Assessing antimicrobial resistance occurrence in the Portuguese food system: Poultry, pigs and derived food, 2014-2018

Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract

Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.

The Importance of the Slaughterhouse in Surveilling Animal and Public Health: A Systematic Review

From the point of public health, the objective of the slaughterhouse is to guarantee the safety of meat in which meat inspection represent an essential tool to control animal diseases and guarantee the public health. The slaughterhouse can be used as surveillance center for livestock diseases. However, other aspects related with animal and human health, such as epidemiology and disease control in primary production, control of animal welfare on the farm, surveillance of zoonotic agents responsible for food poisoning, as well as surveillance and control of antimicrobial resistance, can be monitored. These controls should not be seen as a last defensive barrier but rather as a complement to the controls carried out on the farm. Regarding the control of diseases in livestock, scientific research is scarce and outdated, not taking advantage of the potential for disease control. Animal welfare in primary production and during transport can be monitored throughout ante-mortem and post-mortem inspection at the slaughterhouse, providing valuable individual data on animal welfare. Surveillance and research regarding antimicrobial resistance (AMR) at slaughterhouses is scarce, mainly in cattle, sheep, and goats. However, most of the zoonotic pathogens are sensitive to the antibiotics studied. Moreover, the prevalence at the slaughterhouse of zoonotic and foodborne agents seems to be low, but a lack of harmonization in terms of control and communication may lead to underestimate its real prevalence.

Prevalence of Extended-Spectrum β-Lactamase-Resistant Genes in Escherichia coli Isolates from Central China during 2016-2019

The emergence and dissemination of Escherichia coli (E. coli) strains that produce extended-spectrum beta-lactamases (ESBLs) represents a major public health threat. The present study was designed to evaluate the prevalence and characteristics of ESBL-producing Escherichia coli isolates from chickens in central China during 2016-2019. A total of 407 E. coli strains isolated from 581 chicken swabs were identified conventionally and analyzed for various cephalosporin susceptibility by disk-diffusion assay. ESBL-producing strains were screened using the double=disk synergy test and ESBL-encoding genes were carried out by PCR/sequencing. A total of 402 E. coli isolates exhibited strong resistance to first- to fourth-generation cephalosporins and monobactam antibiotics, especially cefazolin (60.69%), cefuroxime (54.05%), cefepime (35.14%), ceftriaxone (54.30%), and aztreonam (40.29%). Piperacillin/tazobactam (1.72%) was the most effective drug against the strains, but the resistance rates increased each year. Among the isolates, 262 were identified as ESBL producers and the isolation rates for the ESBL producers increased from 63.37% to 67.35% over the four years. CTX-M (97.33%) was the most prevalent type, followed by TEM (76.72%) and SHV (3.05%). The most common ESBL genotype combination was bla_TEM + bla_CTX-M (74.46%), in which the frequency of carriers increased steadily, followed by bla_CTX-M + bla_SHV (3.05%). In addition, the most predominant specific CTX-M subtypes were CTX-M-55 (48.47%) and CTX-M-1 (17.94%), followed by CTX-M-14 (11.01%), CTX-M-15 (8.02%), CTX-M-9 (6.11%), CTX-M-65 (4.58%), and CTX-M-3 (1.15%). Moreover, a novel multiplex qPCR assay was developed to detect bla_CTX-M, bla_TEM, and bla_SHV, with limits of detection of 2.06 × 10¹ copies/μL, 1.10 × 10¹ copies/μL, and 1.86 × 10¹ copies/μL, respectively, and no cross-reactivity with other ESBL genes and avian pathogens. The assays exhibited 100% sensitivity and specificities of 85%, 100%, and 100% for bla_CTX-M, bla_TEM, and bla_SHV, respectively. In conclusion, our findings indicated that ESBL-producing E.coli strains isolated from chickens in central China were highly resistant to cephalosporins and frequently harbored diversity in ESBL-encoding genes. These isolates can pose a significant public health risk. The novel multiplex qPCR method developed in this study may be a useful tool for molecular epidemiology and surveillance studies of ESBL genes.

Recognition of quinolone antibiotics by the multidrug efflux transporter MexB of Pseudomonas aeruginosa

The drug/proton antiporter MexB is the engine of the major efflux pump MexAB-OprM in Pseudomonas aeruginosa. This protein is known to transport a large variety of compounds, including antibiotics, thus conferring a multi-drug resistance phenotype. Due to the difficulty of producing co-crystals, only two X-ray structures of MexB in a complex with ligands are available to date, and mechanistic aspects are largely hypothesized based on the body of data collected for the homologous protein AcrB of Escherichia coli. In particular, a recent study (Ornik-Cha, Wilhelm, Kobylka et al., Nat. Commun., 2021, 12, 6919) reported a co-crystal structure of AcrB in a complex with levofloxacin, an antibiotic belonging to the important class of (fluoro)-quinolones. In this work, we performed a systematic ensemble docking campaign coupled to the cluster analysis and molecular-mechanics optimization of docking poses to study the interaction between 36 quinolone antibiotics and MexB. We additionally investigated surface complementarity between each molecule and the transporter and thoroughly assessed the computational protocol adopted against the known experimental data. Our study reveals different binding preferences of the investigated compounds towards the sub-sites of the large deep binding pocket of MexB, supporting the hypothesis that MexB substrates oscillate between different binding modes with similar affinity. Interestingly, small changes in the molecular structure translate into significant differences in MexB–quinolone interactions. All the predicted binding modes are available for download and visualization at the following link: https://www.dsf.unica.it/dock/mexb/quinolones.

Putative binding modes (BMs) of quinolones to the bacterial efflux transporter MexB were identified. Multiple interaction patterns are possible, supporting the hypothesis that substrates oscillate between different BMs with similar affinity.