Identification of antimicrobial resistance genes and drug resistance analysis of Escherichia coli in the animal farm environment

Abstract Background The discovery of mcr-1-positive Escherichia coli (MCRPEC), a notable superbug, attracted great attention worldwide. Swine-origin multi-drug resistance MCRPEC is a potential threat to public health and safety. To date, few detailed studies regarding swine-origin MCRPEC in Guangxi, South China, have been reported. Results In this study, thirty-three MCRPEC harbored mcr-1 genes were identified from 142 E. coli strains isolated from swine droppings and entrails in Guangxi in 2018. All MCRPEC isolates were assigned to 8 unique STs, including ST10, ST224 and ST410, which overlapped with the human-origin MCRPEC. Additionally, a total of six plasmid replicon types (IncFI, IncHI1, IncY, IncN, IncI1 and IncX1) were found. Moreover, the drug susceptibility of the MCRPEC isolates was tested with 27 antimicrobial agents belonging to 17 antimicrobial categories that are usually used in hospitals. There were 19 extended spectrum beta lactamase (ESBL) E. coli and 12 carbapenem resistant E. coli among the 33 MCRPEC strains. Importantly, the MCRPEC showed a high rate of resistance against two broad-spectrum carbapenem antibiotics, imipenem and meropenem, which are forbidden in livestock production use. Three MCRPEC strains were further identified to be extensively drug-resistant (XDR), and other isolates were recognized as multi-drug-resistant (MDR). Meanwhile, to detect whether plasmid-carrying antimicrobial resistance genes coexisted with the mcr-1 gene in the MCRPEC isolates, a total of 22 plasmid-carrying antimicrobial resistance genes were tested for. The results showed that four ESBL genes and one pAmpC gene were identified. Eight of the MCRPEC isolates also contained the carbapenem gene blaNDM-5, which could cause untreatable infections. Moreover, ten non-lactamase genes were also detected. Conclusion This study indicated that swine-origin MCRPEC isolated in Guangxi seemed to have a high rate of resistance to both regular and final line of defense drugs as well as drug resistance genes, which pose a great threat to human public safety and health.

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Antimicrobial Resistance of Escherichia coli From Aquaculture Farms and Their Environment in Zhanjiang, China

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.806653 ◽

2021 ◽

Vol 8 ◽

Author(s):

Cui-Yi Liao ◽

Balamuralikrishnan Balasubramanian ◽

Jin-Ju Peng ◽

Song-Ruo Tao ◽

Wen-Chao Liu ◽

...

Keyword(s):

Escherichia Coli ◽

Drug Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Detection Rate ◽

Resistance Rate ◽

Antimicrobial Drugs ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Soil And Sediment

Antimicrobial resistance (AMR) has become a major concern worldwide. To evaluate the AMR of Escherichia coli in aquaculture farms of Zhanjiang, China, a total of 90 samples from the water, soil, and sediment of three aquaculture farms (farms I, II, and III) in Zhanjiang were collected, and 90 strains of E. coli were isolated for drug resistance analysis and AMR gene detection. The results indicated that the isolated 90 strains of E. coli have high resistance rates to penicillin, amoxicillin, ampicillin, tetracycline, compound sulfamethoxazole, sulfisoxazole, chloramphenicol, florfenicol, and rifampin (≥70%). Among these antimicrobial drugs, the resistance rate to rifampicin is as high as 100%. Among the isolated 90 strains of E. coli, all of them were resistant to more than two kinds of antimicrobial drugs, the number of strains resistant to nine kinds of drugs was the largest (19 strains), and the most resistant strain showed resistance to 16 kinds of antibacterial drugs. Regarding the AMR genes, among the three aquaculture farms, the most resistance genes were detected in farm II (28 species). The detection rate of blaTEM, blaCIT, blaNDM, floR, OptrA, cmlA, aphA1, Sul2, oqxA, and qnrS in 90 isolates of E. coli was high (≥50%). The detection rate of carbapenem-resistant genes, such as blaKPC, blaIMP, and cfr, was relatively lower ( ≤ 30%), and the detection rate of mcr2 was the lowest (0). At least four AMR genes were detected for each strain, and 15 AMR genes were detected at most. Among them, the number of strains that carried 10 AMR genes was the largest (15 strains). Finally, a correlation analysis found that the AMR genes including blaTEM, blaCIT, floR, OptrA, cmlA, aac(3)-II, Sul2, ereA, ermB, oqxB, qnrA, mcr1, and mcr2 had a high correlation rate with drug resistance (≥50%). To summarize, the 90 strains of E. coli isolated from water, surrounding soil, and sediment samples showed resistance to multi-antimicrobial drugs and carried various antimicrobial resistance genes. Thus, it is essential to strengthen the rational use of antimicrobial drugs, especially the amide alcohol drugs, and control the AMR in the aquaculture industry of Zhanjiang, China.

