Phylogenetic of Shiga Toxin-Producing Escherichia coli and a typical Enteropathogenic Escherichia coli Strains Isolated From Human and Cattle in Kerman, Iran

Background: Shiga toxin-producing Escherichia coli (STEC) have emerged as the important zoonotic food-borne pathogens and confrming the risk to public health. Enteropathogenic Escherichia coli (EPEC) is a major cause of children diarrhoea in developing countries. E. coli strains can be assigned to four main phylogenetic groups, A, B1, B2 and D. Objectives: The aim of the current study was to analyze the distribution of phylogenetic groups and presence of STEC and atypical EPEC pathotypes in E. coli isolated from human diarrhea and fecal samples of healthy cattle in Kerman, Iran by PCR. Materials and Methods: A total of 188 E. coli isolates were isolated from human diarrheic (94 isolates) and fecal healthy cattle (94 isolates) samples. The isolates were identifed by standard bacteriological tests. The confrmed isolates were examined to detect the phylogenetic groups and a selection of virulence genes including stx1, stx2 and eae by PCR. Results: Phylotyping of isolates from diarrheic human showed that 38.29% belonged to A, 20.21% to B1, 14.89% to B2 and 26.59% to D phylo groups. The isolates of healthy cattle distributed in A (34.04%), B1 (47.88%), B2 (7.44 %) and D (10.64%) phylo-groups. Prevalence of eae gene in human diarrheic isolates was 5.32% (5 isolates), whereas none of the human diarrheic isolates were positive for stx1 and stx2 genes. Among cattle isolates 7.44% (7 isolates) were positive for stx1 gene and 5.32% (5 isolates) possessed eae gene. Of the all isolates examined, none were positive for the stx2 gene. The eae gene were positive for isolates of human diarrhea distributed in A and B2 phylo-groups and isolates possessed stx1 and eae genes from healthy cattle fell into A (4 isolates), B1 (7) and B2 (one isolate). Conclusions: The isolates of human diarrhea samples and fecal healthy cattle were distributed into different phylogenetic groups, which mostly distributed in A and B1 phylo-groups. In addition, results of this study revealed the lower prevalence of SETC and aEPEC in isolates

Shiga toxin and beta-lactamases genes in Escherichia coli phylotypes isolated from carcasses of broiler chickens slaughtered in Iran

Two hundred and four Escherichia coli strains were isolated from external and visceral cavity surfaces of 102 slaughtered broiler carcasses. The isolates were screened to determine the phylogenetic background and presence of Shiga toxins (stx1, stx2), intimin (eae) and beta-lactamase (blaTEM, blaSHV) genes. Phylotyping results revealed that the E. coli isolates segregated in four phylogenetic groups A (56.86%), B1 (19.12%), B2 (4.90%) and D (19.12%). PCR assays revealed that 13 isolates (6.37%) from 12 carcasses were positive for eae (12 isolates) and/or stx2 (2) genes. The eae positive isolates belonged to phylogenetic groups A (A0, A1), B1, B2 (B22) and D (D2). Two stx2 positive and seven eae positive isolates were recovered from visceral cavity surface, whereas only 5 eae positive isolates were from the external surface of the carcasses. On the other hand, thirty one E. coli strains isolated from visceral cavity and external surface of 26 carcasses carried the blaTEM (27) and blaSHV (4) genes and belonged to different phylo-groups. This study suggests that broiler carcasses could be considered as an important source of EPEC and STEC pathotypes in southeast of Iran; as well as the examined antibiotic resistance genes, which were carried by some isolates and could be transferred to pathogens through the food chain

Molecular study on diarrheagenic Escherichia coli pathotypes isolated from under 5 years old children in southeast of Iran

Objective: To determine the phylogenetic groups and prevalence of diarrheagenic Escherichia coli (E. coli) (DEC) genes from children less than five years of age with diarrhea in southeast of Iran. Methods: A total of 142 E. coli isolates were isolated from diarrheic samples. The isolates were examined for detection of virulence determinants and their phylogenetic background by PCR technique. Results: The E. coli isolates fall into four phylogenetic groups: A (40.14%), B1 (18.31%), B2 (16.90%) and D (24.65%). Eighty isolates were positive for at least one of the examined DEC genes. E. coli isolates were classified in enterotoxigenic E. coli (52 isolates), enteroaggregative E. coli (23), atypical enteropathogenic E. coli (9), enteroinvasive E. coli (2). Conclusions: This study demonstrated the importance of enterotoxigenic E. coli and enteroaggregative E. coli pathotypes in the childhood diarrhea. An epidemiologic surveillance especially for DEC, would be useful in control and prevention of infectious diarrhea in children

