Pyomelanin biosynthetic pathway in pigment-producer strains from the pandemic Acinetobacter baumannii IC-5.

BACKGROUND: Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baumannii. OBJECTIVES: This study aimed to characterise the reddish-brown pigment produced by A. baumannii strains, and to determine its biosynthetic pathway by genomic approaches. METHODS: Pigment characterisation and antimicrobial susceptibility were conducted by phenotypic tests. The clonal relationship was obtained by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genome of an A. baumannii was obtained for characterisation of genes involved with pigment production. FINDINGS: The pyomelanin was the pigment produced by A. baumannii. Strains were extensively drug resistant and belonged to the IC-5/ST79. The pyomelanin biosynthetic pathway was determined and presented a particular architecture concerning the peripheral (tyrB, phhB and hpd) and central (hmgB, hmgC and hmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDE and a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEF and barAB) were characterised. MAIN CONCLUSION: There is a biosynthetic pathway compatible with the pyomelanin production observed in persistent A. baumannii IC-5 strains.

Acinetobacter baumannii infections in Amazon Region driven by extensively drug resistant international clones, 2016-2018.

BACKGROUND: Acinetobacter baumannii is a leading cause of nosocomial infections. This species is characterised by the presence of pandemic lineages (International Clones) that present a broad antimicrobial resistance profile. OBJECTIVE: To perform the molecular epidemiology of carbapenem-resistant A. baumannii from a clinical setting in the Amazon Basin, and to characterise their antimicrobial resistance determinants. METHODS: The genetic relationship of carbapenem-resistant A. baumannii were assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Class A, B and D ß-lactamase genes were screened by polymerase chain reaction (PCR) and sequencing. The antimicrobial susceptibility profile was obtained by Disc-diffusion method and minimum inhibitory concentration (MIC) determination. FINDINGS: All carbapenem-resistant A. baumannii strains belonged to three international clones, IC-1, IC-5 and IC-6, the latter recently reported by the first time in Brazil. The major determinant of carbapenem resistance in IC-1 and IC-5 strains was bla OXA-23, associated with ISAba1 and ISAba3, respectively, while IC-6 harboured the bla OXA-72. CONCLUSIONS: The A. baumannii epidemiology in Brazilian Amazon Region was unknown. It was demonstrated that A. baumannii XDR international clones were responsible for nosocomial infections in Boa Vista during 2016-2018, revealing that the epidemiological scenario of A. baumannii infections in Amazon Region resembles those from the cosmopolitan regions worldwide.

In-silico genomic characterization of Staphylococcus haemolyticus on a global scale: lineages, resistome, and virulome.

BACKGROUND: Staphylococcus haemolyticus belongs to the Coagulase-Negative Staphylococci (CoNS), exhibiting the highest levels of antibiotic resistance within this group of bacteria. This species has been increasingly implicated in nosocomial and animal infections worldwide, with a prevalence of methicillin-resistant Staphylococcus haemolyticus (MRSH). Most information about this organism comes from regional analyzes or with the absence of typing data, thus not revealing the real role of S. haemolyticus strains in world public health. METHODS: Here, we performed an enhanced global epidemiological analysis considering all available S. haemolyticus genomes from all continents, including genomes of nosocomial, environmental, and animal origin (n = 310). Furthermore, we added original genomic information from a clinical MRSH from the Brazilian Amazon region. The resistome and virulome of the genomes were associated with their mobilome, being inferred based on the presence of specific genes and databases such as CARD, VFDB, and PlasmidFinder, respectively. RESULTS: Phylogenetic analysis revealed three main groups, the main one covering most of the clinical clonal complex 3 (CC3) genomes in the world. The virulome of some genomes in this cluster showed the complete capsule operon (capA-capM). Importantly, this virulome trait could be associated with the mobilome, since the capsule operon, as well as a whole set of genes of the type VII secretion system, were observed in plasmids. In addition, the resistome of the main cluster (CC3) was larger, characterized mainly by the presence of the mecA gene, in addition to a set of other genes (aad, aac-aph, aph, erm), contrasting with the poor resistome of the other two clusters. Several insertion sequences were identified, some of them linked to specific clusters, and resistance genes, such as the rare cfrA (IS257). CONCLUSIONS: Therefore, successful lineages of CC3 S. haemolyticus causing human infections are widespread worldwide, raising concern about the impact of this scenario on public health.

