Quality Assurance/Quality Control Manual

Ohio Water Microbiology Laboratory

ABSTRACT

The U.S. Geological Survey (USGS), Ohio Water Microbiology Laboratory (the OWML) provides water-quality data on microorganisms of public health significance for a variety of projects within the USGS. Currently, the OWML analyzes samples for and provides training on bacterial indicators, coliphage, enteric viruses, and two protozoan pathogens—Cryptosporidium and Giardia.

Quality-assurance and quality-control (QA/QC) practices for the operation of OWML are described in this manual. The Laboratory Manager, Laboratory Coordinator, Chemical Hygiene Officer, and laboratory and field staff are responsible for implementing QA/QC procedures. This includes correctly following methods of analysis, media and reagent preparation and storage, and analytical quality-control procedures. A sample management and documentation system involves the use of service request forms and login ID’s for each sample. A laboratory information management system (LIMS) has been implemented to store sample login information and results. Laboratory equipment maintenance and calibration records are also stored in the LIMS.

INTRODUCTION

The USGS Ohio Water Center Ohio Water Microbiology Laboratory (the OWML) mainly provides analytical data for projects within the Ohio Center. With the growth of microbiological monitoring within the WRD, however, the OWML has begun analyzing samples for other Water Center programs by request. Samples are collected to determine the presence of microbiological organisms of public health significance in ground waters and surface waters for a variety of study objectives. For example, some local studies are done to judge compliance with standards for protection of public health in swimmable or drinkable waters. Other studies investigate the occurrence, distribution, and trends of pathogenic organisms and indicators in surface and ground waters and relate these to environmental and water-quality factors.

The OWML fulfills analytical requirements of the WRD by analyzing environmental samples for bacterial indicators, coliphage, enteric viruses, and two protozoan pathogens—Cryptosporidium and Giardia. OWML personnel provide assistance for project planning and training on three major groups of microorganisms of public health significance in the United States: bacteria, viruses, and protozoa. As funds become available for expansion, the OWML plans to add other analytical methods and types of microorganisms to its analytical list. The OWML is not involved in method development at the present time, but instead tests new methods developed by others for applicability to ambient monitoring programs.

The OWML is committed to providing quality microbiological analytical services to the USGS. The quality assurance/quality control (QA/QC) program is designed to ensure the production of scientifically sound, legally defensible data of known and documented quality. The effectiveness of this program relies on clearly defined objectives, well-documented procedures, and management support.

Purpose and Scope

The purpose of this manual is to identify and document practices and standard operating procedures for those activities of the OWML that affect quality of data. The manual provides OWML personnel and customers with general descriptions of quality practices and goals to aid in the interpretation of data. This manual is intended to be an unpublished, dynamic document that will be frequently updated as laboratory activities expand or change.

Organizational Structure

The Laboratory Manager (1) oversees the daily operations of the OWML, (2) directs technical personnel in the proper performance of laboratory procedures and the reporting of results, (3) ensures that appropriate methods are used, (4) plans activities leading to testing and modification of analytical procedures, and (5) designs and implements a comprehensive QA/QC program. The Laboratory Manager is responsible for initiating the QA/QC program, providing information and training to the staff, and periodically reviewing QA/QC activities.

The Laboratory Coordinator oversees the daily operations of the OWML, ensures that the equipment is properly maintained and calibrated, orders supplies and equipment, and oversees and performs analytical work. The Laboratory Coordinator implements the QA/QC program in the daily tasks of conducting analyses, performing quality control checks, and calculating and reporting results.

The Chemical Hygiene Officer oversees safety operations in the laboratory with assistance from the Laboratory Manager and Laboratory Coordinator.

The laboratory and field staffs are responsible for correctly implementing collection and analysis procedures and for identifying and working with supervisors to correct and avoid potential problems.

Table 1. Current laboratory personnel and qualifications.

NAME	LABORATORY TITLE	USGS TITLE	Education/experience
Donna Francy	Microbiology/ Water Quality Specialist	Hydrologist GS-13	B.A. Biology, M.S. Environmental Science, Certified Clinical Microbiologist 15 years experience in water quality and environmental microbiology
Rebecca Bushon	Laboratory Manager	Hydrologist GS-12	B.S. Biology 10 years experience in microbiology
Don Stoeckel	Project Chief/ Special Projects	Hydrologist GS-12	B.S. Microbiology M.S. Environmental Science Ph.D. Soil Science 10 years experience in microbiology
Chris Kephart	Molecular Analyst	StuTrain(Hyd) GS-9	B.S. Microbiology Working on M.S. Environmental Science 7 years experience in microbiology
Amie Brady	Laboratory Coordinator	Hydrologist GS-9	B. S. Environmental Science B.S. Plant Biology M.S. Environmental Science 7 years experience in microbiology
Christina Likirdopulos	Specialized Lab Analyst/ Chemical Hygiene Officer	Hydrologist GS-9	B.A. Chemistry M.S.P.H. Environmental Sciences & Engineering 7 years experience in microbiology
Erin Bertke	General Lab Analyst	Biologist GS-7	B.S. Environmental Science 3 years experience in microbiology

GENERAL LABORATORY QUALITY ASSURANCE/QUALITY- CONTROL PRACTICES

An overview of analytical methods, training policies, safety, laboratory maintenance, sample management, and data documentation is given in this section.

Analytical methods

The methods used by the OWML can be categorized into four groups: compliance, official, provisional, and experimental. The United States Environmental Protection Agency (USEPA) and others in the research community are continuously developing new methods for detecting and quantifying microbiological pathogens and indicators in water; therefore, several types of methods for target organisms may be currently in use at the OWML.

Compliance methods are those published by USEPA in the Federal Register and are used to determine compliance with standards for protection of public health in swimmable or drinkable waters. Analytical methods for fecal-indicator bacteria are often in this group because they are straightforward, quantitative, and routinely used.

Official methods are those noncompliance methods published by water-analysis authorities such as American Public Health Association, the U.S. Environmental Protection Agency, or the USGS. Official methods should be well established, have known levels of bias and variability, and be relatively easy to apply in field operations or have holding times long enough to allow shipping to a central laboratory for analysis.