Determination of phylogenetic background, fimbrial genes, and antibiotic susceptibility of Escherichia coli isolates from urinary tract infections in Bam region, Iran

Phylogenetic analysis have shown that Escherichia coli (E. coli) strains segregate in four main phylogenetic groups A, B1, B2, and D. E. coli fimbriae increase invasive capability of bacteria to renal tissues. The purpose of this study was to determine the distribution of phylogenetic groups/subgroups among fimbrial genes and antibiotic resistance patterns of E. coli isolates from urinary tract infections (UTI), in Bam (southeast of Iran). A total of 122 E. coli isolates from patients with UTI, which were confirmed by biochemical tests, were collected. Antibiotic susceptibility of isolates was examined against six antibiotic agents by disk diffusion method. DNA was extracted and examined for detection of phylogenetic group/subgroups and also for determination of afaI BC, sfa/focDE, and papEF genes using PCR technique. E. coli isolates were distributed in phylogroups A (45.08 %), D (43.45 %), B2 (7.83 %), and B1 (4.09 %). The examined isolates belonged to six phylogenetic subgroups A0 (28.69 %), D2 (24.59 %), D1 (18.85 %), A1 (16.39 %), B2–3 (7.39 %), and B1 (4.09 %). Fimbrial genes were found in 27.85 % of isolates. Phylogroups A and D were more prevalent in antibiotic resistance patterns than other phylogenetic groups. The findings of the current study showed that A and D phylogenetic groups were dominant among our isolates. These results differ with that of other researches in other parts of the world. Further studies are required to clarify the phylogenetic background in Bam area. Antibiotic resistant seems to be a common feature of most E. coli isolates in this area

Determination of phylogenetic groups and antibiotic resistance pattern of Enterotoxigenic Escherishia coli isolates from diarrheoic cases in Bam City by PCR

Background and Aim: Purposes of this study were to determine the phylogenetic groups, prevalence of enterotoxigenic pathotype and antibiotic resistance of Escherichia coli (E. coli) isolates from diarrheic cases in Bam city. Materials and Methods: In this study 155 E. coli were isolated from diarrheic samples in Bam city. Phylogenetic groups of isolates and enterotoxigenic pathotype were determined by detection of chuA, yjaA, TspE4C2 and ST, LT genes respectively. Results: One hundred fifty five examined isolates were distributed in phylogenetic groups: A (71.60%), B1 (3.22%), B2 (9.67%) and D (15.48%). The genes for enterotoxigenic pathotype were detected in 52 isolates (33.54%), which ST gene were found in 29 isolates, LT in 16 isolates and LT, ST genes in 7 isolates. Twenty nine ST gene positive isolates were distributed in three phylogenetic groups A (48.28%), D (41.38%) and B2 (10.34%). According to the antibiotic susceptibility tests maximum and minimum antibiotic resistance rate was against to trimethoprim/sulfamethoxazole (74.19%) and ciprofloxacin and gentamycin (9.67%). Fifteen multiple antibiotic resistance patterns were detected in four phylogenetic groups. Conclusions: Escherichia coli isolates from enterotoxigenic pathotype have a considerable antibiotic resistance rate in Bam city and were distributed in different phylogenetic groups. Since a considerable number of isolates were negative for LT and ST genes, it is necessary to study the other virulence genes and their phylogenetic background in E. coli isolates from diarrheic cases in Bam city

Antibiotic Resistance Profle in Relation to Phylogenetic Background in Escherichia coli Isolated From Fecal Samples of Healthy Ostrich

