Application of latent semantic indexing to evaluate the similarity of sets of sequences without multiple alignments character-by-character.

Most molecular analyses, including phylogenetic inference, are based on sequence alignments. We present an algorithm that estimates relatedness between biomolecules without the requirement of sequence alignment by using a protein frequency matrix that is reduced by singular value decomposition (SVD), in a latent semantic index information retrieval system. Two databases were used: one with 832 proteins from 13 mitochondrial gene families and another composed of 1000 sequences from nine types of proteins retrieved from GenBank. Firstly, 208 sequences from the first database and 200 from the second were randomly selected and compared using edit distance between each pair of sequences and respective cosines and Euclidean distances from SVD. Correlation between cosine and edit distance was -0.32 (P < 0.01) and between Euclidean distance and edit distance was +0.70 (P < 0.01). In order to check the ability of SVD in classifying sequences according to their categories, we used a sample of 202 sequences from the 13 gene families as queries (test set), and the other proteins (630) were used to generate the frequency matrix (training set). The classification algorithm applies a voting scheme based on the five most similar sequences with each query. With a 3-peptide frequency matrix, all 202 queries were correctly classified (accuracy = 100%). This algorithm is very attractive, because sequence alignments are neither generated nor required. In order to achieve results similar to those obtained with edit distance analysis, we recommend that Euclidean distance be used as a similarity measure for protein sequences in latent semantic indexing methods.

Application of latent semantic indexing to evaluate the similarity of sets of sequences without multiple alignments character-by-character

Most molecular analyses, including phylogenetic inference, are based on sequence alignments. We present an algorithm that estimates relatedness between biomolecules without the requirement of sequence alignment by using a protein frequency matrix that is reduced by singular value decomposition (SVD), in a latent semantic index information retrieval system. Two databases were used: one with 832 proteins from 13 mitochondrial gene families and another composed of 1000 sequences from nine types of proteins retrieved from GenBank. Firstly, 208 sequences from the first database and 200 from the second were randomly selected and compared using edit distance between each pair of sequences and respective cosines and Euclidean distances from SVD. Correlation between cosine and edit distance was -0.32 (P < 0.01) and between Euclidean distance and edit distance was +0.70 (P < 0.01). In order to check the ability of SVD in classifying sequences according to their categories, we used a sample of 202 sequences from the 13 gene families as queries (test set), and the other proteins (630) were used to generate the frequency matrix (training set). The classification algorithm applies a voting scheme based on the five most similar sequences with each query. With a 3-peptide frequency matrix, all 202 queries were correctly classified (accuracy = 100%). This algorithm is very attractive, because sequence alignments are neither generated nor required. In order to achieve results similar to those obtained with edit distance analysis, we recommend that Euclidean distance be used as a similarity measure for protein sequences in latent semantic indexing methods.

Prospective surveillance applying the national nosocomial infection surveillance methods in a Brazilian pediatric public hospital.

BACKGROUND: A hospital-wide, traditional prospective surveillance for nosocomial infections was commenced in 1992 in Centro Geral de Pediatria in Minas Gerais, Brazil, to describe the epidemiology of nosocomial infection in this pediatric hospital and to implement cross-infection prevention and control policies. METHODS: We performed a prospective cohort nosocomial infection surveillance of all patients receiving acute care according to the hospital-wide and intensive care unit components of the National Nosocomial Infections Surveillance System from January 1993 to December 1997 (14,892 discharges; 131,764 patient-days). The Centers for Disease Control and Prevention (Atlanta) 1988-definitions and the Brazilian Ministry of Health-Legislation 930 (1992) were used. RESULTS: The average overall nosocomial infection rate per 1000 patient-days was 8.9 in units 2 and 3 and 16.4 in the pediatric intensive care unit. Over time, the overall hospital infection rate decreased from 16.6 nosocomial infections per 1000 patient-days in 1993 to 7.0 in 1997 (P <.05). We believe this can be attributed to interventions and data reporting during the period. The five most frequent sites of infections were eye-ear-nose-throat (38%), skin (22%), pneumonia (12%), soft tissue (5%) and laboratory-confirmed bloodstream infection (4%). In the pediatric intensive care unit, the most frequent nosocomial infection sites were pneumonia related to mechanical ventilators (22%), with rates ranging from 0 to 42 per 1000 ventilator-days; and sepsis related to central lines (11%), with rates ranging from 0 to 32 per 1000 central line-days. CONCLUSIONS: Describing the epidemiology of nosocomial infections in this hospital enabled us to establish infection occurrence, distribution, and expected incidence, as well as to recognize trends and keep track of possible outbreaks. The knowledge acquired through this surveillance allowed us to target more specific and continuous quality improvement projects, to upgrade health care quality in pediatric public hospitals in Brazil, and to implement preventive strategies. Methods from the National Nosocomial Infections Surveillance System can be successfully applied in pediatric public hospitals in Brazil.

