scholarly journals Comparison of Antimicrobial Resistance Detected in Environmental and Clinical Isolates from Historical Data for the US

2020 ◽  
Vol 2020 ◽  
pp. 1-11 ◽  
Author(s):  
Megan Hua ◽  
William Huang ◽  
Albert Chen ◽  
Michael Rehmet ◽  
Cade Jin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Pathogen Detection ◽  
Historical Data ◽  
Clinical Isolates ◽  
Public Health Issue ◽  
Environmental Isolates ◽  
Multivariate Statistical ◽  
E Coli ◽  
Environmental Setting ◽  
The Us

Antimicrobial resistance (AMR) has become an urgent public health issue, as pathogens are becoming increasingly resistant to commonly used antimicrobials. While AMR isolate data are available in the NCBI Pathogen Detection Isolates Browser (NPDIB) database, few researches have been performed to compare antimicrobial resistance detected in environmental and clinical isolates. To address this, this work conducted the first multivariate statistical analysis of antimicrobial-resistance pathogens detected in NPDIB clinical and environmental isolates for the US from 2013 to 2018. The highly occurring AMR genes and pathogens were identified for both clinical and environmental settings, and the historical profiles of those genes and pathogens were then compared for the two settings. It was found that Salmonella enterica and E. coli and Shigella were the highly occurring AMR pathogens for both settings. Additionally, the genes fosA, oqxB, ble, floR, fosA7, mcr-9.1, aadA1, aadA2, ant(2”)-Ia, aph(3”)-Ib, aph(3’)-Ia, aph(6)-Id, blaTEM-1, qacEdelta1, sul1, sul2, tet(A), and tet(B) were mostly detected for both clinical and environmental settings. Ampicillin, ceftriaxone, gentamicin, tetracycline, and cefoxitin were the antimicrobials which got the most resistance in both settings. The historical profiles of these genes, pathogens, and antimicrobials indicated that higher occurrence frequencies generally took place earlier in the environmental setting than in the clinical setting.

scholarly journals An Analysis of Antimicrobial Resistance of Clinical Pathogens from Historical Samples for Six Countries

Processes ◽  
2019 ◽  
Vol 7 (12) ◽  
pp. 964 ◽  
Author(s):  
Karen Li ◽  
Joanna Zheng ◽  
Thomas Deng ◽  
James Peng ◽  
Dagmar Daniel ◽  
...  
Keyword(s):  
South Africa ◽  
Antimicrobial Resistance ◽  
Pathogen Detection ◽  
Clinical Settings ◽  
Multivariate Statistical ◽  
E Coli ◽  
Time Profiles ◽  
Antimicrobial Resistance Gene ◽  
The Us ◽  
The Uk

The spread of antimicrobial resistance pathogens in humans has increasingly become an issue that threatens public health. While the NCBI Pathogen Detection Isolates Browser (NPDIB) database has been collecting clinical isolate samples over time for various countries, few studies have been done to identify genes and pathogens responsible for the antimicrobial resistance in clinical settings. This study conducted the first multivariate statistical analysis of the high-dimensional historical data from the NPDIB database for six different countries from majorly inhabited landmasses, including Australia, Brazil, China, South Africa, the UK, and the US. The similarities among different countries in terms of genes and pathogens were investigated to understand the potential avenues for antimicrobial-resistance gene spreading. The genes and pathogens that were closely involved in antimicrobial resistance were further studied temporally by plotting time profiles of their frequency to evaluate the trend of antimicrobial resistance. It was found that several of these significant genes (i.e., aph(3″)-Ib, aph(6)-Id, blaTEM-1, and qacEdelta1) are shared among all six countries studied. Based on the time profiles, a large number of genes and pathogens showed an increasing occurrence. The most shared pathogens responsible for carrying the most important genes in the six countries in the clinical setting were Acinetobacter baumannii, E. coli and Shigella, Klebsiella pneumoniae and Salmonella enterica. South Africa carried the least similar antimicrobial genes to the other countries in clinical isolates.

scholarly journals Investigation of Virulence Genes Detected in Antimicrobial-Resistance Pathogens Isolates for Five Countries across the World

