Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil.

This study analyzes the genomic findings of the first report of Salmonella isolate carrying the blaCTX-M-55 gene, recovered from a bacteremic patient from Brazil. A bacterial isolate positive for the blaCTX-M-55 gene was submitted to antimicrobial susceptibility testing by disk diffusion and epsilometric test. Whole genome sequencing was performed using Illumina technology. Conjugation assay was performed; plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinION long reads sequencing. Isolate 288_18 was identified as sequence type ST13, resistant to ampicillin, cefotaxime, ceftazidime, cefepime, ceftriaxone, and aztreonam. A transferable IncFII plasmid sized approximately 67 kb was found to carry the blaTEM-1 and blaCTX-M-55 in a module consisting of IS26-blaTEM-1B-WbuC-blaCTX-M-55-IS26. In addition, an 117 kb IncI1plasmid was also identified in the 288_18 isolate, but without additional resistance genes. To the best of our knowledge, this is the first report of blaCTX-M-55 in Salmonella isolated from human infection in Brazil. The occurrence of blaCTX-M-55 in the IncFII epidemic plasmid in a relevant clinical human isolate of Salmonella Agona underscores the urgent need for enhanced and effective continuous surveillance for controlling its dissemination.

Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil

This study analyzes the genomic findings of the first report of Salmonella isolate carrying the blaCTX-M-55 gene, recovered from a bacteremic patient from Brazil. A bacterial isolate positive for the blaCTX-M-55 gene was submitted to antimicrobial susceptibility testing by disk diffusion and epsilometric test. Whole genome sequencing was performed using Illumina technology. Conjugation assay was performed; plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinION long reads sequencing. Isolate 288_18 was identified as sequence type ST13, resistant to ampicillin, cefotaxime, ceftazidime, cefepime, ceftriaxone, and aztreonam. A transferable IncFII plasmid sized approximately 67 kb was found to carry the blaTEM-1 and blaCTX-M-55 in a module consisting of IS26-blaTEM-1B-WbuC-blaCTX-M-55-IS26. In addition, an 117 kb IncI1plasmid was also identified in the 288_18 isolate, but without additional resistance genes. To the best of our knowledge, this is the first report of blaCTX-M-55 in Salmonella isolated from human infection in Brazil. The occurrence of blaCTX-M-55 in the IncFII epidemic plasmid in a relevant clinical human isolate of Salmonella Agona underscores the urgent need for enhanced and effective continuous surveillance for controlling its dissemination.

Salmonella enterica serotypes from human and nonhuman sources in Sao Paulo State, Brazil, 2004-2020.

Salmonellosis ranks among the most frequently reported zoonosis worldwide and is often associated with foodborne outbreaks. Since the 1950s, the distribution of Salmonella serotypes in Sao Paulo State, Brazil, has been documented and periodically reported. In this study, we updated the data on the distribution of Salmonella serotypes received in our reference laboratory, isolated from human infections and nonhuman sources, from 2004 to 2020. In that period, a total of 9,014 Salmonella isolates were analyzed, of which 3,553 (39.4%) were recovered from human samples, mainly of stool (65%) and blood (25.6%), and 5,461 (60.6%) were isolated from nonhuman origins, such as animals (47.2%), food (27.7%) and animal environments (18.6%). In human isolates, a total of 104 serotypes were identified and the most frequent ones were Enteritidis, Typhimurium, S . I. 4,[5],12:i:-, Dublin and Typhi. A consistent reduction of the Enteritidis proportion was observed over the years. Among the 156 serotypes identified in isolates with nonhuman origins, Enteritidis, Mbandaka, Typhimurium, Agona and Anatum were ranked as the top five Salmonella serotypes; in more recent years, S . Heidelberg has increased in frequency. Although with different proportions, the top 10 prevalent serotypes were identified in both human and nonhuman origins, underscoring the role of animals, food products and environment as reservoirs of Salmonella with potential to cause human salmonellosis.

earlyMYCO: A Pilot Mother-Child Cohort Study to Assess Early-Life Exposure to Mycotoxins-Challenges and Lessons Learned.

