Slum health: diseases of neglected populations.

BackgroundUrban slums, like refugee communities, comprise a social cluster that engenders a distinct set of health problems. With 1 billion people currently estimated to live in such communities, this neglected population has become a major reservoir for a wide spectrum of health conditions that the formal health sector must deal with.DiscussionUnlike what occurs with refugee populations, the formal health sector becomes aware of the health problems of slum populations relatively late in the course of their illnesses. As such, the formal health sector inevitably deals with the severe and end-stage complications of these diseases at a substantially greater cost than what it costs to manage non-slum community populations. Because of the informal nature of slum settlements, and cultural, social, and behavioral factors unique to the slum populations, little is known about the spectrum, burden, and determinants of illnesses in these communities that give rise to these complications, especially of those diseases that are chronic but preventable. In this article, we discuss observations made in one slum community of 58,000 people in Salvador, the third largest city in Brazil, to highlight the existence of a spectrum and burden of chronic illnesses not likely to be detected by the formal sector health services until they result in complications or death. Lack of health-related data from slums could lead to inappropriate and unrealistic allocation of health care resources by the public and private providers. Similar misassumptions and misallocations are likely to exist in other nations with large urban slum populations.SummaryContinued neglect of ever-expanding urban slum populations in the world could inevitably lead to greater expenditure and diversion of health care resources to the management of end-stage complications of diseases that are preventable. A new approach to health assessment and characterization of social-cluster determinants of health in urban slums is urgently needed

A phylogenomic analysis of the Actinomycetales mce operons

BACKGROUND: The genome of Mycobacterium tuberculosis harbors four copies of a cluster of genes termed mce operons. Despite extensive research that has demonstrated the importance of these operons on infection outcome, their physiological function remains obscure. Expanding databases of complete microbial genome sequences facilitate a comparative genomic approach that can provide valuable insight into the role of uncharacterized proteins. RESULTS: The M. tuberculosis mce loci each include two yrbE and six mce genes, which have homology to ABC transporter permeases and substrate-binding proteins, respectively. Operons with an identical structure were identified in all Mycobacterium species examined, as well as in five other Actinomycetales genera. Some of the Actinomycetales mce operons include an mkl gene, which encodes an ATPase resembling those of ABC uptake transporters. The phylogenetic profile of Mkl orthologs exactly matched that of the Mce and YrbE proteins. Through topology and motif analyses of YrbE homologs, we identified a region within the penultimate cytoplasmic loop that may serve as the site of interaction with the putative cognate Mkl ATPase. Homologs of the exported proteins encoded adjacent to the M. tuberculosis mce operons were detected in a conserved chromosomal location downstream of the majority of Actinomycetales operons. Operons containing linked mkl, yrbE and mce genes, resembling the classic organization of an ABC importer, were found to be common in Gram-negative bacteria and appear to be associated with changes in properties of the cell surface. CONCLUSION: Evidence presented suggests that the mce operons of Actinomycetales species and related operons in Gram-negative bacteria encode a subfamily of ABC uptake transporters with a possible role in remodeling the cell envelope

Identification of novel antimicrobial resistance genes from microbiota on retail spinach

BackgroundDrug resistance genes and their mobile genetic elements are frequently identified from environmental saprophytic organisms. It is widely accepted that the use of antibiotics in animal husbandry selects for drug resistant microorganisms, which are then spread from the farm environment to humans through the consumption of contaminated food products. We wished to identify novel drug resistance genes from microbial communities on retail food products. Here, we chose to study the microbial communities on retail spinach because it is commonly eaten raw and has previously been associated with outbreaks of bacterial infections.ResultsWe created metagenomic plasmid libraries from microbiota isolated from retail spinach samples. We identified five unique plasmids that increased resistance to antimicrobial drugs in the E. coli host. These plasmids were identified in E. coli that grew on plates that contained ampicillin (pAMP), aztreonam (pAZT), ciprofloxacin (pCIP), trimethoprim (pTRM), and trimethoprim-sulfamethoxazole (pSXT). We identified open reading frames with similarity to known classes of drug resistance genes in the DNA inserts of all 5 plasmids. These drug resistance genes conferred resistance to fluoroquinolones, cephalosporins, and trimethoprim, which are classes of antimicrobial drugs frequently used to treat human Gram negative bacterial infections. These results show that novel drug resistance genes are found in microbiota on retail produce items.ConclusionsHere we show that microbiota of retail spinach contains DNA sequences previously unidentified as conferring antibiotic resistance. Many of these novel sequences show similarity to genes found in species of bacteria, which have previously been identified as commensal or saprophytic bacteria found on plants. We showed that these resistance genes are capable of conferring clinically relevant levels of resistance to antimicrobial agents. Food saprophytes may serve as an important reservoir for new drug-resistance determinants in human pathogens

Risk factors for fecal carriage of drug-resistant Escherichia coli: a systematic review and meta-analysis.