Provisional methods are published methods that are still being validated by the method developer, usually the USEPA. For these methods, the method developer establishes precision and accuracy and ensures the methods are adequately tested. Because methods for detection of protozoa are complex, qualitative to semiquantitative, expensive, and very time consuming, these methods are often provisional.

Experimental methods are unpublished methods that are currently being testing to establish QA/QC practices and determine applicability to ambient monitoring programs.

Training

The Laboratory Manager and Laboratory Coordinator are responsible for ensuring that laboratory employees receive proper training in analytical methods and laboratory procedures and for documenting any training received. In particular, laboratory employees will be trained in sterile technique before handling samples for microbiological analysis. A new employee will receive orientation and skills training. New or established employees may receive training on new methods given by the method developer. The Laboratory Coordinator will maintain training records for microbiological methods on file by employee; this includes on-the-job training as certification of proficiency in microbiology.

The Laboratory Coordinator, Chemical Hygiene Officer, and Water Center Safety Officer provide safety orientation to new employees and safety education to all employees. The employee orientation covers general safety issues, emergency procedures, standard-safety operations, the chemical-hygiene plan, hazardous-waste management, waste disposal, and location of safety equipment.

Safety

Detailed laboratory safety practices and responsibilities are described in the Chemical Hygiene Plan. Safety activities include safeguards to avoid electric shock; prevent fire; prevent accidental chemical spills; and minimize microbiological dangers, facility deficiencies, and equipment failures.

Laboratory personnel that are isolating microorganisms from natural sources must be made aware that pathogens may be present in environmental samples. Technicians are to wear disposable gloves and lab coats when handling samples that are likely to contain pathogens. Safety glasses are worn if there is a chance of projectiles, aerosols, or other foreign matter entering the eye. This includes when using positive-pressure air to blow out any remaining liquid during the ultrafiltration process for Cryptosporidium and Giardia. Laboratory personnel will receive immunizations for pathogens on a project-specific basis. Each project sending samples to the OWML is required to have a project safety plan--copies are available for OWML employees. Immunizations are offered to all OWML workers for Hepatitis A virus, Hepatitis B virus, and tetanus.

Safety equipment is tested at regular intervals. Safety showers and eyewash stations are tested annually and recorded in the LIMS. Fire extinguishers are inspected annually. The Chemical Hygiene Officer maintains a list of chemicals and arranges for a contract for disposal of hazardous waste.

Laboratory materials and equipment

The Laboratory Manager sets policies for preventive maintenance and calibration of laboratory materials and equipment. Two QA/QC logbooks are kept in the laboratory bookshelf with records of quality-assurance checks of materials and equipment up through September 30, 2006. The logbooks are for (1) equipment -autoclaves, balances, pipettors, hoods, and thermometers; and (2) laboratory water. Examples of equipment log sheets are in Appendix AA. Results of quality-assurance checks of materials and equipment starting in FY 04 are stored in the LIMS. Quality-control checks that are required LIMS entries are listed in italics below.

· The Laboratory Manager or Laboratory Coordinator must review QA/QC quarterly reports from LIMS to ensure procedures are followed and problems are properly addressed.

For some pieces of equipment, the use of daily logbooks to record operating times and other types of frequent entries are required. A daily logbook is kept with the autoclaves and the water-quality meters (pH, specific conductance, and turbidity).

General sterility and cleanliness

The sterility and cleanliness of the laboratory is necessary to ensure the integrity of samples and analytical procedures.

· Traffic through the laboratory is restricted to those doing work in the laboratory, especially when analytical work is being done.

· The countertops are wiped down with surface disinfectants, such as Conflikt (Decon Labs, Inc., King of Prussia, PA) or 70 percent ethanol, before and after use.

· Antimicrobial soap is available at various laboratory sinks to facilitate hand washing before and after laboratory work.

Clean and sterile glassware that is free of detergent residue is crucial to ensure valid results in microbiology.

· Dirty dishes are placed on a moveable laboratory cart after use and are not to be stored on countertops. Dishes are washed in a dishwasher or by hand with hot water and laboratory-grade phosphate-free detergent. Dishes are rinsed with tap water and then deionized water.

Autoclaves

Sterilization is the process that eliminates living organisms from substances or objects. The OWML is equipped with three autoclaves for sterilization of glassware, reagents, media, and disposables—two medium-sized autoclaves (Market Forge) that are operated in the side laboratory and one large autoclave (Consolidated) that is operated in the warehouse.

· Dishes that need to be sterilized are wrapped in aluminum foil or kraft paper and placed in the autoclave for moist heat sterilization. Clean and sterile dishes are stored in closed cupboards until use.

· The autoclaves are operated at 15 lb/in² steam pressure, producing an inside temperature of 121 to 124^oC (American Public Health Association, 1998, Section 9020B). Do not overload the autoclave. Autoclave time depends on the type and amount of equipment as follows:

· Glassware and up to 250 mL of liquid—15 minutes

· 500 to 2,000 mL liquid—30 minutes

· Greater than 2,000 mL to 6,000 mL liquid—15 minutes per 1,000 mL

· Greater than 6,000 mL liquid—90 minutes

· Carbohydrate-containing media—15 minutes (no more than 250 mL volumes)

· Contaminated materials and discarded cultures—30 minutes, allow autoclave chamber pressure to decrease, then run for a 60 minute cycle

· Operating temperature and pressure are checked once a week. Heat-sterilizing tape is used with each run to identify supplies that have been properly sterilized and checks the performance of the autoclave. The performance is also checked monthly by using spore indicators and recorded in the LIMS.

· If the autoclave does not reach the specified temperature or fails the spore indicator test, service the autoclave and re-sterilize all glassware and reagents that were insufficiently sterilized.

For the two medium-sized autoclaves, general maintenance is as follows:

· The autoclaves are operated using deionized water.

· At the end of the day, autoclaves are drained. Twice a month, autoclaves are cleaned with mild soap, rinsed with water, and drained. The condensate holding tank is drained daily or as needed. The cleaning date is recorded in the LIMS.

· Twice a year, have a contractor inspect and calibrate the autoclaves and perform preventive maintenance. Preventive maintenance dates are recorded in the LIMS.

· Twice a year, clean the chambers with 10% muriatic acid and flush well with water. Cleaning dates are recorded in the LIMS.

