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Help with Bacteria

CDC Releases Recommendations for the Laboratory-Based Detection of Chlamydia trachomatis and Neisseria gonorrhoeae
An update on the 2002 CDC recommendations for screening of Chlamydia trachomatis and Neisseria gonorrhoeae infections. These recommendations discuss new recommendations for optimal specimen types, the use of tests to detect rectal and oropharyngeal C. trachomatis and N. gonorrhoeae infections, and the conditions in which supplemental testing is warranted.

Transportation of Specimens for Neisseria gonorrhoeae Culture
An APHL document that describes the transport systems suitable for transporting N. gonorrhoeae specimens and it highlights available performance data and outlines the benefits and limitations of each system.

The following helpful tables are from the Manual of Clinical Microbiology, 10th ed. (J. Versalovic, K.C. Carroll, G. Funke, J.H. Jorgensen, M.L. Landry, and D.W. Warnock, ed.; ASM Press, Washington, DC, 2011), ASMscience
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 Bacterial Collection, Transport and Storage Guidelines
Collection, transport, and storage guidelines for microbiological laboratory diagnostic studies.

 Diagnosis of BV using a Gram Stain Smear of Vaginal Secretions
Gram-stained smears should be examined and interpreted.

 Interpretation of Bacterial Lower Respiratory Tract Culture Results 
Interpretative criteria used with respiratory tract specimens.

 Interpretation of Urine Culture Results
Interpretative criteria used with urine specimens.

 Recommendations for Gram Stain and Plating Media for Bacterial Specimens or Organisms
Gram stains can deliver rapid, actionable results to clinicians, can determine if a specimen is acceptable for culture based on cellularity, and should be used to aid the microbiologist in interpretation of the culture. 

 Screening Specimens for Routine Bacterial Culture to Ensure Quality
Examples of acceptable and unacceptable specimens based on screening criteria. 

 Selection of Common Clinical Specimens for Bacterial Culture 
One of the key principles of good specimen collection is to avoid introduction of colonizing bacteria surrounding the site of infection or on the skin or mucous membranes near the infectious site. This table lists anatomic sites with appropriate and inappropriate clinical specimens. 

From E. J. Baron and R. B. Thomson, Jr., “Specimen Collection, Transport, and Processing: Bacteriology,” chapter 16, p. 228–271, in J. Versalovic, K. C. Carroll, G. Funke, J. H. Jorgensen, M. L. Landry, and D. W. Warnock (ed.), Manual of Clinical Microbiology, 10th ed., vol. 1 (© ASM Press, Washington, DC, 2011). 

Visit ASMscience to purchase MCM10 in print and/or electronic format.

Cystic Fibrosis Pathogens
A Clinical Microbiology Reviews article on microbial infection and adaptation in cystic fibrosis.

Bacterial Identification Tools

Practical Approach to the Identification of Glucose Non-Fermenting Gram-Negative Bacilli
Dr. Paul Schreckenberger’s Clinical Microbiology webpage and the home of the ASHEX Glucose Non-Fermenting Bacteria ID Database. This site was founded in 2004 to provide a home for their project, the ASHEX matrix, which utilizes a program called PIBWin to identify glucose non-fermenting bacteria with a set array of phenotypic tests.

Abbreviated Identification of Bacteria and Yeast; Approved Guidelines
A CLSI document that provides the minimum identification criteria that can be used to rapidly identify organisms commonly isolated from clinical specimens. The FDA has evaluated and recognized this approved-level consensus guideline for use in satisfying a regulatory requirement.

Advanced Bacterial Identification Software (ABIS)
ABIS online is a software developed as a lab tool for bacterial identification. You only have to enter a name and hit the button. Bacteria identification results are purely informative and are not intended to be an official point of view. Because of the permanent changes in bacterial nomenclature and classification, some bacterial names and taxa may not comply with the Approved Lists of Bacterial Names.

Probabilistic Identification of Bacteria for Windows
The University of Southhampton's, United Kingdom, software program, PIBWin, provides probabilistic identification of unknown bacterial isolates against identification matrices of known strains. It has three major functions: the identification of an unknown isolate; the selection of additional tests to distinguish between possible strains if identification is not achieved; and the storage and retrieval of results.

NamesforLife Technology
Provides a completely new approach to bibliographic retrieval, based upon the use of nomenclature as a means of linking to content.

Taxonomy of Bacterial Species
The increasing use of both MALFI-TOF and 16s rRNA sequencing for identification of bacteria has resulted in the recognition of many new species of bacteria associated with animal and human infections.

ASM's Practical Guidance Document for the Laboratory Detection of Vibrio cholerae
ASM's Practical Guidance Document for the Laboratory Detection of Toxigenic Clostridium difficile

Pediatric Pneumonia Guidelines
Guidelines on the diagnosis and treatment of community-acquired pneumonia (CAP) in infants and children, from the Pediatric Infectious Diseases Society (PIDS) and the Infectious Diseases Society of America (IDSA), emphasize the importance of immunizations, including a yearly influenza vaccine, to protect children from life-threatening pneumonia.

Vancomycin-Intermediate/Resistant Staphylococcus aureus Laboratory Testing Algorithm
All laboratories should develop a step-by-step problem-solving procedure or algorithm for detecting VISA/VRSA that is specific for their laboratory. A sample algorithm is available and highlights the recommended testing methodologies for detecting VISA/VRSA and actions based on results.

Detection of Enterobacteriaceae Isolates Carrying Metallo-Beta-Lactamase
During January--June 2010, three Enterobacteriaceae isolates carrying a newly described resistance mechanism, the New Delhi metallo-beta-lactamase (NDM-1) (1), were identified from three U.S. states at the CDC antimicrobial susceptibility laboratory. This is the first report of NDM-1 in the U.S., and the first report of metallo-beta-lactamase carriage among Enterobacteriaceae in the U.S.

Recommendation for Diagnosis of Shiga Toxin--Producing Escherichia coli Infection by Clinical Laboratories
Shiga toxin--producing Escherichia coli (STEC) This report provides comprehensive and detailed recommendations for STEC testing by clinical laboratories; detailed procedures for specimen selection, handling, and transport; a review of culture and nonculture tests for STEC detection; and clinical considerations and recommendations for management of patients with STEC infection.

What Happened to the Streptococci: Overview of Taxonomic and Nomenclature Changes
A 2002 Clinical Microbiology Reviews' article presents a combination of conventional tests and specific chromogenic tests as suggested by several investigators.
R. Fackham
Clin. Microbio. Rev. October 2002 15: 613-630
Abstract and PDF
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The Life and Times of the Enterococcus
An article published in Clinical Microbiology Reviews in 1990 about Enterococci which are important human pathogens that are increasingly resistant to antimicrobial agents.
B.E. Murray
Clin. Microbiol. Rev. January 1990 3: 46-65
Abstract and PDF
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