Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains.

A curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible (https://ngstar.canada.ca). The N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA, mtrR, porB, ponA, gyrA, parC, and 23S rRNA) associated with resistance to ß-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entire penA sequence, combining the historical nomenclature for penA types I to XXXVIII with novel nucleotide sequence designations; the full mtrR sequence and a portion of its promoter region; portions of ponA, porB, gyrA, and parC; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) (n = 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs (n = 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 (n = 100; 13.0%), ST-42 and ST-91 (n = 45; 5.9%), ST-64 (n = 44; 5.72%), and ST-139 (n = 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 (n = 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 (n = 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 (n = 196; 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 (n = 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistant N. gonorrhoeae strains.

Risk factors for sporadic domestically acquired Salmonella serovar Enteritidis infections: a case-control study in Ontario, Canada, 2011.

In Ontario, Canada, the number of Salmonella Enteritidis (SE) cases increased over the years 2005-2010. A population-based case-control study was undertaken from January to August 2011 for the purpose of identifying risk factors for acquiring illness due to SE within Ontario. A total of 199 cases and 241 controls were enrolled. After adjustment for confounders, consuming any poultry meat [adjusted odds ratio (aOR) 2·24, 95% confidence interval (CI) 1·31-3·83], processed chicken (aOR 3·32, 95% CI 1·26-8·76) and not washing hands following handling of raw eggs (OR 2·82, 95% CI 1·48-5·37) were significantly associated with SE infection. The population attributable fraction was 46% for any poultry meat consumption and 10% for processed chicken. Poultry meat continues to be identified as a risk factor for SE illness. Control of SE at source, as well as proper food handling practices, are required to reduce the number of SE cases.

Subtyping of a large collection of historical Listeria monocytogenes strains from Ontario, Canada, by an improved multilocus variable-number tandem-repeat analysis (MLVA).

Listeria monocytogenes is responsible for severe and often fatal food-borne infections in humans. A collection of 2,421 L. monocytogenes isolates originating from Ontario's food chain between 1993 and 2010, along with Ontario clinical isolates collected from 2004 to 2010, was characterized using an improved multilocus variable-number tandem-repeat analysis (MLVA). The MLVA method was established based on eight primer pairs targeting seven variable-number tandem-repeat (VNTR) loci in two 4-plex fluorescent PCRs. Diversity indices and amplification rates of the individual VNTR loci ranged from 0.38 to 0.92 and from 0.64 to 0.99, respectively. MLVA types and pulsed-field gel electrophoresis (PFGE) patterns were compared using Comparative Partitions analysis involving 336 clinical and 99 food and environmental isolates. The analysis yielded Simpson's diversity index values of 0.998 and 0.992 for MLVA and PFGE, respectively, and adjusted Wallace coefficients of 0.318 when MLVA was used as a primary subtyping method and 0.088 when PFGE was a primary typing method. Statistical data analysis using BioNumerics allowed for identification of at least 8 predominant and persistent L. monocytogenes MLVA types in Ontario's food chain. The MLVA method correctly clustered epidemiologically related outbreak strains and separated unrelated strains in a subset analysis. An MLVA database was established for the 2,421 L. monocytogenes isolates, which allows for comparison of data among historical and new isolates of different sources. The subtyping method coupled with the MLVA database will help in effective monitoring/prevention approaches to identify environmental contamination by pathogenic strains of L. monocytogenes and investigation of outbreaks.

Carbapenemase-producing Enterobacterales in hospital drains in Southern Ontario, Canada.

BACKGROUND: Hospital drains may be an important reservoir for carbapenemase-producing Enterobacterales (CPE). AIM: To determine prevalence of CPE in hospital drains exposed to inpatients with CPE, relatedness of drain and patient CPE, and risk factors for drain contamination. METHODS: Sink and shower drains in patient rooms and communal shower rooms exposed to 310 inpatients with CPE colonization/infection were cultured at 10 hospitals. Using short- and long-read whole-genome sequencing, inpatient and corresponding drain CPE were compared. Risk factors for drain contamination were assessed using multi-level modelling. FINDINGS: Of 1209 exposed patient room and communal shower room drains, 53 (4%) yielded 62 CPE isolates in seven (70%) hospitals. Of 49 CPE isolates in patient room drains, four (8%) were linked to prior room occupants. Linked drain/room occupant pairs included Citrobacter freundii ST18 isolates separated by eight single nucleotide variants (SNVs), related blaKPC-containing IncN3-type plasmids (different species), related blaKPC-3-containing IncN-type plasmids (different species), and related blaOXA-48-containing IncL/M-type plasmids (different species). In one hospital, drain isolates from eight rooms on two units were Enterobacter hormaechei separated by 0-6 SNVs. Shower drains were more likely to be CPE-contaminated than hand hygiene (odds ratio: 3.45; 95% confidence interval: 1.66-7.16) or patient-use (13.0; 4.29-39.1) sink drains. Hand hygiene sink drains were more likely to be CPE-contaminated than patient-use sink drains (3.75; 1.17-12.0). CONCLUSION: Drain contamination was uncommon but widely dispersed. Drain CPE unrelated to patient exposure suggests contamination by undetected colonized patients or retrograde (drain-to-drain) contamination. Drain types had different contamination risks.

Representing clinical guidelines in GLIF: individual and collaborative expertise.

OBJECTIVE: An evaluation of the cognitive processes used in the translation of a clinical guideline from text into an encoded form so that it can be shared among medical institutions. DESIGN: A comparative study at three sites regarding the generation of individual and collaborative representations of a guideline for the management of encephalopathy using the GuideLine Interchange Format (GLIF) developed by members of the InterMed Collaboratory. MEASUREMENTS: Using theories and methods of cognitive science, the study involves a detailed analysis of the cognitive processes used in generating representations in GLIF. The resulting process-outcome measures are used to compare subjects with various types of computer science or clinical expertise and from different institutions. RESULTS: Consistent with prior studies of text comprehension and expertise, the variability in strategies was found to be dependent on the degree of prior experience and knowledge of the domain. Differing both in content and structure, the representations developed by physicians were found to have additional information and organization not explicitly stated in the guidelines, reflecting the physicians' understanding of the underlying pathophysiology. The computer scientists developed more literal representations of the guidelines; addition were mostly limited to specifications mandated by the logic of GLIF itself. Collaboration between physicians and computer scientists resulted in consistent representations that were more than the sum of the separate parts, in that both domain-specific knowledge of medicine and generic knowledge of guideline structure were seamlessly integrated. CONCLUSION: Because of the variable construction of guideline representations, understanding the processes and limitations involved in their generation is important in developing strategies to construct shared representations that are both accurate and efficient. The encoded guidelines developed by teams that include both clinicians and experts in computer-based representations are preferable to those developed by individuals of either type working alone.

Evaluation of humoral immune responses in cattle grazing endophyte-infected or endophyte-free fescue.

Anecdotal reports suggest cattle with fescue toxicosis may not respond to vaccination and thus, experience increased incidence of Bovine Respiratory Disease Complex (BRDC) when shipped to feedlots. Fescue toxicosis causes hypoprolactemia in cattle. Hypoprolactemia decreases humoral immune responses in mice. Therefore, a study was conducted to compare the magnitude of primary and secondary humoral immune responses against specific antigens in cattle grazing endophyte-infected or endophyte-free fescue. Angus steers were blocked by weight and allocated into four groups. Two groups grazed endophyte-infected (EI) fescue and the other two groups grazed endophyte-free (EF) fescue. All steers were injected IM on d 0 and 21 with lysozyme without adjuvant and concanavalin. A (Con A) with sheep red blood cells (SRBC) in incomplete adjuvant of Freund. Steers were bled on days 0, 21 and 35 post-vaccination. Average daily gains (ADG), alkaline phosphatase (ALP) activity, cholesterol concentrations, rectal temperatures, and serum prolactin concentrations were measured to confirm fescue toxicosis in steers grazing EI fescue. Antibodies to Con A and SRBC were determined by ELISA and hemagglutination assay, respectively. The ADG were decreased for the EI group during the first month. Rectal temperature were elevated and serum prolactin concentrations were decreased in the EI group. Cholesterol and ALP concentrations also were decreased in the EI group. Primary and secondary immune responses against Con A tended to be increased and were increased against SRBC in the EI group. Antibodies against lysozyme were not induced in either group. In conclusion, cattle grazing EI fescue mounted similar humoral immune responses to vaccination, despite hypoprolactemia, as cattle grazing EF fescue. Increases in bovine respiratory disease in cattle maintained on EI fescue probably is not associated with lack of humoral immune response to vaccination protocols as a result of fescue toxicosis.

Ascophyllum nodosum supplementation: a preharvest intervention for reducing Escherichia coli O157:H7 and Salmonella spp. in feedlot steers.

Ascophyllum nodosum (Tasco-14) decreased the prevalence of enterohemorrhagic Escherichia coli (EHEC) O157:H7 in animals fed prior to harvest. Tasco-14 was supplemented on a 2% dry matter basis 14 days prior to harvest to determine its effects on EHEC and Salmonella spp. prevalence. Two hundred mixed crossbred steers and heifers (Bos indicus x Bos taurus), in a large commercial finishing facility, served as experimental units. Treatment (TRT, n = 100) animals received a steam-rolled corn-based diet containing 2% Tasco-14 on a dry matter basis, and control (CON, n = 100) animals received only the steam-rolled corn-based diet. Hide swabs and fecal samples were obtained for EHEC and Salmonella spp. evaluations. Animals were sampled 1 day prior to (d - 1) the feeding of Tasco-14 and immediately following exsanguinations. The prevalence of EHEC O157 on hide swabs and in fecal samples (P = 0.0001 and P < 0.0001, respectively) and the prevalence of EHEC O157:H7 on hide swabs and in fecal samples (P < 0.0001 and P < 0.0001, respectively) was reduced by 33 and 36% from d - 1 levels on TRT hide swabs and by 9 and 11% in TRT fecal samples. The prevalence of EHEC O157 and EHEC O157:H7 was reduced by 33 and 36% from d - 1 levels on TRT hide swabs and by 9 and 11% in TRT fecal samples. The prevalence of Salmonella spp. on hide swabs did not change for TRT animals (P = 0.64). CON animals showed an increase in Salmonella spp. prevalence (P < 0.0001) from d - 1 feeding levels on hide swabs. The prevalence of Salmonella spp. increased in both TRT and CON fecal samples when compared to d - 1 levels (P = 0.002). However, TRT samples exhibited a lower (P < 0.05) postfeeding prevalence of Salmonella spp. in fecal samples than did CON samples. Results from this study indicate that 2% Tasco-14 supplementation in feedlot cattle diets reduces EHEC O157 and EHEC O157:H7 prevalence on hide swabs and in fecal samples and may suppress increases in Salmonella spp.

Toward a framework for computer-mediated collaborative design in medical informatics.

The development and implementation of enabling tools and methods that provide ready access to knowledge and information are among the central goals of medical informatics. The need for multi-institutional collaboration in the development of such tools and methods is increasingly being recognized. Collaboration involves communication, which typically involves individuals who work together at the same location. With the evolution of electronic modalities for communication, we seek to understand the role that such technologies can play in supporting collaboration, especially when the participants are geographically separated. Using the InterMed Collaboratory as a subject of study, we have analyzed their activities as an exercise in computer- and network-mediated collaborative design. We report on the cognitive, sociocultural, and logistical issues encountered when scientists from diverse organizations and backgrounds use communications technologies while designing and implementing shared products. Results demonstrate that it is important to match carefully the content with the mode of communication, identifying, for example, suitable uses of E-mail, conference calls, and face-to-face meetings. The special role of leaders in guiding and facilitating the group activities can also be seen, regardless of the communication setting in which the interactions occur. Most important is the proper use of technology to support the evolution of a shared vision of group goals and methods, an element that is clearly necessary before successful collaborative designs can proceed.

Influence of dietary aluminum on nutrient utilization in ruminants.

Aluminum enters the ruminant diet through plant-accumulated Al, soil ingestion, feed and water contamination, and as an additive to alter metabolism or absorption of other minerals. Ingested Al is usually poorly absorbed and has been shown to depress utilization of dietary F and P, largely due to the formation of insoluble, nonabsorbable Al complexes. Aluminum has been suggested for use in alleviating F toxicosis in ruminants. Increases in fecal F and decreases in dental lesions and bone F content have been observed by some researchers in response to dietary Al. The Al content of certain P supplements has been associated with poor P utilization. Levels of 1,450 ppm Al as AlCl3 in the diet of lambs lowered P absorption and resulted in a need for increased dietary P. It has been suggested that absorbed Al decreases P incorporation into DNA and RNA, with shifts of ATP to AMP and ADP. Aluminum administration has resulted in alterations in carbohydrate metabolism in rats and in parathyroid function in man. In sheep, 2,000 ppm dietary Al as AlCl3 depressed kidney Mg and plasma Mg and P concentrations. Sheep dosed via rumen cannula with 2,000 ppm Al as citrate, exhibited lower serum Mg and increased urinary Ca excretion. Steers dosed via rumen cannula with 4,000 ppm Al as Al2 (SO4)3 had lowered serum Mg values within 24 h.

Managing replacement stock within the environment of the south--plant, soil, and animal interactions: a review.

The South extends from the Atlantic Coast and the Gulf of Mexico north through Virginia and Kentucky and west to the 100th meridian, which extends through Texas and Oklahoma. The soils, environment, and range of adapted forage species offer many and varied opportunities for designing forage-livestock systems for rearing replacement stock. Anti-quality factors of concern when using forages for replacement stock include the presence of Acremonium coenophialum (Morgan-Jones and Gams) in tall fescue (Festuca arundinacea Schreb.), phytoestrogens potentially in several species of Trifolium and Medicago, toxins in some species of brush that contribute to infertility, and imbalances of several minerals including Ca, P, K, Fe, I, Zn, Na, Cu, and Se. Systems should be designed to provide appropriate quality and quantity of forage to produce reproductively active female animals of the desired weight and condition for breeding at the target age, usually 15 mo for beef and dairy heifers and 8 to 9 mo for ewe lambs. Systems generally require sequence grazing of two or more forage species or mixtures to provide extended or year-round grazing opportunities. Stockpiling of tall fescue in the Upper South and use of cool-season annuals in the Lower South extend grazing in autumn, winter, and early spring. Successful systems coordinate plant growth potential with changing animal forage requirements for both quantity and quality of forage to achieve optimum growth rates for replacement stock.