Clinical Microbiology Issues Update - December 2012


  • Joint ASM-CDC Developed Group B Streptococcus Protocols Available
  • ASM Attends HHS Avian Influenza Workshop
  • ASM Attends Congressional Hearings on Fungal Meningitis Outbreak
  • ASM Staff Attends FDA Public Workshop on Burkholderia
  • ASM Participates in Fiscal Cliff Discussions
  • ASM Signs Clinical Laboratory Coalition Letter to House Leaders
  • ASM Sends Letter to CDC Commenting on HPAI H5N1 Questions
  • ASM Staff Meet with CDC Board of Scientific Counselors
  • Minority Microbiology Mentor Newsletter


  • ASM Conferences
  • ASM Journal Articles of Interest
  • ASM2013 Website and Registration Now Open


  • Contamination Found in Other NECC Products
  • TEST Act Signed Into Law
  • FDA Approves Raxibacumab to Treat Inhalational Anthrax
  • CMS Releases 2013 Update for CLFS
  • CMS Publishes New Laboratory Codes and Fees
  • National Select Agents Registry Makes Documents Available
  • FDA Approves First Seasonal Influenza Vaccine Manufactured Using Cell Culture Technology
  • NIH-Funded Trial Launched to Assess Experimental TB Drug
  • MMWR Articles of Interest


  • Developing and Strengthening the Global Supply Chain for Second-Line Drugs for Multidrug-Resistant Tuberculosis: Workshop Summary
  • Articles of Interest



Joint ASM-CDC Developed Group B Streptococcus Protocols Available
Standard operating procedures, developed by the ASM and CDC's Streptococcus Laboratory, are available to assist laboratory scientists in processing group B Streptococcus specimens. The documents are tailored for use in different settings, depending on the procedures and assays used in each laboratory (e.g. pigmented or non-pigmented broth, sub-culture versus serologic or molecular methods, etc.). To access these protocols, go to

ASM Attends HHS Avian Influenza Workshop
The U.S. Department of Health and Human Services (HHS) sponsored an international workshop on December 17-18 on Gain-of-Function Research on Highly Pathogenic Avian Influenza H5N1 Viruses. The purpose of this workshop is to provide a forum for sharing multidisciplinary international perspectives on research that aims to increase transmissibility, increase pathogenicity, and/or alter host range of highly pathogenic avian influenza (HPAI) H5N1 viruses. Dr. Ronald Atlas, cochair of the PSAB Biological Defense Committee attended the workshop. Specific issues for discussion will include the implications of such research for global public health; risks and concerns associated with this research; the risks of not conducting such research; fundamental principles regarding the conduct and oversight of such research; and conditions under which such research might be conducted. For more information on the workshop, please click

ASM Attends Congressional Hearings on Fungal Meningitis Outbreak
ASM staff attended the House Subcommittee on Oversight and Investigations hearing entitled “The Fungal Meningitis Outbreak: Could It Have Been Prevented?” on November 14. Committee lawmakers reviewed the history of complaints associated with sterile compounding pharmacies and possible limitations of FDA oversight of compounding. The three panels included Lauren Smith, Interim Commissioner, Massachusetts Department of Public Health (MDPH), Margaret A. Hamburg, Commissioner, U.S. Food and Drug Administration (FDA), and Barry Cadden, President, Co-Owner, and Director of Pharmacy, New England Compounding Center (NECC). To view the archived hearing, see

The Senate Health Education Labor and Pensions (HELP) committee held a hearing entitled “Pharmacy Compounding: Implications of the 2012 Meningitis Outbreak”, which ASM staff also attended. The Committee requested records on October 25 from the NECC, the Massachusetts Board of Pharmacy, and the FDA to aid their investigation into why federal and state regulatory agencies failed to detect and prevent the outbreak. In addition to Dr. Hamburg and Dr. Smith, Beth Bell, Director, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC); Marion Kainer, Director, Healthcare Associated Infections & Antimicrobial Resistance Program, Tennessee Department of Health; David Miller, Executive Vice President and CEO, International Academy of Compounding Pharmacy; and Dr. Kasey Thompson, Vice President, Office of Policy, Planning and Communications, American Society of Health-System Pharmacists all testified. Barry Cadden, Owner and Director of Pharmacy, NECC failed to appear. More information about the hearing can be found here

ASM Staff Attends FDA Public Workshop on Burkholderia
The White Oak campus of the U.S. Food and Drug Administration hosted a Public Workshop entitled “Burkholderia: Exploring Current Issues and Identifying Regulatory Science Gaps” On November 29 and 30. Its goals were to identify solutions or future areas of research needed to further animal model development and to advance candidate medical countermeasures (MCMs) for approval, licensure, or clearance. The first day was composed of research presentations on the state of animal models, the role of auto transporters and other research and the workshop concluded with a draft plan for moving forward.   For more information, please see the following link

