NICL Laboratories is introducing new technology to Microbiology in May 2022. The new technology is MALDI-TOF or matrix assisted laser desorption/ionization-time of flight, and it will be performed on the Bruker Sirius ONE MALDI Biotyper® CA System.
This technology uses high mass spectrometric resolution to rapidly and accurately identify microorganisms in a matter of minutes after isolation of the organism.
RAPID IDENTIFICATION
Turnaround time for this method is equivalent to a gram stain, but unlike a gram stain it provides definitive identification (ID) of the microorganism with over 98% certainty. The accuracy of this methodology is comparable to nucleic acid sequencing, but it is more cost effective and easily accessible, as it doesn’t require nucleic acid specific testing materials or kits and a longer time to results. If the organism requires specific resistance classification the report will indicate so, and a preliminary identification will be reported, with the organism and resistance reported later.
Included in this method’s compendium are organisms such as Candida auris, a deadly yeast, which is primarily only identifiable via this method. Historically, Candida auris has been transferred to a reference laboratory for identification, adding up to 48 hours to turnaround time.
Blood Cultures and Sepsis
The MBT Sensityper® test will also be available, and when used with the Bruker MALDI Biotyper® allows for identification of the organism directly from a positive blood culture bottle. When the bottle is flagged as positive, this method will allow us to provide a sample for identification on the MALDI in 15 to 20 minutes. This will effectively reduce the turnaround time for organism ID from a blood culture by up to 48 hours.
NICL Laboratories also has a PCR method available for a small menu of organisms, to provide antimicrobial susceptibility test results within a few hours of organism isolation and identification, and it can now be performed in a more selective manner, based upon the organism identified.
Antimicrobial Stewardship
Rapid organism identification from a culture bottle or a culture plate will provide for focused antimicrobial treatment and intervention. Coupled with NICL Laboratories annual MASTR™ report, the Bruker MALDI Biotyper® will assist the Infection Surveillance personnel in appropriate antimicrobial utilization. It will also provide for early determination of contamination, reducing the use of needless treatments.
Use of Broad Spectrum Antimicrobials and intravenous (IV) antimicrobials is very expensive. The use of PIC line and Midline catheters adds to the cost. The cost of use of Daptomycin over the period of a month can cost $9-10,000 and other drugs can cost as much as $33,000 for a one-month Medicare A stay. There is also risk attached to the use of these IV methods as they relate to nosocomial infections.
Use of this technology has an added benefit in that the microtiter wells on the plates used for organism ID can now be used to add a larger menu of antimicrobials for each organism identified, and for some antimicrobials, to provide a greater range of microtiters. BRUKER MALDI Biotyper® will help us to provide you with improved antimicrobial stewardship and patient outcomes.
Sepsis impact on Reimbursement
Hospital Acquired Conditions (HAC) such as sepsis, may impact a facility’s reimbursement. Every year the worst performing 25% are penalized by losing up to 1% of their Medicare payments. Targeted treatment may assist in reducing sepsis, and early successful treatment of other nosocomial infections, which will not only improve patient care and outcome, but it can also significantly impact the financial bottom line.
https://nicl.com/wp-content/uploads/2022/05/Bruker-mbt-sirius-with-user-bruker-md-web-thumbnail.jpeg511512NICL/wp-content/uploads/2022/04/nicl-logo-300x86.pngNICL2022-05-24 11:24:002022-09-23 14:40:18Antimicrobial Stewardship and the War on Sepsis
NOTE: Wear a gown, gloves, mask (N95 preferred), and eyewear when collecting these specimen.
1. Obtain specimen using only the mini-tip swab provided in the kit. Due to supply shortages, please use one swab per patient, please!
When collecting just a SARS CoV-2 sample, you may use an anterior nasal swab.
All other viral pathogen tests require a thin-tipped nasopharyngeal swab.
Swab Type
Collection Procedure
Nasopharyneal (N/P) swab
Has a very thin swab end; diameter of swab end is not much larger than swab handle
Push forward using gentle downward pressure to keep the swab on the floor of the nasal cavity until the tip reaches the posterior wall of the nasopharynx. Gently rub and roll the swab, and leave in place for several seconds to absorb fluid.*
It is not necessary to swab both sides if the swab is fully saturated from one side, but if both sides are collected, use a single swab on both the left and right nasal cavity.
A single swab may be used for SARS-CoV-2 and Influenza/RSV or Respiratory Viral Panel.
