Molecular Microbiology Research, 2025, Vol.15, No.1, 18-27 http://microbescipublisher.com/index.php/mmr 22 5.2 Role of environmental factors in the emergence of pathogenic strains Many factors in the environment, especially antibiotics and diet, can affect whether E. coli becomes a "bad bacteria". Antibiotics are frequently used in farmed animals, which may make symbiotic E. coli in the gut “resistant”. These drug-resistant genes may also be passed on to other pathogenic bacteria and eventually become “multi-drug-resistant” superbies (Ramos et al., 2020). E. coli’s genes are flexible and can quickly learn new abilities through “horizontal transfer”, such as how to fight drugs (Navarro-García et al., 2019). In addition, what you eat can also affect the intestinal bacterial flora. Some diets may make pathogenic bacteria grow faster, while the number of good bacteria becomes smaller. The use of antibiotics and dietary changes will create better survival opportunities for these "bad bacteria" and make the originally harmless E. coli more dangerous. 5.3 Cross-species transmission and zoonotic potential of pathogenic E. coli Pathogenic E. coli can spread between humans and animals, and this is called "zoonotic". Especially some strains with special enzymes (such as ESBLs) that are resistant to many antibiotics, which makes them more difficult to deal with (Ramos et al., 2020). The study found that the E. coli strains isolated from humans, animals, and food were very genetically similar, suggesting that they can be spread across species (Sarowska et al., 2019). E. coli can gain new abilities through “gene exchange”, which allows them to survive between different hosts, such as jumping from animals to humans (Figure 3) (Desvaux et al., 2020). To reduce this kind of transmission, we need to have an in-depth understanding of how it occurs so that effective prevention and control measures can be formulated to protect everyone's health. Figure 3 Structure and motility functions of PAIs (Adopted from Desvaux et al., 2020) Image caption: A: Insertion and excision processes of PAIs. PAIs are chromosomal fragments of pathogenic bacteria that encode biological functions involved in virulence. Their insertion in the chromosome is due to the presence of att sites at a chromosomal acceptor site (attB) and in the episomal PAI (attP). They are recognized by integrases, which catalyze a recombination of att sites. It results in the insertion of the episomal element at the attB site and the formation of direct repeated sequences (DRS) also named attL (left DRS) and attR (right DRS) in the ends of the inserted PAI. The excision of the PAI results from recombination between the direct repeats attL and attR. Catalyzed by integrases and recombination directionality factors (RDFs) also called excisionases, it generates an episomal element that contains one of the att sites (attP), while the other att site remains in the chromosome (attB); B: Horizontal transfer of PAIs via conjugative plasmids, ICEs, and phages harboring att sites. Episomal PAIs can be inserted at att sites in conjugative plasmids, ICEs and phages as described above and then transferred into a bacterial recipient via conjugation for ICE-type and plasmid-type navettes or via transduction for phage-type navettes (Adopted from Desvaux et al., 2020) 6 Case Study 6.1 Background and epidemiology of the outbreak In May 2011, a severe outbreak of E. coli (EHEC) broke out in Germany, the largest ever. This epidemic mainly occurred in Hamburg. What caused the outbreak was an E. coli strain called O104. This bacteria is particularly powerful, causing 3 128 people to suffer from gastroenteritis, of which 782 also developed hemolytic uremic syndrome (HUS), and 46 people eventually died. Initially, local doctors discovered that a group of HUS patients
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