ASM Participates in Fiscal Cliff Discussions
On December 11, the ASM signed onto a letter from the Ad Hoc Group for Medical Research Coalition that was sent to all members of the House of Representatives. The letter outlined the coalition's concerns about the impact of continued cuts, including sequestration, on medical research supported by the National Institutes of Health (NIH) and the subsequent negative health consequences for all Americans. To see the letter click here

ASM also joined with more than one hundred organizations, scientific societies and universities in a letter urging the President and Congress to work together to find a solution to sequestration or the “fiscal cliff” without cuts to science and technology R&D funding. The letter, sent on December 7, warns that sequestration would cut $11.3 billion from the National Institutes of Health (NIH) over the next ten years, $4.6 billion in nondefense R&D from the Department of Energy (DOE) by 2017 and the National Science Foundation (NSF) would lose $2.1 billion over five years. A copy of the letter can be found at:

On December 4, ASM staff attended an NDD (non-defense discretionary) Summit meeting on Capitol Hill entitled “Planning for the Plan.” Senator Patty Murray addressed the group on sequestration negotiations and the importance of preserving R&D programs funded with nondefense discretionary funds. The NDD summit is a coalition of organizations, societies, including ASM, and academic institutions among others who support nondefense discretionary funding.

ASM Signs Clinical Laboratory Coalition Letter to House Leaders
On November 30, ASM joined with 49 members of the Clinical Laboratory Coalition, representing America’s community, regional, hospital-based, and national clinical laboratories in a letter to House leadership. The letter requests protection of access to Medicare Part B clinical laboratory services as Congress works to address end of year fiscal matters, including sequestration and the pending Medicare SGR cuts to physicians. The letter specifically urges legislators to oppose any additional reductions in the Medicare Part B Clinical Laboratory Fee Schedule, which was cut by Congress earlier this year. Further reductions to the fee schedule, whether through a direct cut or the imposition of new laboratory cost sharing requirements, threaten laboratory providers’ ability to serve their communities and specifically meet the needs of the Medicare population. The letter can be found here

ASM Sends Letter to CDC Commenting on HPAI H5N1 Questions
The Public and Scientific Affairs Board sent a letter December 14 in response to the Centers for Disease Control and Prevention’s (CDC) announcement in the October 17 Federal Register opening a docket for 60 days to obtain information and comments from the public on questions concerning highly pathogenic avian influenza (HPAI) H5N1 viruses that contain a hemagglutinin (HA) from the Goose/Guangdong/1/96 lineage, and their potential to pose a severe threat to public health and safety. This information will be considered in a determination of whether such viruses should be listed as HHS select agents, by revising the HHS Select Agent Regulations (42 CFR Part 73).  The ASM letter stated that all highly pathogenic avian influenza viruses are already USDA select agents and the question is whether designating the specific HPAI H5N1 influenza viruses containing the HA gene from the Goose/Guangdong/1/96 lineage an HHS tier 1 agent increases biosafety and biosecurity, i.e., whether it would enhance public health and safety. The ASM letter said that doing so is not warranted at this time. The complete letter is available at

ASM Staff Meet with CDC Board of Scientific Counselors
ASM participated in the Dec 5 meeting of the Centers for Disease Control and Prevention (CDC) Board of Scientific Counselors, Office of Infectious Diseases. The day-long Atlanta meeting covered six separate topics in detail, including addressing increasing numbers of pertussis cases, implementing new recommendations for reducing HCV morbidity and mortality, the CDC response to the fungal meningitis outbreak, and a report from the Antimicrobial Resistance Working Group. Speaking at the board meeting were CDC Director Thomas Frieden, Rima Khabbaz, CDC Deputy Director for Infectious Diseases, and Beth Bell, the director of the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID). This full board meets twice a year. For more information about it, including its charter and roster, see  

Minority Microbiology Mentor Newsletter
The December issue of the Minority Microbiology Newsletter has been published by the Committee on Microbiological Issues Impacting Minorities.


ASM Conferences

3rd ASMET - The ASM Emerging Technologies Conference
June 25-28, 2013
Ismir, Turkey

For a complete list of upcoming ASM conferences, please see

ASM/APHL Joint Webinar on Sentinel Clinical Laboratory Testing Protocols
Understanding the Sentinel Clinical Laboratory Testing Protocols
January 29, 2013 • 1:00 pm – 2:00 PM ET
Registration Deadline: January 27, 2013

For more information on this seminar, click

ASM Journal Articles of Interest
Cigarette Smoke Boosts Virulence in Staphylococcus aureus
Ritwij Kulkarni of Columbia University, New York, NY, and colleagues show that cigarette smoke actually boosts virulence of Staphylococcus aureus. Their study appears in the November 2012 issue of the journal Infection and Immunity.

