Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil.

Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca. However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The blaNDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes.

Surveillance system for Healthcare-associated endophthalmitis at state level in a middle-income country: preliminary results.

PURPOSE: To describe the implementation pro cess and the preliminary results of a surveillance system for healthcare-associated endophthalmitis. METHODS: This is a case study of the implementation of a surveillance system for healthcare-associated endophthalmitis. The system for healthcare-associated endophthalmitis is a structured system that enables surveillance of cases of healthcare-associated endophthalmitis after intraocular procedures, developed and coordinated by the Division of Hospital Infection at the State Health Department, São Paulo, Brazil. The implementation process included a pilot phase, followed by a scaling-up phase. Data were reported monthly to the Division of Hospital Infection by participating healthcare facilities that performed intraocular procedures in the state of São Paulo, Brazil, from September 2017 to December 2019. RESULTS: Among the 1,483 eligible healthcare facilities, 175 engaged in the study (participation rate of 11.8%), reporting 222,728 intraocular procedures performed, of which 164,207 were cataract surgery and 58,521 were intravitreal injections. The overall incidence rate of endophthalmitis was reported to be 0.05% (n=105; 80 cases after cataract surgery and 25 cases after intravitreal injections). The incidence rates for healthcare facilities ranged from 0.02% to 4.55%. Most cases were caused by gram-positive bacteria, mainly Staphylococcus spp. In 36 (46.2%) of the cases, there was no bacterial growth; no sample was collected in 28 (26.7%) cases. This system for healthcare-associated endophthalmitis enabled the identification of an outbreak of four cases of endophthalmitis after intravitreal injections. CONCLUSION: The system for healthcare-associated endophthalmitis proved to be operationally viable and efficient for monitoring cases of endophthalmitis at the state level.

Genomic Diversity of NDM-Producing Klebsiella Species from Brazil, 2013-2022.

Background: Since its first report in the country in 2013, NDM-producing Enterobacterales have been identified in all the Brazilian administrative regions. In this study, we characterized by antimicrobial susceptibility testing and by molecular typing a large collection of NDM-producing Klebsiella isolates from different hospitals in Brazil, mainly from the state of Sao Paulo, over the last decade. Methods: Bacterial isolates positive for blaNDM-genes were identified by MALDI-TOF MS and submitted to antimicrobial susceptibility testing by disk diffusion or broth microdilution (for polymyxin B). All isolates were submitted to pulsed-field gel electrophoresis, and isolates belonging to different clusters were submitted to whole genome sequencing by Illumina technology and downstream analysis. Mating out assays were performed by conjugation, plasmid sizes were determined by S1-PFGE, and plasmid content was investigated by hybrid assembly after MinIon long reads sequencing. Results: A total of 135 NDM-producing Klebsiella were identified, distributed into 107 different pulsotypes; polymyxin B was the only antimicrobial with high activity against 88.9% of the isolates. Fifty-four isolates presenting diversified pulsotypes were distributed in the species K. pneumoniae (70%), K. quasipneumoniae (20%), K. variicola (6%), K. michiganensis (a K. oxytoca Complex species, 2%), and K. aerogenes (2%); blaNDM-1 was the most frequent allele (43/54, 80%). There was a predominance of Clonal Group 258 (ST11 and ST340) encompassing 35% of K. pneumoniae isolates, but another thirty-one different sequence types (ST) were identified, including three described in this study (ST6244 and ST6245 for K. pneumoniae, and ST418 for K. michiganensis). The blaNDM-1 and blaNDM-7 were found to be located into IncF and IncX3 type transferable plasmids, respectively. Conclusions: Both clonal (mainly driven by CG258) and non-clonal expansion of NDM-producing Klebsiella have been occurring in Brazil in different species and clones, associated with different plasmids, since 2013.

Statewide evaluation of infection control measures for preventing coronavirus disease 2019 in hemodialysis facilities.

OBJECTIVE: This study aimed to evaluate the occurrence of coronavirus disease 2019 (COVID-19) in hemodialysis facilities and the occurrence of and risk factors for clustering of COVID-19 cases. METHODS: We conducted a cross-sectional online survey between March and July 2020, in all dialysis facilities in São Paulo state, using Google Forms. The online questionnaire contained questions addressing specific components of infection prevention and control practices and the number of cases during the COVID-19 pandemic. RESULTS: A total of 1,093 (5%) COVID-19 cases were reported among 20,984 patients; approximately 56% of the facilities had ≥1 cluster. Most facilities implemented various measures (such as allocation of dedicated COVID-19 areas/shifts, symptom screening, environmental disinfection, and maintenance of adequate ventilation) to prevent the transmission of severe acute respiratory syndrome coronavirus 2. Clustering of COVID-19 cases was suspected in only 7% of dialysis facilities. The only variable associated with this event was the performance of aerosol-generating procedures (odds ratio: 4.74; 95% confidence interval: 1.75-12.86). CONCLUSION: Attention should be paid to avoiding the performance of aerosol-generating procedures in dialysis facilities and monitoring the clustering of cases.

