Bacterial Enteropathogens Research Articles

Comparison of the Microflex LT and Vitek MS Systems for Routine Identification of Bacteria by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

This study compared the performance of three matrix-assisted laser desorption ionization-time of flight mass spectrometry systems: Microflex LT (Bruker Daltonics, Bremen, Germany), Vitek MS RUO (Axima Assurance-Saramis database; bioMérieux, Marcy l'Etoile, France), and Vitek MS IVD (bioMérieux). A total of 1,129 isolates, including 1,003 routine isolates, 73 anaerobes, and 53 bacterial enteropathogens, were tested on the Microflex LT and Axima Assurance devices. The spectra were analyzed using three databases: Biotyper (Bruker Daltonics), Saramis, and Vitek MS (bioMérieux). Among the routine isolates requiring identification to the species level (n = 986), 92.7% and 93.2% were correctly identified by the Biotyper and Vitek MS databases, respectively. The Vitek MS database is more specific for the identification of Streptococcus viridans. For the anaerobes, the Biotyper database often identified Fusobacterium isolates to only the genus level, which is of low clinical significance, whereas 20% of the Bacteroides species were not identified or were misidentified by the Vitek MS database. For the enteropathogens, the poor discrimination between Escherichia coli and Shigella explains the high proportion of unidentified organisms. In contrast to the Biotyper database, the Vitek MS database properly discriminated all of the Salmonella entrica serovar Typhi isolates (n = 5). The performance of the Saramis database was globally poorer. In conclusion, for routine procedures, the Microflex LT and Vitek-MS systems are equally good choices in terms of analytical efficiency. Other factors, including price, work flow, and lab activity, will affect the choice of a system.

Long-term trends in the epidemiology and resistance of childhood bacterial enteropathogens in Crete

In this study, we investigated the long-term trends in the epidemiology and susceptibility of bacterial enteropathogens among children in a well-defined area of adequate health standards. The study included all children younger than 14 years of age treated for enteritis at Heraklion University General Hospital on the island of Crete during the 18-year period from January 1993 to December 2010. Stool specimens were tested for Salmonella, Shigella, Campylobacter, enteropathogenic Escherichia coli (EPEC), Yersinia, and Aeromonas species. Of the 33,032 stool samples from patients of any age, 2,912 (8.82%) were positive for bacterial enteropathogens. The 1,597 isolates from children were identified as S. enterica (42.3%), Campylobacter spp. (33.6%), EPEC (17.4%), Y. enterocolitica (5.82%), A. hydrophila (0.44%), and Shigella spp. (0.38%). A decline in prevalence was observed for all bacterial enteropathogens. Taken as a total, enteropathogens were susceptible to gentamicin, ceftriaxone, ciprofloxacin, co-trimoxazole, and amoxicillin in 98.8%, 88.0%, 83.0%, 67.1%, and 59.6%, respectively. During the study period, the susceptibility rates decreased for co-trimoxazole (p<0.0001) and ciprofloxacin (p<0.001), and increased for amoxicillin (p<0.0001). Our findings suggest declining long-term trends in the prevalence of bacterial enteropathogens and changes in susceptibility rates to first-line antibacterial agents. These changing trends in the long-term morbidity and susceptibility call for ongoing surveillance and tailored management.

The Role of Innate Immunity in the Host Defense Against Intestinal Bacterial Pathogens

Eradication of infectious disease is our global health challenge. After encountering intestinal infection with a bacterial pathogen, the host defense program is initiated by local antigen-presenting cells (APCs) that eliminate invading pathogens by phagocytosis and establish localized inflammation by secreting cytokines and chemokines. These pathogen-experienced APCs migrate to the mesenteric lymph nodes, where host immune responses are precisely orchestrated. Initiation and regulation of this defense program appear to be largely dependent on innate immunity which is antigen non-specific and provides a rapid defense against broader targets. On the other hand, many bacterial enteropathogens have evoked abilities to modify the host defense program to their advantage. Therefore, better understanding of the host-pathogen interactions is essential to establish effective eradication strategies for enteric infectious diseases. In this review, we will discuss the current understanding of innate immune regulation of the host defense mechanisms against intestinal infection by bacterial pathogens.

