NDM-producing Enterobacterales prevalence associated to COVID-19 in a tertiary hospital.

Colonizations/Infections caused by carbapenem-resistant Enterobacterales are of great clinical and epidemiological importance due to their rapid dissemination and high mortality rates. In this scenario, the use of antibiotics intensified by the COVID-19 pandemic has brought about a great warning on the real impact that this pandemic could have on antimicrobial management programs and long-term antimicrobial resistance rates. The objective of this study was to evaluate the increase of New Delhi Metallo ß-Lactamase (NDM)-producing Enterobacterales cases in COVID-19 units of a complex Brazilian tertiary hospital. This retrospective observational study included all patients admitted to the hospital identified as colonized or infected by NDM-producing Gram negative bacilli (GNB), from January 2017 to April 2021. Forty-two NDM-producing Enterobacterales were identified in 39 patients. The rate of NDM cases per total surveillance cultures increased progressively between 2017 and 2021 (chi-2 for trend, p < 0.0001) and was associated with a higher occurrence specifically in COVID units (Fisher exact, p < 0.0001). The molecular investigation of the NDM-producing Klebsiella pneumoniae strains revealed the emergence of diverse clones during the COVID-19 period, also with possible evidence of horizontal transmission among patients within COVID units. NDM-producing Enterobacterales with multiple and different clonalities in the COVID-19 units also raised questions about the importance of other factors besides horizontal clonal transfer, including the increase of antimicrobial consumption by these patients.

NDM-producing enterobacterales prevalence associated to COVID-19 in a tertiary hospital

Colonizations/Infections caused by carbapenem-resistant Enterobacterales are of great clinical and epidemiological importance due to their rapid dissemination and high mortality rates. In this scenario, the use of antibiotics intensified by the COVID-19 pandemic has brought about a great warning on the real impact that this pandemic could have on antimicrobial management programs and long-term antimicrobial resistance rates. The objective of this study was to evaluate the increase of New Delhi Metallo b-Lactamase (NDM)-producing Enterobacterales cases in COVID-19 units of a complex Brazilian tertiary hospital. This retrospective observational study included all patients admitted to the hospital identified as colonized or infected by NDM-producing Gram negative bacilli (GNB), from January 2017 to April 2021. Forty-two NDM-producing Enterobacterales were identified in 39 patients. The rate of NDM cases per total surveillance cultures increased progressively between 2017 and 2021 (chi-2 for trend, p < 0.0001) and was associated with a higher occurrence specifically in COVID units (Fisher exact, p < 0.0001). The molecular investigation of the NDM-producing Klebsiella pneumoniae strains revealed the emergence of diverse clones during the COVID-19 period, also with possible evidence of horizontal transmission among patients within COVID units. NDM-producing Enterobacterales with multiple and different clonalities in the COVID-19 units also raised questions about the importance of other factors besides horizontal clonal transfer, including the increase of antimicrobial consumption by these patients.

NDM-producing Enterobacterales prevalence associated to COVID-19 in a tertiary hospital

Abstract Colonizations/Infections caused by carbapenem-resistant Enterobacterales are of great clinical and epidemiological importance due to their rapid dissemination and high mortality rates. In this scenario, the use of antibiotics intensified by the COVID-19 pandemic has brought about a great warning on the real impact that this pandemic could have on antimicrobial management programs and long-term antimicrobial resistance rates. The objective of this study was to evaluate the increase of New Delhi Metallo β-Lactamase (NDM)-producing Enterobacterales cases in COVID-19 units of a complex Brazilian tertiary hospital. This retrospective observational study included all patients admitted to the hospital identified as colonized or infected by NDM-producing Gram negative bacilli (GNB), from January 2017 to April 2021. Forty-two NDM-producing Enterobacterales were identified in 39 patients. The rate of NDM cases per total surveillance cultures increased progressively between 2017 and 2021 (chi-2 for trend, p < 0.0001) and was associated with a higher occurrence specifically in COVID units (Fisher exact, p < 0.0001). The molecular investigation of the NDM-producing Klebsiella pneumoniae strains revealed the emergence of diverse clones during the COVID-19 period, also with possible evidence of horizontal transmission among patients within COVID units. NDM-producing Enterobacterales with multiple and different clonalities in the COVID-19 units also raised questions about the importance of other factors besides horizontal clonal transfer, including the increase of antimicrobial consumption by these patients.

