# Current Challenges in _Yersinia_ Diagnosis and Treatment
## 9 Diagnosis
pseudotuberculosis_, due to the unique band patterns for each species from the fecal samples. To establish specific species, four primer pairs are chosen to detect the genes that are responsible for the virulence in pathogenic _Yersinia_ species. These genes include _Ail_ (attachment invasion locus, present on the chromosome of pathogenic _Y. enterocolitica_ strains), gen _FyuA_ (ferric yersiniabactin uptake receptor A, present on the chromosomal DNA of highly pathogenic _Y. enterocolitica_), _Inv_ (invasion, present on the chromosome of pathogenic _Y. pseudotuberculosis_), and _VirF_ (virulence regulon transcriptional activator, encoded on a plasmid of pathogenic _Y. enterocolitica_ and _Y. pseudotuberculosis_), which are responsible for the virulence in pathogenic Yersinia species [15]  
Since traditional stool cultures are insufficient, many laboratories have recently adopted PCR-based gastrointestinal pathogen panels (GIPP) to increase the speed and efficiency of pathogen detection; for example, commercial multiplex assays such as Verigene EP, FilmArray GI, xTAG GPP, Go-GutDx(r), and BD MAXTM GIPP have been adopted [16; 17; 18]. For example, Go-GutDx(r) is the DNA stool testing kit used for the confirmation of infectious diarrhea, including not only Yersinia, but also other pathogens such as _Clostridium difficile_, _Campylobacter jejuni_, _Salmonella enterica Typhimurium_, _Shigella_ spp., _STEC (stx1, stx2)_, _Vibrio_ spp., and _Yersinia enterocolitica_[17]. In contrast, the BD MAXTM GIPP system detects significantly more _Yersinia enterocolitica_ than traditional cultures, with most of these positive results not recoverable by culture. Interestingly, irregular PCR amplification curvesoccurred if the viable organisms were not recovered in culture, but still yielded positive automated interpretations [18]. The results of nucleic acid amplification interpretation tests for many pathogens must be related to the clinical picture because these tests detect DNA and do not necessarily involve living organisms. Clinical isolates from Yersinia-infected patients have recently been characterized at the molecular subtyping level using whole genome sequencing (WGS). WGS is a powerful tool for subtyping _Yersinia enterocolitica_. It showed that _Y. enterocolitica_ BT 1A strains and BT 4/O:3 strains are genetically diverse, while BT 2/O:3 strains are all ST12 strains and clustered closely [162]. WSG also allows the comparison of the \"New World\" 8081 strain (1B/O:8), which predominates in the United States (1B/O:8), to the epidemiological pattern in Europe, Japan, and China [biotype 3 strain, 105.5R (r) (O:9) are representatives of the Old World biogroup]. The comparison of the sequenced genome of the mentioned biotypes shows that both strains have more than 14% conservation of specific genes. Many of the loci representing ancestral clusters contributing to enteric survival and pathogenesis are present in strain 105.5R (r) but are lost in strain 8081. The comparative genome analysis indicated that these two strains [biotype 3 strain, 105.5R (r) (O:9) and strain 8081--91B/O:8)] may have attained their pathogenicity by completely separate evolutionary events [163]. The WGS can also be used for food analysis. For example, the study by [PERSON] et al. shows that the pathogenic _Y. enterocolitica_ strains were isolated from 32 of 100 pork samples, from 25 of 100 chicken meat samples, and 22 of 97 produce samples (fresh herbs and salads), all collected at the retail level in Switzerland in 2024. The whole-genome sequencing (WGS) results revealed that three strains belonged to biotype 4 (from pork) and each of them carried a pYV-like plasmid harboring 44 virulence factors. The other 86 strains belonged to biotype 1A, and all isolates belonged to 45 sequence types. Interestingly, plasmids from the same type were identified in different sequence types, showing that genetic exchange between them does occur. Fortunately, none of the isolates harbored plasmid-mediated antimicrobial resistance genes. The _Y.