Antimicrobial resistance in clinical Escherichia coli isolates from poultry and livestock, China

Yassin, Afrah Kamal; Gong, Jicheng; Kelly, Patrick J.; Lu, Guangyu; Guardabassi, Luca; Wei, Lanjing; Han, Xiangan; Qiu, Haixiang; Price, Stuart; DaRong, Cheng; Wang, Chengming

doi:10.1371/journal.pone.0185326

Cited by 106 publications

(108 citation statements)

References 25 publications

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“…More recently, a study sampled 862 clinical isolates of E. coli from a variety of animals including chickens, pigs, and cows and found that 94% of strains were resistant to one drug and 83% were resistant to three antimicrobial classes (Yassin et al, 2017).…”

Section: Studies Have Shown That Approximately 54% Of Predominantmentioning

confidence: 99%

“…More recently, a study was carried out where 137 E. coli clinical isolates were tested for resistance to 11 commonly used antibiotics and showed 50 of the isolates tested were resistant to 10 of the 11 antibiotics, highlighting the urgent requirement for alternative therapies (Olorunmola, Kolawole, & Lamikanra, ). More recently, a study sampled 862 clinical isolates of E. coli from a variety of animals including chickens, pigs, and cows and found that 94% of strains were resistant to one drug and 83% were resistant to three antimicrobial classes (Yassin et al, ).…”

Section: Introductionmentioning

confidence: 99%

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A scaled‐down model for the translation of bacteriophage culture to manufacturing scale

Ali

Rafiq

Ratcliffe

2019

Biotech & Bioengineering

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Therapeutic bacteriophages are emerging as a potential alternative to antibiotics and synergistic treatment of antimicrobial‐resistant infections. This is reflected by their use in an increasing number of recent clinical trials. Many more therapeutic bacteriophage is being investigated in preclinical research and due to the bespoke nature of these products with respect to their limited infection spectrum, translation to the clinic requires combined understanding of the biology underpinning the bioprocess and how this can be optimized and streamlined for efficient methods of scalable manufacture. Bacteriophage research is currently limited to laboratory scale studies ranging from 1–20 ml, emerging therapies include bacteriophage cocktails to increase the spectrum of infectivity and require multiple large‐scale bioreactors (up to 50 L) containing different bacteriophage–bacterial host reactions. Scaling bioprocesses from the milliliter scale to multi‐liter large‐scale bioreactors is challenging in itself, but performing this for individual phage‐host bioprocesses to facilitate reliable and robust manufacture of phage cocktails increases the complexity. This study used a full factorial design of experiments approach to explore key process input variables (temperature, time of infection, multiplicity of infection, agitation) for their influence on key process outputs (bacteriophage yield, infection kinetics) for two bacteriophage–bacterial host bioprocesses (T4 – Escherichia coli; Phage K – Staphylococcus aureus). The research aimed to determine common input variables that positively influence output yield and found that the temperature at the point of infection had the greatest influence on bacteriophage yield for both bioprocesses. The study also aimed to develop a scaled down shake‐flask model to enable rapid optimization of bacteriophage batch bioprocessing and translate the bioprocess into a scale‐up model with a 3 L working volume in stirred tank bioreactors. The optimization performed in the shake flask model achieved a 550‐fold increase in bacteriophage yield and these improvements successfully translated to the large‐scale cultures.

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Section: Studies Have Shown That Approximately 54% Of Predominantmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A scaled‐down model for the translation of bacteriophage culture to manufacturing scale

Ali

Rafiq

Ratcliffe

2019

Biotech & Bioengineering

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“…Increasing antibiotic resistance and the lack of new antibacterial agents have revived 260 interest in old compounds such as nitrofurantoin in clinical [46,47]. Despite the renewed 261 importance of nitrofurantoin and the known role of food animals in resistance 262 dissemination, only a few studies include this antibiotic in antimicrobial resistance 263 screenings [48,49].…”

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confidence: 99%

“…resistance to nitrofurantoin in extra-intestinal clinical isolates of E. coli from chickens has 267 been reported in China [48]. Due to the possibility that the resistance to nitrofurantoin 268 could increase over time, it is important to include it in antimicrobial resistance 269 surveillance plans in poultry production systems.…”

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confidence: 99%

Characterization of cefotaxime resistant Escherichia coli isolated from broiler farms in Ecuador

