Legionella pneumophila monoclonal antibody subgroups and DNA sequence types isolated in Canada between 1981 and 2009: Laboratory Component of National Surveillance

Legionella in drinking water: the detection method matters

Legionella concentrations in drinking water have been regulated for decades and are evaluated with regard to their concentrations in drinking water plumbing systems (DWPS). The respective action levels differ at the international level. In Germany, the Federal Environment Agency (UBA) specifies the application of ISO 11731 for the detection of legionella in drinking water and gives a binding recommendation for the methods to be used for culturing and evaluation. Effective from 01 March 2019, the UBA recommendation was revised. The utilized culture media in the culture approach were altered, consequently affecting the spectrum of legionella colonies detected in drinking water. Using data from a routine legionella monitoring of a large laboratory, over a period of 6 years and 17,270 individual drinking water samples, allowed us to assess the impact of the alteration on the assessment of DWPS. By comparing the amount of action level exceedances before and after the method change, it could be demonstrated that exceedances are reported significantly more often under the new method. Consequently, the corresponding action level for evaluation of legionella contamination and the resulting risk to human health needs to be revised to avoid the misleading impression of increased health risk.

Sequence-based typing of clinical and environmental Legionella pneumophila isolates in Shenyang, China

INTRODUCTION

We performed SBT (sequence-based typing) on clinical and environmental Legionellapneumophila isolates in Shenyang (China). We analyzed and compared the results with those obtained by PFGE (pulsed field gel electrophoresis).

METHODS

Twenty-two L. pneumophila isolates were collected from two patients with L. pneumophila infection, two hospitals, and 13 office buildings. There were two clinical isolates, one strain isolated from domestic tap water, another from shower water and 18 strains from cooling tower water. All these isolates were analyzed by SBT and PFGE methods.

RESULTS

The 22 isolates were divided into 7 types by SBT. Five isolates belonged to novel sequence types (ST2345, ST2344, ST2406, ST2407, and ST2408) and one isolate belonged to ST328. The STs were not obtained for two of the isolates. The remaining 14 isolates belonged to ST1. PFGE typing divided the 22 isolates into 14 pulsotypes. The main pulsotype was SYC, which included seven isolates.

CONCLUSION

Both typing methods showed that predominant clonal lines exist in the Shenyang region, with high levels of genetic polymorphisms. Five novel STs were identified, indicating a unique genetic composition of L. pneumophila strains in this region, which are significantly different from those found in other environmental water systems in the world.

Distribution of Virulence Genes and Sequence-Based Types Among Legionella pneumophila Isolated From the Water Systems of a Tertiary Care Hospital in India

Background: Legionnaires' disease (LD) is a potentially fatal pneumonia predominantly caused by infection due to Legionella pneumophila although more than 50 other Legionella species are described. Water systems contaminated with Legionella spp. are the implicated sources of Legionnaires' disease. In this study, we aimed to assess Legionella contamination in the water sources of a tertiary care hospital and to determine the virulence properties and molecular characteristics of L. pneumophila environmental isolates.

Methods: During May 2015 through August 2018, a total of 201 hospital water samples were tested for L. pneumophila by standardized culture procedures; environmental isolates were examined for the presence of two virulence genes: Legionella vir homolog (lvh) and repeats in structural toxin (rtxA) by PCR. The genotyping of isolates was performed by sequence-based typing (SBT) according to the protocol of the European Study Group for Legionella Infections (ESGLI).

Results:L. pneumophila was isolated from 38/201 (18.9%) water samples; among the 46 isolates, the lvh locus was present in 45 (97.8%), the rtxA locus was found in 45 (97.8%), and both loci were found in 44 (95.7%) isolates. A total of 23 sequence types (STs) were identified among the 44 isolates (index of discrimination [IOD] of 0.929), and 11/23 (47.8%) STs were new to the ESGLI database.

Conclusions: The study results showed genetic diversity in L. pneumophila isolates from the hospital environment along with a high percentage of pathogenicity loci. Besides, certain STs may have an increased ability to cause legionellosis, thus requires specific infection control and prevention strategies whenever identified.

Characterization of Legionella pneumophila Populations by Multilocus Variable Number of Tandem Repeats (MLVA) Genotyping from Drinking Water and Biofilm in Hospitals from Different Regions of the West Bank

The West Bank can be considered a high-risk area for Legionnaires' disease (LD) due to its hot climate, intermittent water supply and roof storage of drinking water. Legionella, mostly L. pneumophila, are responsible for LD, a severe, community-acquired and nosocomial pneumonia. To date, no extensive assessment of Legionella spp and L. pneumophila using cultivation in combination with molecular approaches in the West Bank has been published. Two years of environmental surveillance of Legionella in water and biofilms in the drinking water distribution systems (DWDS) of eight hospitals was carried out; 180 L. pneumophila strains were isolated, mostly from biofilms in DWDS. Most of the isolates were identified as serogroup (Sg) 1 (60%) and 6 (30%), while a minor fraction comprised Sg 8 and 10. Multilocus Variable number of tandem repeats Analysis using 13 loci (MLVA-8(12)) was applied as a high-resolution genotyping method and compared to the standard Sequence Based Typing (SBT). The isolates were genotyped in 27 MLVA-8(12) genotypes (Gt), comprising four MLVA clonal complexes (VACC 1; 2; 5; 11). The major fraction of isolates constituted Sequence Type (ST)1 and ST461. Most of the MLVA-genotypes were highly diverse and often unique. The MLVA-genotype composition showed substantial regional variability. In general, the applied MLVA-method made it possible to reproducibly genotype the isolates, and was consistent with SBT but showed a higher resolution. The advantage of the higher resolution was most evident for the subdivision of the large strain sets of ST1 and ST461; these STs were shown to be highly pneumonia-relevant in a former study. This shows that the resolution by MLVA is advantageous for back-tracking risk sites and for the avoidance of outbreaks of L. pneumophila. Overall, our results provide important insights into the detailed population structure of L. pneumophila, allowing for better risk assessment for DWDS.

