Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis.

Mutations in the SARS-CoV-2 genome can alter the virus' fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 × 10-4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.

Virulomic Analysis of Multidrug-Resistant Klebsiella pneumoniae Isolates and Experimental Virulence Model Using Danio rerio (Zebrafish).

This study evaluates a possible correlation between multidrug-resistant Klebsiella pneumoniae strains and virulence markers in a Danio rerio (zebrafish) model. Whole-genome sequencing (WGS) was performed on 46 strains from three Brazilian hospitals. All of the isolates were colistin-resistant and harbored blaKPC-2. Ten different sequence types (STs) were found; 63% belonged to CC258, 22% to ST340, and 11% to ST16. The virulence factors most frequently found were type 3 fimbriae, siderophores, capsule regulators, and RND efflux-pumps. Six strains were selected for a time-kill experiment in zebrafish embryos: infection by ST16 was associated with a significantly higher mortality rate when compared to non-ST16 strains (52% vs. 29%, p = 0.002). Among the STs, the distribution of virulence factors did not differ significantly except for ST23, which harbored a greater variety of factors than other STs but was not related to a higher mortality rate in zebrafish. Although several virulence factors are described in K. pneumoniae, our study found ST16 to be the only significant predictor of a virulent phenotype in an animal model. Further research is needed to fully understand the correlation between virulence and sequence types.

Molecular characterization of Enterobacteriaceae resistant to carbapenem antimicrobials / Caracterização molecular de enterobactérias resistentes aos carbapenêmicos

ABSTRACT The present study aimed to genotypically and phenotypically characterize clinical isolates of carbapenem-resistant Enterobacteriaceae collected from inpatients at the University Hospital of Santa Maria, during seven months. Among the clinical isolates subjected to the modified Hodge test (MHT), 62.5% were positive, indicating possible production of carbapenemase. Polymerase chain reaction (PCR) demonstrated that blaKPC was the most frequently found gene (31%), followed by blaIMP (12.5%). Combined use of the methods is needed to identify carbapenem resistance in enterobacteria to prevent their spread and control the infections caused by these organisms.

RESUMO Objetivou-se caracterizar fenotípica e genotipicamente isolados clínicos de enterobactérias resistentes aos carbapenêmicos (CRE) provenientes do Hospital Universitário de Santa Maria (RS). Entre os isolados clínicos submetidos ao teste modificado de Hodge (MHT), 62,5% apresentaram positividade, indicando possível produção de carbapenemase. A reação em cadeia da polimerase (PCR) demonstrou que o blaKPC foi o gene mais encontrado (31%), seguido de blaIMP (12,5%). O uso conjunto de distintas metodologias faz-se necessário para identificar a resistência aos carbapenêmicos produzida pelas enterobactérias, de modo a auxiliar o controle de infecção prevenindo a disseminação desses microrganismos.

Methicillin-resistant Staphylococcus aureus carrying SCCmec type II was more frequent than the Brazilian endemic clone as a cause of nosocomial bacteremia.

Fifty consecutive MRSA blood isolates were evaluated: 30(60%) carried SCCmec type II (single PFGE clone; sequence type 5 or ST105); 12 (26%), IV; 5 (10%), III; 3 (6%), I. Brazilian endemic clone, carrying SCCmec type III, has been the main nosocomial clone in Brazil; however, this study showed that a clone carrying type II predominated.

Methicillin-resistant Staphylococcus aureus (MRSA) carriage in a dermatology unit.

OBJECTIVE: The aim of this study was to characterize Staphylococcus aureus (MRSA) carriage in a dermatology unit. METHODS: This was a prospective and descriptive study. Over the course of 26 weeks, surveillance cultures were collected weekly from the anterior nares and skin of all patients hospitalized in a 20-bed dermatology unit of a tertiary-care hospital. Samples from healthcare workers (HCWS) were cultured at the beginning and end of the study. Colonized patients were put under contact precautions, and basic infection control measures were enforced. Staphylococcus aureus colonization pressure was determined monthly. Colonized and non-colonized patients were compared, and isolates were evaluated for antimicrobial susceptibility, SCCmec type, virulence factors, and type. RESULTS: Of the 142 patients evaluated, 64 (45%) were colonized by MRSA (39% hospital acquired; 25% community acquired; 36% indeterminate). Despite isolation precautions, hospital-acquired Staphylococcus aureus occurred in addition to the continuous entry of Staphylococcus aureus from the community. Colonization pressure increased from 13% to 59%, and pemphigus and other bullous diseases were associated with MRSA colonization. Eleven out of 71 HCWs (15%) were Staphylococcus aureus carriers, although only one worker carried a persistent clone. Of the hospital-acquired MRSA cases, 14/28 (50%) were SCCmec type IV (3 PFGE types), 13 were SCCmec type III (46%), and one had an indeterminate type. These types were also present among the community-acquired Staphylococcus aureus isolates. SSCmec type IV isolates were shown to be more susceptible than type III isolates. There were two cases of bloodstream infection, and the pvl and tst virulence genes were absent from all isolates. CONCLUSIONS: Dermatology patients were colonized by community- and hospital-acquired Staphylococcus aureus. Half of the nosocomial Staphylococcus aureus isolates were SCCmec type IV. Despite the identification of colonized patients and the subsequent contact precautions and room placement, Staphylococcus aureus colonization continued to occur, and colonization pressure increased. Pemphigus and other bullous diseases were associated with Staphylococcus aureus.

