Impact of In-Hospital infection with SARS-CoV-2 among Inpatients at a university hospital.

OBJECTIVE: The objective of this study was to evaluate the incidence of nosocomial infection and the impact of cross-transmission of SARS-CoV-2 among inpatients at a tertiary care teaching hospital. METHODS: This was a retrospective cohort study involving inpatients admitted to a tertiary university hospital in the city of São Paulo, Brazil, between March 2020 and February 2021. Cases were identified on the basis of a positive reverse-transcription polymerase chain reaction result for SARS-CoV-2 and the review of electronic medical records. Nosocomial transmission was defined by applying the criteria established by the Brazilian National Health Regulatory Agency. RESULTS: We identified 2146 cases of SARS-CoV-2 infection, 185 (8.6%) of which were considered cases of nosocomial transmission. The mean age was 58.3 years. The incidence density was 1.78 cases per 1,000 patient-days on the general wards, being highest on the cardiac surgery ward, and only 0.16 per 1,000 patient-days on the COVID-19 wards. Of the 185 patients evaluated, 115 (62.2%) were men, 150 (81.1%) cases had at least one comorbidity, and 104 (56.2%) evolved to death. CONCLUSIONS: Despite the preventive measures taken, nosocomial transmission of SARS-CoV-2 occurred throughout our hospital. Such measures should be intensified when the incidence of community transmission peaks.

Pseudomonas aeruginosa in the ICU: prevalence, resistance profile, and antimicrobial consumption

Abstract INTRODUCTION: Pseudomonas aeruginosa is one of the main pathogens causing infection in intensive care units (ICUs) and usually presents antimicrobial resistance. METHODS: Data were obtained from ICUs between 2010 and 2013. RESULTS: P. aeruginosa had a prevalence of 14.5% of which 48.7% were multidrug resistant. We observed increasing resistance to carbapenems and polymyxin B and growing consumption of aminoglycosides, meropenem, ceftazidime, and polymyxin B. The regression impact between resistance and consumption was significant with respect to amikacin, imipenem, meropenem, and polymyxin B. CONCLUSIONS: Monitoring antimicrobial consumption and resistant microorganisms should be reinforced to combat antimicrobial- and multi-drug resistance.

Pseudomonas aeruginosa in the ICU: prevalence, resistance profile, and antimicrobial consumption.

INTRODUCTION: Pseudomonas aeruginosa is one of the main pathogens causing infection in intensive care units (ICUs) and usually presents antimicrobial resistance. METHODS: Data were obtained from ICUs between 2010 and 2013. RESULTS: P. aeruginosa had a prevalence of 14.5% of which 48.7% were multidrug resistant. We observed increasing resistance to carbapenems and polymyxin B and growing consumption of aminoglycosides, meropenem, ceftazidime, and polymyxin B. The regression impact between resistance and consumption was significant with respect to amikacin, imipenem, meropenem, and polymyxin B. CONCLUSIONS: Monitoring antimicrobial consumption and resistant microorganisms should be reinforced to combat antimicrobial- and multi-drug resistance.

Comparison of DNA Extraction Protocols and Molecular Targets to Diagnose Tuberculous Meningitis.

Tuberculous meningitis (TBM) is a severe form of extrapulmonary tuberculosis. The aims of this study were to evaluate in-house molecular diagnostic protocols of DNA extraction directly from CSF samples and the targets amplified by qPCR as an accurate and fast diagnosis of TBM. One hundred CSF samples from 68 patients suspected of TBM were studied. Four DNA extraction techniques (phenol-chloroform-thiocyanate guanidine, silica thiocyanate guanidine, resin, and resin with ethanol) were compared and CSF samples were used to determine the best target (IS6110, MPB64, and hsp65 KDa) by qPCR. The extraction protocol using the phenol-chloroform-thiocyanate guanidine showed the best results in terms of quantification and sensitivity of PCR amplification, presenting up to 10 times more DNA than the second best protocol, the silica guanidine thiocyanate. The target that showed the best result for TBM diagnosis was the IS6110. This target showed 91% sensitivity and 97% specificity when we analyzed the results by sample and showed 100% sensitivity and 98% specificity when we analyzed the results by patient. The DNA extraction with phenol-chloroform-thiocyanate guanidine followed by IS6110 target amplification has been shown to be suitable for diagnosis of TBM in our clinical setting.