Sequence-based typing of clinical and environmental Legionella pneumophila isolates in Shenyang, China

INTRODUCTION

We performed SBT (sequence-based typing) on clinical and environmental Legionellapneumophila isolates in Shenyang (China). We analyzed and compared the results with those obtained by PFGE (pulsed field gel electrophoresis).

METHODS

Twenty-two L. pneumophila isolates were collected from two patients with L. pneumophila infection, two hospitals, and 13 office buildings. There were two clinical isolates, one strain isolated from domestic tap water, another from shower water and 18 strains from cooling tower water. All these isolates were analyzed by SBT and PFGE methods.

RESULTS

The 22 isolates were divided into 7 types by SBT. Five isolates belonged to novel sequence types (ST2345, ST2344, ST2406, ST2407, and ST2408) and one isolate belonged to ST328. The STs were not obtained for two of the isolates. The remaining 14 isolates belonged to ST1. PFGE typing divided the 22 isolates into 14 pulsotypes. The main pulsotype was SYC, which included seven isolates.

CONCLUSION

Both typing methods showed that predominant clonal lines exist in the Shenyang region, with high levels of genetic polymorphisms. Five novel STs were identified, indicating a unique genetic composition of L. pneumophila strains in this region, which are significantly different from those found in other environmental water systems in the world.

Comparison of Whole-Genome Sequences of Legionella pneumophila in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016

During the water crisis in Flint, Michigan, USA (2014-2015), 2 outbreaks of Legionnaires' disease occurred in Genesee County, Michigan. We compared whole-genome sequences of 10 clinical Legionella pneumophila isolates submitted to a laboratory in Genesee County during the second outbreak with 103 water isolates collected the following year. We documented a genetically diverse range of L. pneumophila strains across clinical and water isolates. Isolates belonging to 1 clade (3 clinical isolates, 3 water isolates from a Flint hospital, 1 water isolate from a Flint residence, and the reference Paris strain) had a high degree of similarity (2-1,062 single-nucleotide polymorphisms), all L. pneumophila sequence type 1, serogroup 1. Serogroup 6 isolates belonging to sequence type 2518 were widespread in Flint hospital water samples but bore no resemblance to available clinical isolates. L. pneumophila strains in Flint tap water after the outbreaks were diverse and similar to some disease-causing strains.

Legionella pneumophila levels and sequence-type distribution in hospital hot water samples from faucets to connecting pipes

Recent studies have reported increased levels of Legionella pneumophila (Lp) at points of use compared to levels in primary and secondary components of hot water systems, suggesting possible selection by environmental conditions. In this study, concentrations of Lp in a hospital hot water system were evaluated by profile sampling, collecting successive water samples to determine the prevalence at the faucet (distal) and upstream piping before and after a system intervention to increase temperature. Lp strain diversity was compared between different points of use and different areas of the hot water system (i.e., tap, intermediate piping and main upflow piping). In total, 47 isolates were recovered from 32 positive hot water samples collected from designated taps, showers and recirculation loops; these isolates were subsequently analyzed by sequence-based typing (SBT). Lp levels were comparable between first draw (500 mL) and flushed (2 and 5 min) samples, whereas a decrease was observed in the amount of culturable cells (1 log). Two sequence types (STs) were identified throughout the system. ST378 (sg4/10) was present in 91% of samples, while ST154-like (sg1) was present in 41%; both STs were simultaneously recovered in 34% of samples. Isolated STs displayed comparable tolerance to copper (0.8-5 mg/L) and temperature (55 °C, 1 h) exposure. The ability to replicate within THP1 cells and Acanthamoeba castellanii was similar between the two STs and a comparative environmental outbreak strain. The low Lp diversity and the detection of both Lp sequence types in repeated subsequent samples collected from positive faucets in a hospital wing suggest a minimal impact of the distal conditions on strain selection for the sampled points, as well as a possible adaptation to stressors present in the system, leading to the predominance of a few strains.

Travel-associated Legionnaires' disease: would changing cluster definition lead to the prevention of a larger number of cases?

According to European Guidelines for Legionnaires' Disease prevention and control, travel-associated Legionnaires' disease (TALD) cases are managed differently if classified as sporadic or as part of a cluster and more stringent control measures are deployed after clusters are identified. In this study, we propose to modify the current cluster definition: 'two or more cases of Legionnaires' disease (LD) who stayed at, or visited, the same commercial accommodation site 2-10 days before onset of illness and whose onset is within the same 2-year period' with a new cluster definition, i.e. accommodation sites associated with multiple cases regardless of the time elapsed between them. TALD cases occurred in Italy and in the Balearic Islands between 2005 and 2015 were analysed applying the current European Legionnaires' Disease Surveillance Network (ELDSNet) cluster definition. In a sample of selected accommodation sites with multiple cases, a microbiological study was also conducted. Using the new definition, 63 additional sites (16.4% increase) and 225 additional linked cases (19.5% increase) were identified. Legionella pneumophila sg1 was isolated from 90.7% of the selected accommodation sites. The use of the here proposed TALD cluster definition would warrant a full investigation for each new identified case. This approach should therefore increase the number of sites that will require a risk assessment and, in the presence of an increased risk, the adoption of LD control measures to hopefully prevent additional cases.

Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1

Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations and environmental source attribution. In the United States (US), ST1 is the most prevalent clinical and environmental Lp sequence type. In order to characterize the ST1 population, we sequenced 289 outbreak and non-outbreak associated clinical and environmental ST1 and ST1-variant Lp strains from the US and, together with international isolate sequences, explored their genetic and geographic diversity. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant and environmental isolates unassociated with human disease (n = 99) contained ~65% more nucleotide diversity compared to clinical-sporadic (n = 139) or outbreak-associated (n = 28) ST1 subgroups. The accessory pangenome of environmental isolates was also ~30-60% larger than other subgroups and was enriched for transposition and conjugative transfer-associated elements. Up to ~10% of US ST1 genetic variation could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and from different decades. These findings provide new insight into the ST1 population structure and establish a foundation for interpreting genetic relationships among ST1 strains; these data may also inform future analyses for improved outbreak investigations.