Methicillin-resistant Staphylococcus aureus (MRSA) carriage in a dermatology unit

OBJECTIVE: The aim of this study was to characterize Staphylococcus aureus (MRSA) carriage in a dermatology unit. METHODS: This was a prospective and descriptive study. Over the course of 26 weeks, surveillance cultures were collected weekly from the anterior nares and skin of all patients hospitalized in a 20-bed dermatology unit of a tertiary-care hospital. Samples from healthcare workers (HCWS) were cultured at the beginning and end of the study. Colonized patients were put under contact precautions, and basic infection control measures were enforced. Staphylococcus aureus colonization pressure was determined monthly. Colonized and non-colonized patients were compared, and isolates were evaluated for antimicrobial susceptibility, SCCmec type, virulence factors, and type. RESULTS: Of the 142 patients evaluated, 64 (45 percent) were colonized by MRSA (39 percent hospital acquired; 25 percent community acquired; 36 percent indeterminate). Despite isolation precautions, hospital-acquired Staphylococcus aureus occurred in addition to the continuous entry of Staphylococcus aureus from the community. Colonization pressure increased from 13 percent to 59 percent, and pemphigus and other bullous diseases were associated with MRSA colonization. Eleven out of 71 HCWs (15 percent) were Staphylococcus aureus carriers, although only one worker carried a persistent clone. Of the hospital-acquired MRSA cases, 14/28 (50 percent) were SCCmec type IV (3 PFGE types), 13 were SCCmec type III (46 percent), and one had an indeterminate type. These types were also present among the community-acquired Staphylococcus aureus isolates. SSCmec type IV isolates were shown to be more susceptible than type III isolates. There were two cases of bloodstream infection, and the pvl and tst virulence genes were absent from all isolates. CONCLUSIONS: Dermatology patients were colonized by community- and hospital-acquired Staphylococcus aureus. Half of the nosocomial Staphylococcus aureus isolates were SCCmec type IV. Despite the identification of colonized patients and the subsequent contact precautions and room placement, Staphylococcus aureus colonization continued to occur, and colonization pressure increased. Pemphigus and other bullous diseases were associated with Staphylococcus aureus.

Differences between "classical" risk factors for infections caused by methicillin-resistant Staphylococcus aureus (MRSA) and risk factors for nosocomial bloodstream infections caused by multiple clones of the staphylococcal cassette chromosome mec type IV MRSA strain.

OBJECTIVE: To identify risk factors associated with nosocomial bloodstream infections caused by multiple clones of the staphylococcal cassette chromosome mec (SCCmec) type IV strain of methicillin-resistant Staphylococcus aureus (MRSA). DESIGN: An unmatched case-control study (at a ratio of 1:2) performed during the period from October 2002 through September 2003. SETTING: A 2,000-bed tertiary care teaching hospital affiliated with the University of São Paulo in São Paulo, Brazil. METHODS: Case patients (n=30) were defined either as patients who had a bloodstream infection due to SCCmec type IV MRSA diagnosed at least 48 hours after hospital admission or as neonates with the infection who were born in the hospital. Control patients (n=60) were defined as patients with SCCmec type III MRSA infection diagnosed at least 48 hours after hospital admission. Genes encoding virulence factors were studied in the isolates recovered from case patients, and molecular typing of the SCCmec type IV MRSA isolates was also done by pulsed-field gel electrophoresis and multilocus sequence typing. RESULTS: In multivariate analysis, the following 3 variables were significantly associated with having a nosocomial bloodstream infection caused by SCCmec type IV strains of MRSA: an age of less than 1 year, less frequent use of a central venous catheter (odds ratio [OR], 0.07 [95% confidence interval {CI}, 0.02-0.28]; p= .025), and female sex. A second analysis was performed that excluded the case and control patients from the neonatal unit, and, in multivariate analysis, the following variables were significantly associated with having a nosocomial bloodstream infection caused by SCCmec type IV strains of MRSA: less frequent use of a central venous catheter (OR, 0.12 [95% CI, 0.03-0.55]; p= .007), lower Acute Physiology and Chronic Health Evaluation II score on admission (OR, 0.14 [95% CI, 0.03-0.61]; p= .009), less frequent surgery (OR, 0.21 [95% CI, 0.06-0.83]; p= .025), and female sex (OR, 5.70 [95% CI, 1.32-24.66]; p= .020). Of the 29 SCCmec type IV MRSA isolates recovered from case patients, none contained the Panton-Valentine leukocidin, gamma-hemolysin, enterotoxin B or C, or toxic shock syndrome toxin-1. All of the isolates contained genes for the LukE-LukD leukocidin and alpha-hemolysin. Genes for enterotoxin A were present in 1 isolate, and genes for beta-hemolysin were present in 3 isolates. CONCLUSIONS: "Classical" risk factors do not apply to patients infected with the SCCmec type IV strain of MRSA, which is an important cause of nosocomial bacteremia. This strain infects a patient population that is less ill and has had less frequent invasive procedures than a patient population infected with the multidrug-resistant strain of SCCmec type III MRSA. We found that virulence factors were rare and that Panton-Valentine leukocidin was absent. There were multiple clones of the SCCmec type IV strain in our hospital. Children under 1 year of age were at a higher risk. There was a predominant clone (sequence type 5) in this patient population.