In the past 30 years, improvement in preoperative diagnostics, surgical techniques, intensive therapy, and adjuvant chemoradiation enabled expert centers to achieve excellent results in operative mortality and 5-year survival, introducing the term “cure” among goals of esophageal cancer treatment.¹ x 1 Stein, HJ, von Rahden, BH, and Siewert, JR. Survival after oesophagectomy for cancer of the oesophagus. Langenbecks Arch Surg. 2005; 390: 280–285 Crossref | PubMed | Scopus (30) | Google Scholar See all References Nevertheless, little is known if these patients are really cured of their malignant disease, or the reported, admittedly improved survival rates are just consequences of an institutional selection bias, changing epidemiology of esophageal carcinoma, or in cases of early cancer, products of lead time bias and a short follow-up.² x 2 Welch, HG, Schwartz, LM, and Woloshin, S. Are increasing 5-year survival rates evidence of success against cancer?. JAMA. 2000; 283: 2975–2978 Crossref | PubMed | Scopus (290) | Google Scholar See all References x 3 MacDonald, AJ, McEwan, H, McCabe, M et al. Age at death of patients with colorectal cancer and the effect of lead-time bias on survival in elective vs emergency surgery. Colorectal Dis. 2011; 13: 519–525 Crossref | PubMed | Scopus (12) | Google Scholar See all References – ⁴ x 4 Croswell, JM, Ransohoff, DF, and Kramer, BS. Principles of cancer screening: lessons from history and study design issues. Semin Oncol. 2010; 37: 202–215 Abstract | Full Text | Full Text PDF | PubMed | Scopus (102) | Google Scholar See all References To minimize these biases and assess national temporal trends in long-term survival and possible cure rates in patients with carcinoma of the esophagus and the gastric cardia, we analyzed Surveillance, Epidemiology, and End Results (SEER) cancer registry data, comparing cancer-related survival in each stage through the last 3 decades in the United States.

The increasing prevalence of antimicrobial resistance (AMR) is a significant threat to global health. More and more multi-drug-resistant bacterial strains cause life-threatening infections and the death of thousands of people each year. Beyond disease control animals are often given antibiotics for growth promotion or increased feed efficiency, which further increase the chance of the development of multi-resistant strains. After the consumption of unprocessed animal products, these strains may meet the human bacteriota. Among the foodborne and the human populations, antimicrobial resistance genes (ARGs) may be shared by horizontal gene transfer. This study aims to test the presence of antimicrobial resistance genes in milk metagenome, investigate their genetic position and their linkage to mobile genetic elements. We have analyzed raw milk samples from public markets sold for human consumption. The milk samples contained genetic material from various bacterial species and the in-depth analysis uncovered the presence of several antimicrobial resistance genes. The samples contained complete ARGs influencing the effectiveness of acridine dye, cephalosporin, cephamycin, fluoroquinolone, penam, peptide antibiotics and tetracycline. One of the ARGs, PC1 beta-lactamase may also be a mobile element that facilitates the transfer of resistance genes to other bacteria, e.g. to the ones living in the human gut.

As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the pre-antibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are widespread used in many areas of biological research and antibiotic resistance is no exception. For the rapid annotation of whole genome sequencing and metagenomic results considering antibiotic resistance, several tools and data resources were developed. These databases, however, can differ fundamentally in the number and type of genes and resistance determinants they comprise. Furthermore, the annotation structure and metadata stored in these resources can also contribute to their differences. Several previous reviews were published on the tools and databases of resistance gene annotation; however, to our knowledge, no previous review focused solely and in depth on the differences in the databases. In this review, we compare the most well-known and widely used antibiotic resistance gene databases based on their structure and content. We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation.

Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.