RESUMEN
Early detection of pathogen cross-transmission events and environmental reservoirs is needed to control derived nosocomial outbreaks. Whole-genome sequencing (WGS) is considered the gold standard for outbreak confirmation, but, in most cases, it is time-consuming and has elevated costs. Consequently, the timely incorporation of WGS results to conventional epidemiology (CE) investigations for rapid outbreak detection is scarce. Fourier transform infrared spectroscopy (FTIR) is a rapid technique that establishes similarity among bacteria based on the comparison of infrared light absorption patterns of bacterial polysaccharides and has been used as a typing tool in recent studies. The aim of the present study was to evaluate the performance of the FTIR as a first-line typing tool for the identification of extended-spectrum ß-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) outbreaks in the hospital setting in comparison with CE investigations using WGS as the gold standard method. Sixty-three isolates of ESBL-Kp collected from 2018 to 2021 and classified according to CE were typed by both FTIR and WGS. Concordance was measured using the Adjusted Rand index (AR) and the Adjusted Wallace coefficient (AW) for both CE and FTIR clustering considering WGS as the reference method. Both AR and AW were significantly higher for FTIR clustering than CE clustering (0.475 vs. 0.134, p = 0.01, and 0.521 vs. 0.134, p = 0.009, respectively). Accordingly, FTIR inferred more true clustering relationships than CE (38/42 vs. 24/42, p = 0.001). However, a similar proportion of genomic singletons was detected by both FTIR and CE (13/21 vs. 12/21, p = 1). This study demonstrates the utility of the FTIR method as a quick, low-cost, first-line tool for the detection of ESBL-Kp outbreaks, while WGS analyses are being performed for outbreak confirmation and isolate characterization. Thus, clinical microbiology laboratories would benefit from integrating the FTIR method into CE investigations for infection control measures in the hospital setting.
RESUMEN
The present study was developed in the São Pedro and São Paulo Archipelago, with the objective to describe the structure of the microphytoplankton community, and establish its diurnal and spatial variation. The samplings were carried out in two stations (Enseada and Cabeço da Tartaruga) during five consecutive days (May 12 to 16, 2008) of the rainy season, during early morning and late afternoon, by subsurface horizontal hauls of 10 minutes duration with plankton net of 45 μm of mesh size. A total of 131 taxa were recorded, out of which 117 in Cabeço station and 89 in Enseada. The group of dinoflagellates was the most diverse, represented by 90 taxa belonging to 17 genera, highlighting the Ceratium genus with 33 species. The cyanophyceae Trichodesmium thiebautti Gomon ex Gomont was the only dominant species in the area, influencing the community structure, and serving as indicator species for the area. There was a greater number of species at the Cabeço than in Enseada. The marine planktonic oceanic species predominated, with 61.26 percent of the overall species richness. The diversity and evenness were in general higher in both sampling stations. At Cabeço station, the values of species diversity were between a minimum of 0.76 bits.cell-1 and a maximum of 4.27 bits.cell-1 and evenness varied between 0.16 and 0.84. At the Enseada station, it was registered a minimum of 2.91 bits.cell-1 and a maximum of 3.87 bits.cell-1, and evenness with minimum and maximum values of 0.64 and 0.84, respectively. The cluster analysis showed the formation of three distinct associations of species, with Cabeço and Enseada species in separate groups, highlighting the differences between the communities of the two studied sites. In each station, there was no significant difference between samples of different hours. The study area is characterized by a floristic composition typical of stable, transparent and oligotrophic waters.
O presente trabalho foi desenvolvido no Arquipélago de São Pedro e São Paulo, com o objetivo de descrever a estrutura da comunidade microfitoplanctônica, assim como estabelecer sua variação diurna e espacial. As amostras foram coletadas em duas estações (Cabeço da Tartaruga e Enseada) durante cinco dias consecutivos (12 a 16/05/08) do período chuvoso, nos horários da manhã e da tarde, por meio de arrastos horizontais subsuperficiais de 10 minutos de duração, com uma rede de plâncton com abertura de malha de 45 µm. Um total de 131 táxons foram registrados, dos quais 117 foram na estação Cabeço da Tartaruga e 89 na Enseada. O grupo dos dinoflagelados foi o mais diverso, representado por 90 táxons pertencentes a 17 gêneros, destacando-se o gênero Ceratium com 33 espécies. A cianofícea Trichodesmium thiebautti Gomont ex Gomon foi a única espécie dominante na área, influenciando a estrutura da comunidade, servindo como a espécie indicadora da área. Houve um número maior de espécies na estação Cabeço do que na Enseada. As espécies marinhas planctônicas oceânicas predominaram, com 61,26 por cento da riqueza total de espécies. A diversidade e a equitabilidade foram, no geral, altas em ambos locais de coleta. Na estação Cabeço, os valores de diversidade específica situaram-se entre o mínimo de 0,76 bits.cél-1 e máximo de 4,27 bits.cél-1 e a equitabilidade oscilou entre 0,16 e 0,84. Na Enseada, registraram-se mínimo de diversidade específica de 2,91 bits.cél-1 e máximo de 3,87 bits.cél-1, e equitabilidade com valores mínimo e máximo de 0,64 e 0,84, respectivamente. A análise de agrupamento mostrou a formação de três associações distintas de espécies, com espécies do Cabeço e da Enseada em grupos separados, evidenciando a diferença entre as comunidades dos dois locais estudados. Em cada estação, não houve diferença significativa entre as amostras dos diferentes horários. A área estudada está caracterizada por uma composição florística típica de ambiente estável, águas transparentes e oligotróficas.