Early-life exposure occurs during gestation through transfer to the fetus and later, during lactation. Recent monitoring data revealed that the Portuguese population is exposed to mycotoxins, including young children. This study aimed to develop a pilot study to assess the early-life exposure to mycotoxins through a mother-child cohort, and to identify the associated challenges. Participants were recruited during pregnancy (1st trimester) and followed-up in three moments of observation: 2nd trimester of pregnancy (mother), and 1st and 6th month of the child's life (mother and child), with the collection of biological samples and sociodemographic and food consumption data. The earlyMYCO pilot study enrolled 19 mother-child pairs. The analysis of biological samples from participants revealed the presence of 4 out of 15 and 5 out of 18 mycotoxins' biomarkers of exposure in urine and breast milk samples, respectively. The main aspects identified as contributors for the successful development of the cohort were the multidisciplinary and dedicated team members in healthcare units, reduced burden of participation, and the availability of healthcare units for the implementation of the fieldwork. Challenges faced, lessons learned, and suggestions were discussed as a contribution for the development of further studies in this area.

Genomic characterization of a multi-drug resistant, CTX-M-65-producing clinical isolate of Salmonella Infantis isolated in Brazil.

A multi-drug resistant, CTX-M-65 producing Salmonella Infantis was identified from a patient in Brazil. Whole genome sequencing followed by hybrid assembly (short and long reads) indicated the presence of blaCTX-M-65 in a pESI-like megaplasmid in this ST32 isolate and phylogenetic analysis showed high similarity with IncFIB S. Infantis isolates from food and poultry in the USA.

A interdisciplinaridade na construção da Educação Permanente em Saúde com equipes gestoras / Interdisciplinarity in the construction of Permanent Education in Health with management teams

RESUMO A gestão no Sistema Único de Saúde (SUS) requer das equipes gestoras a compreensão e o desenvolvimento de um conjunto de habilidades e competências que os auxiliem no cotidiano e nos desafios da gestão pública. Este artigo apresenta um processo de Educação Permanente em Saúde (EPS) desenvolvido com equipes gestoras de duas regiões de saúde do Paraná, com intuito de ampliar o olhar dos participantes para a reorganização da gestão e da implementação do SUS no território, pautado na interdisciplinaridade. Trata-se de um relato de experiência desenvolvido com equipes gestoras, realizada no ano de 2019, apresentado em cinco seções: a primeira descreve o contexto em que a experiência foi desenvolvida, elucidando motivos, atores e a localidade em que ocorreu; a segunda apresenta a proposta de trabalho, a confecção das oficinas e os recursos metodológicos utilizados; a terceira relata o caminho percorrido na sua operacionalização; a quarta discute as características de interdisciplinaridade existentes no processo de EPS e a última apresenta algumas considerações. A proposta mostra-se como uma potente estratégia para promover o diálogo entre diferentes atores e instituições, principalmente no contexto de crise sanitária e fiscal do Estado, qualificar e tornar reflexivo o trabalho no campo da gestão em saúde.

ABSTRACT Government in the Unified Health System (SUS) is admittedly complex, requiring management teams to understand and develop a set of skills and competencies that help into their routines and in the challenges of public administration. This article presents a continuing education process developed with leadership teams from two health regions in Paraná, with the aim of broadening the participants' view of the reorganization of the management and implementation of the SUS in the territory, based on interdisciplinarity and interprofessional. This is an experience report developed with teams, carried out in 2019, presented in five sections: the first describes the context in which the experience was developed, elucidating reasons, actors, and where it took place; the second section presents the work proposal, the preparation of the workshops, and the methodological resources used; the third reports the pathway travelled in its operation; the fourth discussions the characteristics of interdisciplinarity that exists in the continuing education process; and the last section presents some considerations. The proposal presents a powerful strategy to promote dialogue between different actors and institutions, and especially in the context of the State's sanitary and fiscal crisis, to qualify and make reflective the work in the field of health management.

Salmonella enterica serotypes from human and nonhuman sources in Sao Paulo State, Brazil, 2004-2020

ABSTRACT Salmonellosis ranks among the most frequently reported zoonosis worldwide and is often associated with foodborne outbreaks. Since the 1950s, the distribution of Salmonella serotypes in Sao Paulo State, Brazil, has been documented and periodically reported. In this study, we updated the data on the distribution of Salmonella serotypes received in our reference laboratory, isolated from human infections and nonhuman sources, from 2004 to 2020. In that period, a total of 9,014 Salmonella isolates were analyzed, of which 3,553 (39.4%) were recovered from human samples, mainly of stool (65%) and blood (25.6%), and 5,461 (60.6%) were isolated from nonhuman origins, such as animals (47.2%), food (27.7%) and animal environments (18.6%). In human isolates, a total of 104 serotypes were identified and the most frequent ones were Enteritidis, Typhimurium, S . I. 4,[5],12:i:-, Dublin and Typhi. A consistent reduction of the Enteritidis proportion was observed over the years. Among the 156 serotypes identified in isolates with nonhuman origins, Enteritidis, Mbandaka, Typhimurium, Agona and Anatum were ranked as the top five Salmonella serotypes; in more recent years, S . Heidelberg has increased in frequency. Although with different proportions, the top 10 prevalent serotypes were identified in both human and nonhuman origins, underscoring the role of animals, food products and environment as reservoirs of Salmonella with potential to cause human salmonellosis.