Background: E. coli is regarded as a reservoir for antibiotic resistance in foods of animal origin. E. coli can be categories into four main phylogenetic groups (A, B1, B2 and D). The commensal E. coli strains mostly are assigned to the phylo-groups A and B1. Objectives: The purposes of this study were to determine the phylogenetic group/subgroups and antibiotic resistance patterns of ostrich E. coli isolates in Iran. Materials and Methods: A total of 126 E. coli isolates were obtained from cloacae swabs of the healthy ostrich in Kerman, Iran. The E. coli isolates were confrmed using biochemical API 20E identifcation system. The confrmed isolates were studied to determine phylogenetic background by PCR. The isolates were tested for antibiotic resistance against 12 different antibiotic disk by disk diffusion method. Results: Phylotyping of E. coli isolates indicated that 74 isolates belonged to A, 27 isolates to B1, 7 isolates to B2, and 18 isolates to D groups. Also the isolates fell into six phylogenetic subgroups, including 34 isolates in A0, 40 isolates in A1, one isolate in B22, 6 isolates in B23, 11 isolates in D 1 and 7 isolates in subgroup D2. In the examined E. coli isolates, the maximum rate of resistance was against tetracycline, and the minimum rate of resistance was against amoxicillin. Twenty three antibiotic resistance patterns were detected among the isolates. The cefoxitin and tetracycline resistance pattern was the most prevalent in the isolates that belonged to phylo-group A. Conclusions: In conclusion, the result of the present study revealed a low frequency of antibiotic resistance in ostrich E. coli isolates. The antibiotic resistance patterns were in relation to A and D phylogenetic groups. Further studies are needed to better understand the distribution of phylogenetic groups in poultry isolates

High Frequency of Diarrheagenic Escherichia coli in HIV-Infected Patients and Patients with Thalassemia in Kerman, Iran

This study was conducted on patients with thalassemia and HIV-infected patients to determine the frequency of diarrheagenic Escherichia coli in Kerman, Iran. We analyzed 68 and 49 E coli isolates isolated from healthy fecal samples of patients with thalassemia and HIV-infected patients, respectively. The E coli isolates were studied using a multiplex polymerase chain reaction to identify the enterotoxigenic E coli (ETEC), enterohemorrhagic E coli (EHEC), and enteropathogenic E coli (EPEC) groups. Statistical analysis was carried out to determine the correlation of diarrheagenic E coli between HIVinfected patients and patients with thalassemia using Stata 11.2 software. The frequency of having at least 1 diarrheagenic E coli was more common in patients with thalassemia (67.64%) than in HIV-infected patients (57.14%; P ¼ .25), including ETEC (67.64% versus 57.14%), EHEC (33.82% versus 26.53%), and EPEC (19.11% versus 16.32%). The results of this study indicate that ETEC, EHEC, and EPEC pathotypes are widespread among diarrheagenic E coli isolates in patients with thalassemia and HIV-infected patients

Mapping local patterns of childhood overweight and wasting in low- and middle-income countries between 2000 and 2017

A double burden of malnutrition occurs when individuals, household members or communities experience both undernutrition and overweight. Here, we show geospatial estimates of overweight and wasting prevalence among children under 5 years of age in 105 low- and middle-income countries (LMICs) from 2000 to 2017 and aggregate these to policy-relevant administrative units. Wasting decreased overall across LMICs between 2000 and 2017, from 8.4% (62.3 (55.1–70.8) million) to 6.4% (58.3 (47.6–70.7) million), but is predicted to remain above the World Health Organization’s Global Nutrition Target of <5% in over half of LMICs by 2025. Prevalence of overweight increased from 5.2% (30 (22.8–38.5) million) in 2000 to 6.0% (55.5 (44.8–67.9) million) children aged under 5 years in 2017. Areas most affected by double burden of malnutrition were located in Indonesia, Thailand, southeastern China, Botswana, Cameroon and central Nigeria. Our estimates provide a new perspective to researchers, policy makers and public health agencies in their efforts to address this global childhood syndemic

Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and population estimates in 204 countries and territories, 1950-2019 : a comprehensive demographic analysis for the Global Burden of Disease Study 2019

