Next-generation sequencing for typing and detection of resistance genes: performance of a new commercial method during an outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli.

Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131) Escherichia coli infections in a nursing home in The Netherlands. The assay was performed on 56 extended-spectrum-beta-lactamase (ESBL) E. coli isolates collected during 2 prevalence surveys (March and May 2013). Typing results were compared to those of amplified fragment length polymorphism (AFLP), whereby we visually assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP. A microarray was considered the gold standard for detection of resistance genes. AFLP identified a large cluster of 31 indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree showed that all isolates of this outbreak cluster were strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. The BioDetection assay detected ESBL genes in all but 1 isolate (sensitivity, 98%) but was unable to discriminate between ESBL and non-ESBL TEM and SHV beta-lactamases or to specify CTX-M genes by group. The performance of the hospital-acquired infection (HAI) BioDetection System for typing of E. coli isolates compared well with the results of AFLP. Its performance with larger collections from different locations, and for typing of other species, was not evaluated and needs further study.

Changes in the bovine teat canal during the nonlactating period and early lactation, as measured by teat canal impressions.

Changes in dimensions of impressions of the lumen of the teat canals of 13 cows were examined at 17 intervals during the nonlactating period and early lactation. Impressions were made of teats of 2 diagonally opposed quarters of each cow, using dental impression material. Impression length was measured and cross sections of the impressions at the proximal (distal to Furstenburg rosette), distal (proximal to the teat orifice), and middle (midway between the 2), portions of the teat canal were prepared. Cross sections were photographed and enlarged, and circumference and area were determined by use of planimetry. Effects of making repeated impressions during the nonlactating period and early lactation on new infection rates and somatic cell counts were also assessed. Mean length of teat canal impressions decreased between days 0 and 3 of involution and during the prepartum periods. Depending on the level from which they were taken, cross-sectional areas of impressions tended to increase or increased significantly during the period of involution and again in the prepartum period. Significant changes in cross-sectional area were not observed during early lactation. Changes in circumference of proximal, middle, and distal cross sections followed trends similar to area measurements, but were more variable and differences were less statistically significant. On the basis of our findings, we suggest that heightened susceptibility to new infection during mammary involution and the prepartum period may be attributable, in part, to changes in the patency of the teat canal. Making impressions repeatedly throughout the nonlactating period and early lactation did not affect the number of new intramammary infections.