Phylogenetically related Argentinean and Australian Escherichia coli O157 isolates are distinguished by virulence clades and alternative shiga toxin 1 and 2 prophages

Shiga toxigenic Escherichia coli O157 is the leading cause of hemolytic uremic syndrome (HUS) worldwide. The frequencies of stx genotypes and the incidences of O157-related illness and HUS vary significantly between Argentina and Australia. Locusspecific polymorphism analysis revealed that lineage I/II (LI/II) E. coli O157 isolates were most prevalent in Argentina (90%) and Australia (88%). Argentinean LI/II isolates were shown to belong to clades 4 (28%) and 8 (72%), while Australian LI/II isolates were identified as clades 6 (15%), 7 (83%), and 8 (2%). Clade 8 was significantly associated with Shiga toxin bacteriophage insertion (SBI) type stx2 (locus of insertion, argW) in Argentinean isolates (P<0.0001). In Argentinean LI/II strains, stx2 is carried by a prophage inserted at argW, whereas in Australian LI/II strains the argW locus is occupied by the novel stx1 prophage. In both Argentinean and Australian LI/II strains, stx2c is almost exclusively carried by a prophage inserted at sbcB. However, alternative q933- or q21-related alleles were identified in the Australian stx2c prophage. Argentinean LI/II isolates were also distinguished from Australian isolates by the presence of the putative virulence determinant ECSP_3286 and the predominance of motile O157:H7 strains. Characteristics common to both Argentinean and Australian LI/II O157 strains included the presence of putative virulence determinants (ECSP_3620, ECSP_0242, ECSP_2687, ECSP_2870, and ECSP_2872) and the predominance of the tir255T allele. These data support further understanding of O157 phylogeny and may foster greater insight into the differential virulence of O157 lineages. © 2012, American Society for Microbiology.Facultad de Ciencias Veterinaria

Genomic epidemiology of NDM-1-encoding plasmids in latin American clinical isolates reveals insights into the evolution of multidrug resistance

Bacteria that produce the broad-spectrum Carbapenem antibiotic NewDelhi Metallo-b-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistancemechanism.Although it is believed that theassociated resistancegenebla NDM-1 originated inAcinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we usedwhole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) aswell as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian dollmodel for the dissemination of blaNDM-1 in LatinAmerica,with P. rettgeri playing a central role in this process, andrevealnewinsights into the evolution and disseminationof plasmids carrying such antibiotic resistance genes

Persistent Salmonella enterica serovar Typhi sub-populations within host interrogated by whole genome sequencing and metagenomics.

Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever and, in some cases, chronic carriage after resolution of acute disease. This study examined sequential isolates of S. Typhi from a single host with persistent asymptomatic infection. These isolates, along with another S. Typhi isolate recovered from a household contact with typhoid fever, were subjected to whole genome sequencing and analysis. In addition, direct sequencing of the bile fluid from the host with persistent infection was also performed. Comparative analysis of isolates revealed three sub-populations of S. Typhi with distinct genetic patterns. Metagenomic sequencing recognised only two of the three sub-populations within the bile fluid. The detection and investigation of insertion sequences IS10R and associated deletions complemented analysis of single nucleotide polymorphisms. These findings improve our understanding of within-host dynamics of S. Typhi in cases of persistent infection and inform epidemiological investigations of transmission events associated with chronic carriers

Discriminatory SNPs and gene products for each of the three sub-populations.

Discriminatory SNPs and gene products for each of the three sub-populations.</p

Multiple genomic comparison of the genomes in this study.

The reference genome, as demarcated in the figure, is presented in the centre of the ring. Each coloured rings represents a different query genome and coloured regions represent BLASTN matches to the reference. Query genomes along with percent BLASTN identity are colour coded in the figure key. The outermost ring in alternating red and blue represent the contigs of the reference genome, separated by black lines. Image was generated using BRIG version 0.95-dev.0004. (TIF)</p

Sub-consensus variation from CIDM-STyphi-BMG identified from mapping of reads onto 129-0238-M and the detection of variation in the sequencing data of the seven isolates.

Sub-consensus variation from CIDM-STyphi-BMG identified from mapping of reads onto 129-0238-M and the detection of variation in the sequencing data of the seven isolates.</p

Missing genes of the <i>rfb</i> cluster in CIDM-Styphi-B01 relative to genomic locations in 129-0238-M.

Missing genes of the rfb cluster in CIDM-Styphi-B01 relative to genomic locations in 129-0238-M.</p

Separation of the seven isolates into three subpopulations.

(A) ML tree based on core SNP alignments of the seven isolates along with contextual sequences. Number of detected homoplasic SNPs are labelled on the branches. Number of nucleotide substitutions per site is represented in the scale bar. (B) Comparison of 41 SNPs between the seven S. Typhi pseudomolecules and the reference genome. Discriminatory SNP positions are marked in the figure and expanded upon in Table 2. S. Typhi populations of the source genomes are represented next to the isolate name and colour-coded according to the Figure Key. Image was generated using snipit (https://github.com/aineniamh/snipit).</p

Coverage across virulence genes detected in the assemblies of the seven <i>S</i>. Typhi isolates when screened against VFDB.

Coverage across virulence genes detected in the assemblies of the seven S. Typhi isolates when screened against VFDB.</p

Proportion of the classified bacteria reads from the kitome.

Classification was performed against Centrifuge’s prebuild p+h+v index (12/06/2016 version). Image was generated using Krona version 2.8. (TIF)</p