WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil.

The dissemination of carbapenem-resistant and third generation cephalosporin-resistant pathogens is a critical issue that is no longer restricted to hospital settings. The rapid spread of critical priority pathogens in Brazil is notably worrying, considering its continental dimension, the diversity of international trade, livestock production, and human travel. We conducted a nationwide genomic investigation under a One Health perspective that included Escherichia coli strains isolated from humans and nonhuman sources, over 45 years (1974-2019). One hundred sixty-seven genomes were analyzed extracting clinically relevant information (i.e., resistome, virulome, mobilome, sequence types [STs], and phylogenomic). The endemic status of extended-spectrum ß-lactamase (ESBL)-positive strains carrying a wide diversity of blaCTX-M variants, and the growing number of colistin-resistant isolates carrying mcr-type genes was associated with the successful expansion of international ST10, ST38, ST115, ST131, ST354, ST410, ST648, ST517, and ST711 clones; phylogenetically related and shared between human and nonhuman hosts, and polluted aquatic environments. Otherwise, carbapenem-resistant ST48, ST90, ST155, ST167, ST224, ST349, ST457, ST648, ST707, ST744, ST774, and ST2509 clones from human host harbored blaKPC-2 and blaNDM-1 genes. A broad resistome to other clinically relevant antibiotics, hazardous heavy metals, disinfectants, and pesticides was further predicted. Wide virulome associated with invasion/adherence, exotoxin and siderophore production was related to phylogroup B2. The convergence of wide resistome and virulome has contributed to the persistence and rapid spread of international high-risk clones of critical priority E. coli at the human-animal-environmental interface, which must be considered a One Health challenge for a post-pandemic scenario. IMPORTANCE A One Health approach for antimicrobial resistance must integrate whole-genome sequencing surveillance data of critical priority pathogens from human, animal and environmental sources to track hot spots and routes of transmission and developing effective prevention and control strategies. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we present genomic data of WHO critical priority carbapenemase-resistant, ESBL-producing, and/or colistin-resistant Escherichia coli strains isolated from humans and nonhuman sources in Brazil, a country with continental proportions and high levels of antimicrobial resistance. The present study provided evidence of epidemiological and clinical interest, highlighting that the convergence of wide virulome and resistome has contributed to the persistence and rapid spread of international high-risk clones of E. coli at the human-animal-environmental interface, which must be considered a One Health threat that requires coordinated actions to reduce its incidence in humans and nonhuman hosts.

Treating Staphylococcus aureus infections in an intensive care unit at a University Hospital in Brazil.

BACKGROUND: Optimizing antimicrobial therapy is important for treating patients who are critically ill with Staphylococcus aureus infection, and susceptibility tests are necessary. OBJECTIVE: The aim of the present study was to evaluate antibacterial therapy after susceptibility testing of S. aureus infections. Setting The setting was an intensive care unit at a University Hospital in Brazil. METHODS: An observational and retrospective study was conducted over 6 years. The antimicrobials that were used for S. aureus infection treatment were calculated as the defined daily dose per 1000 patient-days (DDD1000). Antimicrobial susceptibility data were obtained by reviewing bacteriological tests. Patient profiles and treatment were determined by analyzing patient charts. RESULTS: Methicillin-resistant S. aureus (MRSA) was prevalent in this study (76.13 %). Patients who were infected with MRSA had total antimicrobial consumption that was three-times higher (9567.2 DDD1000) than patients who were infected with methicillin-susceptible S. aureus (MSSA; 3101.1 DDD1000). The average length of stay in the intensive care unit was 19 days (interquartile range 17 days) for MSSA and 20 days (interquartile range 20 days) for MRSA. Mortality in patients who were infected with MSSA was higher (52.17 %) than in patients who were infected with MRSA (33.80 %), and de-escalation was not identified in 73.90 % of MSSA patients.

Plasmid-mediated quinolone resistance by genes qnrA1 and qnrB19 in Salmonella strains isolated in Brazil.

Considering the importance of the mechanisms involved in quinolone resistance, this study evaluate the presence of PMQR in 126 epidemic and not epidemic strains of Salmonella spp. It was noted that presence of PMQR, by itself, did not generate resistance to ciprofloxacin; but detection of qnr genes in Salmonella spp. and the identification of the qnrB19 variant in a strain of poultry origin alert for the indiscriminate use of quinolones in poultry production, that can result in a pressure for mutant selection of resistant strains with a clinical limitation use of FQs in the near future. And last but not least, is the need to continued study of resistance mechanisms and to monitor the microbial resistance profile of epidemiological strains.

Ciprofloxacin susceptibility reduction of salmonella strains isolated from outbreaks

The antimicrobial susceptibility of 212 Salmonella strains isolated from patients and foods was evaluated and 45 percent were found to be resistant to nalidixic acid. Nalidixic acid resistant strains showed a higher minimal inhibitory concentration for ciprofloxacin than sensitive strains. During the study an increase of strains with reduced susceptibility to ciprofloxacin was also observed.