Vinueza-Burgos

Ortega-Paredes

Narváez

et al. 2018

Preprint

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Antimicrobial resistance (AR) is a worldwide concern. Up to a 160% increase in antibiotic usage in food animals is expected in Latin American countries. The poultry industry is an increasingly important segment of food production and contributor to AR. The objective of this study was to evaluate the prevalence, AR patterns and the characterization of relevant resistance genes in Extended Spectrum β-lactamases (ESBL) and AmpC E. coli from large poultry farms in Ecuador. Sampling was performed from June 2013 to July 2014 in 6 slaughterhouses that slaughter broilers from 115 farms totaling 384 flocks. Each sample of collected caeca was streaked onto TBX agar supplemented with cefotaxime (3 mg/l). In total, 176 isolates were analyzed for antimicrobial resistance patterns by the disk diffusion method and for blaCTX-M, blaTEM, blaCMY, blaSHV, blaKPC, and mcr-1 by PCR and sequencing. ESBL and AmpC E. coli were found in 362 flocks (94.3%) from 112 farms (97.4%). We found that 98.3% of the isolates were multi-resistant to antibiotics. Low resistance was observed for ertapenem and nitrofurantoin. The most prevalent ESBL genes were the blaCTX-M (90.9%) blaCTX-M-65, blaCTX-M-55 and blaCTX-M-3 alleles. Most of the AmpC strains presented the blaCMY-2 gene. Three isolates showed the mcr-1 gene. Poultry production systems represent a hotspot for antimicrobial resistance in Ecuador, possibly mediated by the extensive use of antibiotics. Monitoring this sector in national and regional plans of antimicrobial resistance surveillance should therefore be considered.

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“…The variation in resistance reflects the difference in the antimicrobial usage policy of this drug in food-producing animals among the different countries (Kools et al, 2008). China and Brazil use fluoroquinolones for the treatment and prevention of infections in chickens (Gouvêa et al, 2015;Yassin et al, 2017).…”

Section: Quinolonesmentioning

confidence: 99%

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Awawdeh¹,

Turni²,

Henning³

et al.

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Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, a localised or systemic infection resulting in clinical diseases such as colisepticemia, chronic respiratory disease and swollen-head syndrome. Globally, avian colibacillosis is the leading cause of morbidity and mortality in poultry, and it has been associated with massive economic losses and welfare problems.This organism is of public health significance as APEC is communicable to humans. The diagnosis of avian colibacillosis relies on clinical signs, typical pathological lesions and culture of E. coli from affected tissue(s). Antimicrobial therapy is often used both for treatment and control. Previous overseas studies have characterised APEC and identified virulence genes (VGs) that can be used as molecular markers for the identification of APEC. Little is known about APEC in broiler chickens in Australia.The aim of this thesis was to gain a better understanding of the epidemiology of APEC in Australian broiler flocks and how factors including presence of VGs and phylogenetic group can improve the identification of this pathotype in Australia. Firstly, three faecal DNA extraction methods were evaluated. Faeces were collected from healthy chickens and chickens with colibacillosis from commercial broiler farms in South East Queensland (SEQ). The extracted DNA was screened by a pentaplex-PCR for five APEC-associated VGs (iroN, iutA, iss, hlyF and ompT). DNA extracted from E. coli isolates cultured from the cloaca and organs of the birds were screened using the same PCR.Repeated bead beating plus column elution was the preferred DNA extraction method, as it yielded good PCR quality and adequate quantity DNA. However, identifying APEC by direct detection of the five VGs from the faecal material was not feasible as all of these genes were also detected in all of the birds. However, the VGs were more commonly detected in E. coli isolates cultured from birds with colibacillosis.A cross-sectional study was performed to estimate APEC farm-level prevalence in healthy broiler chickens in SEQ and to identify potential risk factors associated with the carriage of APEC. At the farm-level, all of the 40 farms sampled were positive for APEC, that is at least one bird per farm carried APEC, while the within-farm prevalence was 63% (95% Confidence Interval: 55.8, 70.2).Higher APEC within-farm bird-level prevalence was significantly associated with the usage of well water as a source of drinking water, failure to disinfect the water line after each flock, farm visitors not showering before entering the shed, distances greater than 20 metres between the car park and the poultry shed and the presence of wild birds within 50 metres of the shed. Chlorinating the drinking water combined with automatic water filtration reduced within-farm bird-level APEC prevalence. Page | 3Therefore, based on the results concluded from the multivariable model, improving biosecurity and water treatments might reduce APEC prevalence, decrease the risk of co...

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Antimicrobial resistance in clinical Escherichia coli isolates from poultry and livestock, China

Cited by 106 publications

References 25 publications

A scaled‐down model for the translation of bacteriophage culture to manufacturing scale

A scaled‐down model for the translation of bacteriophage culture to manufacturing scale

Characterization of cefotaxime resistant Escherichia coli isolated from broiler farms in Ecuador

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

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