Characterization of a new multidrug-resistant Brazilian K. pneumoniae isolate and 172 Klebsiella spp. sequenced strains: Genomic island, multilocus sequence typing and capsule locus dataset.

The genus Klebsiella comprises species that cause nosocomial and community-acquired infections. A dataset was created to compile the sequence type (ST) and capsule type (K-locus) information predicted for 172 worldwide isolates of Klebsiella spp. whose complete genomes could be retrieved from the GenBank (NCBI) repository. The dataset also includes information related to one multidrug-resistant strain (B31) isolated from a patient who was admitted to an intensive care unit in the Northeast region of Brazil. This strain was phenotypically characterized and submitted to whole-genome sequencing and comparative genomics analysis as we recently reported [1]. The dataset also compiles information on Pathogenicity Islands (PIs), Resistance Islands (RIs) and Miscellaneous Islands (MIS) present in the genome of strain B31. The information provided here may support outbreak prevention policies and future epidemiological studies involving Klebsiella spp.

Comparative genomics with a multidrug-resistant Klebsiella pneumoniae isolate reveals the panorama of unexplored diversity in Northeast Brazil.

The emergence of community acquired infections increases the public health concern on K. pneumoniae and closely related bacteria among which antimicrobial resistance spreads. We report a multidrug-resistant K. pneumoniae isolate, B31, of a patient infected in the community and admitted to an intensive care unit in Northeast Brazil. Antimicrobial susceptibility and genome information were thoroughly investigated to characterize B31 in front of 172 sequenced strains of different countries. Assigned to the Sequence Type 15, which is globally spread, B31 presented extended spectrum beta-lactamase, tigecycline and ciprofloxacin resistance. Genome sequencing revealed most resistance genes being carried by plasmids with high dissemination potential. The absence of main virulence factors, like yersiniabactin and colibactin, apparently suggests a mild pathogenic strain which, on the contrary, persisted and caused severe infection in a previously healthy patient. The present study contributes to unveil the unclear genomic scenario of virulent and multidrug-resistant K. pneumoniae in Brazil.

Prevalence of fungemia in a tertiary hospital: Analysis of the last decade.

INTRODUCTION: The prevalence of nosocomial fungemia has increased worldwide, and mortality caused by this disease is high. OBJECTIVE: To assess progress in the last decade, and the prevalence and profile of fungal agents isolated in blood cultures performed in a tertiary university hospital. METHOD: All the results of blood cultures processed at Hospital das Clínicas, Universidade Federal de Minas Gerais (HC-UFMG), in the time intervals 2001-2003 and 2011-2013 were analyzed retrospectively. For each three-year period, the number of collected blood cultures, the overall positivity rate and the percentage of fungemia were recorded. In addition, all identified fungal species were cataloged. All blood samples were incubated in the BacT/ALERT® (bioMérieux) automation system. RESULTS: In 2001-2003, 34,822 samples were evaluated, with 5,510 (15.8%) positive results. In 2011-2013, the number of blood cultures processed increased to 55,052 samples, with 4,873 (8.9%) positive results. There was an increase in the number of positive cultures for fungi in the analyzed period (2001-2003: 4.16%; 2011-2013: 5.95%; p<0.001). Among the agents, candidemias were predominant, especially those caused by non-albicans Candida species (2001-2003: 57.64%; 2011-2013: 65.17%; p<0.05). There was also an increase in fungemia caused by other genera (2001-2003: 2.62%; 2011-2013: 4.48%; p<0.01). CONCLUSION: There was an increase in the prevalence of fungemia in the last decade at HC-UFMG. Although candidemias have been responsible for most of the cases, there has been an increase in fungemias caused by other species.

Prevalence of fungemia in a tertiary hospital: Analysis of the last decade / Prevalência de fungemia em um hospital terciário: análise da última década

Summary Introduction: The prevalence of nosocomial fungemia has increased worldwide, and mortality caused by this disease is high. Objective: To assess progress in the last decade, and the prevalence and profile of fungal agents isolated in blood cultures performed in a tertiary university hospital. Method: All the results of blood cultures processed at Hospital das Clínicas, Universidade Federal de Minas Gerais (HC-UFMG), in the time intervals 2001-2003 and 2011-2013 were analyzed retrospectively. For each three-year period, the number of collected blood cultures, the overall positivity rate and the percentage of fungemia were recorded. In addition, all identified fungal species were cataloged. All blood samples were incubated in the BacT/ALERT® (bioMérieux) automation system. Results: In 2001-2003, 34,822 samples were evaluated, with 5,510 (15.8%) positive results. In 2011-2013, the number of blood cultures processed increased to 55,052 samples, with 4,873 (8.9%) positive results. There was an increase in the number of positive cultures for fungi in the analyzed period (2001-2003: 4.16%; 2011-2013: 5.95%; p<0.001). Among the agents, candidemias were predominant, especially those caused by non-albicans Candida species (2001-2003: 57.64%; 2011-2013: 65.17%; p<0.05). There was also an increase in fungemia caused by other genera (2001-2003: 2.62%; 2011-2013: 4.48%; p<0.01). Conclusion: There was an increase in the prevalence of fungemia in the last decade at HC-UFMG. Although candidemias have been responsible for most of the cases, there has been an increase in fungemias caused by other species.