For the large autoclave, general maintenance is as follows:

· Once a month, clean chamber with water and liquinox. Cleaning dates are recorded in the LIMS.

· Twice a year, have a contractor perform preventive maintenance and inspection, clean and service the generator, clean the door gasket and head ring, apply graphite to the door gasket, oil the door hinge pins, and lubricate the door hub. Preventive maintenance dates are recorded in the LIMS.

· Twice a year, clean the chamber with 10% muriatic acid and flush well with water. Cleaning dates are recorded in the LIMS.

Laboratory water

The OWML has three types of laboratory water:

(1) Type III deionized water (“deionized water”) produced from City of Columbus tap water for general laboratory use. The deionized water unit and tap are stored in the warehouse. The system is described in Francy and others (1998). The vendor changes the cation and anion columns, moves forward the standby mixed-bed column, installs a new standby tank, and changes the carbon filter when the red service light illuminates. Maintenance checks are recorded in the LIMS.

(2) Reagent-grade water produced using a Millipore MilliQ system (“MilliQ water”). Deionized water is used as source water for the MilliQ system. Reagent water is used for cultivation media and additives (mTEC, MI, mEI, antibiotic stocks, and others) as well as for preparation of reagents for sensitive procedures (elutions, PCR, hybridization, and others). The MilliQ cartridges are changed by OWML laboratory personnel when the service light blinks and the display message reads “EXCH. CARTRIDGES.” Indicate the date of cartridge change in the LIMS.

(3) Deionized water is stored in a laboratory carboy (“stored water”) and used for rinsing of dishware and other supplies.

A variety of quality-control checks are routinely done on the three types of water and may differ depending on the type of water. Acceptance criteria are listed in table 2. For deionized water, two levels of acceptance criteria are listed—(1) a warning level wherein the system is inspected and constituents are retested and (2) a shut-down level. For MilliQ water, only a shut-down level is listed in table 2. For stored water, if criteria are not met, the container is cleaned out, refilled, and retested.

· Quarterly checks of specific conductance and turbidity are done on all three types of water and recorded in the LIMS. Instructions for performing this check are in the back of the equipment QA/QC logbook.

· Quarterly checks of bacterial growth are done on the MilliQ water and recorded in the LIMS. Instructions for performing this check are in the back of the equipment QA/QC logbook.

· A blank of deionized water is submitted to the National Water Quality Laboratory (NWQL) annually and analyzed for low level nutrients (Schedule 1217), and total-organic carbon (Labcode 114), and the results are recorded in the LIMS. We no longer analyze a blank for trace elements and low-level major ions because the need for these low-level analyses is project specific.

· The stored deionized water carboy is to be emptied completely and cleaned with Liquinox and water every other week. Record cleanings in the LIMS.

Table 2. Acceptance criteria for laboratory water quality-assurance checks

[Adopted from USEPA (1978), APHA (1998), and ASTM (1999); NA is not applicable; constituents highlighted in gray are no longer required tests]

	DEIONIZED		MILLIQ	STORED
ACTION	warning	shut down	shut down	clean and refill
Specific conductance (ms/cm)	3	5	2	3
Turbidity	1	5	1	1
Heterotrophic plate count (colonies/mL)	NA	NA	<1	NA
Total organic carbon (mg/L)	0.2	10	NA	NA
Sodium (mg/L)	0.1	1	NA	NA
Nutrients individual (mg/L)	0.1	1	NA	NA
Heavy metals, individual (Cd, Cr, Cu, Ni, Pb, Zn) (mg/L)	1	10	NA	NA
Other trace elements (mg/L)	3	50	NA	NA

Analytical balances

Analytical balances are used for accurate weighing of reagents and media. They are checked and calibrated annually by the manufacturer’s service technician, and the results are recorded in the LIMS. Balances must rest on a firm, level surface. Balance trays are wiped off after each use with water or a surface disinfectant, such as Conflikt or 70 percent ethanol.

Hoods

The Ohio Water Center has four types of hoods— (1) two biosafety cabinets, (2) a laminar-flow hood, (3) a hazardous-waste fume hood, and (4) a PCR workstation. To ensure proper use of hoods 1, 2, and 3, “quick check” criteria for properly running each hood are posted on the hoods.

· The operation of all hoods are checked and certified by a qualified inspector annually and recorded in the LIMS.

The biosafety and laminar flow hoods have magnehelic pressure gauges (MAG) that are used to monitor operation of the hoods. When using these hoods, check to make sure the pressure gauge is reading at a level approximately equal to the annually recorded MAG level on the calibration sticker. A significant increase in pressure indicates that the filters are dirty whereas a significant decrease in pressure indicates an electrical problem.

The biosafety cabinets, laminar-flow hood, and PCR workstation (Hoods 1, 2, and 4) must be free from contamination by live organisms.

· The working surfaces of the laminar-flow hood, the biosafety cabinets, and the PCR workstation (Hoods 1, 2, and 4) are wiped down with a surface disinfectant, such as Conflikt or 70 percent ethanol before and after general use. When working with pathogenic organisms, the hoods are wiped down with Dispatch Hospital Cleaner Disinfectant towels with bleach (Caltech Industries Inc., Midland, MI) followed with 70 percent ethanol. For the biosafety cabinets, be sure to lift up the work surface and clean under this area periodically.

· The biosafety cabinets and PCR workstation (Hoods 1 and 4) have ultraviolet bulbs for germicidal purposes. The ultraviolet lights in the biosafety cabinets and PCR workstation are cleaned quarterly by wiping the bulbs with a soft cloth. Cleaning dates are recorded in the LIMS. A bulb that is dull in the center needs to be replaced. Record the bulb change in the LIMS.

· Biannually, nonselective agar plates are exposed to airflow in the laminar-flow hood, the biosafety cabinets, and PCR workstation for 1 hour (Hoods 1, 2, and 4). The plates are incubated at 35^oC for 24 hours and examined for contamination. The results are record in the LIMS.

The hazardous-waste fume hood (Hood 3) must be checked to ensure that it is operating properly.

· Check the operation of the hazardous-waste fume hood (Hood 3) quarterly by use of fume cartridges and record results in the LIMS.

