Danieli Conte - Academia.edu (original) (raw)

Papers by Danieli Conte

Research paper thumbnail of Matrix-assisted laser desorption ionization-time of flight: a promising alternative method of identifying the major coagulase-negative Staphylococci species

Revista da Sociedade Brasileira de Medicina Tropical, 2018

Introduction. This study aimed to evaluate different methods for differentiation of species of co... more Introduction. This study aimed to evaluate different methods for differentiation of species of coagulase-negative staphylococci (CoNS) that caused infections in hospitalized immunocompromised patients. Methods. A total of 134 CoNS strains were characterized using four different methods. Results. The results of matrix assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) analysis were in complete agreement with those of tuf gene sequencing (kappa index = 1.00). The kappa index of Vitek 2 ® Compact analysis was 0.85 (very good) and that of the conventional method was 0.63 (moderate). Conclusions. MALDI-TOF MS provided rapid and accurate results for the identification of CoNS (134; 100%).

Research paper thumbnail of Bacteremia and meningitis caused by OXA-23-producing Acinetobacter baumannii – molecular characterization and susceptibility testing for alternative antibiotics

Brazilian Journal of Microbiology, 2018

Research paper thumbnail of Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR

Journal of Microbiological Methods, 2017

Research paper thumbnail of Detection of Extended-Spectrum β-Lactamase in Enterobacter spp.– Evaluation of Six Phenotypic Tests

Microbial Drug Resistance, 2012

Extended-spectrum β-lactamases (ESBL) are plasmid-mediated enzymes that hydrolyze cephalosporins ... more Extended-spectrum β-lactamases (ESBL) are plasmid-mediated enzymes that hydrolyze cephalosporins and monobactams. The lack of a standard method to detect ESBL in Enterobacter spp. has led to underestimating its frequency. The aim of this study was to evaluate ESBL detection in Enterobacter spp. By the double-disk synergy test (DDST) and combined disk test (CDT) assay using cefepime, cefotaxime, and ceftazime as substrates for ESBL, plus AmpC inhibitors in different associations. A total of 83 Enterobacter spp. ESBL and 31 non-ESBL Enterobacter spp. were tested, and a cutoff point ≥3 mm was defined using a receiver operating characteristic (ROC) curve for combined disc methods. All tests showed 100% specificity. The sensitivity was 89.2% for DDST and CDT without AmpC inibitor, 90.4% in the combined disc test in Mueller-Hinton agar containing phenylboronic acid (CDT-PBAA), and 94% in the combined disc test in Mueller-Hinton agar containing cloxacillin (CDT-CLXA). Cefepime was the best substrate, mainly when AmpC inhibitors were not used. However, superior results were achieved when all cephalosporins were evaluated together. In conclusion, to improve ESBL detection in Enterobacter spp., some modifications in phenotypic tests are needed, such as to reduce the distance between the discs to 20 mm in DDST, to use a cutoff point for ≥3 mm on the CDT, and to include a cefepime disk or an inhibitor of AmpC in all tests.

Research paper thumbnail of Novel Insights into bla GES Mobilome Reveal Extensive Genetic Variation in Hospital Effluents

Microbiology Spectrum

In the “One Health” approach, which encompasses human, animal, and environmental health, emerging... more In the “One Health” approach, which encompasses human, animal, and environmental health, emerging issues of antimicrobial resistance are associated with hospital effluents that contain clinically relevant antibiotic-resistant bacteria along with a wide range of antibiotic concentrations, and lack regulatory status for mandatory prior and effective treatment. bla GES genes have been reported in aquatic environments despite the low detection of these genes among clinical isolates within the studied hospitals. Carbapenemase enzymes, which are relatively unusual globally, such as GES type inserted into new integrons on plasmids, are worrisome.

Research paper thumbnail of Title: COAGULASE-NEGATIVE STAPHYLOCOCCI: MALDI-TOF VERSUS GENE tuf SEQUENCE-BASED IDENTIFICATION

Coagulase-negative staphylococci (CoNS) is an important opportunistic pathogens, associated with ... more Coagulase-negative staphylococci (CoNS) is an important opportunistic pathogens, associated with catheter infections and others medical devices which involve biofilm’s formation. In hospital services these microorganisms represent a serious complication for immunocompromised patients, contributing to higher morbidity and mortality. Although the identification of species of CoNS have a clinical importance, laboratory limitations are still a challenge in distinguishing these pathogens. The purpose of this study was to characterize 182 CoNS species isolated from sterile body sites of hospitalized patients of tertiary care in Curitiba – PR by four different methodologies: phenotypic conventional (biochemical tests), automated (Vitek 2®), genotype (sequencing of the tuf gene) and proteomic (Matrix-assisted laser desorption ionization time of flight mass spectrometry, MALDI-TOF). Susceptibility test to commonly used antibiotics for treating infections caused by CoNS (oxacillin, daptomycin...

