Culture or Not?

The traditional culture method is all about growing what’s there, slowly but surely and observing phenotypic characters like shape, size, staining property, reactions in biochemical tests etc. It often involves the process of trial and error, ruling out species after species until you have only one option left using observable characteristics. These methods for diagnosing infection have relied largely on clinical microbiology laboratories selecting, isolating and then identifying pathogenic organisms. This can be very time consuming. For some fastidious or slow-growing organisms, the delay to definitive microbiological diagnosis can stretch to weeks, while some organisms cannot be cultured at all. Other drawbacks with culture methods include problems with sensitivity, cost (resource intensive) and potential safety concerns with pathogenic organisms.


Convergent Diagnostics offers real time, quantitative PCR testing (RT-qPCR) to diagnose pathogens and to identify antibiotic resistance genes. RT-qPCR technology provides genetic identification of each pathogen with an accuracy rate of 99.8%. PCR can precisely analyze the genetic material of pathogens, provide a more definitive diagnosis than POC antigen assays, and can be done at lower costs and within 24-hour turn-around times.

Convergents pathogen detection panels provide comprehensive and targeted results for the following: Respiratory, UTI, STI, Wound, and Gastrointestinal.

In addition, Convergent’s testing solution provides you with antibiotic resistance reporting to help you better understand identified infections and options for treatment. Identifying the right pathogen is the crucial step in developing an appropriate treatment plan for an infection. The gold standard has been traditional culture and sensitivity. Now providers have an additional diagnostic tests available – molecular testing through PCR and NGS.

NGS Testing

Once a specimen is received in the laboratory, Convergent will perform a standard probe(s), RT-qPCR test covering an array of the most common (or prescribed) infectious microbes. Within 24-48 hours, the laboratory findings and antibiotic resistance gene markers will be available to you in order to begin a treatment protocol.

The DNA / RNA that was amplified during the RT-qPCR test will be used with our NGS test, if prescribed. NGS requires a longer testing time (usually a few weeks) to detect the precise microbe known to cause a certain infection. NGS technology allows the test to canvass the universe of pathogens and infectious microbes, attempting to match DNA / RNA sequence codes with tens of thousands of known microbes.

NGS is extremely beneficial to physicians who are concerned about chronic infections, hard to treat infections and biofilms.




Biofilms – Infectious Communities

A biofilm is a cluster of closely-packed microbial cells that grow on both living and inert surfaces and surround themselves in a matrix comprised primarily of a thick polysaccharide material. This thick layer encases the microbial cells, thereby protecting them from antimicrobials and from the host immune response.

Many single-cell bacteria species form biofilms. Investigation has revealed these species to be complex and diverse. The complexity of biofilms composition has led to the idea that single-cell bacteria are coordinated and cooperative groups, comparable to multicellular organisms.

There is a perception that single-celled organisms are asocial, but that is misguided. When bacteria are under stress—which is the story of their lives—they team up and form this collective called a biofilm. If you look at naturally occurring biofilms, they have very complicated architecture. They are like cities with channels for nutrients to go in and waste to go out.

Andre Levchenko, PhD, Johns Hopkins University

Researchers have estimated that 60-80 percent of microbial infections in the body are caused by bacteria growing as a biofilm – as opposed to planktonic (free-floating) bacteria. Biofilm communities have more resistance mechanisms as compared to the free-floating planktonic bacterial cells. This resistance contributes to chronic infections and hampers effective treatment options.

The most prolific of these infections include:

Chronic Prostatitis
Chronic Sinusitis
Chronic Wounds
Cystic Fibrosis
Inner Ear Infections

Biofilm Antibiotic Resistance

The development of a biofilm allows for the cells inside the biofilm colony to become more resistant to the body’s natural antimicrobials as well as the antibiotics administered in a standard fashion. In fact, depending on the organism and type of antimicrobial and experimental system, biofilm bacteria can be up to a thousand times more resistant to antimicrobial stress than free-swimming bacteria of the same species.

Approximately 80% of chronic and recurrent microbial infections in the human
body are due to bacterial biofilm. Microbial cells within biofilms have shown
10–1000 times more antibiotics resistance than the planktonic cells.

Sharma, D., Misba, L. & Khan, A.U.
Antibiotics versus biofilm:an emerging battleground in microbial communities.
Antimicrob Resist Infect Control (2019).

Magnet S, Smith TA, Zheng R, Nordmann P, Blanchard JS.
Aminoglycosides resistance resulting from tight drug binding to an altered
aminoglycosides acetyl transferase. Antomicrob Agents Chemother. 2003;47:1577–83


Biofilm Treatment Protocol

Biofilm’s are immense, complex structures that can be treated in a variety of ways. DNA sequencing technologies has allowed us not only to identify the vast colonies of bacteria and develop strategies to address them, but to begin to examine the cells and colonies specific to the effect of the therapies we employ.

Our NGS technology will identify all of the microbes in a particular sample. So instead of reporting RT-qPCR findings that accurately target only a handful of micro-organism, our NGS platform will match DNA sequences to tens of thousands of bacterial and fungal species from the National Database.

The power of NGS resides in its ability to generate a massive amount of genetic information in a relatively simple and rapid manner, especially when combined with the most prevalently used marker to study microbiological communities (SSU rRNA). The analysis involves extensive parallel sequencing, where information is gathered from several sets of primers, targeting hypervariable regions and taking data from several sources simultaneously.

Next Generation DNA sequencing (NGS) for infectious disease holds the promise of accuracy with greater sensitivity and specificity than culture, serologic and PCR methods. NGS allows for better discrimination between strains, species, detection of novel variants and new organisms, detection of an ever-growing array of uncultivable organisms, and the ability to detect eukaryotes that were previously undetectable.