Norovirus Disinfection: How Much is Enough?
Norovirus is the most common cause of gastroenteritis, according to the CDC. A variety of institutions and governments have developed “commonsense-based” disinfection guidelines to control norovirus contamination, but now, for the first time, a Dutch team has come up with science-based guidelines. The research is published in the November 2012 issue of the journal Applied and Environmental Microbiology.

New Coronavirus Has Ability to Pass Through Many Hosts
A novel type of human coronavirus can infect cells from humans and bats alike. According to a study published in mBio® on December 11, the new coronavirus, called hCoV-EMC, is blamed for five deaths and several other cases of severe disease originating in countries in the Middle East. According to the new results, hCoV-EMC uses a different receptor in the human body than the SARS virus, and can infect cells from a wide range of animal species.

Evaluation of a Simple Protein Extraction Method for Species Identification of Clinically Relevant Staphylococci by MALDI-TOF Mass Spectrometry
In this study, authors evaluated a modified protein extraction method of identification performed on target plates (on-plate extraction method) with MALDI-TOF (Bruker Microflex LT with Biotyper version 3.0) and compared it to 2 previously described methods: the direct colony method and a standard protein extraction method. 

Swab Protocol for Rapid Laboratory Diagnosis of Cutaneous Anthrax
This study developed a rapid protocol for detection of B. anthracis on clinical swabs. Three types of swabs were evaluated by 3 extraction methods, the swab extraction tube system (SETS), sonication, and vortex. Swabs were spiked with virulent B. anthracis cells, and the methods were compared for their efficiency over time by culture and real-time PCR. 

ASM2013 Website and Registration Now Open
You can now register and submit abstracts through the general meeting website at The general meeting will take place in Denver, CO from May 18-21, 2013.


Contamination Found in Other NECC Products
FDA and CDC have identified bacterial and/or fungal contamination in unopened vials of betamethasone, cardioplegia, and triamcinolone solutions distributed and recalled from NECC. These are in addition to the methylprednisolone acetate implicated in the current outbreak. For more information, see

TEST Act Signed into Law
S. 3391, Taking Essential Steps for Testing Act of 2012 passed the Senate by unanimous vote November 13. The bill amends the Public health Service Act to revise sanctions for laboratories that refer proficiency testing samples required for certification to another laboratory for analysis. This bill has passed both chambers and was signed by the President on December 4, making it Public Law No: 112-202. To read the text, see

FDA Approves Raxibacumab to Treat Inhalational Anthrax
On December 14, The U.S. Food and Drug Administration approved raxibacumab injection to treat inhalational anthrax. Raxibacumab, a monoclonal antibody that neutralizes anthrax toxin, also is approved to prevent inhalational anthrax when alternative therapies are not available or not appropriate. For the full press release, see

CMS Releases 2013 Update for CLFS
The Centers for Medicare & Medicaid Services (CMS), through their Medical Learning Network MLN Matters information service, has released the Calendar Year (CY) 2013 Annual Update for Clinical Laboratory Fee Schedule and Laboratory Services Subject to Reasonable Charge Payment document.

This document provides instructions to Medicare contractors for the 2013 Clinical Laboratory Fee Schedule, mapping for new codes for clinical laboratory tests, and updates for laboratory costs subject to the reasonable charge payment. According to this transmitted document, Medicare fees for services on the Part B clinical laboratory fee schedule are to be cut by 2.95 percent in CY 2013. To see the document, which contains both mapping information and links, go to

CMS Publishes New Laboratory Codes and Fees
On October 16, CMS published Revisions to Payment Policies under the Physician Fee Schedule.   This comprehensive revision places some 115 newly created molecular pathology Current Procedural Terminology (CPT) codes under the Clinical Laboratory Fee Schedule (CLFS) for 2012-2013. In addition, a new code, G0452, has been set aside for use when physician interpretation of a molecular pathology procedure is medically necessary. This G code has been designated as an interim code on the Physicians Fee Schedule (PFS) and will be monitored by CMS throughout calendar year 2013.   There is no corresponding code for interpretation by a doctoral level scientist or other appropriately trained nonphysician health care professional on either the CLFS or the PFS since they do not have a Medicare benefit category that allows them to bill and be paid for their interpretation services.   To see the revisions in their entirety, please see

National Select Agents Registry Makes Documents Available
The National Select Agents Registry has made guidance documents for Final Rule compliance assistance available on their website. Users will be able to select from a list of documents to assist in complying with the requirements of the Select Agents regulations by going to this site A Webcast from their November 16 detailed 2012 Select Agent Workshop training will be available shortly at   This training included precise instructions on how to fill out forms, so may be beneficial to laboratory personnel.