BackgroundAntimicrobial resistance is a serious public health problem. Fecal carriage of drug-resistant bacteria has been suggested as an important source of antimicrobial resistant genes (ARGs). We aimed to identify risk factors associated with fecal carriage of drug-resistant commensal Escherichia coli among healthy adult population.MethodsWe conducted a systematic review and meta-analysis following the PRISMA guideline. We identified observational studies published from 2014 to 2019 through PubMed, Embase, and Web of Science. Studies were eligible if they investigated and reported risk factors and accompanying measure of associations for fecal carriage of drug-resistant E. coli for healthy population aged 18-65. Data on risk factors assessed in three or more studies were extracted.ResultsFifteen of 395 studies involving 11480 healthy individuals were included. The pooled prevalence of drug-resistant Enterobacteriaceae was 14% (95% confidence interval [CI] 8-23%). Antimicrobial use within the 12 months prior to stool culture (odds ratio [OR] 1.84 [95%CI 1.35-2.51]), diarrhea symptoms (OR 1.56 [95%CI 1.09-2.25]), travel to India (OR 4.15 [95%CI 2.54-6.78]), and vegetarian diet (OR 1.60 [95%CI 1.00(1.0043)-2.56(2.5587)]) were associated with increased risk of fecal carriage of drug-resistant E. coli. Among travellers, antimicrobial use (OR 2.81 [95%CI 1.47-5.36]), diarrhea symptoms (OR 1.65 [95%CI 1.02-2.68]), travel to India (OR 3.80 [95%CI 2.23-6.47]), and vegetarian diet (OR 1.92 [95%CI 1.13-3.26]) were associated with increased risk. Among general adult population, antimicrobial use (OR 1.51 [95%CI 1.17-1.94]), diarrhea symptoms (OR 1.53 [95%CI 1.27-1.84]), and travel to Southeast Asia (OR 1.67 [95%CI 1.02-2.73]) were associated with the increased risk of drug-resistant E. coli carriage.ConclusionsThe findings indicate that dietary habit as well as past antimicrobial use and travel to high-risk country are associated with the risk of fecal carriage of drug-resistant commensal E. coli

A Population-Based Surveillance Study of Shared Genotypes of Escherichia coli Isolates from Retail Meat and Suspected Cases of Urinary Tract Infections.

There is increasing evidence that retail food may serve as a source of Escherichia coli that causes community-acquired urinary tract infections, but the impact of this source in a community is not known. We conducted a prospective, population-based study in one community to examine the frequency of recovery of uropathogenic E. coli genotypes from retail meat samples. We analyzed E. coli isolates from consecutively collected urine samples of patients suspected to have urinary tract infections (UTIs) at a university-affiliated health service and retail meat samples from the same geographic region. We genotyped all E. coli isolates by multilocus sequence typing (MLST) and tested them for antimicrobial susceptibility. From 2016 to 2017, we cultured 233 E. coli isolates from 230 (21%) of 1,087 urine samples and 177 E. coli isolates from 120 (28%) of 427 retail meat samples. Urine samples contained 61 sequence types (STs), and meat samples had 95 STs; 12 STs (ST10, ST38, ST69, ST80, ST88, ST101, ST117, ST131, ST569, ST906, ST1844, and ST2562) were common to both. Thirty-five (81%) of 43 meat isolates among the 12 STs were from poultry. Among 94 isolates in the 12 STs, 26 (60%) of 43 retail meat isolates and 15 (29%) of 51 human isolates were pan-susceptible (P < 0.005). We found that 21% of E. coli isolates from suspected cases of UTIs belonged to STs found in poultry. Poultry may serve as a possible reservoir of uropathogenic E. coli (UPEC). Additional studies are needed to demonstrate transmission pathways of these UPEC genotypes and their food sources.IMPORTANCE Community-acquired urinary tract infection caused by Escherichia coli is one of the most common infectious diseases in the United States, affecting approximately seven million women and costing approximately 11.6 billion dollars annually. In addition, antibiotic resistance among E. coli bacteria causing urinary tract infection continues to increase, which greatly complicates treatment. Identifying sources of uropathogenic E. coli and implementing prevention measures are essential. However, the reservoirs of uropathogenic E. coli have not been well defined. This study demonstrated that poultry sold in retail stores may serve as one possible source of uropathogenic E. coli This finding adds to a growing body of evidence that suggests that urinary tract infection may be a food-borne disease. More research in this area can lead to the development of preventive strategies to control this common and costly infectious disease

Molecular epidemiology of tuberculosis in Prague: Analysis by restriction fragment length polymorphism

AbstractObjectives: To characterize by restriction fragment length polymorphism (RFLP) patterns, the distribution of different Mycobacterium tuberculosisstrains isolated consecutively from 75 tuberculosis patients who resided in Prague and had culture-confirmed cases during a 4-month period in 1995.Methods: The insertion sequence IS6110-based RFLP analysis of M. tuberculosis isolates was carried out.Results: There were a total of 75 patients with various forms of tuberculosis (54 males; 21 females). The sources of M. tuberculosis isolates were sputum (n = 64), pleura or lymph node drainage (n = 8), and urine (n = 3). Fifty-three of the patients (70.7%) had isolates with unique RFLP patterns, while 22 (29.3%) had isolates that belonged to seven clusters of related RFLP patterns. The seven clusters consisted of four groups of two patients, two groups of four patients, and one group of six patients. Most of the patients whose isolates fell within a clustered RFLP pattern lived in different quarters of the city and had no identifiable contacts with other patients whose isolates had the same pattern.Conclusions: The finding that isolates from most patients (70.7%) had unique rather than clustered RFLP patterns suggests that endogenous reactivation rather than exogenous transmission is the major determinant of most of the tuberculosis cases in Prague. The occurrence of seven distinct clusters comprising 29.3% of the isolates suggests that approximately one third of cases developed active tuberculosis from recent exogenous transmission