Resumo Introdução: a prevalência de fungemia hospitalar tem aumentado em todo o mundo e a mortalidade por essa afecção é elevada. Objetivo: avaliar a evolução, na última década, da prevalência e do perfil dos agentes fúngicos isolados em hemoculturas realizadas em um hospital universitário terciário. Método: foram analisados retrospectivamente todos os resultados de hemocultura processados no Hospital das Clínicas da Universidade Federal de Minas Gerais (HC-UFMG), entre os períodos de 2001-2003 e de 2011-2013. Para cada triênio foram registrados o número de hemoculturas coletadas, o percentual de positividade geral e o percentual de fungemia. Também foram catalogadas todas as espécies fúngicas identificadas. Todas as amostras sanguíneas foram incubadas no sistema de automação BacT/ALERT® (bioMérieux). Resultados: entre 2001-2003, foram avaliadas 34.822 amostras, sendo 5.510 (15,8%) positivas. Entre 2011-2013, o número de hemoculturas processadas aumentou para 55.052 amostras, sendo 4.873 (8,9%) positivas. Observou-se um aumento do número de culturas positivas para fungos no período analisado (2001-2003: 4,16%; 2011-2013: 5,95%; p<0,001). Dentre os agentes, as candidemias foram predominantes, principalmente por espécies de Candida não albicans (2001-2003: 57,64%; 2011-2013: 65,17%; p<0,05). Houve também aumento da fungemia por outros gêneros (2001-2003: 2,62%; 2011-2013: 4,48%; p<0,01). Conclusão: houve aumento da prevalência de fungemia na última década no HC-UFMG. Embora as candidemias tenham sido responsáveis pela maioria dos casos, houve aumento de fungemias causadas por outras espécies.

Implementation of criteria for automatic release of clinical chemistry test results in a laboratory at an academic public hospital / Implantação de critérios de liberação automática de resultados de bioquímica em um laboratório de hospital público universitário

ABSTRACT Introduction: Autoverification is the release of laboratory test results from clinical instruments to hospital interface, or to patients' records, with no human intervention. Verification rules are inserted in the middleware and/or in the laboratory information system (LIS), based on criteria established by the laboratory. As a result, it ensures that every result is consistently reviewed in the same way, improving the entire verification process and patient safety. Objective: Describe the implementation of autoverification of clinical chemistry tests results at the core laboratory of Hospital das Clínicas da Universidade Federal de Minas Gerais (HC/UFMG), Brazil. Material and methods: Twenty-six automated chemistry assays were chosen. They were fully automated including internal quality control, interfaced with LIS, available 24 hours a day, seven days a week. Rules were set up in the middleware and in the LIS. Instrument flags, evaluation of sample integrity, test linearity, delta check and critical values were used to construct the verification algorithms. Results: An autoverification algorithm was constructed; delta check values were calculated and defined, as well as automatic verification ranges. The results retained for manual verification followed a flowchart prepared for this purpose. Conclusion: Autoverification implementation led to a more consistent reviewing process of test results, efficiency and improved patient safety.

RESUMO Introdução: A verificação automática dos resultados consiste na liberação dos resultados dos exames diretamente do equipamento, sem intervenção humana. São inseridas regras para avaliar os resultados no middleware e/ou no sistema de informação laboratorial (SIL), com base em critérios estabelecidos pelo laboratório. A autoverificação uniformiza os critérios de liberação e melhora a eficiência no processo, garantindo a segurança do paciente. Objetivo: Descrever a implantação da autoverificação nos testes bioquímicos do menu de urgência no Serviço de Medicina Laboratorial (SML) do Hospital das Clínicas da Universidade Federal de Minas Gerais (HC/UFMG). Material e métodos: Foram configurados 26 testes bioquímicos disponíveis 24 horas por dia, plenamente interfaceados, inclusive o controle interno da qualidade. Definiram-se parâmetros e algoritmos usados para configuração do SIL e no middleware. No algoritmo elaborado para autoverificação, foram incluídos flags de equipamento, presença de interferentes na amostra, linearidade, delta check e valores críticos. Resultados O algoritmo de liberação automática de resultados, os valores de delta check, os intervalos de liberação automática e o fluxograma para liberação manual dos resultados retidos foram definidos e implantados. Conclusão: A implantação da autoverificação nos testes bioquímicos do menu de urgência no serviço possibilitou padronização e segurança na liberação dos resultados.