Prevalence of resistance to macrolides and aminoglycosides in Mycobacterium avium, M. abscessus, and M. chelonae identified in the Laboratorio Nacional de Referencia of Colombia from 2018 to 2022 / Prevalencia de la resistencia a macrólidos y aminoglucósidos en los complejos Mycobacterium avium y M. abscessus y en Mycobacterium chelonae identificados en el Laboratorio Nacional de Referencia de Colombia entre el 2018 y el 2022.

Introduction: The Mycobacterium chelonae species and the M. avium and M. abscessus complexes are emerging pathogens that cause mycobacteriosis. Treatment depends on the species and subspecies identified. The drugs of choice are macrolides and aminoglycosides. However, due to the resistance identified to these drugs, determining the microbe's sensitivity profile will allow clinicians to improve the understanding of the prognosis and evolution of these pathologies. Objective: To describe the macrolide and aminoglycoside susceptibility profile of cultures identified by Colombia's Laboratorio Nacional de Referencia de Mycobacteria from 2018 to 2022, as Mycobacterium avium complex, M. abscessus complex, and M. chelonae. Materials and methods. This descriptive study exposes the susceptibility profile to macrolides and aminoglycosides of cultures identified as M. avium complex, M. abscessus complex, and M. chelonae using the GenoType® NTM-DR method. Materials and methods: This descriptive study exposes the susceptibility profile to macrolides and aminoglycosides of cultures identified as M. avium complex, M. abscessus complex, and M. chelonae using the GenoType® NTM-DR method. Results: We identified 159 (47.3 %) cultures as M. avium complex, of which 154 (96.9 %) were sensitive to macrolides, and 5 (3.1 %) were resistant; all were sensitive to aminoglycosides. From the 125 (37.2 %) cultures identified as M. abscessus complex, 68 (54.4 %) were sensitive to macrolides, 57 (45.6 %) were resistant to aminoglycosides, and just one (0.8 %) showed resistance to aminoglycosides. The 52 cultures (15.5 %) identified as M. chelonae were sensitive to macrolides and aminoglycosides. Conclusions: The three studied species of mycobacteria have the least resistance to Amikacin. Subspecies identification and their susceptibility profiles allow the establishment of appropriate treatment schemes, especially against M. abscessus.

Introducción. Mycobacterium chelonae y los complejos Mycobacterium avium y M. abscessus, son agentes patógenos emergentes causantes de micobacteriosis. El tratamiento de esta infección depende de la especie y la subespecie identificadas. Los fármacos de elección son los macrólidos y aminoglucósidos, contra los cuales se ha reportado resistencia; por esta razón, el determinar el perfil de sensibilidad le permite al médico tratante comprender mejor el pronóstico y la evolución de estas infecciones. Objetivo. Describir los perfiles de sensibilidad ante macrólidos y aminoglucósidos, de los cultivos identificados como complejo Mycobacterium avium, complejo M. abscessus o especie M. chelonae, en el Laboratorio Nacional de Referencia de Micobacterias durante los años 2018 a 2022. Materiales y métodos. Se llevó a cabo un estudio descriptivo del perfil de sensibilidad a macrólidos y aminoglucósidos, de los cultivos identificados como complejo M. avium, complejo M. abscessus o M. chelonae, mediante la metodología GenoType® NTM-DR. Resultados. Los cultivos del complejo M. avium fueron 159 (47,3 %), de los cuales, 154 (96,9 %) fueron sensibles y 5 (3,1 %) resistentes a los macrólidos; todos fueron sensibles a los aminoglucósidos. Del complejo M. abscessus se estudiaron 125 (37,2 %) cultivos, 68 (54,4 %) resultaron sensibles y 57 (45,6 %) resistentes a los macrólidos; solo un cultivo (0,8 %) fue resistente a los aminoglucósidos. De M. chelonae se analizaron 52 cultivos (15,5 %), todos sensibles a los macrólidos y aminoglucósidos. Conclusiones. En las tres especies de micobacterias estudiadas, la resistencia contra la amikacina fue la menos frecuente. La identificación de las subespecies y los perfiles de sensibilidad permiten instaurar esquemas de tratamiento adecuados, especialmente en las micobacteriosis causadas por M. abscessus.

RpoS role in antibiotic resistance, tolerance and persistence in E. coli natural isolates.

