scholarly journals Pseudomonas Species Prevalence, Protein Analysis, and Antibiotic Resistance: An Evolving Public Health Challenge

2021 ◽  
Author(s):  
Ayman Elbehiry ◽  
Eman Marzouk ◽  
Ihab Moussa ◽  
Adil Abalkhail ◽  
Mai Ibrahim ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Pseudomonas Stutzeri ◽  
Protein Analysis ◽  
Incidence Rates ◽  
Chicken Meat ◽  
Species Level ◽  
Pseudomonas Fragi ◽  
High Incidence ◽  
Pseudomonas Species ◽  
Public Health Challenge

Abstract Psychrotrophic Pseudomonas is one of the significant microbes that lead to putrefaction in chilled meat. One of the biggest problems in the detection of Pseudomonas is that several species are seemingly identical. Antibiotic resistance is an alternative considerable challenge worldwide. Therefore, this study was designed to apply an accurate technique for the discrepancy of Pseudomonas species and to study their resistance against various antimicrobials. A total of 320 chicken meat specimens were cultivated, and phenotypically recognized the isolated bacteria. Protein analysis was carried out for cultured isolates via Microflex LT. The resistance of Pseudomonas isolates was recorded through Vitek®ฏ 2 AST-GN83 cards. Overall, 69 samples were identified as Pseudomonas spp. and included 18 Pseudomonas lundensis (P. lundensis), 16 Pseudomonas fragi (P. fragi), 13 Pseudomonas oryzihabitans (P. oryzihabitans), 10 Pseudomonas stutzeri (P. stutzeri), 5 Pseudomonas fluorescens (P. fluorescens), 4 Pseudomonas putida (P. putida), and 3 Pseudomonas aeruginosa (P. aeruginosa) isolates. Microflex LT identified all Pseudomonas isolates (100%) correctly with a score value ≥2.00. PCA positively discriminated the identified isolates into various groups. The antimicrobial resistance levels against Pseudomonas isolates were 81.16% for nitrofurantoin, 71% for ampicillin and ampicillin/sulbactam, 65.22% for cefuroxime and ceftriaxone, 55% for aztreonam, and 49.28% for ciprofloxacin. The susceptibilities were 100% for cefotaxime, 98.55% for ceftazidime, 94.20% for each piperacillin/tazobactam and cefepime, 91.3% for cefazolin. In conclusion, chicken meat was found to be contaminated with different Pseudomonas spp., with high incidence rates of P. lundensis. Microflex LT is a potent tool for distinguishing Pseudomonads at the species level.

scholarly journals Evaluating Metagenomic Analysis for Pathogen Transmission in Healthcare Settings

2020 ◽  
Vol 41 (S1) ◽  
pp. s224-s224
Author(s):  
Curt Hewitt ◽  
Katharina Weber ◽  
Danielle LeSassier ◽  
Anthony Kappell ◽  
Kathleen Schulte ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Dna Analysis ◽  
Pathogen Transmission ◽  
Species Level ◽  
Metagenomic Analysis ◽  
Skin Microbiome ◽  
Limited Information ◽  
Culture Methods ◽  
Data Set ◽  
Skin Contact

Background: The prevalence of healthcare-acquired infections (HAIs) and rising levels of antimicrobial resistance place a significant burden on modern healthcare systems. Cultures are typically used to track HAIs; however, culture methods provide limited information and are not applicable to all pathogens. Next-generation sequencing (NGS) can detect and characterize pathogens present within a sample, but few research studies have explored how NGS could be used to detect pathogen transmission events under HAI-relevant scenarios. The objective of this CDC-funded project was to evaluate and correlate sequencing approaches for pathogen transmission with standard culture-based analysis. Methods: We modeled pathogen transfer via hand contact using synthetic skin. These skin coupons were seeded with a community of commensal organisms to mimic the human skin microbiome. Pathogens were added at physiologically relevant high or low levels prior to skin-to-skin contact. The ESKAPE pathogens: E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp plus C. difficile were employed because they are the most common antibiotic resistant HAIs. Pathogen transfer between skin coupons was measured following direct skin contact and fomite surface transmission. The effects of handwashing or fomite decontamination were also evaluated. Transferred pathogens were enumerated via culture to establish a robust data set against which DNA and RNA sequence analyses of the same samples could be compared. These data also provide a quantitative assessment of individual ESKAPE+C pathogen transfer rates in skin contact scenarios. Results: Metagenomic and metatranscriptomic analysis using custom analysis pipelines and reference databases successfully identified the commensal and pathogenic organisms present in each sample at the species level. This analysis also identified antibiotic resistance genes and plasmids. Metatranscriptomic analysis permitted not only gene identification but also confirmation of gene expression, a critical factor in the evaluation of antibiotic resistance. DNA analysis does not require cell viability, a key differentiator between sequencing and culturing reflected in simulated handwashing data. Sensitivity remains a key limitation of metagenomic analysis, as shown by the poor species identification and gene content characterization of pathogens present at low abundance within the simulated microbial community. Species level identification typically failed as ratios fell below 1:1,000 pathogen CFU:total community CFU. Conclusions: These findings demonstrate the strengths and weaknesses of NGS for molecular epidemiology. The data sets produced for this study are publicly available so they can be employed for future metagenomic benchmarking studies.Funding: NoneDisclosures: None

scholarly journals Temporal and geographic analysis of trichinellosis incidence in Chile with risk assessment