Anterior nasal swab
Swab end resembles a Q-tip. Do not attempt to collect a nasopharyngeal specimen using this type of swab.
Insert the swab at least one-half inch inside the nostril (naris) and firmly sample the nasal membrane by rotating the swab and leaving in place for 10 to 15 seconds.
Sample both nostrils with the same swab.
This type of swab can only be used for SARS-CoV-2 testing. It cannot be used for Influenza, RSV or other Respiratory Viral Pathogen testing.
*For a demonstration of N/P specimen collection please go to http://www.youtube.com/watch?v=DVJNWefmHjE (NEJM | Collection of Nasopharyngeal Specimens with the Swab Technique).
2. Break the shaft at the molded mark so that it can be placed in the tube without restricting the cap, and replace the cap tightly to prevent leakage and specimen rejection.
3. Label the vial with patient information (Name, DOB, collection date & time, specimen source and the test requested). Refrigerate it immediately.
4. Store the specimen refrigerated, and send it to the lab as soon as possible.
5. Complete the requisition. Indicate the swab type, and if the patient is symptomatic or if testing is for preoperative procedures. Race and ethnicity are also required by Health and Human Services. This is essential!
The above are M4RT media and other Viral transport media (check the label to see if the media should be kept refrigerated prior to collection). They are appropriate for Influenza, RSV, Respiratory Viral Panels and SARS-CoV-2 testing. NICL requires the use Viral transport media for its viral pathogens testing.
This procedure will guide you through indications, timing, number of sets, volume of draw per set, and PICC line collection.
INDICATION
Routine blood cultures should be performed on patients with suspected bacteremia or candidemia.
TIMING
Blood cultures should be drawn prior to the administration of antibiotics whenever possible, or as soon as possible after administration begins. There is no data to support that timing in relationship to febrile state or chills will improve yield or detection.
VOLUME
Literature suggests that the volume of specimen collected is directly proportional to the positivity rate. It also shows that low volume collections contain a higher number of contaminants. Two to three (2-3) sets of cultures should be used to rule out bacteremia or candidemia.
COLLECTION
PICC line collection (should be performed only when absolutely necessary):
1. Make sure you are wearing proper personal protection equipment (PPE), including gown and gloves.
2. Gather the required equipment:
Blood culture bottles
4 alcohol preps
1 3-5 cc syringe
10 cc syringes with a sterile needle
3. It is essential to AVOID DRAWING FROM LINES WITHIN AN HOUR OF COMPLETION OF ANTIMICROBIAL AGENT ADMINISTRATION, as the antimicrobial agent may be passed into the blood culture bottles and prohibit growth.
4. Using two separate alcohol preps wipes (70% alcohol), scrub catheter hub connection for 15 seconds with each wipe. Let it air dry.
5. Using the last two alcohol preps carefully wipe the tops of the blood culture bottles for 15 seconds each.
6. Disconnect the tubing from the cap of the catheter and attach the small syringe to collect discard blood. The suggested amounts for adults are 3 ml and 0.2 ml for pediatric patients. This blood is used to wash the line, and it is not used for culture. The entire syringe and contents can be discarded into a biohazard container.
7. Using a new syringe, collect blood for culture through the hub. 2-4 ml is required for each of two blood culture vials. When enough blood has been obtained for the two vials, detach the syringe from the catheter and reconnect the tubing to the cap of the catheter.
8. Place a sterile needle on the syringe, and transfer the blood, using sterile technique into the blood culture vials. Sterile technique requires that you DO NOT touch the top of the alcohol cleaned vials with anything but the tip of a sterile needle, and that you do not touch the syringe head with anything but the sterile needle.
9. Gently mix the blood culture vials thoroughly to prevent clotting.
10. Label each specimen with the patient’s name, date of birth, date and time of collection, and collection site, and place them with a completed requisition at room temperature for pickup by laboratory personnel.
Enterococci are part of normal gastrointestinal and genital tract flora.
Enterococci are gram positive cocci included in the Streptococci group D species; they are widely distributed in nature, animals and humans.
Among the 17 species currently recognized, E. faecalis and E. faecium are the most prominent in humans.
Infections that can be caused by enterococci include: UTI, bacteremia, wound, abdominal-pelvic infections and endocarditis.
Vancomycin is an important antibiotic used alone or in combination with other antibiotics for the treatment of serious infections caused by enterococci.