BACKGROUND: The intrinsic concentration of RpoS, the second most abundant sigma factor, varies widely across the E. coli species. Bacterial isolates that express high levels of RpoS display high resistance to environmental stresses, such as temperature, pH and osmolarity shifts, but are less nutritional competent, making them less capable of utilising alternative nutrient sources. The role of RpoS in antibiotic resistance and persistence in standard laboratory domesticated strains has been examined in several studies, most demonstrating a positive role for RpoS. RESULTS: Using disk diffusion assays we examined bacterial resistance to 15 different antibiotics, including ß -lactams (penicillins, monobactams, carbapenems and cephalosporins), aminoglycosides, quinolones and anti-folates, in a representative collection of 328 E. coli natural isolates displaying a continuum of different levels of RpoS. There was an overall trend that isolates with higher levels of RpoS were slightly more resistant to these antibiotics. In addition, the effect of RpoS on bacterial tolerance and persistence to 3 different antibiotics - ampicillin, ciprofloxacin and kanamycin was evaluated through time-kill curves. Again, there was a small beneficial effect of RpoS on tolerance and persistence to these antibiotics, but this difference was not statistically significant. Finally, a K-12 strain expressing high levels of RpoS was compared with its isogenic RpoS-null counterpart, and no significant effect of RpoS was found. CONCLUSION: Based on a representative collection of the species E. coli, RpoS was found to have a very small impact on antibiotic resistance, tolerance, or persistence.

Prevalence of Brucella melitensis and Brucella abortus aminoglycoside-resistant isolates: a systematic review and meta-analysis.

INTRODUCTION: Aminoglycosides are vital antibiotics for treating Brucella infections, because they interfere with bacterial protein production and are often combined with other antibiotics. They are cost-effective, have fewer side effects, and can penetrate biofilms. The prevalence of brucellosis has increased in recent years, increasing the need for effective treatments. In addition, the emergence of multidrug-resistant Brucella strains has highlighted the need for an updated and comprehensive understanding of aminoglycoside resistance. This systematic review aimed to provide a comprehensive overview of the global prevalence of aminoglycoside resistance in B. melitensis and B. abortus. METHODS: A systematic search of online databases was conducted and eligible studies met certain criteria and were published in English. Quality assessment was performed using the JBI Checklist. A random-effects model was fitted to the data, and meta-regression, subgroup, and outlier/influential analyses were performed. The analysis was performed using R and the metafor package. RESULTS: The results of this systematic review and meta-analysis suggested that the average prevalence rates of streptomycin, gentamicin, and amikacin resistance were 0.027 (95% confidence interval [CI], 0.015-0.049), 0.023 (95% CI, 0.017-0.032), and 0.008 (95% CI, 0.002-0.039), respectively. The prevalence of streptomycin resistance was higher in the unidentified Brucella group than in the B. abortus and B. melitensis groups (0.234, 0.046, and 0.017, respectively; p < 0.02). The prevalence of gentamicin resistance increased over time (r = 0.064; 95% CI, 0.018 to 0.111; p = 0.007). The prevalence of resistance did not correlate with the quality score for any antibiotic. Funnel plots showed a potential asymmetry for streptomycin and gentamicin. These results suggest a low prevalence of antibiotic resistance in the studied populations. CONCLUSION: The prevalence of aminoglycoside resistance in B. melitensis and B. abortus was low. However, gentamicin resistance has increased in recent years. This review provides a comprehensive and updated understanding of aminoglycoside resistance in B. melitensis and B. abortus.

Impact of the national shortage of polymyxin B in critically ill patients during the COVID-19 pandemic / Impacto da escassez nacional de polimixina B em pacientes gravemente enfermos durante a pandemia de COVID-19 / Impacto del desabasto nacional de polimixina B en pacientes críticos durante la pandemia de COVID-19

Background and Objectives: during the COVID-19 pandemic, the number of critical patients requiring intensive care increased considerably, resulting in an increase in infections due to multi-resistant microorganisms. In Brazil, in 2021, due to the high demand for polymyxin B use, there was a national shortage of the medication. One strategy used to overcome this situation was aminoglycoside use. The work aimed to analyze the impact of replacing polymyxin B with amikacin and gentamicin in the final stage of patients. Method: an analytical study with an observational, cross-sectional design, with a quantitative approach, through a retrospective analysis through the analysis of medical records, with the primary stages being discharges or deaths. Results: mortality was similar between the group treated with aminoglycoside and the group treated with polymyxin B. Within the aminoglycoside group, mortality was higher in the group that had bacteria resistant to the drug than in the group that had infection with an organism sensitive to this drug. Mortality was not affected by comorbidities, age, or number of hospital infections. The main factor that led to the need for dialysis was the combination of two nephrotoxic medications. Conclusion: two hypotheses emerged: the first would be that replacing polymyxin B with aminoglycosides did not impact mortality; the other would be that, regardless of the antibiotic group used, patients had a high risk of death. Despite sample limitations, the study corroborates the adoption of strategies for the rational use of antimicrobials.(AU)