Total antibiotic use in a state-wide area and resistance patterns in Brazilian hospitals: an ecologic study.

INTRODUCTION: Use of antibiotic and bacterial resistance is the result of a complex interaction not completely understood. OBJECTIVES: To evaluate the impact of entire antimicrobial use (community plus hospitals) on the incidence of bloodstream infections in intensive care units adjusted by socioeconomic factors, quality of healthcare, and access to the healthcare system. DESIGN: Ecologic study using a hierarchical spatial model. SETTING: Data obtained from 309 hospitals located in the state of São Paulo, Brazil from 2008 to 2011. PARTICIPANTS: Intensive care units located at participant hospitals. OUTCOME: Hospital acquired bloodstream infection caused by MDRO in ICU patients was our primary outcome and data were retrieved from São Paulo Health State Department. Socioeconomic and healthcare indexes data were obtained from IBGE (Brazilian Foundation in charge of national decennial census) and SEADE (São Paulo Planning and Development Department). Information on antimicrobial sales were obtained from IMS Brazil. We divided antibiotics into four different groups (1-4). RESULTS: We observed a direct association between the use of group 1 of antibiotics and the incidences of bloodstream infections caused by MRSA (1.12; 1.04-1.20), and CR-Acinetobacter sp. (1.19; 1.10-1.29). Groups 2 and 4 were directly associated to VRE (1.72; 1.13-2.39 and 2.22; 1.62-2.98, respectively). Group 2 was inversely associated to MRSA (0.87; 0.78-0.96) and CR-Acinetobacter sp. (0.79; 0.62-0.97). Group 3 was inversely associated to Pseudomonas aeruginosa (0.69; 0.45-0.98), MRSA (0.85; 0.72-0.97) and VRE (0.48; 0.21-0.84). No association was observed for third generation cephalosporin-resistant Klebsiella pneumoniae and Escherichia coli. CONCLUSIONS: The association between entire antibiotic use and resistance in ICU was poor and not consistent for all combinations of antimicrobial groups and pathogens even after adjusted by socioeconomic indexes. Selective pressure exerted at the community level seemed not to affect the incidences of MDRO infection observed in intensive care setting.

Surveillance system for Healthcare-associated endophthalmitis at state level in a middle-income country: preliminary results / Sistema de vigilância epidemiológica para endoftalmites em nível estadual em um país de renda média: resultados preliminares

ABSTRACT Purpose: To describe the implementation pro cess and the preliminary results of a surveillance system for healthcare-associated endophthalmitis. Methods: This is a case study of the implementation of a surveillance system for healthcare-associated endophthalmitis. The system for healthcare-associated endophthalmitis is a structured system that enables surveillance of cases of healthcare-associated endophthalmitis after intraocular procedures, developed and coordinated by the Division of Hospital Infection at the State Health Department, São Paulo, Brazil. The implementation process included a pilot phase, followed by a scaling-up phase. Data were reported monthly to the Division of Hospital Infection by participating healthcare facilities that performed intraocular procedures in the state of São Paulo, Brazil, from September 2017 to December 2019. Results: Among the 1,483 eligible healthcare facilities, 175 engaged in the study (participation rate of 11.8%), reporting 222,728 intraocular procedures performed, of which 164,207 were cataract surgery and 58,521 were intravitreal injections. The overall incidence rate of endophthalmitis was reported to be 0.05% (n=105; 80 cases after cataract surgery and 25 cases after intravitreal injections). The incidence rates for healthcare facilities ranged from 0.02% to 4.55%. Most cases were caused by gram-positive bacteria, mainly Staphylococcus spp. In 36 (46.2%) of the cases, there was no bacterial growth; no sample was collected in 28 (26.7%) cases. This system for healthcare-associated endophthalmitis enabled the identification of an outbreak of four cases of endophthalmitis after intravitreal injections. Conclusion: The system for healthcare-associated endophthalmitis proved to be operationally viable and efficient for monitoring cases of endophthalmitis at the state level.

