scholarly journals Comparison of Phenotypical Antimicrobial Resistance between Clinical and Non-Clinical E. coli Isolates from Broilers, Turkeys and Calves in Four European Countries

2021 ◽  
Vol 9 (4) ◽  
pp. 678
Author(s):  
Octavio Mesa-Varona ◽  
Rodolphe Mader ◽  
Martina Velasova ◽  
Jean-Yves Madec ◽  
Sophie A. Granier ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Statistical Analyses ◽  
Clinical Isolates ◽  
Resistance Level ◽  
Laboratory Methods ◽  
Bacterial Populations ◽  
E Coli ◽  
Use Patterns ◽  
The Uk ◽  
Animal Category

Livestock data on antimicrobial resistance (AMR) are commonly collected from bacterial populations of clinical and non-clinical isolates. In contrast to data on non-clinical isolates from livestock, data on clinical isolates are not harmonized in Europe. The Normalized Resistance Interpretation (NRI) method was applied to overcome the lack of harmonization of laboratory methods and interpretation rules between monitoring systems. Statistical analyses were performed to identify associations between the isolate type (clinical vs. non-clinical) and resistance to four antimicrobials (ampicillin, tetracycline, gentamicin, and nalidixic acid) per animal category in Germany and France. Additional statistical analyses comparing clinical and non-clinical isolates were performed with the available data on the same antimicrobial panel and animal categories from the UK and Norway. Higher resistance prevalence was found in clinical isolates compared to non-clinical isolates from calves to all antimicrobials included in Germany and France. It was also found for gentamicin in broilers from France. In contrast, in broilers and turkeys from Germany and France and in broilers from the UK, a higher resistance level to ampicillin and tetracycline in non-clinical isolates was encountered. This was also found in resistance to gentamicin in isolates from turkeys in Germany. Resistance differed within countries and across years, which was partially in line with differences in antimicrobial use patterns. Differences in AMR between clinical and non-clinical isolates of Escherichia coli are associated with animal category (broiler, calf, and turkey) and specific antimicrobials. The NRI method allowed comparing results of non-harmonized AMR systems and might be useful until international harmonization is achieved.

scholarly journals High Levels of Antibiotic Resistance in Isolates From Diseased Livestock

2021 ◽  
Vol 8 ◽  
Author(s):  
Nurul Asyiqin Haulisah ◽  
Latiffah Hassan ◽  
Siti Khairani Bejo ◽  
Saleh Mohammed Jajere ◽  
Nur Indah Ahmad
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Sensitivity ◽  
Clinical Isolates ◽  
Situational Analysis ◽  
Sensitivity Testing ◽  
Resistance Level ◽  
Diagnostic Laboratory ◽  
E Coli ◽  
Livestock Health ◽  
High Level

Overuse of antimicrobials in livestock health and production beyond therapeutic needs has been highlighted in recent years as one of the major risk factors for the acceleration of antimicrobial resistance (AMR) of bacteria in both humans and animals. While there is an abundance of reports on AMR in clinical isolates from humans, information regarding the patterns of resistance in clinical isolates from animals is scarce. Hence, a situational analysis of AMR based on clinical isolates from a veterinary diagnostic laboratory was performed to examine the extent and patterns of resistance demonstrated by isolates from diseased food animals. Between 2015 and 2017, 241 cases of diseased livestock were received. Clinical specimens from ruminants (cattle, goats and sheep), and non-ruminants (pigs and chicken) were received for culture and sensitivity testing. A total of 701 isolates were recovered from these specimens. From ruminants, Escherichia coli (n = 77, 19.3%) predominated, followed by Staphylococcus aureus (n = 73, 18.3%). Antibiotic sensitivity testing (AST) revealed that E. coli resistance was highest for penicillin, streptomycin, and neomycin (77–93%). In addition, S. aureus was highly resistant to neomycin, followed by streptomycin and ampicillin (68–82%). More than 67% of E. coli isolates were multi-drug resistant (MDR) and only 2.6% were susceptible to all the tested antibiotics. Similarly, 65.6% of S. aureus isolates were MDR and only 5.5% were susceptible to all tested antibiotics. From non-ruminants, a total of 301 isolates were recovered. Escherichia coli (n = 108, 35.9%) and Staphylococcus spp. (n = 27, 9%) were the most frequent isolates obtained. For E. coli, the highest resistance was against amoxicillin, erythromycin, tetracycline, and neomycin (95–100%). Staphylococcus spp. had a high level of resistance to streptomycin, trimethoprim/sulfamethoxazole, tetracycline and gentamicin (80–100%). The MDR levels of E. coli and Staphylococcus spp. isolates from non-ruminants were 72.2 and 74.1%, respectively. Significantly higher resistance level were observed among isolates from non-ruminants compared to ruminants for tetracycline, amoxicillin, enrofloxacin, and trimethoprim/sulfamethoxazole.

