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1.5 - Microbiology General Information
Message1.5 - Microbiology General Information
Message
Director of Microbiology
BACL Microbiology Laboratory Supervisor
Microbiology Lead Technologist
Kristen Houghton
Microbiology Laboratory: 857-203-5954
Hours of Operation
Monday-Friday: 7:00 AM to 5:00 PM
Weekends and Holidays: 7:00 AM to 3:00 PM
GENERAL INFORMATION
The Microbiology Laboratory performs routine gram stains, aerobic, anaerobic, and mycology on a variety of specimen types from various body sources. Identification and susceptibility testing will be performed as applicable, and reporting of specific antibiotics will follow guidelines for CLSI (Clinical Laboratory Standards Institute).
Select molecular PCR assays are performed and will detect or not detect specific analytes that are listed on the assay/panel. SARS-CoV-2, Influenza (A and B) and RSV testing is performed using PCR with a turnaround time of 2 hours from receipt in the West Roxbury Laboratory. This assay is performed 24/7 and requires a properly obtained nasopharyngeal/nasal swab submitted in VTM/UTM from individuals with signs and symptoms of respiratory tract infection which can be obtained from the laboratory. This assay is also available at the Brockton, JP, and Bedford facilities but only during their routine laboratory hours. A Respiratory Pathogen Panel is also available to test for additional respiratory pathogens from a properly obtained nasopharyngeal/nasal swab collected in VTM/UTM. Respiratory Panels should only be requested after ruling out SARS CoV-2, Influenza A, Influenza B, and RSV. Additional molecular PCR assays are listed below.
Microbiologic detection of pathogenic organisms begins with properly collected specimens and timely delivery to the laboratory. Please take the extra effort to collect an optimal specimen (e.g., a small piece of tissue, fluid or aspirate rather than a swab).
All specimens for culture must be collected and transported to the laboratory according to accepted standard procedure. Individual test listings provide full details. Complete patient identification (first name, last name and entire social security number), specimen type, tests ordered with order number, date/time of collection, and collector initials must be provided. Specimen body site/source is required for all cultures.
All specimens other than the following should be refrigerated immediately upon collection:
The following specimens should be left at room temperature
Blood Culture Bottles
Body fluids (Do not collect in blood culture bottles)
Tissues/bones/biopsy
Cultures for N. gonorrhoeae*(Genital)/meningitidis
Aspirates/syringes
Swab cultures for anaerobes in anaerobic transport media/anaerobic swabs
*PCR for N. gonorrhoeae/Chlamydia in COBAS media is the optimal specimen and culture is discouraged. PCR is a send out test performed at West Haven.
ROUTINE TESTS PERFORMED IN MICROBIOLOGY
GRAM STAIN’s
Exceptions: Urine, Throat, Catheter Tip
ANAEROBIC CULTURE
Automatically performed on body fluids, tissues, bones, abscesses, aspirate, new drainages, medical devices
BLOOD CULTURE
Gram stains are only performed after a bottle has alerted as positive.
CRYPTOCOCCUS AG PANEL, CSF (if CJD is suspected – notify the laboratory)
CRYPTOCOCCUS AG PANEL, SERUM
CULTURE, ABSCESS
CULTURE, ASPIRATE
CULTURE, BODY FLUID (if CJD is suspected – notify the laboratory)
CULTURE, BONE
CULTURE, BONE MARROW
CULTURE, BRONCHIAL
CULTURE, CATHETER TIP
CULTURE, CSF (If CJD is suspected – notify the laboratory)
CULTURE, CALCULUS
CULTURE, DRAINAGE
CULTURE, EAR
CULTURE, EYE (if CJD is suspected – notify the laboratory)
Corneal Scraping’s may be collected and plated bedside. Agar may be retrieved directly from the Laboratory.
