Problems associated with identification of Legionella species from the environment and isolation of six possible new species

Legionella quinlivanii strain isolated from a human: A case report and whole genome sequencing analysis

We describe a strain of Legionella quinlivanii isolated from a bronchoalveolar lavage specimen from an 83-year-old patient in the province of Québec. Identification was done using 16S rRNA sequencing. The strain could replicate efficiently in human THP-1 macrophages and maintained a low level of cytotoxicity. Upon analyzing the whole genome sequencing data, the icm/dot secretion system was present, but the strain lacked some effector genes known to express proteins toxic to cells. The pathogenicity of this Legionella species should be investigated further.

Current and emerging Legionella diagnostics for laboratory and outbreak investigations

Legionnaires' disease (LD) is an often severe and potentially fatal form of bacterial pneumonia caused by an extensive list of Legionella species. These ubiquitous freshwater and soil inhabitants cause human respiratory disease when amplified in man-made water or cooling systems and their aerosols expose a susceptible population. Treatment of sporadic cases and rapid control of LD outbreaks benefit from swift diagnosis in concert with discriminatory bacterial typing for immediate epidemiological responses. Traditional culture and serology were instrumental in describing disease incidence early in its history; currently, diagnosis of LD relies almost solely on the urinary antigen test, which captures only the dominant species and serogroup, Legionella pneumophila serogroup 1 (Lp1). This has created a diagnostic "blind spot" for LD caused by non-Lp1 strains. This review focuses on historic, current, and emerging technologies that hold promise for increasing LD diagnostic efficiency and detection rates as part of a coherent testing regimen. The importance of cooperation between epidemiologists and laboratorians for a rapid outbreak response is also illustrated in field investigations conducted by the CDC with state and local authorities. Finally, challenges facing health care professionals, building managers, and the public health community in combating LD are highlighted, and potential solutions are discussed.

Identification of water pathogens by Raman microspectroscopy

Legionella species can be found living in water mostly in a viable but nonculturable state or associated with protozoa and complex biofilm formations. Isolation and afterwards identification of these pathogens from environmental samples by using common identification procedures based on cultivation are extremely difficult and prolonged. The development of fast and sensitive method based on the cultivation free identification of bacteria is necessary. In this study Raman microspectroscopy combined with multiclass support vector machines have been used to discriminate between Legionella and other common aquatic bacteria, to distinguish among clinically relevant Legionella species and to classify unknown Raman spectra for a fast and reliable identification. Recorded Raman spectra of the twenty-two Legionella species as well as the Raman spectra of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa were utilized to build the classification model. Afterwards, independent Raman spectra of eleven species were used to identify them on the basis of the classification model that was created. The present study shows that Raman microspectroscopy can be used as a rapid and reliable method to distinguish between Legionella species recognized as human pathogens and to identify samples which are unknown to the model based on multiclass support vector machines (MC-SVM).

Sequence-based identification of legionella

Legionella strains are considered biologically inert with respect to traditional identification schemes. Various phenotypic alternatives have been attempted but all have lacked resolution as additional species have been added to what is proving to be a large genus. Only sequence-based schemes have the required resolution to confidently speciate or recognize potentially novel strains. The mip gene target is the most comprehensive currently available, with the added advantage of a Web-based analysis tool. Other gene targets are available for most if not all species, the best of which target 16S rRNA, rpoB, rnpB, or proA genes. One or several of these should be used to confirm important strains or clarify apparent novelness. The increased resolution of these sequence-based schemes has recognized many new species, and many more remain to be characterized. I provide a mip analysis of 44 such strains along with the recognized species, and a SplitsTree network analysis of recognized species and 20 novel strains for which sequence for the five targets is available.

Legionella nagasakiensis sp. nov., isolated from water samples and from a patient with pneumonia

A novel Legionella species was identified based on analysis of 16S rRNA and mip (macrophage infectivity potentiator) gene sequences, cellular fatty acids, isoprenoid quinones, biochemical reactions, antigens and quantitative DNA–DNA hybridization. Strain CDC-1796-JAP-ET was isolated from well water at the Nagasaki Municipal Medical Center, Japan. Two strains, CDC-3041-AUS-E and CDC-3558-AUS-E, were isolated from water samples during an outbreak of legionellosis in South Australia. Strain CDC-5427-OH-H was isolated from a 66-year-old female patient diagnosed with Legionnaires’ disease in the US. Cells from these four strains were Gram-negative, non-fluorescent, rod-shaped, and positive for alkaline phosphatase, esterase, leucine arylamidase, catalase, gelatinase, β-lactamase and tyrosine browning assay. Phylogenetic analysis of 16S rRNA and mip genes revealed that the four strains formed a distinct cluster within the genus Legionella. The bacteria contained branched-chain fatty acids and quinones that are typical of members of the genus Legionella. Slide agglutination tests demonstrated no cross-reaction with 52 previously described members of the Legionellaceae. DNA–DNA hybridization studies indicated that DNAs from the four strains were highly related (78–84 %) but they showed 29 % relatedness to Legionella oakridgensis ATCC 33761T and less than 10 % to strains of other Legionella species tested. These characterizations suggest that the isolates represent a novel species, for which the name Legionella nagasakiensis sp. nov. is proposed; the type strain is CDC-1796-JAP-ET ( = ATCC BAA-1557T = JCM 15315T).

Legionella anisa, a possible indicator of water contamination by Legionella pneumophila

Legionella anisa is one of the most frequent species of Legionella other than Legionella pneumophila in the environment and may be hospital acquired in rare cases. We found that L. anisa may mask water contamination by L. pneumophila, suggesting that there is a risk of L. pneumophila infection in immunocompromised patients if water is found to be contaminated with Legionella species other than L. pneumophila.

Rapid identification of clinically relevant Legionella spp. by analysis of transfer DNA intergenic spacer length polymorphism

Analysis of PCR-amplified transfer DNA (tDNA) intergenic spacers was evaluated as a rapid method for identification to the species level of 18 species of Legionella known as human pathogens. Type strains (n = 19), reference strains (n = 16), environmental strains (n = 31), and clinical strains (n = 32) were tested. PCR products using outwardly directed tDNA consensus primers were separated on polyacrylamide gels and analyzed with automated laser fluorescence. Test results were obtained in 8 h starting with 72-h-old bacterial growth on solid medium. Species-specific patterns were obtained for all 18 Legionella species tested: Legionella anisa, L. bozemanii serogroups 1 and 2, L. cincinnatiensis, L. dumoffii, L. feeleii serogroups 1 and 2, L. gormanii, L. hackeliae serogroups 1 and 2, L. jordanis, L. lansingensis, L. longbeachae serogroups 1 and 2, L. lytica, L. maceachernii, L. micdadei, L. oakridgensis, L. parisiensis, L. pneumophila serogroups 1 to 14, L. sainthelensi serogroup 2, L. tucsonensis, and L. wadsworthii. Computer-assisted matching of tDNA-intergenic length polymorphism (ILP) patterns identified all 63 environmental and clinical strains to the species level and to serogroup for some strains. tDNA-ILP analysis is proposed as a routinely applicable method which allows rapid identification of environmental and clinical isolates of Legionella spp. associated with legionellosis.

Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms

As a technique allowing simultaneous visualization, identification, enumeration and localization of individual microbial cells, fluorescence in situ hybridization (FISH) is useful for many applications in all fields of microbiology. FISH not only allows the detection of culturable microorganisms, but also of yet-to-be cultured (so-called unculturable) organisms, and can therefore help in understanding complex microbial communities. In this review, methodological aspects, as well as problems and pitfalls of FISH are discussed in an examination of past, present and future applications.

Stability of cyclopropane and conjugated linoleic acids during fatty acid quantification in lactic acid bacteria

Seven methods commonly used for fatty acid analysis of microorganisms and foods were compared to establish the best for the analysis of lyophilized lactic acid bacteria. One of these methods involves fat extraction followed by methylation of fatty acids, while the other methods use a direct methylation of the samples, under different operating conditions (e.g., reaction temperature and time, reagents, and pH). Fatty acid methyl esters were identified by gas chromatography-mass spectrometry and quantified by on-column capillary gas chromatography. Two reliable methods for the analysis of fatty acids in bacteria were selected and further improved. They guarantee high recovery of classes of fragile fatty acids, such as cyclopropane and conjugated acids, and a high degree of methylation for all types of fatty acid esters. These two direct methylation methods have already been successfully applied to the analysis of fatty acids in foods. They represent a rapid and highly reliable alternative to classical time- and solvent-consuming methods and they give the fatty acid profile and the amount of each fatty acid. Using these methods, conjugated linoleic acids were identified and quantified in lactic acid bacteria.

Specific detection of Legionella pneumophila: construction of a new 16S rRNA-targeted oligonucleotide probe

Based on comparative sequence analysis, we have designed an oligonucleotide probe complementary to a region of 16S rRNA of Legionella pneumophila which allows the differentiation of L. pneumophila from other Legionella species without cultivation. The specificity of the new probe, LEGPNE1, was tested by in situ hybridization to a total of four serogroups of six strains of L. pneumophila, five different Legionella spp. and three nonlegionella species as reference strains. Furthermore, L. pneumophila cells could be easily distinguished from Legionella micdadei and Pseudomonas aeruginosa cells by using in situ hybridization with probes LEGPNE1, LEG705, and EUB338 after infection of the protozoan Acanthamoeba castellanii.