In-depth analysis of Klebsiella aerogenes resistome, virulome and plasmidome worldwide.

Klebsiella aerogenes is an emergent pathogen associated with outbreaks of carbapenem-resistant strains. To date, studies focusing on K. aerogenes have been small-scale and/or geographically restricted. Here, we analyzed the epidemiology, resistome, virulome, and plasmidome of this species based on 561 genomes, spanning all continents. Furthermore, we sequenced four new strains from Brazil (mostly from the Amazon region). Dozens of STs occur worldwide, but the pandemic clones ST93 and ST4 have prevailed in several countries. Almost all genomes were clinical, however, most of them did not carry ESBL or carbapenemases, instead, they carried chromosomal alterations (omp36, ampD, ampG, ampR) associated with resistance to ß-lactams. Integrons were also identified, presenting gene cassettes not yet reported in this species (blaIMP, blaVIM, blaGES). Considering the virulence loci, the yersiniabactin and colibactin operons were found in the ICEKp10 element, which is disseminated in genomes of several STs, as well as an incomplete salmochelin cluster. In contrast, the aerobactin hypervirulence trait was observed only in one ST432 genome. Plasmids were common, mainly from the ColRNAI replicon, with some carrying resistance genes (mcr, blaTEM, blaNDM, blaIMP, blaKPC, blaVIM) and virulence genes (EAST1, senB). Interestingly, 172 genomes of different STs presented putative plasmids containing the colicin gene.

Emergence of a VIM-2-producing extensively drug-resistant (XDR) Pseudomonas aeruginosa ST309 in South America: a comparative genomic analysis.

Pseudomonas aeruginosa is considered a top priority pathogen associated with elevated morbidity and mortality. Worldwide outbreaks have been associated with a few high-risk epidemic P. aeruginosa lineages. However, the biological features involved in the persistence and spread of such lineages in clinical settings remain to be unravelled. This study reports the emergence of an extensively drug-resistant (XDR) sequence type 309 (ST309) P. aeruginosa in South America (Brazil), specifically in the Amazon region. Genomic analyses were performed with 42 complete and draft ST309 genomes, giving insights into its epidemiology, resistome and mobilome. A heterogeneous distribution of acquired antimicrobial resistance genes among ST309 genomes was observed, which included blaVIM-2, blaIMP-15 and qnrVC1, all associated with class 1 integrons. Mobilome mining showed the presence of integrative and conjugative elements (ICEs), transposons and genomic islands (GIs) harbouring a huge arsenal of heavy metal resistance determinants, which probably provided adaptive advantages to the ST309 lineage.

Global Genomic Epidemiology of Escherichia coli (ExPEC) ST38 Lineage Revealed a Virulome Associated with Human Infections.

BACKGROUND: Most of the extraintestinal human infections worldwide are caused by specific extraintestinal pathogenic Escherichia coli (ExPEC) lineages, which also present a zoonotic character. One of these lineages belongs to ST38, a high-risk globally disseminated ExPEC. To get insights on the aspects of the global ST38 epidemiology and evolution as a multidrug-resistant and pathogenic lineage concerning the three axes of the One Health concept (humans, animals, and natural environments), this study performed a global phylogenomic analysis on ST38 genomes. METHODS: A phylogenetic reconstruction based on 376 ST38 genomes recovered from environments, humans, livestock, and wild and domestic animals in all continents throughout three decades was performed. The global information concerning the ST38 resistome and virulome was also approached by in silico analyses. RESULTS: In general, the phylogenomic analyses corroborated the zoonotic character of the ExPEC ST38, since clonal strains were recovered from both animal and human sources distributed worldwide. Moreover, our findings revealed that, independent of host sources and geographic origin, the genomes were distributed in two major clades (Clades 1 and 2). However, the ST38 accessory genome was not strictly associated with clades and sub-clades, as found for the type 2 T3SS ETT2 that was evenly distributed throughout Clades 1 and 2. Of note was the presence of the Yersinia pestis-like high-pathogenicity island (HPI) exclusively in the major Clade 2, in which prevails most of the genomes from human origin recovered worldwide (2000 to 2020). CONCLUSIONS: This evidence corroborates the HPI association with successful E. coli ST38 establishment in human infections.

