scholarly journals Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica

2020 ◽  
Author(s):  
Jingqiu Liao ◽  
Renato Hohl Orsi ◽  
Laura Carroll ◽  
Martin Wiedmann
Keyword(s):  
Population Structure ◽  
Comparative Genomics ◽  
Causative Agent ◽  
Salmonella Enterica ◽  
Geographic Origin ◽  
Health Concern ◽  
Ecological Niches ◽  
Evolutionary Forces ◽  
Geographic Origins ◽  
The Impact

SummaryGenetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco-evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York state and Washington state to understand host- and geographic-associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large-scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic-associated single-nucleotide polymorphisms (SNPs), rather than geographic-associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein-encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter-population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins.Originality/Significance StatementSalmonella enterica, which is the causative agent of salmonellosis, poses a growing public health concern due to the emergence and spread of antimicrobial resistant (AMR) strains. The mechanisms underlying the population structure associated with different hosts and geographic origins of AMR S. enterica are underexplored due to limited genome-wide studies assessing the impact of ecological niches on genetic variations. By employing comparative genomics, our study provided insights into the genomic profiles of AMR S. enterica associated with two distinct hosts and two distant geographic locations, improving the mechanistic understanding of how bacterial population structure is shaped by different ecological niches. Our findings have broad implications for elucidating the impact of ecological and evolutionary forces on the adaptation, antimicrobial resistance, and pathogenicity of bacteria. Also, specific genetic markers we identified may help predict host or geographic origin of AMR Salmonella isolates, which could benefit the source tracking (e.g., host and geographic origins) of human disease cases and contamination events caused by AMR S. enterica.

scholarly journals Evolution and Population Structure of Salmonella enterica Serovar Newport

2010 ◽  
Vol 192 (24) ◽  
pp. 6465-6476 ◽  
Author(s):  
Vartul Sangal ◽  
Heather Harbottle ◽  
Camila J. Mazzoni ◽  
Reiner Helmuth ◽  
Beatriz Guerra ◽  
...  
Keyword(s):  
Population Structure ◽  
North America ◽  
Salmonella Enterica ◽  
Health Concern ◽  
Global Public Health ◽  
Multiple Sequence ◽  
Monophyletic Lineage ◽  
Population Structures ◽  
Paratyphi B ◽  
Multiple Drugs

ABSTRACT Salmonellosis caused by Salmonella enterica serovar Newport is a major global public health concern, particularly because S. Newport isolates that are resistant to multiple drugs (MDR), including third-generation cephalosporins (MDR-AmpC phenotype), have been commonly isolated from food animals. We analyzed 384 S. Newport isolates from various sources by a multilocus sequence typing (MLST) scheme to study the evolution and population structure of the serovar. These were compared to the population structure of S. enterica serovars Enteritidis, Kentucky, Paratyphi B, and Typhimurium. Our S. Newport collection fell into three lineages, Newport-I, Newport-II, and Newport-III, each of which contained multiple sequence types (STs). Newport-I has only a few STs, unlike Newport-II or Newport-III, and has possibly emerged recently. Newport-I is more prevalent among humans in Europe than in North America, whereas Newport-II is preferentially associated with animals. Two STs of Newport-II encompassed all MDR-AmpC isolates, suggesting recent global spread after the acquisition of the bla CMY-2 gene. In contrast, most Newport-III isolates were from humans in North America and were pansusceptible to antibiotics. Newport was intermediate in population structure to the other serovars, which varied from a single monophyletic lineage in S. Enteritidis or S. Typhimurium to four discrete lineages within S. Paratyphi B. Both mutation and homologous recombination are responsible for diversification within each of these lineages, but the relative frequencies differed with the lineage. We conclude that serovars of S. enterica provide a variety of different population structures.

