Genomic Investigation of a Legionellosis Outbreak in a Persistently Colonized Hotel

Characterisation of Legionella Clinical Isolates in Spain from 2012 to 2022

Although cases of Legionnaires' disease are notifiable, data on the phenotypic and genotypic characterisation of clinical isolates are limited. This retrospective study aims to report the results of the characterisation of Legionella clinical isolates in Spain from 2012 to 2022. Monoclonal antibodies from the Dresden panel were used for phenotypic identification of Legionella pneumophila. Genotypic characterisation and sequence type assignment were performed using the Sequence-Based Typing scheme. Of the 1184 samples, 569 were identified as Legionella by culture. Of these, 561 were identified as L. pneumophila, of which 521 were serogroup 1. The most common subgroups were Philadelphia (n = 107) and Knoxville (n = 106). The SBT analysis revealed 130 different STs, with the most common genotypes being ST1 (n = 87), ST23 (n = 57), ST20 (n = 30), and ST42 (n = 29). Knoxville has the highest variability with 32 different STs. ST23 is mainly found in Allentown/France (n = 46) and ST42 in Benidorm (n = 18), whereas ST1 is widely distributed. The results demonstrate that clinical isolates show high genetic diversity, although only a few sequence types (STs) are responsible for most cases. However, outbreaks can also occur with rare genotypes. More data on LD and associated epidemiological studies are needed to establish the risk of an isolate causing outbreak in the future.

High performance Legionella pneumophila source attribution using genomics-based machine learning classification

Fundamental to effective Legionnaires' disease outbreak control is the ability to rapidly identify the environmental source(s) of the causative agent, Legionella pneumophila. Genomics has revolutionized pathogen surveillance, but L. pneumophila has a complex ecology and population structure that can limit source inference based on standard core genome phylogenetics. Here, we present a powerful machine learning approach that assigns the geographical source of Legionnaires' disease outbreaks more accurately than current core genome comparisons. Models were developed upon 534 L. pneumophila genome sequences, including 149 genomes linked to 20 previously reported Legionnaires' disease outbreaks through detailed case investigations. Our classification models were developed in a cross-validation framework using only environmental L. pneumophila genomes. Assignments of clinical isolate geographic origins demonstrated high predictive sensitivity and specificity of the models, with no false positives or false negatives for 13 out of 20 outbreak groups, despite the presence of within-outbreak polyclonal population structure. Analysis of the same 534-genome panel with a conventional phylogenomic tree and a core genome multi-locus sequence type allelic distance-based classification approach revealed that our machine learning method had the highest overall classification performance-agreement with epidemiological information. Our multivariate statistical learning approach maximizes the use of genomic variation data and is thus well-suited for supporting Legionnaires' disease outbreak investigations.IMPORTANCEIdentifying the sources of Legionnaires' disease outbreaks is crucial for effective control. Current genomic methods, while useful, often fall short due to the complex ecology and population structure of Legionella pneumophila, the causative agent. Our study introduces a high-performing machine learning approach for more accurate geographical source attribution of Legionnaires' disease outbreaks. Developed using cross-validation on environmental L. pneumophila genomes, our models demonstrate excellent predictive sensitivity and specificity. Importantly, this new approach outperforms traditional methods like phylogenomic trees and core genome multi-locus sequence typing, proving more efficient at leveraging genomic variation data to infer outbreak sources. Our machine learning algorithms, harnessing both core and accessory genomic variation, offer significant promise in public health settings. By enabling rapid and precise source identification in Legionnaires' disease outbreaks, such approaches have the potential to expedite intervention efforts and curtail disease transmission.

Rapid adaptations of Legionella pneumophila to the human host

Legionella pneumophila are host-adapted bacteria that infect and reproduce primarily in amoeboid protists. Using similar infection mechanisms, they infect human macrophages, and cause Legionnaires' disease, an atypical pneumonia, and the milder Pontiac fever. We hypothesized that, despite the similarities in infection mechanisms, the hosts are different enough that there exist high-selective value mutations that would dramatically increase the fitness of Legionella inside the human host. By comparing a large number of isolates from independent infections, we identified two genes, mutated in three unrelated patients, despite the short duration of the incubation period (2-14 days). One is a gene coding for an outer membrane protein (OMP) belonging to the OmpP1/FadL family. The other is a gene coding for an EAL-domain-containing protein involved in cyclic-di-GMP regulation, which in turn modulates flagellar activity. The clinical strain, carrying the mutated EAL-domain-containing homologue, grows faster in macrophages than the wild-type strain, and thus appears to be better adapted to the human host. As human-to-human transmission is very rare, fixation of these mutations into the population and spread into the environment is unlikely. Therefore, parallel evolution - here mutations in the same genes observed in independent human infections - could point to adaptations to the accidental human host. These results suggest that despite the ability of L. pneumophila to infect, replicate in and exit from macrophages, its human-specific adaptations are unlikely to be fixed in the population.

