Alfredo Elias Gilio

Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a “flip-flop” phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Clinical patterns and seasonal trends in respiratory syncytial virus hospitalizations in São Paulo, Brazil

The respiratory viruses are recognized as the most frequent lower respiratory tract pathogens for infants and young children in developed countries but less is known for developing populations. The authors conducted a prospective study to evaluate the occurrence, clinical patterns, and seasonal trends of viral infections among hospitalized children with lower respiratory tract disease (Group A). The presence of respiratory viruses in childrens nasopharyngeal was assessed at admission in a pediatric ward. Cell cultures and immunofluorescence assays were used for viral identification. Complementary tests included blood and pleural cultures conducted for bacterial investigation. Clinical data and radiological exams were recorded at admission and throughout the hospitalization period. To better evaluate the results, a non- respiratory group of patients (Group B) was also constituted for comparison. Starting in February 1995, during a period of 18 months, 414 children were included- 239 in Group A and 175 in Group B. In Group A, 111 children (46.4%) had 114 viruses detected while only 5 children (2.9%) presented viruses in Group B. Respiratory Syncytial Virus was detected in 100 children from Group A (41.8%), Adenovirus in 11 (4.6%), Influenza A virus in 2 (0.8%), and Parainfluenza virus in one child (0.4%). In Group A, aerobic bacteria were found in 14 cases (5.8%). Respiratory Syncytial Virus was associated to other viruses and/or bacteria in six cases. There were two seasonal trends for Respiratory Syncytial Virus cases, which peaked in May and June. All children affected by the virus were younger than 3 years of age, mostly less than one year old. Episodic diffuse bronchial commitment and/or focal alveolar condensation were the clinical patterns more often associated to Respiratory Syncytial Virus cases. All children from Group A survived. In conclusion, it was observed that Respiratory Syncytial Virus was the most frequent pathogen found in hospitalized children admitted for severe respiratory diseases. Affected children were predominantly infants and boys presenting bronchiolitis and focal pneumonias. Similarly to what occurs in other subtropical regions, the virus outbreaks peak in the fall and their occurrence extends to the winter, which parallels an increase in hospital admissions due to respiratory diseases.

Risk factors for nosocomial infections in a critically ill pediatric population: a 25-month prospective cohort study.

We studied risk factors for nosocomial infections among 500 critically ill children who were admitted to a pediatric intensive care unit from August 1994 through August 1996 and who were prospectively followed until death, transfer, or discharge. Age, gender, postoperative state, length of stay, device-utilization ratio, pediatric risk of mortality score, and total parenteral nutrition were the risk factors studied. Through multivariate analysis, we identified three independent risk factors for nosocomial infection: device-utilization ratio (odds ratio [OR], 1.6; 95% confidence interval [CI95], 1.10-2.34), total parenteral nutrition (OR, 2.5; CI95, 1.05 5.81) and length of stay (OR, 1.7; CI95, 1.31-2.21).

Epidemiology and genetic variability of human metapneumovirus during a 4-year-long study in Southeastern Brazil.

Epidemiological and molecular characteristics of human metapneumovirus (hMPV) were compared with human respiratory syncytial virus (hRSV) in infants and young children admitted for acute lower respiratory tract infections in a prospective study during four consecutive years in subtropical Brazil. GeneScan polymerase chain assays (GeneScan RT‐PCR) were used to detect hMPV and hRSV in nasopharyngeal aspirates of 1,670 children during January 2003 to December 2006. hMPV and hRSV were detected, respectively, in 191 (11.4%) and in 702 (42%) of the children admitted with acute lower respiratory tract infections at the Sao Paulo University Hospital. Sequencing data of the hMPV F gene revealed that two groups of the virus, each divided into two subgroups, co‐circulated during three consecutive years. It was also shown that a clear dominance of genotype B1 occurred during the years 2004 and 2005, followed by genotype A2 during 2006. J. Med. Virol. 81:915–921, 2009.

Severity of viral coinfection in hospitalized infants with respiratory syncytial virus infection

OBJECTIVE To compare the severity of single respiratory syncytial virus (RSV) infections with that of coinfections. METHODS A historical cohort was studied, including hospitalized infants with acute RSV infection. Nasopharyngeal aspirate samples were collected from all patients to detect eight respiratory viruses using molecular biology techniques. The following outcomes were analyzed: duration of hospitalization and of oxygen therapy, intensive care unit admission and need of mechanical ventilation. Results were adjusted for confounding factors (prematurity, age and breastfeeding). RESULTS A hundred and seventy six infants with bronchiolitis and/or pneumonia were included in the study. Their median age was 4.5 months. A hundred and twenty one had single RSV infection and 55 had coinfections (24 RSV + adenovirus, 16 RSV + human metapneumovirus and 15 other less frequent viral associations). The four severity outcomes under study were similar in the group with single RSV infection and in the coinfection groups, independently of what virus was associated with RSV. CONCLUSION Virus coinfections do not seem to affect the prognosis of hospitalized infants with acute RSV infection.

