Applications of cellular fatty acid analysis

In situmeasurement of microbial biomass, community structure and nutritional status

In sediments and soils the extant microbiota that can be counted by direct microscopy have proved exceedingly difficult to isolate and culture. Classical tests are time consuming and provide little indication of the interactions within the community, the community nutritional status or metabolic activity. Thein situmethod is based on the extraction of ‘signature’ lipid biomarkers (SLB) from the cell membranes and walls of microorganisms. Lipids are cellular components that are recoverable by extraction with organic solvents. Lipids are an essential component of the membrane of all cells and play a role as storage materials. Extraction of the lipid components of the microbiota from soils and sediments provides both purification and concentration together with anin situquantitative analysis of the microbial biomass, community structure, and nutritional status. The determination of the total phospholipid ester-linked fatty acids (PLFA) provides a quantitative measure of the viable biomass. Viable microbes have an intact membrane which contains phospholipids (and PLFA). With cell death enzymes hydrolyze the phosphate group within minutes to hours. The lipid core remains as diglyceride (DG). The resulting DG has the same signature fatty acids as the phospholipids (until it degrades) so a comparison of the ratio of PLFA to DG provides an indication of the viable and nonviable microbes. Analysis by SLB technique provides a quantitative definition of the microbial community structure as specific groups of microbes contain characteristic PLFA patterns. The analysis of other lipids such as the sterols (for the microeukaryotes -nematodes, algae, protozoa), glycolipids (for the phototrophs, gram-positive bacteria), or the hydroxy fatty acids in the lipopolysaccharide of the lipid A (gramnegative bacteria) can provide more detailed community structure analysis. The formation of poly (3-hydroxyalkanoic acid (PHA) in bacteria or triglyceride (TG) in the microeukaryotes relative to the PLFA provides a measure of the nutritional status. Bacteria grown with adequate carbon and terminal electron acceptors form PHA when they cannot divide, because some essential component is missing. Rates of incorporation of14C-acetate into PHA relative to PLFA is a sensitive indicator of disturbance artifacts in estimates of metabolic activity in sediments with redox gradients. Exposure to toxic environments can lead to minicell formation and increases in specific PLFAS. Respiratory quinone structure indicates the proportions of aerobic/anaerobic activities in the community. The SLB technology provides quantitativein situinformation that define the microbial ecology in sedimentary geochemical processes.

Identification of staphylococci with a self-educating system using fatty acid analysis and biochemical tests

We characterized all of the 35 aerobic taxa of the genus Staphylococcus by using an objective, self-learning system combining both whole-cell fatty acid (FA) analysis and the results of 35 biochemical tests. Isolates were compared with the type strain for each taxon to generate an FA profile library and a biochemical table of test responses. Isolates were accepted into the system if they had a similarity index of > or = 0.6 for a taxon within the FA profile library and if they were identified as the same taxon by a computer program using a probability matrix constructed from the biochemical data. These stringent criteria led to acceptance of 1,117 strains assigned to legitimate taxa. Additional FA groups were assembled from selected strains that did not meet the inclusion criteria based on the type strains and were added to the system as separate entries. Currently, 1,512 isolates have bee accepted into the system. This approach has resulted in a comprehensive table of biochemical test results and a FA profile library, which together provide a practical system for valid identifications.

Epidemiological typing of Bacillus spp. isolated from food

Biotypes, fatty acid profiles, and restriction fragment length polymorphisms of a PCR product (PCR-RFLP of the cereolysin AB gene) were compared for 62 isolates of the Bacillus cereus group. Eleven isolates originated from various foods, and 51 isolates were obtained from pasteurized milk which had been processed by two different dairies. The isolates were clustered into 6 biotypes, 10 fatty acid groups, or 7 PCR-RFLP clusters. Isolates with mesophilic or psychrotrophic characteristics were preferentially distributed into specific fatty acid or PCR-RFLP groups (P = 0.004). Unique fatty acid clusters were predominantly found in milk samples of each dairy (P < 0.0001), suggesting that certain dairy plants may harbor plant-specific B. cereus which might constantly contribute to postpasteurization contamination.

Characterization and differentiation of filamentous fungi based on Fatty Acid composition

Cellular fatty acid composition of 100 different filamentous fungi, including oomycetes, zygomycetes, ascomycetes, basidiomycetes, and sterile mycelia, was analyzed to determine if they can be differentiated from one another on this basis and how minor variations in culture temperature and age affect this characteristic. Many fungi were found to possess the same fatty acids but produced different relative concentrations of each. Some fungi differed in both the fatty acids produced and in the relative concentrations of others. Multivariate discriminant analysis demonstrated that all of the species included in this study had significantly different (P < 0.001) fatty acid profiles. Each of the three phyla from which representative species were analyzed and the sterile forms had distinctive fatty acid profiles. Significant differences in fatty acid composition were also found at the intraspecific level. Both culture temperature and age affected fatty acid composition in the fungi examined, but when these factors were held constant, variance in fatty acid composition was not a problem and fungal fatty acid profiles could be differentiated statistically.