RESUMO Objetivo: Descrever o processo de implementação e os resultados preliminares de um sistema de vigilância epidemiológica para endoftalmites associada à assistência à saúde. Métodos: Trata-se de um estudo de caso de implementação de um sistema de vigilância epidemiológica para endoftalmites. O sistema de vigilância epidemiológica para endoftalmites é um sistema estruturado que possibilita a vigilância de casos de endoftalmite associados à assistência à saúde após procedimentos oftalmológicos invasivos, desenvolvido e coordenado pela Divisão de Infecção Hospitalar da Secretaria de Estado da Saúde, São Paulo, Brasil. O processo de implementação incluiu uma fase piloto, seguida pela fase de expansão. Os dados foram enviados mensalmente à Divisão de Infecção Hospitalar pelos estabelecimentos de saúde participantes que realizaram procedimentos oftalmológicos no estado de São Paulo, Brasil no período de setembro de 2017 a dezembro de 2019. Resultados: Entre os 1.483 estabelecimentos de saúde elegíveis, 175 participaram do estudo (taxa de adesão de 11,8%), relatando 222.728 procedimentos oftalmológicos realizados, sendo 164.207 cirurgias de catarata e 58.521 injeções intravítreas. A taxa de incidência global de endoftalmite relatada foi de 0,05% (n=105; 80 casos após cirurgia de catarata e 25 casos após injeção intravítrea). As taxas de incidência entre os estabelecimentos de saúde variaram de 0,02% a 4,55%. A maioria dos casos foi causada por bactérias gram-positivas, principalmente Staphylococcus spp. Em 36 (46,2%) casos não houve crescimento bacteriano; nenhuma amostra foi coletada em 28 (26,7%) casos. O sistema de vigilância epidemiológica para endoftalmites possibilitou a identificação de um surto de quatro casos de endoftalmite após injeção intravítrea. Conclusão: O sistema de vigilância epidemiológica para endoftalmites mostrou-se operacionalmente viável e eficiente para o monitoramento de casos de endoftalmite em nível estadual.

Impact of COVID-19 on healthcare-associated infections: Antimicrobial consumption does not follow antimicrobial resistance

Abstract Background This study aimed to analyze the Healthcare-Associated Infections (HAI) rates and antimicrobial consumption in Intensive Care Units (ICU) in São Paulo city during the COVID-19 pandemic and compare them with the pre-pandemic period. Methods This cohort included all hospitals that reported HAI rates (Central-Line-Associated Bloodstream Infection ‒ CLABSI and Ventilator-Associated Pneumonia ‒ VAP), the proportion of microorganisms that caused CLABSI, the proportion of resistant microorganisms, and antimicrobial consumption from January 2017 ‒ December 2020. Hospitals were stratified by the number of beds, Central Venous Catheter (CVC) utilization rate, Mechanical-Ventilation (MV) utilization rate, and type of funding. Statistical analyses were based on time-series plots and regression models. Results 220 ICUs were included. The authors observed an abrupt increase in CLABSI rates after the pandemic onset. High CLABSI rates during the pandemic were associated with hospital size, funding (public and non-profit private), and low CVC use (≤ 50%). An increase in VAP rates was associated with public hospitals, and high MV use (> 35%). The susceptibility profile of microorganisms did not differ from that of the pre-pandemic period. polymyxin, glycopeptides, and antifungal use increased, especially in COVID-19 ICUs. Conclusions HAI increased during COVID-19. The microorganisms' susceptibility profile did not change with the pandemic, but the authors observed a disproportionate increase in large-spectrum antimicrobial drug use.

Genomic diversity of NDM-producing Klebsiella species from Brazil, 2013-2022

Since its first report in the country in 2013, NDM-producing Enterobacterales have been identified in all the Brazilian administrative regions. In this study, we characterized by antimicrobial susceptibility testing and by molecular typing a large collection of NDM-producing Klebsiella isolates from different hospitals in Brazil, mainly from the state of Sao Paulo, over the last decade. Methods: Bacterial isolates positive for blaNDM-genes were identified by MALDI-TOF MS and submitted to antimicrobial susceptibility testing by disk diffusion or broth microdilution (for polymyxin B). All isolates were submitted to pulsed-field gel electrophoresis, and isolates belonging to different clusters were submitted to whole genome sequencing by Illumina technology and downstream analysis. Mating out assays were performed by conjugation, plasmid sizes were determined by S1-PFGE, and plasmid content was investigated by hybrid assembly after MinIon long reads sequencing. Results: A total of 135 NDM-producing Klebsiella were identified, distributed into 107 different pulsotypes; polymyxin B was the only antimicrobial with high activity against 88.9% of the isolates. Fifty-four isolates presenting diversified pulsotypes were distributed in the species K. pneumoniae (70%), K. quasipneumoniae (20%), K. variicola (6%), K. michiganensis (a K. oxytoca Complex species, 2%), and K. aerogenes (2%); blaNDM-1 was the most frequent allele (43/54, 80%). There was a predominance of Clonal Group 258 (ST11 and ST340) encompassing 35% of K. pneumoniae isolates, but another thirty-one different sequence types (ST) were identified, including three described in this study (ST6244 and ST6245 for K. pneumoniae, and ST418 for K. michiganensis). The blaNDM-1 and blaNDM-7 were found to be located into IncF and IncX3 type transferable plasmids, respectively. Conclusions: Both clonal (mainly driven by CG258) and non-clonal expansion of NDM-producing Klebsiella have been occurring in Brazil in different species and clones, associated with different plasmids, since 2013.

