All the isolates with IP-1 amplified a strong band with intI1, but only four isolates amplified strong bands for qacEΔ1. Most of the isolates with IP-1 (76%) did not amplify qacEΔ1 or produced very weak bands (16%) [see Additional file2]. This result suggests that most of these integrons contain an unusual 3′ CS, as recently reported for this integron in Salmonella and Staphylococcus [40, 49–51]. Twenty isolates that did not amplify the cassette region using the CS-F and CS-R primers were selected to test the amplification of intI1 and qacEΔ1. Most of these isolates did not produce amplifications, or produced very weak bands; only four isolates presented an intense intI1 band. Macro-restriction

PFGE dendrogram and association among molecular markers BAY 73-4506 ic50 The PFGE fingerprints were clustered

using the UPGMA algorithm. The dendrogram was divided in five clusters using a cut-off value of 78% similarity (Figure 4). Cluster I grouped all the ST213 isolates Ibrutinib manufacturer and four ST19 isolates. Using the information provided by the accessory genes, this cluster can be further subdivided in four main groups. Group Ia contained only ST213 isolates from three different states, many of which carried cmy-2 and IP-1. Groups Ib and Ic contained ST213 isolates mostly without cmy-2 and ST19 isolates without pSTV, and comprising five of the six IP-2. Group Id was similar to group Ia; it contained ST213 isolates, most of which harboured cmy-2 and IP-1. It is distinguished from groups Ia and Ib by the lack of a large restriction fragment of about 665 kb. Cluster II was formed by ST19 isolates carrying both pSTV and SGI1. Clusters III and

IV grouped ST19 isolates and the four ST302 strains, most of them carrying pSTV. Cluster IV contained the two ST19 isolates for which rck could not be amplified, and one of them carried the IP-4 integron. Finally, cluster V was composed by ST19 strains lacking pSTV. A few exceptions to these general patterns were detected, such as a cluster I ST213 Bcl-w isolate harbouring pSTV (yuhs03–80) or a ST19 isolate harbouring pSTV and SGI1 in cluster I (sorapus02–4). The whole set of genetic markers targeting both housekeeping and accessory genes allowed us to discover genetic subgroups within the isolate set. Discussion Low genetic diversity of core and accessory genes Both housekeeping and accessory genes displayed extremely low levels of genetic diversity; even the third codon positions were invariable. The low genetic diversity and the clonal pattern of descent of accessory elements could be explained by several evolutionary processes, such as rapid clonal expansion of the population, genetic drift, the existence of barriers to genetic exchange among subgroups within the population, or a combination of these possibilities [4, 5, 8, 52, 53].