Perfil microbiológico da unidade de queimaduras da EPM/UNIFESP, São Paulo, Brasil / Microbiological surveillance of burn unit of EPM/UNIFESP in São Paulo, Brazil

Introdução: Apesar dos grandes avanços em seu tratamento, infecção de pele com queimadura continua a ser um grande desafio. O objetivo deste estudo é avaliar os aspectos microbiológicos do primeiro ano de funcionamento de uma unidade de queimadura em um Hospital Universitário. Métodos: Estudo retrospectivo. Dados microbiológicos foram coletados e analisados a partir de pacientes internados na Unidade de Queimadura (UTQ) do Hospital São Paulo, Hospital Universitário da Escola Paulista de Medicina (EPM) da Universidade Federal de São Paulo (UNIFESP), entre junho de 2009 e julho de 2010. Resultados: O tempo médio de permanência hospitalar foi de 13,8 dias, com uma taxa de mortalidade de 5,9%. A média da superfície corpórea queimada foi de 10,3%. Avaliou-se 159 culturas de 101 pacientes. Culturas de sangue foram as mais solicitadas (41%). Também foram acessadas 245 culturas de vigilância, coletadas de 75 pacientes. A análise microbiológica revelou um índice de positividade total de 34,5%. Os agentes mais prevalentes foram Staphylococcus coagulase-negativo - CoNS - (33%), Pseudomonas aeruginosa (24%), Acinetobacter spp. (22%) e Klebsiella pneumoniae (5%). Conclusão: A avaliação microbiológica do primeiro ano de funcionamento da UTQ da EPM/ UNIFESP revelou que, embora o agente mais prevalente tenha sido a CoNS, bacilos Gram negativos ainda são muito prevalentes, como a Pseudomonas aeruginosa e a Acinetobacter baumannii. Apesar de pouco tempo de operação, observou-se um grande número de microrganismos multirresistentes, que pode ser explicado por longa exposição a agentes antimicrobianos e alta taxa de transferência de outros hospitais.

Introduction: Despite great advances in treatment, burned skin infection remains a major challenge. The aim of this study is to evaluate the microbiological aspects of the first year's operation of a Burn Unit in a University Hospital. Methods: Retrospective study. Microbiological data were collected and analyzed from patients admitted to the Burn Unit of São Paulo Hospital, a University Hospital of the Paulista Medical School (EPM) of the Federal University of São Paulo (UNIFESP) from June 2009 to July 2010. Results: The average length of stay was 13.8 days with a mortality rate of 5.9%, and median of TBSA was 10.3%. Evaluated 159 cultures from 101 patients. Blood cultures were the most requested (41%). It was also accessed 245 surveillance cultures collected from 75 patients. The microbiological analysis revealed a total positivity rate of 34,5%. The most prevalent agents were Coagulase-negative Staphylococcus - CoNS - (33%), Pseudomonas aeruginosa (24%), Acinetobacter spp. (22%) and Klebsiella pneumoniae (5%). Conclusion: The microbiological evaluation of the first year's activity of EPM/UNIFESP Burn Care Unit revealed that, although the most prevalent agent was CoNS, Gram negative bacilli are still very prevalent, such as Pseudomonas aeruginosa and Acinetobacter baumannii. Despite the short time of operation, was observed large number of multiresistant microorganisms which can be explained by long exposure to antimicrobials and high transfer rate from other hospitals.

Evaluation of the presence of microorganisms in solid-organ preservation solution

OBJECTIVE: To assess the presence of microorganism contamination in the preservation solution for transplant organs (kidney/pancreas). Method: Between August 2007 and March 2008, 136 samples of preservation solution were studied prior to graft implantation. Variables related to the donor and to the presence of microorganisms in the preservation solution of organs were evaluated, after which the contamination was evaluated in relation to the "recipient culture" variable. Univariate and multivariate statistical analyses were performed. RESULTS: The contamination rate of the preservation solution was 27.9 percent. Coagulase-negative Staphylococcus was the most frequently isolated microorganism. However, highly virulent agents, such as fungi and enterobacteria, were also isolated. In univariate analysis, the variable "donor antibiotic use" was significantly associated to the contamination of the preservation solution. On the other hand, multivariate analysis found statistical significance in "donor antibiotic use" and "donor's infectious complications" variables. CONCLUSIONS: In this study, 27.9 percent of the preservation solutions of transplant organs were contaminated. Infectious diseases and non-use of antibiotics by the donor were significantly related to the presence of microorganisms in organ preservation solutions. Contamination in organ preservation solutions was not associated with infection in the recipient.

