Carbapenem resistant Enterobacteriaceae colonization in patients admitted to the emergency department and in intensive care units: epidemiology, prevalence and risk factors

Enterobactérias resistentes a carbapenêmicos (ERC) já foram relatadas em todo o mundo e são associadas a altas taxas de mortalidade. A colonização intestinal atua como um reservatório e favorece a transmissão de mecanismos de resistência. O objetivo desta tese foi investigar a prevalência de pacientes portadores de CRE na admissão hospitalar, fatores de risco associados e a taxa de aquisição no Pronto Socorro (PS) e seu impacto na colonização por ERC na admissão em Unidades de Terapia Intensiva (UTI). Realizamos um estudo transversal com 676 pacientes admitidos no prontosocorro. Foram coletados swabs retais de pacientes na admissão e após uma semana, para cultura e para reação em cadeia da polimerase multiplex em tempo real (RT-PCR). Quarenta e seis pacientes (6,8%) foram colonizados e a taxa de aquisição foi de 18%. A exposição prévia à assistência médica no último ano, hepatopatia e uso de antibióticos no último mês foram fatores de risco para a colonização. Seis pacientes sem exposição prévia aos cuidados de saúde foram colonizados por ERC na admissão, sugerindo transmissão de ERC dentro da comunidade. No outro estudo, avaliamos o impacto de hospitalizações anteriores no setor de emergência na colonização por ERC na admissão na UTI. Neste estudo caso-controle, comparamos pacientes colonizados por ERC com pacientes que não foram colonizados na admissão na UTI. Os fatores de risco encontrados foram: tempo de internação no Pronto Socorro, aumentando a cada dia de internação, porém com maior impacto após o segundo dia, uso de carbapenem, Simplified Acute Physiology Score 3 (SAPS 3), endoscopia digestiva alta e transferência de outro hospital. O conjunto de achados desta tese demonstra que a internação no PS aumenta o risco de colonização por ERC no PS e leva ao aumento de risco de colonização por ERC na admissão na UTI. Nossos achados indicam que atuar no controle de ERC no PS ajudará a controlar a resistência a carbapenem nas UTIsCarbapenem Resistant Enterobacteriaceae (CRE) are worldwide reported and associated with high mortality rates. Intestinal colonization acts as a reservoir and fosters resistance mechanisms exchange. The aim of this thesis was to investigate the prevalence of patients harboring CRE on hospital admission, risk factors associated and the acquisition rate within the emergency department (ED) and its impact on colonization by CRE on admission to the Intensive Care Units (ICU). We conducted a cross-sectional study with 676 patients admitted to the ED. We collected rectal swabs from patients on admission, and after one week, for culture and for multiplex realtime polymerase chain-reaction (RT-PCR). Forty-six patients (6.8%) were colonized and the acquisition rate was 18%. Previous exposure to healthcare in the last year, hepatopathy and use of antibiotics in the last month were risk factors for colonization. Six patients with no previous exposure to healthcare were CRE-colonized on admission, suggesting transmission of CRE within the community. In the other study, we evaluated the impact of previous hospitalization in the emergency department on CRE colonization at ICU admission. In this case-control study we compared patients colonized by CRE to patients that were not colonized on admission to ICU. The risk factors found were emergency-department stay, increasing every day, but more importantly after 2 days of hospitalization in the ED, use of carbapenem, Simplified Acute Physiology Score (SAPS 3), upper digestive endoscopy, and transfer from another hospital. This thesis demonstrates that ED hospitalization increases the risk for CRE colonization and it has impacts on colonization on ICU admission. Our findings indicate that addressing problems in the ED will help to control carbapenem resistance in IC

SARS-CoV-2 Detection and Culture in Different Biological Specimens from Immunocompetent and Immunosuppressed COVID-19 Patients Infected with Two Different Viral Strains

Introduction—The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods—We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested via RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results—A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS-CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions—Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication