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6. Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar Enteritidis

Author

den Bakker, Henk C., Allard, Marc W., Bopp, Dianna, Brown, Eric W., Fontana, John, Iqbal, Zamin, Kinney, Aristea, Limberger, Ronald, Musser, Kimberlee A., Shudt, Matthew, Strain, Errol, Wiedmann, Martin, and Wolfgang, William J.

Subjects
Nucleotide sequencing -- Genetic aspects -- Analysis, Genomics -- Genetic aspects -- Analysis, DNA sequencing -- Genetic aspects -- Analysis, Genomes -- Genetic aspects -- Analysis, Public health -- Analysis, Salmonella -- Analysis, Health
Abstract

For genetically monomorphic bacteria, current typing methods often prove inadequate for outbreak detection, trace back, and identification of transmission routes. Some of these bacteria, such as Salmonella enterica serovar Enteritidis, [...]

Published
2014
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10. Escherichia coli O157:H7 Cluster Associated With Deer Harvested at a Single Wildlife Hunting Area, Oregon, 2017.

Author

Ladd-Wilson, Stephen G., Morey, Karim, Turpen, Lauren, DeMarco, Kara, Van Der Veen, Gary, Fontana, John L., Dannenhoffer, Robert L., Tenney, Kristina, Kutumbaka, Kirthi K., Samadpour, Mansour, and Cieslak, Paul R.

Subjects
ESCHERICHIA coli, SEQUENCE analysis, SINGLE nucleotide polymorphisms, INTERVIEWING, POPULATION geography, GENE expression, ESCHERICHIA coli diseases, HUNTING, CASE studies, DESCRIPTIVE statistics, EPIDEMICS, FOOD handling, MAMMALS
Abstract

The Oregon Health Authority routinely investigates clusters of reportable enteric diseases identified by whole-genome sequencing. While investigating 2 cases of Escherichia coli O157:H7 in 2019, in which both patients were exposed to the same home-processed "jerky" and clinical isolates matched within 2 single nucleotide polymorphisms (SNPs), we discovered, by searching the National Library of Medicine's National Center for Biotechnology Information website, 3 other cases of E coli O157:H7 from 3 Oregon counties—Tillamook, Umatilla, and Douglas—whose clinical isolates were within 9 SNPs of the 2 initial matched cases. We analyzed interview data for 3 case patients and followed up with additional hypothesis-generating questions. Onset of illness for the Tillamook, Umatilla, and Douglas county cases were October 7, 2017, October 27, 2017, and April 30, 2018, respectively. The median age of the 5 case patients was 16 years. Parents of 2 of the 5 case patients, each from a different county, had harvested deer approximately 20 miles from each other in the same Douglas County wildlife hunting unit in late September 2017. The case from Umatilla County was lost to follow-up. Although it is well documented that deer are a viable and substantial reservoir of E coli O157:H7, to our knowledge, this is the first time that venison from a common wildlife hunting unit was found to be associated with a cluster of illnesses. This finding suggests a geographic nidus for E coli O157:H7. We recommend routinely asking about wildlife hunting units when developing exposure hypotheses involving potential venison-associated clusters. [ABSTRACT FROM AUTHOR]

Published
2022
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14. Genetic Diversity of Non-O157 Shiga Toxin-Producing Escherichia coli Recovered From Patients in Michigan and Connecticut.

Author

Blankenship, Heather M., Mosci, Rebekah E., Phan, Quyen, Fontana, John, Rudrik, James. T., and Manning, Shannon D.

