RESUMO
We reconstructed the SARS-CoV-2 epidemic caused by Omicron variant in Puerto Rico by sampling genomes collected during October 2021-May 2022. Our study revealed that Omicron BA.1 emerged and replaced Delta as the predominant variant in December 2021. Increased transmission rates and a dynamic landscape of Omicron sublineage infections followed.
Assuntos
COVID-19 , Epidemias , Humanos , Porto Rico/epidemiologia , SARS-CoV-2/genética , COVID-19/epidemiologiaRESUMO
Background: Puerto Rico has experienced the full impact of the COVID-19 pandemic. Since SARS-CoV-2, the virus that causes COVID-19, was first detected on the island in March of 2020, it spread rapidly though the island's population and became a critical threat to public health. Methods: We conducted a genomic surveillance study through a partnership with health agencies and academic institutions to understand the emergence and molecular epidemiology of the virus on the island. We sampled COVID-19 cases monthly over 19 months and sequenced a total of 753 SARS-CoV-2 genomes between March 2020 and September 2021 to reconstruct the local epidemic in a regional context using phylogenetic inference. Results: Our analyses reveal that multiple importation events propelled the emergence and spread of the virus throughout the study period, including the introduction and spread of most SARS-CoV-2 variants detected world-wide. Lineage turnover cycles through various phases of the local epidemic were observed, where the predominant lineage was replaced by the next competing lineage or variant after ~4 months of circulation locally. We also identified the emergence of lineage B.1.588, an autochthonous lineage that predominated in Puerto Rico from September to December 2020 and subsequently spread to the United States. Conclusions: The results of this collaborative approach highlight the importance of timely collection and analysis of SARS-CoV-2 genomic surveillance data to inform public health responses.
RESUMO
Puerto Rico has experienced the full impact of the COVID-19 pandemic. Since SARS-CoV-2, the virus that causes COVID-19, was first detected on the island in March of 2020, it spread rapidly though the islandâ™s population and became a critical threat to public health. We conducted a genomic surveillance study through a partnership with health agencies and academic institutions to understand the emergence and molecular epidemiology of the virus on the island. We sampled COVID-19 cases monthly over 19 months and sequenced a total of 753 SARS-CoV-2 genomes between March 2020 and September 2021 to reconstruct the local epidemic in a regional context using phylogenetic inference. Our analyses revealed that multiple importation events propelled the emergence and spread of the virus throughout the study period, including the introduction and spread of most SARS-CoV-2 variants detected world-wide. Lineage turnover cycles through various phases of the local epidemic were observed, where the predominant lineage was replaced by the next competing lineage or variant after approximately 4 months of circulation locally. We also identified the emergence of lineage B.1.588, an autochthonous lineage that predominated circulation in Puerto Rico from September to December 2020 and subsequently spread to the United States. The results of this collaborative approach highlight the importance of timely collection and analysis of SARS-CoV-2 genomic surveillance data to inform public health responses.
RESUMO
We reconstructed the 2016-2017 Zika virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic's origin, spread, and evolutionary dynamics. Our study revealed that the epidemic was propelled by multiple introductions that spread across the island, intricate evolutionary patterns, and ≈10 months of cryptic transmission.
Assuntos
Epidemias , Infecção por Zika virus , Zika virus , Evolução Molecular , Humanos , Porto Rico/epidemiologia , Zika virus/genética , Infecção por Zika virus/epidemiologiaRESUMO
The global expansion of dengue viruses (DENV-1 to DENV-4) has contributed to the divergence, transmission, and establishment of genetic lineages of epidemiological concern; however, tracking the phylogenetic relationships of these virus is not always possible due to the inability of standardized sequencing procedures in resource-limited public health laboratories. Consequently, public genomic data banks contain inadequate representation of geographical regions and historical periods. In order to improve detection of the DENV-1 to DENV-4 lineages, we report the development of a serotype-specific Sanger-based method standardized to sequence DENV-1 to DENV-4 directly from clinical samples using universal primers that detect most DENV genotypes. The resulting envelope protein coding sequences are analyzed for genotyping with phylogenetic methods. We evaluated the performance of this method by detecting, amplifying, and sequencing 54 contemporary DENV isolates, including 29 clinical samples, representing a variety of genotypes of epidemiological importance and global presence. All specimens were sequenced successfully and phylogenetic reconstructions resulted in the expected genotype classification. To further improve genomic surveillance in regions where dengue is endemic, this method was transferred to 16 public health laboratories in 13 Latin American countries, to date. Our objective is to provide an accessible method that facilitates the integration of genomics with dengue surveillance.
