ABSTRACT Objective: To compare pre-extubation physiological characteristics and ultrasound variables between patients intubated for COVID-19 compared to a clinical population and those intubated for other reasons. Methods: This was a secondary analysis of a prospective cohort study of patients undergoing invasive mechanical ventilation (IMV) for more than 48 h. Patients were divided into two groups: those intubated for COVID-19-induced ARDS and those intubated for other clinical reasons. Ultrasound assessment of lung and diaphragm function was performed before extubation. The results were compared between the two groups of patients. Results: In comparison with the patients without COVID-19, those with the disease were younger (a median age of 58 [46-76] years vs. a median age of 75 [69-85] years; p = 0.01), had fewer comorbidities (a median Charlson Comorbidity Index of 2 [1-4] vs. a median Charlson Comorbidity Index of 5 [4-6]; p < 0.01), and were less severely ill at admission (a median APACHE II score of 9 [8-14] vs. a median APACHE II score of 18 [13-22]; p < 0.01). In addition, the median duration of IMV was longer in the COVID-19 patients (11 [9-23] days vs. 6 [3-8] days; p < 0.01). Although extubation success rates were similar between the COVID-19 and non-COVID-19 groups (22 [71%] vs. 35 [77.8%]), median lung ultrasound score differed between the two groups (23 [18-25] vs. 15 [11-18]; p < 0.01), as did median diaphragmatic excursion (2.1 [1.7-2.4] vs. 1.7 [1.2-2.0]; p < 0.01). Conclusions: Although patients with COVID-19 requiring ventilatory support are younger and have fewer comorbidities than those intubated for other clinical reasons, they experience longer hospital stays. Although lung ultrasound score can differ between patients with and without COVID-19, these differences do not significantly translate into extubation success rates. Therefore, the utility of ultrasound scores in weaning COVID-19 patients from IMV needs further study. Objective preextubation pre COVID19 COVID 19 COVID-1 reasons Methods (IMV 4 h COVID19induced COVIDinduced induced Results COVID19, 19, 4676 46 76 [46-76 vs 7 6985 69 85 [69-85 0.01, 001 0.01 , 0 01 0.01) 14 1 [1-4 [4-6] 814 8 [8-14 1322 13 22 [13-22] 0.01. . addition 11 (1 923 23 [9-23 38 3 [3-8 nonCOVID19 nonCOVID non non-COVID-1 (2 71% 71 [71% 77.8%, 778 77.8% 77 [77.8%]) 1825 25 [18-25 1118 [11-18] 2.1 21 (2. 1.72.4 1724 2.4 [1.7-2.4 17 1. 1.22.0 1220 1.2 2.0 [1.2-2.0] Conclusions stays Therefore COVID1 COVID- 467 [46-7 698 [69-8 00 0.0 [1- [4-6 81 [8-1 132 [13-22 ( 92 [9-2 [3- nonCOVID1 non-COVID- [71 77.8 [77.8%] 182 [18-2 111 [11-18 2. 72 1.72. 172 24 [1.7-2. 1.22. 122 12 20 [1.2-2.0 [46- [69- 0. [1 [4- [8- [13-2 [9- [3 non-COVID [7 77. [77.8% [18- [11-1 1.72 [1.7-2 1.22 [1.2-2. [46 [69 [ [4 [8 [13- [9 [77.8 [18 [11- [1.7- [1.2-2 [6 [13 [77. [11 [1.7 [1.2- [77 [1. [1.2

Abstract Tuberculosis (TB) is one of the infectious diseases with high mortality in the world. DNA amplification techniques have been used to overcome barriers to the diagnosis of this disease. However, the success of these methodologies is highly dependent on the DNA obtained from the sample. This study was carried out to verify whether the DNA extracted by sonication (in house method) could yield suitable DNA for amplification by real-time PCR (qPCR). Sixty sputum samples were submitted to DNA extraction using sonication compared to a commercial method (Detect-TB kit, Labtest/MG-Brazil). All DNA samples were amplified by qPCR for IS6110 region (IS6110-qPCR/SYBR Green assay). Out of 60 samples, 40 were positive for TB; of these, all had positive results when extracted by sonication (100%) and 80% when extracted by the commercial method. The limit of detection (LOD) of Mycobacterium tuberculosis (H37Rv strain) by qPCR was 14CFU/mL when the DNA was extracted by sonication, compared to countless colonies when extracted by commercial kit. In conclusion, the sonication protocol (without purification step) proved to be a simple, fast, and suitable method for obtaining DNA for use in qPCR from sputum samples.