Resistance to Vancomycin
Vancomycin resistant enterococci (VRE) are multidrug resistant strains which present a serious difficulty in treating patients.
The resistance to vancomycin is induced by a genetic mechanism; the “VAN A gene” confers high-level resistance to vancomycin; it is plasmid mediated and can be transferred to other microorganisms such as Staphylococcus aureus. This may increase a possible emergence of VRSA (vancomycin resistant Staphylococcus aureus).
The patients can be “colonized” (carrying VRE without symptoms of infection), or “infected” (the presence of the VRE accompanied by clinical symptoms). They are both sources for nosocomial infection.
The most frequent sites for colonization are: stool, perineal, anus, axilla, umbilicus, wounds, foley catheter, and colostomy sites.
Epidemiology
Most infections and colonizations with VRE are attributed to the patient’s endogenous flora.
VRE can be spread by direct patient to patient contact or indirectly via hands of personnel, contaminated environmental surface or patient care equipment.
Prevention
Since vancomycin use has been reported consistently as a risk factor for colonization and infection with VRE, a restriction in the use of vancomycin should be imposed (see Hospital Infection Control Practices Advisory Committee recommendations).
It is strongly recommended for each facility to develop its own policies regarding the prevention and control of nosocomial transmission of VRE (isolation, culture survey, education program) according to the Hospital Infection Control Practices Advisory Committee (a copy is available from NICL).
Cultures of central venous catheter tips are frequently ordered to help determine the source of bacteremia. Correct collection and submission are essential for accurate results and personnel safety.
The intracutaneous segment and distal tip of long catheters should be submitted, but in practice the catheter tip is usually received and should be accepted. The catheter tip must be in a sterile container and must not remain at room temperature for more than 4 hours.
Catheter tips should be requested only if there are signs of infections, i.e. inflammation at the site of insertions, fever, signs of sepsis, or documented bacteremia in which source is not apparent. The routine culture of catheter tips without signs and symptoms is discouraged.
COLLECTION OF CATHETER TIP BY NURSE OR PHYSICIAN
Thoroughly cleanse skin around the insertion site with 70% alcohol. Allow to dry.
Using sterile forceps, carefully withdraw the catheter keep externalized portion directed upward and away from the skin surface.
Holding the distal end of the catheter over a sterile container, cut the tip with sterile scissors, dropping the last 2-3 inches into the sterile container. Avoid contact with the outside of the container. Avoid drying of the specimen.
Inspect the catheter exit site and note if any purulence can be expelled.
If pus can be expelled from the catheter exit site, swab drainage with a culturette swab and send to the laboratory requesting a routine wound culture. Label the source as: Drainage from (location of) IV exit site, (e.g. drainage from Right IJ exit site).
Send the catheter segment(s) to the laboratory requesting a routine culture. Label the source as: Location/type of IV catheter, (e.g. Right IJ swan).
Send the accompanying blood cultures to confirm bacteremia.
SPECIMEN STORAGE
Store in refrigerator (must not remain at room temperature for more than 4 hours). Must arrive within 24 hours.
REJECTION CRITERIA
Do not send Foley catheter tips.
Do not send catheter tips in saline or transport media.
Do not send the whole catheter line.
Catheter received in a nonsterile container.
Unlabeled specimen (always have Patient’s name, date of birth, and source)
References:
Linares J, Sitges-Serra, Grarav J, Percex JL, Martin R: Pathogenesis of catheter sepsis: a prospective study with quantitative and semi-quantitative cultures of catheter hub and segments. J Clin Microbiology 1985;21:357-360
Maki, D.G., Wise CE, Safarin H.W. : A semiquantitative culture method for identifying intravenous catheter-related infections. New Engl J Med 1977;296:1305-1309.
3/5/2020 NICL Laboratories, Ltd All Rights Reserved
Previously known as Flavobacterium meningosepticum, and more recently as Chryseobacterium meningosepticum, Elizabethkingia meningoseptica is a gram-negative bacterium found in soil and water. Although it is rarely isolated from clinical specimens, this organism is resistant to several classes of antimicrobials and is capable of causing infection in blood, cerebrospinal fluid, skin and soft tissue, the respiratory system, and other body sites. Nosocomial transmission of E. meningoseptica among immunocompromised adults in intensive care units has been reported. Further, long-term acute care hospitals with mechanically ventilated patients could serve as an important transmission setting for E. meningoseptica. This multidrug-resistant bacterium could pose additional risk when patients are transferred between long-term acute care facilities and other hospitals.