Enteropathogenic Bacteria in Dogs and Cats: Diagnosis, Epidemiology, Treatment, and Control

This report offers a consensus opinion on the diagnosis, epidemiology, treatment, and control of the primary enteropathogenic bacteria in dogs and cats, with an emphasis on Clostridium difficile, Clostridium perfringens, Campylobacter spp., Salmonella spp., and Escherichia coli associated with granulomatous colitis in Boxers. Veterinarians are challenged when attempting to diagnose animals with suspected bacterial-associated diarrhea because well-scrutinized practice guidelines that provide objective recommendations for implementing fecal testing are lacking. This problem is compounded by similar isolation rates for putative bacterial enteropathogens in animals with and without diarrhea, and by the lack of consensus among veterinary diagnostic laboratories as to which diagnostic assays should be utilized. Most bacterial enteropathogens are associated with self-limiting diarrhea, and injudicious administration of antimicrobials could be more harmful than beneficial. Salmonella and Campylobacter are well-documented zoonoses, but antimicrobial administration is not routinely advocated in uncomplicated cases and supportive therapy is recommended. Basic practices of isolation, use of appropriate protective equipment, and proper cleaning and disinfection are the mainstays of control. Handwashing with soap and water is preferred over use of alcohol-based hand sanitizers because spores of C. difficile and C. perfringens are alcohol-resistant, but susceptible to bleach (1:10 to 1:20 dilution of regular household bleach) and accelerated hydrogen peroxide. The implementation of practice guidelines in combination with the integration of validated molecular-based testing and conventional testing is pivotal if we are to optimize the identification and management of enteropathogenic bacteria in dogs and cats.

Systematic review: the use of proton pump inhibitors and increased susceptibility to enteric infection

The use of proton pump inhibitors (PPIs) is increasing worldwide. Suppression of gastric acid alters the susceptibility to enteric bacterial pathogens. AIM This systematic review was undertaken to examine the relationship between PPI use and susceptibility to enteric infections by a specific pathogen based on published literature and to discuss the potential mechanisms of PPI enhanced pathogenesis of enteric infections. METHODS PubMed, OVID Medline Databases were searched. Search terms included proton pump inhibitors and mechanisms of, actions of, gastric acid, enteric infections, diarrhoea, Clostridium difficile, Salmonella, Shigella and Campylobacter. RESULTS The use of PPIs increases gastric pH, encourages growth of the gut microflora, increases bacterial translocation and alters various immunomodulatory and anti-inflammatory effects. Enteric pathogens show variable gastric acid pH susceptibility and acid tolerance levels. By multiple mechanisms, PPIs appear to increase susceptibility to the following bacterial enteropathogens: Salmonella, Campylobacter jejuni, invasive strains of Escherichia coli, vegetative cells of Clostridium difficile, Vibrio cholerae and Listeria. We describe the available evidence for enhanced susceptibility to enteric infection caused by Salmonella, Campylobacter and C. difficile by PPI use, with adjusted relative risk ranges of 4.2-8.3 (two studies); 3.5-11.7 (four studies); and 1.2-5.0 (17 of 27 studies) for the three respective organisms. CONCLUSIONS Severe hypochlorhydria generated by PPI use leads to bacterial colonisation and increased susceptibility to enteric bacterial infection. The clinical implication of chronic PPI use among hospitalized patients placed on antibiotics and travellers departing for areas with high incidence of diarrhoea should be considered by their physicians.