Specific conductance, pH, and turbidity meters

With each use of the specific conductance, pH, or turbidity meter, calibrate the instrument according to the manufacturer’s instructions (kept with the meter). Use a calibrated solution that is within the range of the water sample to be measured. Label specific conductance and pH buffer solutions with the date opened and discard working solution weekly. Each piece of equipment has a daily logbook; record all calibrations in the appropriate logbook.

Micropipettors

Micropipettors are used for the accurate delivery of small volumes.

· Pipettors are sent to the manufacturer annually for cleaning, preventative maintenance, calibration, and adjustment, if necessary. Preventive maintenance dates are recorded in the LIMS. Preventative maintenance includes a new seal and piston cleaning annually, and a new shaft and reconditioned piston every 3 years.

Vacuum pump

The vacuum pump is mainly used for membrane filtration. The oil is changed in the pump every 2 years. Record the oil change in the LIMS.

Thermometers, incubators, water baths, refrigerators, and freezers

Thermometers are kept in three areas and are inventoried according to storage and use: (1) extra thermometers for general laboratory use, including the National Institute of Standards and Technology (NIST) thermometer (2) daily-use water-bath, incubator, and refrigerator thermometers, (3) digital thermometers, and (4) back-lab thermometers.

· The NIST thermometer is calibrated and certified annually by an outside service technician. Certification dates are recorded in the LIMS.

· Extra and daily-use thermometers are checked quarterly against the NIST thermometer. Results are recorded in the LIMS and acceptance criteria are listed in table 4. Criteria are based on use.

· Digital thermometers are checked quarterly against the NIST thermometer and are calibrated annually by the manufacturer. Results and calibration dates are recorded in the LIMS.

Table 3. Acceptance criteria for laboratory thermometers
Thermometer use	Thermometer identification (will vary)	Location	Test Temperature	Criteria
NIST	NIST	Drawer	Certified	Certified
Daily use water baths	L	W/B 1	48°C	± 1°C
	S	W/B 2	37°C and 70°C	± 1°C
	O	W/B 3	36°C	± 1°C
	T	W/B 5	70°C	± 1°C
	K	W/B 6	36°C and 48°C	± 1°C
Daily use incubators	U	Inc 5	35°C	± 1°C
	R	Inc 6	35°C	± 1°C
	Q	Inc 7	35°C	± 1°C
Daily use refrigerators	M	Refrig 1	0°C	± 1°C
	N	Refrig 2	0°C	± 1°C
	V	Refrig 3	0°C	± 1°C
	B	Refrig 4	0°C	± 1°C
	W	Refrig 5	0°C	± 1°C
Digital	Dig F, Dig G, Dig H	Drawer	0°C, 36°C, and 48°C	± 0.3°C
Back lab	F	Freezer 5, Back lab	30°C and 0°C	± 1°C
	X	W/B 4, back lab	51°C	± 0.1°C
	C	back lab	0°C	± 1°C

There are 7 incubators, 6 water baths, 5 refrigerators and 5 freezers in use in the laboratory. Temperature settings and criteria for acceptance are dependent on use (table 3). Approximately 11 aluminum-block blue field incubators and 2 double-chamber gray incubators are used for laboratory and field operations.

· The temperatures of the laboratory incubators, water baths, and refrigerators are checked quarterly with NIST-calibrated laboratory thermometers and recorded in the LIMS. During use, the incubators, water baths, and refrigerators are checked daily and recorded on a designated daily log sheet.

· The temperatures of the freezers are checked quarterly with NIST-calibrated laboratory thermometers and recorded in the LIMS. The -70ºC freezers are equipped with automatic alarms that are set to respond when temperatures rise above -60ºC; the alarm system sounds during regular working hours and is attached to a telephone notification system after hours.

· The operating temperatures of microbiological aluminum-block incubators are checked annually (or in preparation for a major study) and recorded on the outside of each incubator and in the LIMS. During periods of heavy use, the temperatures are checked and recorded weekly.

· The two –70^oC freezers (freezers 3 and 4) are used to store samples and microbiological cultures. A filter is cleaned and fans behind the filter are checked by laboratory personnel for operation quarterly and dates are recorded in the LIMS. The condenser is dusted or vacuumed every 6 months and recorded in the LIMS. A temperature chart is changed after a single pass around the chart (weekly).

· Water baths are filled with distilled water and are cleaned with mild soap quarterly, or more often as needed. Record quarterly cleanings in the LIMS.

Table 4. Acceptance criteria for laboratory refrigerators, freezers, incubators, and waterbaths
Equipment identification	Use	Acceptance criteria
INC 2	*Actinomycetes*	28°C ± 1.0°C
INC 3	Hybridization oven	51°C ± 1.0°C, 80°C ± 1.0°C
INC 4	Fungi, general use	36°C ± 1°C
INC 5	Method 1601/1602, transfer cultures, general use	35°C ± 1.0°C
INC 6	*Method 1601/1602, Clostridium, transfer cultures, general use*	35°C ± 1.0°C, 42°C ± 0.5°C
INC 7	Method 1601/1602, transfer cultures, general use	35°C ± 1.0°C
W/B 1	Melt and temper agar	48°C ± 3.0°C
W/B 2	Method 1602, heat treatments	37°C ± 1.0°C, 70°C ± 3.0°C
W/B 3	Grow hosts/1602	36°C ± 1.0°C, 48°C ± 1.0°C
W/B 4	Shaking bath for hybridization	51°C ± 0.2°C
W/B 5	Heat treatments	70°C ± 3.0°C
W/B 6	Grow hosts/1602	36°C ± 1.0°C, 48°C ± 1.0°C
REFRIG 1	Sample storage	1 to 4°C
REFRIG 2	Sample storage	1 to 4°C
REFRIG 3	Reagent storage	1 to 4°C
REFRIG 4	Sample storage	1 to 4°C
REFRIG 5	Reagent/ media storage	1 to 4°C
FREEZ 1	Reagent storage	-20°C to -30°C
FREEZ 2	Ice packs, biological sample storage	-20°C to -30°C
FREEZ 3	Bacteria stocks, virus stocks, samples	Shelf 1 -70°C ± 10°C Shelf 2 -70°C ± 10°C Shelf 3 -60°C ± 10°C Shelf 4 -60°C ± 10°C Shelf 5 -60°C ± 10°C
FREEZ 4	Sample storage	-70°C ± 10°C
FREEZ 5	Probes, hybridization reagents	-20°C to -30°C
FIELD INCUBATORS	Membrane filtration	35°C ± 1.0°C, 44.5°C ± 0.5°C, 41.5°C ± 0.5°C