BACKGROUND Early diagnosis of tuberculosis (TB) and identification of strains of Mycobacterium tuberculosis resistant to anti-TB drugs are considered the main factors for disease control. OBJECTIVES To standardise a real-time polymerase chain reaction (qPCR) assay technique and apply it to identify mutations involved in M. tuberculosis resistance to Isoniazid (INH) directly in Ziehl-Neelsen (ZN) stained slides. METHODS Were analysed 55 independent DNA samples extracted from clinical isolates of M. tuberculosis by sequencing. For application in TB diagnosis resistance, 59 ZN-stained slides were used. The sensitivity, specificity and Kappa index, with a 95% confidence interval (CI95%), were determined. FINDINGS The agreement between the tests was, for the katG target, the Kappa index of 0.89 (CI95%: 0.7-1.0). The sensitivity and specificity were 97.6% (CI95%: 87.7-99.9) and 91.7% (CI95%: 61.5-99.5), respectively. For inhA, the Kappa index was 0.92 (CI95%: 0.8-1.0), the sensitivity and specificity were 94.4% (CI95%: 72.7-99.8) and 97.3% (CI95%: 85.8-99.9), respectively. The use of ZN-stained slides for drug-resistant TB detection showed significant results when compared to other standard tests for drug resistance. MAIN CONCLUSIONS qPCR genotyping proved to be an efficient method to detect genes that confer M. tuberculosis resistance to INH. Thus, qPCR genotyping may be an alternative instead of sequencing.

ABSTRACT Introduction: Nontyphoidal Salmonella serotypes are the main cause of human food-borne infection, including several hospitalization cases in the developing countries. Aim: To detect the main serotypes and to characterize the antibiotic resistance of human non-enteric and enteric nontyphoidal Salmonella from clinical isolates in Brazil. Methods: Salmonella serotypes were identified by microbiological and molecular methods. Susceptibility testing to antibiotics was performed by agar disk diffusion. Real-time PCRs were carried out for the detection of the genus Salmonella as well as serotypes Typhimurium and Enteritidis. Results: A total of 307 nontyphoidal Salmonella were isolated from 289 different patients in a reference laboratory (LACEN-RS) from Southern Brazil in a six-year period (2010–2015). There were 45 isolates from emerging cases and 244 from sporadic cases in hospitalized patients. Non-enteric isolates were detected in 42.6% of the patients from sources such as urine, blood and other clinical fluids. Serological and PCR-specific tests demonstrated that Typhimurium (48.4%) and Enteritidis (18.3%) were the most frequent serotypes. Typhimurium isolates were generally resistant to three or more antibiotic classes, while Enteritidis isolates to one or two classes. Typhimurium was the most frequent serotype in all samples (48.4%), mainly among the hospitalized patients (55.6%), and presented the highest rates of multidrug resistance (59.3% of the isolates of this serotype). Further, the prevalence of this serotype increased along the years of the study in comparison to other nontyphoidal Salmonella serotypes. Conclusion: Greater public health attention should be given to prevent salmonellosis in the community and in hospital settings to reduce the rates of Typhimurium strains with multidrug resistance.

ABSTRACT Background Hepatitis B virus (HBV) infection is a major public health problem in Brazil. HBV endemicity is usually moderate to low according to geographic regions, and high prevalence of this virus has been reported in people of some specific Brazilian counties, including those with a strong influence of Italian colonization in southern Brazil. Analysis of HBV diversity and identification of the main risk factors to HBV infection are necessary to understand hepatitis B epidemiology in these high prevalence regions in southern Brazil. Objective To investigate epidemiological characteristics and HBV genotypes and subgenotypes circulating in a specific city with high HBV prevalence. Methods A cross-sectional study was performed with 102 HBV chronically infected individuals, recruited in reference outpatient clinics for viral hepatitis in a city of high HBV prevalence (Bento Gonçalves) in Rio Grande do Sul state, Brazil between July and December 2010. Socio-demographic, clinical and behavior-related variables were collected in a structured questionnaire. HBV serological markers (HBsAg, anti-HBc), viral load, genotypes/subgenotypes and drug resistance were evaluated and comparatively analyzed among all patients. Results The HBV infected subjects had a mean age of 44.9 (±12.2) years, with 86 patients (84.3%) reporting to have a family history of HBV infection, 51 (50.0%) to share personal objects, and were predominantly of Italian descendants (61; 64.9%). There was a predominance of genotype D (49/54; 90.7%), but genotype A was also detected (5/54; 9.3%). Subgenotypes D1 (1; 4.7%), D2 (3; 14.3%), and D3 (17; 81.0%) were identified. LAM-resistant mutation (rtM204I) and ADV-resistant mutations (rtA181V) were detected in only one patient each. Conclusions These results demonstrate a pivotal role of intrafamilial transmission for HBV spreading in this population. Furthermore, there is a high prevalence of HBV genotype D in this region.

