Ands AnalysisAnnotated draft genomes were submitted to IslandViewer three (Dhillon et al., 2015) applying L. monocytogenes EGD-e (NC_003210.1) as a reference for contig reordering. Genomic islands have been predicted employing IslandPath-DIMOB (Hsiao et al., 2005) and SIGI-HMM (Waack et al., 2006). Predicted genomic islands positioned on the genome within 10 kb of every other had been merged into one single region. To form groups of related genomic islands, the genetic distance between genomic island sequences was computing using Mash (parameter 2000; Ondov et al., 2016) and groups of comparable sequences had been identified making use of hclust and cutree in R.Frontiers in Microbiology www.frontiersin.orgMarch 2017 Volume 8 ArticleHingston et al.L. monocytogenes Pressure Tolerance GenotypesTABLE 1 Genetic characteristics and prevalence of sensitive and tolerant phenotypes amongst L. monocytogenes belonging to diverse serotypes. Serotype n ( ) Plasmid+ ( )a Full length inlA ( )a 14 (56) 15 (83) 85 (92) 3 (12) 0 1 0 1 0 119 SSI-1+ ( )a CS ( )a CT ( )a SS ( )a ST ( )a AS ( )a AT ( )a DS ( )a DT ( )a4b 12b 12a 12c 3a 3b 4c 12b, 3b, 7 12a, 3a Sum25 (15) 18 (11) 92 (55) 25 (15) two (1) 1 1 1 14 (16) 14 (78) 49 PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/21359215 (53) 21 (84) 2 (100) 1 0 0 14 (16) 17 (94) 65 (71) 25 (one hundred) two (100) 1 0 1 14 (16) 0 4 (4) five (20) 0 0 0 0 02 (eight) two (11) 11 (12) three (12) 0 0 0 0 01 (4) 3 (17) 18 (20) 4 (16) 1 0 0 0 13 (12) 2 (11) 12 (13) 0 0 0 0 0 01 (4) 0 22 (24) two (8) 1 0 0 0 04 (16) 7 (39) 7 (8) 4 (16) 0 0 0 0 02 (eight) two (11) 10 (11) 4 (16) 0 0 1 0 13 (12) four (22) 11 (12) four (16) 0 1 0 0 0a PercentagesCS, cold sensitive; CT, cold tolerant; SS, salt sensitive; ST, salt tolerant; AS, acid sensitive; AT, acid tolerant; DS, desiccation sensitive; DT, desiccation tolerant. relate to prevalence inside the serotype.inlA PMSC’s at 700aa (Table S1). An more 13 isolates, all from the serotype 4b CCs six and 315, contained a 3 codon deletion mutation previously reported in Kovacevic et al. (2013). Together with the exception of CCs five and 9, all isolates from the exact same CC either contained complete length inlA or maybe a truncated version. In the course of the screening of your whole genome sequences, the absence of E4CPG price lmo1078 was noted among serotype 4b isolates. This gene, which encodes a UDP-glucose pyrophosphorylase, has been previously demonstrated to possess a function in L. monocytogenes cold development (Chassaing and Auvray, 2007). It was also observed that 70 (n = 116) of strains possessed SSI-1 with this island getting most prevalent amongst serotype 12c isolates (one hundred ) followed by 12b (94 ), 12a (71 ), and 4b (16 ; Table 2). Moreover, all isolates from CCs three, 5, 7, 8, 9, 155, 224, 315, and 321 contained SSI-1 (Table 2). All remaining isolates possessed a homolog to F2365_0481 in location of SSI-1 (Ryan et al., 2010), with all the exception with the CC121 isolate which possessed lin0464 and lin0465 homologs as reported in Hein et al. (2011). The LGI1 indicator gene, emrE, was identified in 16 of our isolates and as previously reported (Gilmour et al., 2010; Althaus et al., 2014; Kovacevic et al., 2015), all originated from Canada and 14 were serotype 12a ST120-CC8. The remaining two isolates represented novel STs (ST1022 and 1025) that also belonged to CC8. All emrE containing isolates also harbored SSI-1 and full length inlA.desiccation tolerance assays, the Baranyi and Roberts (1994) was suitable for modeling the spectrophotometrically obtained information with typical R2 and MSE-values ranging from 0.997 to 0.998 and 0.003 to 0.017, respectively. General, 27 and.