Research paper thumbnail of Characterization of CTX-M enzymes, quinolone resistance determinants, and antimicrobial residues from hospital sewage, wastewater treatment plant, and river water

Ecotoxicology and Environmental Safety, 2017

Multidrug-resistant (MDR) bacteria are widespread in hospitals and have been increasingly isolate... more Multidrug-resistant (MDR) bacteria are widespread in hospitals and have been increasingly isolated from aquatic environments. The aim of the present study was to characterize extended-spectrum β-lactamase (ESBL) and quinolone-resistant Enterobacteriaceae from a hospital effluent, sanitary effluent, inflow sewage, aeration tank, and outflow sewage within a wastewater treatment plant (WWTP), as well as river water upstream and downstream (URW and DRW, respectively), of the point where the WWTP treated effluent was discharged. β-lactamase (bla) genes, plasmid-mediated quinolone resistance (PMQR), and quinolone resistance-determining regions (QRDRs) were assessed by amplification and sequencing in 55 ESBL-positive and/or quinolone-resistant isolates. Ciprofloxacin residue was evaluated by high performance liquid chromatography. ESBL-producing isolates were identified in both raw (n=29) and treated (n=26) water; they included Escherichia coli (32), Klebsiella pneumoniae (22) and Klebsiella oxytoca (1). Resistance to both cephalosporins and quinolone was observed in 34.4% of E. coli and 27.3% of K. pneumoniae. Resistance to carbapenems was found in 5.4% of K. pneumoniae and in K. oxytoca. Results indicate the presence of blaCTX-M (51/55, 92.7%) and blaSHV (8/55, 14.5%) ESBLs, and blaGES (2/55, 3.6%) carbapenemase-encoding resistance determinants. Genes conferring quinolone resistance were detected at all sites, except in the inflow sewage and aeration tanks. Quinolone resistance was primarily attributed to amino acid substitutions in the QRDR of GyrA (47%) or to the presence of PMQR (aac-(6')-Ib-cr, oqxAB, qnrS, and/or qnrB; 52.9%) determinants. Ciprofloxacin residue was absent only from URW. Our results have shown strains carrying ESBL genes, PMQR determinants, and mutations in the gyrA QRDR genes mainly in hospital effluent, URW, and DRW samples. Antimicrobial use, and the inefficient removal of MDR bacteria and antibiotic residue during sewage treatment, may contribute to the emergence and spreading of resistance in the environment, making this a natural reservoir.

Research paper thumbnail of Antimicrobial resistance in Aeromonas species isolated from aquatic environments in Brazil

Journal of Applied Microbiology, 2020

The current study was conducted to determine the antimicrobial resistance profile and genetic rel... more The current study was conducted to determine the antimicrobial resistance profile and genetic relatedness of Aeromonas sp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP) and river water.

Research paper thumbnail of Diversity of Antimicrobial-Resistant Aeromonas Species Isolated from Aquatic Environments in Brazil

ABSTRACTIn the present study, we characterized antimicrobial resistance profile and genetic relat... more ABSTRACTIn the present study, we characterized antimicrobial resistance profile and genetic relatedness of Aeromonas spp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP), and river water. We detected the presence of genes responsible for the resistance to β-lactam, quinolone, and aminoglycoside. Enterobacterial Repetitive Intergenic Consensus PCR and multilocus sequence typing (MLST) were carried out to differentiate the strains and multilocus phylogenetic analysis (MLPA) was used to identify species. A total of 28 Aeromonas spp. cefotaxime-resistant strains were identified that carried a variety of resistance determinants, including uncommon GES-type β-lactamases. Multidrug-resistant Aeromonas spp. were found in hospital wastewater, WWTP, and sanitary effluent. Among these isolates, we detected A. caviae producing GES-1 or GES-5, as well as A. veronii harboring GES-7 or GES-16. We successfully identified Aeromonas spp. by using MLPA and found that A....