Emergence of extensively drug-resistant international clone IC-6 Acinetobacter baumannii carrying blaOXA-72 and blaCTX-M-115 in the Brazilian Amazon region.

OBJECTIVES: The extensively drug-resistant (XDR) Acinetobacter baumannii international clone VI (IC-6) has been identified worldwide since 2006. This study reports the emergence of IC-6 in the Brazilian Amazon region and reveals the particular genomic features considering its mobilome and resistome. METHODS: A total of 32 carbapenem-resistant A. baumannii strains recovered from Boa Vista city (Roraima, Brazil) in 2016 were characterised by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The whole genome sequences of the Brazilian IC-6 strains were obtained. The mobilome and resistome were assessed by in silico analyses. RESULTS: PFGE and MLST demonstrated that the 32 A. baumannii strains belonged to four clones. One XDR clone corresponded to the high-risk pandemic IC-6 lineage from ST944Oxf/78Pas. The IC-6 resistome was composed of aadA5, aac(3'')-IIa, aph(3')-Ia, armA, aadB, msrE, blaTEM-1, IS15DIV-blaCTX-M-115-IS15DIV, blaOXA-90, ISAba1-blaADC-152, blaOXA-72, qacEΔ1 and sul1. Mobilome prediction revealed that blaOXA-72 was embedded in a 15.5-kb plasmid and that it was flanked by putative XerC/D-binding sites, possibly involved in blaOXA-72 mobilisation. Several resistance genes were in a 48-kb multidrug resistance genomic island inserted in the chromosome, which also harboured genes involved in host pathogenicity and adaptive traits. Interestingly, the Brazilian strains shared the blaOXA-72 and blaCTX-M-115 with IC-6/ST944Oxf/78Pas recovered in a distinct spatiotemporal context, pointing to an epidemiological link among them. CONCLUSION: This study highlights the importance of surveillance of XDR A. baumannii strains, even outside of densely populated cosmopolitan regions, to reveal the epidemiology of pandemic lineages, stressing their threat to public health.

Riscos domiciliares: análises ambientais realizadas com pessoas idosas e enfermeiros da atenção primária à saúde / Domestic risks: environmental analyses carried out with elderly people and primary health care nurses

Objetivo: Analisar os riscos presentes no ambiente domiciliar das pessoas idosas. Métodos: Estudo exploratório-descritivo de abordagem qualitativa, desenvolvido na rede municipal de Atenção Primária à Saúde de Boa Vista -Roraima. O grupo social envolvido nesta investigação foi constituído por 22 participantes, distribuídos em dois subgrupos: 11 pessoas idosas e 11 enfermeiros que acompanham os idosos selecionados em seu domicílio. Foram realizadas entrevistas semiestruturadas e os achados foram analisados segundo o referencial teórico-analítico de conteúdo de Laurence Bardin. Resultados: Os riscos presentes no ambiente domiciliar das pessoas idosas foram organizados em três grandes dimensões categóricas: comportamentais, biológicas e físicos. Nesse sentido, ações como limpar, lavar, cozinhar, o uso ineficaz de medicamentos, hábitos alimentares inapropriados, diagnóstico de doenças crônicas, declínio das funções fisiológicas, vasos sanitários desalinhados, objetos no chão, uso de tapetes, piso liso, quebrado e molhado, foram considerados elementos indutores de risco à saúde da pessoa idosa em seu lar. Conclusão: A tríade comportamento, biologia e ambiente representou um complexo-chave para pensar os riscos que influenciam o processo saúde-doença das pessoas idosas domiciliadas a partir de análises nightingaleanas. Descritores: Ambiente Domiciliar; Atenção Primária à Saúde; Acidentes por Quedas; Vulnerabilidade em Saúde; Enfermagem Geriátrica.