Statewide evaluation of infection control measures for preventing coronavirus disease 2019 in hemodialysis facilities

OBJECTIVE: This study aimed to evaluate the occurrence of coronavirus disease 2019 (COVID-19) in hemodialysis facilities and the occurrence of and risk factors for clustering of COVID-19 cases. METHODS: We conducted a cross-sectional online survey between March and July 2020, in all dialysis facilities in São Paulo state, using Google Forms. The online questionnaire contained questions addressing specific components of infection prevention and control practices and the number of cases during the COVID-19 pandemic. RESULTS: A total of 1,093 (5%) COVID-19 cases were reported among 20,984 patients; approximately 56% of the facilities had ≥1 cluster. Most facilities implemented various measures (such as allocation of dedicated COVID-19 areas/shifts, symptom screening, environmental disinfection, and maintenance of adequate ventilation) to prevent the transmission of severe acute respiratory syndrome coronavirus 2. Clustering of COVID-19 cases was suspected in only 7% of dialysis facilities. The only variable associated with this event was the performance of aerosol-generating procedures (odds ratio: 4.74; 95% confidence interval: 1.75-12.86). CONCLUSION: Attention should be paid to avoiding the performance of aerosol-generating procedures in dialysis facilities and monitoring the clustering of cases.

Total antibiotic use in a state-wide area and resistance patterns in Brazilian hospitals: an ecologic study

ABSTRACT Introduction: Use of antibiotic and bacterial resistance is the result of a complex interaction not completely understood. Objectives: To evaluate the impact of entire antimicrobial use (community plus hospitals) on the incidence of bloodstream infections in intensive care units adjusted by socioeconomic factors, quality of healthcare, and access to the healthcare system. Design: Ecologic study using a hierarchical spatial model. Setting: Data obtained from 309 hospitals located in the state of São Paulo, Brazil from 2008 to 2011. Participants: Intensive care units located at participant hospitals. Outcome: Hospital acquired bloodstream infection caused by MDRO in ICU patients was our primary outcome and data were retrieved from São Paulo Health State Department. Socioeconomic and healthcare indexes data were obtained from IBGE (Brazilian Foundation in charge of national decennial census) and SEADE (São Paulo Planning and Development Department). Information on antimicrobial sales were obtained from IMS Brazil. We divided antibiotics into four different groups (1-4). Results: We observed a direct association between the use of group 1 of antibiotics and the incidences of bloodstream infections caused by MRSA (1.12; 1.04-1.20), and CR-Acinetobacter sp. (1.19; 1.10-1.29). Groups 2 and 4 were directly associated to VRE (1.72; 1.13-2.39 and 2.22; 1.62-2.98, respectively). Group 2 was inversely associated to MRSA (0.87; 0.78-0.96) and CR-Acinetobacter sp. (0.79; 0.62-0.97). Group 3 was inversely associated to Pseudomonas aeruginosa (0.69; 0.45-0.98), MRSA (0.85; 0.72-0.97) and VRE (0.48; 0.21-0.84). No association was observed for third generation cephalosporin-resistant Klebsiella pneumoniae and Escherichia coli. Conclusions: The association between entire antibiotic use and resistance in ICU was poor and not consistent for all combinations of antimicrobial groups and pathogens even after adjusted by socioeconomic indexes. Selective pressure exerted at the community level seemed not to affect the incidences of MDRO infection observed in intensive care setting.

