Public Health Laboratory

Required Submissions to Public Health (Title 17)

When a laboratory receives a specimen or request for the laboratory diagnosis of a suspected human case of one of the following diseases, the laboratory must communicate with Contra Costa Communicable Diseases immediately by telephone 925-313-6740.

• Anthrax
• Botulism
• Brucellosis
• Glanders
• Novel influenza
• Melioidosis
• Plague
• Smallpox
• Tularemia
• Viral hemorrhagic fevers

• Drug resistant Neisseria gonorrhoeae (cephalosporin or azithromycin only)
• Listeria monocytogenes
• Mycobacterium tuberculosis
• Neisseria meningitidis from sterile sites
• Salmonella
• Shiga toxin-producing Escherichia coli (STEC), includes O157 & non-O157 strains
• Shigella
• Candida auris(w/in 10 working days)

Specimens:

• Malaria positive blood film slides
• Neisseria meningitidis eye specimens
• Shiga toxin-positive fecal broths
• Zika virus immunoglobulin M (IgM)-positive sera

Upon request:

• HIV-1/2
• SARS-CoV-2

Food Poisoning and Water Pollution

If deemed appropriate/necessary, the Communicable Disease Program or Environmental Health Program will submit suspect samples to CCPHL for testing. Samples suspected of causing food or waterborne illnesses will only be accepted if deemed appropriate by the aforementioned entities.

Please call the Communicable Disease Program at 925-313-6740 or the Environmental Health Program at 925-608-5500 for further information.

Influenza

CCPHL along with the CDC California Emerging Infections Program (CEIP) requests that all clinical laboratories collect and submit influenza specimens from patients who meet the following criteria:

• Hospitalized within 14 days of positive influenza result AND
• Positive result for influenza by rapid test; OR
• Positive type A result for influenza by molecular test and no definitive influenza A subtype result available

Contra Costa County participates in the national Hospitalized Influenza Surveillance Program (FluSurv-NET). Clinical respiratory specimens submitted to CCPHL for testing have assisted the CDC with yearly monitoring of influenza viruses circulating in the United States.

Malaria

Blood films for the detection of malaria parasites may be submitted to the CCPHL. Blood films on which the diagnosis of malaria has been established must be sent to the CCPHL for confirmation (Title 17, California Code of Regulations, Section 1075).

NGHA Renewal Form

An NGHA program is a program in which bioanalytical screening is provided to an asymptomatic individual to screen for a non-infectious chronic health condition. Individuals who appear likely to have a marker or risk factor are then referred to licensed sources of care for appropriate follow up. NGHA programs must provide significant public health benefit as determined by accepted public health protocols and practice.

Facilities must comply with the requirements of CLIA waived testing and meet requirements of Section 1265 of the California Business and Professions Code. If blood collection is to be performed during the nondiagnostic general health assessment, finger prick method is the only "skin puncture" method permitted per California regulations, and does not include venipuncture, arterial puncture, or any other blood collection procedure.

California Business and Professions Code: Nondiagnostic General Health Assessments

• California Code, Business and Professions Code - BPC § 1244 | FindLaw
• California Code, Business and Professions Code - BPC § 1244.1 | FindLaw

Orthopox/mpox

CCPHL accepts Orthopox/mpox specimens for testing. If sending specimens to CCHPL, please contact the Communicable Disease Program (CoCoCD@cchealth.org) for additional guidance.

Further information and forms regarding mpox testing can be found below:

• Monkeypox Screening Form
• Specimen Collection Instruction
• Viral and Rickettsial Disease Laboratory General Purpose Specimen Submittal Form

Rabies

CCPHL tests various animals at high risk for rabies. Animal species tested include both domestic and wild species and varies from dogs and cats to raccoons and bats. Rabies testing may be necessary if there is confirmed or suspect human contact with a wild animal, if a bite occurs with a domestic animal or for general surveillance purposes.

Arrangements for animal testing are made through Martinez Animal Control at 925-646-2995, Antioch Animal Control at 925-779-6989 or the Communicable Disease Program at 925-313-6740. A fee is charged for a rabies test for an animal which is not required for Public Health control.

Salmonellosis

A culture on which the diagnosis of salmonellosis (other than typhoid fever) has been established must be submitted to the CCPHL for definitive identification. Following treatment, stool specimens from individuals in certain occupations must be submitted to the CCPHL for culture and Public Health clearance.

Sexually Transmitted Diseases

Diagnostic services for syphilis such as darkfield, RPR/VDRL and TP-PA confirmatory testing are available. Other diagnostic services include detection of gonorrhea and chlamydia by highly sensitive molecular assays and microscopic detection of genital infections by protozoa, fungi and Gardnerella vaginalis. Providers may wish to refer patients to Public Health STD clinics in Richmond, Pittsburg and Concord.