Subtyping of plasmid-mediated quinolone resistance among Salmonella serotypes by whole genome sequencing.

Most known plasmids are identified by conferring virulence or antimicrobial resistance phenotypes and such characteristics aid in the success of the dispersion of different plasmid types between bacteria from different sources. This study aimed to perform the subtyping of the plasmid-mediated quinolone resistance, detected in Salmonella spp. A total of 34 Salmonella strains non-susceptible to ciprofloxacin were evaluated. Strains were selected based on the presence of PMQR determined by Polymerase Chain Reaction and further submitted to Next Generation Sequencing. Most of the strains presented the qnrB19 in small ColE-like plasmids and qnrB2 gene associated with IncN/ST5 plasmids also detected. Our results indicated the co-occurrence of PMQR and ESBLs in plasmids that are a lineage of epidemic plasmids circulating in Salmonella in which additional resistances were detected, highlighting the potential threat of resistance Salmonella to public health, particularly in infections in which antimicrobial therapy is needed.

Molecular analysis of clonally related Salmonella Typhi recovered from epidemiologically unrelated cases of typhoid fever, Brazil.

BACKGROUND: The primary method of molecular subtyping for the identification and investigation of outbreaks has been pulsed-field gel electrophoresis (PFGE). In some cases, this technique has not been able to show discrimination between the unrelated strains that can be achieved by whole genome sequencing (WGS). METHODS: The aim of this study was to determine the strengths and drawbacks of WGS using different analytic approaches compared to traditional typing method, PFGE, for retrospectively typing clusters cases of 28 S. Typhi. RESULTS: We evaluated three analytical approaches on the WGS data set (Nucleotide Difference (ND), (SNPs) and Whole genome multi locus sequence typing (wgMLST) that identically classified the clusters-related strains into two clusters, cluster A (with strains from 2017), and Cluster B (with strains from 2007). CONCLUSIONS: In this study WGS based typing, was able to compete with PFGE for differentiation of the clusters of S. Typhi strains.

Genetic diversity, antimicrobial resistance and virulence profile of Salmonella isolated from the peanut supply chain.

Thirty-Eight Salmonella isolates recovered from different stages of the peanut supply chain in three Brazilian States (São Paulo, Minas Gerais and Bahia) were subtyped by pulsed-field gel electrophoresis (PFGE) and characterized by phenotypic and genotypic tests for antimicrobial resistance and virulence genes. The isolates were distributed into seven PFGE pulsotypes. All the isolates were resistant to sulfonamide. However, only one isolate from a production site in Minas Gerais had resistance to two types of antimicrobials (sulfonamide and ampicillin). Furthermore, the isolates had intermediary resistance to kanamycin (16/38), streptomycin (14/38) and ceftazidime (12/38). Four isolates had the antimicrobial resistance gene related to phenicols (floR) and 37 related to aminoglycosides (strA). The blashv gene related to ß-lactams was detected in isolates recovered from all the production regions. Six virulence genes (invA, sefA, sivH, mgtC, ssaQ and agfA) were observed in all isolates. The sopE gene was detected in 24 isolates, avrA in 12. The gtgB, ipfA and rck genes were not detected. The results showed that the pulsotype 1 was restricted to Minas Gerais whereas the pulsotype 7 was present in São Paulo and Bahia. In addition, most of the isolates were not multidrug resistant.

Draft Genome Sequence of a Pathogenic Vibrio vulnificus Strain Isolated in Brazil.

We describe the draft genome sequence of the clinical Vibrio vulnificus strain 03_7315, isolated in 2016 from the blood of a diabetic patient who died of septicemia after ingestion of seafood. The draft genome, with 4,755,588 bp covering two chromosomes, presented 4,434 genes, 4,213 coding sequences, and 117 pseudogenes.

Long-Term Management of RAP Lesions in Clinical Practice: Treatment Efficacy and Predictors of Functional Improvement.