Processes ◽  
2020 ◽  
Vol 8 (12) ◽  
pp. 1589
Author(s):  
Kevin Cui ◽  
Iris Gong ◽  
Alvin Dong ◽  
Jacob Yan ◽  
Max Wang ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Salmonella Enterica ◽  
Pathogen Detection ◽  
Virulence Genes ◽  
Principal Component ◽  
Multivariate Statistical ◽  
E Coli ◽  
The Us ◽  
The World ◽  
The Uk

A large portion of annual deaths worldwide are due to infections caused by disease-causing pathogens. These pathogens contain virulence genes, which encode mechanisms that facilitate infection and microbial survival in hosts. More recently, antimicrobial resistance (AMR) genes, also found in these pathogens, have become an increasingly large issue. While the National Center for Biotechnology Information (NCBI) Pathogen Detection Isolates Browser (NPDIB) database has been compiling genes involved in microbial virulence and antimicrobial resistance through isolate samples, few studies have identified the genes primarily responsible for virulence and compared them to those responsible for AMR. This study performed the first multivariate statistical analysis of the multidimensional NPDIB data to identify the major virulence genes from historical pathogen isolates for Australia, China, South Africa, UK, and US—the largely populated countries from five of the six major continents. The important virulence genes were then compared with the AMR genes to study whether there is correlation between their occurrences. Among the significant genes and pathogens associated with virulence, it was found that the genes fdeC, iha, iss, iutA, lpfA, sslE, ybtP, and ybtQ are shared amongst all five countries. The pathogens E. coli and Shigella, Salmonella enterica, and Klebsiella pneumoniae mostly contained these genes and were common among four of the five studied countries. Additionally, the trend of virulence was investigated by plotting historical occurrences of gene and pathogen frequency in the annual samples. These plots showed that the trends of E. coli and Shigella and Salmonella enterica were similar to the trends of certain virulence genes, confirming the two pathogens do indeed carry important virulence genes. While the virulence genes in the five countries are not significantly different, the US and the UK share the largest amount of important virulence genes. The plots from principal component analysis and hierarchical clustering show that the important virulence and AMR genes were not significantly correlated, with only few genes from both types of genes clustered into the same groups.

scholarly journals Antimicrobial Resistance Traits of Escherichia coli Isolated from Dairy Manure and Freshwater Ecosystems Are Similar to One Another but Differ from Associated Clinical Isolates

2020 ◽  
Vol 8 (5) ◽  
pp. 747
Author(s):  
Rachelle E. Beattie ◽  
Ellen Bakke ◽  
Nicholas Konopek ◽  
Rebecca Thill ◽  
Erik Munson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Freshwater Ecosystems ◽  
Dairy Manure ◽  
Clinical Isolates ◽  
Resistant Bacteria ◽  
Freshwater Ecosystem ◽  
Environmental Isolates ◽  
E Coli ◽  
Resistance Traits

Antimicrobial resistance (AMR) is a prevalent global health problem across human and veterinary medicine. The One Health approach to AMR is necessary to mitigate transmission between sources of resistance and decrease the spread of resistant bacteria among humans, animals, and the environment. Our primary goal was to identify associations in resistance traits between Escherichia coli isolated from clinical (n = 103), dairy manure (n = 65), and freshwater ecosystem (n = 64) environments within the same geographic location and timeframe. Clinical E. coli isolates showed the most phenotypic resistance (47.5%), followed by environmental isolates (15.6%) and manure isolates (7.7%), with the most common resistances to ampicillin, ampicillin-sulbactam, and cefotaxime antibiotics. An isolate subset was screened for extended spectrum beta-lactamase (ESBL) production resulting in the identification of 35 ESBL producers. The most common ESBL gene identified was blaTEM-1. Additionally, we found nine different plasmid replicon types including IncFIA-FIB, which were frequently associated with ESBL producer isolates. Molecular phylotyping revealed a significant portion of clinical E. coli were associated with phylotype B2, whereas manure and environmental isolates were more diverse. Manure and environmental isolates were significantly different from clinical isolates based on analyzed traits, suggesting more transmission occurs between these two sources in the sampled environment.

scholarly journals Investigation of the Genes Involved in the Outbreaks of Escherichia coli and Salmonella spp. in the United States

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1274
Author(s):  
Michelle Li ◽  
Kyle Wang ◽  
Ashley Tang ◽  
Aaron Tang ◽  
Andrew Chen ◽  
...  
Keyword(s):  
Stress Response ◽  
Antimicrobial Resistance ◽  
Pathogen Detection ◽  
Dimensional Space ◽  
Virulence Gene ◽  
Principal Component ◽  
The United States ◽  
Salmonella Spp ◽  
E Coli ◽  
Antimicrobial Resistance Genes