Genotyping of selected bacterial enteropathogens in Norway

In Norway the Norwegian Institute of Public Health (NIPH) is the primary facility for nationwide surveillance of foodborne infections, and it is vital that we can perform rapid and high resolution identification of foodborne bacteria at the strain level. During the last decade a rapid introduction of DNA-based methods has been introduced, which show promise in enhancing the speed and discriminatory capability of the typing laboratory. The laboratory responsible for genotyping enteropathogens at NIPH is limited in staff, thus methods demanding reduced labour, high degree of automation and increased ease of interpretation is essential. We found that this could be achieved by focusing on MLVA for some of the most predominant enteropathogenic species. Bacterial genotyping is performed by several laboratories in Norway, however this review will address the use of routine genotyping by MLVA of common foodborne bacteria at NIPH. The emphasis will be on Escherichia coli, Salmonella typhimurium, Shigella spp. Yersinia enterocolitica and Listeria monocytogenes. This review is based on an oral presentation given at the 9th International Meeting on Microbial Epidemiological Markers in Wernigerode Germany on September 1st 2010.

Bacterial enteropathogens associated with diarrhea in a rural population of Haiti.

Diarrheal disease is one of the leading causes of morbidity in developing countries. To further understand the epidemiology of diarrheal disease among a rural population surrounding Robillard, Haiti, fecal swabs from patients with diarrhea were screened for the presence of enteropathogenic bacteria. Fecal swabs were collected from 34 patients with signs and symptoms of diarrhea and stored in BBL™ Cary-Blair transport medium (Becton, Dickinson and Company, Sparks, MD) until transit to the USA. Swab material was inoculated on to different enrichment and selective agars for incubation. Fermenting and nonfermenting bacteria that grew on the enteric selection media were identified by the BBL™ Crystal™ Enteric/Nonferementing Identification system (Becton, Dickinson and Company). Organisms identified as Escherichia coli were further screened for the presence of virulence factors by polymerase chain reaction (PCR). Of 34 patients, no Campylobacter, Shigella, Salmonella, or Vibrio spp. were isolated from swabs transported to the USA for culture. Of 73 E. coli isolates cultured from the swabs, one enteropathogenic strain of E. coli was identified by multiplex PCR. Escherichia fergusonii and Cronobacter sakazakii, both potential gastrointestinal pathogens, were also isolated from patient stools. This study was undertaken to determine if bacterial enteropathogens could be detected in the stools of patients suffering from diarrhea or dysentery and, in the absence of sufficient facilities, rectal swabs could be transported to the USA for culture. Although several genera of overt enteropathogens were not detected, one enteropathogenic E. coli and other pathogenic enterobacteriaceae were successfully cultured and identified.

Antimicrobial susceptibilities of enteric bacterial pathogens isolated in Kathmandu, Nepal, during 2002-2004

The prevalence and antimicrobial susceptibility patterns of the bacterial enteropathogens Vibrio cholerae, Salmonella species and Shigella species were investigated. A total of 877 stool samples were received for culture at the National Public Health Laboratory (NPHL), Kathmandu, Nepal, during January 2002 to December 2004, from diarrhoea patients attending Shukraraj Tropical Infectious Hospital and referral outpatients. All samples collected were processed for isolation and antibiotic susceptibility testing of Vibrio cholerae, Salmonella spp. and Shigella spp. Of the 877 stool samples, 148 (16.8%) were culture positive for one of the three bacterial enteropathogens investigated. Among them, Vibrio cholerae, Shigella spp. and Salmonella spp. accounted for 98/877 (11.1%), 41/877 (4.6%), 9/877 (1.02%) of the isolates respectively. A year-to-year variation was seen in the type of predominant organism, with Shigella spp. being the most prevalent in 2002 and 2003 and Vibrio spp. in 2004. In all three years, Vibrio cholerae were encountered only during the months of April to June while Salmonella spp. and Shigella spp. were isolated throughout the whole year. All Vibrio cholerae and Salmonella isolates were susceptible to ciprofloxacin. All Shigella isolates were susceptible to ceftriaxone. Ciprofloxacin resistance was observed among isolates of Shigella dysenteriae type-1 isolated after 2003. Vibrio cholerae, Salmonella and Shigella infections are prevalent in Kathmandu, Nepal. A gradual increase in resistance to commonly used antimicrobials was seen among bacterial enteropathogens. Antimicrobial resistance surveillance is necessary to guide empirical treatment.