Ciprofloxacin susceptibility reduction of Salmonella strains isolated from outbreaks.

The antimicrobial susceptibility of 212 Salmonella strains isolated from patients and foods was evaluated and 45% were found to be resistant to nalidixic acid. Nalidixic acid resistant strains showed a higher minimal inhibitory concentration for ciprofloxacin than sensitive strains. During the study an increase of strains with reduced susceptibility to ciprofloxacin was also observed.

High prevalence of children colonized with penicillin-resistant Streptococcus pneumoniae in public day-care centers.

OBJECTIVES: To investigate the prevalence of Streptococcus pneumoniae (pneumococci) in the nasopharynx of healthy children enrolled in public day-care centers of the municipality of Umuarama, state of Paraná, Brazil. The susceptibility of the pneumococcal strains to antimicrobial agents was also studied. METHODS: Nasopharyngeal specimens from 212 children were collected from April to October 2008. After the specimens were seeded in blood agar and incubated at 37 degrees C for 24-48 hours, the colonies suspected of belonging to S. pneumoniae were identified using alpha-hemolysis, optochin sensitivity, and bile solubility test. Penicillin susceptibility was investigated using the disk diffusion and dilution tests. Susceptibility to the other antimicrobial agents indicated for the treatment of pneumococcal infections was investigated using the disk diffusion test. RESULTS: The prevalence of nasopharyngeal pneumococci was 43.4% (92/212), with higher rates in children between 2 and 5 years old (p = 0.0005). There was no significant difference between sexes. Intermediate and full resistance to penicillin were found in 34.8 (32/92) and 22.8% (21/92) isolates, respectively. Sixty-seven strains (72.8%) were resistant to sulfamethoxazole-trimethoprim, eight (8.7%) were resistant to erythromycin, and six (6.5%) to tetracycline. One strain was resistant to clindamycin (1.1%) and another was resistant to chloramphenicol (1.1%). All strains were sensitive to levofloxacin, ofloxacin, rifampicin, telithromycin, linezolid, and vancomycin. Nine strains were considered multiresistant because they were resistant to three or more classes of antimicrobial agents. CONCLUSIONS: The present study detected a high prevalence of healthy children colonized with penicillin-resistant S. pneumoniae strains who may be important reservoirs of this pathogen in the community.

Alta prevalência de crianças portadoras de Streptococcus pneumoniae resistentes à penicilina em creches públicas / High prevalence of children colonized with penicillin-resistant Streptococcus pneumoniae in public day-care centers

OBJETIVOS: Investigar a prevalência de Streptococcus pneumoniae (pneumococos) na nasofaringe de crianças sadias atendidas em creches municipais da cidade de Umuarama (PR). Avaliar a susceptibilidade aos antimicrobianos dos pneumococos isolados. MÉTODOS: Secreção da nasofaringe de 212 crianças foi coletada no período de abril a outubro de 2008. Após semeadura dos espécimes em ágar sangue e incubação a 37 °C por 24-48 horas, as colônias suspeitas de pertencerem a S. pneumoniae foram identificadas pela α-hemólise, sensibilidade à optoquina e bile solubilidade. A susceptibilidade à penicilina foi investigada pelos testes de disco-difusão e de diluição. A susceptibilidade aos demais antimicrobianos indicados no tratamento das infecções pneumocócicas foi realizada por disco-difusão RESULTADOS: A prevalência de pneumococos na nasofaringe foi de 43,4 por cento (92/212), sendo maior em crianças com idade entre 2 e 5 anos (p = 0,0005). Não houve diferença significativa entre os sexos. Resistência intermediária e resistência plena à penicilina foram encontradas respectivamente em 34,8 (32/92) e 22,8 por cento (21/92) dos isolados. Sessenta e sete amostras (72,8 por cento) foram resistentes ao sulfametoxazol-trimetoprim, oito (8,7 por cento) à eritromicina e seis (6,5 por cento) à tetraciclina. Uma amostra apresentou resistência à clindamicina (1,1 por cento), e outra ao cloranfenicol (1,1 por cento). Todas as amostras foram sensíveis a levofloxacina, ofloxacina, rifampicina, telitromicina, linezolide e vancomicina. Nove amostras foram consideradas multirresistentes, por apresentarem resistência a três ou mais classes de antimicrobianos. CONCLUSÕES: O presente estudo registrou uma alta prevalência de crianças portadoras sadias de amostras de S. pneumoniae resistentes à penicilina que podem constituir importantes reservatórios desse patógeno na comunidade.