Justificativa e Objetivos: durante a pandemia de COVID-19, o número de pacientes críticos que necessitaram de cuidados intensivos aumentou consideravelmente, resultando em aumento de infecções por microrganismos multirresistentes. No Brasil, em 2021, devido à grande demanda pelo uso da polimixina B, houve escassez nacional do medicamento. Uma estratégia utilizada para superar essa situação foi o uso de aminoglicosídeos. O trabalho teve como objetivo analisar o impacto da substituição da polimixina B por amicacina e gentamicina na fase final dos pacientes. Método: estudo analítico com desenho observacional, transversal, com abordagem quantitativa, por meio de análise retrospectiva por meio de análise de prontuários, sendo as etapas primárias as altas ou óbitos. Resultados: a mortalidade foi semelhante entre o grupo tratado com aminoglicosídeo e o grupo tratado com polimixina B. Dentro do grupo aminoglicosídeo, a mortalidade foi maior no grupo que apresentava bactérias resistentes ao medicamento do que no grupo que apresentava infecção por organismo sensível a este medicamento. medicamento. A mortalidade não foi afetada por comorbidades, idade ou número de infecções hospitalares. O principal fator que levou à necessidade de diálise foi a combinação de dois medicamentos nefrotóxicos. Conclusão: surgiram duas hipóteses: a primeira seria que a substituição da polimixina B por aminoglicosídeos não impactou a mortalidade; a outra seria que, independentemente do grupo de antibióticos utilizado, os pacientes apresentavam alto risco de morte. Apesar das limitações amostrais, o estudo corrobora a adoção de estratégias para o uso racional de antimicrobianos.(AU)

Antecedentes y Objetivos: durante la pandemia de COVID-19, el número de pacientes críticos que requirieron cuidados intensivos aumentó considerablemente, resultando en un aumento de infecciones por microorganismos multirresistentes. En Brasil, en 2021, debido a la alta demanda del uso de polimixina B, hubo escasez nacional del medicamento. Una estrategia utilizada para superar esta situación fue el uso de aminoglucósidos. El trabajo tuvo como objetivo analizar el impacto de la sustitución de la polimixina B por amikacina y gentamicina en la etapa final de los pacientes. Método: estudio analítico con diseño observacional, transversal, con enfoque cuantitativo, mediante un análisis retrospectivo mediante el análisis de historias clínicas, siendo las etapas primarias las altas o defunciones. Resultados: la mortalidad fue similar entre el grupo tratado con aminoglucósido y el grupo tratado con polimixina B. Dentro del grupo de aminoglucósido, la mortalidad fue mayor en el grupo que tenía bacterias resistentes al fármaco que en el grupo que tenía infección con un organismo sensible a este. droga. La mortalidad no se vio afectada por las comorbilidades, la edad o el número de infecciones hospitalarias. El principal factor que llevó a la necesidad de diálisis fue la combinación de dos medicamentos nefrotóxicos. Conclusión: surgieron dos hipótesis: la primera sería que la sustitución de polimixina B por aminoglucósidos no impactó la mortalidad; la otra sería que, independientemente del grupo de antibióticos utilizado, los pacientes tenían un alto riesgo de muerte. A pesar de las limitaciones de la muestra, el estudio corrobora la adopción de estrategias para el uso racional de antimicrobianos.(AU)

Experience of the use of lock therapy in pediatric patients with central venous catheter. / Experiencia del uso de terapia de sello en pacientes pediátricos con catéter venoso central.

Lock therapy is useful for preserving indwelling catheters. Few lock therapy studies have been published in Latin America. OBJECTIVE: To describe the clinical characteristics of pediatric patients using therapeutic and prophylactic lock therapy for six years in a high-complexity hospital in Colombia. PATIENTS AND METHOD: Cross-sectional descriptive study of patients aged < 18 years who received lock therapy. Collected variables included demographic data, clinical characteristics, blood test results, therapeutic interventions, frequency of admission to the pediatric critical care unit, and mortality. Descriptive analysis was performed. RESULTS: 54 patients were included in the study, most of them males, with 67 episodes of therapeutic lock therapy use. The most frequent diagnosis was hematological neoplasm (61%). Among these patients, 88% presented neutropenia while receiving lock therapy. Catheter preservation was achieved in 75% of the cases. Aminoglycosides were the most commonly used antibiotics (38%). Mortality due to catheter-related bacteremia was 6%. Catheter preservation using ethanol solution 70% was achieved in 62% of the patients with prophylactic lock therapy, all of whom had chronic gastrointestinal pathology. CONCLUSION: Catheter preservation rates were 75% and 62% in patients with therapeutic and prophylactic lock therapy, respectively, with a higher rate achieved among cancer patients with neutropenia (80%). Aminoglycosides and vancomycin were the most commonly used antibiotics.

[Advances of the novel immunosuppressant brasilicardin A].

Brasilicardin A (BraA) is a natural diterpene glycoside isolated from the pathogenic actinomycete Nocardia brasiliensis IFM 0406 with highly potent immunosuppressive activity (IC50=0.057 µg/mL). BraA potently inhibits the uptake of amino acids that are substrates for amino acid transport system L of T cells, which is different from the existing clinical immunosuppressants. BraA is more potent in a mouse mixed lymphocyte reaction and less toxic against various human cell lines compared with the known clinical immunosuppressants, such as cyclosporin A, ascomycin and tacrolimus. Therefore, BraA attracted more attention as a new promising immunosuppressant. However, the development of this promising immunosuppressant as drug for medical use is so far hindered because BraA has the unusual and synthetically challenging skeleton and shows the low-yield production in the natural pathogenic producer. This review introduces the molecular structure of BraA, its activity, mechanism of action, chemical synthesis of BraA analogs, heterologous expression of gene cluster, and an application of combining microbial and chemical synthesis for production of BraA, with the aim to facilitate the efficient production of BraA and its analogs.