Population structure of Environmental and Clinical Legionella pneumophila isolates in Catalonia

Legionella is the causative agent of Legionnaires’ disease (LD). In Spain, Catalonia is the region with the highest incidence of LD cases. The characterisation of clinical and environmental isolates using molecular epidemiology techniques provides epidemiological data for a specific geographic region and makes it possible to carry out phylogenetic and population-based analyses. The aim of this study was to describe and compare environmental and clinical isolates of Legionella pneumophila in Catalonia using sequence-based typing and monoclonal antibody subgrouping. A total of 528 isolates were characterised. For data analysis, the isolates were filtered to reduce redundancies, and 266 isolates (109 clinical and 157 environmental) were finally included. Thirty-two per cent of the clinical isolates were ST23, ST37 and ST1 while 40% of the environmental isolates were ST284 and ST1. Although the index of diversity was higher in clinical than in environmental ST isolates, we observed that clinical STs were similar to those recorded in other regions but that environmental STs were more confined to particular study areas. This observation supports the idea that only certain STs trigger cases or outbreaks in humans. Therefore, comparison of the genomes of clinical and environmental isolates could provide important information about the traits that favour infection or environmental persistence.

Molecular typing of Legionella pneumophila isolates from environmental water samples and clinical samples using a five-gene sequence typing and standard Sequence-Based Typing

Inadequate discriminatory power to distinguish between L. pneumophila isolates, especially those belonging to disease-related prevalent sequence types (STs) such as ST1, ST36 and ST47, is an issue of SBT scheme. In this study, we developed a multilocus sequence typing (MLST) scheme based on two non-virulence loci (trpA, cca) and three virulence loci (icmK, lspE, lssD), to genotype 110 L. pneumophila isolates from various natural and artificial water sources in Guangdong province of China, and compared with the SBT. The isolates were assigned to 33 STs of the SBT and 91 new sequence types (nSTs) of the MLST. The indices of discrimination (IODs) of SBT and MLST were 0.920 and 0.985, respectively. Maximum likelihood trees of the concatenated SBT and MLST sequences both showed distinct phylogenetic relationships between the isolates from the two environments. More intragenic recombinations were detected in nSTs than in STs, and they were both more abundant in natural water isolates. We found out the MLST had a high discriminatory ability for the disease-associated ST1 isolates: 22 ST1 isolates were assigned to 19 nSTs. Furthermore, we assayed the discrimination of the MLST for 29 reference strains (19 clinical and 10 environmental). The clinical strains were assigned to eight STs and ten nSTs. The MLST could also subtype the prevalent clinical ST36 or ST47 strains: eight ST36 strains were subtyped into three nSTs and two ST47 strains were subtyped into two nSTs. We found different distribution patterns of nSTs between the environmental and clinical ST36 isolates, and between the outbreak clinical ST36 isolates and the sporadic clinical ST36 isolates. These results together revealed the MLST scheme could be used as part of a typing scheme that increased discrimination when necessary.

Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires' Disease

Background.

Legionnaires’ disease is an important cause of hospital-acquired pneumonia and is caused by infection with the bacterium Legionella. Because current typing methods often fail to resolve the infection source in possible nosocomial cases, we aimed to determine whether whole-genome sequencing (WGS) could be used to support or refute suspected links between cases and hospitals. We focused on cases involving a major nosocomial-associated strain, L. pneumophila sequence type (ST) 1.

Methods.

WGS data from 229 L. pneumophila ST1 isolates were analyzed, including 99 isolates from the water systems of 17 hospitals and 42 clinical isolates from patients with confirmed or suspected hospital-acquired infections, as well as isolates obtained from or associated with community-acquired sources of Legionnaires’ disease.

Results.

Phylogenetic analysis demonstrated that all hospitals from which multiple isolates were obtained have been colonized by 1 or more distinct ST1 populations. However, deep sampling of 1 hospital also revealed the existence of substantial diversity and ward-specific microevolution within the population. Across all hospitals, suspected links with cases were supported with WGS, although the degree of support was dependent on the depth of environmental sampling and available contextual information. Finally, phylogeographic analysis revealed that hospitals have been seeded with L. pneumophila via both local and international spread of ST1.

Conclusions.

WGS can be used to support or refute suspected links between hospitals and Legionnaires’ disease cases. However, deep hospital sampling is frequently required due to the potential coexistence of multiple populations, existence of substantial diversity, and similarity of hospital isolates to local populations.

Microbiology and Epidemiology of Legionnaire's Disease

Legionnaire's disease (LD) is the pneumonic form of legionellosis caused by aerobic gram-negative bacilli of the genus Legionella. Individuals become infected when they inhale aerosolized water droplets contaminated with Legionella species. Forty years after the identification of Legionella pneumophila as the cause of the 1976 pneumonia outbreak in a hotel in Philadelphia, we have non-culture-based diagnostic tests, effective antibiotics, and preventive measures to handle LD. With a mortality rate still around 10%, underreporting, and sporadic outbreaks, there is still much work to be done. In this article, the authors review the microbiology, laboratory diagnosis, and epidemiology of LD.

Differential Proteome Between Patient-Related and Non-related Environmental Isolates of Legionella pneumophila

Molecular epidemiologic studies of Legionella have shown different molecular types coexisting in the same environment, with only one having the ability to trigger an outbreak. We therefore studied the proteome of isolates of these different molecular types in search of the proteins responsible for infection. In this study, we performed a differential proteomic analysis between patient-related and non-patient-related environmental isolates using two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry. Sixty-three spots were observed as being different between the two groups; 31 spots were identified corresponding to 23 different proteins. Patient-related isolates overexpressed proteins associated with metabolism, with enzymes of the tricarboxylic acid cycle and the degradation pathways being the most abundant proteins identified. However, the largest group of non-patient-related proteins was associated with stress response. Furthermore, the MOMP protein was located in different spots depending on their patient-related or non-patient-related origin, suggesting different post-translational modifications. According to these results, different bacterial adaptation pathways are activated in stress conditions which influence their ability to produce infection.