Research paper thumbnail of Assessment of clinical and epidemiological characteristics of patients with and without sepsis in intensive care units of a tertiary hospital

Einstein (São Paulo)

Assessment of clinical and epidemiological characteristics of patients with and without sepsis in... more Assessment of clinical and epidemiological characteristics of patients with and without sepsis in intensive care units of a tertiary hospital Avaliação das características clínicas e epidemiológicas de pacientes com e sem sepse nas unidades de terapia intensiva de um hospital terciário

Research paper thumbnail of Matrix-assisted laser desorption ionization-time of flight: a promising alternative method of identifying the major coagulase-negative Staphylococci species

Revista da Sociedade Brasileira de Medicina Tropical

Introduction. This study aimed to evaluate different methods for differentiation of species of co... more Introduction. This study aimed to evaluate different methods for differentiation of species of coagulase-negative staphylococci (CoNS) that caused infections in hospitalized immunocompromised patients. Methods. A total of 134 CoNS strains were characterized using four different methods. Results. The results of matrix assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) analysis were in complete agreement with those of tuf gene sequencing (kappa index = 1.00). The kappa index of Vitek 2 ® Compact analysis was 0.85 (very good) and that of the conventional method was 0.63 (moderate). Conclusions. MALDI-TOF MS provided rapid and accurate results for the identification of CoNS (134; 100%).

Research paper thumbnail of Procalcitonin, C-Reactive Protein, Albumin, and Blood Cultures as Early Markers of Sepsis Diagnosis or Predictors of Outcome: A Prospective Analysis

Sepsis is a condition with high mortality rates and its diagnosis remains a challenge. We assesse... more Sepsis is a condition with high mortality rates and its diagnosis remains a challenge. We assessed epidemiological, clinical data, multiple biomarker profiles, and blood culture with respect to sepsis diagnosis and predictors of outcome. METhODS: In total, 183 patients who were suspected of having sepsis and underwent blood culture collection were followed up for 7 days. Sepsis-related Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation (APACHE) II scores were calculated daily; biomarkers and blood culture test results were evaluated. RESulTS: In total, 78 (43%) had sepsis, 50 (27%) had septic shock, and 55 (30%) had no sepsis. Blood culture was positive in 28% and 42% of the sepsis and septic shock groups, respectively (P < .001). Regarding clinical profiles and biomarker values, there were no differences between the sepsis and non-sepsis groups, but significant differences were observed in the septic shock group. Multivariate logistic regression models revealed that age, serum albumin level, APACHE II, and SOFA 1 st day scores were the independent variables for death. COnCluSiOnS: The challenge in the diagnosis of sepsis continues as clinical and laboratory differences found between the groups were due to septic shock. Older aged patients with lower albumin levels and higher APACHE II and SOFA 1 st day scores have a greater probability of mortality.

Research paper thumbnail of Matrix-assisted laser desorption ionization-time of flight: a promising alternative method of identifying the major coagulase-negative Staphylococci species

Revista da Sociedade Brasileira de Medicina Tropical, 2018

Introduction. This study aimed to evaluate different methods for differentiation of species of co... more Introduction. This study aimed to evaluate different methods for differentiation of species of coagulase-negative staphylococci (CoNS) that caused infections in hospitalized immunocompromised patients. Methods. A total of 134 CoNS strains were characterized using four different methods. Results. The results of matrix assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) analysis were in complete agreement with those of tuf gene sequencing (kappa index = 1.00). The kappa index of Vitek 2 ® Compact analysis was 0.85 (very good) and that of the conventional method was 0.63 (moderate). Conclusions. MALDI-TOF MS provided rapid and accurate results for the identification of CoNS (134; 100%).

Research paper thumbnail of Bacteremia and meningitis caused by OXA-23-producing Acinetobacter baumannii – molecular characterization and susceptibility testing for alternative antibiotics

Brazilian Journal of Microbiology, 2018

Research paper thumbnail of Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR

Journal of Microbiological Methods, 2017

Research paper thumbnail of Detection of Extended-Spectrum β-Lactamase in Enterobacter spp.– Evaluation of Six Phenotypic Tests

Microbial Drug Resistance, 2012

Extended-spectrum β-lactamases (ESBL) are plasmid-mediated enzymes that hydrolyze cephalosporins ... more Extended-spectrum β-lactamases (ESBL) are plasmid-mediated enzymes that hydrolyze cephalosporins and monobactams. The lack of a standard method to detect ESBL in Enterobacter spp. has led to underestimating its frequency. The aim of this study was to evaluate ESBL detection in Enterobacter spp. By the double-disk synergy test (DDST) and combined disk test (CDT) assay using cefepime, cefotaxime, and ceftazime as substrates for ESBL, plus AmpC inhibitors in different associations. A total of 83 Enterobacter spp. ESBL and 31 non-ESBL Enterobacter spp. were tested, and a cutoff point ≥3 mm was defined using a receiver operating characteristic (ROC) curve for combined disc methods. All tests showed 100% specificity. The sensitivity was 89.2% for DDST and CDT without AmpC inibitor, 90.4% in the combined disc test in Mueller-Hinton agar containing phenylboronic acid (CDT-PBAA), and 94% in the combined disc test in Mueller-Hinton agar containing cloxacillin (CDT-CLXA). Cefepime was the best substrate, mainly when AmpC inhibitors were not used. However, superior results were achieved when all cephalosporins were evaluated together. In conclusion, to improve ESBL detection in Enterobacter spp., some modifications in phenotypic tests are needed, such as to reduce the distance between the discs to 20 mm in DDST, to use a cutoff point for ≥3 mm on the CDT, and to include a cefepime disk or an inhibitor of AmpC in all tests.