Bacterial keratitis in a tertiary hospital in São Paulo: a 21-year review of the epidemiological, laboratory, and clinical data.

Infectious keratitis is a sight-threatening condition that is usually an ocular emergency. The visual outcome depends on prompt and accurate clinical management as well as geographic and epidemiological awareness. We conducted a retrospective observational study to define the epidemiological and laboratory profile, as well as the clinical course of bacterial keratitis in a tertiary hospital in São Paulo over 21 years. Information about age, sex, predisposing factors, topical and surgical treatment, visual acuity, ulcers' classification, bacterioscopy, culture, and antibiotic sensitivity tests were collected. This study included 160 patients. The mean age was 65.1 ± 18.4 years and risk factors were identified in 83.1 % of the patients. Empirical topical fortified cephalosporin with an aminoglycoside or fourth-generation fluoroquinolone was curative for 66.2 % of the cases. The mean treatment duration was 22.5 ± 9 days. The mean variation of visual acuity was -0.25 logMAR, p < 0.001. Culture revealed 64 % of Gram-positive bacteria. All Gram-positive bacteria were sensitive to cephalothin, vancomycin, and quinolones. All Gram-negative bacteria were sensitive to gentamicin, tobramycin, amikacin, and ciprofloxacin. These findings reinforce the importance of prompt empirical treatment of severe corneal ulcers with a fortified cephalosporin and aminoglycoside or a fourth-generation fluoroquinolone as there are equally effective. Collected data was insufficient to evaluate resistance of ocular infections over time in this population.

Invasive non-typhoidal Salmonella (iNTS) aminoglycoside-resistant ST313 isolates feature unique pathogenic mechanisms to reach the bloodstream.

Invasive non-typhoidal Salmonella (iNTS) from the clonal type ST313 (S. Typhimurium ST313) is the primary cause of invasive salmonellosis in Africa. Recently, in Brazil, iNTS ST313 strains have been isolated from different sources, but there is a lack of understanding of the mechanisms behind how these gut bacteria can break the gut barrier and reach the patient's bloodstream. Here, we compare 13 strains of S. Typhimurium ST313, previously unreported isolates, from human blood cultures, investigating aspects of virulence and mechanisms of resistance. Initially, RNAseq analyses between ST13-blood isolate and SL1344 (ST19) prototype revealed 15 upregulated genes directly related to cellular invasion and replication, such as sopD2, sifB, and pipB. Limited information is available about S. Typhimurium ST313 pathogenesis and epidemiology, especially related to the global distribution of strains. Herein, the correlation of strains isolated from different sources in Brazil was employed to compare clinical and non-clinical isolates, a total of 22 genomes were studied by single nucleotide polymorphism (SNPs). The epidemiological analysis of 22 genomes of S. Typhimurium ST313 strains grouped them into three distinct clusters (A, B, and C) by SNP analysis, where cluster A comprised five, group B six, and group C 11. The 13 clinical blood isolates were all resistant to streptomycin, 92.3% of strains were resistant to ampicillin and 15.39% were resistant to kanamycin. The resistance genes acrA, acrB, mdtK, emrB, emrR, mdsA, and mdsB related to the production of efflux pumps were detected in all (100%) strains studied, similar to pathogenic traits investigated. In conclusion, we evidenced that S. Typhimurium ST313 strains isolated in Brazil have unique epidemiology. The elevated frequencies of virulence genes such as sseJ, sopD2, and pipB are a major concern in these Brazilian isolates, showing a higher pathogenic potential.

Global scenario of the RmtE pan-aminoglycoside-resistance mechanism: emergence of the rmtE4 gene in South America associated with a hospital-related IncL plasmid.

Antimicrobial resistance (AMR) mechanisms, especially those conferring resistance to critically important antibiotics, are a great concern for public health. 16S rRNA methyltransferases (16S-RMTases) abolish the effectiveness of most clinically used aminoglycosides, but some of them are considered sporadic, such as RmtE. The main goals of this work were the genomic analysis of bacteria producing 16S-RMTases from a 'One Health' perspective in Venezuela, and the study of the epidemiological and evolutionary scenario of RmtE variants and their related mobile genetic elements (MGEs) worldwide. A total of 21 samples were collected in 2014 from different animal and environmental sources in the Cumaná region (Venezuela). Highly aminoglycoside-resistant Enterobacteriaceae isolates were selected, identified and screened for 16S-RMTase genes. Illumina and Nanopore whole-genome sequencing data were combined to obtain hybrid assemblies and analyse their sequence type, resistome, plasmidome and pan-genome. Genomic collections of rmtE variants and their associated MGEs were generated to perform epidemiological and phylogenetic analyses. A single 16S-RMTase, the novel RmtE4, was identified in five Klebsiella isolates from wastewater samples of Cumaná. This variant possessed three amino acid modifications with respect to RmtE1-3 (Asn152Asp, Val216Ile and Lys267Ile), representing the most genetic distant among all known and novel variants described in this work, and the second most prevalent. rmtE variants were globally spread, and their geographical distribution was determined by the associated MGEs and the carrying bacterial species. Thus, rmtE4 was found to be confined to Klebsiella isolates from South America, where it was closely related to ISVsa3 and an uncommon IncL plasmid related with hospital environments. This work uncovered the global scenario of RmtE and the existence of RmtE4, which could potentially emerge from South America. Surveillance and control measures should be developed based on these findings in order to prevent the dissemination of this AMR mechanism and preserve public health worldwide.

