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Shiga toxin (Stx) is the definitive virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx variants are currently organized into a taxonomic system of three Stx1 (a, c, and d) and seven Stx2 (a, b, c, d, e, f, and g) subtypes. In this study, seven STEC isolates from food and clinical samples possessing stx2 sequences that do not fit current Shiga toxin taxonomy were identified. Genome assemblies of the STEC strains were created from Oxford Nanopore and Illumina sequence data. The presence of atypical stx2 sequences was confirmed by Sanger sequencing, as were Stx2 expression and cytotoxicity. A strain of O157:H7 was found to possess stx1a and a truncated stx2a , which were originally misidentified as an atypical stx 2 . Two strains possessed unreported variants of Stx2a (O8:H28) and Stx2b (O146:H21). In four of the strains, we found three Stx subtypes that are not included in the current taxonomy. Stx2h (O170:H18) was identified in a Canadian sprout isolate; this subtype has only previously been reported in STEC from Tibetan Marmots. Stx2o (O85:H1) was identified in a clinical isolate. Finally, Stx2j (O158:H23 and O33:H14) was found in lettuce and clinical isolates. The results of this study expand the number of known Stx subtypes, the range of STEC serotypes, and isolation sources in which they may be found. The presence of the Stx2j and Stx2o in clinical isolates of STEC indicates that strains carrying these variants are potential human pathogens.

The presence of clusters in units with a high incidence of candidemia suggests the need for the prevention of candidemia. We analyzed the percentage of patients involved in clusters and its evolution over a large period of time in a tertiary hospital. We studied 432 patients admitted to Gregorio Marañón Hospital with candidemia caused by Candida albicans ( n = 276) or Candida parapsilosis ( n = 156) between January 2007 and December 2014. Incident isolates were genotyped. A cluster was defined as a group of ≥2 patients infected by an identical genotype; we considered clusters to be "tracking clusters" when the patients involved in the cluster were admitted to the same ward within a period of 24 months. The study period was split into two periods, 2007 to 2010 (period 1) and 2011 to 2014 (period 2). The number of episodes of C. albicans and C. parapsilosis candidemia ( n = 262 versus n = 170, respectively), the mean incidence (1.62 versus 1.36 episodes per 1,000 admissions, respectively), and the percentage of episodes caused by clusters (overall clusters [40% versus 12%] and tracking clusters [18% versus 3%], respectively) were significantly lower in period 2 than in period 1. Linear regression analysis showed a positive correlation between the overall number of episodes of candidemia and episodes caused by clusters ( r 2 = 0.89). We found a reduction in the number of episodes of candidemia caused by C. albicans and C. parapsilosis and a decrease in the percentage of episodes caused by clusters over time. Interestingly, the reduction was accompanied by the implementation of a campaign to reduce the number of catheter-related infections., (Copyright © 2018 American Society for Microbiology.)

Genotyping of Candida albicans strains causing candidemia can uncover the presence of endemic genotypes in the hospital. Using a highly reproducible and discriminatory microsatellite marker panel, we studied the genetic diversity of 217 C. albicans isolates from the blood cultures of 202 patients with candidemia (from January 2007 to December 2011). Each isolate represented 1 candidemia episode. Multiple episodes were defined as the isolation of C. albicans in further blood cultures taken ≥7 days after the last isolation in blood culture. Of the 202 patients, 188 had 1 episode, 13 had 2 episodes, and 1 had 3 episodes. Identical genotypes showed the same alleles for all 6 markers. The genotypes causing both episodes were identical in most patients with 2 episodes (11/13; 84.6%). In contrast, 2 different genotypes were found in the patient with 3 episodes, one causing the first and second episodes and the other causing the third episode (isolated 6 months later). We found marked genetic diversity in 174 different genotypes: 155 were unique, and 19 were endemic and formed 19 clusters (2 to 6 patients per cluster). Up to 25% of the patients were infected by endemic genotypes that infected 2 or more different patients. Some of these endemic genotypes were found in the same unit of the hospital, mainly neonatology, whereas others infected patients in different wards.

We prospectively determined the antifungal susceptibility of yeast isolates causing fungemia using the Etest on direct blood samples (195 prospectively collected and 133 laboratory prepared). We compared the Etest direct (24 h of incubation) with CLSI M27-A3 and the standard Etest methodologies for fluconazole, voriconazole, posaconazole, isavuconazole, caspofungin, and amphotericin B. Strains were classified as susceptible, resistant, or nonsusceptible using CLSI breakpoints (voriconazole breakpoints were used for posaconazole and isavuconazole). Categorical errors between Etest direct and CLSI M27-A3 for azoles were mostly minor. No errors were detected for caspofungin, and high percentages of major errors were detected for amphotericin B. For the azoles, false susceptibility (very major errors) was found in only two (0.6%) isolates (Candida tropicalis and C. glabrata). False resistance (major errors) was detected in 46 (14%) isolates for the three azoles (in 23 [7%] after excluding posaconazole). Etest direct of posaconazole yielded a higher number of major errors than the remaining azoles, especially for C. glabrata, Candida spp., and other yeasts. Excluding C. glabrata, Candida spp., and other yeasts, the remaining species did not yield major errors. Etest direct for fluconazole, voriconazole, isavuconazole, and caspofungin shows potential as an alternative to the CLSI M27-A3 procedure for performing rapid antifungal susceptibility tests on yeast isolates from patients with fungemia. Etest direct is a useful tool to screen for the presence of azole-resistant and caspofungin-nonsusceptible strains.

Enterococcus faecium has emerged as an important nosocomial pathogen worldwide, and this trend has been associated with the dissemination of a genetic lineage designated clonal cluster 17 (CC17). Enterococcal isolates were collected prospectively (2006 to 2008) from 32 hospitals in Colombia, Ecuador, Perú, and Venezuela and subjected to antimicrobial susceptibility testing. Genotyping was performed with all vancomycin-resistant E. faecium (VREfm) isolates by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. All VREfm isolates were evaluated for the presence of 16 putative virulence genes (14 fms genes, the esp gene of E. faecium [espEfm], and the hyl gene of E. faecium [hylEfm]) and plasmids carrying the fms20-fms21 (pilA), hylEfm, and vanA genes. Of 723 enterococcal isolates recovered, E. faecalis was the most common (78%). Vancomycin resistance was detected in 6% of the isolates (74% of which were E. faecium). Eleven distinct PFGE types were found among the VREfm isolates, with most belonging to sequence types 412 and 18. The ebpAEfm-ebpBEfm-ebpCEfm (pilB) and fms11-fms19-fms16 clusters were detected in all VREfm isolates from the region, whereas espEfm and hylEfm were detected in 69% and 23% of the isolates, respectively. The fms20-fms21 (pilA) cluster, which encodes a putative pilus-like protein, was found on plasmids from almost all VREfm isolates and was sometimes found to coexist with hylEfm and the vanA gene cluster. The population genetics of VREfm in South America appear to resemble those of such strains in the United States in the early years of the CC17 epidemic. The overwhelming presence of plasmids encoding putative virulence factors and vanA genes suggests that E. faecium from the CC17 genogroup may disseminate in the region in the coming years.