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 bla_CTX-M-55 gene, recovered from a bacteremic patient from Brazil. A bacterial isolate positive for the bla_CTX-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 bla_TEM-1 and bla_CTX-M-55 in a module consisting of IS26-bla_TEM-1B-WbuC-bla_CTX-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 bla_CTX-M-55 in Salmonella isolated from human infection in Brazil. The occurrence of bla_CTX-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.

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.

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

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% mostraram-se positivas para bacilo álcool-acidorresistente e 72,9% negativas. Nos cultivos em Lowenstein-Jensen, 34,7% foram positivas e 63% negativas; no sistema automatizado, 37,1% foram positivas e 56,9% negativas. Observou-se sensibilidade de 98,1% e 91.9% no sistema automatizado e no Lowenstein-Jensen, respectivamente. A especificidade e o valor preditivo positivo foram de 100% nos dois métodos. O valor preditivo negativo foi de 98,9% no sistema automatizado e de 95,5% no Lowenstein-Jensen. A acurácia foi de 99,3% no sistema automatizado e 97% 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.

Aspectos epidemiológicos da tuberculose multirresistente em serviço de referência na cidade de São Paulo

Com o objetivo de estudar algumas características epidemiológicas dos portadores de tuberculose pulmonar multirresistente e suas influências sobre o controle e o tratamento, foi avaliada uma coorte de 4 anos de pacientes selecionados pela recuperação do Mycobacterium tuberculosis no escarro, resistência à rifampicina, isoniazida e mais uma terceira droga usual ou falência do esquema de reserva, matriculados em uma referência na cidade de São Paulo. As variáveis estudadas foram: sexo e idade, tipo de multirresistência, contágio, condições associadas, perfil de resistência às drogas usuais e distribuição das lesões na radiologia convencional. Revistos 182 pacientes, 112 (61,5%) masculinos, com idade variando entre 16 e 64 anos (35,7±6,8). Com base na história terapêutica foram discriminados os seguintes tipos: MR-primária (com teste de sensibilidade inicial), 11 (6%), MR-pós-primária (irregularidade no tratamento anterior), 134 (74%) e MR-indeterminada (falência após uso regular informado dos esquemas usuais), 37 (20%). Contágio presente em 41 de 170 pacientes, predominando o intradomiciliar sobre o institucional. Identificados 4 surtos familiares e nenhum institucional. O abandono (45%) foi a mais freqüente condição associada, seguido do etilismo (27%), falência seqüencial aos esquemas de retratamento (23%), contágio com multirresistência (15%), reações adversas às drogas (6%), HIV-positivo (4%) e diabetes (3%). Resistência à rifampiina+isoniazida em 100%, 83% à estreptomicina e 47% ao etambutol. Todos com cavidades no Rx de tórax convencional, unilaterais em 35 (19%). Discutem-se os achados e apresentam-se sugestões.

[Epidemiological features of multidrug-resistant tuberculosis in a reference service in São Paulo city]

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.