PURPOSE: To evaluate the long-term efficacy of ranibizumab in the treatment of retinal angiomatous proliferation (RAP) and to identify predictors of functional outcome. METHODS: Retrospective case series comprised 79 eyes of 68 consecutive patients with RAP followed up ≥36 months. Primary end-points were best-corrected visual acuity (BCVA) and central macular thickness (CMT) variation at 36 months and at the last visit. RESULTS: Mean follow-up time was 59.8 ± 16.0 months. All eyes were treated with pro re nata ranibizumab, with (n = 33) or without (n = 46) photodynamic therapy (PDT). Stabilization or improvement in BCVA was observed in 50.6% of the patients at 36 months, and in 40.5% at the end of the follow-up, where 20.3% preserved reading vision. A significant decrease in CMT was observed at 36 months (p < 0.001), but not at the end of the follow-up. Geographic atrophy (GA) was present in 59.5% of the eyes at the final visit. Baseline subretinal fluid was associated with better visual outcomes (p = 0.001). Results of combination treatment with intravitreal ranibizumab and PDT did not significantly differ from ranibizumab monotherapy. CONCLUSION: Modest functional outcomes can be expected from the long-term treatment of RAP lesions in clinical practice, most likely due to the advent of GA. Baseline subretinal fluid positively correlated with final BCVA.

Treatment of Retinal Vein Occlusion with Ranibizumab in Clinical Practice: Longer-Term Results and Predictive Factors of Functional Outcome.

PURPOSE: To evaluate long-term results and predictors of efficacy in patients with macular edema due to retinal vein occlusion (RVO) treated with intravitreal ranibizumab in a clinical practice setting. METHODS: The clinical records of patients with a minimum follow-up of 3 years were retrospectively analyzed. Sixteen eyes with branch RVO (BRVO) and 16 with central RVO (CRVO) were included. All patients performed cross-sectional evaluation with best-corrected visual acuity (BCVA), spectral domain optical coherence tomography and fluorescein angiography. The foveal avascular zone (FAZ) was assessed and microstructural morphology of the retina was characterized. RESULTS: Follow- up was 42.9 ± 9.0 and 44.8 ± 8.0 months in the CRVO and BRVO groups, respectively. Patients with CRVO received on average 6.9 injections, with a final VA gain of 8.3 ± 15.0 letters (p = 0.05). BRVO eyes had on average 5.9 injections, with a final VA gain of 1.6 ± 21.0 letters (p > 0.05). The FAZ area remained stable in both groups (p > 0.05). Baseline BCVA and disruption of the retinal pigment epithelium (RPE) were predictors of final BCVA (p = 0.001 and 0.011, respectively). CONCLUSION: Although functional outcomes were inferior to those reported in clinical trials, ranibizumab was satisfactory in the long-term treatment of macular edema secondary to RVO and was not associated with increased macular ischemia. Final BCVA depends on baseline BCVA and RPE integrity.

Characterization of the genetic diversity of Mycobacterium tuberculosis in São Paulo city, Brazil.

BACKGROUND: Tuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis). FINDINGS: Spoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International-types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated. CONCLUSIONS: Our data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients.

Avaliação de uma sonda genética (Sistema Accuprobe, Gen Probe®) para identificação de organismos do complexo Mycobacterium tuberculosis, em comparação com métodos tradicionais de caracterização / Evaluation of a genetic probe (Gen-Probe Accuprobe® system) in comparison to traditional methods for identifying members of the Mycobacterium tuberculosis complex

INTRODUÇÃO: O aparecimento da co-infecção tuberculose/síndrome da imunodeficiência adquirida, o aumento de doenças por micobactérias não tuberculosas e as confusões que estas podem ter com as emergentes cepas multirresistentes exigem respostas laboratoriais mais rápidas e de melhor rendimento, não só com isolamento das micobactérias, mas também com a sua identificação. OBJETIVO: Estudo comparativo entre uma nova ferramenta de identificação molecular com sonda genética baseada na unidade 16S do gene rDNA do Mycobacterium tuberculosis (Accuprobe Gen Probe®, Gen Probe Inc.) e a metodologia clássica. MÉTODO: Foram selecionados 55 isolados do gênero Mycobacterium, mantidos em bacterioteca, obtidos de escarros de pacientes de uma unidade de referência para tuberculose. Foram feitos repiques em três tubos: um destinado à identificação genética, outro para realização dos testes clássicos (produção e acumulação da niacina, e crescimento em meio de Lowenstein-Jensen com agentes inibidores - ácido p-nitrobenzóico e hidrazida do ácido tiofeno-2-carboxílico), e outro reserva. RESULTADOS: A sonda identificou 51 amostras do complexo M. tuberculosis (uma associada ao M. kansasii) e 4 como micobactérias não tuberculosas, posteriormente identificadas como M. kansasii (3) e M. avium (1). Os métodos tradicionais identificaram 47 amostras como do complexo M. tuberculosis, 4 com perfil de micobactérias não tuberculosas (concordante com o obtido pela sondagem genética) e 4 provas inconclusivas, uma delas exatamente a que associava duas espécies de micobactérias. CONCLUSÃO: Os benefícios da técnica de biologia molecular justificam sua implantação e uso rotineiro, associado aos métodos clássicos, numa unidade com alta demanda e que atenda casos de tuberculose de alta complexidade.