Research paper thumbnail of Novel Insights into bla GES Mobilome Reveal Extensive Genetic Variation in Hospital Effluents

Microbiology Spectrum

In the “One Health” approach, which encompasses human, animal, and environmental health, emerging... more In the “One Health” approach, which encompasses human, animal, and environmental health, emerging issues of antimicrobial resistance are associated with hospital effluents that contain clinically relevant antibiotic-resistant bacteria along with a wide range of antibiotic concentrations, and lack regulatory status for mandatory prior and effective treatment. bla GES genes have been reported in aquatic environments despite the low detection of these genes among clinical isolates within the studied hospitals. Carbapenemase enzymes, which are relatively unusual globally, such as GES type inserted into new integrons on plasmids, are worrisome.

Research paper thumbnail of Title: COAGULASE-NEGATIVE STAPHYLOCOCCI: MALDI-TOF VERSUS GENE tuf SEQUENCE-BASED IDENTIFICATION

Coagulase-negative staphylococci (CoNS) is an important opportunistic pathogens, associated with ... more Coagulase-negative staphylococci (CoNS) is an important opportunistic pathogens, associated with catheter infections and others medical devices which involve biofilm’s formation. In hospital services these microorganisms represent a serious complication for immunocompromised patients, contributing to higher morbidity and mortality. Although the identification of species of CoNS have a clinical importance, laboratory limitations are still a challenge in distinguishing these pathogens. The purpose of this study was to characterize 182 CoNS species isolated from sterile body sites of hospitalized patients of tertiary care in Curitiba – PR by four different methodologies: phenotypic conventional (biochemical tests), automated (Vitek 2®), genotype (sequencing of the tuf gene) and proteomic (Matrix-assisted laser desorption ionization time of flight mass spectrometry, MALDI-TOF). Susceptibility test to commonly used antibiotics for treating infections caused by CoNS (oxacillin, daptomycin...

Research paper thumbnail of Characterization of CTX-M enzymes, quinolone resistance determinants, and antimicrobial residues from hospital sewage, wastewater treatment plant, and river water

Ecotoxicology and Environmental Safety, 2017

Multidrug-resistant (MDR) bacteria are widespread in hospitals and have been increasingly isolate... more Multidrug-resistant (MDR) bacteria are widespread in hospitals and have been increasingly isolated from aquatic environments. The aim of the present study was to characterize extended-spectrum β-lactamase (ESBL) and quinolone-resistant Enterobacteriaceae from a hospital effluent, sanitary effluent, inflow sewage, aeration tank, and outflow sewage within a wastewater treatment plant (WWTP), as well as river water upstream and downstream (URW and DRW, respectively), of the point where the WWTP treated effluent was discharged. β-lactamase (bla) genes, plasmid-mediated quinolone resistance (PMQR), and quinolone resistance-determining regions (QRDRs) were assessed by amplification and sequencing in 55 ESBL-positive and/or quinolone-resistant isolates. Ciprofloxacin residue was evaluated by high performance liquid chromatography. ESBL-producing isolates were identified in both raw (n=29) and treated (n=26) water; they included Escherichia coli (32), Klebsiella pneumoniae (22) and Klebsiella oxytoca (1). Resistance to both cephalosporins and quinolone was observed in 34.4% of E. coli and 27.3% of K. pneumoniae. Resistance to carbapenems was found in 5.4% of K. pneumoniae and in K. oxytoca. Results indicate the presence of blaCTX-M (51/55, 92.7%) and blaSHV (8/55, 14.5%) ESBLs, and blaGES (2/55, 3.6%) carbapenemase-encoding resistance determinants. Genes conferring quinolone resistance were detected at all sites, except in the inflow sewage and aeration tanks. Quinolone resistance was primarily attributed to amino acid substitutions in the QRDR of GyrA (47%) or to the presence of PMQR (aac-(6&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;)-Ib-cr, oqxAB, qnrS, and/or qnrB; 52.9%) determinants. Ciprofloxacin residue was absent only from URW. Our results have shown strains carrying ESBL genes, PMQR determinants, and mutations in the gyrA QRDR genes mainly in hospital effluent, URW, and DRW samples. Antimicrobial use, and the inefficient removal of MDR bacteria and antibiotic residue during sewage treatment, may contribute to the emergence and spreading of resistance in the environment, making this a natural reservoir.