Whole genome analysis of Gram-negative bacteria using the EPISEQ CS application and other bioinformatic platforms.

OBJECTIVES: To determine genomic characteristics and molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa from medical centres of Mexico using whole genome sequencing data analysed with the EPISEQⓇ CS application and other bioinformatic platforms. METHODS: Clinical isolates collected from 28 centres in Mexico included carbapenem-non-susceptible K. pneumoniae (n = 22), E. coli (n = 24), A. baumannii (n = 16), and P. aeruginosa (n = 13). Isolates were subjected to whole genome sequencing using the Illumina (MiSeq) platform. FASTQ files were uploaded to the EPISEQⓇ CS application for analysis. Additionally, the tools Kleborate v2.0.4 and Pathogenwatch were used as comparators for Klebsiella genomes, and the bacterial whole genome sequence typing database was used for E. coli and A. baumannii. RESULTS: For K. pneumoniae, both bioinformatic approaches detected multiple genes encoding aminoglycoside, quinolone, and phenicol resistance, and the presence of blaNDM-1 explained carbapenem non-susceptibility in 18 strains and blaKPC-3 in four strains. Regarding E. coli, both EPISEQⓇ CS and bacterial whole genome sequence typing database analyses detected multiple virulence and resistance genes: 20 of 24 (83.3%) strains carried blaNDM, 3 of 24 (12.4%) carried blaOXA-232, and 1 carried blaOXA-181. Genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, trimethoprim, and macrolides were also detected by both platforms. Regarding A. baumannii, the most frequent carbapenemase-encoding gene detected by both platforms was blaOXA-72, followed by blaOXA-66. Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, blaVIM, blaIMP, and blaGES were the more frequently detected. Multiple virulence genes were detected in all strains. CONCLUSION: Compared to the other available platforms, EPISEQⓇ CS enabled a comprehensive resistance and virulence analysis, providing a reliable method for bacterial strain typing and characterization of the virulome and resistome.

Antimicrobial profile of non-typhoidal Salmonella isolated from raw sewage in the Metropolitan Region of São Paulo, Brazil.

INTRODUCTION: Non-typhoidal Salmonella (NTS), are frequently found in sewage and are one of the main causes of diarrhea in developed and developing countries due to poor sanitation conditions. In addition, NTS can potentially act as reservoirs and vehicles for the transmission of antimicrobial resistance (AMR), which can be facilitated by the discharge of sewage effluents into environmental matrices. This study aimed to analyze a NTS Brazilian collection, focusing on their antimicrobial susceptibility profile and the presence of clinically relevant AMR-encoding genes. METHODOLOGY: Forty-five non-clonal NTS strains from serotypes Salmonella enteritidis (n = 6), Salmonella enterica serovar 1,4,[5],12:i:- (S. 1,4,[5],12:i:-) (n = 25), Salmonella cerro (n = 7), Salmonella typhimurium (n = 3) and Salmonella braenderup (n = 4) were studied. Antimicrobial susceptibility testing was done using the Clinical and Laboratory Standards Institute guidelines (2017) and genes encoding resistance to beta-lactams, fluoroquinolones and aminoglycosides were identified by polymerase chain reaction and sequencing. RESULTS: Resistance to ß-lactams, fluoroquinolones, tetracyclines and aminoglycosides was frequent. The highest rates were observed for nalidixic acid (89.0%), followed by tetracycline (67.0%), ampicillin (67.0%), amoxicillin + clavulanic acid (64.0%); ciprofloxacin (47.0%) and streptomycin (42.0%). The AMR-encoding genes detected were qnrB, oqxAB, blaCTX-M and rmtA. CONCLUSIONS: Raw sewage has been considered a valuable tool to evaluate epidemiological population patterns and this study supports the view that NTS with pathogenic potential and resistance to antimicrobials are circulating in the studied region. This is worrisome due to the dissemination of these microorganisms throughout the environment.

The antibiotic resistome in Escherichia coli isolated from human, food, and animal sources.