Molecular Typing of Legionella pneumophila Isolates in the Province of Quebec from 2005 to 2015

Legionella is found in natural and man-made aquatic environments, such as cooling towers and hot water plumbing infrastructures. Legionella pneumophila serogroup 1 (Lp1) is the most common etiological agent causing waterborne disease in the United States and Canada. This study reports the molecular characterization of Lp strains during a 10 year period. We conducted sequence-based typing (SBT) analysis on a large set of Lp isolates (n = 284) to investigate the province of Quebec sequence types (STs) distribution in order to identify dominant clusters. From 2005 to 2015, 181 clinical Lp isolates were typed by SBT (141 sporadic cases and 40 outbreak related cases). From the same period of time, 103 environmental isolates were also typed. Amongst the 108 sporadic cases of Lp1 typed, ST-62 was the most frequent (16.6%), followed by ST-213 (10.2%), ST-1 (8.3%) and ST-37 (8.3%). Amongst other serogroups (SG), ST-1327 (SG5) (27.3%) and ST-378 (SG10) (12.2%) were the most frequent. From the environmental isolates, ST-1 represent the more frequent SBT type (26.5%). Unweighted pair group method with arithmetic mean (UPGMA) dendrogram from the 108 sporadic cases of SG1 contains 4 major clusters (A to D) of related STs. Cluster B contains the majority of the strains (n = 61) and the three most frequent STs in our database (ST-62, ST-213 and ST-1). During the study period, we observed an important increase in the incidence rate in Quebec. All the community associated outbreaks, potentially or confirmed to be associated with a cooling tower were caused by Lp1 strains, by opposition to hospital associated outbreaks that were caused by serogroups of Lp other than SG1. The recent major Quebec City outbreak caused by ST-62, and the fact that this genotype is the most common in the province supports whole genome sequencing characterization of this particular sequence type in order to understand its evolution and associated virulence factors.

Characterization of unrelated clinical Legionella pneumophila isolates in Catalonia by monoclonal subgrouping and sequence-based typing

AIM

To characterize the genetic diversity of unrelated Legionella pneumophila clinical isolates in Catalonia and compare with other European regions.

METHODS

95 unrelated isolates were analyzed using monoclonal antibodies and sequence-based typing, 1989-2013.

RESULTS

The isolates showed a high diversity (IOD 0.964) with a predominance of some profiles (ST37-Phialdelphia, ST23-Philadelphia and ST1-OLDA). All regions had predominant sequence types (STs) that differed between regions, and only 3% of STs were shared between the three regions.

CONCLUSION

L. pneumophila clinical isolates from Catalonia presented a high diversity and can be used in epidemiological surveillance studies. The heterogeneous predominance of STs between European regions suggested a relationship between geographical distribution and virulence of some STs.

Population structure and minimum core genome typing of Legionella pneumophila

Legionella pneumophila is an important human pathogen causing Legionnaires’ disease. In this study, whole genome sequencing (WGS) was used to study the characteristics and population structure of L. pneumophila strains. We sequenced and compared 53 isolates of L. pneumophila covering different serogroups and sequence-based typing (SBT) types (STs). We found that 1,896 single-copy orthologous genes were shared by all isolates and were defined as the minimum core genome (MCG) of L. pneumophila. A total of 323,224 single-nucleotide polymorphisms (SNPs) were identified among the 53 strains. After excluding 314,059 SNPs which were likely to be results of recombination, the remaining 9,165 SNPs were referred to as MCG SNPs. Population Structure analysis based on MCG divided the 53 L. pneumophila into nine MCG groups. The within-group distances were much smaller than the between-group distances, indicating considerable divergence between MCG groups. MCG groups were also supplied by phylogenetic analysis and may be considered as robust taxonomic units within L. pneumophila. Among the nine MCG groups, eight showed high intracellular growth ability while one showed low intracellular growth ability. Furthermore, MCG typing also showed high resolution in subtyping ST1 strains. The results obtained in this study provided significant insights into the evolution, population structure and pathogenicity of L. pneumophila.

Microbiological diagnosis and molecular typing of Legionella strains during an outbreak of legionellosis in Southern Germany

An explosive outbreak of Legionnaires' disease with 64 reported cases occurred in Ulm/Neu-Ulm in the South of Germany in December 2009/January 2010 caused by Legionella (L.) pneumophila serogroup 1, monoclonal (mAb) subtype Knoxville, sequence type (ST) 62. Here we present the clinical microbiological results from 51 patients who were diagnosed at the University hospital of Ulm, the results of the environmental investigations and of molecular typing of patients and environmental strains. All 50 patients from whom urine specimens were available were positive for L. pneumophila antigen when an enzyme-linked immunosorbent assay (EIA) was used following concentration of those urine samples that tested initially negative. The sensitivity of the BinaxNow rapid immunographic assay (ICA), after 15 min reading and after 60 min reading were 70% and 84%, respectively. Direct typing confirmed the monoclonal subtype Knoxville in 5 out of 8 concentrated urine samples. Real time PCR testing of respiratory tract specimens for L. pneumophila was positive in 15 out of 25 (60%) patients. Direct nested sequence based typing (nSBT) in some of these samples allowed partial confirmation of ST62. L. pneumophila serogroup 1, monoclonal subtype Knoxville ST62, defined as the epidemic strain was isolated from 8 out of 31 outbreak patients (26%) and from one cooling tower confirming it as the most likely source of the outbreak. While rapid detection of Legionella antigenuria was crucial for the recognition and management of the outbreak, culture and molecular typing of the strains from patients and environmental specimens was the clue for the rapid identification of the source of infection.