FDA Approves First Seasonal Influenza Vaccine Manufactured Using Cell Culture Technology
The U.S. Food and Drug Administration announced the approval of Flucelvax, the first seasonal influenza vaccine licensed in the United States produced using cultured animal cells, instead of fertilized chicken eggs. Flucelvax is approved to prevent seasonal influenza in people ages 18 years and older.

Cell culture technology has already been in use for several decades to produce other U.S. licensed vaccines. For the full announcement, see

NIH-Funded Trial Launched to Assess Experimental TB Drug
A clinical trial will examine an investigational drug’s early bacteria-killing activity in patients newly diagnosed with drug-sensitive pulmonary tuberculosis. The clinical trial, sponsored by the National Institute of Allergy and Infectious Diseases (NIAID), is being led by researchers at the Tuberculosis Research Unit at Case Western Reserve University. The study will take place in Cape Town, South Africa, will enroll 75 men and women with TB ages 18 to 65, including individuals who are also infected with HIV but not yet taking antiretroviral treatment. See the link for more information

Get Smart About Antibiotics Week
Get Smart About Antibiotics Week, observed November 12-18, has been an annual effort to coordinate the work of CDC’s Get Smart: Know When Antibiotics Work campaign, state-based appropriate antibiotic use campaigns, non-profit partners, and for-profit partners during a one week observance of antibiotic resistance and the importance of appropriate antibiotic use. As in past years, the effort coincided with European Antibiotic Awareness Day, Australia's Antibiotic Awareness Week and Canada's Antibiotic Awareness Week. For more, see

MMWR Articles of Interest

Multistate Outbreak of Salmonella Serotype Bovismorbificans Infections Associated with Hummus and Tahini
On September 27, 2011, three clinical isolates of Salmonella enterica serotype Bovismorbificans with indistinguishable pulsed-field gel electrophoresis (PFGE) patterns were identified by the District of Columbia Public Health Laboratory (PHL). Human infection with S. Bovismorbificans is rare in the United States. Through query of PulseNet, the national molecular subtyping network for foodborne disease surveillance, six additional cases with indistinguishable PFGE patterns were identified in three states (Maryland, Michigan, and Virginia) during the prior 60 days. All nine patients had eaten at restaurants in the District of Columbia (DC) or northern Virginia <2 weeks before illness onset.

Mumps Outbreak on a University Campus: California, 2011
On September 29, 2011, the California Department of Public Health (CDPH) confirmed three cases of mumps by PCR among students recently evaluated at their university's student health services with symptoms suggestive of mumps. An investigation by CDPH, student health services, and the local health department identified 29 mumps cases. The presumed source patient was an unvaccinated student with a history of recent travel to Western Europe, where mumps is circulating.

National Influenza Vaccination Week: December 2–8, 2012
To highlight the importance of annual influenza vaccination, and to foster greater use of influenza vaccine in the months of December, January, and beyond, the U.S. Department of Health and Human Services, CDC, and other agencies conducted educational and promotional activities during National Influenza Vaccination Week, December 2–8, 2012.

Announcement: World AIDS Day December 1, 2012
World AIDS Day draws attention to the current status of the human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) epidemic worldwide. The theme for this year's observance on December 1 was “Working Together for an AIDS-Free Generation.”


Developing and Strengthening the Global Supply Chain for Second-Line Drugs for Multidrug-Resistant Tuberculosis: Workshop Summary
The Institute of Medicine (IOM)’s Forum on Drug Discovery, Development, and Translation held a workshop on July 31 – August 1, 2012, to explore options and opportunities to improve the effectiveness of the global supply chain in delivering drugs to patients. The workshop was part of a series to gather information from experts around the world on drug resistant tuberculosis prevention, diagnosis, treatment, and management. This document summarizes the workshop.

Articles of Interest

Direct Conversion of Quiescent Cardiomyocytes to Pacemaker Cells by Expression of Tbx18
Nature Biotechnology
December 12, 2012
A recent breakthrough at Cedars-Sinai Heart Institute shows it may be possible to convert ordinary heart cells into “pacemaker” cells with a known gene and a modified virus.

Faster Testing Comes at a Cost
The new tests, which could shave a few days off the time needed to tell whether E. coli, Salmonella or other food-borne bacteria caused a patient’s illness, could reach medical laboratories as early as next year.   One problem: these new tests can’t detect crucial differences between different subtypes of bacteria. And that fingerprint is what states and the federal government use to match patients to a contaminated food source. 

Massachusetts Chemist in Drug Lab Testing Scandal Indicted on 27 Charges
Washington Post
December 18, 2012
Annie Dookhan, 35, of Franklin, was indicted Monday by a grand jury on 17 counts of obstruction of justice, eight counts of tampering with evidence, perjury and pretending to hold a college degree.