AIMS: The aim of this study was to analyze and compare the prevalence and distribution of resistance genes in Escherichia coli genomes isolated from human clinical samples and animal-based foods worldwide. METHODS AND RESULTS: We download from NCBI Pathogen Detection Database the corresponding metadata of the 7,123 E. coli genome to access the information about the antimicrobial resistance gene content. The geographic location and the source of isolation were also obtained and compiled with the antimicrobial resistance gene for statistical analysis, results and discussion. Our criteria considered four groups for analyzing the antimicrobial resistance gene distribution. The first group of genomes from invasive clinical human (ICH) samples from countries with Human Development Index (HDI) ≥ 0.850; the second group of ICH from countries with an HDI ≤ 0.849; the third group of animal-based foods (ABF) from countries with HDI ≥ 0.850 and the fourth group of ABFs from countries with HDI ≤ 0.849. The most prevalent genes in the first group were blaCTX-M-134 (96.53%) and blaCTX-M-27 (86.35%). In the second group, ere(A) (95.96%), soxS (94.49%), qepA8 (90.81%), blaCTX-M-15 (85.66%), and fosA3 (80.88%). In the third group, the most frequently detected were aadA12 (98.5%), ant(3") (89.92%), and blaCARB-2 (87.2%). In the fourth group, aadA12 and aac(3)-IV were identified in 100% of the analyzed genomes. CONCLUSIONS: It was clear that the use of aminoglycosides in animal production is increasing the selective pressure on micro-organisms in both groups of countries since genes linked to aminoglycoside resistance are related to E. coli from ABF samples. The genomic profile of E. coli from HDI ≥ 0.850 countries indicates a selective pressure aimed at cephalosporins given the high prevalence in both sources.

Aminoglycosides' dosage in hematological malignancies and febrile neutropenia: extended interval or conventional dosage?

A patient with acute myeloid leukemia presented various episodes of febrile neutropenia, for which there was no positive response to antibiotic treatments. Following an episode of bacteremia by extensively drug-resistant Klebsiella pneumoniae, amikacin was prescribed, pharmacokinetic analyses of its plasma concentrations were performed and the dosage interval was narrowed to 12 and 8 h in order to counteract the reduced postantibiotic effect due to the patient being immunocompromised. The patient responded positively, with procalcitonin decreasing and body temperature normalizing. Recovery was finally achieved, without renal or auditory damage. This case proposes tightening dosage intervals for aminoglycosides as an effective strategy in immunocompromised patients. Aminoglycosides are given over extended intervals (24 h), considering concentration-dependent effectiveness, nephrotoxicity and postantibiotic effect. Leukocytes appear to play a determining role in the postantibiotic effect, with no proposed dosing strategy for strongly immunocompromised patients.

Plague Meningitis: A Systematic Review of Clinical Course, Antimicrobial Treatment, and Outcomes.

Plague meningitis is a serious and often fatal manifestation of Yersinia pestis infection. In the aftermath of a bioweapon attack with Y pestis, this typically rare manifestation may develop in a substantial number of patients, particularly if treatment delays occur. Risk factors, clinical evolution, and optimal treatment strategies for plague meningitis are not well understood. We searched PubMed Central and other databases for reports of plague meningitis in any language. Articles containing descriptions of patients with plague meningitis and their treatment and outcomes were included. Among 1,496 articles identified in our search, 56 articles describing 84 cases from 1898 to 2015 met inclusion criteria. The median age of patients was 16 years (range 6 weeks to 64 years); 68% were male. Most patients (n = 50, 60%) developed meningitis following primary bubonic plague. Common signs and symptoms included fever (n = 56, 66%), nuchal rigidity (n = 38, 45%), and headache (n = 33, 36%); 29% (n = 24) of patients had focal neurologic deficits such as cranial nerve abnormalities. Almost all (n = 23, 96%) of the 24 patients who did not receive antimicrobials died, and 42% (n = 25) of the 59 patients treated with antimicrobials died. The case fatality rate of patients grouped by antimicrobial received was 50% (1 out of 2) for fluoroquinolones, 19% (4 out of 21) for aminoglycosides, 14% (2 out of 14) for sulfonamides, 11% (2 out of 18) for chloramphenicol, and 0% (0 out of 13) for tetracyclines. Plague meningitis most often occurs as a complication of bubonic plague and can cause focal neurologic deficits. Survival is more likely in patients who receive antimicrobials; tetracyclines, aminoglycosides, and chloramphenicol had the lowest associated case fatality rates.

GenoType MTBDRsl for detection of second-line drugs and ethambutol resistance in multidrug-resistant Mycobacterium tuberculosis isolates at a high-throughput laboratory.