Prevalence and Molecular Characteristics of Waterborne Pathogen Legionella in Industrial Cooling Tower Environments

Cooling towers are a source of Legionnaires' disease. It is important from a public health perspective to survey industrial cooling towers for the presence of Legionella. Prospective surveillance of the extent of Legionella pollution was conducted at factories in Shijiazhuang, China between March 2011 and September 2012. Overall, 35.7% of 255 industrial cooling tower water samples showed Legionella-positive, and their concentrations ranged from 100 Colony-Forming Units (CFU)/liter to 88,000 CFU/liter, with an average concentration of 9100 CFU/liter. A total of 121 isolates were obtained. All isolates were L. pneumophila, and the isolated serogroups included serogroups 1 (68 isolates, 56.2%), 6 (25, 20.7%), 5 (12, 9.9%), 8 (8, 6.6%), 3 (6, 5.0%) and 9 (2, 1.6%). All 121 isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and 64 different patterns were obtained. All 121 isolates were analyzed sequence-based typing (SBT), a full 7-allele profile was obtained from 117 isolates. One hundred and seventeen isolates were divided into 49 sequence types. Two virulence genes, lvh and rtxA, are analyzed by polymerase chain reaction (PCR). 92.6% (112/121) and 98.3% (119/121) isolates carried lvh and rtxA respectively and 90.9% (110/121) of tested isolates carried both genes. Our results demonstrated high prevalence and genetic polymorphism of L. pneumophila in industrial cooling tower environments in Shijiazhang, China, and the SBT and virulence gene PCR results suggested that the isolates were pathogenic. Improved control and prevention strategies are urgently needed.

Prevalence of 7 virulence genes of Legionella strains isolated from environmental water sources of public facilities and sequence types diversity of L. pneumopila strains in Macau

In this study, we analyzed 7 virulence genes in 55 Legionella species (including 29 L. pneumophila and 26 non-L. pneumophila strains) which isolated from environmental water sources of the public facilities in Macau by using PCR and real-time PCR. In addition, 29 Legionella pneumophila isolates were subjected to genotyping by sequence-based typing scheme and compared with the data reported. The detection rate of flaA, pilE, asd, mip, mompS, proA and neuA genes in the L. pneumophila were 100.0%, respectively. The neuA gene was not detected in the non-L. pneumophila strains, but flaA, pilE, asd, mip, mompS, and proA genes could be amplified with a positive rate of 15.4%, 15.4%, 53.8%, 38.5%, 15.4%, and 38.5%, respectively. The results from real-time PCR were generally consistent with that of PCR. Those L. pneumophila strains were assigned into 10 sequence types (STs) and ST1 (9/29) was the dominant STs. Four new STs were found to be unique in Macau. The analysis of population structure of L. pneumophila strains which isolated from Macau, Guangzhou and Shenzhen indicated that the similar clones were existed and ST1 was the most prevalent STs. However, the distribution of the subtypes isolated from Macau was not the same extensive as those from Guangzhou and Shenzhen. The different detection rates of the 7 virulence genes in different species of Legionella might reflect their own potential for environmental adaptability and pathogenesis. And the data analyzed from STs diversity indicated the Macau L. pneumophila possessed obvious regional specificity and high genetic diversity.

Legionella detection and subgrouping in water air-conditioning cooling tower systems in Kuwait

The main aim of the study was to test for the presence of Legionnaires' disease-causing microorganisms in air-conditioned buildings in Kuwait using molecular technologies. For this purpose, 547 samples were collected from 38 cooling towers for the analysis of Legionella pneumophila. These samples included those from water (n = 178), air (n = 231), and swabs (n = 138). Out of the 547 samples, 226 (41%) samples were presumptive positive for L. pneumophila, with L. pneumophila viable counts in the positive water samples ranging from 1 to 88 CFU/ml. Of the Legionella culture-positive samples, 204 isolates were examined by latex agglutination. These isolates were predominately identified as L. pneumophila serogroup (sg) 2-14. Using the Dresden panel of monoclonal antibodies, 74 representatives isolates were further serogrouped. Results showed that 51% of the isolates belonged to serogroup 7 followed by 1 (18%) and 3 (18%). Serogroups 4 (4%) and 10 (7%) were isolated at a lower frequency, and two isolates could not be assigned to a serogroup. These results indicate the wide prevalence of L. pneumophila serogroup 7 as the predominant serogroup at the selected sampling sites. Furthermore, the 74 L. pneumophila (sg1 = 13; sg3 = 13; sg4 = 3; sg7 = 38; sg10 = 5; sgX = 2) isolates were genotyped using the seven gene protocol sequence-based typing (SBT) scheme developed by the European Working Group for Legionella Infections (EWGLI). The results show that Legionella isolates were discriminated into nine distinct sequence typing (ST) profiles, five of which were new to the SBT database of EWGLI. Additionally, all of the ST1 serogroup 1 isolates were of the OLDA/Oxford subgroup. These baseline data will form the basis for the development of a Legionella environmental surveillance program and used for future epidemiological investigations.

Genetic diversity and evolutionary relationships among Legionella pneumophila clinical isolates, Portugal, 1987 to 2012

The genetic diversity of 89 clinical Legionella isolates, collected between 1987 and 2012, in 22 hospitals from the five regions of Portugal, was analysed in this study using monoclonal antibodies (MAbs) of the Dresden panel and the sequence-based typing (SBT) protocol. The eBURST algorithm was used to infer levels of relatedness between isolates. All isolates collected were Legionella pneumophila, which were further characterised into four subgroups by MAbs, and 30 sequence types (STs) by SBT. Twelve of the STs were unique to Portugal; one of them (ST100) was represented by 32 epidemiologically related isolates. The ST44 was the profile with the highest number of epidemiologically unrelated isolates. The eBURST analyses indicate that, within the group formed by the 30 STs identified in this study, 17 STs were genetically close to at least another ST in the group. The comparison between the eBURST diagrams obtained with the STs from this study and the entire SBT database of the European Working Group for Legionella, showed that 24 (seven of them unique to Portugal) of our 30 STs were related with STs identified in others countries. These results suggest that the population of L. pneumophila clinical strains in Portugal includes both worldwide and local strains.