CULTURE, EMPYEMA
CULTURE, GENITAL
CULTURE, LEGIONELLA
CULTURE, MEDICAL DEVICE
CULTURE, SPUTUM
CULTURE, THROAT
CULTURE, TISSUE (if CJD is suspected – notify the laboratory)
CULTURE, URINE
CULTURE, WOUND
FECAL LEUKOCYTES (LACTOFERRIN)
GC CULTURE (discouraged: use COBAS media for PCR GC/Chlamydia)
NOCARDIA CULTURE
MYCOLOGY CULTURE
AFB CULTURE AND SMEAR (Mycobacteriology sent out to West Haven VA AFB Lab)
Cultures vary in the time they are held before being finalized due to a variety of reasons such as slow growing organisms, additional identification and susceptibility testing or questionable rule out results.
Nonetheless routine bacterial cultures are held for 48 hours except for throat cultures. A culture that has an anaerobe culture is held for 7 days. Blood Cultures are held for 5 days unless the bottles alert as positive.
Routine TESTS performed in MOLECULAR
C. diff/epi toxin B gene (Cepheid) PCR
Limit one loose or watery specimen per patient per week.
Stools that test positive to PCR will be reflexed to the C. diff Toxin/GDH Antigen. See reflex details below.
COVID-19 and FLU/RSV DIAGNOSTIC PANEL (Cepheid) PCR
SARS-CoV-2 PCR(Cepheid) PCR
Carba-R Perirectal Screen (Cepheid) PCR
Norovirus Genogroup I (GI) and Genogroup II (GII) (Cepheid) PCR
MTB/Rif complex (Rule/Out) (Cepheid) PCR
Performed only on sputum with approval through Infectious Disease.
Respiratory Pathogen Panel (RP2.1 on BioFire) - alias COVID-19 DIAGNOSTIC PANEL(BIOFIRE)
Blood Culture Identification Panel (BCID2 on BioFire) PCR
Performed only on positive blood cultures only. See reflex details below
Gastrointestinal panel (GI on BioFire) PCR
Automatic Reflex Testing on Microbiology tests:
Mycology culture, AFB Culture & Smear AFB smear and AFB culture: Will be added to bronchial specimens and respiratory tissues.
Anaerobic culture: Added to specimens (surgical, aspirate, etc) that require anaerobic cultures and that are not received on red top swab culturettes. They are allowed on blue top swab culturettes. (Stored in laboratory)
Carba-R PCR will be added to any culture isolates that test intermediate or resistant to a carbapenem antibiotic and is identified as an Enterobacterales, Pseudomonas aeruginosa, or Acinetobacter baumannii complex.
Positive Blood Cultures: Gram stain and BCID2 PCR will be added on and performed on positive blood cultures ONLY. Only the first sets of positives will be reflexed for PCR unless an additional organism or morphology of bacteria/yeast is seen.
C diff toxin/GDH Antigen will be reflex to all stool specimens that test positive for C. diff tox B Gene by PCR.
A stool culture will be performed as reflex after a Gastrointestinal (GI) panel by PCR is positive for a bacterium that can be isolated by this lab such as Campylobacter, Plesiomonas, Salmonella, Vibrio, Yersinia or Shigella.
ANTIMICROBIAL SUSCEPTIBILITY TESTING
Susceptibility testing is performed on pathogens to antibiotics that have CLSI/FDA breakpoints. MIC values (in micrograms/ml) and interpretations of S/I/R will be reported. Certain antibiotics do have SDD (Susceptible Dose-Dependent) interpretations and disclaimers will be added as necessary.
Certain antibiotics may be reported by manual testing methods due to updated CLSI standards that are not reflective of current automated susceptibility testing methods.
Testing for organism/antibiotic combinations with no interpretative criteria is not recommended. Consult infectious disease for testing of additional antibiotics.
Repeat antibiotic susceptibility testing on the same patient with the same organism is not performed on specimens from the same site within 3 days for unit patients and 7 days for ward patients. Consult the Technical Director of Microbiology and/or supervisor for technical questions related to susceptibility/resistance testing.
MYCOLOGY CULTURES
Mycology cultures will be read initially to screen for yeast and/or mould and then final reports will be issued at four weeks or sooner if appropriate.
KOH/Fungal Smears are NOT PERFORMED
Yeast Susceptibility Testing: This is a send out test and should be requested only after consulting the Infectious Disease Service. Exception: Yeast from blood cultures.