Microscope

There are two Zeiss microscopes used to perform microscopy. The Zeiss Axio Imager microscope has the capability to perform fluorescence microscopy and differential interference contrast (DIC). Additionally, it is equipped with a digital camera. This microscope is used for specialized laboratory work and for enumerating Cryptosporidium oocysts and Giardia cysts by USEPA Method 1623. The microscope has three objectives: 20X, 40X and 100X (oil), as well as stage and ocular micrometers. Furthermore, the microscope is equipped with excitation/band-pass filters for the immunofluorescence assay (FA) and 4’, 6-diamidino-2-pheylindole (DAPI) analysis. The microscope also has optics for DIC analysis under the 100X objective. It is kept in a room capable of being almost completely darkened.

The older Zeiss microscope is used for general laboratory work, Gram Stains, and Actinomycetes analysis. It is equipped for fluorescence microscopy, so it can also be used to enumerate Cryptosporidium oocysts and Giardia cysts, if necessary. It has five objectives: 10X, 25X, 40X, 63X and 100X (oil), as well as stage and ocular micrometers.

· The mercury bulb power supply for the Zeiss Axio Imager has an automated timer to monitor the number of hours the bulb has been on. After 150-200 hours, the mercury bulb should be changed. Note: the maximum life expectancy of the bulb is 300 hours. Call the manufacturer’s local representative or a professional company for assistance. The bulb must be disposed of in accordance with legal regulations, not in domestic waste. Contact the Carl Zeiss microscopy service for assistance. Record the mercury bulb number and date of installation in the LIMS.

· The mercury bulb power supply for the older Zeiss microscope has a log book to record the number of hours the bulb has been in use. As explained above, the bulb should be changed after 150-200 hours and the appropriate information recorded in the LIMS.

The cleaning procedures are the same for both microscopes.

· The microscope is cleaned by a professional company and the ocular micrometer is calibrated yearly by the company or the manufacturer’s local representative. Record this maintenance in the LIMS.

· After each use, clean the objectives and stage with lens paper and lens cleaner. A Q-tip and lens cleaner can be used to help remove oil from the end of the objective, as well as keep the oculars clean. Keep the dust protection cover on the microscopes while not in use and let the lamp housing cool before putting on the cover.

· As needed, blow dust off of the microscope (especially the condenser, field aperature, and the oculars) with compressed air.

Centrifuges

There are three types of centrifuges that are used to perform separation of particles by centrifugal force. The refrigerated floor centrifuge is used to concentrate Cryptosporidium oocysts and Giardia cysts by USEPA Method 1623, for DNA extraction, and to process concentrated samples. The ultracentrifuge is used to isolate virus particles eluted from water samples and for concentrating bacterial spores. Two microcentrifuges are used for processing bacterial extractions, purifications, concentrations, and phase separations.

Refrigerated floor centrifuge

· Each run of the centrifuge is recorded in the centrifuge log book.

· The temperature is monitored quarterly with the digital thermometer (acceptance criteria is 4+ 3ºC).

· The buckets are disinfected with dilute bleach and dechlorinated quarterly.

· Rotors and adapters are checked for deterioration, as needed.

· Lubrication is done annually, or as needed.

· All maintenance is recorded in the LIMS.

Ultracentrifuge

· Each run of the centrifuge is recorded in the centrifuge log book.

· The rotor and buckets are disinfected with dilute bleach and dechlorinated quarterly.

· Lubrication of the O-ring with vacuum grease, and lubrication of the buckets and cap mating surfaces with Spinkote lubricant are done quarterly.

· The O-rings on the buckets are replaced twice a year.

· The vacuum pump oil is changed every 2 years.

· All maintenance is recorded in the LIMS.

Microcentrifuge (2)

· The chamber and the rotor are cleaned with soap and water quarterly.

· The air intake and exhaust vents are cleared from obstructions quarterly.

· Lubrication of the drive shaft and threads and O-ring with vacuum grease is done quarterly.

· All maintenance is recorded in the LIMS.

Thermal Cyclers

There are two thermal cyclers used to perform the polymerase chain reaction (PCR). The PCR is done to amplify microbial DNA targets through a series of temperatures changes. Numerous projects use the PCR for a variety of applications including microbial source tracking, detection and/or quantification of enteric viruses, and detection and/or quantification of bacterial indicators. The thermal cycler used for end-point PCR performs the PCR to completion so that the amplified DNA products can be subsequently detected using gel electrophoresis. The thermal cycler used for real-time quantitative PCR (QPCR) detects and quantifies the targeted DNA sequence as it is being amplified.

End-point PCR thermal cycler

· The temperature is monitored twice a year (Appendix V).

· Results of the temperature QC are kept in the Master Cycler QC logbook.

· Temperature monitoring dates are recorded in the LIMS.

QPCR thermal cycler

· Background calibration is performed monthly.

· A pure-spectra assay is done twice a year.

· A RNase P verification run is done annually.

· A regions of interest (ROI) plate is run as needed (following lamp replacement or if the system is jostled).

· All quality assurance checks are recorded in the LIMS.

Sample Management and Documentation

Samples for the bacterial indicators, E. coli, enterococci, fecal coliform, and total coliforms, are most commonly processed and analyzed in the field; however, they may be done in the OWML. Holding times are 6 hours for compliance purposes and 24 hours for noncompliance purposes (American Public Health Association, 1998, Section 9060 B.) Adhering to a 6-hour holding time for all bacteriological samples, however, is highly recommended.

Samples for Clostridium perfringens, coliphage, and enteric viruses are processed and analyzed in the OWML; samples are kept on ice and processed within 48 hours of sample collection. Samples for the analysis of coliphage that arrive chilled within 48 to 96 hours from collection are acceptable, but the results are qualified. Samples for Cryptosporidium and Giardia are processed in the OWML within 48 hours of sample collection. Although the samples for Cryptosporidium and Giardia are not kept on ice during transport, they are stored in the refrigerator upon receipt in the OWML.