Avaliação das metodologias M.I.C.E.®, Etest® e microdiluição em caldo para determinação da CIM em isolados clínicos / Evaluation of M.I.C.E.TM, Etest® and CLSI broth microdilution methods for antimicrobial susceptibility testing of nosocomial bacterial isolates

INTRODUÇÃO: As fitas Oxoid® M.I.C.Evaluator® (M.I.C.E., Thermo Fisher Scientific, Basingstoke, UK), recém-lançadas no mercado brasileiro, representam uma alternativa rápida para a realização de testes de sensibilidade a antimicrobianos (TSA). OBJETIVO: Avaliar o desempenho da metodologia M.I.C.E. em relação à microdiluição em caldo (teste de referência) e ao Etest® (BioMérieux, Marcy l'Étoile, France). Material e métodos: Foram selecionados 160 isolados bacterianos, sendo P. aeruginosa (20), Acinetobacter spp. (20), K. pneumoniae (20), E. coli (20), S. aureus (20), Staphylococcus coagulase-negativa (20), E. faecalis (20) e E. faecium (20). Os TSAs foram realizados por microdiluição em caldo, Etest e M.I.C.E., seguindo-se as recomendações do Clinical Laboratory Standards Institute (CLSI, 2009) e dos respectivos fabricantes. Os resultados foram interpretados segundo os critérios estabelecidos pelo CLSI e comparados por análise de regressão. RESULTADOS: Avaliando-se todas as combinações de antimicrobianos vs. a espécie bacteriana, o desempenho da metodologia M.I.C.E. foi muito bom, apresentando uma concordância geral (variação na concentração inibitória mínima [CIM] ± 1-log2) > 90 por cento, exceto para cefotaxima (85 por cento) e vancomicina (76,3 por cento), quando em comparação com os resultados da metodologia de referência. Quando comparado com o Etest, a metodologia M.I.C.E. apresentou concordância geral > 96 por cento, com exceção para a combinação amoxicilina/ácido clavulânico (67,5 por cento). CONCLUSÃO: Os resultados do TSA obtidos pela metodologia M.I.C.E. apresentaram boa correlação com aqueles obtidos pela microdiluição em caldo e pelo Etest, indicando que essa metodologia é uma alternativa rápida para a determinação da CIM pelos laboratórios de microbiologia clínica. Atenção especial deve ser dada á determinação da CIM para a combinação amoxicilina/ácido clavulânico.

INTRODUCTION: The Oxoid® M.I.C.EvaluatorTM methodology (M.I.C.E., Thermo Fisher Scientific, Basingstoke, UK), recently released into the market, represents a rapid alternative to antimicrobial susceptibility testing. OBJECTIVE: The objective of this study was to evaluate the performance of M.I.C.E. methodology in relation to broth microdilution (reference test) and Etest® (BioMérieux, Marcy l'Étoile, France). Material and method: A total of 160 bacterial isolates were collected comprising the following species: P. aeruginosa (20), Acinetobacter spp. (20), K. pneumoniae (20), E. coli (20), S. aureus (20), coagulase-negative Staphylococcus (20), E. faecalis (20) and E. faecium (20). Following Clinical Laboratory Standands Institute (CLSI) standards (2009) and the manufacturers' recommendations, antimicrobial susceptibility testing was performed using broth microdilution method, Etest and M.I.C.E. The results were interpreted according to the criteria established by CLSI and compared through regression analysis. RESULTS: All antimicrobial combinations vs. bacterial species were evaluated and M.I.C.E. methodology yielded good results with general correlation (MIC variation ± 1-log2) > 90 percent, except for cefotaxime (85 percent) and vancomycin (76.3 percent) when compared with the reference method. The M.I.C.E. results compared to Etest showed general correlation (> 96 percent), except for amoxicillin/clavulanic acid (67.5 percent) combination. CONCLUSION: AST results obtained from M.I.C.E. methodology showed a good correlation with those from broth microdilution and Etest, which corroborates its time effectiveness in the determination of MIC. However, the combination of amoxicillin/clavulanic acid requires further attention.

Evaluation of the presence of microorganisms in solid-organ preservation solution.

OBJECTIVE: To assess the presence of microorganism contamination in the preservation solution for transplant organs (kidney/pancreas). METHOD: Between August 2007 and March 2008, 136 samples of preservation solution were studied prior to graft implantation. Variables related to the donor and to the presence of microorganisms in the preservation solution of organs were evaluated, after which the contamination was evaluated in relation to the "recipient culture" variable. Univariate and multivariate statistical analyses were performed. RESULTS: The contamination rate of the preservation solution was 27.9%. Coagulase-negative Staphylococcus was the most frequently isolated microorganism. However, highly virulent agents, such as fungi and enterobacteria, were also isolated. In univariate analysis, the variable "donor antibiotic use" was significantly associated to the contamination of the preservation solution. On the other hand, multivariate analysis found statistical significance in "donor antibiotic use" and "donor's infectious complications" variables. CONCLUSIONS: In this study, 27.9% of the preservation solutions of transplant organs were contaminated. Infectious diseases and non-use of antibiotics by the donor were significantly related to the presence of microorganisms in organ preservation solutions. Contamination in organ preservation solutions was not associated with infection in the recipient.