MYCOBACTERIOLOGY
Rule Out M. tuberculosis Complex PCR. PCR for MTB complex will be performed on one to three specimens (sputum only) by the Microbiology laboratory following approval of the request by Infection Prevention (one specimen for lower risk patients and 2 specimens for higher risk patients per APHL guidelines). The specimens will also be sent to the VA Connecticut (West Haven) Laboratory for smear and culture.
Acid Fast Bacilli (AFB) smear and cultures: Submit to the Microbiology Laboratory for shipment to the VA Connecticut Lab.
AFB in blood: Consult infectious disease. After consultation Myco-F lytic bottles can be obtained from the microbiology lab.
Final negative reports will be issued after 6 - 8 weeks. Any positive culture and susceptibility report (if appropriate) will be issued when available.
PARASITOLOGY
Parasitology identification is not performed in-house due to low yields in the population. Please contact the send-out department. Exception: The Multiplex Vaginal Panel (MVP) does include the detection of Trichomonas vaginalis.
Message
Director of Microbiology
| Dr. Merry Spradling | 857-203-5020 |
BACL Microbiology Laboratory Supervisor
| Scott Connolly 857-203-6021 |
Microbiology Lead Technologist
Kristen Houghton
Microbiology Laboratory: 857-203-5954
Hours of Operation
Monday-Friday: 7:00 AM to 5:00 PM
Weekends and Holidays: 7:00 AM to 3:00 PM
GENERAL INFORMATION
The Microbiology Laboratory performs routine gram stains, aerobic, anaerobic, and mycology on a variety of specimen types from various body sources. Identification and susceptibility testing will be performed as applicable, and reporting of specific antibiotics will follow guidelines for CLSI (Clinical Laboratory Standards Institute).
Select molecular PCR assays are performed and will detect or not detect specific analytes that are listed on the assay/panel. SARS-CoV-2, Influenza (A and B) and RSV testing is performed using PCR with a turnaround time of 2 hours from receipt in the West Roxbury Laboratory. This assay is performed 24/7 and requires a properly obtained nasopharyngeal/nasal swab submitted in VTM/UTM from individuals with signs and symptoms of respiratory tract infection which can be obtained from the laboratory. This assay is also available at the Brockton, JP, and Bedford facilities but only during their routine laboratory hours. A Respiratory Pathogen Panel is also available to test for additional respiratory pathogens from a properly obtained nasopharyngeal/nasal swab collected in VTM/UTM. Respiratory Panels should only be requested after ruling out SARS CoV-2, Influenza A, Influenza B, and RSV. Additional molecular PCR assays are listed below.
Microbiologic detection of pathogenic organisms begins with properly collected specimens and timely delivery to the laboratory. Please take the extra effort to collect an optimal specimen (e.g., a small piece of tissue, fluid or aspirate rather than a swab).
All specimens for culture must be collected and transported to the laboratory according to accepted standard procedure. Individual test listings provide full details. Complete patient identification (first name, last name and entire social security number), specimen type, tests ordered with order number, date/time of collection, and collector initials must be provided. Specimen body site/source is required for all cultures.
All specimens other than the following should be refrigerated immediately upon collection:
The following specimens should be left at room temperature
Blood Culture Bottles
Body fluids (Do not collect in blood culture bottles)
Tissues/bones/biopsy
Cultures for N. gonorrhoeae*(Genital)/meningitidis
Aspirates/syringes
Swab cultures for anaerobes in anaerobic transport media/anaerobic swabs
*PCR for N. gonorrhoeae/Chlamydia in COBAS media is the optimal specimen and culture is discouraged. PCR is a send out test performed at West Haven.
ROUTINE TESTS PERFORMED IN MICROBIOLOGY
GRAM STAIN’s
Exceptions: Urine, Throat, Catheter Tip
ANAEROBIC CULTURE
Automatically performed on body fluids, tissues, bones, abscesses, aspirate, new drainages, medical devices
BLOOD CULTURE
Gram stains are only performed after a bottle has alerted as positive.