Please find more information on the STD website.

Typhoid Fever

A culture of the organism from which the diagnosis of typhoid fever is established must be submitted to the CCPHL for definitive identification. Following treatment, stool and urine specimens submitted are to be sent to the CCPHL for culture and clearance.

Tuberculosis

Isolation and identification of acid-fast bacilli and antibiotic susceptibility tests on Mycobacterium tuberculosis are available at the CCPHL. A culture on which the diagnosis of tuberculosis has been established must be submitted to the CCPHL for definitive diagnosis and drug susceptibility testing (if required).

The name, address and date of birth of the person from whom the specimen was obtained, the date the specimen was obtained and the name, address and telephone number of the health care provider of the patient must be provided (Title 17, California Code of Regulations, Section 1075).

Whole Genome Sequencing (WGS) for SARS-CoV-2

The currently available COVID-19 vaccines have high efficacy for prevention of symptomatic SARS-CoV-2 infection. However, breakthrough cases among fully vaccinated people are expected. The Contra Costa Public Health Department is seeking to investigate whether these cases and other high-risk scenarios may be caused by particular SARS-CoV-2 variants or current Variants of Concern (VOC). As such, the department is encouraging clinicians and clinical laboratories located within Contra Costa County to forward positive specimens (≥500uL) for WGS that meet criteria.

WGS is not currently a validated assay and you will not receive laboratory reports from the Contra Costa Public Health Laboratory or California Department of Public Health (CDPH). However, the Contra Costa Public Health Department may reach out for purposes of Contact Tracing to control the spread of SARS-CoV-2 and certain variants.

Notification about cases and questions please call 925-370-5775.

• Vaccine Breakthrough: Person who has SARS-CoV-2 RNA detected by a molecular test (e.g., PCR or NAAT) on a respiratory specimen collected ≥14 days after completing the primary vaccination series (i.e., ≥14 days following receipt of the second dose in a 2-dose series or ≥14 days following receipt of one dose of a single-dose FDA-authorized COVID-19 vaccine). Symptomatic breakthrough cases (also referred to as Vaccine Breakthrough cases of interest [VBCI]) will be prioritized for WGS, but asymptomatic vaccine breakthrough cases can be reviewed to see if potential follow up with WGS is appropriate;
• Hospitalized Patients (or ICU Patients);
• Outbreaks with high attack rate in a given outbreak or more cases than expected;
• Concerns for variants due to drop in diagnostic assay target (ex: N target, ORF target, S target) or any marked difference in real-time RT-PCR viral target(s) cycle threshold values (CT);
• Concern for variants due to other clinical history, such as, patient is immunocompromised, prolonged infection, failed to improve after receiving monoclonal antibody, death, etc.;
• Travel Associated: (1) case with recent travel or (2) case with contact to someone that had recent international travel;
• Reinfection: positive SARS-CoV-2 PCR or NAAT >90 days after first positive test. (please submit original specimens from both original infection and subsequent infection.

AND

Original positive respiratory specimen must be available for WGS and the Cycle threshold (Ct) value ≤30 (if Ct available) or RLU ≥1150. (e.g. nasal or NP swabs in viral transport medium (VTM), saline, or molecular transport medium, Hologic Aptima media, sputa. Please note that dry swabs, are not acceptable for WGS.)

Sample Storage and Shipment:

Sample Storage and Shipment:

Include a requisition form OR CDPH Specimen Submittal Form

• Patient Demographics: Name, DOB, description of symptoms and onset, clinical information (hospitalization, death, etc).
• Test Information: collection date, Ct ≤30 or or RLU ≥1150, COVID-19 test type, lab that performed test.
• Reason WGS is being requested. If Vaccine Breakthrough, please provide dates of vaccination and manufacturer.

For both WGS, please request the lab store the original positive sample or a portion of the original positive sample ( ≥500 uL) frozen until shipment and shipped on dry ice to the CCPHL. Please ship using the following:

Attn: Stephanie Trammell or Kelly Riddle
Contra Costa County Public Health Laboratory
2500 Alhambra Ave, Rm. 209
Martinez, CA 94553
925-370-5775

For additional information please see: cchealth.org/covid19/providers/

For questions regarding Contra Costa County's other COVID-19 surveillance efforts for which you are a participant, please contact Stephanie Trammell at Contra Costa Public Health Laboratory, stephanie.trammell@cchealth.org.

• SARS-CoV-2 surveillance submission form