Evaluation of the Microbial Identification System for identification of clinically isolated yeasts

The Microbial Identification System (MIS; Microbial ID, Inc., Newark, Del.) was evaluated for the identification of 550 clinically isolated yeasts. The organisms evaluated were fresh clinical isolates identified by methods routinely used in our laboratory (API 20C and conventional methods) and included Candida albicans (n = 294), C. glabrata (n = 145), C. tropicalis (n = 58), C. parapsilosis (n = 33), and other yeasts (n = 20). In preparation for fatty acid analysis, yeasts were inoculated onto Sabouraud dextrose agar and incubated at 28 degrees C for 24 h. Yeasts were harvested, saponified, derivatized, and extracted, and fatty acid analysis was performed according to the manufacturer's instructions. Fatty acid profiles were analyzed, and computer identifications were made with the Yeast Clinical Library (database version 3.8). Of the 550 isolates tested, 374 (68.0%) were correctly identified to the species level, with 87 (15.8%) being incorrectly identified and 89 (16.2%) giving no identification. Repeat testing of isolates giving no identification resulted in an additional 18 isolates being correctly identified. This gave the MIS an overall identification rate of 71.3%. The most frequently misidentified yeast was C. glabrata, which was identified as Saccharomyces cerevisiae 32.4% of the time. On the basis of these results, the MIS, with its current database, does not appear suitable for the routine identification of clinically important yeasts.

The inhibitory action of fatty acids on oral bacteria

Saturated and unsaturated fatty acids and fatty acid derivatives were examined for their growth-inhibitory effects towards three selected oral bacteria: Porphyromonas gingivalis, Selenomonas artemidis, and Streptococcus sobrinus. Of the 45 compounds surveyed, only one, myristoleic acid, was inhibitory towards S. artemidis at a concentration < 100 micrograms/ml. cis-Hexadecenoic and cis-octadecenoic acids were generally inhibitory towards P. gingivalis and S. sobrinus, but there was no correlation between the position of the double bond and the minimum inhibitory concentration. Supra-minimum inhibitory concentrations of palmitoleic acid did not promote leakage of intracellular materials from either P. gingivalis or S. sobrinus, nor was L-isoleucine uptake by S. sobrinus inhibited. Fatty acids and derivatives were also examined for prospective synergistic or antagonistic interactions with thymol vis-à-vis growth inhibition of the test strains. Lauric acid and myristic acid each behaved synergistically with thymol to inhibit the growth of at least one test strain, whereas cis-10-heptadecenoic acid and thymol were noticeably antagonistic towards the growth of S. sobrinus.

Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics

Most of the bacterial species are still unknown. Consequently, our knowledge about bacterial ecology is poor and expectations about specialized species with novel enzymatic functions or new products are high. Thus, bacterial identification is a growing field of interest within microbiology. In this review, suitability of developments for identification based on miniaturized biochemical and physiological investigations of bacteria are evaluated. Special emphasis is given to chemotaxonomic methods such as analysis of quinone system, fatty acid profiles, polar lipid patterns, polyamine patterns, whole cell sugars, peptidoglycan diaminoacids, as well as analytical fingerprinting methods and cellular protein patterning. 16S rDNA sequencing introduced to investigate the phylogenetic relationships of bacteria, nucleic acids hybridization techniques and G + C content determination are discussed as well as restriction fragment length polymorphism (RFLP), macrorestriction analysis and random amplified polymorphic DNA (RAPD). The importance of the different approaches in classification and identification of bacteria according to phylogenetic relationships are demonstrated on selected examples.

Polyphasic taxonomy, a consensus approach to bacterial systematics

Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.

Characteristics of Bordetella hinzii strains isolated from a cystic fibrosis patient over a 3-year period

Over a 3-year period, an adult cystic fibrosis patient underwent eight episodes of pulmonary exacerbation of his disease. At least one of two different strains of Bordetella hinzii could be isolated from sputum samples in every instance. The differentiation of B. hinzii from related taxa and its role as an etiologic agent of infections are discussed. The two isolates of B. hinzii reported are the third and fourth human-derived strains described in the literature.