Seasonality of DiarrheagenicEscherichia coliPathotypes in the US Students Acquiring Diarrhea in Mexico

Up to 60% of the US visitors to Mexico develop travelers' diarrhea (TD). In Mexico, rates of diarrhea have been associated with the rainy season and increase in ambient temperature. However, the seasonality of the various diarrheagenic Escherichia coli pathotypes in travelers has not been well described. A study was undertaken to determine if ambient temperature and rainfall have an impact on the acquisition of TD due to different diarrheagenic E coli pathotypes in Mexico. We conducted a cohort study of the US adult students traveling to Cuernavaca, Mexico, who were followed during their stay and provided a stool sample with the onset of TD. The presence of E coli was analyzed by a direct fecal multiplex polymerase chain reaction for common E coli pathotypes including enterotoxigenic, enteropathogenic, enteroinvasive, shiga toxin-producing, and enteroaggregative E coli (ETEC, EPEC, EIEC, STEC, and EAEC respectively). The presence of pathotypes was correlated with daily rainfall, average, maximum, and minimum temperatures. A total of 515 adults were enrolled from January 2006 to February 2007. The weekly attack rate of TD for newly arrived travelers was lower in the winter months (range 6.8%-16.3%) than in summer months (range 11.5%-25%; p = 0.05). The rate of ETEC infection increased by 7% for each degree centigrade increase in weekly ambient temperature (p = 0.003). In contrast, EPEC and EAEC were identified in similar proportions during the winter and summer seasons. Temperature variations in central Mexico influenced the rate of ETEC but not EAEC-associated diarrhea in the US visitors. This epidemiological finding could influence seasonal recommendations for the use of ETEC vaccines in Mexico.

In vitro antimicrobial susceptibility of bacterial enteropathogens isolated from international travelers to Mexico, Guatemala, and India from 2006 to 2008.

The incidence rates of travelers' diarrhea (TD) have remained high for the last 50 years. More recently, there have been increasing recommendations for self-initiated therapy and use of prophylactic drugs for TD. We last examined the in vitro susceptibilities of commonly used antibiotics against TD pathogens in 1997. We now examine 456 enteropathogens isolated from adult travelers to Mexico, India, and Guatemala with diarrhea acquired between 2006 and 2008 to determine changes in susceptibility against 10 different antimicrobials by the agar dilution method. Traditional antibiotics, such as ampicillin, trimethoprim-sulfamethoxazole, and doxycycline, continue to show high levels of resistance. Current first-line antibiotic agents, including fluoroquinolones and azithromycin, showed significantly higher MICs than in our earlier study, and MIC(90) levels were above the Clinical and Laboratory Standards Institute cutoffs for resistance. There were significant geographical differences in resistance patterns when Central America was compared with India. Entertoxigenic Escherichia coli (ETEC) isolates showed increased resistance to ciprofloxacin (P = 0.023) and levofloxacin (P = 0.0078) in India compared with Central America. Enteroaggregative E. coli (EAEC) isolates from Central America showed increased resistance to nearly all of the antibiotics tested. Compared to MICs of isolates 10 years prior, there were 4- to 10-fold increases in MIC(90) values for ceftriaxone, ciprofloxacin, levofloxacin, and azithromycin for both ETEC and EAEC. There were no significant changes in rifaximin MICs. Rising MICs over time imply the need for continuous surveillance of susceptibility patterns worldwide and geographically specific recommendations in TD therapy.