Evaluation of different monitoring methods of surface cleanliness in operating rooms.

OBJECTIVES: to evaluate different monitoring methods for detecting the presence of organic or biological matter before and after the cleaning and disinfection processes of the operating room. METHODS: this is a cross-sectional study based on visual inspection, adenosine triphosphate levels and microbiological culture for the assessment of cleaning and disinfection. RESULTS: 93.3% of the surfaces inspected visually for this study purpose were considered clean, even when high levels of adenosine triphosphate and microbiological analysis detected presence of microorganisms relevant to biofilm formation. CONCLUSIONS: the cleaning and disinfection processes reduced the microbial load and organic matter of the inspected surfaces, demonstrated by the values obtained by the adenosine triphosphate bioluminescence assay and microbiological analysis, but the visual inspection as a unique tool to assess the surfaces' cleanliness may give a false impression of clean environment.

Evaluation of different monitoring methods of surface cleanliness in operating rooms / Avaliação dos diferentes métodos de monitoramento de limpeza de superfície em sala operatória / Evaluación de diferentes métodos de monitoreo de limpieza de superficie en sala operatoria

ABSTRACT Objectives: to evaluate different monitoring methods for detecting the presence of organic or biological matter before and after the cleaning and disinfection processes of the operating room. Methods: this is a cross-sectional study based on visual inspection, adenosine triphosphate levels and microbiological culture for the assessment of cleaning and disinfection. Results: 93.3% of the surfaces inspected visually for this study purpose were considered clean, even when high levels of adenosine triphosphate and microbiological analysis detected presence of microorganisms relevant to biofilm formation. Conclusions: the cleaning and disinfection processes reduced the microbial load and organic matter of the inspected surfaces, demonstrated by the values obtained by the adenosine triphosphate bioluminescence assay and microbiological analysis, but the visual inspection as a unique tool to assess the surfaces' cleanliness may give a false impression of clean environment.

RESUMO Objetivos: avaliar diferentes métodos de monitoramento da presença de matéria orgânica ou biológica entre a limpeza e a desinfecção da sala cirúrgica. Métodos: trata-se de um estudo transversal utilizando a inspeção visual, amostras de trifosfato de adenosina e cultura microbiológica como indicadores para avaliação da limpeza e a desinfecção. Resultados: 93,3% das áreas avaliadas visualmente neste estudo apresentavam-se visualmente limpas, mesmo na presença de altos níveis de bioluminescência no resultado de trifosfato de adenosina e análises microbiológicas detectando a presença de microrganismos relevantes para a formação de biofilmes. Conclusões: o processo de limpeza e desinfecção reduziu a carga microbiana e matéria orgânica das superfícies avaliadas, demonstrada pelos resultados obtidos pelo trifosfato de adenosina e avaliação microbiológica, mas a inspeção visual como ferramenta única para avaliar a eficácia da limpeza das superfícies, pode gerar uma falsa impressão de ambiente limpo.

RESUMEN Objetivos: evaluar diferentes métodos de monitoreo de la presencia de materia orgánica o biológica entre la limpieza y desinfección de la sala quirúrgica. Métodos: estudio transversal utilizando la inspección visual, muestras de adenosina trifosfato y cultura microbiológica como indicadores para evaluación de la limpieza y desinfección. Resultados: 93,3% de las áreas evaluadas visualmente en este estudio se presentaban visualmente limpias, mismo en la presencia de altos niveles de bioluminiscencia en el resultado de adenosina trifosfato y análisis microbiológicos detectando la presencia de microorganismos relevantes para la formación de biofilms. Conclusiones: el proceso de limpieza y desinfección redujo la carga microbiana y materia orgánica de las superficies evaluadas, demostrada por los resultados obtenidos por el adenosina trifosfato y evaluación microbiológica, pero la inspección visual como herramienta única para evaluar la eficacia de la limpieza de las superficies, puede generar una falsa impresión de ambiente limpio.