CRYPTOCOCCUS AG PANEL, CSF (if CJD is suspected – notify the laboratory)
CRYPTOCOCCUS AG PANEL, SERUM
CULTURE, ABSCESS
CULTURE, ASPIRATE
CULTURE, BODY FLUID (if CJD is suspected – notify the laboratory)
CULTURE, BONE
CULTURE, BONE MARROW
CULTURE, BRONCHIAL
CULTURE, CATHETER TIP
CULTURE, CSF (If CJD is suspected – notify the laboratory)
CULTURE, CALCULUS
CULTURE, DRAINAGE
CULTURE, EAR
CULTURE, EYE (if CJD is suspected – notify the laboratory)
Corneal Scraping’s may be collected and plated bedside. Agar may be retrieved directly from the Laboratory.
CULTURE, EMPYEMA
CULTURE, GENITAL
CULTURE, LEGIONELLA
CULTURE, MEDICAL DEVICE
CULTURE, SPUTUM
CULTURE, THROAT
CULTURE, TISSUE (if CJD is suspected – notify the laboratory)
CULTURE, URINE
CULTURE, WOUND
FECAL LEUKOCYTES (LACTOFERRIN)
GC CULTURE (discouraged: use COBAS media for PCR GC/Chlamydia)
NOCARDIA CULTURE
MYCOLOGY CULTURE
AFB CULTURE AND SMEAR (Mycobacteriology sent out to West Haven VA AFB Lab)
Cultures vary in the time they are held before being finalized due to a variety of reasons such as slow growing organisms, additional identification and susceptibility testing or questionable rule out results.
Nonetheless routine bacterial cultures are held for 48 hours except for throat cultures. A culture that has an anaerobe culture is held for 7 days. Blood Cultures are held for 5 days unless the bottles alert as positive.
Routine TESTS performed in MOLECULAR
C. diff/epi toxin B gene (Cepheid) PCR
Limit one loose or watery specimen per patient per week.
Stools that test positive to PCR will be reflexed to the C. diff Toxin/GDH Antigen. See reflex details below.
COVID-19 and FLU/RSV DIAGNOSTIC PANEL (Cepheid) PCR
SARS-CoV-2 PCR(Cepheid) PCR
Carba-R Perirectal Screen (Cepheid) PCR
Norovirus Genogroup I (GI) and Genogroup II (GII) (Cepheid) PCR
MTB/Rif complex (Rule/Out) (Cepheid) PCR
Performed only on sputum with approval through Infectious Disease.
Respiratory Pathogen Panel (RP2.1 on BioFire) - alias COVID-19 DIAGNOSTIC PANEL(BIOFIRE)
Blood Culture Identification Panel (BCID2 on BioFire) PCR
Performed only on positive blood cultures only. See reflex details below
Gastrointestinal panel (GI on BioFire) PCR
Automatic Reflex Testing on Microbiology tests:
Mycology culture, AFB Culture & Smear AFB smear and AFB culture: Will be added to bronchial specimens and respiratory tissues.
Anaerobic culture: Added to specimens (surgical, aspirate, etc) that require anaerobic cultures and that are not received on red top swab culturettes. They are allowed on blue top swab culturettes. (Stored in laboratory)
Carba-R PCR will be added to any culture isolates that test intermediate or resistant to a carbapenem antibiotic and is identified as an Enterobacterales, Pseudomonas aeruginosa, or Acinetobacter baumannii complex.
Positive Blood Cultures: Gram stain and BCID2 PCR will be added on and performed on positive blood cultures ONLY. Only the first sets of positives will be reflexed for PCR unless an additional organism or morphology of bacteria/yeast is seen.
C diff toxin/GDH Antigen will be reflex to all stool specimens that test positive for C. diff tox B Gene by PCR.
A stool culture will be performed as reflex after a Gastrointestinal (GI) panel by PCR is positive for a bacterium that can be isolated by this lab such as Campylobacter, Plesiomonas, Salmonella, Vibrio, Yersinia or Shigella.