Outcomes of North American, Japanese, and European extensive-disease small cell lung cancer (ED-SCLC) patients under irinotecan-platinum or etoposide-platinum therapy: Systematic review and meta-analysis.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e18534-e18534
Author(s):  
Joao Paulo Da S.N. Lima ◽  
Andre Deeke Sasse ◽  
Emma C. Sasse ◽  
Lucas Vieira dos Santos
Keyword(s):  
Systematic Review ◽  
North American ◽  
Meta Analysis ◽  
Geographic Origin ◽  
First Line ◽  
First Line Therapy ◽  
Geographic Origins ◽  
One Year ◽  
Meta Analyses ◽  
The Impact

e18534 Background: Superiority of irinotecan-platinum (IP) regimens over etoposide-platinum (EP) in ED-SCLC has been extensively debated, with ethnic and pharmacogenomics issues hypothesized as causes of the divergent findings. We undertook a systematic review to scrutinize the data according to geographic origin. Methods: Randomized controlled trials comparing first-line EP doublets versus IP in ED-SCLC patients were searched in major meeting proceedings and databases. The outcomes were overall survival (OS), one-year survival, two-year survival, and safety. Meta-analyses were performed using random-effects model. Subgroup analyses and meta-regression were undertaken to compare and measure the impact of geographical origin of study over the estimated effect size. Results: Seven studies (2,029 patients) were included. IP improved OS worldwide (HR = 0.83; 95% CI 0.76-0.92; P>0.001; I²=0%). However, the impact of IP on OS was different according to geographic origin, with relevant benefit for Japanese, little benefit for North American/Australian and intermediate for European patients (P for interaction = 0.029, table 1). One year survival was homogenously improved from 34% with EP to 40% with IP (P=0.006). IP improved two year survival just for Japanese and European patients but not to North American ones (Table). Toxicity was not impacted by trial origin. Conclusions: IP improved survival for both Western and Eastern patients, but seems to exist a gradient of benefit according to geographic origins, with maximal benefit for Japanese, some relevant for European ones and little, if any, for North American/Australian patients. These findings should be taken in account when considering IP or EP as first-line therapy for ED-SCLC patients worldwide. [Table: see text]

scholarly journals Whole genome analysis and characterization of Salmonella enterica subsp. enterica serovar Typhimurium strain UPM 260 for mediated genetic manipulation

2020 ◽  
Author(s):  
Najwa Syahirah Roslan ◽  
Nurulfiza Mat Isa ◽  
Abdul Rahman Omar ◽  
Mohd. Hair Bejo ◽  
Aini Ideris
Keyword(s):  
Salmonella Enterica ◽  
Functional Characterization ◽  
Poultry Meat ◽  
Whole Genome Sequence ◽  
Health Concern ◽  
Type I ◽  
Whole Genome ◽  
Typhimurium Strain ◽  
Serovar Typhimurium ◽  
The Impact

Abstract Background Salmonella enterica serovar Typhimurium persists as one of the most frequent food-borne zoonoses, causing a major public health concern worldwide. Furthermore, Salmonella infection has a large economic impact. Globally, the main sources of infection for humans include the consumption of contaminated poultry meat and eggs. In animals however, Salmonella transmission usually occurs horizontally from infected birds and contaminated environments. Hence, to delve further on how the impact of this disease can be lessened, an epidemiological study needs to be performed. It is vital to determine the genomic sequences of microorganisms to understand their biology and functional characterization. Thus, we determined the whole-genome sequence and virulence profile of S. enterica serovar Typhimurium strain UPM 260 isolated from Perak, Malaysia. Whole genome sequencing (WGS) using paired-end sequencing generated 107 contigs with a total genome size of 4.9 Mbp and 52% G+C content. The contigs were annotated for phylogenetic and functional analysis. Results Through the analysis, it is revealed that the genome were resistant to a number of antimicrobial drug classes including aminoglycoside, fluoroquinolone, tetracycline and phenicol. Also found in UPM 260 genome were three intact prophages (Fels-1, Gifsy-2 and one unique prophage, mEp390). The genome housed four types of restriction-modification systems (RMS) and Type I-E subtype of CRISPR-Cas system. Two metal resistance operons (mer and cop) and six pathogenicity islands (SPIs) were also discovered in UPM 260 genome. The SPIs contributed mostly to the bacterial virulence properties since 1054 CDS were reported to be homologous to the virulence factors in the database VFDB. Conclusion This study benefits us specifically in the field of genome engineering where gene-based genetic manipulations can be applied in reducing the prevalence and pathogenicity in Salmonella.