Please articulate and reinforce your established policies of infection control: handwashing and disinfection practices, isolation policies, the use of gowns and gloves, the proper disposal of body fluids and body fluid– contaminated items, and the use of sterile water for cleaning of respiratory equipment and any other devices that come into contact with mucous membranes or nonintact skin of patients. Additionally, adherence to the current CDC guidelines for prevention of Ventilator-Associated Pneumonia (VAP) is important for reducing these types of infections in the long-term acute care facility.
References:
Weaver, KN et al. Acute Emergence of Elizabethkingia meningoseptica Infection among Mechanically Ventilated Patients in a Long-Term Acute Care Facility. Infection Control and Hospital Epidemiology 2010, Vol. 31 (No. 1), pp. 54-58.
Walkey, AJ et al. Epidemiology of Ventilator-Associated Pneumonia in a Long-Term Acute Care Hospital. Infection Control and Hospital Epidemiology 2009, Vol. 30 (No. 4), pp 319-324.
Tablan OC, et al.; Centers for Disease Control and Prevention (CDC); Healthcare Infection Control Practices Advisory Committee. Guidelines for preventing health-care–associated pneumonia, 2003: recommendations of CDC and the Healthcare Infection Control Practices Advisory Committee. MMWR Recomm Rep 2004; 53(RR-3):1-36.
3/5/2020 NICL Laboratories, Ltd All Rights Reserved
NICL Laboratories will be providing new rapid molecular tests to aid in diagnosis of blood stream infections which could lead to sepsis. These new tests, called the Verigene® Blood Culture Nucleic Acid BC-GP or BC-GN, are for detection and identification of gram positive and gram negative organisms, respectively. These tests are also capable of detection of drug resistance markers. The test(s) will be automatically performed when a blood culture becomes positive.
Once a blood culture has been shown to be positive, a gram stain is performed to determine whether the organism is gram positive or gram negative, or if both are present. A sample is then submitted to the Verigene system for BC-GP (Gram Positive) or BC-GN (Gram Negative) organism identification. The results are available in approximately 3 hours. This will reduce the time for identification of the organism and resistance markers for 90% of organisms by nearly two days. The lists below indicate the organisms and resistance markers that can be detected.
Studies have shown that delayed administration of appropriate antibiotics is associated with a decrease in survival rate for each hour that the appropriate antimicrobial treatment is delayed*1. Rapid molecular testing of blood cultures has been shown to reduce this time and is associated with significant institutional cost savings*2.
The laboratory will continue to provide complete susceptibility profiles for blood culture isolates using conventional culture methods, to identify organisms not detected by this method, differentiate mixed culture growth, and to associate antimicrobial resistance marker genes to a specific organism.
*1.Bauer et al.2010. Clin Infect Dis, 51:1074-80
*2.Ly et al. 2008. Clin Risk Manag, 4:637-40
Bacterial Genera, Species and Resistance Markers
GRAM POSITIVE ORGANISMS
Organisms
Staphylococcus spp
Staphylococcus aureus
Staphulococcus epidermidis
Stahylococcus lugdunensis
Streptococcus spp
Streptococcus pneumonia
Streptococcus pyogenes
Streptococcus agalactiae
Streptococcus anginosus group
Enterococcus faecalis
Enterococcus faecium
Listeria spp
Resistance Markers
mecA gene, conferring methicillin resistance
vanA and vanB genes, conferring vancomycin resistance
GRAM NEGATIVE ORGANISMS
Organisms
Acinetobacter spp
Citrobacter spp
Enterobacter spp
Proteus spp
Escherichia coli
Klebsiella pneumonia
Klebsiella oxytoca
Pseudomonas aeruginosa
Resistance Markers
CTX-M (blaCTX-M)
KPC (blaKPC)
NDM (blaNDM)
VIM (blaVIM)
IMP (blaIMP)
OXA (blaOXA)
9/8/2017 NICL Laboratories, Ltd All Rights Reserved
NICL Laboratories is pleased to add Procalcitonin to our in-house esoteric testing menu. This test will be available seven (7) days per week.
Procalcitonin (PCT) is the precursor to calcitonin, and a specific marker for detection of severe bacterial infection and sepsis. Noninfectious inflammations need to be extremely severe for an increase in PCT to occur, making it a better indicator for sepsis than other inflammatory markers, such as cytokines, acute phase reactants, and interleukins. The elevations of PCT are also more sustained than most other markers and will also occur in neutropenic patients. This will reduce false negative results.