Genomic characterization of a large outbreak of Legionella pneumophila serogroup 1 strains in Quebec City, 2012

During the summer of 2012, a major Legionella pneumophila serogroup 1 outbreak occurred in Quebec City, Canada, which caused 182 declared cases of Legionnaire's disease and included 13 fatalities. Legionella pneumophila serogroup 1 isolates from 23 patients as well as from 32 cooling towers located in the vicinity of the outbreak were recovered for analysis. In addition, 6 isolates from the 1996 Quebec City outbreak and 4 isolates from patients unrelated to both outbreaks were added to allow comparison. We characterized the isolates using pulsed-field gel electrophoresis, sequence-based typing, and whole genome sequencing. The comparison of patients-isolated strains to cooling tower isolates allowed the identification of the tower that was the source of the outbreak. Legionella pneumophila strain Quebec 2012 was identified as a ST-62 by sequence-based typing methodology. Two new Legionellaceae plasmids were found only in the epidemic strain. The LVH type IV secretion system was found in the 2012 outbreak isolates but not in the ones from the 1996 outbreak and only in half of the contemporary human isolates. The epidemic strains replicated more efficiently and were more cytotoxic to human macrophages than the environmental strains tested. At least four Icm/Dot effectors in the epidemic strains were absent in the environmental strains suggesting that some effectors could impact the intracellular replication in human macrophages. Sequence-based typing and pulsed-field gel electrophoresis combined with whole genome sequencing allowed the identification and the analysis of the causative strain including its likely environmental source.

Distribution of sequence-based types of legionella pneumophila serogroup 1 strains isolated from cooling towers, hot springs, and potable water systems in China

Legionella pneumophila serogroup 1 causes Legionnaires' disease. Water systems contaminated with Legionella are the implicated sources of Legionnaires' disease. This study analyzed L. pneumophila serogroup 1 strains in China using sequence-based typing. Strains were isolated from cooling towers (n = 96), hot springs (n = 42), and potable water systems (n = 26). Isolates from cooling towers, hot springs, and potable water systems were divided into 25 sequence types (STs; index of discrimination [IOD], 0.711), 19 STs (IOD, 0.934), and 3 STs (IOD, 0.151), respectively. The genetic variation among the potable water isolates was lower than that among cooling tower and hot spring isolates. ST1 was the predominant type, accounting for 49.4% of analyzed strains (n = 81), followed by ST154. With the exception of two strains, all potable water isolates (92.3%) belonged to ST1. In contrast, 53.1% (51/96) and only 14.3% (6/42) of cooling tower and hot spring, respectively, isolates belonged to ST1. There were differences in the distributions of clone groups among the water sources. The comparisons among L. pneumophila strains isolated in China, Japan, and South Korea revealed that similar clones (ST1 complex and ST154 complex) exist in these countries. In conclusion, in China, STs had several unique allelic profiles, and ST1 was the most prevalent sequence type of environmental L. pneumophila serogroup 1 isolates, similar to its prevalence in Japan and South Korea.

Prevalence of sequence types among clinical and environmental isolates of Legionella pneumophila serogroup 1 in the United States from 1982 to 2012

Since the establishment of sequence-based typing as the gold standard for DNA-based typing of Legionella pneumophila, the Legionella laboratory at the Centers for Disease Control and Prevention (CDC) has conducted routine sequence-based typing (SBT) analysis of all incoming L. pneumophila serogroup 1 (Lp1) isolates to identify potential links between cases and to better understand genetic diversity and clonal expansion among L. pneumophila bacteria. Retrospective genotyping of Lp1 isolates from sporadic cases and Legionnaires' disease (LD) outbreaks deposited into the CDC reference collection since 1982 has been completed. For this study, we compared the distribution of sequence types (STs) among Lp1 isolates implicated in 26 outbreaks in the United States, 571 clinical isolates from sporadic cases of LD in the United States, and 149 environmental isolates with no known association with LD. The Lp1 isolates under study had been deposited into our collection between 1982 and 2012. We identified 17 outbreak-associated STs, 153 sporadic STs, and 49 environmental STs. We observed that Lp1 STs from outbreaks and sporadic cases are more similar to each other than either group is to environmental STs. The most frequent ST for both sporadic and environmental isolates was ST1, accounting for 25% and 49% of the total number of isolates, respectively. The STs shared by both outbreak-associated and sporadic Lp1 included ST1, ST35, ST36, ST37, and ST222. The STs most commonly found in sporadic and outbreak-associated Lp1 populations may have an increased ability to cause disease and thus may require special attention when detected.

A structural comparison of lipopolysaccharide biosynthesis loci of Legionella pneumophila serogroup 1 strains

Background

The lipopolysaccharide (LPS) is the major immuno-dominant antigen of all Legionella species including L. pneumophila. Its diversity is the basis for the classification of L. pneumophila into serogroups and monoclonal subgroups and is thought to be involved in strain specific virulence. The understanding of the genetic basis of the LPS-antigen is incomplete. Thus, we analyzed the genetic locus involved in LPS-biosynthesis of L. pneumophila serogroup 1 (Sg1) strains with the focus on strain specific gene composition.

Results

The LPS-biosynthesis loci of 14 L. pneumophila Sg1 strains comprise two distinct regions: A 15 kb region containing LPS-biosynthesis genes that can be found in all L. pneumophila strains and a Sg1-specific 18 kb region. The 15 kb region is highly conserved among Sg1 strains as reflected by high homologies of single ORFs and by a consistent ORF arrangement. In contrast, the Sg1 specific 18 kb region is variable and partially disrupted by phage related genes. We propose that the region spanning from ORF 6 to ORF 11 of the Sg1-specific region is likely involved in late LPS-modification. Due to the high variability of this small region and various combinations of single ORFs within this region a strain specific LPS-structure could be synthesized including modifications of legionaminic acid derivates.

Conclusions

Our data clearly demonstrate that the gene structure of the LPS-biosynthesis locus of L. pneumophila Sg1 strains show significant interstrain variability. These data can be used for further functional analysis of the LPS synthesis to understand pathogenesis and reactivity with monoclonal antibodies. Moreover, variable but strain specific regions can serve as basis for the development of novel genotyping assays.

Characterization of legionella lipopolysaccharide

The lipopolysaccharide(LPS) of Legionella spp. is an immuno-dominant antigen and the basis for Legionella pneumophila serogroup classification. The LPS shows a peculiar structure composed of a very hydrophobic lipid A acylated by long chain fatty acids and an O-antigen-specific chain consisting of homopolymeric legionaminic acid. In this chapter we describe a method for the isolation of LPS from L. pneumophila. In the first part we describe the chemical purification, in the second part we outline the application of monoclonal antibody (mAb) in Western blot and immuno-localization by indirect immunofluorescence. This report does not describe physico-chemical methods that analyze the structure of lipopolysaccharide entities.