ANTIMICROBIAL SUSCEPTIBILITY TESTING
Susceptibility testing is performed on pathogens to antibiotics that have CLSI/FDA breakpoints. MIC values (in micrograms/ml) and interpretations of S/I/R will be reported. Certain antibiotics do have SDD (Susceptible Dose-Dependent) interpretations and disclaimers will be added as necessary.
Certain antibiotics may be reported by manual testing methods due to updated CLSI standards that are not reflective of current automated susceptibility testing methods.
Testing for organism/antibiotic combinations with no interpretative criteria is not recommended. Consult infectious disease for testing of additional antibiotics.
Repeat antibiotic susceptibility testing on the same patient with the same organism is not performed on specimens from the same site within 3 days for unit patients and 7 days for ward patients. Consult the Technical Director of Microbiology and/or supervisor for technical questions related to susceptibility/resistance testing.
Antibiotic reporting cascade for Enterobacterales only. 1st line antibiotics that will be reported on this cascade include:
• Amoxicillin-clavulanate
• Ampicillin
• Ampicillin-sulbactam
• Cefazolin
• Cefoxitin
• Ceftriaxone
• Ciprofloxacin
• Levofloxacin
• Gentamycin
• Nitrofurantoin (Urine specimens only)
• Piperacillin-tazobactam
• Trimethoprim-sulfamethoxazole
If certain 1st line antibiotics are Intermediate or Resistant then this will trigger a 2nd line of reportable antibiotics:
• If Cefazolin is Intermediate or Resistant:
Cefuroxime will be reported.
Cefuroxime will be reported.
• If Gentamicin is Intermediate or Resistant
Tobramycin will be reported.
Tobramycin will be reported.
Amikacin will be reported by disc diffusion with interpretation only (No MIC)
• If Ceftriaxone is Intermediate/Resistant OR isolate is ESBL positive:
Cefepime will be reported.
Meropenem/Ertapenem will be reported.
If Meropenem/Ertapenem 2nd line antibiotics are Intermediate or Resistant, then a Carba-R PCR test will be reflexed to screen for Carbapenemase producing genes.
• If confirmed CRE(Carbapenem resistant Enterobacterales)/CP(Carbapenem producing) via Carba-R PCR:
Ceftazidime-avibactam and Meropenem-vaborbactam will be reported.
Additional Notes for this cascade for Enterobacterales:
• AmpC inducible Enterobacterales may have additional antibiotics suppressed.
• Ceftazidime may be tested and reported upon request when other 1st and 2nd line antimicrobials are non-susceptible.
• Fosfomycin may be tested and reported upon request for E. coli in urine cultures only. This is done by disc diffusion with interpretation only (No MIC)
• Isolates from Cerebrospinal Fluid (CSF) may have additional antibiotics suppressed.
MYCOLOGY CULTURES
Mycology cultures will be read initially to screen for yeast and/or mould and then final reports will be issued at four weeks or sooner if appropriate.
KOH/Fungal Smears are NOT PERFORMED
Yeast Susceptibility Testing: This is a send out test and should be requested only after consulting the Infectious Disease Service. Exception: Yeast from blood cultures.
MYCOBACTERIOLOGY
Rule Out M. tuberculosis Complex PCR. PCR for MTB complex will be performed on one to three specimens (sputum only) by the Microbiology laboratory following approval of the request by Infection Prevention (one specimen for lower risk patients and 2 specimens for higher risk patients per APHL guidelines). The specimens will also be sent to the VA Connecticut (West Haven) Laboratory for smear and culture.
Acid Fast Bacilli (AFB) smear and cultures: Submit to the Microbiology Laboratory for shipment to the VA Connecticut Lab.
AFB in blood: Consult infectious disease. After consultation Myco-F lytic bottles can be obtained from the microbiology lab.
Final negative reports will be issued after 6 - 8 weeks. Any positive culture and susceptibility report (if appropriate) will be issued when available.
PARASITOLOGY
Parasitology identification is not performed in-house due to low yields in the population. Please contact the send-out department. Exception: The Multiplex Vaginal Panel (MVP) does include the detection of Trichomonas vaginalis.
Test Code
Microbiology
Additional Information
Microbiology Specimens that need site or source
Last Updated: May 19, 2025