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Virulence and antimicrobial resistance genes are enriched in the plasmidome of clinical Escherichia coli isolates compared with wastewater isolates from western Kenya

Infection Genetics and Evolution ◽

10.1016/j.meegid.2021.104784 ◽

2021 ◽

Vol 91 ◽

pp. 104784

Author(s):

Sifuna Anthony Wawire ◽

Oleg N. Reva ◽

Thomas J. O'Brien ◽

Wendy Figueroa ◽

Victor Dinda ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Western Kenya ◽

Antimicrobial Resistance Genes

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Distribution of Virulence and Antimicrobial Resistance Genes in Phylogenetic Groups of Escherichia coli Strains Isolated from Mexican Patients with Urinary Infection

Jundishapur Journal of Microbiology ◽

10.5812/jjm.83711 ◽

2019 ◽

Vol In Press (In Press) ◽

Cited By ~ 1

Author(s):

Juan Carlos Bravata-Alcantara ◽

Juan Manuel Bello-Lopez ◽

Iliana Alejandra Cortes-Ortiz ◽

Juan Jose Mendez-Velazquez ◽

Brandon Aviles-Soto ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Urinary Infection ◽

Phylogenetic Groups ◽

Antimicrobial Resistance Genes ◽

Mexican Patients

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Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

10.1101/2020.02.19.952366 ◽

2020 ◽

Author(s):

B Constantinides ◽

KK Chau ◽

TP Quan ◽

G Rodger ◽

M Andersson ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Bacterial Infections ◽

Wide Spectrum ◽

Klebsiella Oxytoca ◽

Clinical Disease ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Wide Range

ABSTRACTEscherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonised with diverse populations of E. coli, Klebsiella pneumoniae and Klebsiella oxytoca, including both antimicrobial-resistant and susceptible strains. Using whole genome sequencing (WGS) of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies which may vary as a result of different inputs and selection pressures. WGS of 46 contemporaneous patient isolates identified one (2%; 95% CI 0.05-11%) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10% of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including blaCTX-M, blaSHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention.IMPORTANCEEscherichia coli and Klebsiella spp. cause a wide range of bacterial infections, including bloodstream, urine and lung infections. Previous studies have shown that sink drains in hospitals may be part of transmission chains in outbreaks of antimicrobial-resistant E. coli and Klebsiella spp., leading to colonisation and clinical disease in patients. We show that even in non-outbreak settings, contamination of sink drains by these bacteria is common across hospital wards, and that many antimicrobial resistance genes can be found and potentially exchanged in these sink drain sites. Our findings demonstrate that the colonisation of handwashing sink drains by these bacteria in hospitals is likely contributing to some infections in patients, and that additional work is needed to further quantify this risk, and to consider appropriate mitigating interventions.

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Molecular and Phenotypic Characterization of Some Antimicrobial Resistance Genes in Escherichia coli Isolated from Human and Broiler Chickens

International Journal of Current Microbiology and Applied Sciences ◽

10.20546/ijcmas.2016.512.104 ◽

2016 ◽

Vol 5 (12) ◽

pp. 953-965

Author(s):

Mohamed Elmahdy Shehata ◽

Gamal Mohamed EL-Sherbiny ◽

Amira Hussainy Mohamed ◽

Hesham Mohamed Shafik

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Broiler Chickens ◽

Phenotypic Characterization ◽

Antimicrobial Resistance Genes

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Impact of UV and Peracetic Acid Disinfection on the Prevalence of Virulence and Antimicrobial Resistance Genes in Uropathogenic Escherichia coli in Wastewater Effluents

Applied and Environmental Microbiology ◽

10.1128/aem.00418-14 ◽

2014 ◽

Vol 80 (12) ◽

pp. 3656-3666 ◽

Cited By ~ 24

Author(s):

Basanta Kumar Biswal ◽

Ramzi Khairallah ◽

Kareem Bibi ◽

Alberto Mazza ◽

Ronald Gehr ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Peracetic Acid ◽

Content Type ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Antimicrobial Resistance Gene ◽

Municipal Wastewaters ◽

The Impact

ABSTRACTWastewater discharges may increase the populations of pathogens, includingEscherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenicEscherichia coli(UPEC), the most abundantE. colipathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766E. coliisolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm2and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.

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