Bacterial Enteropathogens and Risk Factors Associated with Childhood Diarrhea

To investigate the etiology of bacterial enteropathogens causing diarrhea among children; to elucidate the risk factors, sign and symptoms involved in developing of infection; and to identify the antimicrobial susceptibility pattern. Stool samples from diarrheal cases with clinical diagnosis of gastroenteritis compared to matched controls, were examined for detection of bacterial enteropathogens by conventional cultural method from February 2006 through January 2007. Ninety three of diarrheal cases comprising enteropathogen isolates. A recognized bacterial enteric pathogen was identified in 31% of the cases and 8% of the control group. The frequency of isolated enteropathogens from faeces of diarrheal cases was recorded in the following order, Enterohemorrhagic E. coli 8.3%, Shigella spp. 6.7%, Campylobacter jejuni 5%, Salmonella spp. 4%, Yersinia enterocolitica 2.7%, Aeromonas spp. 4.7%, and Plesiomonas spp. 1.3%. E.H.E coli, Shigella and Salmonella had shown a significant statistical association with diarrhea (p<0.05). Compared to matched uninfected control, multivariate analysis revealed that malnutrition status (OR adjusted 8.37; p<0.001) was the only independent factor associated with infection. Antibiotic susceptibility profile indicated that enteropathogens were generally susceptible to meropenem, ceftriaxone, followed by amikacin and ciprofloxacin. Almost all enteropathogens were resistant to ampicillin and amoxicillin. The results of this study emphasize the importance of bacterial enteropathogens in causing severe diarrhea in children. E.H.E. coli was the most predominant pathogen. Malnutrition was identified as the main independent risk factor associated with developing of infection. Ampicillin and amoxicillin should not be used as empirical treatment in acute diarrhea.

The ability of disease and non-disease producing strains of Clostridium perfringens from chickens to adhere to extracellular matrix molecules and Caco-2 cells

Clostridium perfringens is a major enteric pathogen that is responsible for causing necrotic enteritis of poultry. The ability to adhere to the host’s intestinal epithelium and to extracellular matrix molecules (ECMM) in the gut, are strategies used by numerous bacterial enteropathogens, however, C. perfringens has received comparatively little attention in this respect. The present study investigated sixteen type A C. perfringens isolates from chickens, with varying disease producing ability with respect to necrotic enteritis in chickens, for their ability to adhere to nine different extracellular matrix molecules (ECMM) and to the intestinal epithelial cell line Caco-2. C. perfringens strains were able to bind to ECMMs and there was strain variation. Strains of C. perfringens that produced severe disease, were capable of binding to collagen type III, IV and V, fibrinogen, laminin and vitronectin at higher levels than less severe disease producing strains, suggesting that the ability to adhere to ECMMs might enhance virulence with respect to induction of necrotic enteritis. In addition, severe disease producing strains also bound better to collagen type III and IV and fibrinogen, than non-disease producing strains. The present study also showed that some strains of C. perfringens possessed the ability to adhere to Caco-2 cells; however no relationship was found between the ability to adhere to Caco-2 cells and disease producing ability.

An Epidemiologic Review of Enteropathogens in Gaborone, Botswana: Shifting Patterns of Resistance in an HIV Endemic Region

BackgroundThe epidemiology of diarrheal disease in Botswana, an HIV endemic region, is largely unknown. Our primary objective was to characterize the prevalent bacterial and parasitic enteropathogens in Gaborone, Botswana. Secondary objectives included determining corresponding antimicrobial resistance patterns and the value of stool white and red blood cells for predicting bacterial and parasitic enteropathogens.Methodology/Principal FindingsA retrospective cross-sectional study examined laboratory records of stool specimens analyzed by the Botswana National Health Laboratory in Gaborone, Botswana from February 2003 through July 2008. In 4485 specimens the median subject age was 23 [interquartile range 1.6–34] years. Overall, 14.4% (644 of 4485) of samples yielded a pathogen. Bacteria alone were isolated in 8.2% (367 of 4485), parasites alone in 5.6% (253 of 4485) and both in 0.5% (24 of 4485) of samples. The most common bacterial pathogens were Shigella spp. and Salmonella spp., isolated from 4.0% (180 of 4485) and 3.9% (175 of 4485) of specimens, respectively. Escherichia coli (22 of 4485) and Campylobacter spp. (22 of 4485) each accounted for 0.5% of pathogens. Comparing antimicrobial resistance among Shigella spp. and Salmonella spp. between two periods, February 2003 to February 2004 and July 2006 to July 2008, revealed an increase in ampicillin resistance among Shigella spp. from 43% to 83% (p<0.001). Among Salmonella spp., resistance to chloramphenicol decreased from 56% to 6% (p<0.001). The absence of stool white and red blood cells correlated with a high specificity and negative predictive value.Conclusions/SignificanceMost gastroenteritis stools were culture and microscopy negative suggesting that viral pathogens were the majority etiologic agents in this Botswana cohort. Shigella spp. and Salmonella spp. were the most common bacteria; Isospora spp. and Cryptosporidium spp. were the most common parasites. Resistance to commonly used antimicrobials is high and should be closely monitored.

