resistant isolates had additional substitutions near the transpeptidase active sites of pbp1 and pbp3. These clones could disseminate and contribute to imipenem resistance.
Joana Isidro; Andrea Santos; Alexandra Nunes; Vítor Borges; Catarina Silva; Luís Vieira; Aristides L. Mendes; Mónica Serrano; Adriano O. Henriques; João Paulo Gomes; Mónica Oleastro. Imipenem Resistance in Clostridium difficile Ribotype 017, Portugal. Emerging Infectious Diseases 2018, 24, 741 -745.
AMA StyleJoana Isidro, Andrea Santos, Alexandra Nunes, Vítor Borges, Catarina Silva, Luís Vieira, Aristides L. Mendes, Mónica Serrano, Adriano O. Henriques, João Paulo Gomes, Mónica Oleastro. Imipenem Resistance in Clostridium difficile Ribotype 017, Portugal. Emerging Infectious Diseases. 2018; 24 (4):741-745.
Chicago/Turabian StyleJoana Isidro; Andrea Santos; Alexandra Nunes; Vítor Borges; Catarina Silva; Luís Vieira; Aristides L. Mendes; Mónica Serrano; Adriano O. Henriques; João Paulo Gomes; Mónica Oleastro. 2018. "Imipenem Resistance in Clostridium difficile Ribotype 017, Portugal." Emerging Infectious Diseases 24, no. 4: 741-745.
The use of antimicrobial agents and acquired resistances explains in part the emergence and spreading of epidemic strains of . Continued use of antimicrobial therapy still represents an acute danger in triggering the emergence and spreading of new resistant and multiresistant strains including against first-line antibiotics. We examine the pathway of peptidoglycan synthesis in this organism and associated resistances, as well as resistance to other classes of antibiotics. The life cycle of involves growth, spore formation and germination. Spores endow the organism with a formidable capacity of persistence in the environment and in the host, resistance, dissemination and infectious potential. Highly resistant spores produced by antibiotic-resistant/multiresistant strains may be one of the most serious challenges we face in what concerns the containment of . Finally, we review recent developments in the treatment and prevention of infection.
Joana Isidro; Aristides Lopes Mendes; Mónica Serrano; Adriano O. Henriques; Mónica Oleastro. Overview of Clostridium difficile Infection: Life Cycle, Epidemiology, Antimicrobial Resistance and Treatment. Clostridium Difficile - A Comprehensive Overview 2017, 1 .
AMA StyleJoana Isidro, Aristides Lopes Mendes, Mónica Serrano, Adriano O. Henriques, Mónica Oleastro. Overview of Clostridium difficile Infection: Life Cycle, Epidemiology, Antimicrobial Resistance and Treatment. Clostridium Difficile - A Comprehensive Overview. 2017; ():1.
Chicago/Turabian StyleJoana Isidro; Aristides Lopes Mendes; Mónica Serrano; Adriano O. Henriques; Mónica Oleastro. 2017. "Overview of Clostridium difficile Infection: Life Cycle, Epidemiology, Antimicrobial Resistance and Treatment." Clostridium Difficile - A Comprehensive Overview , no. : 1.
Clostridium difficile infection (CDI) represents a great healthcare burden in developed countries. The emergence of the epidemic PCR ribotype (RT) 027 and its acquired fluoroquinolones resistance have accentuated the need for an active surveillance of CDI. Here we report the first countrywide study of CDI in Portugal with the characterization of 498 C. difficile clinical isolates, from 20 hospitals, comprising four regions in Portugal, regarding RT, virulence factors and antimicrobial susceptibility. We identified 96 RTs with marked variations between and within regions, as only six RTs appeared in all four regions. RT027 was the most frequent RT overall (18.5%) and among healthcare facility-associated isolates (19.6%), while RT014 was the most common among community-associated isolates (12%). The North showed a high RT diversity among isolates and a low moxifloxacin (MXF) resistance rate (11.9%), being the only region in which RT027 was not predominant. In contrast, the isolates from the Centre presented the highest RT027 frequency and 53.4% were resistant to MXF. Overall MXF resistance (33.2%) was associated (p<0.001) with the presence of binary toxin genes and mutations in tcdC regardless of the RT. Both traits appeared in almost 30% of the strains. RT027 showed a reduced susceptibility to metronidazole (p<0.01) and RT126 had higher MICs to vancomycin (p=0.03), when compared with other RTs. The present study highlights an unusual heterogeneity of RTs in Portugal, with a high frequency of hypervirulent RTs, and the emergence of virulence factors in non-027 RTs, emphasizing the need for a surveillance system for CDI in Portugal.
Andrea Santos; Joana Isidro; Catarina Silva; Luísa Boaventura; José Diogo; Alberta Faustino; Cristina Toscano; Mónica Oleastro. Molecular and epidemiologic study of Clostridium difficile reveals unusual heterogeneity in clinical strains circulating in different regions in Portugal. Clinical Microbiology and Infection 2016, 22, 695 -700.
AMA StyleAndrea Santos, Joana Isidro, Catarina Silva, Luísa Boaventura, José Diogo, Alberta Faustino, Cristina Toscano, Mónica Oleastro. Molecular and epidemiologic study of Clostridium difficile reveals unusual heterogeneity in clinical strains circulating in different regions in Portugal. Clinical Microbiology and Infection. 2016; 22 (8):695-700.
Chicago/Turabian StyleAndrea Santos; Joana Isidro; Catarina Silva; Luísa Boaventura; José Diogo; Alberta Faustino; Cristina Toscano; Mónica Oleastro. 2016. "Molecular and epidemiologic study of Clostridium difficile reveals unusual heterogeneity in clinical strains circulating in different regions in Portugal." Clinical Microbiology and Infection 22, no. 8: 695-700.