Background: Accurate and up-to-date assessment of demographic metrics is crucial for understanding a wide range of social, economic, and public health issues that affect populations worldwide. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 produced updated and comprehensive demographic assessments of the key indicators of fertility, mortality, migration, and population for 204 countries and territories and selected subnational locations from 1950 to 2019. Methods: 8078 country-years of vital registration and sample registration data, 938 surveys, 349 censuses, and 238 other sources were identified and used to estimate age-specific fertility. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate age-specific fertility rates for 5-year age groups between ages 15 and 49 years. With extensions to age groups 10–14 and 50–54 years, the total fertility rate (TFR) was then aggregated using the estimated age-specific fertility between ages 10 and 54 years. 7417 sources were used for under-5 mortality estimation and 7355 for adult mortality. ST-GPR was used to synthesise data sources after correction for known biases. Adult mortality was measured as the probability of death between ages 15 and 60 years based on vital registration, sample registration, and sibling histories, and was also estimated using ST-GPR. HIV-free life tables were then estimated using estimates of under-5 and adult mortality rates using a relational model life table system created for GBD, which closely tracks observed age-specific mortality rates from complete vital registration when available. Independent estimates of HIV-specific mortality generated by an epidemiological analysis of HIV prevalence surveys and antenatal clinic serosurveillance and other sources were incorporated into the estimates in countries with large epidemics. Annual and single-year age estimates of net migration and population for each country and territory were generated using a Bayesian hierarchical cohort component model that analysed estimated age-specific fertility and mortality rates along with 1250 censuses and 747 population registry years. We classified location-years into seven categories on the basis of the natural rate of increase in population (calculated by subtracting the crude death rate from the crude birth rate) and the net migration rate. We computed healthy life expectancy (HALE) using years lived with disability (YLDs) per capita, life tables, and standard demographic methods. Uncertainty was propagated throughout the demographic estimation process, including fertility, mortality, and population, with 1000 draw-level estimates produced for each metric. Findings: The global TFR decreased from 2·72 (95% uncertainty interval [UI] 2·66–2·79) in 2000 to 2·31 (2·17–2·46) in 2019. Global annual livebirths increased from 134·5 million (131·5–137·8) in 2000 to a peak of 139·6 million (133·0–146·9) in 2016. Global livebirths then declined to 135·3 million (127·2–144·1) in 2019. Of the 204 countries and territories included in this study, in 2019, 102 had a TFR lower than 2·1, which is considered a good approximation of replacement-level fertility. All countries in sub-Saharan Africa had TFRs above replacement level in 2019 and accounted for 27·1% (95% UI 26·4–27·8) of global livebirths. Global life expectancy at birth increased from 67·2 years (95% UI 66·8–67·6) in 2000 to 73·5 years (72·8–74·3) in 2019. The total number of deaths increased from 50·7 million (49·5–51·9) in 2000 to 56·5 million (53·7–59·2) in 2019. Under-5 deaths declined from 9·6 million (9·1–10·3) in 2000 to 5·0 million (4·3–6·0) in 2019. Global population increased by 25·7%, from 6·2 billion (6·0–6·3) in 2000 to 7·7 billion (7·5–8·0) in 2019. In 2019, 34 countries had negative natural rates of increase; in 17 of these, the population declined because immigration was not sufficient to counteract the negative rate of decline. Globally, HALE increased from 58·6 years (56·1–60·8) in 2000 to 63·5 years (60·8–66·1) in 2019. HALE increased in 202 of 204 countries and territories between 2000 and 2019

Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw values of the posterior distribution. Findings: Global health has steadily improved over the past 30 years as measured by age-standardised DALY rates. After taking into account population growth and ageing, the absolute number of DALYs has remained stable. Since 2010, the pace of decline in global age-standardised DALY rates has accelerated in age groups younger than 50 years compared with the 1990–2010 time period, with the greatest annualised rate of decline occurring in the 0–9-year age group. Six infectious diseases were among the top ten causes of DALYs in children younger than 10 years in 2019: lower respiratory infections (ranked second), diarrhoeal diseases (third), malaria (fifth), meningitis (sixth), whooping cough (ninth), and sexually transmitted infections (which, in this age group, is fully accounted for by congenital syphilis; ranked tenth). In adolescents aged 10–24 years, three injury causes were among the top causes of DALYs: road injuries (ranked first), self-harm (third), and interpersonal violence (fifth). Five of the causes that were in the top ten for ages 10–24 years were also in the top ten in the 25–49-year age group: road injuries (ranked first), HIV/AIDS (second), low back pain (fourth), headache disorders (fifth), and depressive disorders (sixth). In 2019, ischaemic heart disease and stroke were the top-ranked causes of DALYs in both the 50–74-year and 75-years-and-older age groups. Since 1990, there has been a marked shift towards a greater proportion of burden due to YLDs from non-communicable diseases and injuries. In 2019, there were 11 countries where non-communicable disease and injury YLDs constituted more than half of all disease burden. Decreases in age-standardised DALY rates have accelerated over the past decade in countries at the lower end of the SDI range, while improvements have started to stagnate or even reverse in countries with higher SDI. Interpretation: As disability becomes an increasingly large component of disease burden and a larger component of health expenditure, greater research and developm nt investment is needed to identify new, more effective intervention strategies. With a rapidly ageing global population, the demands on health services to deal with disabling outcomes, which increase with age, will require policy makers to anticipate these changes. The mix of universal and more geographically specific influences on health reinforces the need for regular reporting on population health in detail and by underlying cause to help decision makers to identify success stories of disease control to emulate, as well as opportunities to improve. Funding: Bill & Melinda Gates Foundation. © 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 licens