In-house nucleic acid amplification tests for the detection of Mycobacterium tuberculosis in sputum specimens: meta-analysis and meta-regression

BACKGROUND: More than 200 studies related to nucleic acid amplification (NAA) tests to detect Mycobacterium tuberculosis directly from clinical specimens have appeared in the world literature since this technology was first introduced. NAA tests come as either commercial kits or as tests designed by the reporting investigators themselves (in-house tests). In-house tests vary widely in their accuracy, and factors that contribute to heterogeneity in test accuracy are not well characterized. Here, we used meta-analytical methods, including meta-regression, to identify factors related to study design and assay protocols that affect test accuracy in order to identify those factors associated with high estimates of accuracy. RESULTS: By searching multiple databases and sources, we identified 2520 potentially relevant citations, and analyzed 84 separate studies from 65 publications that dealt with in-house NAA tests to detect M. tuberculosis in sputum samples. Sources of heterogeneity in test accuracy estimates were determined by subgroup and meta-regression analyses. Among 84 studies analyzed, the sensitivity and specificity estimates varied widely; sensitivity varied from 9.4% to 100%, and specificity estimates ranged from 5.6% to 100%. In the meta-regression analysis, the use of IS6110 as a target, and the use of nested PCR methods appeared to be significantly associated with higher diagnostic accuracy. CONCLUSION: Estimates of accuracy of in-house NAA tests for tuberculosis are highly heterogeneous. The use of IS6110 as an amplification target, and the use of nested PCR methods appeared to be associated with higher diagnostic accuracy. However, the substantial heterogeneity in both sensitivity and specificity of the in-house NAA tests rendered clinically useful estimates of test accuracy difficult. Future development of NAA-based tests to detect M. tuberculosis from sputum specimens should take into consideration these findings in improving accuracy of in-house NAA tests

Compositions and methods for detecting mycobacterium

The present disclosure provides methods of detecting mycobacterium in an individual, generally involving detecting antibody to a mycobacterial lipid in a biological sample obtained from the individual. The present disclosure further provides compositions and kits for carrying out the methodsThe present disclosure provides methods of detecting mycobacterium in an individual, generally involving detecting antibody to a mycobacterial lipid in a biological sample obtained from the individual. The present disclosure further provides compositions and kits for carrying out the method

Draft Genome Sequence of a Community-Associated Methicillin- Resistant Panton-Valentine Leukocidin-Positive Staphylococcus aureus Sequence Type 30 Isolate from a Pediatric Patient with a Lung Infection in Brazil

The sequence of methicillin-resistant Staphylococcus aureus strain B6 (sequence type 30 [ST30], spa type t433, staphylococcal chromosomal cassette mec element [SCCmec] type IVc, Panton-Valentine leukocidin [PVL] positive), isolated from a pediatric patient with a lung infection in Niterói, Rio de Janeiro, Brazil, is described here. The draft genome sequence includes a 2.8-Mb chromosome, accompanied by a 20-kb plasmid containing blaZ and two small cryptic plasmids

Differences in the Prevalence of Non-Communicable Disease between Slum Dwellers and the General Population in a Large Urban Area in Brazil.

Residents of urban slums are at greater risk for disease than their non-slum dwelling urban counterparts. We sought to contrast the prevalences of selected non-communicable diseases (NCDs) between Brazilian adults living in a slum and the general population of the same city, by comparing the age and sex-standardized prevalences of selected NCDs from a 2010 survey in Pau da Lima, Salvador Brazil, with a 2010 national population-based telephone survey. NCD prevalences in both populations were similar for hypertension (23.6% (95% CI 20.9⁻26.4) and 22.9% (21.2⁻24.6), respectively) and for dyslipidemia (22.7% (19.8⁻25.5) and 21.5% (19.7⁻23.4)). Slum residents had higher prevalences of diabetes mellitus (10.1% (7.9⁻12.3)) and of overweight/obesity (46.5% (43.1⁻49.9)), compared to 5.2% (4.2⁻6.1) and 40.6% (38.5⁻42.8) of the general population in Salvador. Fourteen percent (14.5% (12.1⁻17.0)) of slum residents smoked cigarettes compared to 8.3% (7.1⁻9.5) of the general population in Salvador. The national telephone survey underestimated the prevalence of diabetes mellitus, overweight/obesity, and smoking in the slum population, likely in part due to differential sampling inside and outside of slums. Further research and targeted policies are needed to mitigate these inequalities, which could have significant economic and social impacts on slum residents and their communities