Evaluation of different monitoring methods of surface cleanliness in operating rooms / Avaliação dos diferentes métodos de monitoramento de limpeza de superfície em sala operatória / Evaluación de diferentes métodos de monitoreo de limpieza de superficie en sala operatoria

ABSTRACT Objectives: to evaluate different monitoring methods for detecting the presence of organic or biological matter before and after the cleaning and disinfection processes of the operating room. Methods: this is a cross-sectional study based on visual inspection, adenosine triphosphate levels and microbiological culture for the assessment of cleaning and disinfection. Results: 93.3% of the surfaces inspected visually for this study purpose were considered clean, even when high levels of adenosine triphosphate and microbiological analysis detected presence of microorganisms relevant to biofilm formation. Conclusions: the cleaning and disinfection processes reduced the microbial load and organic matter of the inspected surfaces, demonstrated by the values obtained by the adenosine triphosphate bioluminescence assay and microbiological analysis, but the visual inspection as a unique tool to assess the surfaces' cleanliness may give a false impression of clean environment.

RESUMO Objetivos: avaliar diferentes métodos de monitoramento da presença de matéria orgânica ou biológica entre a limpeza e a desinfecção da sala cirúrgica. Métodos: trata-se de um estudo transversal utilizando a inspeção visual, amostras de trifosfato de adenosina e cultura microbiológica como indicadores para avaliação da limpeza e a desinfecção. Resultados: 93,3% das áreas avaliadas visualmente neste estudo apresentavam-se visualmente limpas, mesmo na presença de altos níveis de bioluminescência no resultado de trifosfato de adenosina e análises microbiológicas detectando a presença de microrganismos relevantes para a formação de biofilmes. Conclusões: o processo de limpeza e desinfecção reduziu a carga microbiana e matéria orgânica das superfícies avaliadas, demonstrada pelos resultados obtidos pelo trifosfato de adenosina e avaliação microbiológica, mas a inspeção visual como ferramenta única para avaliar a eficácia da limpeza das superfícies, pode gerar uma falsa impressão de ambiente limpo.

RESUMEN Objetivos: evaluar diferentes métodos de monitoreo de la presencia de materia orgánica o biológica entre la limpieza y desinfección de la sala quirúrgica. Métodos: estudio transversal utilizando la inspección visual, muestras de adenosina trifosfato y cultura microbiológica como indicadores para evaluación de la limpieza y desinfección. Resultados: 93,3% de las áreas evaluadas visualmente en este estudio se presentaban visualmente limpias, mismo en la presencia de altos niveles de bioluminiscencia en el resultado de adenosina trifosfato y análisis microbiológicos detectando la presencia de microorganismos relevantes para la formación de biofilms. Conclusiones: el proceso de limpieza y desinfección redujo la carga microbiana y materia orgánica de las superficies evaluadas, demostrada por los resultados obtenidos por el adenosina trifosfato y evaluación microbiológica, pero la inspección visual como herramienta única para evaluar la eficacia de la limpieza de las superficies, puede generar una falsa impresión de ambiente limpio.

Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry and real-time PCR in a combined protocol for diagnosis of bloodstream infections: a turnaround time approach.

Bloodstream infections (BSIs) are serious infections associated with high rates of morbidity and mortality. Every hour delay in initiation of an effective antibiotic increases mortality due to sepsis by 7%. Turnaround time (TAT) for conventional blood cultures takes 48h, forcing physicians to streamline therapy by exposing patients to broad-spectrum antimicrobials. Our objective was (1) to evaluate the accuracy and TAT of an optimized workflow combining direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and in-house real-time polymerase chain reaction (PCR) for bacterial identification and antimicrobial resistance profiling directly from positive blood bottles for diagnosing bloodstream infections and (2) to verify the effect of reporting results to medical staff. A total of 103 BSI episodes from 91 patients admitted to three hospitals in São Paulo, Brazil were included. TAT from molecular versus conventional methods was measured and compared. Our protocol showed an overall agreement of 93.5% for genus and 78.5% for species identification; 74.2% for methicillin resistance detection, 89.2% for extended-spectrum ß-lactamase profiling, 77.8% for metallo-ß-lactamase profiling, and 100% for carbapenemase profile and vancomycin-resistance detection when compared with conventional testing. TAT of molecular sample processing according to our protocol was 38h shorter than conventional methods. Antimicrobial interventions were possible in 27 BSI episodes. Antimicrobial discontinuation was achieved in 12 BSI episodes while escalation of therapy occurred in 15 episodes. Antimicrobial therapy was inadequate in three (12%) BSI episodes diagnosed using results of molecular testing. Our in-house rapid protocol for identifying both bacteria and antimicrobial resistance provided rapid and accurate results, having good agreement with conventional testing results. These results could contribute to faster antimicrobial therapy interventions in BSI episodes.

Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry and real-time PCR in a combined protocol for diagnosis of bloodstream infections: a turnaround time approach

ABSTRACT Bloodstream infections (BSIs) are serious infections associated with high rates of morbidity and mortality. Every hour delay in initiation of an effective antibiotic increases mortality due to sepsis by 7%. Turnaround time (TAT) for conventional blood cultures takes 48 h, forcing physicians to streamline therapy by exposing patients to broad-spectrum antimicrobials. Our objective was (1) to evaluate the accuracy and TAT of an optimized workflow combining direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and in-house real-time polymerase chain reaction (PCR) for bacterial identification and antimicrobial resistance profiling directly from positive blood bottles for diagnosing bloodstream infections and (2) to verify the effect of reporting results to medical staff. A total of 103 BSI episodes from 91 patients admitted to three hospitals in São Paulo, Brazil were included. TAT from molecular versus conventional methods was measured and compared. Our protocol showed an overall agreement of 93.5% for genus and 78.5% for species identification; 74.2% for methicillin resistance detection, 89.2% for extended-spectrum β-lactamase profiling, 77.8% for metallo-β-lactamase profiling, and 100% for carbapenemase profile and vancomycin-resistance detection when compared with conventional testing. TAT of molecular sample processing according to our protocol was 38 h shorter than conventional methods. Antimicrobial interventions were possible in 27 BSI episodes. Antimicrobial discontinuation was achieved in 12 BSI episodes while escalation of therapy occurred in 15 episodes. Antimicrobial therapy was inadequate in three (12%) BSI episodes diagnosed using results of molecular testing. Our in-house rapid protocol for identifying both bacteria and antimicrobial resistance provided rapid and accurate results, having good agreement with conventional testing results. These results could contribute to faster antimicrobial therapy interventions in BSI episodes.

Fatal case of donor-derived colistin-resistant carbapenemase-producing Klebsiella pneumoniae transmission in cardiac transplantation

ABSTRACT Herein we report a fatal case of donor-derived transmission of XDR-resistant carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) in cardiac transplantation. A 59-year-old male patient with non-obstructive hypertrophic cardiomyopathy underwent heart transplantation. On day 5 post-operation, blood cultures from the donor were positive for colistin-resistant carbapenemase-producing K. pneumoniae (ColR KPC-Kp) susceptible only to amikacin. Recipient blood cultures were also positive for ColR KPC-Kp with the same sensitivity profile as the donor isolate with an identical PFGE pattern. The patient was treated with double-carbapenems and amikacin. The patient evolved to pericarditis, osteomyelitis, and pulmonary necrosis, all fragment cultures positive for the same agent. The patient developed septic shock, multiple organ failure and died on day 50 post-transplantation. Based on current microbiological scenario worldwide the possibility of transmitting multidrug resistant (MDR) organisms should be considered.

Fatal case of donor-derived colistin-resistant carbapenemase-producing Klebsiella pneumoniae transmission in cardiac transplantation.

Herein we report a fatal case of donor-derived transmission of XDR-resistant carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) in cardiac transplantation. A 59-year-old male patient with non-obstructive hypertrophic cardiomyopathy underwent heart transplantation. On day 5 post-operation, blood cultures from the donor were positive for colistin-resistant carbapenemase-producing K. pneumoniae (ColR KPC-Kp) susceptible only to amikacin. Recipient blood cultures were also positive for ColR KPC-Kp with the same sensitivity profile as the donor isolate with an identical PFGE pattern. The patient was treated with double-carbapenems and amikacin. The patient evolved to pericarditis, osteomyelitis, and pulmonary necrosis, all fragment cultures positive for the same agent. The patient developed septic shock, multiple organ failure and died on day 50 post-transplantation. Based on current microbiological scenario worldwide the possibility of transmitting multidrug resistant (MDR) organisms should be considered.