Objective: To analyze the risks present in the home environment of elderly people.Methods: Exploratory-descriptive study with a qualitative approach, developed in the Primary Health Care municipal network of Boa Vista -Roraima. The social group involved in this investigation consisted of 22 participants, divided into two subgroups: 11 elderly people and 11 nurses who accompany theselected elderly in their homes. Semi-structured interviews were carried out and the findings were analyzed according to the theoretical-analytical framework of Laurence Bardin's content.Results: The current risks in the home environment of elderly people were organized into three major categorical dimensions: behavioral, biological and physical. In this sense, actions such as cleaning, washing, cooking, the ineffective use of medication, inappropriate eating habits, diagnosis of chronic diseases, declinein physiological functions, misaligned toilets, objects on the floor, use of rugs, smooth, broken and wet floors, they were considered risk-inducing elements to the health of the elderly person in their home. Conclusion: The triad of behavior, biology andenvironment represented a key-complex for thinking about the risks that influence the health-disease process of elderly people living at home based on Nightingale's analyses. Descriptors: Home Environment; Primary Health Care; Fall Accidents; Health Vulnerability; Geriatric Nursing.

Identificação precoce e tratamento inicial da sepse por enfermeiros da emergência / Early identification and initial treatment of sepsis by emergency nurses

Objetivo: Identificar o conhecimento dos enfermeiros atuantes no setor de emergência sobre a identificação e tratamento inicial da sepse. Métodos: Estudo descritivo, transversal, quantitativo, desenvolvido na emergência de um hospital público de Roraima, com 25 enfermeiros. Os dados sociodemográficos, ocupacionais e de conhecimento dos enfermeiros sobre sepse foram coletados por meio de um formulário estruturado online através do Google Forms e analisados utilizando-se estatística descritiva por meio do programa Statistical Package for the Social Sciences(SPSS) versão 20.0. Resultados: Dentre os participantes, 76,0% relataram não terem recebido treinamento sobre sepse e não possuírem conhecimento sobre a existência de protocolos de sepse na instituição. Quanto às questões específicas sobre sepse, 68,0% apresentaram conhecimento desatualizado sobre a definição atual e os sinais clínicos dasepse. O manejo inicial de sepse, tempo ideal para administrar a primeira dose do antibiótico e iniciar antibiótico de amplo espectro, foram as questões que obtiveram melhores percentuais de acerto, com 88,0% e 80,0%, respectivamente. Conclusão: Verificou-se que há lacunas no conhecimento dos enfermeiros da emergência sobre a identificação e o tratamento precoce da sepse, justificando a necessidade urgente de realização de capacitações e implantação de protocolos clínicos sobre o tema na instituição. Descritores:Identificação da Emergência. Sepse. Enfermeiras e Enfermeiros. Planejamento de Assistência ao Paciente. Emergências

Objective: To identify the knowledge of nurses working in the emergency sector about the identification and initial treatment of sepsis.Methods: Descriptive, cross-sectional, quantitative study, developed in the emergency room of a public hospital in Roraima, with 25 nurses. Sociodemographic, occupational and nurses' knowledge of sepsis data were collected by applying a structured online form using Google Forms and analyzed using descriptive statistics employing the Statistical Package for the Social Sciences (SPSS) version 20.0. Results:Among the participants, 76.0% reported not having received training on sepsis and not having knowledge about the existence of sepsis protocols in the institution. As for the specific questions about sepsis, 68.0% had outdated knowledge about the current definition and clinical signs of sepsis. The initial management of sepsis, the ideal time to administer the first dose of the antibiotic and start a broad-spectrum antibiotic, were the questions that obtained the best percentages of correct answers, with 88.0% and 80.0%, respectively. Conclusion:It was found that there are gaps in the knowledge of emergency nurses on the identification and early treatment of sepsis, justifying the urgent need for training and implementation of clinical protocols on the subject in the institution.Descriptors:Emergency Identification. Sepsis. Nurses. Patient Care Planning. Emergencies.

