You can always do a qPCR to verify the copy numbers.

If pMLST (plasmid multilocus sequence typing) is different within a specific plasmid replicon, such as IncFII, it suggests that there are genetic variations within that particular plasmid replicon. In this case, the plasmid environment as a whole may still have similarities, but there could be dissimilarities in certain genetic elements or regions associated with the pMLST.

Plasmids are genetic elements that can exist independently within a bacterial cell and often carry accessory genes that provide various advantages, such as antibiotic resistance or virulence factors. Plasmids are typically categorized into different replicon types based on the replication machinery they use, and IncFII is one such replicon type.

The pMLST scheme is used to characterize the genetic diversity of plasmids by sequencing specific conserved genes or regions within the plasmid. It allows for the identification of different sequence types (STs) within a specific replicon type. If the pMLST is different within the IncFII plasmid replicon, it indicates that there are different sequence types or genetic variants within that particular replicon.

However, while the pMLST may be different, other aspects of the plasmid environment, such as the backbone structure, replication mechanisms, and some shared genetic elements, may still be similar. These shared features contribute to the overall classification of the plasmid as an IncFII replicon. So, while there may be some dissimilarities in specific regions associated with the pMLST, the plasmid as a whole may still exhibit similarities in terms of its general replicon characteristics and functionality.