Genome analysis of Legionella pneumophila ST23 from various countries reveals highly similar strains

ST23 isolated in Italy are analysed by cgMLST and SNP approaches and they are also compared with ST23 from other countries. They are found to be phylogenetically related independently on year, town, or country of isolation.

Legionella pneumophila serogroup 1 (Lp1) sequence type (ST) 23 is one of the most commonly detected STs in Italy where it currently causes all investigated outbreaks. ST23 has caused both epidemic and sporadic cases between 1995 and 2018 and was analysed at genomic level and compared with ST23 isolated in other countries to determine possible similarities and differences. A core genome multi-locus sequence typing (cgMLST), based on a previously described set of 1,521 core genes, and single-nucleotide polymorphisms (SNPs) approaches were applied to an ST23 collection including genomes from Italy, France, Denmark and Scotland. DNAs were automatically extracted, libraries prepared using NextEra library kit and MiSeq sequencing performed. Overall, 63 among clinical and environmental Italian Lp1 isolates and a further seven and 11 ST23 from Denmark and Scotland, respectively, were sequenced, and pangenome analysed. Both cgMLST and SNPs analyses showed very few loci and SNP variations in ST23 genomes. All the ST23 causing outbreaks and sporadic cases in Italy and elsewhere, were phylogenetically related independent of year, town or country of isolation. Distances among the ST23s were further shortened when SNPs due to horizontal gene transfers were removed. The Lp1 ST23 isolated in Italy have kept their monophyletic origin, but they are phylogenetically close also to ST23 from other countries. The ST23 are quite widespread in Italy, and a thorough epidemiological investigation is compelled to determine sources of infection when this ST is identified in both LD sporadic cases and outbreaks.

A Community Outbreak of Legionnaires' Disease with Two Strains of L. pneumophila Serogroup 1 Linked to an Aquatic Therapy Centre

An outbreak of Legionnaires' disease affected 18 people in Montpellier, a town of the south of France, between December 2016 and July 2017. All cases were diagnosed by a positive urinary antigen test. No deaths were reported. Epidemiological, environmental and genomic investigations (nested Sequence-Based Typing (nSBT) and whole genome sequencing) were undertaken. For the cases for which we had information, four had a new isolate (ST2471), one had a different new isolate (ST2470), one had a genomic pattern compatible with the ST2471 identified by nSBT (flaA = 3), and one had a genomic pattern not compatible with two previous identified STs (pilE = 6). The analysis conducted on the pool of an aquatic therapy center revealed seven isolates of Legionella pneumophila. Whole genome analysis confirmed the link between the environmental and clinical isolates for both ST2470 and ST2471. As the outbreak occurred slowly, with several weeks between new cases, it was not possible to immediately identify a common source. The sixth case was the first to report having aquatic therapy care. Of the 18 cases, eight had attended the aquatic therapy center and the other 10 were inhabitants who lived, worked or walked close to the center. The main cause for this outbreak was the lack of facility maintenance. This investigation highlights the risk to public health of aquatic therapy centers for users and nearby populations, and emphasizes the need for risk reduction measures with specific guidelines to improve health and safety in aquatic facilities.

Legionellosis Cluster Associated With Working at a Racetrack Facility in West Virginia, 2018

In October 2018, the Centers for Disease Control and Prevention was notified of a cluster of Legionnaires' disease cases in workers at a racetrack facility. The objective of the resulting investigation was to determine the extent of the outbreak and identify potential sources of exposure to halt transmission. Case-finding and interviews were conducted among symptomatic racetrack workers who were known to be at the facility within 14 days prior to symptom onset. An environmental assessment of the facility and surrounding area was conducted for sources of potential Legionella exposure. In total, 17 legionellosis cases were identified. The environmental assessment revealed a poorly maintained hot tub in the jockey locker room as the most likely source. Further investigation identified deficiencies in the facility's ventilation systems, which suggested a transmission mechanism for workers who never entered the locker room floor. Considering indirect exposure routes via air handling systems can be useful for source identification and case-finding in legionellosis outbreaks.

Travel-associated cases of Legionnaires' disease in the United States, 2015-2016

BACKGROUND

Recent travel is associated with ~20% of reported Legionnaires' disease (LD) cases worldwide.

METHODS

We analyzed LD cases reported to the Centers for Disease Control and Prevention (CDC) during 2015-2016. Travel-associated cases met case criteria for confirmed LD in someone who spent ≥1 night away from home during the 10 days before symptom onset. Most analyses were limited to travel-associated, public accommodation stay (TAPAS) cases. We used reported travel dates to estimate the number of TAPAS cases acquired during travel.