scholarly journals Reproduction in Trypanosomatids: Past and Present

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 471
Author(s):  
Camino Gutiérrez-Corbo ◽  
Bárbara Domínguez-Asenjo ◽  
María Martínez-Valladares ◽  
Yolanda Pérez-Pertejo ◽  
Carlos García-Estrada ◽  
...  
Keyword(s):  
Low Income ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Genetic Exchange ◽  
Health Concern ◽  
Current Debate ◽  
Naturally Occurring ◽  
Experimental Works ◽  
Genomic Recombination ◽  
The Impact

Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.

scholarly journals Breakfast Cereals Intended for Children: Opportunities for Reformulation and Potential Impact on Nutrient Intake

Foods ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1772
Author(s):  
Mariana Santos ◽  
Filipa Matias ◽  
Ana Isabel Rito ◽  
Isabel Castanheira ◽  
Duarte Torres ◽  
...  
Keyword(s):  
Dietary Fiber ◽  
Nutritional Quality ◽  
Saturated Fatty Acids ◽  
World Health ◽  
Health Concern ◽  
Regional Office ◽  
Nutrient Profile ◽  
Dietary Fiber Intake ◽  
Directorate General ◽  
The Impact

Ready-to-eat cereals (RTECs) have become a popular breakfast option claiming to provide important nutrients to children’s diets, despite being a source of excess sugar and, therefore, a health concern. Thus, food reformulation constitutes an important public health strategy that could benefit from inputs provided by nutrient profiling. This study aimed to assess the adequacy of the RTECs for children available in Portuguese supermarkets, applying three nutrient profile models (NPMs)—the nutrient profile model of the World Health Organization’s Regional Office for Europe (WHO-EURO), the profile of the private-sector EU Pledge (EU-Pledge), and the national model developed by the Directorate-General of Health (NPM-PT)—in order to explore the potential for reformulation of the RTECs identified as not adequate and evaluate the impact of RTECs’ reformulation on the nutritional quality of Portuguese children’s diets. In total, 78 RTECs intended for children were assessed and two scenarios—current (not considering reformulation) and alternative (considering reformulation to accomplish the nutrient profile requirements)—were considered to assess the impact of reformulation on nutritional quality. Across all RTECs, only 5.1% could be promoted to children according to the considered NPMs. The most common nutrients requiring reformulation were sugar, saturated fatty acids (SFA), salt, and dietary fiber. The scenarios of reformulation considered could reduce the RTECs average content of total sugars, SFA, and salt by 43%, 8.7%, and 1.1%, respectively, and dietary fiber intake could be increased by 34%. Thus, these results support policies to implement reformulation strategies for developing healthier food products to be promoted to children.

scholarly journals Virulence and Antimicrobial Resistance Profiles of Salmonella enterica Serovars Isolated from Chicken at Wet Markets in Dhaka, Bangladesh

2021 ◽  
Vol 9 (5) ◽  
pp. 952
Author(s):  
Nure Alam Siddiky ◽  
Md Samun Sarker ◽  
Md. Shahidur Rahman Khan ◽  
Ruhena Begum ◽  
Md. Ehsanul Kabir ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Salmonella Enterica ◽  
Virulence Genes ◽  
Health Concern ◽  
Production Cycle ◽  
Salmonella Spp ◽  
Native Chicken ◽  
Resistance Patterns ◽  
Research Findings ◽  
Native Chickens

Virulent and multi drug resistant (MDR) Salmonellaenterica is a foremost cause of foodborne diseases and had serious public health concern globally. The present study was undertaken to identify the pathogenicity and antimicrobial resistance (AMR) profiles of Salmonellaenterica serovars recovered from chicken at wet markets in Dhaka, Bangladesh. A total of 870 cecal contents of broiler, sonali, and native chickens were collected from 29 wet markets. The overall prevalence of S. Typhimurium, S. Enteritidis, and untyped Salmonella spp., were found to be 3.67%, 0.57%, and 1.95% respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namely invA, agfA, IpfA, hilA, sivH, sefA, sopE, and spvC. S. Enteritidis isolates carried all virulence genes whilst S. Typhimurium isolates carried six virulence genes except sefA and spvC. A diverse phenotypic and genotypic AMR pattern was found. Harmonic descending trends of resistance patterns were observed among the broiler, sonali, and native chickens. Interestingly, virulent and MDR Salmonella enterica serovars were found in native chicken, although antimicrobials were not used in their production cycle. The research findings anticipate that virulent and MDR Salmonella enterica are roaming in the wet markets which can easily anchor to the vendor, consumers, and in the food chain.