Research paper thumbnail of Antimicrobial resistance in Aeromonas species isolated from aquatic environments in Brazil

Journal of Applied Microbiology, 2020

The current study was conducted to determine the antimicrobial resistance profile and genetic rel... more The current study was conducted to determine the antimicrobial resistance profile and genetic relatedness of Aeromonas sp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP) and river water.

Research paper thumbnail of Diversity of Antimicrobial-Resistant Aeromonas Species Isolated from Aquatic Environments in Brazil

ABSTRACTIn the present study, we characterized antimicrobial resistance profile and genetic relat... more ABSTRACTIn the present study, we characterized antimicrobial resistance profile and genetic relatedness of Aeromonas spp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP), and river water. We detected the presence of genes responsible for the resistance to β-lactam, quinolone, and aminoglycoside. Enterobacterial Repetitive Intergenic Consensus PCR and multilocus sequence typing (MLST) were carried out to differentiate the strains and multilocus phylogenetic analysis (MLPA) was used to identify species. A total of 28 Aeromonas spp. cefotaxime-resistant strains were identified that carried a variety of resistance determinants, including uncommon GES-type β-lactamases. Multidrug-resistant Aeromonas spp. were found in hospital wastewater, WWTP, and sanitary effluent. Among these isolates, we detected A. caviae producing GES-1 or GES-5, as well as A. veronii harboring GES-7 or GES-16. We successfully identified Aeromonas spp. by using MLPA and found that A....

Research paper thumbnail of Assessment of clinical and epidemiological characteristics of patients with and without sepsis in intensive care units of a tertiary hospital

Einstein (São Paulo)

Assessment of clinical and epidemiological characteristics of patients with and without sepsis in... more Assessment of clinical and epidemiological characteristics of patients with and without sepsis in intensive care units of a tertiary hospital Avaliação das características clínicas e epidemiológicas de pacientes com e sem sepse nas unidades de terapia intensiva de um hospital terciário

Research paper thumbnail of Matrix-assisted laser desorption ionization-time of flight: a promising alternative method of identifying the major coagulase-negative Staphylococci species

Revista da Sociedade Brasileira de Medicina Tropical

Introduction. This study aimed to evaluate different methods for differentiation of species of co... more Introduction. This study aimed to evaluate different methods for differentiation of species of coagulase-negative staphylococci (CoNS) that caused infections in hospitalized immunocompromised patients. Methods. A total of 134 CoNS strains were characterized using four different methods. Results. The results of matrix assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) analysis were in complete agreement with those of tuf gene sequencing (kappa index = 1.00). The kappa index of Vitek 2 ® Compact analysis was 0.85 (very good) and that of the conventional method was 0.63 (moderate). Conclusions. MALDI-TOF MS provided rapid and accurate results for the identification of CoNS (134; 100%).

Research paper thumbnail of Procalcitonin, C-Reactive Protein, Albumin, and Blood Cultures as Early Markers of Sepsis Diagnosis or Predictors of Outcome: A Prospective Analysis

Sepsis is a condition with high mortality rates and its diagnosis remains a challenge. We assesse... more Sepsis is a condition with high mortality rates and its diagnosis remains a challenge. We assessed epidemiological, clinical data, multiple biomarker profiles, and blood culture with respect to sepsis diagnosis and predictors of outcome. METhODS: In total, 183 patients who were suspected of having sepsis and underwent blood culture collection were followed up for 7 days. Sepsis-related Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation (APACHE) II scores were calculated daily; biomarkers and blood culture test results were evaluated. RESulTS: In total, 78 (43%) had sepsis, 50 (27%) had septic shock, and 55 (30%) had no sepsis. Blood culture was positive in 28% and 42% of the sepsis and septic shock groups, respectively (P < .001). Regarding clinical profiles and biomarker values, there were no differences between the sepsis and non-sepsis groups, but significant differences were observed in the septic shock group. Multivariate logistic regression models revealed that age, serum albumin level, APACHE II, and SOFA 1 st day scores were the independent variables for death. COnCluSiOnS: The challenge in the diagnosis of sepsis continues as clinical and laboratory differences found between the groups were due to septic shock. Older aged patients with lower albumin levels and higher APACHE II and SOFA 1 st day scores have a greater probability of mortality.