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General Microbiology Section

As part of the Biological Sciences Bureau, the General Microbiology Section includes General bacteriology (or General Microbiology (GM), as we like to call it), Tuberculosis (TB), and Mycology. In the GM area, there are three primary benches, each with their particular analyses. The three benches are the Enteric Bench, the Miscellaneous Bench, and the Reference Bench. We have a separate laboratory area for routine processing and manipulation of TB, and an area for fungal testing. Each bench strives to serve the public of New Mexico with excellence in their own way, from assisting in identification by serotyping for surveillance of enteric pathogens on the Enteric Bench to screening patient specimens for Legionella on the Miscellaneous Bench to working up cultures for the Office of the Medical Investigator on the Reference Bench, and much more.

Recent Activity



Enteric Bench

Serotyping for Salmonella H Poly groups, showing flocculation (or clumping) in the poly groups B and G. Serotyping for Salmonella somatic factors showing agglutination in the somatic factor 9, or D, as seen in the fourth rectangle of the grid. Photo of four different microscopic biological lifeforms. Photograph of testubes. The Enteric Bench in General Microbiology aims to support public health improvement by assisting with identification and serotyping of bacterial isolates, screening clinical specimens for a number of enteric pathogens, and by participating in the National Antimicrobial Resistance Monitoring System (NARMS). The Enteric Bench receives clinical specimens from throughout the state of New Mexico from patients suspected of being made ill due to an enteric pathogen. The pathogens worked up on the Enteric Bench include Salmonella, Shigella, Campylobacter, Shiga toxin producing E. Coli, Vibrio, Aeromonas, Pleisiomonas, Yersinia enterocolitica, Bacillus cereus, and Staphylococcus aureus. Specimens may be sent to be screened for any or all of these organisms or to be confirmed and fully identified by serotyping for the purposes of epidemiology and surveillance. When an outbreak of an enteric pathogen occurs, the Enteric Bench is one factor in assisting the state epidemiologists in identifying which clinical specimens are directly linked to a specific outbreak.


Diagram describing the antigenic structure of a Salmonella bacterial cell.After biochemically identifying the genus and species, serotyping may be performed on certain enteric isolates, such as Salmonella, Shigella, Shiga toxin producing E. coli, and Vibrio cholera, to identify the bacterial strain, also known as the serotype or serovar. Antisera are used to detect specific antigens found on the bacterial cell, typically somatic O antigens (located within the cell wall) or flagellar H antigens. Less common is the K antigen, or capsular antigen. The serotype Salmonella A Typhi may possess a K antigen known as the Vi antigen, which contributes to the virulence of the microorganism. Although not used for diagnostic purposes, determining the specific serotype of a microorganism serves to contribute to epidemiologic and research purposes.

National Antimicrobial Resistance Monitoring System

O157 Chromagar showing mixed growth of Shiga toxin producing E. coli O157 (mauve colonies) and a non-Shiga toxin producing E. coli (blue colonies)The Enteric Bench also participates in the National Antimicrobial Resistance Monitoring System (NARMS). NARMS is a study coordinated by the Center for Disease Control and Prevention (CDC) that monitors trends of antimicrobial resistance of enteric bacteria on three fronts, specifically human enteric illness, retail meats, and in food-producing animals. The Enteric Bench participates in NARMS by submitting bacterial isolates of Salmonella, Shigella, E. coli O157, Campylobacter, and Vibrio that have been received from clinical labs throughout the state of New Mexico. The isolates of these enteric pathogens assist the CDC in monitoring patterns of antimicrobial resistance and in investigating possible outbreaks related to foodbourne illnesses.