Factors associated with pneumonia in Yanomami children hospitalized for Ambulatory Care sensitive conditions in the north of Brazil. / Fatores associados à pneumonia em crianças Yanomami internadas por condições sensíveis à atenção primária na região norte do Brasil.

In developing countries, pneumonia is the leading cause of sickness and mortality in childhood, especially among vulnerable groups. The scope of this study was to analyze the factors associated with pneumonia in Yanomami children hospitalized for Ambulatory Care Sensitive Conditions (ACSC). Hospital admissions were divided into two groups: i) pneumonia; and ii) other causes, according to the Brazilian ACSC list. Adjusted hospitalization rates were estimated and unconditional logistic regression was used to analyze factors associated with pneumonia. Over 90% of the registered cases were considered ACSC. The adjusted rate of ACSC was 18.6/1000. The odds ratio of hospitalization for pneumonia was 2.7 (CI: 1.3-5.4) times higher in children aged between 0.1 and 5.9 months; 1.9 (CI: 1.1-3.3) times higher in children who were hospitalized for 8-14 days; and three (CI: 1.2-7.5) times higher in children with a secondary diagnosis of malnutrition. The excess of avoidable hospitalizations is a clear indication of the low quality of care and limited accessibility to primary health care in indigenous territories, which is contrary to the assistance model proposed by the indigenous healthcare subsystem in Brazil, which should in theory focus on welfare technologies based on primary health care.

Pyomelanin biosynthetic pathway in pigment-producer strains from the pandemic Acinetobacter baumannii IC-5

BACKGROUND Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baumannii. OBJECTIVES This study aimed to characterise the reddish-brown pigment produced by A. baumannii strains, and to determine its biosynthetic pathway by genomic approaches. METHODS Pigment characterisation and antimicrobial susceptibility were conducted by phenotypic tests. The clonal relationship was obtained by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genome of an A. baumannii was obtained for characterisation of genes involved with pigment production. FINDINGS The pyomelanin was the pigment produced by A. baumannii. Strains were extensively drug resistant and belonged to the IC-5/ST79. The pyomelanin biosynthetic pathway was determined and presented a particular architecture concerning the peripheral (tyrB, phhB and hpd) and central (hmgB, hmgC and hmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDE and a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEF and barAB) were characterised. MAIN CONCLUSION There is a biosynthetic pathway compatible with the pyomelanin production observed in persistent A. baumannii IC-5 strains.

Análise da cobertura vacinal em menores de cinco anos em um estado fronteiriço da Amazônia

Objetivou-se realizar uma análise temporal da cobertura vacinal em menores de cinco anos em um estado fronteiriço da região amazônica. Trata-se de um estudo quantitativo, epidemiológico, de série histórica, por meio de dados do Departamento de Informática do Sistema Único de Saúde (DATASUS) sobre a cobertura vacinal no estado de Roraima entre os anos de 2013 e 2017. De maneira geral, a cobertura vacinal mostrou-se instável no período analisado, apontando para um aumento nos anos de 2013 a 2015 e uma tendência de redução entre o período de 2015 a 2017 nas três esferas avaliadas (Brasil, Região Norte e Roraima). Todavia, o estado de Roraima apresentou indicadores acima da média nacional a partir de 2015. Com relação aos imunobiológicos, somente a BCG alcançou a meta preconizada em toda série histórica. Diante disso, verificou-se heterogeneidade nas coberturas quando avaliados os imunobiológicos isoladamente e houve uma redução geral na cobertura vacinal, apontando a necessidade de criar estratégias eficazes para direcionar as ações em saúde de maneira a controlar ou erradicar as doenças imunopreviníveis.