In addition to identifying components of the microbiome, Convergent Diagnostics will return to our customer a comprehensive NGS findings reports outlining drug resistance and sensitivity. NGS technology has also been utilized to identify antibiotic resistance genes (ARGs) within a given microbiome, with the intended purpose of tailoring antibiotic therapy and promoting antibiotic stewardship.

Biofilms pose a threat to the human race because of their persistent nature
and plays a major role in certain pathogenic infections.


Sharma, D., Misba, L. & Khan, A.U. Antibiotics versus biofilm: an emerging battleground in microbial communities.
Antimicrob Resist Infect Control 8, 76 (2019).

Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms:
an emergent form of bacterial life. Nat Rev Microbiol. 2016;14(9):563–75



Antibiotic Stewardship is the effort to measure and improve how antibiotics are prescribed by clinicians and used by patients. Improving antibiotic prescribing and use is critical to effectively treat infections, protect patients from harms caused by unnecessary antibiotic use, and combat antibiotic resistance. Antimicrobial stewardship is a collective set of strategies to improve the appropriateness and minimize the adverse effects of antibiotic use including resistance, toxicity and costs. Stewardship is achieved by promoting the selection of the optimal antibiotic regimen, dose, duration and route of administration.

LTC Facilities

Long-Term Care (LTC) Facilities have health and safety standards that facilities must meet in order participate in Medicare or Medicaid programs. These standards include new mandates and language related to Infection Prevention and Control, and Antibiotic Stewardship.

Antibiotic Stewardship Monthly Report

The purpose of the Antibiotic Stewardship Program is to provide statistical data for every patient tested for the possibility of infectious diseases. These monthly reports will provide the vital information to the state surveyors as they review each facility to see the CMS standards for ASP are met. The surveyors will know which patients had a bacterial infection, which had an antibiotic resistance and see that the CMS criteria has been met.

The Antibiotic Stewardship Monthly Report Includes:

1. The Infectious Disease Panels ordered.
2. The number of patients tested during the month.
3. The number of patients positive for bacteria including specific organisms.
4. The number of patients positive for antibiotic resistant bacteria and type of resistance.
5. A list of the medication recommendations for each resistant bacterium.
6. A signature section for the ASP committee members to sign each report along with a comment section.
7. Cumulative statistical report on each SNF within a company be given as well as a comparative analysis using the national averages.

Sanford Guide


Our mission is to improve the quality of patient outcomes with concise, reliable, and accessible clinical guidance for infectious diseases treatment decision-making at the point of care.

IDSA/SHEA Guidelines for the implementation of Antibiotic Stewardship Programs (ASPs) recommend the development and use of facility-specific practice guidelines to improve appropriate use of antibiotics (Clin Infect Dis.(2016)62(10):e51-e77.).

Specific improvements you can expect are:

  • increased likelihood of adequate initial therapy
  • use of narrower-spectrum antibiotic regimens
  • earlier switch from IV to oral therapy
  • shorter duration of treatment
  • reductions in adverse events, mortality, length of stay, and readmission
  • greater efficiency and lower treatment costs


Sanford Guide provides superior content and service through our commitment to:

  • Expertise – Our distinguished editorial board of experts from leading academic
    institutions brings depth and breadth of expertise in the field of infectious diseases.
  • Reliability – Since 1969, The Sanford Guide has been the essential infectious diseases treatment reference for generations of clinicians.
  • Usability – We maintain an ongoing dialogue with our users to continually improve the quality of our content and user experience of our products.
  • Transparency – Our recommendations are evidence-based, extensively vetted by our editorial board with source references throughout.
  • Independence – While our content is available through many channels, editorial
    independence has always been and remains a hallmark of The Sanford Guide.

Article: Be Antibiotics Aware: Protect Your Patient

The Centers for Disease Control and Prevention (CDC) is urging healthcare professionals to prescribe antibiotics only when necessary to help fight antibiotic resistance and the spread of superbugs and to protect their patients from antibiotic adverse events. During U.S. Antibiotic Awareness Week and throughout the year, CDC promotes Be Antibiotics Aware, an educational effort to raise awareness about the importance of safe antibiotic prescribing and use.
The Be Antibiotics Aware initiative provides resources to help improve antibiotic prescribing among healthcare professionals and use among consumers.

CDC’s Be Antibiotics Aware educational effort encourages healthcare professionals to:

  • Follow clinical guidelines on whether to prescribe antibiotics and when prescribing antibiotics, to prescribe the right antibiotic at the right dose for the right duration at the right time.
  • Shortening the duration of antibiotic therapy to the minimum effective duration is a key antibiotic stewardship strategy in all settings of health care. The goal is to maximize the benefit to the patient by curing the infection while at the same time minimizing the risks of antibiotic resistance and side effects from antibiotics.
  • Protect your patients. Only prescribe antibiotics when they are needed. You can do harm by prescribing antibiotics that aren’t needed.
  • Tell your patients why they don’t need antibiotics for a viral infection, what to do to feel better, and when to seek care again if they don’t feel better.
  • Talk to your patients and their families about possible harms from antibiotics, such as allergic reactions, C. difficile, and antibiotic-resistant infections.
  • Watch for signs of sepsis, which can be life threatening. If you suspect sepsis, send the patient for emergency care, obtain cultures, and start antibiotics immediately.
  • Perform hand hygiene and follow infection prevention measures with every patient.

Be Antibiotics Aware has resources to help healthcare professionals (in outpatient and inpatient settings) educate patients and families about antibiotic use and risks for potential side effects.

For more information visit:

– CDC US Antibiotic Awareness Week, Sept 11, 2020