New approach for diagnosis of candidemia based on detection of a 65-kilodalton antigen.

Nosocomial candidiasis is a major concern in tertiary care hospitals worldwide. This infection generally occurs in patients with degenerative and neoplastic diseases and is considered the fourth most frequent cause of bloodstream infections. Diagnosis of candidemia or hematogenous candidiasis has been problematic because clinical signs and symptoms are nonspecific, leading to delays in diagnosis and, consequently, delays in appropriate antifungal therapy. We developed an inhibition enzyme-linked immunosorbent assay (ELISA) for detection of a 65-kDa antigen in an experimental model of candidemia and for diagnosis of patients in intensive care units (ICUs) with suspected candidemia. An anti-65-kDa monoclonal antibody was tested for detection of the 65-kDa antigen produced by Candida albicans, Candida tropicalis, and Candida parapsilosis in murine candidemia models. The 65-kDa antigen was detected in sera at concentrations ranging from 0.012 to 3.25 microg/ml. A total of 20 human patients with candidemia were then evaluated with the inhibition ELISA using sequential sera. Sixteen (80%) patients had the 65-kDa antigen in concentrations ranging from 0.07 to 5.0 microg/ml. Sequential sera from patients with candidemia presented three different patterns of antigenemia of the 65-kDa molecule: (i) total clearance of antigenemia, (ii) initial clearance and relapse of antigenemia, and (iii) partial clearance of antigenemia. Our results indicate detection of the 65-kDa protein may be a valuable tool for the diagnosis of candidemia by C. albicans, C. tropicalis, and C. parapsilosis.

Oligella urethralis isolada em hemocultura de paciente internada no complexo HSP/UNIFESP / Oligella urethralis isolated in hemoculture from patient interned in HSP-UNIFESP complex

Primeiro isolado de Oligella urethralis em duas amostras de sangue periférico detectado por metodologia de monitoração contínua de metabolismo (sistema Bactec®) e identificado pelo sistema automatizado Phoenix® (BD System) em paciente com linfoma retroperitoneal com metástase em sistema nervoso central (SNC) no Hospital São Paulo da Universidade Federal de São Paulo (HSP/UNIFESP).

First time isolation of Oligella urethralis in two samples of peripheral blood detected by continuous metabolism monitoring methodology (Bactec 61650 system) and identified by the automatized Phoenix 61650 system (BD System) in patient with retro-peritoneal lymphoma with metastasis in the central nervous system at São Paulo hospital of Federal University of São Paulo (HSP/UNIFESP).

Avaliação do risco de contaminação por bactérias, no paciente submetido à broncoscopia, após o reprocessamento do broncoscópio / Evaluation of the risk of bacterial contamination in the patient submitted to bronchoscopy, after reprocessing the bronchoscope

Introdução: A broncoscopia é um procedimento diagnóstico e terapêutico realizado com a introdução nas vias aéreas de um tubo flexível que permite visualizar até as menores delas. Para evitar ou reduzir o risco de infecções, o broncoscópio deve ser adequadamente desinfetado com, pelo menos, desinfecção de alto nível. Objetivo: Verificar se há risco de contaminação bacteriana para os pacientes submetidos à broncoscopia do Hospital São Paulo da Unifesp, Estado de São Paulo. Métodos: No período de 1997 a 1998, o reprocessamento do broncoscópio incluiu limpeza e enxágüe com água estéril ou potável, seguida de rinsagem com glutaraldeído a 2 por cento por 20 minutos, novo enxágüe com água estéril ou potável e rinsagem com álcool etílico a 70 por cento e secagem com ar forçado pelo canal de sucção. Foram colhidas amostras de 65 pacientes para exames microbiológicos, instalando-se soro fisiológico estéril pelo canal de sucção do broncoscópio. Resultados: Após o reprocessamento foram encontrados nas amostras Staphylococcus epidermidis, Enterobacter sp, Acinetobacter baumanni, Streptococcus viridans, Staphylococcus aureus, Streptococcus beta hemoliticus A, Staphylococcus coagulase negativa e em cinco amostras houve crescimento de microbactéria na cultura. Conclusões: A desinfecç ão do broncoscópio com glutaraldeído a 2 por cento não foi suficiente para garantir a desinfecção do aparelho e a presença de Staphylococcus epidermidis indica que houve contaminação do broncoscópio pela manipulação após a desinfecção