Comparison of MIDI Sherlock system and pulsed-field gel electrophoresis in characterizing strains of methicillin-resistant Staphylococcus aureus from a recent hospital outbreak

An outbreak of methicillin-resistant Staphylococcus aureus infections at the University of Utah Health Sciences Center occurred over a 7-month period. While the isolates phenotypically appeared to be similar in gross morphology and have similar Vitek antibiotic susceptibility patterns, two additional methods of strain characterization were evaluated to enhance the epidemiological investigation: pulsed-field gel electrophoresis and gas chromatography with the MIDI Sherlock system. Sherlock uses gas chromatography to qualitatively and quantitatively analyze the cellular fatty acid composition of organisms and creates two-dimensional plots based on principal-component analysis to define groups of closely related organisms. All isolates were also evaluated by digesting their chromosomal DNAs with the low-frequency-cutting enzyme SmaI and separating the restriction fragments by contour-clamped homogeneous electric field gel electrophoresis. Sample preparation for this pulsed-field gel electrophoresis included a novel cell lysis procedure involving achromopeptidase, greatly reducing the turnaround time. Isolates tested were recovered from the following: 45 suspected outbreak patients, 6 hospitalized patients believed to be unrelated to the outbreak, 6 patients from outside the hospital, and one health care practitioner implicated in the outbreak. Of 45 phenotypically similar suspect strains, 43 clustered tightly on the Sherlock two-dimensional plot. All outbreak patient isolates were also identical by pulsed-field gel electrophoresis with the exception of the same two outliers identified by Sherlock. In this epidemiologic investigation, we found an excellent correlation between the Sherlock and pulsed-field gel electrophoresis results for strain characterization of methicillin-resistant S. aureus.

Temperature-dependent membrane fatty acid and cell physiology changes in coccoid forms of Campylobacter jejuni

The effect of temperature and the availability of nutrients on the transition of spiral Campylobacter jejuni cells to coccoid forms was investigated. Ageing of spiral C. jejuni cells in either nutrient-poor or nutrient-rich environments resulted in the formation of nonculturable coccoid cells at 4, 12, and 25 degrees C after different periods, with the cells incubated at 4 degrees C in nutrient-deficient media remaining culturable the longest. To study the phenomenon, ATP levels, protein profiles, and fatty acid compositions were monitored under conditions where the transition from spiral to coccoid cells occurred. During storage, the levels of intracellular ATP were highest in cells incubated at low temperatures (4 and 12 degrees C) and remained constant after a small initial decrease. During the transformation from spiral to coccoid forms, no alteration in protein profiles could be detected; indeed, inhibition of protein synthesis by chloramphenicol did not influence the transition. Furthermore, DNA damage by gamma irradiation had no effect on the process. Membrane fatty acid composition of cocci formed at low temperatures was found to be almost identical to that of spiral cells, whereas that of cocci formed at 25 degrees C was clearly different. Combining these results, it is concluded that the formation of cocci is not an active process. However, distinctions between cocci formed at different temperatures were observed. Cocci formed at 4 degrees C show characteristics comparable to those of spirals, and these cocci may well play a role in the contamination cycle of C. jejuni.(ABSTRACT TRUNCATED AT 250 WORDS)

Further Evidence that the N(inf2)-Fixing Endophytic Bacterium from the Intercellular Spaces of Sugarcane Stems Is Acetobacter diazotrophicus

Nitrogen-fixing bacteria, isolated from the sugar solution in intercellular spaces of sugarcane stems, were compared with the type strain of Acetobacter diazotrophicus (PAL-5) and found to be congruent with it in all characters studied. These characters were 37 morphological and biochemical tests, cellular fatty acid composition, and nitrogenase activity. The nitrogenase activity was measured by acetylene reduction and H(inf2) evolution and found to be unusual in that the H(inf2) evolution was suppressed much less than expected by high concentrations of acetylene.

Typing of Staphylococcus epidermidis strains by random amplification of polymorphic DNA

The polymerase chain reaction was used to obtain randomly amplified polymorphic DNA profiles for typing of Staphylococcus epidermidis strains. Epidemiologically unrelated S. epidermidis isolates were screened with randomly amplified polymorphic DNA analysis. The discriminating ability of 45 randomly designed 10-mer primers was assessed. The highest discriminatory power was obtained with the 10-mer oligonucleotide OPAM-12. In typing a total of 13 unrelated S. epidermidis strains with OPAM-12, 11 different banding profiles were obtained reproducibly by agarose gel electrophoresis. The discriminatory power of the method with OPAM-12 was estimated using the D value of Hunter and Gaston (1988) to be 0.961. A reproducibility index of 1 was obtained after typing a total of 40 cultures including 12 triplicates and one quadruplicate of the 13 unrelated strains. Following the described procedure, the randomly amplified polymorphic DNA method provided a rapid, simple and reproducible alternative to other S. epidermidis typing systems.