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Carlos Landaeta-Aqueveque ◽  
Salvador Ayala ◽  
Denis Poblete-Toledo ◽  
Mauricio Canals
Keyword(s):  
Relative Risk ◽  
Poverty Rate ◽  
Incidence Rates ◽  
Temporal Data ◽  
Rate Fluctuation ◽  
High Incidence ◽  
Domestic Cycle ◽  
Model Residuals ◽  
Free Ranging ◽  
Spearman’S Correlation

AbstractTrichinellosis is a foodborne disease caused by several Trichinella species around the world. In Chile, the domestic cycle was fairly well-studied in previous decades, but has been neglected in recent years. The aims of this study were to analyze, geographically, the incidence of trichinellosis in Chile to assess the relative risk and to analyze the incidence rate fluctuation in the last decades. Using temporal data spanning 1964–2019, as well as geographical data from 2010 to 2019, the time series of cases was analyzed with ARIMA models to explore trends and periodicity. The Dickey-Fuller test was used to study trends, and the Portmanteau test was used to study white noise in the model residuals. The Besag-York-Mollie (BYM) model was used to create Bayesian maps of the level of risk relative to that expected by the overall population. The association of the relative risk with the number of farmed swine was assessed with Spearman’s correlation. The number of annual cases varied between 5 and 220 (mean: 65.13); the annual rate of reported cases varied between 0.03 and 1.9 cases per 105 inhabitants (mean: 0.53). The cases of trichinellosis in Chile showed a downward trend that has become more evident since the 1980s. No periodicities were detected via the autocorrelation function. Communes (the smallest geographical administrative subdivision) with high incidence rates and high relative risk were mostly observed in the Araucanía region. The relative risk of the commune was significantly associated with the number of farmed pigs and boar (Sus scrofa Linnaeus, 1758). The results allowed us to state that trichinellosis is not a (re)emerging disease in Chile, but the severe economic poverty rate of the Mapuche Indigenous peoples and the high number of backyard and free-ranging pigs seem to be associated with the high risk of trichinellosis in the Araucanía region.

High Incidence Rates of Stroke in Örebro, Sweden: Further Support for Regional Incidence Differences within Scandinavia

2002 ◽  
Vol 14 (3-4) ◽  
pp. 161-168 ◽  
Author(s):  
Peter Appelros ◽  
Ingegerd Nydevik ◽  
Åke Seiger ◽  
Andreas Terént
Keyword(s):  
Incidence Rates ◽  
High Incidence

scholarly journals Prevalence and diversity of Arcobacter spp. in retail chicken meat in Turkey

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Celenk Molva ◽  
Halil Ibrahim Atabay
Keyword(s):  
Polymerase Chain Reaction ◽  
Multiplex Pcr ◽  
Chicken Meat ◽  
Species Level ◽  
Waterborne Pathogens ◽  
Chain Reaction ◽  
Retail Markets ◽  
Specific Polymerase Chain Reaction ◽  
Polymerase Chain ◽  
Retail Chicken Meat

Arcobacters are food and waterborne pathogens associated with human and animal infections. The objective of the present study was to investigate the prevalence and diversity of <em>Arcobacter</em> spp. in commercially sold chicken meat in İzmir region of Turkey. For this purpose, 100 samples including legs (n=40), 17 chicken quarters (n=17), drumstickers (n=16), breasts (n=11), wings (n=10), and carcasses (n=6) were collected from different retail markets. A total of 65 isolates were confirmed as <em>Arcobacter</em> spp. from 55 samples by genus-specific polymerase chain reaction (PCR). The prevalence of <em>Arcobacter</em> spp. was 32.5, 81.3, 64.7, 72.7, 83.3, and 50% for legs, drumstickers, chicken quarters, breasts, carcasses and wings, respectively. Based on the multiplex-PCR, most of the isolates were identified as <em>A. butzleri</em> (n=45, 80%), followed by <em>A. cryaerophilus</em> (n=2, 3.6%), <em>A. skirrowii</em> (n=1, 1.8%) and 17 isolates (30.9%) could not be identified at the species level.

scholarly journals Incidence Of Diarrheal Infections In Ukraine: Epidemiological Peculiarities

2019 ◽  
Author(s):  
Nina Malysh ◽  
Oksana Chemych ◽  
Roman Rodyna ◽  
Inna Chorna ◽  
Svitlana Doan
Keyword(s):  
Drinking Water ◽  
Food Item ◽  
Analytical Study ◽  
Incidence Rates ◽  
Epidemiological Surveillance ◽  
Statistical Research ◽  
Factors Influencing ◽  
High Incidence ◽  
The World ◽  
Low Incidence