Salmonella spp. and Escherichiacoli (E. coli) are two of the deadliest foodborne pathogens in the US. Genes involved in antimicrobial resistance, virulence, and stress response, enable these pathogens to increase their pathogenicity. This study aims to examine the genes detected in both outbreak and non-outbreak Salmonella spp. and E. coli by analyzing the data from the National Centre for Biotechnology Information (NCBI) Pathogen Detection Isolates Browser database. A multivariate statistical analysis was conducted on the genes detected in isolates of outbreak Salmonella spp., non-outbreak Salmonella spp., outbreak E. coli, and non-outbreak E. coli. The genes from the data were projected onto a two-dimensional space through principal component analysis. Hierarchical clustering was then used to quantify the relationship between the genes in the dataset. Most of the outlier genes identified in E. coli isolates are virulence genes, while outlier genes identified in Salmonella spp. are mainly involved in stress response. Gene epeA, which encodes a high-molecular-weight serine protease autotransporter of Enterobacteriaceae (SPATE) protein, along with subA and subB that encode cytotoxic activity, may contribute to the pathogenesis of outbreak E. coli. The iro operon and ars operon may play a role in the ecological success of the epidemic clones of Salmonella spp. Concurrent relationships between esp and ter operons in E. coli and pco and sil operons in Salmonella spp. are found. Stress-response genes (asr, golT, golS), virulence gene (sinH), and antimicrobial resistance genes (mdsA and mdsB) in Salmonella spp. also show a concurrent relationship. All these findings provide helpful information for experiment design to combat outbreaks of E. coli and Salmonella spp.

scholarly journals Retrospective Analysis on Antimicrobial Resistance Trends and Prevalence of β-lactamases in Escherichia coli and ESKAPE Pathogens Isolated from Arabian Patients during 2000–2020

2020 ◽  
Vol 8 (10) ◽  
pp. 1626
Author(s):  
Mahfouz Nasser ◽  
Snehal Palwe ◽  
Ram Naresh Bhargava ◽  
Marc G. J. Feuilloley ◽  
Arun S. Kharat
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Enterococcus Faecium ◽  
Arab Countries ◽  
Clinical Isolates ◽  
Arab Region ◽  
E Coli ◽  
Extended Spectrum ◽  
Eskape Pathogens

The production of diverse and extended spectrum β-lactamases among Escherichia coli and ESKAPE pathogens is a growing threat to clinicians and public health. We aim to provide a comprehensive analysis of evolving trends of antimicrobial resistance and β-lactamases among E. coli and ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acine to bacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) in the Arabian region. A systematic review was conducted in Medline PubMed on papers published between January 2000 and February 2020 on countries in the Arab region showing different antibiotic resistance among E. coli and ESKAPE pathogens. A total of n = 119,144 clinical isolates were evaluated for antimicrobial resistance in 19 Arab countries. Among these clinical isolates, 74,039 belonged to E. coli and ESKAPE pathogen. Distribution of antibiotic resistance among E. coli and ESKAPE pathogens indicated that E. coli (n = 32,038) was the predominant pathogen followed by K. pneumoniae (n = 17,128), P. aeruginosa (n = 11,074), methicillin-resistant S. aureus (MRSA, n = 4370), A. baumannii (n = 3485) and Enterobacter spp. (n = 1574). There were no reports demonstrating Enterococcus faecium producing β-lactamase. Analyses revealed 19 out of 22 countries reported occurrence of ESBL (Extended-Spectrum β-Lactamase) producing E. coli and ESKAPE pathogens. The present study showed significantly increased resistance rates to various antimicrobial agents over the last 20 years; for instance, cephalosporin resistance increased from 37 to 89.5%, fluoroquinolones from 46.8 to 70.3%, aminoglycosides from 40.2 to 64.4%, mono-bactams from 30.6 to 73.6% and carbapenems from 30.5 to 64.4%. An average of 36.9% of the total isolates were reported to have ESBL phenotype during 2000 to 2020. Molecular analyses showed that among ESBLs and Class A and Class D β-lactamases, blaCTX-M and blaOXA have higher prevalence rates of 57% and 52.7%, respectively. Among Class B β-lactamases, few incidences of blaVIM 27.7% and blaNDM 26.3% were encountered in the Arab region. Conclusion: This review highlights a significant increase in resistance to various classes of antibiotics, including cephalosporins, β-lactam and β-lactamase inhibitor combinations, carbapenems, aminoglycosides and quinolones among E. coli and ESKAPE pathogens in the Arab region.

scholarly journals Comparison of Consumption Data and Phenotypical Antimicrobial Resistance in E. coli Isolates of Human Urinary Samples and of Weaning and Fattening Pigs from Surveillance and Monitoring Systems in Germany

Antibiotics ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 28
Author(s):  
Octavio Mesa-Varona ◽  
Ides Boone ◽  
Matthias Flor ◽  
Tim Eckmanns ◽  
Heike Kaspar ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Rural Areas ◽  
Molecular Data ◽  
Clinical Isolates ◽  
E Coli ◽  
Rural And Urban ◽  
Consumption Data ◽  
Gentamicin Resistance ◽  
Urban And Rural Areas ◽  
Fattening Pigs

Antimicrobial resistance (AMR) data from humans are mostly collected from clinical isolates, whereas from livestock data also exist from colonizing pathogens. In Germany, livestock data are collected from clinical and nonclinical isolates. We compared resistance levels of clinical and nonclinical isolates of Escherichia coli from weaning and fattening pigs with clinical outpatient isolates of humans from urban and rural areas. We also studied the association of AMR with available antimicrobial use (AMU) data from humans and pigs. Differences between rural and urban isolates were minor and did not affect the comparison between human and pig isolates. We found higher resistance levels to most antimicrobials in human isolates compared to nonclinical isolates of fattening pigs. Resistance to ampicillin, however, was significantly more frequent in clinical isolates of fattening pigs and in clinical and nonclinical isolates of weaning pigs compared to isolates from humans. The opposite was observed for ciprofloxacin. Co-trimoxazole resistance proportions were higher in clinical isolates of weaning and fattening pigs as compared to isolates from humans. Resistance proportions were higher in clinical isolates than in nonclinical isolates from pigs of the same age group and were also higher in weaner than in fattening pigs. Significant associations of AMU and AMR were found for gentamicin resistance and aminoglycoside use in humans (borderline) and for ampicillin resistance in clinical isolates and penicillin use in fattening pigs. In summary, we found significant differences between isolates from all populations, requiring more detailed analyses supported by molecular data and better harmonized data on AMU and AMR.

scholarly journals Escherichia Coli From Urine Samples of Pregnant Women as an Indicator for Antimicrobial Resistance in the Community: a Field Study From Rural Burkina Faso.

2021 ◽  
Author(s):  
A.S. Post ◽  
I. Guiraud ◽  
M. Peeters ◽  
P. Lompo ◽  
S. Ombelet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Burkina Faso ◽  
Pregnant Women ◽  
Urine Analysis ◽  
Urine Samples ◽  
Clinical Isolates ◽  
Antibiotic Residues ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli

Abstract Introduction: In low- and middle-income countries, surveillance of antimicrobial resistance (AMR) is mostly hospital-based and, in view of poor access to clinical microbiology, biased to more resistant pathogens. We assessed AMR among Escherichia coli isolates obtained from urine cultures of pregnant women as an indicator for community AMR and compared the AMR results with those from E. coli isolates obtained from febrile patients in previously published clinical surveillance studies conducted within the same population in Nanoro, rural Burkina Faso.Results: Between October 2016 – September 2018, midstream urine samples collected as part of routine antenatal in Nanoro district were cultured by a dipslide method and screened for antibiotic residues. Among 6018 consenting women (median (IQR) age 25 (20 - 30)), 84 (1.4%) were excluded because of symptoms of urinary tract infection and 96 (1.6%) screened positive for antibiotic residues. Significant growth - defined as a monoculture of Enterobacterales at counts of ≥ 104 colony forming units/ml – was observed in 202 (3.4%) cultures; E. coli represented 155 (76.7%) of isolates. Among these E. coli isolates, resistance rates to ampicillin, cotrimoxazole and ciprofloxacin were respectively 65.8%, 64.4% 16.2%, compared to 89.5%, 89.5% and 62.5% among E. coli from historical clinical isolates (n = 48 of which 45 from blood cultures). Proportions of extended spectrum beta-lactamase producers and multidrug resistance were 3.2% and 5.2% among E. coli isolates from urine in pregnant women versus 35.4%, and 60.4% respectively among clinical isolates. Adding urine culture to the routine urine analysis (protein and glucose) of antenatal was feasible. The dipslide culture method was affordable and user-friendly and allowed on-site inoculation and easy transport; challenges were contamination (midstream urine sampling) and the semi-quantitative reading. Conclusions: The E. coli isolates obtained from healthy pregnant women had significantly lower AMR rates compared to clinical E. coli isolates, probably reflecting the lower antibiotic pressure in the pregnant women population. Provided confirmation of the present findings in other settings, E. coli from urine samples in pregnant women may be a potential indicator for benchmarking, comparing, and monitoring community AMR rates across populations over different countries and regions.