Traveling Internationally: Avoiding and Treating Travelers' Diarrhea

Traveling Internationally: Avoiding and Treating Travelers' Diarrhea

Symptomatic and Asymptomatic Rotavirus and Norovirus Infections During Infancy in a Chilean Birth Cohort

Rotavirus and more recently norovirus have been recognized as 2 of the most common causes of acute diarrhea in children. Comparative analysis of these infections in a birth cohort has not been performed and can provide relevant insight on clinical and viral behaviors. Mother-infant pairs from middle-low socioeconomic background living in the Metropolitan Region of Chile are being followed for 18 months in 2 outpatient clinics. Infants are evaluated monthly for asymptomatic excretion of rotavirus and norovirus and during acute diarrhea episodes (ADE) for rotavirus, norovirus, and bacterial enteropathogens. Severity of ADE is evaluated using the Vesikari score. Between July 1, 2006 and September 1, 2008 a total of 198 children were followed for a mean of 15.7 months. Asymptomatic rotavirus and norovirus infections were detected in 1.3% and 8% of 2278 stool samples compromising 14% and 57% of infants, respectively. Incidence of ADE was approximately 0.8 for the first year of life and approximately 0.6 for the 13 to 18 month age group. Rotavirus and norovirus were detected in 15% and 18% of 145 ADE evaluated. Mean Vesikari score was 10.4 and 7.4 for rotavirus and norovirus respectively (P = 0.01) and severity was not associated with age of patients for either virus. Reinfections were more common for norovirus asymptomatic episodes: 44% versus 19% (P = 0.01) and borderline for symptomatic episodes: 40% versus 11% (P = 0.08). Rotavirus genotype G9P8 and norovirus genogroup II (GII) predominated although most asymptomatic episodes for both viruses were nontypable. None of 19 symptomatic GII norovirus infections had a previous documented GII infection compared with 10 of 31 asymptomatic GII infections (OR = 0. 95% CL = 0, 0.59; P = 0.008). Children had suffered a mean of approximately 1.4 ADE by 18 months of age of which 15% and 18% were caused by rotavirus and norovirus, respectively. In general rotavirus infections were more severe than norovirus infections and for both viruses severity was not related to age. Norovirus reinfections were significantly more common than rotavirus reinfections but for GII norovirus a primary infection seems to confer protection against clinically significant reinfections.

Evaluación de un modelo de coprocultivo en las guardias de microbiología para el aislamiento de enteropatógenos bacterianos

Gastrointestinal infection is still a common problem in emergencies. We have evaluated a routine faecal culture method for isolating bacterial enteropathogens for urgent use. We studied 2201 faeces specimens by culturing in Skirrow, MacConkey agar and Selenite broth, the study and the whole culture procedure being completed during normal laboratory hours. The final results were reported significantly earlier; Campylobacter (36.1%), Salmonella (35.1%) and Shigella (90%) ( P<0.001). Isolates were recovered from 10% of the samples. The faecal culture method used in microbiology emergencies is feasible and effective.

Systematic review: the epidemiology and clinical features of travellers’ diarrhoea

Travellers' diarrhoea is the most common medical complaint among persons venturing into developing areas from industrialized regions. To review recent developments dealing with microbiological, clinical, pathophysiological and therapeutic aspects of travellers' diarrhoea. The author's extensive file plus a review of publications listed in PubMed on January 22, 2009 on the topic of travellers' diarrhoea were reviewed. Travellers' diarrhoea is largely caused by detectable and undetected bacterial enteropathogens, explaining the remarkable effectiveness of antibacterial agents in prophylaxis and therapy of the illness. A number of host genetic polymorphisms have been recently linked with susceptibility to travellers' diarrhoea. Novel antisecretory agents are being developed for treatment considering their physiological effects in acute diarrhoea. All travellers should be armed with one of three antibacterial drugs, ciprofloxacin, rifaximin or azithromycin, before their trips to use in self therapy should diarrhoea occur during travel. Loperamide may treat milder forms of travellers' diarrhoea and can be employed with antibacterial drugs. Diarrhoea will continue to plague international travellers to high-risk regions. More studies of the incidence rate, relative important of the various pathogens by geographical region of the world, host risk factors and optimal therapeutic approach are needed.

Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens.

BackgroundThe Enteropathogen Resource Integration Center (ERIC; ) has a goal of providing bioinformatics support for the scientific community researching enteropathogenic bacteria such as Escherichia coli and Salmonella spp. Rapid and accurate identification of experimental conclusions from the scientific literature is critical to support research in this field. Natural Language Processing (NLP), and in particular Information Extraction (IE) technology, can be a significant aid to this process.DescriptionWe have trained a powerful, state-of-the-art IE technology on a corpus of abstracts from the microbial literature in PubMed to automatically identify and categorize biologically relevant entities and predicative relations. These relations include: Genes/Gene Products and their Roles; Gene Mutations and the resulting Phenotypes; and Organisms and their associated Pathogenicity. Evaluations on blind datasets show an F-measure average of greater than 90% for entities (genes, operons, etc.) and over 70% for relations (gene/gene product to role, etc). This IE capability, combined with text indexing and relational database technologies, constitute the core of our recently deployed text mining application.ConclusionOur Text Mining application is available online on the ERIC website . The information retrieval interface displays a list of recently published enteropathogen literature abstracts, and also provides a search interface to execute custom queries by keyword, date range, etc. Upon selection, processed abstracts and the entities and relations extracted from them are retrieved from a relational database and marked up to highlight the entities and relations. The abstract also provides links from extracted genes and gene products to the ERIC Annotations database, thus providing access to comprehensive genomic annotations and adding value to both the text-mining and annotations systems.

Comparison of the prevalence of bacterial enteropathogens, potentially zoonotic bacteria and bacterial resistance to antimicrobials in organic and conventional poultry, swine and beef production: a systematic review and meta-analysis

The prevalences of zoonotic and potentially zoonotic bacteria or bacteria resistant to antimicrobials in organic and conventional poultry, swine and beef production were compared using systematic review and meta-analysis methodology. Thirty-eight articles were included in the review. The prevalence of Campylobacter was higher in organic broiler chickens at slaughter, but no difference in prevalence was observed in retail chicken. Campylobacter isolates from conventional retail chicken were more likely to be ciprofloxacin-resistant (odds ratio 9.62, 95% confidence interval 5.67-16.35). Bacteria isolated from conventional animal production exhibited a higher prevalence of resistance to antimicrobials; however, the recovery of some resistant strains was also identified in organic animal production, where there is an apparent reduced antimicrobial selection pressure. Limited or inconsistent research was identified in studies examining the prevalence of zoonotic and potentially zoonotic bacteria in other food-animal species. There is a need for further research of sufficient quality in this area.

Etiological agents of diarrhea in patients infected by the human immunodeficiency virus-1: a review

Despite the importance of understanding the epidemiology of agents responsible for infectious diarrhea in human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) population, the number of articles about this subject is relatively few. The current article summarizes published data on bacterial, fungal, viral and parasitic enteropathogens in the HIV/AIDS seropositive subjects in different countries, regions and localities. In general, there is a great difference in the frequencies of etiological agents due to factors which include immune status, geographical location, climate and socioeconomic conditions. It is important to stress that a great prevalence of infection by emergent agents has been reported in the more advanced stages of AIDS. Therefore, to establish specific treatment depends directly on knowledge of these agents and risk factors associated to their distribution. Moreover, the colonization by potential pathogenic agents verified in these individuals is high thus implicating that they act as carriers. Finally, public health measures of control and prevention must take into consideration the regional previously identified enteropathogens, especially in areas where HIV prevalence is high.