PCT begins to rise 2 to 4 hours after onset of severe infection or sepsis and peaks in 12-24 hours. The rise also parallels the severity of the infection/inflammation, as higher levels are found in the more severe infections, and the levels will fall as the inflammation subsides. PCT has a half life of 24-35 hours, making serial testing a useful tool for monitoring the patient’s inflammation or response to therapeutics. As PCT levels will decline as the inflammation subsides, it is also useful for identification of a secondary infection. If serial testing is indicated, the same sample type and testing location are recommended.
It should be noted that the sensitivity and specificity of PCT for sepsis ranges from 60% to 100%, and heterophile antibodies may interfere with all immunometric assays of this sort.
Interpretations
In adults, PCT levels less than 0.5 ng/mL represent a low risk of severe sepsis or septic shock, but cannot exclude local infection or systemic infection in early stages of less than 6 hours.
PCT levels between 0.2 and 2.0 ng/mL do not exclude an infection, because localized infections without systemic signs may be seen in these situations.
PCT levels greater than 2.0 ng/mL are highly suggestive of system bacterial infection or sepsis, or a very severe localized infection such as pneumonia, meningitis, or peritonitis.
PCT can also rise in non-infectious situations, such as major burns, severe trauma, acute multi-organ failure or with major abdominal surgery or cardiothoracic surgery, or prolonged or cardiogenic shock, but will generally begin to fall in 24 to 48 hours in these situations.
Autoimmune diseases, chronic inflammation, viral infections, and mild localized infections rarely lead to levels greater than 0.5 ng/mL.
Renal failure or insufficiency may also influence PCT values, and may confound diagnosis when present.
PCT can also be used to differentiate a viral from a bacterial infection.
If there is any disagreement between the laboratory results and the clinical signs, additional testing may be necessary.
5/30/2018 NICL Laboratories, Ltd All Rights Reserved
https://nicl.com/wp-content/uploads/2022/04/nicl-lab-bg.jpg10001500NICL/wp-content/uploads/2022/04/nicl-logo-300x86.pngNICL2018-05-30 11:44:002022-09-14 11:54:38Procalcitonin – for Detection of Severe Infection and Sepsis
Guidelines have emerged to increase the sensitivity of assays for Clostridium difficile (C. difficile). The primary two guidelines in the U.S. support the use of testing for a common antigen knownas glutamate dehyrogenase (GDH) as a primary screen.1,2 GDH has been shown to have sensitivity levels equivalent to molecular methods. It is produced by non-toxic strains, however, making the testing for the toxin also necessary.
NICL Laboratories will be performing C. difficile testing using an algorithm. This algorithm will consist of a combination test which includes an Enzyme immunoassay test for the antigen GDH and C. difficile toxin (CDT). If both tests are negative, the patient will be considered negative for C. difficile Toxin A/B. If both tests are positive, the patient will be considered positive for C.difficile Toxin A/B. When the results disagree, this combination test will be followed, with a test for the toxin gene using a real-time polymerase chain (PCR) based qualitative test. The test targets C. difficile Toxin A gene (tcdA), and Toxin B gene (tcdB). This algorithm appears in teal blue in the chart below.
The laboratory will also be providing a Lactoferrin immunochromatographic assay for detecting the presence of WBCs in stool, to rule out inflammation. This additional testing, which appears in green in the chart below, will be performed only upon request.
The new test code for C. difficile, including the nucleic acid probe confirmation is 27449. This testing will continue to be available on a daily basis. The test code for Lactoferrin for detecting white blood cells in stool is 13630.
NOTE: This testing will only be performed on uniform (liquid or soft) stool specimen. Solid or hard formed samples will be rejected.
1 Cohen,et al. Clinical Practice Guidelines for Clostridium difficile infection in adults: 2010 update by the Society of Healthcare Epidemiology of America (SHEA) and the Infectious Diseases Society of America (IDSA). Infection Control and Hospital Epidemiology. 2010
2American Society for Microbiology. 20103Noren, Torbjorn, Alriksson, Ingegard, Andersson, Josefin, Akerlund, Thomas, Unemo, Magnus Rapid and Sensitive LoopMediated Isothermal Amp0lification Test for Clostridium difficile Detection Challenges Cytotoxin B Cell Test and Culture as Gold Standard, Journal of Clinical Microbiology, Feb 2011, p 710-711