Serotype distribution of Streptococcus pneumoniae isolated from patients with invasive pneumococcal disease in Brazil before and after ten-pneumococcal conjugate vaccine implementation

The ten-pneumococcal conjugate vaccine (PCV10) was introduced into the national immunization program for childhood vaccination schedules by the Brazilian Health Public Service in March 2010. The aim of this study was to compare Streptococcus pneumoniae serotype distribution, antibiotic resistance patterns, and potential coverage before (January 2006-June 2010) and after (July 2010-September 2012) PCV10 introduction. The incidence of invasive pneumococcal disease (IPD), patient demographics, and disease characteristics were recorded. This study was conducted at the University Hospital of Sao Paulo University in Brazil from January 2006 to September 2012. Serotyping was performed using multiplex PCR typing, and antimicrobial sensitivity by Clinical and Laboratory Standards Institute (CLSI). A total of 259 S. pneumoniae strains were isolated from patients with IPD. The ages of the patients ranged from 3 months to 95 years old. The strains were isolated from cerebrospinal fluid, pleural fluid, and blood. The incidence of IPD among patients at HU-USP changed after the introduction of PCV10. The overall incidence of IPD was 3.42 cases per 1000 admissions in the vaccine pre- implementation period and of 2.99 cases per 1000 admissions in the vaccine post-implementation period. The incidence of IPD among children<2 y.o. attended at HU-USP changed significantly after the introduction of PCV10, from 20.30 to 3.97 of incidence. The incidence of PCV10- serotypes decrease from 16.47 to 0.44 in the same age, before and after PC10 implementation, respectively. Moreover, it was possible to realize the sensitivity to penicillin among isolates increased significantly in the post-vaccine period. Data from this study suggest that PCV10 contributed to decrease with PID rate among children less than 2 y.o. The resistance rate among pneumococcal isolates also could be observed since serotypes with greater resistance to beta lactam antibiotics were not easily isolated after vaccination.

Perfil etiológico das diarréias agudas de crianças atendidas em São Paulo

Objetivo: determinar o perfil etiologico das diarreias agudas de um grupo de criancas de baixo nivel socioeconomico atendidas em um servico regional de pronto-atendimento pediatrico. Metodo: durante dois anos, as criancas com diarreia aguda atendidas durante um horario pre-estabelecido do dia e da semana foram incluidas no estudo. Os outros criterios seletivos eram: a) idade inferior a 5 anos; b) nao utilizacao de antibiotico no mes precedente; c) ausencia de viagem para fora da cidade no mes precedente. Foram pesquisados nas fezes: a) rotavirus (imunofluorescencia e contra-imunoeletroforese); b) bacterias - cultura em agar MacConkey, agar SS, agar Columbia, verde brilhante, soroaglutinacao, deteccao de toxinas - INV, LT,ST,SLT I, SLT II, teste de Sereny, deteccao de fatores de virulencia -- EAF, eae ,BFP; c) protozoarios (Hoffman e Faust). No mesmo periodo, um grupo controle sem diarreia foi tambem avaliado para os mesmos patogenos fecais. Resultados: no periodo de marco de 1994 a junho de 1996, foram selecionadas para o estudo 154 criancas com diarreia aguda (GDA) e 42 criancas sem diarreia (GSDA). Foram detectados agentes enteropatogenicos em 112 casos (72,8%) do GDA, e em 9 (21,5%) do GSDA. A associacao de dois ou mais enteropatogenos ocorreu em 47 (30,5%) casos do GDA, e em 3 (7,1%) do GSDA. Os patogenos encontrados por caso, do GDA, foram: rotavirus 32 (20,8%), bacterias 53 (34,4%), ambos 25 (16,2%), e 2 (1,4%) com Giardia lamblia (em um caso associada a rotavirus e noutro a bacteria). No GSDA, foram detectadas bacterias em 8 casos (19,1%), e bacteria associada a Giardia lamblia em 1 (2,4%) caso. Das 105 bacterias isoladas no GDA, 90 eram Escherichia coli (EPEC 27, DAEC 24, ETEC 21, EAEC 18), 12 eram Shigella sp, 2 eram Salmonella sp, e uma era Yersinia sp. As criancas com infeccao mista - viral e bacteriana - apresentaram maior ocorrencia de vomitos repetidos, desidratacao e internacao.Conclusoes: as bacterias foram os enteropatogenos mais detectados nos casos de diarreia aguda, sendo a Escherichia coli a mais frequente. Na maior parte, as cepas de Escherichia coli eram de biovariedade nao-EPEC, habitualmente nao investigadas nos laboratorios de patologia clinica. O rotavirus foi encontrado em grande parcela dos casos, muitas vezes em associacao com as bacterias. Os protozoarios tiveram importância reduzida.