. In Vitro assessment of combined Polymyxin B and minocycline therapy against klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae

The multidrug resistance profiles of Klebsiella pneumoniae carbapenemase (KPC) producers have led to increased clinical polymyxin use. Combination therapy with polymyxins may improve treatment outcomes, but it is uncertain which combinations are most effective. Clinical successes with intravenous minocycline-based combination treatments have been reported for infections caused by carbapenemase-producing bacteria. The objective of this study was to evaluate the in vitro activity of polymyxin B and minocycline combination therapy against six KPC-2-producing K. pneumoniae isolates (minocycline MIC range, 2 to 32 mg/liter). Polymyxin B monotherapy (0.5, 1, 2, 4, and 16 mg/liter) resulted in a rapid reduction of up to 6 log in bactericidal activity followed by regrowth by 24 h. Minocycline monotherapy (1, 2, 4, 8, and 16 mg/liter) showed no reduction of activity of >1.34 log against all isolates, although concentrations of 8 and 16 mg/liter prolonged the time to regrowth. When the therapies were used in combination, rapid bactericidal activity was followed by slower regrowth, with synergy (60 of 120 combinations at 24 h, 19 of 120 combinations at 48 h) and additivity (43 of 120 combinations at 24 h, 44 of 120 combinations at 48 h) against all isolates. The extent of killing was greatest against the more susceptible polymyxin B isolates (MICs of ≤0.5 mg/liter) regardless of the minocycline MIC. The pharmacodynamic activity of combined polymyxin B-minocycline therapy against KPC-producing K. pneumoniae is dependent on polymyxin B susceptibility...

Differentiation of Klebsiella pneumoniae carbapenemase (KPC) variants by pyrosequencing.

A fast and reliable protocol using the pyrosequencing technique was developed to identify 11 different types of the KPC enzyme. A total of 65 blaKPC positive bacterial isolates were tested and characterized. In the end, the pyrosequencing proved to be a powerful tool for epidemiological studies of KPC producer isolates.

Oral infection by the Human Papilloma Virus in women with cervical lesions at a prison in São Paulo, Brazil.

UNLABELLED: Carcinoma of the head and neck is the 6th cause of death by cancer in the world. In recent decades the human papillomavirus (HPV) has been implicated in the etiology of this disease. OBJECTIVE: To characterize the types of HPV detected in the oral mucosa in women with cytological abnormalities suggesting intraepithelial squamous lesions in the uterine cervix. METHODS: Four-hundred-nine cervical-vaginal and oral pap-smears of women interned in a Female Prison in São Paulo were examined. The relationship between cervical and oral lesion was analyzed by PCR/RFLP and DNA sequencing. RESULTS: Of 27 (6.67%) specimens showing cervical cytological abnormalities suggesting LSIL and HSIL, 22 (81.48%) had oncogenic high-risk HPV infection, of which HPV 59 was the most prevalent. Three (11.1%) samples showed cytological changes suggesting mild dysplasia in the oral cavity. CONCLUSION: Our study suggests an association between carcinoma of the oral cavity and HPV infection, regardless of the virus type.

Infecção oral pelo HPV em mulheres com lesão escamosa de colo uterino no sistema prisional da cidade de São Paulo, Brasil / Oral infection by the Human Papilloma Virus in women with cervical lesions at a prison in São Paulo, Brazil

O carcinoma de cabeça e pescoço é 6ª maior causa de mortes por neoplasia no mundo. Nas últimas décadas, tem-se associado a relação da infecção pelo Papilomavírus Humano (HPV) e seu envolvimento na etiologia desta doença, bem como acontece com o câncer de colo de útero. OBJETIVO: A caracterização molecular dos tipos de HPV diagnosticados na mucosa oral de mulheres que apresentavam alterações citológicas compatíveis com lesão escamosa no colo uterino. MÉTODOS: Foram estudadas 409 amostras cérvico-vaginais e de cavidade oral de mulheres internas no Presídio Feminino da cidade de São Paulo. A correlação entres lesões cervicais e orais foram avaliadas em 27 mulheres que apresentavam lesões pré-malignas e malignas no colo uterino pela caracterização molecular dos tipos de HPV por PCR/ RFLP e Sequenciamento. RESULTADOS: Das 27 (6,67%) amostras compatíveis com LSIL e HSIL no colo uterino, 22 (81,48%) apresentaram infecção pelo HPV de alto risco oncogênico, sendo o HPV 59 o mais prevalente, dentre elas, três amostras (11,1%) evidenciaram alterações celulares compatíveis com displasia leve na cavidade oral. CONCLUSÃO: Nosso estudo sugere uma relação entre o desenvolvimento de lesões da cavidade oral e a infecção pelo HPV, independentemente do tipo viral presente.

