Surveillance of multi-resistant microrganisms and epidemiological investigation of intensive care unit patients: Análise de parâmetros relevantes em culturas de vigilância epidemiológica de pacientes internados no centro de tratamento intensivo e colonizados por microrganismos multirresistentes

It is of great importance to detect the presence of microorganisms in healthcare services. On this basis, strategies should be developed to maintain safety inside the hospital environment by preventing the transmission of microorganisms, thus preventing healthcare-associated infections (HAI). In the Intensive Care Unit (ICU), the precocious detection of infection and/or colonization by multidrug-resistant (MDR) microorganisms is key. For this reason, the routine monitoring of patients that are infected or colonized by MDR microorganisms is mandatory. In this context, this study aimed to evaluate the performance of epidemiological surveillance swabs and microbiological cultures in ICU patients in a university public hospital in Belo Horizonte, Minas Gerais State, Brazil. Medical records of patients admitted to the ICU from January 1st, 2018 to December 31st, 2020, submitted to epidemiological surveillance cultures, and presenting factors correlated to the development of HAI were evaluated. This was a descriptive, retrospective and observational, non-interventional study. The study population was composed mainly of male patients (66.3%), with a mean age of 59 years, coming from the Medical Clinic department, and septicemia was the main cause of hospitalization in the ICU. The analyses showed that 9.5% of the patients were colonized by MDR microorganisms. The samples were collected at the ICU, and a higher frequency of gram-negative bacteria was observed, including A. baumannii, P. aeruginosa, K. pneumoniae, and carbapenem-resistant Enterobacteriaceae. The most frequently prescribed antimicrobials were β-lactams and glycopeptides, and the same patient was treated using more than one class of antimicrobials. The surveillance culture is key to understanding the microbiological profile of the institution. The collection of swabs and microbiological cultures from different sites could be used to adopt routines and recommend measures aimed at controlling and reducing the HAI rates as well as the emergence of MDR outbreaks. These procedures could contribute to the creation and maintenance of a safe and effective healthcare service

Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone

The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids’ transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem

Relationship between clinical-epidemiological parameters and outcomes of patients with COVID-19 admitted to the intensive care unit: a report from a Brazilian hospital

BackgroundPeople in low-income countries, especially those with low socio-economic conditions, are likelier to test positive for SARS-CoV-2. The unequal conditions of public health systems also increase the infection rate and make early identification and treatment of at-risk patients difficult. Here, we aimed to characterize the epidemiological profile of COVID-19 patients in intensive care and identify laboratory and clinical markers associated with death.Materials and methodsWe conducted an observational, descriptive, and cross-sectional study in a reference hospital for COVID-19 treatment in the Southern Region of Bahia State, in Brazil, to evaluate the epidemiological, clinical, and laboratory characteristics of COVID-19 patients admitted to the intensive care unit (ICU). Additionally, we used the area under the curve (AUC) to classify survivors and non-survivors and a multivariate logistic regression analysis to assess factors associated with death. Data was collected from the hospital databases between April 2020 and July 2021.ResultsThe use of bladder catheters (OR 79.30; p < 0.0001) and central venous catheters (OR, 45.12; p < 0.0001) were the main factors associated with death in ICU COVID-19 patients. Additionally, the number of non-survivors increased with age (p < 0.0001) and prolonged ICU stay (p < 0.0001). Besides, SAPS3 presents a higher sensibility (77.9%) and specificity (63.1%) to discriminate between survivors and non-survivor with an AUC of 0.79 (p < 0.0001).ConclusionWe suggest that multi-laboratory parameters can predict patient prognosis and guide healthcare teams toward more assertive clinical management, better resource allocation, and improved survival of COVID-19 patients admitted to the ICU

Estudo comparativo e validação de três técnicas de PCR em tempo real (qPCR) para diagnóstico de Peste Suína Africana