We assessed the performance of MTBDRsl for detection of resistance to fluoroquinolones, aminoglycosides/cyclic peptides, and ethambutol compared to BACTEC MGIT 960 by subjecting simultaneously to both tests 385 phenotypically multidrug-resistant-Mycobacterium tuberculosis isolates from Sao Paulo, Brazil. Discordances were resolved by Sanger sequencing. MTBDRsl correctly detected 99.7% of the multidrug-resistant isolates, 87.8% of the pre-XDR, and 73.9% of the XDR. The assay showed sensitivity of 86.4%, 100%, 85.2% and 76.4% for fluoroquinolones, amikacin/kanamycin, capreomycin and ethambutol, respectively. Specificity was 100% for fluoroquinolones and aminoglycosides/cyclic peptides, and 93.6% for ethambutol. Most fluoroquinolone-discordances were due to mutations in genome regions not targeted by the MTBDRsl v. 1.0: gyrA_H70R and gyrB_R446C, D461N, D449V, and N488D. Capreomycin-resistant isolates with wild-type rrs results on MTBDRsl presented tlyA mutations. MTBDRsl presented good performance for detecting resistance to second-line drugs and ethambutol in clinical isolates. In our setting, multidrug-resistant. isolates presented mutations not targeted by the molecular assay.

High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico.

The spread of beta-lactamase-producing bacteria is of great concern and the environment has been found to be a main source of contamination. Herein, it was proposed to determine the frequency of antimicrobial-resistant-Gram-negative bacteria throughout the Lerma River basin using phenotypic and molecular methods. Resistant bacteria were isolated with chromogenic media and antimicrobial susceptibility tests were used to characterize their resistance. ARGs for beta-lactams, aminoglycosides, and quinolones were detected by PCR. Species were identified by Sanger sequencing the 16S rRNA gene and the representative genomes of MDR strains were sequenced by NGS. A high variation in the number of isolates was observed in the 20 sampled sites, while observing a low diversity among the resistant bacteria. Of the 12 identified bacterial groups, C. freundii, E. coli, and S. marcescens were more predominant. A high frequency of resistance to beta-lactams, quinolones, and aminoglycosides was evidenced, where the blaCTX,qnrB, qnrS y, and aac(6')lb-cr genes were the most prevalent. C. freundii showed the highest frequency of MDR strains. Whole genome sequencing revealed that S. marcescens and K. pneumoniae showed a high number of shared virulence and antimicrobial resistance genes, while E. coli showed the highest number of unique genes. The contamination of the Lerma River with MDR strains carrying various ARGs should raise awareness among environmental authorities to assess the risks and regulations regarding the optimal hygienic and sanitary conditions for this important river that supports economic activities in the different communities in Mexico.

Systematic review on efficacy of preventive measures for surgical site infection by multiple-drug resistant gram-negative bacilli.

BACKGROUND: There are no specific recommendations for prevention of surgical site infection (SSI) caused by multidrug resistant Gram-negative bacilli (MDR-GNB). Our objective was to systematically review the literature evaluating the efficacy and safety of measures specifically designed to prevent MDR-GNB SSI. METHODS: We searched MEDLINE, EMBASE, CINAHL and LILACS databases up to February 18, 2020. Randomized trials and observational cohort studies evaluating the efficacy of preventive measures against MDR-GNB SSI in adult surgical patients were eligible. We evaluated methodological quality of studies and general quality of evidence using Newcastle-Ottawa scale, Cochrane ROBINS-I and GRADE method. Random-effects meta-analyses were performed using Review Manager V.5.3 software. RESULTS: A total of 10,663 titles by searching databases were identified. Two retrospective observational studies, comparing surgical antibiotic prophylaxis (SAP) with or without aminoglycoside in renal transplantation recipients, and one non-randomized prospective study, evaluating ertapenem vs. cephalosporin plus metronidazole for SAP in extended spectrum beta-lactamase producing Enterobacteriales carriers undergoing colon surgery, were included. Risk of bias was high in all studies. Meta-analysis was performed for the renal transplantation studies, with 854 patients included. Combined relative risk (RR) for MDR GNB SSI was 0.57 (95%CI: 0.25-1.34), favoring SAP with aminoglycoside (GRADE: moderate). CONCLUSIONS: There are no sufficient data supporting specific measures against MDR-GNB SSI. Prospective, randomized studies are necessary to assess the efficacy and safety of SAP with aminoglycoside for MDR-GNB SSI prevention among renal transplantation recipients and other populations. PROSPERO 2018 CRD42018100845.

Noncanonical Mismatch Repair Protein NucS Modulates the Emergence of Antibiotic Resistance in Mycobacterium abscessus.