Rendimento da cultura de escarro na comparação de um sistema de diagnóstico automatizado com o meio de Lowenstein-Jensen para o diagnóstico da tuberculose pulmonar / Sputum culture yield: comparing an automated diagnostic system to Lõwenstein-Jensen medium in the diagnosis of pulmonary tuberculosis

INTRODUÇÃO: A tuberculose permanece um problema de saúde pública mundial. OBJETIVO: Avaliar um sistema de diagnóstico automatizado de tuberculose, comparando-o com baciloscopia e cultura em meio de Lowenstein-Jensen. MÉTODO: Estudo comparativo entre os resultados obtidos no sistema automatizado, baciloscopia do escarro e em meio de Lowenstein-Jensen, em 844 amostras de escarro de setembro a dezembro de 1999, em centro de referência para tuberculose em São Paulo (SP). RESULTADOS: Das 844 amostras, 27,1 por cento mostraram-se positivas para bacilo álcool-acidorresistente e 72,9 por cento negativas. Nos cultivos em Lowenstein-Jensen, 34,7 por cento foram positivas e 63 por cento negativas; no sistema automatizado, 37,1 por cento foram positivas e 56,9 por cento negativas. Observou-se sensibilidade de 98,1 por cento e 91.9 por cento no sistema automatizado e no Lowenstein-Jensen, respectivamente. A especificidade e o valor preditivo positivo foram de 100 por cento nos dois métodos. O valor preditivo negativo foi de 98,9 por cento no sistema automatizado e de 95,5 por cento no Lowenstein-Jensen. A acurácia foi de 99,3 por cento no sistema automatizado e 97 por cento no Lowenstein-Jensen e o Kappa de 0,99 no sistema automatizado e 0,94 no Lowenstein-Jensen. O tempo médio de detecção das micobactérias no sistema automatizado (10,5 dias) apresentou diferença estatística significativa quando comparado com o método de Lowenstein-Jensen (34,7 dias). CONCLUSÃO: O rendimento da cultura com o sistema automatizado apresentou diferença estatística significativa quando comparado com o meio de Lowenstein-Jensen. O tempo médio de detecção das micobactérias foi significativamente reduzido no sistema automatizado. O rendimento do sistema automatizado justifica sua utilização em unidade de referência ambulatorial para a tuberculose em São Paulo.

[Epidemiological features of multidrug-resistant tuberculosis in a reference service in São Paulo city]. / Aspectos epidemiológicos da tuberculose multirresistente em serviço de referência na cidade de São Paulo.

In order to study certain epidemiological features of multidrug-resistant tuberculosis (MDR-TB) carriers and their influence on the control and treatment, a group of patients was evaluated over a four-year period, selected by: Mycobacterium tuberculosis isolation from sputum; resistance to Rifampin, Isoniazid and one more drug, or, failure of reserve regimen, all cases were from a tuberculosis reference unit in the City of S o Paulo. A total of 182 patients were reviewed, with a mean age of 35.7 +/- 6.8 years and 112 (61.5%) were male. These patients was classified according to therapeutic history, as: primary MDR-TB (with initial sensitivity test) 11 (6%); post primary MDR-TB (after irregular use previous treatment) 134 (74%), and indeterminate MDR-TB (failure after regular use of initial and reserve regimens) 37 (20%). Contagion was identified in 41/170 patients, acquired through domiciliary rather than institutional transmission. There were four familial outbreaks and none were institutional. The most frequent condition associated with these cases was abandonment of therapy (45%) followed by alcoholism (27%), sequential failure in the treatment regimens (23%), MDR contagion (15%), drug reaction (6%), HIV positive (4%) and diabetes (3%). There was resistance to Rifampin+Isoniazid in 100%, Streptomycin in 83% and Ethambutol in 47%. Conventional X-ray revealed cavities in all, though only 35 (19%) were unilateral. These cases are discussed and some suggestions presented.