Carcinoma of the head and neck is the 6th cause of death by cancer in the world. In recent decades the human papillomavirus (HPV) has been implicated in the etiology of this disease. OBJECTIVE: To characterize the types of HPV detected in the oral mucosa in women with cytological abnormalities suggesting intraepithelial squamous lesions in the uterine cervix. METHODS: four-hundred-nine cervical-vaginal and oral pap-smears of women interned in a Female Prison in São Paulo were examined. The relationship between cervical and oral lesion was analyzed by PCR/RFLP and DNA sequencing. RESULTS: Of 27 (6.67%) specimens showing cervical cytological abnormalities suggesting LSIL and HSIL, 22 (81.48%) had oncogenic high-risk HPV infection, of which HPV 59 was the most prevalent. Three (11.1%) samples showed cytological changes suggesting mild dysplasia in the oral cavity. CONCLUSION: Our study suggests an association between carcinoma of the oral cavity and HPV infection, regardless of the virus type.

[Environmental contamination during a vancomycin-resistant Enterococci outbreak at a hospital in Argentina]. / Contaminación ambiental durante un brote de enterococo resistente a vancomicina en un hospital de Argentina.

INTRODUCTION: Vancomycin-resistant enterococci isolates (VRE) have caused numerous outbreaks in intensive care units (ICUs). A contaminated hospital environment, the hands of health care workers (HCW), and carrier patients may play important roles in perpetuating the chain of transmission in these outbreaks. The aims of this study were to report the first VRE outbreak in our center and assess the role of environmental contamination and HCW hands in the spread of new cases of enterococcal infection. MATERIAL AND METHOD: Between August and December 2003, surveillance cultures were performed with samples from all patients (n = 113) admitted to the ICU, as well as cultures of samples from the environment (n = 69) and HCW hands (n = 23). RESULTS: Eighteen clinical samples from 8 patients and 7 environmental samples yielded Enterococcus faecium (24 strains) and E. avium (1 strain). VRE was not detected on HCW hands. All the VRE isolates belonged to a single clone and carried the vanA gene. CONCLUSION: Environmental contamination provides an important reservoir for future outbreaks of VRE, perpetuating transmission of the microorganism in the hospital setting.

Evaluation of the susceptibility profiles, genetic similarity and presence of qnr gene in Escherichia coli resistant to ciprofloxacin isolated in Brazilian hospitals.

Increasing quinolone resistance has been reported worldwide, mainly among clinical isolates of Escherichia coli. The objectives of this study were to determine the susceptibility profile, the genetic relatedness, and the prevalence of the qnr gene among ciprofloxacin-resistant Escherichia coli isolated from distinct Brazilian hospitals. A total of 144 ciprofloxacin-resistant Escherichia coli were isolated from 17 Brazilian hospitals between January/2002 and June/2003. The antimicrobial susceptibility testing was performed by microdilution according to NCCLS. The presence of the qnr gene was initially screened by colony blotting, and then confirmed by PCR followed by DNA sequencing. Ninety-five urinary ciprofloxacin-resistant Escherichia coli were further selected for molecular typing by pulsed-field gel electrophoresis (PFGE). Imipenem and meropenem showed the highest susceptibility rates (100.0% for both compounds) followed by amikacin (91.0%) and piperacillin/tazobactan (84.8%). A single ciprofloxacin-resistant Escherichia coli isolate was positive for qnr among the 144 ciprofloxacin-resistant Escherichia coli. Forty-six PFGE patterns were observed among the 95 ciprofloxacin-resistant Escherichia coli type. This study shows that therapeutic options are limited for treatment of ciprofloxacin-resistant Escherichia coli due to the presence of additional mechanisms of antimicrobial resistance, such as ESBL production. The qnr gene was uncommon among ciprofloxacin-resistant Escherichia coli clinical isolates, but its identification might indicate the emergence of this mechanism of quinolone resistance in Brazil. The great genomic variability found among the ciprofloxacin-resistant Escherichia coli highlights the importance of the appropriate use of quinolone to restrict the selection of resistant isolates.