NucS/EndoMS-dependent noncanonical mismatch repair (MMR) ensures the stability of genomic DNA in mycobacteria and acts as a guardian of the genome by preventing the accumulation of point mutations. In order to address whether the inactivation of noncanonical MMR could increase the acquisition of drug resistance by mutation, a ΔnucS strain was constructed and explored in the emerging pathogen Mycobacterium abscessus. Deletion of nucS resulted in a mutator phenotype with increased acquisition of resistance to macrolides and aminoglycosides, the two main groups of antimycobacterial agents for M. abscessus treatment, and also to second-line drugs such as fluoroquinolones. Inactivation of the noncanonical MMR in M. abscessus led to increases of 10- to 22-fold in the appearance of spontaneous mutants resistant to the macrolide clarithromycin and the aminoglycosides amikacin, gentamicin, and apramycin, compared with the wild-type strain. Furthermore, emergence of fluoroquinolone (ciprofloxacin) resistance was detected in a nucS-deficient strain but not in a wild-type M. abscessus strain. Acquired drug resistance to macrolides and aminoglycosides was analyzed through sequencing of the 23S rRNA gene rrl and the 16S rRNA gene rrs from independent drug-resistant colonies of both strains. When the acquisition of clarithromycin resistance was examined, a different mutational profile was detected in the M. abscessus ΔnucS strain compared with the wild-type one. To summarize, M. abscessus requires the NucS-dependent noncanonical MMR pathway to prevent the emergence of drug-resistant isolates by mutation. To our knowledge, this is the first report that reveals the role of NucS in a human pathogen, and these findings have potential implications for the treatment of M. abscessus infections. IMPORTANCE Chronic infections caused by M. abscessus are an emerging challenge in public health, posing a substantial health and economic burden, especially in patients with cystic fibrosis. Treatment of M. abscessus infections with antibiotics is particularly challenging, as its complex drug resistance mechanisms, including constitutive resistance through DNA mutation, lead to high rates of treatment failure. To decipher the evolution of antibiotic resistance in M. abscessus, we studied NucS-dependent noncanonical MMR, a unique DNA repair pathway involved in genomic maintenance. Inactivation of NucS is linked to the increase of DNA mutations (hypermutation), which can confer drug resistance. Our analysis detected increased acquisition of mutations conferring resistance to first-line and second-line antibiotics. We believe that this study will improve the knowledge of how this pathogen could evolve into an untreatable infectious agent, and it uncovers a role for hypermutators in chronic infectious diseases under antibiotic pressure.

Evaluation of the antibacterial and inhibitory activity of NorA and MepA efflux pumps from Staphylococcus aureus by diosgenin.

The increase in bacterial resistance to available antibiotics has driven several researchers to search for new agents with therapeutic properties. Diosgenin is a naturally occurring steroidal saponin that has demonstrated several pharmacological properties. In the present study, we report the antimicrobial activity of diosgenin against the standard and multidrug-resistant bacteria of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus, in addition to the efflux pump inhibitory activity against Staphylococcus aureus strains carrying NorA and MepA pumps. For this purpose, the broth microdilution method was used, from which the value of the Minimum Inhibitory Concentration (MIC) was obtained, and this was associated with subinhibitory concentration (MIC/8) with antibiotic of clinical use and ethidium bromide for strains carrier by efflux pump. Diosgenin showed antimicrobial activity for standard S. aureus bacteria and potentiating activity in association with gentamicin and ampicillin for P. aeruginosa multidrug-resistant bacteria, it also showed potentiation in association with norfloxacin against the E. coli strain and gentamicin against the S. aureus strain. Antimicrobial activity against efflux pump-bearing strains revealed that saponin did not interfere with the efflux pump mechanism or intervened antagonistically. Thus, saponin has shown to be very promising against bacterial resistance in association with aminoglycoside, fluoroquinolones and beta-lactam, however additional studies should be carried out to better elucidate the mechanism of action of diosgenin.

Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon river.

OBJECTIVE: Herein, this study aimed to perform the genomic characterization of a blaKPC-2 positive Klebsiella pneumoniae (KP1.1JP) strain isolated from the surface water of river located the Brazilian Amazon region. METHODS: Antimicrobial susceptibility testing was performed following BrCAST/EUCAST recommendations. Genomic DNA was extracted and sequenced using the Illumina® NextSeq platform and the assembly of the generated reads was performed using the SPAdes software. Research on the sequence type, resistance and virulence encoding genes, and plasmid replicon typing was carried out. RESULTS: The KP1.1JP strain was resistant to all ß-lactams, aminoglycosides, and fluoroquinolones tested. The genome size was 5 626 346 bp, distributed in 203 contigs and a guanine and cytosine content of 57.02%. The values of N50 and N75 were 285 583 bp and 173 927 bp, respectively. We verified that KP1.1JP belongs to ST101 and carries genes encoding resistance to ß-lactams (blaCTX-M-15, blaTEM-1B, blaOXA-1, blaSVH-182, and blaKPC-2), aminoglycosides [aac(3')-IIa, aph(3')-Vla], fluoroquinolones [aac(6')-Ib-cr], phenicol (catA1, catA2, catB3), tetracycline [tet(D)], trimethoprim (dfrA14), and fosfomycin (fosA). Additionally, the following virulence encoding genes were also detected: mrkABCDFHIJ (Fimbria type 3); fimABCDRFGHIK (Fimbria type 1); entABCDEFS and fepABCDG (siderophores); iroN, irp1, and irp2 (salmochelins); fyuA and ybtAEPQSTUX (yersiniabactin); and iutA (aerobactin). CONCLUSIONS: We report the occurrence of a K. pneumoniae ST101 strain carrying blaKPC-2 gene in an Amazon river in Brazil. The genomic characteristics of this strain will contribute to a better understanding of the spread of pathogens of clinical importance in the environment based on a One Health perspective.