All requests for laboratory analysis must be submitted using a service request form (Appendix A). The following categories must be filled out when requesting sample analysis: station name, site number, date/time of sample collection, medium code, Water Center user code, and project number. The field personnel must check off requested analyses and make prior arrangements with laboratory personnel. Upon receipt of the sample in the laboratory, personnel will fill in Received By and Date Received on the front of the Service Request form.

Laboratory personnel will then enter sample information on to a log sheet (Appendix B) and log the sample into LIMS, which will assign a login ID. There is one sample logbook that contains a log sheet, service request forms, and results bench sheets. Laboratory personnel will write the login ID on the Service Request form (front and back) and on the sample bottle (or filter cartridge).

The Service Request form is routed to the analyst, who will enter sample login ID, processing times, and analytical information on a separate Results Worksheet (Appendix A). Samples are analyzed within 24 hours of receipt and are stored in the laboratory refrigerators until processing.

Upon completion of the analysis, the analyst writes final results on the back of the Service Request form. A second analyst routinely checks the calculations of the analyst performing the work. The results are entered into the LIMS and then transmitted to the person requesting the analysis by email in a format that can be uploaded into NWIS. The Service Request form and Results Worksheet are then filed together in the sample logbook.

METHODS OF ANALYSIS, MEDIA AND REAGENT PREPARATION, AND ANALYTICAL QUALITY-CONTROL PROCEDURES

Methods of analysis, media and reagent preparation and storage, and analytical quality-control procedures are discussed in this section. Because microbiological analyses measure constantly changing living organisms, the methods are inherently variable. Some quality-control tools used by chemists, therefore, may not be available to the microbiologist (American Public Health Association, 1998, Section 9020 A).

References of published microbiological methods are kept in a notebook in the laboratory. Media-preparation instructions and method summaries written by the OWML are kept in the reference notebook and furnished as Appendixes to this document.

Fecal-indicator bacteria

The methods used for analysis of fecal-indicator bacteria are those of the USGS, USEPA, and APHA and others (table 5). All fecal-indicator bacteria methods used by the OWML are compliance or official methods.

Table 5. Methods for fecal-indicator bacteria analysis used by the Ohio Water Center Microbiology Laboratory (OWML) [DW is drinking water, RW is recreational water]

BACTERIA	METHOD	TYPE OF METHOD	REFERENCE
Total coliforms	mENDO method	Compliance—DW Official—other waters	Britton and Greeson (1987) APHA (1998) Section 9222B
	MI method	Official—all waters	USEPA (2000a and 2002a) (Appendix C)
	Colilert method	Compliance—DW Official—other waters	Idexx Corp., Westbrook, ME APHA (1998) Section 9223 (Appendix D, E)
Fecal coliforms	mFC method	Compliance—DW Official—other waters	Britton and Greeson (1987) APHA (1998) Section 9222D

Enterococci

mEI method

Compliance—RW

Official—other waters

USEPA (1997)

(Appendix H)

Clostridium perfringens

Modified mCP method

Official

USEPA (1996), modified by OWML (Appendix I)

Reagents and media for fecal-indicator analysis are prepared according to the methods and are labeled to indicate media, date prepared, and analyst. Each lot of media is quality-control tested by using a pure culture of the target bacterium or a sewage sample as a positive control; for modified mTEC, Colilert, and MI agars, negative controls are also required (Appendix J). Fresh sewage samples are obtained from the Olentangy Wastewater Treatment Plant as needed. Stock cultures of the positive and negative controls are kept on slants in the refrigerator and transferred once a month. Transfer dates are recorded in the LIMS. When preparing positive and negative controls to be sent to other Water Centers, stock cultures must be transferred within a week before use.

Results are recorded in the “Media and Buffer” logbook on quality-control sheets (Appendix K); documentation of preparation procedures is also kept in this logbook. Media storage requirements and holding times are strictly followed (table 6). Requests for media, buffered-dilution water, and reagent preparation by project personnel are made using the “Expendable supplies request forms” (Appendix L).

The type of buffered-dilution water used by the OWML is phosphate buffer with magnesium chloride dilution water (U.S. EPA, 2000b). Instructions for preparation are listed in Appendix M.

Table 6. Information on media, buffered-dilution water, and reagents prepared and stored in the Ohio Water Cente Microbiology Laboratory (OWML).

TYPE OF MEDIA/BUFFER	SOURCE	STORAGE	HOLDING TIME
mENDO agar	Difco, Detroit, MI	Desiccator	Expiration date for agar kits 3 days as plates
MI agar	OWML	Refrigerator	6 months in dilution bottles 2 weeks as plates
MI agar	Becton Dickinson, Cockeysville, MD	Cabinet	As specified by manufacturer 2 weeks as plates
Colilert	Idexx Corp., Westbrook, ME	Cabinet	As specified by manufacturer
mFC agar	Difco, Detroit, MI	Cabinet	As specified by manufacturer 3 days as plates
mTEC agar	OWML	Refrigerator	6 months in dilution bottles 2 weeks as plates
mTEC agar	Becton Dickinson, Cockeysville, MD	Cabinet	As specified by manufacturer 2 weeks as plates
Modified mTEC	OWML	Refrigerator	6 months in dilution bottles 2 weeks as plates
Modified mTEC	Becton Dickinson, Cockeysville, MD	Cabinet	As specified by manufacturer
mEI	OWML	Refrigerator	6 months in dilution bottles 3 days to 2 weeks as plates*
mCP agar	OWML	Refrigerator	6 months in dilution bottles 1 month as plates
Phosphate buffer with magnesium chloride (Appendix M)	OWML Hardy Diagnostics, CA	Cabinet (unopened) Refrigerator (after opening)	1 year (unopened) 2 weeks (after opening)
Urea-phenol solution (Appendix F)	OWML	Refrigerator	6 months or until it is no longer a straw-yellow color

* If reagents that are added after autoclaving are filter sterilized, the longer holding time is applied.

Analytical quality-control samples for fecal-indicator bacteria by membrane filtration (mENDO, MI, mFC, mTEC, modified mTEC, mEI, and mCP agar methods) include the following:

· Filter blank—a 50-100 mL aliquot of sterile buffered water is plated before the sample to confirm the sterility of equipment and supplies.

