Molecular epidemiology and diversity of Salmonella serovar Typhimurium in pigs using phenotypic and genotypic approaches

Abstract

For epidemiological investigations of the most common and non-host-adapted Salmonella serotypes, such as Typhimurium, highly discriminatory approaches are essential. In the present study, we evaluated three genotyping methods; amplified fragment length polymorphism (AFLP), pulsed-field gel electrophoresis (PFGE) and repetitive palindromic extragenic-PCR (Rep-PCR) using 40 isolates. AFLP showed the highest discriminatory index (0.939), resolution and throughput. To determine clonality of Salmonella Typhimurium isolates and epidemiological relatedness in different commercial pig production units, we employed AFLP in combination with antimicrobial resistance pattern and phage typing. Salmonella serovar Typhimurium isolates (n=196) obtained from a longitudinal study of 18 pig farms over a 3-year period were studied. Using this approach, 16 distinct clonal types were identified. We found two common multidrug- resistant patterns including AmCmStSuTe and AmKmStSuTe. Two commonly multidrug- resistant phage types that are of known public health importance, DT104 and DT193, were also common. AFLP differentiated distinct clones within DT104, a phage type previously reported to be clonal. Fourteen of the clonal types were unique to one of the two production systems, showing diversity between independent commercial pig production systems located in the same geographical area. Clonal types obtained from nursery farms and corresponding finishing units were, however, similar.

Fig. 1

DNA fingerprint patterns of S. Typhimurium isolates using the three genotyping methods evaluated: (a) PFGE macrorestriction of genomic DNA. Lanes 1–4, S. Typhimurium DT193 isolates with AmKmStSuTe resistance pattern; lanes 5–8, DT104 isolates with AmCmStSuTe resistance pattern are shown. (b) Section of AFLP gel: group A, isolates with AmCmStSuTe pattern and group B, isolates with AmKmStSuTe pattern are shown; (c) Rep–PCR. Lanes 1 and 2 are S. Typhimurium DT104 isolates with AmCmStSuTe resistance pattern; lanes 3–5, DT193 isolates with AmKmStSuTe resistance pattern are shown. Lanes marked as ‘M’ indicate the molecular marker lanes in all the three gels.

Fig. 2

Dendrogram representing AFLP fingerprints of 108 Salmonella serovar Typhimurium phage type DT104 isolates. The nine predominant AFLP clonal types as categorized in the Table are represented (3, 2, 6, 7, 8, 16, 9, 11 and 14).

Fig. 3

Dendrogram representing AFLP fingerprints of 48 Salmonella serovar Typhimurium phage type DT193 isolates. The six predominant cluster types as categorized in the Table are represented (5, 4, 1, 10, 13 and 12).