[Joint effort to improve quality in a Brazilian pediatric public hospital through cross-infection control] / Esforço conjunto para melhoria de qualidade em hospital público pediátrico brasileiro através do controle de infecção hospitalar.

OBJECTIVES: To examine the role of the laboratory in nosocomial infection control from January 1993 to December 1996 in Centro Geral de Pediatria of Hospital Foundation of Minas Gerais state. METHODS: Follow -up of 101,139 patient-days (11,147 discharges + deaths + transfers) in the wards and intensive care unit by using the National Nosocomial Infection Surveillance (NNIS) system proposed by the Centers for Disease Control and Prevention (CDC- Atlanta). Prospective surveillance of nosocomial infections at all sites was performed according to the hospital - wide (since 1992) and intensive care unit (since 1996) NNIS components. The CDC definitions since 1988 and Brazilian Ministry of Health regulation number 930 since 1992 were used to diagnose the nosocomial infections. RESULTS: The five most frequent nosocomial pathogens (from a total of 139 isolates) were Klebsiella sp = 24.5%; S. aureus = 18%; P. aeruginosa = 13.7%; E. coli = 12.9%; S. epidermidis = 12.2%. The percentage of identification of pathogens isolated from nosocomial infection sites has increased from 6.2% in 1993 to 13.3% in 1995 and 28.2% in 1996 (p< 0.001) and so has the attempt to isolate the pathogens: 7.5% in 1993, 16.1% in 1995, 33.8% in 1996 (p< 0.001). The time interval taken for lab results (from specimen collected to microbiology result) has decreased from the average of ten days in 1993 to six days in 1996 (p = 0.001). CONCLUSIONS: The continuing education and improved communication among infection control personnel, pediatricians, surgeons and members of the laboratory have proven to play a key role in the epidemiology of nosocomial infections by defining their etiologies in the Centro Geral de Pediatria. A task force to determine the microbiology has been achieved by the understanding of all clinicians that it is important to treat their patients specifically. The NNIS method applied to Brazilian hospitals has shown its impact on the microbiology lab role in nosocomial infection control as well.

Prevalence of nosocomial infections in general hospitals in Belo Horizonte.

OBJECTIVE: To assess the magnitude of nosocomial infections (NI) in general hospitals of Belo Horizonte. DESIGN: Multicenter point-prevalence study of nosocomial infections. SETTING: All of the 11 general hospitals of Belo Horizonte that have more than 20 beds, from August 27 to October 5, 1992. RESULTS: Of the 2,339 patients surveyed, 267 patients had 328 nosocomial infections. The global prevalence rate of NI was 14.0%, ranging from 4.6% to 27.3% in the hospitals surveyed. The most prevalent infections were found to be pneumonia and surgical-wound infections, representing 19.5% and 19.2%, respectively, of the total infections. The highest prevalence rates of NI were observed in the cardiac surgery (31.9%), pediatric (27.2%), and orthopedic (20.7%) services. The most frequently isolated microorganisms were Staphylococcus aureus, Escherichia coli, Pseudomonas species, and Klebsiella species. CONCLUSION: The study allowed a thorough evaluation of the NI distribution profile in Belo Horizonte, Minas Gerais, Brazil, and showed it to be a serious public health problem that requires interinstitutional efforts so that effective action can be taken.

Applying the Centers for Disease Control and Prevention and National Nosocomial Surveillance system methods in Brazilian hospitals.

BACKGROUND: Nosocomial infection is an important public health problem in Brazil. The better to understand and address this problem, we began using the National Nosocomial Infection Surveillance (NNIS) system in five Brazilian hospitals in 1991. METHODS: Data were collected prospectively according to the NNIS protocol, by using nosocomial infection definitions from the Centers for Disease Control and Prevention. RESULTS: From January 1991 to June 1995, the overall nosocomial infection rate was 5.1% or 9.7 nosocomial infections/1000 patient-days. From the detailed epidemiologic information obtained by using the NNIS methods, interventions were designed and implemented that have reduced specific nosocomial infection rates. For example, the incidence of infection caused by methicillin-resistant Staphylococcus aureus was reduced from 0.61 infections/1000 patient-days in 1991 to 0.05 infections/1000 patient-days in 1996 (p < 0.01). The surgical site infection rate after cesarean section was reduced from 11.6% in 1993 to 5.9% in 1996 (p < 0.05). Cost savings from a program to optimize the use of antimicrobial agents in one hospital was more than $1.8 million over a 45-month period. CONCLUSION: The NNIS method was applicable in a wide variety of hospitals, even those with little or no experience with nosocomial infection surveillance. By using this method, we defined the detailed epidemiology of nosocomial infection and implemented interventions that have significantly reduced nosocomial infection rates while achieving substantial cost savings.