· Procedure blank—a 50-100 mL aliquot of sterile buffered water is plated after every fifth sample to measure the effectiveness of the analyst’s rinsing technique or presence of incidental contamination of the buffered water.

· A sewage sample is plated daily when C. perfringens analysis is done to evaluate the test procedure and to ensure anaerobic culture conditions.

· For MI, positive and negative controls are plated every 10 samples to ensure proficiency with the method and evaluate the integrity of the medium. Positive and negative controls include the following:

o Positive controls of E. coli and Serratia marcescens

o Negative controls of Pseudmonas ATCC 10145 (unable to grow on MI and ensures the selectively of the agar) and Providencia alcalifaciens (grows on MI but will not fluoresce and ensures target colonies are correctly identified).

For some projects, a sewage sample is plated with each batch of MI plates at the time of sample analysis to evaluate the effectiveness of cefsulodin (an antibiotic added at the time of plate preparation).

Analytical quality-control samples for Colilert include the following:

· Positive (E. coli) and negative-control (Pseudomonas) cultures are included with every 20^th sample to evaluate the test procedure and aid in interpretation of results.

Enteric viruses

RT-PCR and cell-culture methods are recommended for the detection of enteric viruses in water. To prepare samples for RT-PCR and cell culture, attached viruses are eluted from a 1MDS filter with beef extract (pH 9.5), concentrated using celite (pH 4.0), and eluted with sodium phosphate (pH 9.5). These steps are done in the OWML, and a protocol is included as Appendix N.

The RT-PCR method was written and laboratory tested by USEPA and is experimental (G. Shay Fout, U.S. Environmental Protection Agency, written commun., 1997; Fout and others, 2003). Viruses are isolated from the eluate by ultracentrifugation through a sucrose gradient, and trace contaminants are removed by extraction with a solvent mixture (Appendix N1). An aliquot of the concentrate is used for RT-PCR, wherein any target viral RNA is converted to DNA (by reverse transcriptase) and amplified by the polymerase chain reaction. The RT-PCR products confirmed by hybridization. The enteric viruses detected by use of this method include enterovirus, hepatitis A virus, rotavirus, reovirus, and calicivirus (including Norwalk-like virus).

The OWML consists of a 1,000 ft² main laboratory and a 300 ft²limited-use laboratory. Virus elutions, inhibitor removal, and reaction preparations for RT-PCR are done in the main lab, along with media preparation, membrane filtration, incubation, and culture maintenance. The limited-use lab is the only area in the building in which PCR products are handled. Gel electrophoresis and hybridization are performed in this room. To avoid contamination of incoming samples, staff that have entered the limited-use lab are not allowed to reenter the main lab unless they have showered and changed their clothes. Equipment and supplies are also not to be transferred into the main lab, unless adequate sterilization and decontamination procedures have been followed.

A list describing QC samples for all stages of sample preparation and analysis by the RT-PCR method are listed in Appendix N2. A check list to be used when interpreting all results of RT-PCR analyses is also contained in Appendix N2.

Cell-culture analysis is not done at the OWML; these samples need to be sent to a contract laboratory for analysis. The recommended cell-culture method is an experimental method and was modified from U.S. Environmental Protection Agency (1996) by USEPA (G. Shay Fout, U.S. Environmental Protection Agency, written commun., 1999). The sample eluate is added to a monolayer of a continuous cell line derived from African Green monkey kidney cells. Each cell culture is examined microscopically for the appearance of cytopathic effects (CPE) for a total of 14 days; if CPE is not observed in 14 days, a second passage is done. Results are reported as most probable number of infectious units per volume of water. The following QC samples are included in cell-culture analysis:

· A negative control, containing cells and sodium phosphate buffer, is incubated in a roller bottle with each batch of samples inoculated for the first passage.

· A positive control, containing cells, sodium phosphate buffer, and polio virus vaccine, is incubated in a 75 cm² flask with each batch of samples inoculated for the first passage and the second passage.

Media and reagent preparations are done in the OWML or at the contract laboratory and are prepared and stored per method instructions. The contract laboratory is required to strictly follow the QA/QC guidelines listed in the method documentation (G. Shay Fout, U.S. Environmental Protection Agency, written commun., 1997 and 1999).

Coliphage

The method currently in use for quantitative coliphage analysis by the OWML is the USEPA Method 1602, single-agar layer (SAL) procedure (USEPA, 2001b) (Appendix O). This method is generally most suitable for quantification of coliphage in surface-water samples. Antibiotic-resistant E. coli CN-13 (resistant to nalidixic acid) and E. coli F-amp (resistant to streptomycin and ampicillin) are used as bacterial hosts for somatic and F-specific coliphage, respectively. Procedures for quality-control samples are described in Appendix O. Results are recorded on a QC log form (Appendix P).

The method currently in use for qualitative determination of coliphage in larger sample volumes at the OWML is the USEPA Method 1601, two-step enrichment method (USEPA, 2001a). Sample volumes of 1 L are recommended for detection of coliphage using this method. Because the SAL method is impractical for sample volumes above 100 mL, the two-step enrichment method is often used for ground-water sample analysis. A summary of Method 1601 can be found in Appendix Q. Results from quality-control samples are recorded on a QC log form (Appendix R).

Results from coliphage QC samples are recorded in the LIMS. Coliphage QC log forms are kept in the Sample Logbook with the Service Request Forms. A second book, coliphage QC log book, contains information on media sterility, additional quality-control samples, and coliphage stock enumeration results. Information on host culture strains is maintained in LIMS.

Cryptosporidium and Giardia

USEPA method 1623 (USEPA, 2001c) is the USEPA-recommended method for detection of Cryptosporidium oocysts and Giardia cysts in water. This provisional method involves filtration, immunomagnetic separation, staining with fluorescent antibody, and microscopic evaluation. At the present time, the OWML has the capability to complete the sample processing steps¾filtration and concentration (Appendix T). The OWML is developing the capability for immunomagnetic separation and microscopy.

Actinomycetes

The Actinomycetes are a large group of filamentous gram-positive bacteria that resemble fungi because they produce mycelium and dry spores, called conidia. (Madigan and others, 2000). They are considered nuisance organisms for those in the water industry, as they are one of two types of organisms that impart an earthy-musty odor to waters. The odors are caused by two compounds formed during normal actinomycete development, geosmin and 2-methylisoborneol (American Public Health Association, 1998).