The objective was to carry out a temporal analysis of vaccine coverage in children under five years of age in a border state of the Amazon region. This is a qualitative, epidemiological study of a historical series, using data from the Department of Informatics of the Unified Health System (DATASUS) on vaccination coverage in the state of Roraima between 2013 and 2017. In general, vaccination coverage was unstable during the period analyzed, pointing to an increase in the years 2013- 2015 and a reduction trend between 2015 and 2017 in the three evaluated areas (Brazil, North Region and Roraima). However, the state of Roraima presented indicators above the national average as of 2015. With respect to immunobiologicals, only the BGC reached the goal recommended in all historical series. In view of this, heterogeneity in coverage was observed when immunobiologicals were evaluated separately and there was a general reduction in vaccination coverage, pointing out the need to create effective strategies to direct health actions in order to control or eradicate immunoprevalent diseases.

Fatores associados à pneumonia em crianças Yanomami internadas por condições sensíveis à atenção primária na região norte do Brasil / Factors associated with pneumonia in Yanomami children hospitalized for Ambulatory Care sensitive conditions in the north of Brazil

Resumo Em países em desenvolvimento, a pneumonia é a principal causa de adoecimento e morte na infância, principalmente em grupos vulneráveis. O objetivo deste estudo foi analisar os fatores associados à pneumonia em crianças Yanomami internadas por condições sensíveis à atenção primária (ICSAP). As internações foram divididas em dois grupos: i) pneumonias e ii) demais causas, de acordo com a lista brasileira de ICSAP. Foram estimadas taxas ajustadas de ICSAP e utilizou-se a regressão logística não condicional para analisar fatores associados. Mais de 90% dos registros foram considerados ICSAP. A taxa padronizada de ICSAP foi 18,6/1.000. As chances de internação por pneumonia foram 2,7 (IC: 1,3-5,4) vezes maiores em crianças de 0,1 a 5,9 meses; 1,9 (IC: 1,1-3,3) vezes maiores nas crianças que tiveram a duração da hospitalização variando de 8 a 14 dias; e 3,0 (IC: 1,2-7,5) vezes maiores nas crianças com diagnóstico secundário de desnutrição. O excesso de internações evitáveis é um forte indício da baixa qualidade das ações em terras indígenas e do limitado acesso à atenção primária, contrariando o modelo assistencial proposto pelo subsistema de saúde indígena no Brasil que, em tese, deveria privilegiar tecnologias assistenciais ancoradas na atenção primária.

Abstract In developing countries, pneumonia is the leading cause of sickness and mortality in childhood, especially among vulnerable groups. The scope of this study was to analyze the factors associated with pneumonia in Yanomami children hospitalized for Ambulatory Care Sensitive Conditions (ACSC). Hospital admissions were divided into two groups: i) pneumonia; and ii) other causes, according to the Brazilian ACSC list. Adjusted hospitalization rates were estimated and unconditional logistic regression was used to analyze factors associated with pneumonia. Over 90% of the registered cases were considered ACSC. The adjusted rate of ACSC was 18.6/1000. The odds ratio of hospitalization for pneumonia was 2.7 (CI: 1.3-5.4) times higher in children aged between 0.1 and 5.9 months; 1.9 (CI: 1.1-3.3) times higher in children who were hospitalized for 8-14 days; and three (CI: 1.2-7.5) times higher in children with a secondary diagnosis of malnutrition. The excess of avoidable hospitalizations is a clear indication of the low quality of care and limited accessibility to primary health care in indigenous territories, which is contrary to the assistance model proposed by the indigenous healthcare subsystem in Brazil, which should in theory focus on welfare technologies based on primary health care.