Etiologic profile of acute diarrhea in children in São Paulo

OBJECTIVE: To evaluate the etiologic profile of acute diarrhea in socioeconomically deprived children assisted at a regional pediatric emergency care service. METHODS: During two years all children with acute diarrhea assisted at a previously established day and week time schedule were included in the study. Other selective criteria were: a) age less than 5 years; b) nonuse of antibiotics in the previous month; and c) no travel outside the city in the previous month. Stool examination was used for the detection of the following microorganisms: a) rotavirus (immunofluorescence and counterimmunoelectrophoresis); b) bacteria - culture in MacConkey agar, SS agar, Columbia agar, bright green, serotyping, detection of toxins - INV, LT,ST,SLT I, SLT II, Sereny test, detection of virulence factors- EAF, eae, BFP; and c) protozoa (Hoffman and Faust). In the same period, a control group without diarrhea was also evaluated for the same fecal pathogens. RESULTS: Between March 1994 and June 1996, 154 children with acute diarrhea (AD) and 42 control children (WAD), that is, without acute diarrhea, were selected. In the AD group, intestinal pathogens were detected in 112 (72.8%) cases, and in 9 (21.5%) cases in the WAD group. The association of two or more intestinal pathogens occurred in 47 (30.5%) cases in the AD group, and in 3 (7.1%) cases in the WAD group. The pathogens identified in the AD cases were: Rotavirus: 32 (20.8%), bacteria: 53 (34.4%), both: 25 (16.2%), and 2 (1.4%) with Giardia lamblia (in one case associated with Rotavirus and in another one associated with bacteria). In the WAD group, only bacteria were detected in 8 (19.1%) cases, and bacteria associated with Giardia lamblia in 1 (2.4%) case. Altogether, there were 105 bacteria isolated in the AD group: 90 were Escherichia coli (EPEC 27, DAEC 24, ETEC 21, EAEC 18), 12 were Shigella sp, 2 were Salmonella sp, and one was Yersinia sp. Children with mixed infections (viral and bacterial) had increased incidence of severe vomiting, dehydration and hospitalization. CONCLUSIONS: Bacteria were the most frequent pathogens detected in acute diarrhea cases, among which Escherichia coli was highly predominant. The majority of Escherichia coli strains belong to non-EPEC varieties, strains that are not routinely evaluated in clinical laboratories of pathology. Rotavirus was found in a great number of diarrhea cases, often associated with bacteria. Protozoa showed reduced importance.

Rotavirus Gastroenteritis in Children in 4 Regions in Brazil: A Hospital-Based Surveillance Study

BACKGROUND Rotavirus is a major cause of gastroenteritis in children. Knowledge of rotavirus genotypes is important for vaccination strategies. METHODS During 2005-2006, rotavirus surveillance studies were conducted in São Paulo, Salvador, Goiânia, and Porto Alegre, Brazil. Stool samples were collected from children <5 years of age who had diarrhea and were screened by the Rotaclone Enzyme Immunoassay for the presence of rotavirus. Confirmed rotavirus-positive samples were characterized for P and G genotypes by reverse-transcriptase polymerase chain reaction. RESULTS A total of 510 stool samples were collected. Of these, 221 (43.3%) were positive for rotavirus. Overall, G9 was the predominant G type, followed by G2, and G1; P[4] and P[8] were the predominant P types. The most frequent G/P genotype combination detected was G2P[4], followed by G9P[8], G9P[4], and G1P[8]. G2P[4] was the predominant type in Goiânia and Salvador; G9P[8] and G1P[8] were predominant in São Paulo and Porto Alegre, respectively. CONCLUSIONS The prevalence, seasonality, and genotype distribution of rotavirus infection varied in different regions in Brazil. With immunization programs, continuous monitoring of rotavirus types is important to detect novel and emerging strains.

Infecção urinária comunitária: etiologia segundo idade e sexo

INTRODUCTION Choosing the antimicrobial agent for initial therapy of urinary tract infection (UTI) is usually empirical and should consider the prevalence of uropathogens in different age groups and gender. OBJECTIVE To establish prevalence rates of uropathogens in community-acquired UTI in relation to age and gender. METHODS Cross-sectional study conducted in the emergency department (ED) of a general hospital, from January to December, 2010, in patients younger than 15 years old who had clinical suspicion of UTI and collected quantitative urine culture. UTI was defined as urine culture with growth of a single agent > 100.000 colony forming units (cfu)/mL in a midstream collection or ≥ 50.000 cfu/mL in urethral catheterization. RESULTS There were 63.464 visits to ED. 2577 urine cultures were obtained, of whom 291 were positive for UTI (prevalence = 11.3% of clinical suspicion and 0.46% of visits), 212 cases (72.8%) in females, median age = 2.6 years. The predominant uropathogen was E. coli (76.6%), followed by Proteus mirabilis (10.3%) and Staphylococcus saprophyticus (4.1%). Among infants < 3 months, prevalence rates of E. coli were significantly lower (50% vs 78.4%; OR = 0.276; p = 0.006). Higher prevalences of Staphylococcus saprophyticus occurred among patients > 10 years (24.4% vs 0.4%; OR = 79.265; p < 0.0001). Proteus mirabilis was significantly more prevalent in boys than girls (24.0% vs 5.2%; OR = 5.786; p < 0.001). CONCLUSIONS E. coli was the most prevalent community-acquired uropathogen. Nevertheless, initial empiric antimicrobial treatment of UTI should consider the significant prevalence of other agents different from E. coli in infants < 3 months, the high prevalence of Staphylococcus saprophyticus in patients > 10 years and Proteus mirabilis in males.