The method used for isolation of Actinomycetes from water in the OWML is based on a published method (American Public Health Association, 1998) and a method provided by a commercial supplier of Actinomycetes medium (Difco, Detroit Michigan, The Difco Manual, 2001). A double agar layer method is used (Appendix U). Stock cultures of Streptomycetes albus are used as positive controls. The stock culture is transferred every two months and transfers are recorded in the LIMS.

REFERENCES

American Public Health Association, American Water Works Association, and Water Pollution Control Federation, 1998, Standard methods for the examination of water and wastewater (20th ed.): Washington, D.C., American Public Health Association [variously paginated].

American Society for Testing and Materials, 1999, Annual Book of ASTM Standards, Section 11, Water and Environmental Technology, Designation: D 1193-99, p. 107-109.

Britton , L.J., and Greeson, P.E., eds., 1987, Methods for collection and analysis of aquatic biological and microbiological samples: U.S. Geological Survey Techniques of Water-Resources Investigations, book 5, chap. A4, 363 p.

Fout, G.S., Martinson, B.C., Moyer, M.W.N., and Dahling, D.R., 2003, A multiplex reverse transcription-PCR method for detection of human enteric viruses in groundwater: Applied and Environmental Microbiology, v. 69, no. 6, p. 3158-3164.

Francy, D.S., Jones, A.L., Myers, D.N., Rowe, G.L., Eberle, M., and Sarver, K.M., 1998, Quality-assurance/quality-control manual for collection and analysis of water-quality data in the Ohio District, U.S. Geological Survey: U.S. Geological Survey Water-Resources Investigations Report 98-4057, 71 p.

Francy, D.S., Helsel, D.L., and Nally, R.A., 2000, Occurrence and distribution of microbiological indicators in ground water and stream water: Water Environment Research, v. 72, no. 2, 152 p.

Ijzerman, M.M., and Hagedorn, C., 1992, Improved method for coliphage detection based on b-galactosidase induction: Journal of Virological Methods, v. 40, p. 31-36.

Madigan, M. T., Martinko, J.M., and Parker, J., Brock, Biology of Microoganisms—Ninth Edition: Prentice Hall, Upper Sadlle River, NJ, p. 519.

U.S. Environmental Protection Agency, 1978, Microbiological methods for monitoring the environment—water and wastes: Cincinnati, Ohio, U.S. Environmental Protection Agency, EPA-600/8-78-017, 338 p.

_________________1985, Test methods for Escherichia coli and enterococci in water by the membrane filtered procedure: Cincinnati, Ohio, Environmental Monitoring and Support Laboratory, EPA 600/4-85/076, 24 p.

_________________1996, EPA Information Collection Rule microbial laboratory manual: Washington, D.C., U.S. Environmental Protection Agency, EPA/600/R-95/178.

_________________1997, Method 1600—Membrane filter test method for enterococci in water: U.S. Environmental Protection Agency, Office of Water, Washington, D.C., EPA-821-R-97-004, 9 p.

_________________2000a, Membrane filter method for the simultaneous detection of total coliforms and Escherichia coli in drinking water: U.S. Environmental Protection Agency, Office of Research and Development, EPA 600-R-00-013.

_________________2000b, Improved enumeration methods for the recreational water quality indicators: enterococci and Escherichia coli: U.S. Environmental Protection Agency, Office of Science and Technology, EPA/821/R-97/004.

_________________2001a, Method 1601: Male-specific (F+) and somatic coliphage in water by two-step enrichment procedure: Washington, D.C., U.S. Environmental Protection Agency, EPA-821-R-01-030.

_________________2001b, Method 1602: Male-specific (F+) and somatic coliphage in water by single agar layer (SAL) procedure: Washington, D.C., U.S. Environmental Protection Agency, EPA-821-R-01-029.

_________________ 2001c, Method 1623¾Cryptosporidium and Giardia in water by filtration, immunomagnetic separation, and fluorescent antibody: Washington, D.C., U.S. Environmental Protection Agency, EPA 821-R-01-025.

_________________ 2002a, Method 1604—Total coliforms and Escherichia coli in water by membrane filtration using a simultaneous detection technique (MI medium): Washington D.C., EPA 821-R-02-024, 14 p.

______________ 2002b, Method 1603—Escherichia coli in water by membrane filtration using modified membrane-thermotolerant Escherichia coli agar: Washington, D.C., EPA 821-R-02-23, 9 p.

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*Escherichia coli*	mTEC method	Compliance—RW, DW	USEPA (1985) (Appendix F)
	MI method	Official—all waters	USEPA (2000a and 2002a)
	Colilert method	Compliance—DW Official—other waters	Idexx Corp., Westbrook, ME APHA (1998) Section 9223
	Modified mTEC	Official	USEPA (2000b and 2002b) (Appendix G)

Quality Assurance/Quality Control Manual

Purpose and scope

Organizational structure

Sample management and documentation

Actinomycetes

A. OWML Service request form

G. Modified mTEC agar preparation

H. mEI agar preparation

S. Filtration and elution of samples by USEPA Method 1623 – ultrafiltration method

T. Detection of Actinomycetes in water

Quality Assurance/Quality Control Manual

Ohio Water Microbiology Laboratory

ABSTRACT

INTRODUCTION

Purpose and Scope

Organizational Structure

GENERAL LABORATORY QUALITY ASSURANCE/QUALITY- CONTROL PRACTICES

Analytical methods

Training

Safety

Laboratory materials and equipment

General sterility and cleanliness

Autoclaves

Laboratory water

Analytical balances

Hoods

Specific conductance, pH, and turbidity meters

Thermometers, incubators, water baths, refrigerators, and freezers

Microscope

Centrifuges

Refrigerated floor centrifuge

Ultracentrifuge

Microcentrifuge (2)

Thermal Cyclers

Sample Management and Documentation

METHODS OF ANALYSIS, MEDIA AND REAGENT PREPARATION, AND ANALYTICAL QUALITY-CONTROL PROCEDURES

Fecal-indicator bacteria

Enteric viruses

Coliphage

Cryptosporidium and Giardia

Actinomycetes

REFERENCES