Miscellaneous Bench

Emerging Infections Program

A blood agar plate growing Group B strep (beta hemolysis), Group A strep (pronounced beta hemolysis), and Strep pneumoniae (alpha hemolysis). A microbiologist is inoculating and streaking a Group A Strep isolate to a blood agar plate. The isolate will be frozen in cryovials to be forwarded to the CDC. One vital way in which the GM Miscellaneous Bench aids public health is by participating in is the Emerging Infections Programs (EIP). New Mexico is one of ten states that supports the EIP surveillance of current and up-and-coming infectious diseases. GM participates in the Active Bacterial Core surveillance (ABCs) aspect of the EIP network by collecting pathogens from clinical labs in New Mexico including Group A streptococcus, Group B streptococcus, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis. Both H. influenzae and N. meningitidis isolates are serotyped upon arrival and the Epidemiology and Response Division of New Mexico is notified. These isolates are then forwarded to the CDC where they are examined for epidemiologic purposes, examples being patient risk factors and strategies of prevention in addition to studies of antimicrobial resistance and vaccine development.

Group B Streptococcus (prenatal screening)

Group B Streptococcus (Prenatal Screening) Another way in which the Miscellaneous Bench in General Microbiology improves public health is by screening for Group B Streptococcus (GBS), also known as Streptococcus agalactiae. GBS has been recognized as the leading cause of infections in neonates corresponding to pneumonia, sepsis and meningitis. Neonatal disease and postpartum infections are associated with colonization of GBS in the maternal genital or gastro-intestinal tract. In order to decrease risk of infection, women are screened for GBS at 35-37 weeks of gestation and subsequently treated if positive. The Miscellaneous Bench receives swabs from clinical labs throughout New Mexico that are used to screen for GBS. Colonies suspected of being GBS are confirmed by colony morphology, Gram stain, catalase reaction, Lancefield typing (with PathoDX kit), and optionally, a CAMP test and hippurate hydrolysis. Once GBS is confirmed, the submitter is notified.

Neisseria gonorrhoeae (Gonococcal Isolate Surveillance Project Study)

Gram stain of intracellular Gram-negative N. gonorrhoeae diplococciIn addition to Group B Streptococcus, the Miscellaneous Bench in General Microbiology also receives specimens for screening of Neisseria gonorrhoeae. N. gonorrhoeae is the causative agent of gonorrhea and may cause a variety of infections and complications. Specimens may be received as suspect bacterial isolates from clinical labs for confirmation or as cultures collected by public health offices. Male urethral isolates confirmed as N. gonorrhoeae are included in the Gonococcal Isolate Surveillance Project (GISP). First established in 1986, GISP monitors trends in antimicrobial susceptibilities of strains of N. gonorrhoeae. This data has been used to revise the CDC’s STD Treatment recommendations numerous times since 1986.


Colonies of Legionella as viewed with a dissecting microscope after four days of incubation; note the iridescent and ground-glass appearance.Yet another group of microorganisms that the Miscellaneous Bench screens for is Legionella species, microorganisms typically associated with aqueous environmental sources and recognized as causing pneumonia. Aerosol inhalation is the typical route of infection, with devices like cooling towers or water heaters being the source of contamination and infection. The Miscellaneous Bench receives either isolates suspected of being Legionella or unpreserved raw clinical specimens such as Bronchoalveolar Lavage (BAL) or lung biopsies for testing. Isolates are forwarded to the CDC for confirmation, speciation, and to type for epidemiological purposes.

Bordetella pertussis

Gram-negative Bordetella pertussis Bordetella pertussis on Regan-Lowe media The Miscellaneous Bench also receives specimens to be cultured for Bordetella species. Bordetella pertussis is the causative agent of whooping cough, a highly contagious, yet vaccine-preventable, respiratory disease characterized by convulsive coughing followed by a whooping sound that often afflicts children. While a PCR assay has been developed and routinely used by the Molecular Biology Section to screen clinical specimens for Pertussis, CDC has requested isolated, pure bacteria for further testing and so that improved vaccines may be developed. Specimens are received on a special enriched medium called Regan-Lowe Charcoal Agar because the bacteria has special growth requirements. Colonies whose morphology may match Bordetella species may not appear until after 48-72 hours of incubation.