Assuntos
Vírus da Dengue/genética , Dengue/virologia , Técnicas de Genotipagem/métodos , Análise de Sequência de DNA/métodos , Dengue/epidemiologia , Vírus da Dengue/classificação , Genoma Viral/genética , Genótipo , Humanos , Filogenia , RNA Viral/sangue , RNA Viral/genética , Sorogrupo , Proteínas do Envelope Viral/genéticaRESUMO
Infections in the elderly patient are a challenge, since the classical signs of infection are absent or ill defined. The present paper describes the presentation, diagnosis, clinical manifestations and treatment for a selected group of potential serious infections including influenza, bacterial pneumonia, urinary tract infections as well as infections caused by multiresistant bacteria, like vacomycin-resistant enterococcus and methicillin resistant S. aureus. We conclude with the need for prevention in the older person with the use of vaccines, specifically the influenza and pneumococcal vaccine as well as the prevention of urinary infections. Influenza is a significant cause of morbidity, whose ill effects can be prevented in many older persons with the use of a vaccine. The use in prophylaxis and treatment of antiviral agents like amantadine, rimatadine, and oseltamivir is presented. Bacterial pneumonia is one of the leading causes of death in the USA among the older persons. The emergence of drug resistant Streptococcus pneumoniae leads to the consideration as empiric therapy the newer fluoroquinolones or the use of third or fourth generation cephalosporis. Of importance is the use of pneumococcal vaccine among people age 60 or above. The frequency of urinary tract infections among the elderly is of primary although in many instances important do not require treatment. When infection of the urinary tract is diagnosed, most authors use a fluoroquinolone as empiric theraphy. The emergence of multiresistant bacteria like methicillin resistant S. aureus and or vancomycin resistant enterococci leads to the need to consider new agents like quinipristin-dalfopristin, linezolid and deptomycin in the management of such patients.
Assuntos
Influenza Humana , Pneumonia Bacteriana , Infecções Urinárias , Fatores Etários , Idoso , Antibacterianos/administração & dosagem , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Antivirais/administração & dosagem , Antivirais/uso terapêutico , Farmacorresistência Bacteriana/efeitos dos fármacos , Humanos , Vacinas contra Influenza/administração & dosagem , Influenza Humana/diagnóstico , Influenza Humana/prevenção & controle , Influenza Humana/terapia , Pessoa de Meia-Idade , Vacinas Pneumocócicas/administração & dosagem , Pneumonia Bacteriana/diagnóstico , Pneumonia Bacteriana/prevenção & controle , Pneumonia Bacteriana/terapia , Infecções Urinárias/diagnóstico , Infecções Urinárias/prevenção & controle , Infecções Urinárias/terapiaRESUMO
Antibiotics are frequently prescribed in the older person, the dosification needs special care, since the pharmacokinetic parameters changes with aging and the side effects can be different in the older person. The creatinine clearance changes and we must modify the way we prescribe such antibiotics to the elderly, calculating. The variety of antibiotics now available led us to consider this paper in which we have presented the antimicrobial agents that can be considered in the treatment of the older person. We present several groups: the penicillins, cephalosporins, monobactams, carbapenems and betalactamase inhibitors or the great betalactam group. Other trimetroprin-sulfame-thoxazole, the newer macrolides (azithromycin and clarithromycin) as well as the aminoglycosides, vancomycin, clindamycin, metroridazole. The indications and contraindications are presented and reviewed.