Abstract Background : Diarrheal infections remain relevant for many countries of the world. The processes of globalization, fundamental changes in nutrition and water consumption contributed to the fact that the significance of individual infection sources, etiological structure of diarrheal infections changed. Purpose of the study: on the background of the analytical study of the incidence of diarrheal infections in Ukraine under the current conditions, to determine the factors influencing epidemic situation. Methods: The reports of the Ministry of Health of Ukraine, Main Administrations of Statistics in Kharkiv, Odesa, Zaporizhia oblasts for 2011-2018 are used in the paper. Epidemiological and statistical research methods are applied. Results: The epidemic situation with diarrheal infections in Ukraine is characterized by a low incidence of typhoid fever (from 0.012 to 0.14 per 100 thousand people), shigellosis (from 1.97-6.13 per 100 thousand people), stable incidence rates without the downward trend, salmonellosis (from 17.35 till 24.1 per 100 thousand people), high incidence of diahrreal infections of specified etiology (from 115.5 to141.9 per 100 thousand people) and diahrreal infections of unspecified etiology (from 69.76 to 107.02 per 100 thousand people). The most complicated epidemic situation is observed in economically most developed regions of the country. Most diarrheal infectionsoutbreaks are connected with catering establishments 36.5 % and with children educational establishments 26.1 %. In the region with the highest shigellosis and salmonellosis incidence direct strong correlation relationships are established between the incidence and population, density, natural population movement. The oblasts with the highest diahrreal infections of specified etiology, rotaviral enteritis, diahrreal infections of unspecified etiology incidence are at least provided with water resources and have problems with provision of high-quality drinking water. There is a need to improve the system of epidemiological surveillance over diarrheal infections by extension of the indicators of microbiological study of drinking water quality in the regions of Ukraine, where high diahrreal infections of specified etiology, rotaviral enteritis, diahrreal infections of unspecified etiology incidence is registered; by increasing frequency of food item inspections in the oblasts, where mediana shigellosis and salmonellosis incidence exceeds the average one in Ukraine. Keywords: diarrheal infections, shigellosis, salmonellosis, rotaviral enteritis.

scholarly journals Antibiotic resistance and residue in chicken, cattle, buffalo and goat meats in different southern districts of Bangladesh

2021 ◽  
Vol 5 (1) ◽  
pp. 19-26
Author(s):  
Bidyut Matubber ◽  
Farzana Islam Rume ◽  
Mohammad Enamul Hoque Kayesh ◽  
Mohammad Mahfuzur Rahman ◽  
Mohammad Rohul Amin ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Chicken Meat ◽  
Human Consumption ◽  
Antibiotic Residues ◽  
Salmonella Spp ◽  
Resistance Patterns ◽  
Cattle Meat ◽  
Meat Samples ◽  
Controlling Measures ◽  
Antibiotic Resistance Patterns

The presence of antibiotic residue in chicken and animal meats is a serious threat to human health due to its harmful effects. This study aimed at identifying the antibiotic resistance patterns of the isolates as well as antibiotic residues in chicken, cattle, buffalo and goat meats in different southern districts of Bangladesh. A total of 205 meat samples, including 70 chicken meat, 60 cattle meat, 50 buffalo meat and 25 goat meat were aseptically collected and analysed for the detection of antibiotic residues by thin layer chromatography and the isolates obtained from these samples were subjected to antibiogram study against 16 commonly used antibiotics. The isolates found in this study were Staphylococcus spp., Streptococcus spp., Escherichia coli, and Salmonella spp. and their prevalence were 37.5% (77/205), 22.1% (48/205), 29.7% (61/205), 8.7% (19/205), respectively. The isolates showed different degrees of sensitivity to the antibiotics used in the study. The most resistant phenotype was against cefradine, amoxicillin, penicillin, oxytetracycline, erythromycin, and enrofloxacin. 18.5% (38/205) meat samples were found to be positive for antibiotic residues and the highest prevalence was observed in chicken meat compared to other meat types. Overall, the findings of the study suggest that it is important to take controlling measures for the emergence of antibiotic resistance and also for ensuring healthy meats for human consumption. Asian Australas. J. Food Saf. Secur. 2021, 5 (1), 19-26

scholarly journals The resistome of common human pathogens

2017 ◽  
Author(s):  
Christian Munck ◽  
Mostafa M. Hashim Ellabaan ◽  
Michael Schantz Klausen ◽  
Morten O.A. Sommer
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Species Level ◽  
Natural Environments ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Risk Ranking

AbstractGenes capable of conferring resistance to clinically used antibiotics have been found in many different natural environments. However, a concise overview of the resistance genes found in common human bacterial pathogens is lacking, which complicates risk ranking of environmental reservoirs. Here, we present an analysis of potential antibiotic resistance genes in the 17 most common bacterial pathogens isolated from humans. We analyzed more than 20,000 bacterial genomes and defined a clinical resistome as the set of resistance genes found across these genomes. Using this database, we uncovered the co-occurrence frequencies of the resistance gene clusters within each species enabling identification of co-dissemination and co-selection patterns. The resistance genes identified in this study represent the subset of the environmental resistome that is clinically relevant and the dataset and approach provides a baseline for further investigations into the abundance of clinically relevant resistance genes across different environments. To facilitate an easy overview the data is presented at the species level at www.resistome.biosustain.dtu.dk.

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