Reference/Office of the Medical Investigator Bench

Optochin, or P discs, are used to differentiate Streptococcus pneumoniae (shown with zone of inhibition) and other alpha streptococcus species (no zone of inhibition). (Top) RapID ANA panel used to identify anaerobic microorganisms; (Bottom) Micro ID panel used to identify microorganisms in the family Enterobacteriaceae. One way in which the General Microbiology Section aids the public is by assisting the Office of the Medical Investigator (OMI) in investigating cause of death. As soon as possible following collection during an autopsy, OMI sends specimens to General Microbiology to be plated to the appropriate media, incubated, read at 24 and 48 hours (or longer as needed), and isolates are identified using standard bacterial identification procedures. Although it is only one component of the autopsy, the information gained from postmortem cultures can be added to the deceased’s clinical history and related histological findings to help OMI ascertain whether or not death was due to bacteriological factors.

Listeria monocytogenes showing “umbrella” growth in semisolid media Direct Fluorescent Antibody Stain of Yersinia pestis Yet another way in which the General Microbiology Section serves the public is as a reference lab. The Reference Bench in General Microbiology may receive specimens for three reasons. Reference Bench may be able to give a more complete identification of the microorganism in question. Secondly, a microorganism may be referred to General Microbiology if it is considered to be a possible bioterrorism agent, an example being Bacillus anthracis, or anthrax. Another microorganism that is considered a possible bioterrorism agent, yet is endemic to the state of New Mexico, is Yersinia pestis, also known as plague. Thirdly, microorganisms that are on New Mexico’s list of reportable diseases and conditions are forwarded to the Reference Bench in General Microbiology for confirmation and surveillance purposes. Listeria monocytogenes and Vibrio species are examples of microorganisms on the list of reportable diseases.


A microbiologist works in the Biosafety Level 3 (BSL3)New Mexico has a long history with Tuberculosis (TB) as some of our historic buildings were once TB sanitorums that welcomed patients from across the US to our relaxing warm, dry, sunny state. Thanks to proper treatment and antibiotics, the numbers of new cases of TB has dimished, but due to the devestating severity of the disease, each case is extremely important to us. We strive to identify TB quickly with PCR screening tests and perform direct acid fast bacilli smear and both liquid and solid culture methods to isolate, identify, and provide TB isolates for susceptibility and genotyping. This work helps our TB control program and clinicians properly treat TB patients and provide information for epidemiologic investigation.

Kinyoun smear from liquid culture growth. This is an example of cording where AFB clump together in a distinct pattern, often seen in Mycobacterium tuberculosis This is a close-up of a Mycobacterium tuberculosis culture revealing this organism’s colonial morphology.    Note the colorless, rough surface, which are typical morphologic characteristics seen in Mycobacterium tuberculosis colonies. Macroscopic examination of colonial growth patterns is still one of the ways microorganisms are often identified. In addition to providing testing for human New Mexico residents, we also provide testing for animals at zoos and Veterinary Diagnostic Services. Tuberculosis may be seen in elephants, and we routinely screen our zoo elephants to ensure the public remains safe. We also routinely test other non-TB acid fast bacilli, and provide identification for common pathogenic and non-pathogenic Mycobacterium species.


A microbiologist examines yeast morphology by microscope.The mycology bench serves as both a clinical and reference laboratory. Coccidioides immitis/posadasii causes what is commonly known as Valley Fever, a fungal illness that can range in severity from flu-like respiratory illness, to severe, life-threatening disease. Patients may show symptoms similar to those seen with TB, so often clinics request yeast/mold culture is performed in addition to acid fast bacilli culture on patient sputum specimens.

Microsporum sp. is a dermatophyte, which causes infections of keratinized tissue (hair, skin, nails) Rhizopus sp. from PFA plate Bipolaris sp. from IMA plate We use a combination of conventional culture including colony and microscopic observation with state of the art molecular sequencing to identify fungal or yeast isolates referred to us for identification. Types of fungus identified may be seen commonly in the environment, but if present in a person can cause severe illness, such as Mucormycosis, characterized by disseminated, necrotic infection with severe outcome, caused by several different fungi, including Rhizopus sp. Other types may be more of a nuisance, such as toenail infections caused by a dermatophyte.