Subjects
ESCHERICHIA coli, ARITHMETIC mean, FOOD pathogens, SEROTYPING, NUCLEOTIDE sequencing, LEPTOSPIRA interrogans, ENTEROBACTERIACEAE, RIBOSOMAL DNA
Abstract

Shiga toxin-producing Escherichia coli (STEC) are important foodborne pathogens and non-O157 serotypes have been gradually increasing in frequency. The non-O157 STEC population is diverse and is often characterized using serotyping and/or multilocus sequence typing (MLST). Although spacers within clustered regularly interspaced repeat (CRISPR) regions were shown to comprise horizontally acquired DNA elements, this region does not actively acquire spacers in STEC. Hence, it is useful for further characterizing non-O157 STEC and examining relationships between strains. Our study goal was to evaluate the genetic relatedness of 41 clinical non-O157 isolates identified in Michigan between 2001 and 2005 while comparing to 114 isolates from Connecticut during an overlapping time period. Whole genome sequencing (WGS) was performed, and sequences were extracted for serotyping, MLST and CRISPR analysis. Phylogenetic analysis of MLST and CRISPR data was performed using the Neighbor joining and unweighted pair group method with arithmetic mean (UPGMA) algorithms, respectively. In all, 29 serogroups were identified; eight were unique to Michigan and 13 to Connecticut. "Big-six" serogroup frequencies were similar by state (Michigan: 73.2%, Connecticut: 81.6%), though STEC O121 was not found in Michigan. The distribution of sequence types (STs) and CRISPR profiles was also similar across states. Interestingly, big-six serogroups such as O103 and O26, grouped into different STs located on distinct branches of the phylogeny, further confirming that serotyping alone is not adequate for evaluating strain relatedness. Comparatively, the CRISPR analysis identified 361 unique spacers that grouped into 80 different CRISPR profiles. CRISPR spacers 231 and 317 were isolated from 79.2% (n = 118) and 59.1% (n = 88) of strains, respectively, regardless of serogroup and ST. Spacer profiles clustered according to the MLST analysis, though some discrepancies were noted. Indeed, use of both MLST and CRISPR typing enhanced the discriminatory power when compared to the use of each tool separately. These data highlight the genetic diversity of clinical STEC from different locations and show that CRISPR profiling can be used alongside MLST to discriminate related strains. Use of targeted sequencing approaches are particularly helpful for sites without WGS capabilities and can help define which strains require additional characterization using more discriminatory methods. [ABSTRACT FROM AUTHOR]

Published
2020
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16. Microsoft: Cloud revenue to hit in a couple years; Microsoft waiting for business spending to come back on clients, servers

Author

Fontana, John

Subjects
Microsoft Corp. -- Planning, Computer software industry -- Planning, Company business planning, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Microsoft plans to invest heavily in its cloud platform but expects to see little revenue for two to three years, Bob Muglia, the president of the server [...]

Published
2010

17. Active Directory: 10 years old and thinking cloud; Microsoft eyes new frontiers for directory technology

Author

Fontana, John

Subjects
Microsoft Corp. -- Services, Computer software industry -- Services, Directories -- Technology application, Technology application, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Ten years ago today, Microsoft released its Active Directory technology to skepticism that it could build an infrastructure technology to anchor user management and access control. Now [...]

Published
2010

18. Burton Group identity/privacy expert jumping to security firm; Burton Group's Gerry Gebel joining Axiomatics to set up U.S. operations

Author

Fontana, John

Subjects
Axiomatics Corp. -- Officials and employees, Executives -- Appointments, resignations and dismissals, Computers -- Services, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Identity and privacy expert Gerry Gebel is leaving the Burton Group to take a position leading security firm Axiomatics's expansion into the U.S. market. Gebel, who is [...]

Published
2010

19. Computer hacking charge leveled against disgraced Tour de France cyclist

Author

Fontana, John

Subjects
Computer hackers -- Cases, Company legal issue, Hacker, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Cyclist Floyd Landis, stripped of his 2006 Tour de France title after a positive drug test, is now being labeled a computer hacker by France, which has [...]

Published
2010

20. Symphony 3.0 beta signals IBM attack on Office; Lotus starting three-pronged attack on Microsoft

Author

Fontana, John

Subjects
Business application suite, IBM Lotus Symphony 3.0 (Business application suite) -- Product information, Computer software industry -- Product information, Integrated software -- Product information, International Business Machines Corp. IBM Collaboration Solutions -- Product information
Abstract

Byline: John Fontana IBM/Lotus took another stab at Microsoft Office, releasing a beta 2 version of Symphony 3.0, its free suite of productivity applications. Released Thursday, the beta is the [...]