Sequence-based classification scheme for the genus Legionella targeting the mip gene

The identification and speciation of strains of Legionella is often difficult, and even the more successful chromatographic classification techniques have struggled to discriminate newly described species. A sequence-based genotypic classification scheme is reported, targeting approximately 700 nucleotide bases of the mip gene and utilizing gene amplification and direct amplicon sequencing. With the exception of Legionella geestiana, for which an amplicon was not produced, the scheme clearly and unambiguously discriminated among the remaining 39 Legionella species and correctly grouped 26 additional serogroup and reference strains within those species. Additionally, the genotypic classification of approximately 150 wild strains from several continents was consistent with their phenotypic classification, with the exception of a few strains where serological cross-reactivity was complex, potentially confusing the latter classification. Strains thought to represent currently uncharacterized species were also found to be genotypically unique. The scheme is technically simple for a laboratory with even basic molecular capabilities and equipment, if access to a sequencing laboratory is available.

Restriction fragment length polymorphism of rRNA genes for molecular typing of members of the family Legionellaceae

Typing of Legionella pneumophila remains important in the investigation of outbreaks of Legionnaires' disease and in the control of organisms contaminating hospital water. We found that the discriminatory power of a nonradioactive ribotyping method could be improved by combining results obtained with four restriction enzymes (HindIII, NciI, ClaI, and PstI). Fifty-eight clinical and environmental L. pneumophila strains including geographically unrelated as well as epidemiologically connected isolates were investigated. Epidemiologically related strains had the same ribotypes independent of the combinations of enzymes used. Some strains belonging to the same serogroup were assigned to different ribotypes, and some ribotypes contained members of different serogroups, indicating, as others have found, that serogroup and genotype are not always related. The discriminatory power of the method was estimated by calculating an index of discrimination (ID) for individual enzymes and combinations thereof. The combined result with all four enzymes was highly discriminatory (ID = 0.97), but results for three enzymes also yielded ID values acceptable for epidemiological purposes. In addition, the testing of 27 type strains and 6 clinical isolates representing Legionella species other than L. pneumophila indicated that ribotyping might be of value for species identification within this genus, as previously suggested.

Occurrence and distribution of Legionella species in composted plant materials

Legionellae were found in many samples of composted plant matter obtained from home gardeners and from facilities which undertook bulk composting. The predominant species isolated from these composts was Legionella pneumophila, the strains of which belonged to serogroups other than serogroup 1. Other Legionella species were present in many samples. Legionella longbeachae serogroup 1, which is implicated in human infections in South Australia, was present in samples obtained from two of six facilities composting large volumes of material and from 3 of 30 gardeners. Many of the species or strains isolated from composts have not been implicated as causative agents of legionellosis in South Austrailia, but some cause infection in healthy and immunosuppressed persons.

Hydroxy-fatty acid profiles of Legionella species: diagnostic usefulness assessed by principal component analysis

Twenty-nine species (76 strains) of members of the genus Legionella were analyzed for their cellular hydroxylated fatty acids (OH-FAs). The individual patterns were unusually complex and included both monohydroxylated and dihydroxylated chains of unbranched or branched (iso and anteiso) types. Comparison of the strain profiles by SIMCA (Soft Independent Modelling of Class Analogy) principal component analysis revealed four main groups. Group 1 included Legionella pneumophila plus L. israelensis strains, and group 2 included L. micdadei and L. maceacherneii strains. These two closely related groups were characterized by the occurrence of di-OH-FAs and differed mainly in the amounts of 3-OH-a21:0, 3-OH-n21:0, 3-OH-n22:0, and 3-OH-a23:0. Group 3 (13 species) was distinguished by i14:0 at less than 3%, 3-OH-3-OH-n14:0 at greater than 5%, 3-OH-n15:0 at greater than 2%, and minute amounts of OH-FAs with chains longer than 21:0. Group 4 (12 species) was heterogeneous. Its main characteristics were the presence of 3-OH-n12:0 and 3-OH-n13:0, 3-OH-i14:0 at greater than 5%, as well as significant amounts of 3-OH-a21:0 and 3-OH-n21:0. The groupings obtained by OH-FA profiles were found to reflect DNA-DNA homology groupings reasonably well, and the profiles appear to be useful for differentiation of Legionella species.