Helicobacter pylori isolated from the domestic cat: public health implications

Helicobacter pylori has been directly linked with active chronic gastritis, peptic ulceration, and gastric adenocarcinoma in humans. Although a substantial portion of the human population is colonized with H. pylori, the patterns of transmission of the organism remain in doubt, and reservoir hosts have not been identified. This study documents the isolation of H. pylori from domestic cats obtained from a commercial vendor. The isolation of H. pylori from these cats was confirmed by morphologic and biochemical evaluations, fatty acid analysis, and 16S rRNA sequence analysis. H. pylori was cultured from 6 cats and organisms compatible in appearance with H. pylori were observed in 15 additional cats by histologic examination. In most animals, H. pylori was present in close proximity to mucosal epithelial cells or in mucus layers of the glandular or surface epithelium. Microscopically, H. pylori-infected cat stomachs contained a mild to severe diffuse lymphoplasmacytic infiltrate with small numbers of neutrophils and eosinophils in the subglandular and gastric mucosae. Lymphoid follicles were also noted, particularly in the antrum, and often displaced glandular mucosal tissue. Thus, the domestic cat may be a potential model for H. pylori disease in humans. Also, the isolation of H. pylori from domestic cats raises the possibility that the organism may be a zoonotic pathogen, with transmission occurring from cats to humans.

Determination of microbial chemical markers by gas chromatography-mass spectrometry--potential for diagnosis and studies on metabolism in situ. Review article

Different strategies for the application of gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) in medical microbiology research are discussed. GC can be used to determine specific microbial monomeric constituents and metabolites, so-called chemical markers, in cultures of microorganisms; in particular, analysis of cellular fatty acids has proven useful for species characterization and identification. GC-MS can be applied to study chemical markers directly in complex environmental samples, as exemplified by the analysis of airborne organic material as regards muramic acid (marker of peptidoglycan), 3-hydroxy acids (endotoxins), and ergosterol (fungal biomass). This methodological approach represents an alternative to various biological assays for characterization of airborne microbial structures, and forms a firm basis for correlating inhalation of such structures and development of symptoms. Direct GC-MS analysis of clinical samples provides possibilities for diagnosis (here exemplified by chiral separation of urine D- and L-arabinitol in disseminated candidiasis) and insight into microbial metabolism in the infected host (exemplified by observed indications of mycobacterial build-up of mycolic acids in vivo), with implications for drug development. Continued developments in MS technology will allow rapid advances to be made in GC-MS research in microbiology.

Update on clinical significance of coagulase-negative staphylococci

The clinical significance of coagulase-negative Staphylococcus species (CNS) continues to increase as strategies in medical practice lead to more invasive procedures. Hospitalized patients that are immunocompromised and/or suffering from chronic diseases are the most vulnerable to infection. Since CNS are widespread on the human body and are capable of producing very large populations, distinguishing the etiologic agent(s) from contaminating flora is a serious challenge. For this reason, culture identification should proceed to the species and strain levels. A much stronger case can be made for the identification of a CNS etiologic agent if the same strain is repeatedly isolated from a series of specimens as opposed to the isolation of different strains of one or more species. Strain identity initially can be based on colony morphology, and then one or more molecular approaches can be used to gain information on the genotype. Many of the CNS species are commonly resistant to antibiotics that are being indicated for staphylococcal infections, with the exception of vancomycin. The widespread use of antibiotics in hospitals has provided a reservoir of antibiotic-resistant genes. The main focus on mechanisms of pathogenesis has been with foreign body infections and the role of specific adhesins and slime produced by Staphylococcus epidermidis. Slime can reduce the immune response and opsonophagocytosis, thereby interfering with host defense mechanisms. As we become more aware of the various strategies used by CNS, we will be in a better position to compromise their defense mechanisms and improve treatment.

