**3. Antimicrobial resistance, genetic diversity and molecular epidemiology of the** *Enterobacteriaceae* **foodborne pathogens**

#### **3.1** *E. coli*

*E. coli* is one of the most common food-borne pathogens and may spread a variety of diseases through the food chain in different ecosystems. There are pathogenic and non-pathogenic strains of *E. coli*. Of these, pathogenic strains can cause a variety of intestinal diseases.

The original *E. coli* was sensitive to almost all antibacterial drugs [19], but multiresistance of *E. coli* is now increasingly common. The resistance mechanism of *E. coli* includes the acquisition of encoding ultra-broad-spectrum β-lactamase (resistance to broad-spectrum cephalosporin), carbapenase (resistance to carbapenems), et al. The most common mechanism for the development of resistance in *E. coli* is the production of β-lactamase hydrolyzing β-lactamase antibiotics [20]. Ultra-broadspectrum β-lactamases (ESBLs) are produced by mutations in β-lactamases and could be encoded by genes that effectively hydrolyze third and fourth-generation cephalosporins as well as monoclonal antibodies. However, β-lactamase inhibitors like clavulanate and tarmacadam can stop them [21]. Genes such as *aadA1*, *aadA2*, *mcr-1*, *crf*, and *bla*TEM-1 are related to the drug resistance in *E. coli* (**Table 1**) [19].

The genetic diversity of *E. coli* is reflected not only at the individual level but also at the molecular level. Ramadan et al. [22] used Multilocus sequence typing (MLST) to explore the genetic diversity in *E. coli*, as indicated by the various distribution of *E. coli* lineages among different sources. It was found that a wide range of STs was found in chicken, human and beef isolates. And the most common STs isolated from chicken


#### **Table 1.**

*Resistance phenotype and resistance genes of the strain.*

isolates differed significantly from human and beef isolates, which was consistent with previous research.

The genetic diversity of *E. coli* causes changes at the molecular level. Findlay et al. [23] revealed the cause of Urinary Tract Infection (UTI) was the direct sharing of *E. coli* between local farms and the local population. They found that the *bla*ctX-M or *bla*CMY 2 plasmid isolated from the farm *E. coli* isolates was almost identical to one of the three plasmids isolated from the urine of local people, and these three plasmids are found in almost all humans and animals on earth.

## **3.2** *Salmonella*

*Salmonella* is gram-negative bacteria. Based on the clinical presentation of the patient with their *Salmonella* infection, we usually identify them as typhoidal *Salmonella* and non-typhoidal *Salmonella* (NTS).

*Salmonella* has multidrug resistance because it is resistant to a variety of first-line antibiotics such as ampicillin, chloramphenicol and methicillin/sulfamethoxazole. Lu et al. [24] classified gene products by direct homology through functional annotation of the COG database. COG functional annotation was performed on 13 drug resistance genes of *Salmonella*, such as beta-lactam resistance and macrolide resistance. Also, they found that genes like *ampE*, *macB,* and *macA* are drug resistance genes in *Salmonella* (**Table 1**)*.*

*Salmonella* is an important foodborne pathogen and its genetic diversity is of great significance for the prevention and control of the disease. Methods commonly used in genetic diversity research include serotyping and pulse electrophoresis typing, which are time-consuming and have poor traceability [25]. Zhang et al. [26] conducted multilocus sequence typing of 311 *salmonella* strains, and MLST typing results were divided into 26 ST types.

Molecular epidemiology has been used to document vector to human transmission and to investigate outbreaks of *Salmonellosis* in hospitals. *Salmonella* typing is

### *Foodborne Pathogens of Enterobacteriaceae, Their Detection and Control DOI: http://dx.doi.org/10.5772/intechopen.102086*

epidemiologically important because it provides correlations between cases, foci, and between cases and food or other vectors, animals, regions, and periods. Riley et al. [27] studied an outbreak of enteritis in the northeastern United States in late 1981 caused by *Salmonella* Newport through commercially available raw beef. The outbreak strain is of the same serotype and is sensitive to most antibiotics. Plasmid analysis revealed two plasmids (3.7 and 3.4Md) of strains isolated from raw beef and patients with identical restriction profiles. Meanwhile, 45 percent of intestinal strains from New Jersey and Pennsylvania had the same plasmid profile. Through follow-up of patients, it was also found to be related to raw beef. Without molecular biological analysis, these cases would not be considered part of the outbreak.

## **3.3** *Shigella*

*Shigella* is the most common cause of diarrhoeal disease in humans worldwide, and its drug resistance is already a major public health burden. *Shigella* resistance tests have been reported in some areas of Shanxi Province, China. Of 474 strains, only 2 strains (0.5%) were sensitive to all 21 antimicrobial agents [28], 14 strains (3.0%) were co-resistant to the third-generation cephalosporins and fluoroquinolones. Wang et al. [29] found that *bla*TEM-1, *bla*CTX-M, *bla*OXA-1, *bla*SHV-12 are Cephalosporins and Fluoroquinolones resistance genes (**Table 1**).

*Shigella* is a common cause of diarrhea and death, particularly in children under the age of five. It is critical to investigate the genetic diversity of *Shigella.* Ei-Gendy et al. [28] isolated a total of 70 strains of *Shigella* from children younger than 5 years of age in Egypt, including 40 *Shigella dysenteriae* and 30 *Shigella boydii*. Among them, serotypes 7(30%), 2(28%), and 3(23%) accounted for the majority of *S. dysenteriae* isolates and 50% of *S. boydii* isolates were serotype 2.

*Shigella* is a common foodborne pathogen, and its molecular epidemiology is of great significance for the prevention and control of *Shigella*. Chen et al. [30] collected and typed 161 *Shigella* isolates obtained from Renai and adjacent townships from 1997 to 2000 using serological and PFGE techniques. The finding showed that the strain giving rise to foodborne illnesses remained the most common cause of *Shigellosis* during 4 years. Chen found that the percentage of these outbreak strain isolates among *Shigella flexneri* serotype 2a isolates recovered each year dropped. During this time, although several closely similar strains resembling outbreak strains have also emerged, they are far less transmissible and pathogenic than outbreak strains.