scholarly journals Adolescent depression, early psychiatric comorbidities, and adulthood welfare burden: a 25-year longitudinal cohort study

2021 ◽  
Author(s):  
Iman Alaie ◽  
Richard Ssegonja ◽  
Anna Philipson ◽  
Anne-Liis von Knorring ◽  
Margareta Möller ◽  
...  
Keyword(s):  
Cohort Study ◽  
Early Life ◽  
Adolescent Depression ◽  
Longitudinal Cohort Study ◽  
Health Concern ◽  
Psychiatric Comorbidities ◽  
Longitudinal Cohort ◽  
Transfer Payments ◽  
Social Transfer ◽  
The Impact

Abstract Purpose Depression at all ages is recognized as a global public health concern, but less is known about the welfare burden following early-life depression. This study aimed to (1) estimate the magnitude of associations between depression in adolescence and social transfer payments in adulthood; and (2) address the impact of major comorbid psychopathology on these associations. Methods This is a longitudinal cohort study of 539 participants assessed at age 16–17 using structured diagnostic interviews. An ongoing 25-year follow-up linked the cohort (n = 321 depressed; n = 218 nondepressed) to nationwide population-based registries. Outcomes included consecutive annual data on social transfer payments due to unemployment, work disability, and public assistance, spanning from age 18 to 40. Parameter estimations used the generalized estimating equations approach. Results Adolescent depression was associated with all forms of social transfer payments. The estimated overall payment per person and year was 938 USD (95% CI 551–1326) over and above the amount received by nondepressed controls. Persistent depressive disorder was associated with higher recipiency across all outcomes, whereas the pattern of findings was less clear for subthreshold and episodic major depression. Moreover, depressed adolescents presenting with comorbid anxiety and disruptive behavior disorders evidenced particularly high recipiency, exceeding the nondepressed controls with an estimated 1753 USD (95% CI 887–2620). Conclusion Adolescent depression is associated with considerable public expenditures across early-to-middle adulthood, especially for those exposed to chronic/persistent depression and psychiatric comorbidities. This finding suggests that the clinical heterogeneity of early-life depression needs to be considered from a longer-term societal perspective.

scholarly journals The impact of environmental variables on the spread of COVID-19 in the Republic of Korea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yong Kwan Lim ◽  
Oh Joo Kweon ◽  
Hye Ryoun Kim ◽  
Tae-Hyoung Kim ◽  
Mi-Kyung Lee
Keyword(s):  
Environmental Factors ◽  
Virus Disease ◽  
Environmental Parameters ◽  
Environmental Data ◽  
Republic Of Korea ◽  
Metropolitan Region ◽  
Health Concern ◽  
Ozone Level ◽  
The Republic ◽  
The Impact

AbstractCorona virus disease 2019 (COVID-19) has been declared a global pandemic and is a major public health concern worldwide. In this study, we aimed to determine the role of environmental factors, such as climate and air pollutants, in the transmission of COVID-19 in the Republic of Korea. We collected epidemiological and environmental data from two regions of the Republic of Korea, namely Seoul metropolitan region (SMR) and Daegu-Gyeongbuk region (DGR) from February 2020 to July 2020. The data was then analyzed to identify correlations between each environmental factor with confirmed daily COVID-19 cases. Among the various environmental parameters, the duration of sunshine and ozone level were found to positively correlate with COVID-19 cases in both regions. However, the association of temperature variables with COVID-19 transmission revealed contradictory results when comparing the data from SMR and DGR. Moreover, statistical bias may have arisen due to an extensive epidemiological investigation and altered socio-behaviors that occurred in response to a COVID-19 outbreak. Nevertheless, our results suggest that various environmental factors may play a role in COVID-19 transmission.

Sign in / Sign up

Export Citation Format

Share Document