Long-chain alpha-hydroxy-(omega-1)-oxo fatty acids and alpha-hydroxy-1,omega-dioic fatty acids are cell wall constituents of Legionella (L. jordanis, L. maceachernii and L. micdadei)

Four long-chain fatty acids, 2-hydroxy-27-oxo-octacosanoic acid (n28:0(2-OH,27-oxo)), 2-hydroxy-29-oxo-triacontanoic acid (n30:0(2-OH,29-oxo)), 2-hydroxy-heptacosane-1,27-dioic acid (27:0(2-OH)-dioic) and 2-hydroxy-nonacosane-1,29-dioic acid (29:0(2-OH)-dioic) were identified by GLC-MS analysis in the phenol-chloroform-petroleum ether (PCP) extracts of Legionella jordanis, L. maceachernii and L. micdadei indicating that they are constituents of lipopolysaccharide. Moreover, five long-chain fatty acids (28:0(27-OH), 28:0(27-oxo), 30:0(29-oxo), 27:0-dioic and 29:0-dioic) previously identified in L. pneumophila (Moll, H. et al., FEMS Microbiol. Lett., 97 (1992), 1-6) were also found in these species. This is to our knowledge the first report on the existence of long chain 2-hydroxylated (omega-1)-oxo fatty acids and 2-hydroxylated 1,omega-dioic fatty acids.

Distribution of Legionella spp. in hydrothermal areas in continental Portugal and the island of São Miguel, Azores

Nineteen aquatic environment sites from three hydrothermal areas on continental Portugal and one area on the island of São Miguel, Azores, were examined for the recovery of Legionella spp. Physicochemical and bacteriological parameters were also determined for each site. Water temperatures varied between 22 and 67.5 degrees C, although the majority had temperatures above 40 degrees C; the pH varied between 5.5 and 9.2. The number of Legionella spp. recovered varied between 5.0 x 10(2) and 2.3 x 10(6) CFU/liter. A total of 288 isolates from 14 sites were identified by indirect immunofluorescence assay. The majority of the isolates belonged to Legionella pneumophila (74.3%), of which most belong to serogroup 1, but the relative proportion of L. pneumophila serogroups varied considerably. L. pneumophila serogroup 1 constituted 96.2% of the isolates in area 2 from central Portugal, but no isolates of this serogroup were recovered from São Miguel, where serogroup 6 strains were the predominant isolates. Ninety-six percent of the L. pneumophila serogroup 1 isolates belonged to monoclonal antibody subgroups OLDA and Bellingham. Other species identified were L. bozemanii serogroup 2, L. dumoffii, L. micdadei, L. moravica, L. oakridgensis, L. sainticrucis, and L. sainthelensi. Two undescribed species, which react by indirect immunofluorescence assay to antisera to "L. londoniensis" and "L. nautarum" and a group of isolates with strong cross-reaction to L. cincinnatiensis/L. sainticrucis/L. longbeachae by indirect immunofluorescence assay were also recovered. The latter were the only isolates recovered from area 3, in east central Portugal, over a period of 1 year.

Biochemical fingerprints of Legionella spp. by the BIOLOG system: presumptive identification of clinical and environmental isolates

Six Legionella strains were characterized with the BIOLOG identification system. A specific metabolic pattern for the six Legionella strains was observed after 24 h. Several positive reactions were detected intermittently in all six strains tested. The possible application of the BIOLOG system for identification of Legionella spp. from environmental or clinical samples is discussed.

Legionella adelaidensis, a new species isolated from cooling tower water

A Legionella-like organism (strain 1762-AUS-E) was isolated from a cooling tower of an air-conditioning system in Adelaide, South Australia, Australia. The isolate was presumptively identified as a Legionella strain by its growth requirement for L-cysteine and its cellular branched-chain fatty acids. Strain 1762-AUS-E was serologically distinct in the slide agglutination test with absorbed antisera. DNA hybridization confirmed that it is a new Legionella species for which the name Legionella adelaidensis is proposed.

Distribution of Legionella longbeachae serogroup 1 and other legionellae in potting soils in Australia

Legionella longbeachae serogroup 1 and other Legionella spp. were isolated from 73% of 45 potting soils made in Australia by 13 manufacturers but were not detected in 19 potting soils made in Greece, Switzerland, and the United Kingdom examined between March 1989 and May 1990. Several Legionella species were isolated from a small number of samples of uncomposted pine sawdusts, but it is not known whether sawdust was the source of some of the legionellae found in potting soils. Legionella spp. persisted for periods ranging from 3 to 10 months in a potting soil held at temperatures between -20 and 35 degrees C. Isolates of L. longbeachae serogroup 1 from soil did not grow at 43 degrees C, a temperature which was also lethal for this species in soil. Most Legionella spp. isolated from potting and natural soils belonged to one distinct group according to analysis of ubiquinones and were serologically related to several known species in this group. A small number of potting soils contained L. pneumophila and L. micdadei.