Avaliação do meio de cultura líquido BBL Mycobacteria growth indicator tube (MGIT) em rotina de detecção de micobactérias em amostras de escarro de pacientes com suspeita de tuberculose pulmonar / Evaluation of BBL mycobacteria growth indicator tube (MGIT) for routine detection of mycobacteria from sputum of patients suspected of pulmonary tuberculosis

O Laboratório Clínico de Microbiologia deve fazer uma rápida detecção, identfflcação e teste de susceptibilidade da M.tuberculosis para permitir um efetivo tratamento e controle da infecção, particularmente em ambiente hospitalar. Para avaliar o desempenho do sistema Mycobacteria Growth Indicator Tube (MGIT) na rotina de detecção de micobactérias processamos 559 amostras de escarros, de pacientes com suspeita de tuberculose, pela baciloscopia (BAAR) e cultura utilizando ambos, o meio de Lõwenstein-Jensen(LJ) e o sistema MGIT. Cento e uma (l8,1 por cento ) amostras foram positivas pelo menos por um dos métodos utilizados. A detecção foi 75(13,4 por cento ), 70(14,1 por cento ) e 87(15,6 por cento ) pela BAAR, LJ e MGIT, respectivamente. A concordância entre o LJ e o MGIT foi 96 por cento . A média do tempo para a detecção do MGIT foi 11,43 dias e do LJ foi de 20,29 dias (p

Dosagem de cálcio urinário II: Comportamento da concentraçäo urinária de cálcio em amostras de urinas submetidas a diversas condiçöes experimentais / Urinary calcium dosage II: Behavior of urinary calcium concentration evaluated in urine samples submitted to different experimental conditions

O estudo constou da dosagem e comparaçäo do cálcio urinário em 40 duplicatas de urina, onde um grupo foi colhido com ácido clorídrico concentrado e outro grupo sem o ácido, sendo que, em todas as amostras, o ensaio foi realizado em duas outras condiçöes: no mesmo dia e após dois dias de refrigeraçäo (4-C). A técnica utilizada foi a complexométrica da cresolftaleina automatizada no aparelho ABA-100. A comparaçäo das dosagens de cálcio, com relaçäo à acidificaçäo ou näo, näo evidenciou diferença significante entre os resultados. Quando dosamos o cálcio após dois dias de refrigeraçäo, obtivemos uma diferença significante para maior em relaçäo aos valores médios dos resultados obtidos no dia da coleta

Dosagem de cálcio urinário: I. Avaliaçäo comparativa da concentraçäo urinária de cálcio pelos métodos da cresolftaleina complexona e expectrofotometria de absorçäo atômica / Urinary calcium dosage: I. Comparative evaluation of urinary calcium concentration using cresolphthalein complexona method and atomic absorption spectrophotometry method

Foram utilizadas 50 amostras de urina de indivíduos da rotina normal do laboratório e submetidas simultaneamente à avaliaçäo do cálcio através da espectrofotometria de absorçäo atômica e do método químico da cresolftaleína complexona automatizado em um aparelho ABA-100. Obtivemos como média 14,6 mg/dl + ou - 8,6 mg/dl e 14,4 mg/dl + ou - 8,6 mg/dl, respectivamente. Estes achados mostram que existe correlaçäo entre os dois métodos

Acurácia do método de Papanicolaou, exame a fresco e coloraçäo pelo Gram para o diagnóstico de tricomoníase e micose vaginal / Reliability of cytologic smear, wet smear and Gram smear in the diagnosis of trichomoniasis and vaginal mycosis

As sensibilidades diagnósticas dos métodos de Papanicolaou, de Gram e de preparaçäo a fresco foram comparadas em 60 gestantes quanto à capacidade de revelarem infecçöes provocadas por Trichomonas e por leveduras. Os esfregaços corados pelo Papanicolaou demonstraram o agente causal em todas as pacientes portadoras de Tricomoníase, porém em apenas 75% das portadoras de leveduras. O exame a fresco revelou melhor sensibilidade (91%) do que o Papanicolaou no diagnóstico das infecçöes micóticas. A coloraçäo pelo Gram näo trouxe contribuiçäo de valor e pode ser abolida. Esses resultados sugerem ser melhor associar, no período pré-natal, preparaçöes a fresco e coradas pelo processo de Papanicolaou para as avaliaçöes desses microorganismos