Typing methods for legionella

In this chapter we describe the methods currently used for subgrouping Legionella pneumophila and other non-pneumophila species. In the first part we describe monoclonal antibody (mAb) subgrouping, either by indirect immunofluorescence or indirect ELISA methods. These monoclonal antibodies are not commercially available but can be obtained for noncommercial purposes from one of the authors. Further, we describe pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP) and sequence-based typing (SBT) as well standardized and reproducible methods for genotyping. The SBT schema is currently available for L. pneumophila whereas PFGE and AFLP can be used for all Legionella species. For certain applications it might be useful to use spoligotyping to distinguish strains belonging to the same sequence type (ST).

Facets of small RNA-mediated regulation in Legionella pneumophila

Legionella pneumophila is a water-borne pathogen that causes a severe lung infection in humans. It is able to replicate inside amoeba in the water environment, and inside lung macrophages in humans. Efficient regulation of gene expression is critical for responding to the conditions that L. pneumophila encounters and for intracellular multiplication in host cells. In the last two decades, many reports have contributed to our understanding of the critical importance of small regulatory RNAs (sRNAs) in the regulatory network of bacterial species. This report presents the current state of knowledge about the sRNAs expressed by L. pneumophila and discusses a few regulatory pathways in which sRNAs should be involved in this pathogen.

Molecular characterization of clinical and environmental isolates of Legionella pneumophila in Norway, 2001-2008

BACKGROUND

The aims of the study were to determine the molecular characteristics of a collection of Legionella pneumophila isolates from 45 cases with Legionnaires' disease and from 96 environmental samples, received by the national reference laboratory in Norway between 2001 and 2008, to use these characteristics to identify links between cases and suspected sources of infection, and to compare the isolate characteristics with those in other European countries.

METHODS

The isolates were characterized by 7-gene locus sequence-based typing and dot-blotting with monoclonal antibodies to various serogroups and subgroups.

RESULTS

The clinical isolates represented 12.6% of the 357 cases notified in Norway between 2001 and 2008, during which 3 outbreaks of L. pneumophila serogroup 1 occurred. Outbreak cases constituted 62.2% of the cases, followed by travel-associated (24.4%) and sporadic cases (11.1%). Forty-two (93.3%) of the clinical and 69 (71.9%) of the environmental isolates were serogroup 1, and 39 (86.7%) and 50 (52.1%) isolates, respectively, carried the monoclonal antibody (Mab) 3/1 virulence-associated epitope. The clinical isolates belonged to 17 sequence types and the environmental isolates to 19 sequence types. neuA was not detected in 23 environmental isolates.

CONCLUSIONS

Matching characteristics of sequence types and monoclonal subgroups for case and environmental isolates were obtained for all 3 outbreaks and for 2 of 5 cases of sporadic disease. Sampling during the outbreaks accounted for the higher proportion of serogroup 1 and Mab 3/1-positive environmental isolates in comparison with other European strain collections.

Distribution of monoclonal antibody subgroups and sequence-based types among Legionella pneumophila serogroup 1 isolates derived from cooling tower water, bathwater, and soil in Japan

Legionella pneumophila serogroup (SG) 1 is the most frequent cause of legionellosis. This study analyzed environmental isolates of L. pneumophila SG 1 in Japan using monoclonal antibody (MAb) typing and sequence-based typing (SBT). Samples were analyzed from bathwater (BW; n = 50), cooling tower water (CT; n = 50), and soil (SO; n = 35). The distribution of MAb types varied by source, with the most prevalent types being Bellingham (42%), Oxford (72%), and OLDA (51%) in BW, CT, and SO, respectively. The ratios of MAb 3/1 positive isolates were 26, 2, and 14% from BW, CT, and SO, respectively. The environmental isolates from BW, CT, and SO were divided into 34 sequence types (STs; index of discrimination [IOD] = 0.973), 8 STs (IOD = 0.448), and 11 STs (IOD = 0.879), respectively. Genetic variation among CT isolates was smaller than seen in BW and SO. ST1 accounted for 74% of the CT isolates. The only common STs between (i) BW and CT, (ii) BW and SO, and (iii) CT and SO were ST1, ST129, and ST48, respectively, suggesting that each environment constitutes an independent habitat.

The N-acylneuraminate cytidyltransferase gene, neuA, is heterogenous in Legionella pneumophila strains but can be used as a marker for epidemiological typing in the consensus sequence-based typing scheme

Sequence-based typing (SBT) is the internationally recognized standard method for genotyping Legionella pneumophila. To date all strains of serogroup 1 (SG1) and some of SGs 2 to 14 yield a seven-allele profile and can be assigned a sequence type (ST). However, for some strains belonging to SGs 2 to 14, the targeted region of the neuA gene could not be amplified using the published standard primers. We determined the DNA sequence of a neuA gene homolog located in the lipopolysaccharide synthesis locus of strain Dallas-1E. By using newly designed degenerate consensus primers based on the neuA homolog in strains Dallas-1E, Philadelphia-1, Paris, Lens, and Corby, we were able to obtain DNA sequences for all 48 non-SG1 strains which were untypeable by the standard method. Our data show that the neuA gene is present in all L. pneumophila strains but differs significantly in some non-SG1 strains at both the DNA and amino acid levels. The new primers can be used to amplify and sequence the neuA gene in all strains and can substitute for the standard primers. This offers the possibility of assigning an ST to all strains of L. pneumophila.

