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Archive for the ‘Microbiology’ Category

Varicella vs. Monkeypox

Outbreaks of varicella and monkeypox in Africa are occasionally mistaken for “smallpox”   The following table was generated by an interactive tool in Gideon ( which allows users to generate custom charts that contrast clinical features, drug spectra or microbial phenotypes.




Outbreaks of Non-tubercuous Mycobacterial Infection in the United States

The following chronology of nosocomial mycobacteriosis outbreaks in the United States is abstracted from Gideon and the Gideon e-book series. [1,2] Primary references available on request.

1987 – An outbreak (17 cases) of Mycobacterium chelonae otitis media was caused by contaminated water used by an ENT practice in Louisiana.
1988 – An outbreak (8 cases) of foot infections due to Mycobacterium chelonae subspecies abscessus infections were associated with a jet injector used in a podiatric office.
1989 to 1990 – An outbreak (16 cases) of sputum colonization by Mycobacterium fortuitum was reported among patients on an alcoholism rehabilitation ward in Washington, D.C.
1991 (publication year) – An outbreak (6 cases) of Mycobacterium fortuitum infection in Washington was associated with contaminated electromyography needles.
1995 to 1996 – An outbreak (87 cases) of postinjection abscesses due to Mycobacterium abscessus in several states was ascribed to an adrenal cortex extract.
1998 – An outbreak (6 cases) of Mycobacterium mucogenicum bacteremia among bone marrow transplant and oncology patients in Minnesota was related to contaminated water.
1999 – An outbreak (10 cases) of intra- and periarticular Mycobacterium abscessus infection in Texas was caused by contaminated benzalkonium chloride used for injection.
2000 to 2001 – An outbreak (110 cases) of skin infections due to Mycobacterium fortuitum was caused by contaminated footbaths in California nail salons.
2001 – An outbreak of Mycobacterium chelonae keratitis in California was associated with laser in situ keratomileusis (LASIK).
2001 to 2002 – An outbreak of Mycobacterium simiae in a Texas hospital was related to contaminated tap water.
2002 – An outbreak (14 confirmed and 11 suspected cases) of soft tissue infections due to Mycobacterium abscessus followed injections of cosmetic substances administered by unlicensed practitioners in New York City.
2002 – An outbreak (115 cases or more) of cutaneous infection by Mycobacterium fortuitum was associated with a contaminated footbath in a nail salon in California.
2002 (publication year) – An outbreak (34 cases) of Mycobacterium chelonae soft tissue infection in California was associated with liposuction.
2002 to 2003 – An outbreak (4 cases) of Mycobacterium chelonae infection among patients undergoing rhytidectomies in New Jersey was caused by a contaminated methylene blue solution.
2003 – An outbreak (3 cases) of Mycobacterium goodii infection was associated with surgical implants in a Colorado hospital.
2004 – An outbreak (12 cases) among Americans of soft tissue infections caused by Mycobacterium abscessus following cosmetic surgery performed at various clinics in the Dominican Republic.
2004 – An outbreak (143 cases) of mycobacterial skin and soft tissue infection (presumed M. fortuitum) was reported among persons attending nail salons in California.
2008 – An outbreak (4 cases) of Mycobacterium mucogenicum bloodstream infections was reported among patients with sickle cell disease, in North Carolina.
2009 (publication year) – An outbreak (6 cases) of Mycobacterium chelonae infection was associated with a tattoo establishment.
2009 – An outbreak (2 cases, 1 confirmed) of Mycobacterium haemophilum skin infection was associated with a tattoo parlor in Washington State.
2011 (publication year) – An outbreak (3 cases) of Mycobacterium bolletii/M. massiliense furunculosis was associated with a nail salon in North Carolina.
2011 (publication year) – An outbreak of Mycobacterium abscessus infection was associated with outpatient rhytidectomies.
2011 – An outbreak (2 cases) of Mycobacterium haemophilum infection was reported among persons receiving tattoos in the Seattle, Washington region. {m 201108122444}
2011 (publication year) – An outbreak (11 cases) of Mycobacterium porcinum infection in a Texas hospital was related to contamination of drinking water.
2011 to 2012 – An outbreak (19 cases) of Mycobacterium chelonae infection involving multiple states was associated with contaminated ink used in tattoo parlors.
2011 to 2012 – An outbreak (15 cases) of infection by rapidly-growing mycobacteria was reported among pediatric hematopoietic cell transplant in a Minnesota hospital.
2013 – An outbreak (2 cases) of non-tuberculous mycobacterial infection was associated with fractionated CO2 laser resurfacing procedures performed at a clinic in North Carolina.
2013 to 2014 – An outbreak (19 cases) wound infection was reported among Americans who had traveled to the Dominican Republic for cosmetic surgery – including 12 due to Mycobacterium abscessus and 2 Mycobacterium fortuitum
2014 – An outbreak (15 cases, 4 fatal) of Mycobacterium abscessus infection in a South Carolina hospital was associated with contact of equipment with contaminated tap water.

1. Berger SA. Infectious Diseases of the United States, 2014. 1145 pages, 478 graphs, 12,294 references. Gideon e-books,
2. Berger SA. Non-Tuberculous Mycobacteria: Global Status, 2014. 61 pages, 31 graphs, 584 references. Gideon e-books,

Note featured on ProMED

2014 series of GIDEON eBooks

The 2014 GIDEON ebook series has been released.

This edition incorporates all content added since publication of the last series. Country-series eBooks now include the vaccination schedules for every reporting country as an extra chapter.
Additionally, four new volumes have been added to the series.

Titles now include:

Country series (231 volumes)
Disease series (188 volumes)
GIDEON Guide to Antimicrobial Agents
GIDEON Guide to Vaccines
GIDEON Guide to Medically Important Bacteria
GIDEON Guide to Medically Important Yeasts

The four newer titles incorporate content from GIDEON’s Drugs, Vaccines, Bacteria, Mycobacteria and Yeasts modules. These and all other eBooks in the series are updated annually

These ebooks are available on the GIDEON eBooks website as well as through distributors such as EBSCO and Ingram.

Microbiology References and Vaccination schedules

Over the past couple of months, we have rolled out a number of product updates to the GIDEON web app.

Microbiology References
References have been added to the improved notes and ecology sections for most organisms in the Microbiology sub-modules of Bacteria, Mycobacteria and Yeasts.

Vaccine Schedules
Vaccine schedules for each country have typically appeared in a number of notes in the Diseases module. These vaccine schedules have now been added to the Travel section, so it’s very easy to scroll through countries and compare their vaccination schedules.

For example see the initial travel note for Australia:
Australia vaccination schedule

With easy access to the vaccine abbreviations:

Vaccine abbreviations

Free-living Amoebae in Southeast Asia

To date, infection by free-living amoebae has not been described in Myanmar, Laos or Cambodia. Thailand reported its first case of primary amoebic meningoencephalitis in 1983, and by 1987 an additional five cases had been reported. 22 cases were reported to 2004: 10 due to Naegleria fowleri, 11 Acanthamoeba, and 1 Balamuthia mandrillaris. A study performed during 2001 to 2004 found that amoebae accounted for 2% of ulcerative keratitis cases in Bangkok; and as of 2005, Acanthamoeba, Naegleria, Hartmanella, Vahlkampfia and Vannella had been identified in soil and water samples from 14 provinces. [1,2]

1. Berger SA. Infectious Diseases of Thailand, 2012. 496 pages, 164 graphs, 2316 references. Gideon e-books,
2. Berger SA. Free-living Amoeba: Global Status, 2012. 24 pages, 1 graph, 368 references. Gideon e-books,

Note featured on ProMED

Pathogens Associated with Animal Bites

Gideon lists 31 species of bacteria which have been associated with human infection following the bites of animals:
– Bacteroides tectus
– Bergeyella zoohelcum
– Bisgaard’s taxon
– Capnocytophaga canimorsus
– Corynebacterium canis
– Capnocytophaga cynodegmi
– Corynebacterium freiburgense
– Corynebacterium kutscheri
– CDC NO-1
– Erysipelothrix rhusiopathiae
– Fusobacterium canifelinum
– Halomonas venusta
– Kingella potus
– Moraxella canis
– Mycobacterium vulneris
– Neisseria animaloris
– Neisseria canis
– Neisseria weaveri
– Neisseria zoodegmatis
– Pasteurella caballi
– Pasteurella canis
– Pasteurella dagmatis
– Pasteurella multocida
– Pasteurella stomatis
– Psychrobacter immobilis
– Spirillum minus
– Staphylococcus intermedius
– Streptobacillus moniliformis
– Vibrio charchariae
– Vibrio harveyi

Although virtually all literature on the subject advocates administration of tetanus prophylaxis following animal bites, few if any cases of bite-associated tetanus have been documented.

Updated Microbiology module

GIDEON’s redesigned Microbiology module has been launched (screenshot). Following the update of the GIDEON Diagnosis module, we’ve implemented many of the new features in Microbiology, including

  • New tabs
  • Suggestions
  • Dynamic identification
  • Usability improvements

New tabs

The new tabs in Microbiology replace the older radio buttons and make it easier to reach each function. For each category: Bacteria, Mycobacteria and Yeasts there is easy access to Identify or Lists.


GIDEON’s Microbiology Compare function, until now, has ranked phenotypic tests which are most likely to impact the Identification list. Now, the top four tests which are most likely to focus and shorten the list of possible organisms are displayed and dynamically updated as each new test result is entered. Clickable boxes which allow the user to enter a “yes”, “no” or “unknown”, appear and enlarge each time the mouse passes near a test.

Dynamic identification

The Identify button has been eliminated! Now, the Identification list is automatically updated as test results are entered. This feature demonstrates the effects of each new test result as it is entered.

Diagnosis results buttonsThe familiar buttons: Compare, Why Not, Open case, Save case, Remove All, Print, Email are all in the Identification list area.

Usability improvements

Updated lists

The organism lists have been updated to extend the length of the screen. The organisms can be selected by clicking the check boxes to their left and then Compared. Clicking on expands the list of synonyms.

Collapsible windows

Windows in Identify, such as Suggestions and Phenotypic Tests can be minimized and hidden. For example to not see suggestions, click on the minimize button Minimize button to the left title.

Mouse overs
More mouse-overs have been added: Clickable boxes expand as you mouse over them, and display clear symbols to select “yes” or “no.”

You can now click on the tests  in the Phenotype window.

Quick sorting
Probability sort arrowIdentification results can be sorted alphabetically or by probability easily by clicking the column title.

Window resizing
Changing vertical window size expands size of Phenotypic tests and Identification list sub-windows in Identify and Organism list. This is a great feature for larger monitors.

Previous version
Click “Original Microbiology” to use the older interface.

Update: See video demonstration

Non-tuberculous Mycobacterial Infections

Infection by non-tuberculous mycobacteria is commonly associated with cosmetic surgery, therapeutic injections and other invasive procedures. The following is a list of notable outbreaks:

2007 to 2007 – An outbreak (28 cases) of Mycobacterium immunogenum infection in Buenos Aires was associated with mesotherapy.

2002 to 2004 – An outbreak (14 cases) of mycobacterial wound infection associated with silicone breast implant surgery was reported in Campinas, Sao Paulo.
2003 – An outbreak (5 cases) in Sao Paulo of keratitis due to Mycobacterium immunogenum was associated with myopia surgery.
2004 to 2005 – An outbreak (311 cases) of Mycobacterium abscessus infections in Belem was associated with invasive procedures. Mycobacterium massiliense and M. bolletii were also identified in some cases.
2006 to 2007 – An outbreak (1,051 clinical cases) of Mycobacterium massiliense infections involving 63 hospitals in Rio de Janeiro state was related to contaminated instruments used in video-assisted surgery.
2008 – An outbreak (13 cases) of Mycobacterium fortuitum infections in Sao Paulo was associated with breast implant surgery.

Compare diseases, drugs or pathogens

One of the most important functions of GIDEON is to help users prepare scientific articles, teaching material and other publications (see the Fingerprint case of the month). A new feature now allows users to create custom-designed charts which compare the features of two or more diseases, drugs or pathogens.

For comparison of key clinical and epidemiological features of infectious diseases, in the Diseases tab, click on a disease (step 1 in the image below), and – while holding down the control button – click on other diseases of your choice. Now click on the Compare button (step 2).

Choosing diseases to compare
Choosing diseases to compare


Linking between modules

We’re continuing our progress in making it easier to find the information you’re looking for in GIDEON with minimal effort. We have added a new feature in the Microbiology module that link relevant organisms to their drug susceptibility and appropriate vaccines as demonstrated by the highlighted links in this screen shot of the Vibrio Cholerae general tab:
Microbiology Vibrio Cholerae information
These new links are in addition to links added in the past connecting between disease organisms to microbiology and typical therapy to drugs, vaccines and pathogens.
For example see the links from the Anthrax disease general information tab screen shot below, to the Microbiology organism (Bacillus anthracis), Therapy (eg: Ciprofloxacin) and Anthrax vaccine:
Anthrax general disease information