Published
2010

21. Microsoft's Patch Tuesday to be all about required reboots; Microsoft shops, get ready to restart your servers for these Windows patches

Author

Fontana, John

Subjects
Microsoft Corp. -- Services, Computer software industry -- Services, Company distribution practices, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Here are two keys words for Microsoft Windows shops to remember come this Patch Tuesday: 'six' and 'restart.' Six is the number of a critical bulletins Microsoft [...]

Published
2010

22. Microsoft-funded CodePlex Foundation gets first exec; Microsoft-funded CodePlex lands Paula Hunter as executive director who has held leadership roles at Open Source Development Labs (OSDL) and United Linux

Author

Fontana, John

Subjects
Foundations (Endowments) -- Officials and employees, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana The CodePlex Foundation, an organization funded and created by Microsoft, Wednesday named its first executive director, but still has not begun to form its permanent board as [...]

Published
2010

23. Microsoft juices Visual Studio with secure coding tools; Microsoft security templates, tools aimed at secure code

Author

Fontana, John

Subjects
Microsoft Corp. -- Product enhancement, Computer software industry -- Product introduction -- Safety and security measures -- Product enhancement, Program development software -- Product introduction -- Safety and security measures -- Product enhancement, Source code -- Authorship, Application installation/distribution software, Application development software, Product enhancement, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Microsoft Tuesday said it will deepen ties between its Visual Studio development tools and the secure applications development processes first developed inside the company and now available [...]

Published
2010

24. Win 7 business sales weak, but uptick expected; Microsoft says adoption should come later this year, last 24 to 36 months

Author

Fontana, John

Subjects
Company earnings/profit, Microsoft Windows 7 (Operating system) -- Consumption data, Computer software industry -- Company sales and earnings, Microsoft Corp. -- Company sales and earnings
Abstract

Byline: John Fontana Microsoft Thursday said 60 million Windows 7 licenses have been sold in the past six months, but most of those have been from the consumer side and [...]

Published
2010

25. Apple iPad could give Microsoft fits; iPad tablet computer could impact Microsoft's mobile, tablet and software strategies, industry watchers say

Author

Fontana, John

Subjects
Microsoft Corp. -- Public opinion, Computer software industry -- Public opinion, Computers, High technology industry, Telecommunications industry, Apple iPad (Tablet computer) -- Public opinion
Abstract

Byline: John Fontana Microsoft shouldn't be shaking in its boots after this week's unveiling of the Apple iPad, but the tablet computer could give the software giant fits in the [...]

Published
2010

26. SharePoint 2010 overkill for some, Forrester says; Microsoft's SharePoint 2010 server is growing up but maybe too far out for those not already using software

Author

Fontana, John

Subjects
Microsoft Corp. -- Product information, Computer software industry -- Product information, Work groups -- Computer programs, Workgroup software, Computers, High technology industry, Telecommunications industry, Microsoft SharePoint 2010 (Workgroup software) -- Product information
Abstract

Byline: John Fontana Despite platform improvements coming in Microsoft's SharePoint 2010 server, the software is likely to be overkill for users seeking to meet isolated and specific requirements, according to [...]

Published
2010

27. Free software embraced by CIOs; Survey shows rise in use of free software such as OpenOffice, Google Docs

Author

Fontana, John

Subjects
Public utilities -- Computer programs, Chief information officers -- Surveys, Public utilities software, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Free software is becoming increasingly popular with CIOs, as nearly two-thirds of companies are using it on their desktops and for applications, according to a new survey. [...]