Assuntos
Antibacterianos/uso terapêutico , Fatores Etários , Idoso , Aminoglicosídeos/administração & dosagem , Aminoglicosídeos/uso terapêutico , Antibacterianos/administração & dosagem , Antibacterianos/farmacocinética , Antibacterianos/farmacologia , Anti-Infecciosos/administração & dosagem , Anti-Infecciosos/uso terapêutico , Anti-Infecciosos Urinários/administração & dosagem , Anti-Infecciosos Urinários/uso terapêutico , Carbapenêmicos/administração & dosagem , Carbapenêmicos/uso terapêutico , Cefalosporinas/administração & dosagem , Cefalosporinas/uso terapêutico , Interações Medicamentosas , Fluoroquinolonas/administração & dosagem , Fluoroquinolonas/uso terapêutico , Humanos , Macrolídeos/administração & dosagem , Macrolídeos/uso terapêutico , Monobactamas/administração & dosagem , Monobactamas/uso terapêutico , Penicilinas/administração & dosagem , Penicilinas/uso terapêutico , Combinação Trimetoprima e Sulfametoxazol/administração & dosagem , Combinação Trimetoprima e Sulfametoxazol/uso terapêutico , Inibidores de beta-LactamasesRESUMO
Infections in the older person are common and a significant cause of morbidity and mortality. Infections of the urinary tract, skin and soft tissue infections including decubitus ulcers, antibiotics associated diarrhea and lower respiratory tract infections are particularly important in the elderly because of their frequency. While most initial antibiotic therapy is empiric, its important before treatment to try to document the etiology for better use of antibiotics. Infections of the urinary tract are frequently and potentially serious in the elderly, they must be separated from asymptomatic bacteriuria that requires no therapy. Upper and lower urinary tract infections are frequently caused by aerobic gram negative bacilli and or enterococci. Most authors prefer the use of fluoroquinolones to manage such infections. The elderly with decubitus ulcer presents a problem in management, since these are frequent polymicrobic infections in which anaerobes play an important role. The initial therapy usually involves the combination of a fluoroquinolone plus an antianaerobic agent like clindamycin. C. difficile diarrhea as frequent in nursing home residents as well as the older person with prior antibiotics. The treatment should be with metronidazole and avoid the use of vancomycin. Pneumonias in the elderly can be acquired in the community, the nursing home or during a hospitalization. The etiologic agents that predominate change from S. pneumoniae and atypicals in those from the community to an increase in gram negative pneumonia. The initial treatment as started by most authors as well as guidelines include the use of a new fluoroquinolone like gatifloxacin alone or in combination with a beta-lactamic agent like ceftriaxone. For those infections acquired in the hospital therapy with third or fourth generation cephalosporins, carbapenems, beta-lactams with betalactamase inhibitors alone or in combination with an aminoglucoside and or vancomycin if MRSA is suspected is accepted therapy.
Assuntos
Anti-Infecciosos/uso terapêutico , Pneumonia/tratamento farmacológico , Úlcera por Pressão/tratamento farmacológico , Dermatopatias Infecciosas/tratamento farmacológico , Infecções Urinárias/tratamento farmacológico , Idoso , Humanos , Pneumonia/diagnóstico , Pneumonia/microbiologia , Úlcera por Pressão/diagnóstico , Úlcera por Pressão/microbiologia , Dermatopatias Infecciosas/diagnóstico , Dermatopatias Infecciosas/microbiologia , Infecções Urinárias/diagnóstico , Infecções Urinárias/microbiologiaRESUMO
Se presenta el caso de un neonato a término, producto de madre portadora de dengue hemorrágico , quien desde las 72 horas de vida presentó signos de sepsis complicada con alteraciones hemorrágicas. Se confirmó la transmisiónvertical de la enfermedad por IgM específica para dengue positiva. Evolucionó satisfactoriamente. No se aisló serotipo viral
Assuntos
Humanos , Recém-Nascido , Dengue , Recém-Nascido , Transmissão Vertical de Doenças Infecciosas , Gravidez , Sepse , Pediatria , VenezuelaRESUMO
Se presenta el caso de un neonato a término de madre portadora de dengue hemorrágico, quien desde las 72 horas de vida presentó signos y síntomas de sepsis complicada con alteraciones hemorrágicas. Se confirmó la transmisión vertical de la enfermedad por IgM específica para dengue positiva. Evolucionó viral. No se aisló serotipo viral