Análise dos dados do sistema de vigilância de infecção hospitalar do Estado de São Paulo - ano 2009 / Analysis of the data from the hospital infection surveillance system of the state of São Paulo - 2009

A divulgação anual e a discussão das taxas de infecção hospitalar (IH) são atividades contínuas do Sistema de Vigilância das Infecções Hospitalares do Estado de São Paulo desde sua implantação, em 2004. A tendência de aumento do número de hospitais notificantes, verificada em anos anteriores, manteve-se em 2009, demonstrando a consolidação do sistema. Os dados de infecção hospitalar obtidos permitem o planejamento de ações para a prevenção e controle de IH no Estado. Projetos para a avaliação da relação do consumo de antimicrobianos e resistência microbiana e para a redução das taxas de infecção de corrente sanguínea estão em andamento

Análise dos dados de infecção hospitalar do Estado de São Paulo – 2008 / Hospital Infection data analysis for the State of São Paulo – 2008

A tendência de aumento do número de hospitais notificantes ao Sistema de Vigilância das Infecções Hospitalares do Estado São Paulo, verificada em anos anteriores, manteve-se em 2008. Com isso, há a produção de dados consistente que permitem a comparação entre os hospitais e o direcionamento de ações de prevenção e controle de infecções hospitalares (IH). Esse aumento da adesão é resultado de ações desenvolvidas pela Divisão de Infecção Hospitalar do CVE/CCD/SES-SP, em parceria com os Grupos de Vigilância Epidemiológica (GVE) e municípios. A consolidação do sistema permite avançar na implantação de novos indicadores de IH que propiciam análises mais detalhadas do seu comportamento no Estado.

Análise dos dados de infecção hospitalar do Estado de São Paulo – Ano 2007 / Data analysis of hospital infection in the State of São Paulo – 2007

A tendência de aumento da adesão ao Sistema de Vigilância das Infecções Hospitalares do Estado de São Paulo, já observada nos anos anteriores, manteve-se em 2007. Além disso, é evidente a consolidação do sistema, permitindo a comparação de taxas de infecção hospitalar (IH) de cada hospital com o condensado de taxas de IH do Estado. O desenvolvimento de um sistema para monitorizar infecções selecionadas é de responsabilidade das autoridades de saúde. O Sistema de Vigilância das Infecções Hospitalares do Estado de São Paulo vem cumprindo esta atribuição, caracterizando-se como um sistema de vigilância inédito de base governamental.

Sistema de Vigilância Epidemiológica das Infecções Hospitalares do Estado de São Paulo – Análise dos dados de 2005 / Nosocomial Infection Surveillance System in State of São Paulo, 2005 data analysis

A vigilância epidemiológica (VE) das infecções hospitalares (IH) pretende medir a ocorrência do fenômeno e determinar seus níveis endêmicos. Com o objetivo de produzir dados por meio dos quais ações imediatas e planejamento de programas possam ser elaborados e avaliados, a Divisão de Infecção Hospitalar do CVE apresenta a análise dos dados do Sistema de VE das IH do Estado de São Paulo, implantado em 2004, objetivado nas unidades críticas e cirúrgicas. Os indicadores específicos selecionados avaliaram as principais síndromes infecciosas nas populações de maior risco. A adesão ao sistema de notificação, 60% dos hospitais cadastrados (534/896), foi de superior quando comparada a 2004. A notificação foi constante ao longo do ano, com média de 398 hospitais notificantes por mês. A notificação de dados ocorreu de acordo com a característica de atendimento das instituições: 456 (85,4%) hospitais notificaram a planilha 1, com dados de cirurgia limpa, 275 (51,5%) notificaram a planilha 2, com dados de Unidade de Terapia Intensiva (UTI) Adulto, Pediátrica e Coronariana e 124 (23,2%) notificaram dados de UTI Neonatal (planilha 3). Para cada um dos indicadores foi realizada distribuição das taxas em percentis. Concluiu-se que houve melhora na adesão ao Sistema de Vigilância de Infecções Hospitalares. Contudo, há necessidade de melhorias no que se refere à qualidade da informação.

Análise dos dados de infecção hospitalar do Estado de São Paulo - ano 2006 / Hospital infection data analysis in the State of São Paulo – 2006

Desde sua implantação, em 2004, o Sistema de Vigilância Epidemiológica das Infecções Hospitalares do Estado de São Paulo vem produzindo dados inéditos de infecção hospitalar (IH) e subsidiando ações específicas para prevenção e controle de IH no Estado. A adesão de hospitais ao sistema de notificação e a regularidade de envio dos dados são crescentes. Os indicadores epidemiológicos avaliados apresentaram pouca variação ao longo dos anos, sugerindo consistência dos dados enviados. Importantes objetivos do Sistema de Vigilância Epidemiológica das Infecções Hospitalares do Estado de São Paulo foram atingidos: adesão e consistência dos dados. O próximo desafio é estimular a análise dos dados pelos interlocutores regionais e municipais de IH. Desse modo, as ações de prevenção e controle de IH podem ser desenvolvidas com melhor oportunidade e de acordo com as realidades locais.