Published
2010

28. Lotus bets the house on open collaboration plan; Lotus Project Vulcan is an effort to weave collaboration, BI, analytics into an open architecture

Author

Fontana, John

Subjects
International Business Machines Corp. -- Product information, Spreadsheets -- Product information, Computer industry -- Product information, Spreadsheet add-on, Microcomputer industry, Computer industry, Spreadsheet software, Computers, High technology industry, Telecommunications industry, Lotus (Spreadsheet software) -- Product information
Abstract

Byline: John Fontana ORLANDO - IBM/Lotus is juicing its collaboration tools with a dose of analytics and cloud-based integration with the belief it can redefine the technology, meet the needs [...]

Published
2010

29. IBM/Lotus upgrades set for Notes/Domino, Sametime, Connections and LotusLive; IBM/Lotus to upgrade Notes/Domino, Sametime, Connections and LotusLive

Author

Fontana, John

Subjects
Product enhancement, Computer software industry -- Product enhancement, International Business Machines Corp. IBM Collaboration Solutions -- Product enhancement
Abstract

Byline: John Fontana ORLANDO -- IBM/Lotus is rolling out a set of incremental upgrades across its product lines over the coming 12 month, including new capabilities in Notes/Domino, Sametime, Connections [...]

Published
2010

30. Lotus sets off on 'Vulcanizing' next-gen collaboration; Project Vulcan concept about analytics, integration

Author

Fontana, John

Subjects
Company business planning, Computer software industry -- Planning, International Business Machines Corp. IBM Collaboration Solutions -- Planning
Abstract

Byline: John Fontana ORLANDO -- IBM/Lotus Monday hinted at its collaboration future by unveiling an ambitious plan called Project Vulcan that exists in concept only but is aimed at a [...]

Published
2010

31. IBM plans Blackberry, iPhone, Android applications; IBM takes aim at Blackberry iPhone, Android

Author

Fontana, John

Subjects
International Business Machines Corp. -- Planning, Computer industry -- Planning, Company business planning, Microcomputer industry, Computer industry, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Orlando - IBM is going into the mobile phone business with plans to resell RIM's Blackberry mobile devices pre-loaded with IBM's collaboration software. The effort is part [...]

Published
2010

32. Lotus to set road map for free productivity suite; Lotus Symphony gets support for OpenOffice 3.x

Author

Fontana, John

Subjects
Business application suite, IBM Lotus Symphony (Business application suite) -- Product development, Computer software industry -- Product development, Integrated software -- Product development, International Business Machines Corp. IBM Collaboration Solutions -- Product development
Abstract

Byline: John Fontana IBM/Lotus will ship the next version of its free Symphony productivity suite, code-named Vienna, before the end of June and then follow it up with two more [...]

Published
2010

33. Microsoft, Lotus throw punches; Annual Lotusphere conference rallying point for Lotus, Microsoft battle

Author

Fontana, John

Subjects
Lotusphere, Computer industry -- Conferences, meetings and seminars, Microcomputer industry, Computer industry, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Like clockwork, IBM/Lotus and Microsoft are throwing punches at each other's product lineup just as Lotusphere and its near 7,000 attendees are set to kickoff a weeklong [...]

Published
2010

34. Microsoft's Ballmer: We're staying in China; Google threats not being followed by Microsoft, though Ballmer does call for IP protection in China

Author

Fontana, John

Subjects
Google Inc. -- Investigations, Microsoft Corp. -- Planning, Computer software industry -- Planning, Information services industry -- Investigations, Computer crimes -- Investigations, Information services -- Investigations, Company legal issue, Company business planning, Computer crime, Information services industry, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Microsoft CEO Steve Ballmer said the company is staying in China even though rival Google is talking about pulling out following a cyber attack on its systems. [...]

Published
2010

35. Lotus prepping a deep, broad cloud strategy; IBM Lotus plans Lotus Next and other software improvements

Author

Fontana, John

Subjects
Company business planning, Computer software industry -- Planning, International Business Machines Corp. IBM Collaboration Solutions -- Planning
Abstract

Byline: John Fontana IBM/Lotus will use next week's Lotusphere conference to show its customers a long-term collaboration and cloud strategy that stretches well into the future and across its portfolio [...]

Published
2010

36. Ballmer took Microsoft reins 10 years ago with focus on Internet; Cloud strategy fits under CEO's original promises

Author

Fontana, John

Subjects
Microsoft Corp. -- Officials and employees, Computer software industry -- Officials and employees, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Ten years ago on Jan. 13, 2000, Microsoft's Bill Gates turned over the CEO reins to Steve Ballmer, who emphasized then that the Internet would be the [...]

Published
2010

37. VMware buying Yahoo's Zimbra open source messaging business; Yahoo sells off its Zimbra open source messaging business

Author

Fontana, John

Subjects
VMware Inc. -- Mergers, acquisitions and divestments, Computer software industry -- Mergers, acquisitions and divestments, Company acquisition/merger, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana VMware Tuesday said it was buying Yahoo's Zimbra open source messaging business as a way to bolster its evolving collaboration platform. Terms of the deal were not [...]

Published
2010

38. IBM shuffles Lotus executives, creates new biz units; IBM moves come less than a week before annual Lotusphere conference

Author

Fontana, John

Subjects
Company organization, Company restructuring/company reorganization, Computer software industry -- Reorganization and restructuring, International Business Machines Corp. IBM Collaboration Solutions -- Reorganization and restructuring
Abstract

Byline: John Fontana IBM Tuesday reorganized the structure of its Software Group, including moving Lotus General Manager Bob Picciano back to a leadership role in sales, inserting Alistair Rennie as [...]

Published
2010

39. Facebook joins Apache Foundation; Social networking giant looking to help open source group thrive

Author

Fontana, John

Subjects
Facebook Inc. -- Membership, Computer services industry -- Membership, Computer services industry, Computers, High technology industry, Telecommunications industry, The Apache Software Foundation -- Services
Abstract

Byline: John Fontana Facebook Tuesday joined the Apache Software Foundation as a Gold sponsor, looking to cement its commitment to open source and pledging to help drive the group into [...]

Published
2010

40. Microsoft admits mobile missteps, but fights on; Microsoft mobile chief Robbie Bach hints that Win Mobile 7 is home-run hitter

Author

Fontana, John

Subjects
Microsoft Corp. -- Officials and employees -- Marketing, Computer software industry -- Officials and employees -- Marketing, Smart phones -- Evaluation -- Marketing, Company marketing practices, Company business management, Smart phone, Computers, High technology industry, Telecommunications industry, Microsoft Windows Mobile 7 (Smart phone) -- Evaluation -- Marketing
Abstract

Byline: John Fontana Microsoft doesn't have a business model problem in the mobile market, but its phones are skewed toward business users at the expense of consumers and are not [...]

Published
2010

41. Novell, MSI team on first SUSE Moblin-based netbook; PC features SUSE enhanced version of mobile Linux OS

Author

Fontana, John

Subjects
Suse Inc. -- Alliances and partnerships -- Services, Novell Inc. -- Alliances and partnerships -- Product enhancement, MSI Corp. -- Alliances and partnerships -- Product enhancement, Notebook computers -- Product enhancement, Computer software industry -- Alliances and partnerships -- Product enhancement, Laptop computers -- Product enhancement, Linux (Operating system) -- Product enhancement -- Usage, Linux (Operating system), Laptop/portable computer, Product enhancement, Computers, High technology industry, Telecommunications industry, SUSE Moblin (Laptop/portable computer) -- Product enhancement
Abstract

Byline: John Fontana MSI and Novell will ship in February the first netbook based on the SUSE Moblin open-source Linux operating system. The pair is showing the device at this [...]

Published
2010

42. Microsoft Office coming in ad-supported version; Microsoft will offer virtualized version of Office also available for test drive

Author

Fontana, John

Subjects
Microsoft Corp. -- Marketing, Computer software industry -- Marketing, Company marketing practices, Computers, High technology industry, Telecommunications industry
Abstract

Byline: John Fontana Microsoft Tuesday said it would include an advertising-supported version of Office 2010 on new PCs as well as offer users a virtualized version that stream Office to [...]

Published
2010

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