scholarly journals Virulence factors, antimicrobial resistance, and plasmid content of Escherichia coli isolated in swine commercial farms

2010 ◽  
Vol 62 (1) ◽  
pp. 30-36 ◽  
Author(s):  
M.M. Costa ◽  
G. Drescher ◽  
F Maboni ◽  
S.S. Weber ◽  
A. Schrank ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Factors ◽  
Intestinal Content ◽  
Specific Pattern ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Plasmid Content ◽  
E Coli ◽  
Resistance Patterns

Virulence factors and antimicrobial resistance patterns of Escherichia coli isolates were evaluated. A total of 80 E. coli isolates were evaluated, being 64 from clinical samples (intestinal content and fragments of organs from diarrheic piglets), seven from feces of clinically healthy piglets and sows, and nine environmental samples (five from facilities, two from feed, one from insect, and one from waste). Molecular characterization was performed by PCR detection of fimbriae and toxin genes and plasmid content determination. The isolates were also characterized according to their resistance or sensitivity to the following drugs: ampicillin, trimethoprim:sulfamethoxazole, tetracycline, amikacine, colistin, norfloxacin, florfenicol, enrofloxacin, cefalexin, trimethoprim, neomycin, chloramphenicol, and gentamicin. From 80 E. coli isolates, 53.8% were classified as enterotoxigenic E. coli (ETEC), 2.5% were shiga toxin-producing E. coli (STEC), and 43.8% showed a non specific pattern and were unclassified. One fecal isolate from non-diarrheic piglet was classified as ETEC by PCR. Clinical isolates showed resistance mainly for tetracycline and trimethoprim:sulfamethoxazole. Plasmidial DNA was observed in 70 isolates, being 78.5% of clinical isolates, 8.57% of non-diarrheic feces, and 12.8% of environment.

scholarly journals Novel chromosomal insertions of ISEcp1-blaCTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Misheck Shawa ◽  
Yoshikazu Furuta ◽  
Gillan Mulenga ◽  
Maron Mubanga ◽  
Evans Mulenga ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Chromosomal Location ◽  
Enterobacter Cloacae ◽  
Clinical Isolates ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Genes Encoding ◽  
High Degree ◽  
Genotypic Characteristics

Abstract Background The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. blaCTX-M genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that blaCTX-M-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated blaCTX-M and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements. Methods A total of 46 clinical isolates of cefotaxime-resistant Enterobacteriaceae (1 Enterobacter cloacae, 9 Klebsiella pneumoniae, and 36 Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes, blaCTX-M genes were categorized as either chromosomal or plasmid-borne. Results WGS-based genotyping identified 58 AMR genes, including four blaCTX-M alleles (i.e., blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, and blaCTX-M-55). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of blaCTX-M genes. Out of 45 blaCTX-M gene-carrying strains, 7 harbored the gene in their chromosome. In one E. cloacae and three E. coli strains, chromosomal blaCTX-M-15 was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1 at one end, exhibited a high degree of nucleotide sequence homology with previously reported plasmids, and carried multiple AMR genes that corresponded with phenotypic AMR profiles. Conclusion Our study revealed the co-occurrence of ISEcp1-blaCTX-M-15 and multiple AMR genes on chromosomal insertions in E. cloacae and E. coli, suggesting that ISEcp1 may be responsible for the transposition of diverse AMR genes from plasmids to chromosomes. Stable retention of such insertions in chromosomes may facilitate the successful propagation of MDR clones among these Enterobacteriaceae species.

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