Resumo: Este estudo verificou o desempenho de três técnicas de PCR quantitativa (Real-Time) para o diagnóstico de Peste Suína Africana, uma doença exótica no Brasil, a partir de amostras de tecidos. As três técnicas escolhidas baseiam-se na amplificação de sequências do gene da proteína viral VP72 e são preconizadas, cada uma, por laboratórios oficiais da OIE (PSA-OIE), dos Estados Unidos (PSA-USDA) e da União Europeia (PSA-EU), respectivamente. Oligonucleotídeos iniciadores e sondas de hidrólise marcadas com fluoróforos foram sintetizados conforme a literatura de referência consultada. Sequências-alvo do DNA viral foram inseridos em plasmídeo sintético, os quais serviram de controle positivo para a padronização das técnicas e otimização de reagentes, determinação dos limites de detecção e testes de verificação de desempenho. Para aferição de repetibilidade e reprodutibilidade das técnicas, as técnicas padronizadas foram repetidas em dias diferentes, por um segundo analista, com alteração no mix comercial de reagentes utilizado e em um equipamento diferente, e também por outro laboratório. Realizaram-se, ainda, provas de sensibilidade analítica com amostras de DNA viral de referência e especificidade analítica e diagnóstica, com amostras negativas. As técnicas de PSA-EU e PSA-USDA apresentaram-se mais vantajosas quanto ao consumo de iniciadores. Não houve diferenças significativas nos resultados quantitativos variando-se os dias dos ensaios, os analistas, os equipamentos e o mix de reagentes. As três técnicas apresentaram alta especificidade analítica e diagnóstica e sensibilidade diagnóstica. As três técnicas de qPCR mostraram-se eficazes para serem adotadas por um mesmo laboratório para emissão de diagnósticos oficiais de Peste Suína Africana

PARÂMETROS CLÍNICOS E EPIDEMIOLÓGICOS NA COVID-19 E SUA CORRELAÇÃO COM ÓBITO EM PACIENTES ATENDIDOS EM UNIDADE DE TERAPIA INTENSIVA (UTI)

Introdução/Objetivo: Uma estratégia para compreender a forma grave da COVID-19 está voltada para avaliação de marcadores epidemiológicos, laboratoriais e clínicos capazes de predizer óbito. O presente estudo analisou marcadores epidemiológicos, biomarcadores clínicos e laboratoriais em participantes com COVID-19 grave internados em hospital de referência para tratamento da COVID-19 em Ilhéus/BA, com objetivo de determinar quais marcadores poderiam ser usados como preditores do óbito. Métodos: O estudo foi submetido ao CEP/UESC, aprovado sob CAAE n° 40671720.4.0000.5526. Realizado entre 11/06/2020 a 30/07/2021, onde foram coletados dados epidemiológicos, laboratoriais e clínicos dos prontuários de pacientes internados na UTI de um hospital de referência para COVID-19 em Ilhéus e cidades vizinhas, situadas no Sul da Bahia. Os dados foram registrados no software Epimed Monitor, passando por tratamento estatístico, respeitando categoria da variável: quantitativa ou categórica. As análises foram realizadas por softwares GraphPad Prism 9.0 e Statistical Package for Social Sciences 26.0. A classificação de sobreviventes e não sobreviventes foi analisada via curva ROC pelo método de Wilson/Brown. O estudo englobou 218 participantes com média de idade de 64,37SD± 15,16, 123 do sexo masculino e 95 do sexo feminino. 77 vieram a óbito. Resultados: As análises estatísticas evidenciaram idade superior a 65 anos (ponto de corte >66.5; p 40.5; p 0,895; p 19.4; p 1.350, p = 0.0035.) dosagem de pH arterial (ponto de corte 10.03; p 11,5; p < 0,001) foram associados ao óbito, correlacionados a injúria sistêmica. Conclusão: Os marcadores epidemiológicos, laboratoriais e clínicos encontrados neste estudo podem ser usados pela equipe clínica como preditores para óbito em pacientes com COVID-19

Table_1_Relationship between clinical-epidemiological parameters and outcomes of patients with COVID-19 admitted to the intensive care unit: a report from a Brazilian hospital.DOCX

BackgroundPeople in low-income countries, especially those with low socio-economic conditions, are likelier to test positive for SARS-CoV-2. The unequal conditions of public health systems also increase the infection rate and make early identification and treatment of at-risk patients difficult. Here, we aimed to characterize the epidemiological profile of COVID-19 patients in intensive care and identify laboratory and clinical markers associated with death.Materials and methodsWe conducted an observational, descriptive, and cross-sectional study in a reference hospital for COVID-19 treatment in the Southern Region of Bahia State, in Brazil, to evaluate the epidemiological, clinical, and laboratory characteristics of COVID-19 patients admitted to the intensive care unit (ICU). Additionally, we used the area under the curve (AUC) to classify survivors and non-survivors and a multivariate logistic regression analysis to assess factors associated with death. Data was collected from the hospital databases between April 2020 and July 2021.ResultsThe use of bladder catheters (OR 79.30; p ConclusionWe suggest that multi-laboratory parameters can predict patient prognosis and guide healthcare teams toward more assertive clinical management, better resource allocation, and improved survival of COVID-19 patients admitted to the ICU.</p

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved