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 ◽  
...  

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.

Antibiotics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 744
Author(s):  
Altaf Bandy ◽  
Bilal Tantry

Antimicrobial-resistance in Enterobacterales is a serious concern in Saudi Arabia. The present study retrospectively analyzed the antibiograms of Enterobacterales identified from 1 January 2019 to 31 December 2019 from a referral hospital in the Aljouf region of Saudi Arabia. The revised document of the Centers for Disease Control (CDC) CR-2015 and Magiorakos et al.’s document were used to define carbapenem resistance and classify resistant bacteria, respectively. The association of carbapenem resistance, MDR, and ESBL with various sociodemographic characteristics was assessed by the chi-square test and odds ratios. In total, 617 Enterobacterales were identified. The predominant (n = 533 (86.4%)) isolates consisted of 232 (37.6%), 200 (32.4%), and 101 (16.4%) Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis, respectively. In general, 432 (81.0%) and 128 (24.0%) isolates were of MDR and ESBL, respectively. The MDR strains were recovered in higher frequency from intensive care units (OR = 3.24 (1.78–5.91); p < 0.01). E. coli and K. pneumoniae resistance rates to imipenem (2.55 (1.21–5.37); p < 0.01) and meropenem (2.18 (1.01–4.67); p < 0.04), respectively, were significantly higher in winter. The data emphasize that MDR isolates among Enterobacterales are highly prevalent. The studied Enterobacterales exhibited seasonal variation in antimicrobial resistance rates towards carbapenems and ESBL activity.


2021 ◽  
Vol 9 (2) ◽  
pp. 326
Author(s):  
Frederick Adzitey ◽  
Nurul Huda ◽  
Amir Husni Mohd Shariff

Meat is an important food source that can provide a significant amount of protein for human development. The occurrence of bacteria that are resistant to antimicrobials in meat poses a public health risk. This study evaluated the occurrence and antimicrobial resistance of E. coli (Escherichia coli) isolated from raw meats, ready-to-eat (RTE) meats and their related samples in Ghana. E. coli was isolated using the USA-FDA Bacteriological Analytical Manual and phenotypic antimicrobial susceptibility test was performed by the disk diffusion method. Of the 200 examined meats and their related samples, 38% were positive for E. coli. Notably, E. coli was highest in raw beef (80%) and lowest in RTE pork (0%). The 45 E. coli isolates were resistant ≥ 50% to amoxicillin, trimethoprim and tetracycline. They were susceptible to azithromycin (87.1%), chloramphenicol (81.3%), imipenem (74.8%), gentamicin (72.0%) and ciprofloxacin (69.5%). A relatively high intermediate resistance of 33.0% was observed for ceftriaxone. E. coli from raw meats, RTE meats, hands of meat sellers and working tools showed some differences and similarities in their phenotypic antimicrobial resistance patterns. Half (51.1%) of the E. coli isolates exhibited multidrug resistance. The E. coli isolates showed twenty-two different resistant patterns, with a multiple antibiotic resistance index of 0.0 to 0.7. The resistant pattern amoxicillin (A, n = 6 isolates) and amoxicillin-trimethoprim (A-TM, n = 6 isolates) were the most common. This study documents that raw meats, RTE meats and their related samples in Ghana are potential sources of antimicrobial-resistant E. coli and pose a risk for the transfer of resistant bacteria to the food chain, environment and humans.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jose F. Delgado-Blas ◽  
Cristina M. Ovejero ◽  
Sophia David ◽  
Natalia Montero ◽  
William Calero-Caceres ◽  
...  

AbstractAquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.


Author(s):  
Nahla Omer Eltai ◽  
Hadi M. Yassine ◽  
Sara H. Al-Hadidi ◽  
Tahra ElObied ◽  
Asmaa A. Al Thani ◽  
...  

The dissemination of antimicrobial resistance (AMR) bacteria has been associated with the inappropriate use of antibiotics in both humans and animals and with the consumption of food contaminated with resistant bacteria. In particular, the use of antibiotics as prophylactic and growth promotion purposes in food-producing animals has rendered many of the antibiotics ineffective. The increased global prevalence of AMR poses a significant threat to the safety of the world’s food supply. Objectives: This study aims at determining the prevalence of antibiotic-resistant Escherichia coli (E. coli) isolated from local and imported retail chicken meat in Qatar. Methodology: A total of 270 whole chicken carcasses were obtained from three different hypermarket stores in Qatar. A total of 216 E. coli were isolated and subjected to antibiotic susceptibility testing against 18 relevant antibiotics using disc diffusion and micro- dilution methods. Furthermore, extended-spectrum β-lactamase (ESBL) production was determined via a double-disc synergetic test. Isolates harboring colistin resistance were confirmed using multiplex-PCR and DNA sequencing. Results: Nearly 89% (192/216) of the isolates were resistant to at least one antibiotics. In general, isolates showed relatively higher resistance to sulfamethoxazole (62%), tetracycline (59.7%), ampicillin and trimethoprim (52.3%), ciprofloxacin (47.7%), cephalothin, and colistin (31.9%). On the other hand, less resistance was recorded against amoxicillin/clavulanic acid (6%), ceftriaxone (5.1%), nitrofurantoin (4.2%) and piperacillin/tazobactam (4.2%), cefepime (2.3%), meropenem (1.4%), ertapenem (0.9%), and amikacin (0.9%). Nine isolates (4.2%) were ESBL producers. Furthermore, 63.4% were multidrug-resistant (MDR). The percentage of MDR, ESBL producers, and colistin-resistant isolates was significantly higher among local isolates compared to imported chicken samples. Conclusion: We reported a remarkably high percentage of the antibiotic-resistant E. coli in chicken meat sold at retail in Qatar. The high percentage of MDR and colistin isolates is troublesome to the food safety of raw chicken meat and the potential of antibiotic resistance spread to public health. Our findings support the need for the implementation of one health approach to address the spread of antimicrobial resistance and the need for a collaborative solution.


2020 ◽  
Vol 12 (4) ◽  
pp. 357-365
Author(s):  
H.I. Atta ◽  
A. Gimba ◽  
T. Bamgbose

Abstract. The production of bacteriocins by lactic acid bacteria affords them the ability to inhibit the growth of bacteria; they are particularly important in the biocontrol of human and plant pathogens. Lactic acid bacteria have been frequently isolated from fermented foods due to the high acidity these foods contain. In this study, lactic acid bacteria were isolated from garri, a popular Nigerian staple food, which is fermented from cassava, and their antagonistic activity against clinical and environmental isolates of Escherichia coli was determined. The species of Lactobacillus isolated include: Lactobacillus plantarum (50%), Lactobacillus fermentum (20%), Lactobacillus acidophilus (20%), and Lactobacillus salivarius (10%). Growth inhibition of the strains of E.coli was observed in Lactobacillus plantarum that inhibited the growth of both. The clinical and environmental isolates of E. coli were inhibited by Lactobacillus plantarum, while Lactobacillus acidophilus showed activity against only the clinical isolate. The greatest zone of inhibition against the strains of E. coli was recorded by Lactobacillus acidophilus (22.7±1.53 mm). The bacteriocins produced by Lactobacillus species have a good potential in the biocontrol of pathogens, and should be the focus of further studies on antibiotic resistant bacteria.


2020 ◽  
Vol 8 (10) ◽  
pp. 1626
Author(s):  
Mahfouz Nasser ◽  
Snehal Palwe ◽  
Ram Naresh Bhargava ◽  
Marc G. J. Feuilloley ◽  
Arun S. Kharat

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.


2020 ◽  
Vol 8 (7) ◽  
pp. 1048 ◽  
Author(s):  
Beilei Ge ◽  
Kelly J. Domesle ◽  
Stuart A. Gaines ◽  
Claudia Lam ◽  
Sonya M. Bodeis Jones ◽  
...  

The role animal food plays in the introduction of antimicrobial-resistant bacteria into the human food chain is not well understood. We conducted an analysis of 1025 samples (647 pet food and 378 animal feed) collected across the United States during 2005–2011 for two indicator organisms (Escherichia coli and Enterococcus spp.). The overall prevalence ranged from 12.5% for E. coli to 45.2% for Enterococcus spp., and 11.2% of samples harbored both organisms. Regardless of bacterial genus, animal feed had significantly higher prevalence than pet food (p < 0.001). A general downward trend in prevalence was observed from 2005 to 2009 followed by an upward trend thereafter. Among E. coli isolates (n = 241), resistance was highest to tetracycline (11.2%) and below 5% for fourteen other antimicrobials. Among Enterococcus spp. isolates (n = 1074), Enterococcus faecium (95.1%) was the predominant species. Resistance was most common to tetracycline (30.1%) and ciprofloxacin (10.7%), but below 10% for thirteen other antimicrobials. Multidrug-resistant organisms were observed among both E. coli and Enterococcus spp. isolates at 3.3%. Compared to National Antimicrobial Resistance Monitoring System (NARMS) 2011 retail meat and animal data, the overall resistance for both organisms was much lower in animal food. These findings help establish a historic baseline for the prevalence and antimicrobial resistance among U.S. animal food products and future efforts may be needed to monitor changes over time.


2021 ◽  
Author(s):  
A.S. Post ◽  
I. Guiraud ◽  
M. Peeters ◽  
P. Lompo ◽  
S. Ombelet ◽  
...  

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.


Author(s):  
M.M. Costa ◽  
G. Drescher ◽  
F Maboni ◽  
S.S. Weber ◽  
A. Schrank ◽  
...  

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.


Author(s):  
Misheck Shawa ◽  
Yoshikazu Furuta ◽  
Gillan Mulenga ◽  
Maron Mubanga ◽  
Evans Mulenga ◽  
...  

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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