Abstract INTRODUCTION Infections caused by respiratory viruses are important problems worldwide, especially in children. Human metapneumovirus (hMPV) is a respiratory pathogen and causes severe infections with nonspecific symptoms. This study reports the hMPV occurrence and dissemination in southern Brazil and compares the frequency of occurrence of this virus and the human respiratory syncytial virus (hRSV) in the epidemiological weeks in a three-year period (2009-2011). METHODS: In total, 545 nasopharyngeal (NP) specimens from individuals with Severe Acute Respiratory Syndrome (SARS) who were negative for other seven respiratory viruses were analyzed for the presence of hMPV. Human metapneumovirus was detected by direct immunofluorescence and real-time reverse transcription polymerase chain reaction. RESULTS: hMPV was detected in 109 patients from the main geographic regions of the southernmost state of Brazil, presenting similar overall prevalence in males (46.8%) and females (53.2%). Among children who were less than six years old, hMPV was detected in 99 samples of all age groups, with a higher frequency in infants who were less than one year old (45.7%) compared to all other age groups until six years. hMPV and hRSV infection occurred in almost the same epidemiological weeks (EWs) of each year, with peaks of incidence between EW 31/37 and EW 26/38 for the years 2009 and 2011, respectively. hMPV was further detected in several cases of SARS and it was the only virus detected in three deaths. CONCLUSIONS These findings indicate that hMPV is in circulation in southern Brazil and highlight the importance of diagnosing hMPV for influenza-like illness in the population.

BACKGROUND Hepatitis B virus (HBV) infection is a major public health problem in Brazil. Several risk factors are involved in HBV infection and their identification by a rational and essential approach is required to prevent the transmission of this infection in Brazil. OBJECTIVES To evaluate risk factors associated with HBV infection in South Brazil. METHODS A total of 260 patients with HBV and 260 controls from Caxias do Sul (state of Rio Grande do Sul, Brazil) participated in this study. All participants were given a standard questionnaire to yield the sociodemographic information and to identify HBV risk factors. HBV infection was detected by HBsAg test in all participants. FINDINGS HBV infection in these cases was strongly associated with history of a family member HBV-infected, mainly mother [odds ratio (OR) = 4.86; 95% confidence intervals (CI): 1.69–13.91], father (OR = 5.28; 95% CI: 1.58–17.71), and/or siblings (OR = 22.16; 95% CI: 9.39–52.25); sharing personal objects (OR = 1.40; 95% CI: 1.37–2.38); and having history of blood transfusion (OR = 2.05; 95% CI: 1.10–2.84). CONCLUSIONS HBV infection was strongly associated with having a family member infected with hepatitis B, sharing personal objects, and having history of blood transfusion.

Abstract Human papillomavirus (HPV) infection is common in sexually active women and viral persistence may cause intraepithelial lesions and eventually progress to cervical cancer (CC). The present study aimed to investigate epidemiological factors related to HPV infection and to evaluate viral persistence and CC precursor lesions frequencies in women from a city in the countryside of South Brazil. Three hundred women were recruited from a primary public health care clinic. The patients were interviewed and underwent sampling with cervical brushes for HPV-DNA detection/typing by a PCR-based assay and cytological analysis by Pap smear test. HPV was detected in 47 (15.7%) women. HPV infection was significantly associated with young age (<30 years) and low socio-economic status. Seventeen (5.7%) women presented cytological abnormalities, three of them with precursor CC intraepithelial lesions. A subgroup of 79 women had been previously analyzed and thirteen (16.4%) were persistently infected, two with precursor CC intraepithelial lesions and high-risk HPV types infection (both of them without cervical abnormalities in the first exam). In conclusion, HPV infection was associated with young age (<30 years) and low family income; viral persistence was low (16.4%) but related to CC precursor lesions; and HPV-DNA high risk types detection would help to screen CC in the population.

ABSTRACT INTRODUCTION: Human metapneumovirus (hMPV) is an emergent human respiratory pathogen. This study aimed to evaluate the performance of direct immunofluorescence (DIF) to detect hMPV in a clinical laboratory setting. METHODS: Nasopharyngeal aspirate samples (448) of children and adults with respiratory illness were used to detect hMPV by using DIF and real time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays. RESULTS: In all, 36 (8%) samples were positive by DIF and 94 (21%) were positive by qRT-PCR. Direct immunofluorescence specificity was 99% and sensitivity was 38%. CONCLUSIONS: DIF is not very sensitive under clinical laboratory settings.