OBJECTIVES: To investigate the prevalence of Streptococcus pneumoniae (pneumococci) in the nasopharynx of healthy children enrolled in public day-care centers of the municipality of Umuarama, state of Paraná, Brazil. The susceptibility of the pneumococcal strains to antimicrobial agents was also studied. METHODS: Nasopharyngeal specimens from 212 children were collected from April to October 2008. After the specimens were seeded in blood agar and incubated at 37 °C for 24-48 hours, the colonies suspected of belonging to S. pneumoniae were identified using α-hemolysis, optochin sensitivity, and bile solubility test. Penicillin susceptibility was investigated using the disk diffusion and dilution tests. Susceptibility to the other antimicrobial agents indicated for the treatment of pneumococcal infections was investigated using the disk diffusion test. RESULTS: The prevalence of nasopharyngeal pneumococci was 43.4 percent (92/212), with higher rates in children between 2 and 5 years old (p = 0.0005). There was no significant difference between sexes. Intermediate and full resistance to penicillin were found in 34.8 (32/92) and 22.8 percent (21/92) isolates, respectively. Sixty-seven strains (72.8 percent) were resistant to sulfamethoxazole-trimethoprim, eight (8.7 percent) were resistant to erythromycin, and six (6.5 percent) to tetracycline. One strain was resistant to clindamycin (1.1 percent) and another was resistant to chloramphenicol (1.1 percent). All strains were sensitive to levofloxacin, ofloxacin, rifampicin, telithromycin, linezolid, and vancomycin. Nine strains were considered multiresistant because they were resistant to three or more classes of antimicrobial agents. CONCLUSIONS: The present study detected a high prevalence of healthy children colonized with penicillin-resistant S. pneumoniae strains who may be important reservoirs of this pathogen in the community.

Quinolone-resistant Escherichia coli.

Quinolones (nalidixic acid--NAL, norfloxacin--NOR, ciprofloxacin--CIP and gatifloxacin--GAT) were tested against Escherichia coli isolated from urine (385 patient samples) by disk diffusion (DD) and agar dilution (AD) methods. Fifty-three samples (13.8%) were classified as resistant to at least one of the quinolones tested. CIP and NOR susceptibilities were the same (91.4%) and they were similar to GAT (92.7%). Susceptibility to NAL, detected by the disk diffusion method, was used to predict susceptibility to NOR, CIP and GAT by the agar dilution method. The sensitivity and specificity of NAL were 100% and 95%, respectively. Twelve samples were analyzed for mutations in the quinolone resistance-determining region (QRDR) of the gyrA and parC genes. Sequencing of these genes failed to find any mutations in the quinolone-sensitive isolates. However, three mutations were observed in the isolates resistant to all the quinolones tested--two in gyrA and one in parC. A single mutation in gyrA was found in the strains that were resistant to nalidixic acid but fluoroquinolone-sensitive. These findings support the suggestion that NAL could be used as a marker for susceptibility to fluoroquinolones in routine microbiology laboratories. The overall resistance rate to quinolones in the present study was 13.8%, which is higher than that observed in other studies carried out in developed countries. Our findings serve as a warning that resistance to this group of antimicrobial agents is increasing.

Quinolone-resistant Escherichia coli

Quinolones (nalidixic acid - NAL, norfloxacin - NOR, ciprofloxacin - CIP and gatifloxacin - GAT) were tested against Escherichia coli isolated from urine (385 patient samples) by disk diffusion (DD) and agar dilution (AD) methods. Fifty-three samples (13.8 percent) were classified as resistant to at least one of the quinolones tested. CIP and NOR susceptibilities were the same (91.4 percent) and they were similar to GAT (92.7 percent). Susceptibility to NAL, detected by the disk diffusion method, was used to predict susceptibility to NOR, CIP and GAT by the agar dilution method. The sensitivity and specificity of NAL were 100 percent and 95 percent, respectively. Twelve samples were analyzed for mutations in the quinolone resistance-determining region (QRDR) of the gyrA and parC genes. Sequencing of these genes failed to find any mutations in the quinolone-sensitive isolates. However, three mutations were observed in the isolates resistant to all the quinolones tested - two in gyrA and one in parC. A single mutation in gyrA was found in the strains that were resistant to nalidixic acid but fluoroquinolone-sensitive. These findings support the suggestion that NAL could be used as a marker for susceptibility to fluoroquinolones in routine microbiology laboratories. The overall resistance rate to quinolones in the present study was 13.8 percent, which is higher than that observed in other studies carried out in developed countries. Our findings serve as a warning that resistance to this group of antimicrobial agents is increasing.

Endocarditis due to glycopeptide-intermediate Staphylococcus aureus: case report and strain characterization.

We report a case of infective endocarditis due to vancomycin-intermediate Staphylococcus aureus (VISA) that did not respond to high doses of vancomycin. Initial vancomycin MIC of the last isolate recovered from blood was 8 micro g/mL, but could be induced up to 32 micro g/mL by consecutive growing with vancomycin. Clinical response was only accomplished when linezolid was included in therapy.