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.

Modeling the Emergence of Antibiotic Resistance in Bacterial Populations

2018 ◽  
Vol 80 (3) ◽  
pp. 214-220 ◽  
Author(s):  
Michelle A. Williams ◽  
Patricia J. Friedrichsen ◽  
Troy D. Sadler ◽  
Pamela J. B. Brown
Keyword(s):  
Antibiotic Resistance ◽  
Coli Strain ◽  
Science Standards ◽  
Evolutionary Mechanisms ◽  
Resistance Level ◽  
Random Mutation ◽  
Bacterial Populations ◽  
E Coli ◽  
Disk Diffusion Assay ◽  
High School Classroom

Since antibiotics have become routinely used to treat infections, antibiotic resistance is now an emerging concern for public health. To understand how bacteria become resistant to antibiotics, many students draw from the common misconception that bacteria gain resistance upon antibiotic exposure. We have designed models and a corresponding lab that explores how a population of bacteria can evolve antibiotic resistance, with emphasis on dispelling common misconceptions surrounding the mechanism of antibiotic resistance. Using an antibiotic disk diffusion assay, students compare the antibiotic resistance level of a harmless E. coli strain of bacteria over time. Then, students compare their lab data to the models, which together illustrate the roles that initial genetic variation and random mutation play in the evolution of antibiotic resistance. In this guided investigation, basic microbiology concepts and techniques are made accessible to students in a high school classroom. The models developed here are in line with the practices of the Next Generation Science Standards (NGSS). The models, together with the lab, are used to guide students through the process of argumentation using a claim, evidence, and reasoning (CER) format to explain the evolutionary mechanisms of antibiotic resistance.

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.

scholarly journals Detection of TEM and CTX-M Genes in Escherichia coli Isolated from Clinical Specimens at Tertiary Care Heart Hospital, Kathmandu, Nepal

Diseases ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 15
Author(s):  
Ram Shankar Prasad Sah ◽  
Binod Dhungel ◽  
Binod Kumar Yadav ◽  
Nabaraj Adhikari ◽  
Upendra Thapa Shrestha ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Clinical Isolates ◽  
Diffusion Method ◽  
Gram Negative Bacteria ◽  
Bacterial Isolates ◽  
Disk Diffusion Method ◽  
Gram Negative ◽  
Clinical Specimens ◽  
E Coli ◽  
Esbl Producers

Background: Antimicrobial resistance (AMR) among Gram-negative pathogens, predominantly ESBL-producing clinical isolates, are increasing worldwide. The main aim of this study was to determine the prevalence of ESBL-producing clinical isolates, their antibiogram, and the frequency of ESBL genes (blaTEM and blaCTX-M) in the clinical samples from patients. Methods: A total of 1065 clinical specimens from patients suspected of heart infections were collected between February and August 2019. Bacterial isolates were identified on colony morphology and biochemical properties. Thus, obtained clinical isolates were screened for antimicrobial susceptibility testing (AST) using modified Kirby–Bauer disk diffusion method, while ESBL producers were identified by using a combination disk diffusion method. ESBL positive isolates were further assessed using conventional polymerase chain reaction (PCR) to detect the ESBL genes blaTEM and blaCTX-M. Results: Out of 1065 clinical specimens, 17.8% (190/1065) showed bacterial growth. Among 190 bacterial isolates, 57.4% (109/190) were Gram-negative bacteria. Among 109 Gram-negative bacteria, 40.3% (44/109) were E. coli, and 30.2% (33/109) were K. pneumoniae. In AST, 57.7% (n = 63) Gram-negative bacterial isolates were resistant to ampicillin and 47.7% (n = 52) were resistant to nalidixic acid. Over half of the isolates (51.3%; 56/109) were multidrug resistant (MDR). Of 44 E. coli, 27.3% (12/44) were ESBL producers. Among ESBL producer E. coli isolates, 58.4% (7/12) tested positive for the blaCTX-M gene and 41.6% (5/12) tested positive for the blaTEM gene. Conclusion: Half of the Gram-negative bacteria in our study were MDR. Routine identification of an infectious agent followed by AST is critical to optimize the treatment and prevent antimicrobial resistance.

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.

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