High-throughput typing method to identify a non-outbreak-involved Legionella pneumophila strain colonizing the entire water supply system in the town of Rennes, France

Two legionellosis outbreaks occurred in the city of Rennes, France, during the past decade, requiring in-depth monitoring of Legionella pneumophila in the water network and the cooling towers in the city. In order to characterize the resulting large collection of isolates, an automated low-cost typing method was developed. The multiplex capillary-based variable-number tandem repeat (VNTR) (multiple-locus VNTR analysis [MLVA]) assay requiring only one PCR amplification per isolate ensures a high level of discrimination and reduces hands-on and time requirements. In less than 2 days and using one 4-capillary apparatus, 217 environmental isolates collected between 2000 and 2009 and 5 clinical isolates obtained during outbreaks in 2000 and 2006 in Rennes were analyzed, and 15 different genotypes were identified. A large cluster of isolates with closely related genotypes and representing 77% of the population was composed exclusively of environmental isolates extracted from hot water supply systems. It was not responsible for the known Rennes epidemic cases, although strains showing a similar MLVA profile have regularly been involved in European outbreaks. The clinical isolates in Rennes had the same genotype as isolates contaminating a mall's cooling tower. This study further demonstrates that unknown environmental or genetic factors contribute to the pathogenicity of some strains. This work illustrates the potential of the high-throughput MLVA typing method to investigate the origin of legionellosis cases by allowing the systematic typing of any new isolate and inclusion of data in shared databases.

Investigation of the population structure of Legionella pneumophila by analysis of tandem repeat copy number and internal sequence variation

The population structure of the species Legionella pneumophila was investigated by multilocus variable number of tandem repeats (VNTR) analysis (MLVA) and sequencing of three VNTRs (Lpms01, Lpms04 and Lpms13) in selected strains. Of 150 isolates of diverse origins, 136 (86 %) were distributed into eight large MLVA clonal complexes (VACCs) and the rest were either unique or formed small clusters of up to two MLVA genotypes. In spite of the lower degree of genome-wide linkage disequilibrium of the MLVA loci compared with sequence-based typing, the clustering achieved by the two methods was highly congruent. The detailed analysis of VNTR Lpms04 alleles showed a very complex organization, with five different repeat unit lengths and a high level of internal variation. Within each MLVA-defined VACC, Lpms04 was endowed with a common recognizable pattern with some interesting exceptions. Evidence of recombination events was suggested by analysis of internal repeat variations at the two additional VNTR loci, Lpms01 and Lpms13. Sequence analysis of L. pneumophila VNTR locus Lpms04 alone provides a first-line assay for allocation of a new isolate within the L. pneumophila population structure and for epidemiological studies.

Sporadic Legionnaires' disease: the role of domestic electric hot-water tanks

Sporadic community-acquired legionellosis (SCAL) can be acquired through contaminated aerosols from residential potable water. Electricity-dependent hot-water tanks are widely used in the province of Quebec (Canada) and have been shown to be frequently contaminated with Legionella spp. We prospectively investigated the homes of culture-proven SCAL patients from Quebec in order to establish the proportion of patients whose domestic potable hot-water system was contaminated with the same Legionella isolate that caused their pneumonia. Water samples were collected in each patient's home. Environmental and clinical isolates were compared using pulsed-field gel electrophoresis. Thirty-six patients were enrolled into the study. Legionella was recovered in 12/36 (33%) homes. The residential and clinical isolates were found to be microbiologically related in 5/36 (14%) patients. Contaminated electricity-heated domestic hot-water systems contribute to the acquisition of SCAL. The proportion is similar to previous reports, but may be underestimated.

Insertion sequences as highly resolutive genomic markers for sequence type 1 Legionella pneumophila Paris

The causative agent of legionellosis, Legionella pneumophila, colonizes all natural and human-made water networks, thus constituting the source of contaminated aerosols responsible for airborne human infections. Efficient control of infections, especially during epidemics, necessitates the fastest and most resolutive identification possible of the bacterial source for subsequent disinfection of reservoirs. We thus compared recognized typing approaches for Legionella with a method based on characterization of insertion sequence (IS) content. A total of 86 clinical or environmental isolates of L. pneumophila, including 84 Paris isolates, sampled from 25 clinical investigations in France between 2001 and 2007, were obtained from the Legionella National Reference Center. All strains were typed by monoclonal antibody subgrouping, sequence-based typing, pulsed-field gel electrophoresis, and restriction fragment length polymorphism based on the presence or absence of IS elements. We identified six different types of IS elements in L. pneumophila Paris and used them as genomic markers in hybridization experiments. One IS type, ISLpn11, revealed a high discriminatory power. Simpson's index of discrimination, calculated from the distribution of IS elements, was higher than that obtained with the other typing methods used for L. pneumophila Paris. Moreover, specific ISLpn11 copies were found only in strains isolated from particular cities. In more than half of the cases, each clinical isolate had an ISLpn11 profile that was recovered in at least one environmental isolate from the same geographical location, suggesting that our method could identify the infection source. Phylogenetic analysis suggests a clonal expansion for the L. pneumophila Paris strain.

Characterization of Legionella pneumophila isolates from patients in Japan according to serogroups, monoclonal antibody subgroups and sequence types

We collected 86 unrelated clinical Legionella pneumophila strains that were isolated in Japan during the period 1980–2008. Most (80.2 %) belonged to serogroup 1, followed by serogroups 5, 3 and 2. Interestingly, the patients with L. pneumophila serogroup 1 had a significantly higher male-to-female ratio (12.4) than the patients with other L. pneumophila serogroups (2.0) (OR, 10.5; 95 % CI, 2.5–44.5). When the serogroup 1 strains were analysed by monoclonal antibody (mAb) typing, the most prevalent subgroup was Benidorm (34.9 % of all isolates). Moreover, 79.7 % of the serogroup 1 isolates were bound by mAb 3/1, which recognizes the virulence-associated epitope. When all 86 isolates were subjected to sequence-based typing (SBT) using seven loci, they could be divided into 53 sequence types (STs). The ST with the most isolates (seven) was ST1, to which most isolates from patients and environments around the world belong. However, six of the seven ST1 isolates were isolated before 1994. Other major STs were ST306 (n=6), ST120 (n=5) and ST138 (n=5). All ST306 and ST138 isolates, except for one isolate (ST306), were suspected or confirmed to be derived from bath water, which suggests that these strains prefer bath habitats. The sources of all ST1 and ST120 isolates remain unclear. By combining the SBT and mAb data, the 86 isolates could be divided into 59 types (discrimination index, 0.984). This confirms the usefulness of this combination in epidemiological studies.