Comparative study of the cellular fatty acids of methicillin-resistant and -susceptible Staphylococcus aureus

The cellular fatty acid compositions of 26 strains of methicillin-resistant Staphylococcus aureus (MRSA) and 17 strains of methicillin-susceptible S. aureus (MSSA) were analyzed by gas-liquid chromatography. The fatty acid compositions of the two groups were very similar with 16 identified components. The major fatty acids were Ci14 = 0, Ci15 = 0, C18 = 0 and C20 = 0. Among these fatty acids, the percentage of the Ci15 = 0 fatty acid component of MRSA strains (11.4 +/- 3.9%) was statistically higher than that of MSSA strains (6.2 +/- 2.4%) (p < 0.001). On the other hand, the percentage of the C20 = 0 fatty acid components of MRSA strains (20.2 +/- 8.8%) was statistically lower than that of MSSA strains (30.7 +/- 10.4%) (p < 0.001). The production of beta-lactamase and beta-hemolysin in both groups' strain was also unrelated to the relative amounts of the fatty acid components. These results indicated a statistical tendency for the percentage fatty acid compositions of the MRSA strains to be quantitatively different from those of the MSSA for both the Ci15 = 0 and C20 = 0 fatty acid components. Analysis of the fatty acid compositions may have an application in the differentiation of MRSA and MSSA strains.

Dependence of fatty acid composition of Listeria spp. on growth temperature

In Listeria spp., various fatty acids are produced; by far the most common members are C15 and C17 chain length fatty acids. This pattern is rather similar in all species. At low temperatures, most of the Listeria are able to change the relative composition whereby more of the C15 fatty acids are produced, which could increase the fluidity of the bacterial cell membrane under these conditions.

Effect of crude bacterial lipids on the course of Listeria infection in mice

Crude lipids from 37 strains belonging to 32 bacterial species were isolated. By injecting mice with lipids 5 d prior to challenge with a virulent strain of Listeria monocytogenes, immunostimulatory activity in 19 preparations was found. In general, lipids of Gram-negative bacteria appeared to be more effective. As to bacilli, an extraordinary activity was found in the lipids of Bacillus firmus. Lipids of various species of the genus Listeria were found to be active in approximately one-half of cases. Among other Gram-positive bacteria, significant activity of lipids was found in Corynebacterium xerosis, Propionibacterium acnes and BCG. The composition of fatty acids in the lipids did not differ significantly from that reported in the literature and their mutual differences could not explain the different biological activity. In selected strains of Gram-negative bacteria lipids were repeatedly purified with anhydrous chloroform; these preparations were found to be inactive as compared with original chloroform-methanol lipids.

Identification of some uncommon monounsaturated fatty acids of bacteria

Location of the double-bond position of monounsaturated fatty acids of various bacteria was accomplished with combined gas chromatography-mass spectrometry analysis of dimethyl disulfide (DMDS) derivatives. The monoenoic fatty acids from whole cells were converted to methyl esters and then to DMDS adducts and analyzed by capillary gas chromatography-mass spectrometry. The mass spectra of DMDS adducts gave an easily recognizable molecular ion and two major diagnostic ions attributable to fragmentation between the two CH3S groups located at the original site of unsaturation. Twenty-one relatively novel monoenoic fatty acids were identified among the bacteria studied. All Flavobacterium species contained i17:1 omega 8c, Bacillus alvei contained i16:1 omega 11c and i17:1 omega 12c, and Psychrobacter immobilis contained 12:1 omega 9c. Resolution of cis and trans isomers with capillary gas chromatography and subsequent mass spectrometry permitted positive identification of 16:1 omega 7c and 16:1 omega 7t in Arcobacter (Campylobacter) cryaerophila and 16:1 omega 9c and 16:1 omega 9t in Aerococcus viridans.

Susceptibility testing of clinical isolates of Methylobacterium species

Methylobacterium species represent a relatively new genus which is being increasingly isolated from cases of opportunistic infections. This study reports on 3 reference strains and 15 clinical isolates of Methylobacterium species. Susceptibility tests were performed by the agar dilution and commercial broth microdilution methods at both 30 and 35 degrees C. Readings were made at 24, 48, and 72 h. Incubation conditions of 48 h and 30 degrees C were found to be optimum. Both the agar dilution and broth microdilution methods gave equivalent results. Drugs tested and their MICs for 90% of isolates (in micrograms per milliliter) were as follows: amikacin, less than or equal to 1; gentamicin, 1; ciprofloxacin, 1; trimethoprim-sulfamethoxazole, 2/38; ceftriaxone, 16; and ceftizoxime, 16. The majority of our isolates were resistant to six other beta-lactam drugs tested. Nine of the 15 Methylobacterium isolates were beta-lactamase positive.

Automated systems for identification of microorganisms

Automated instruments for the identification of microorganisms were introduced into clinical microbiology laboratories in the 1970s. During the past two decades, the capabilities and performance characteristics of automated identification systems have steadily progressed and improved. This article explores the development of the various automated identification systems available in the United States and reviews their performance for identification of microorganisms. Observations regarding deficiencies and suggested improvements for these systems are provided.