RESULTS

Of 12,200 LD cases reported among U.S. residents, 12.3% were travel-associated; 8.7% were TAPAS. Median patient age for TAPAS cases was 61 years; 64.4% were male; 67.3% were white; 77.9% were non-Hispanic; 96.1% were hospitalized; 4.5% died. Among 887 TAPAS cases involving U.S. destinations, an estimated 29.8% were acquired during travel; 4.28 TAPAS cases were reported, and an estimated 1.10 TAPAS cases were acquired during travel, per 10,000,000 hotel room nights booked. Sixty-eight U.S. TAPAS clusters were detected.

CONCLUSIONS

While acquisition during travel accounted for a relatively small proportion of all LD cases, clusters of TAPAS cases were frequently detected. Prompt notification of these cases to CDC facilitates cluster detection and expedites intervention.

Legionellosis incidents associated with spa pools, England, 2002-2018

BACKGROUND

Spa pools (SPs) pose risks of Legionella infection for users and bystanders.

METHODS

We searched the National Enhanced Legionella Surveillance System for reported SP-associated legionellosis incidents in England between 2002 and 2018 involving at least two cases.

RESULTS

For seven legionellosis SP-associated incidents, six were in commercial settings such as hotels. The median number of cases per outbreak was four (range 2-115).

CONCLUSION

SP-associated legionellosis incidents were mainly located in commercial settings with a wider range of cases than those recognised in previous publications, reinforcing the need for effective environmental controls for SPs in a range of settings.

A Snapshot of the Prevalence and Molecular Diversity of Legionella pneumophila in the Water Systems of Israeli Hotels

Exposure to Legionella spp. contaminated aerosols in hotel settings confers risk for travel-associated Legionnaire’s disease (TALD). In this study, we investigated the prevalence of Legionella contamination and its molecular diversity in hotels and resorts across Israel. The study was comprised of a convenience sample of water systems from 168 hotels and resorts countrywide, routinely inspected between March 2015 and February 2017. Isolation and quantitation of Legionella were performed in a water laboratory using the ISO 11731 method. The distribution of Legionella isolates was analyzed according to geography and source. The genetic diversity of a subset of isolates was analyzed by sequence-based typing (SBT) at the National Reference Laboratory for Legionella and compared to the national database. Out of 2830 samples tested, 470 (17%) obtained from 102 different premises (60% of hotels) were positive for Legionella spp. In 230 samples (49% of all positive, 8% of total samples), accounting for 37% of hotels, Legionella spp. counts exceeded the regulatory threshold of 1000 CFU/L. The most frequently contaminated water sources were cooling towers (38%), followed by faucets, hot tubs, water lines, and storage tanks (14–17% each). Furthermore, 32% and 17% of samples obtained from cooling towers and hot tubs, respectively, exceeded the regulatory thresholds. SBT was performed on 78 strains and revealed 27 different sequence types (STs), including two novel STs. The most prevalent STs found were ST1 (26%), ST87 (10%), ST93 (6%), and ST461 and ST1516 (5% each). Several L. pneumophila STs were found to be limited to certain geographical regions. This is the first study to investigate the prevalence and diversity of Legionella in hotels and resorts in Israel during non-outbreak environmental inspections. These findings will inform risk assessment, surveillance, and control measures of TALD.

Multiple Sources of the Outbreak of Legionnaires' Disease in Genesee County, Michigan, in 2014 and 2015

BACKGROUND

A community-wide outbreak of Legionnaires' disease (LD) occurred in Genesee County, Michigan, in 2014 and 2015. Previous reports about the outbreak are conflicting and have associated the outbreak with a change of water source in the city of Flint and, alternatively, to a Flint hospital.

OBJECTIVE

The objective of this investigation was to independently identify relevant sources of Legionella pneumophila that likely resulted in the outbreak.

METHODS

An independent, retrospective investigation of the outbreak was conducted, making use of public health, health care, and environmental data and whole-genome multilocus sequence typing (wgMLST) of clinical and environmental isolates.

RESULTS

Strong evidence was found for a hospital-associated outbreak in both 2014 and 2015: a) 49% of cases had prior exposure to Flint hospital A, significantly higher than expected from Medicare admissions; b) hospital plumbing contained high levels of L. pneumophila; c) Legionella control measures in hospital plumbing aligned with subsidence of hospital A-associated cases; and d) wgMLST showed Legionella isolates from cases exposed to hospital A and from hospital plumbing to be highly similar. Multivariate analysis showed an increased risk of LD in 2014 for people residing in a home that received Flint water or was located in proximity to several Flint cooling towers.

DISCUSSION

This is the first LD outbreak in the United States with evidence for three sources (in 2014): a) exposure to hospital A, b) receiving Flint water at home, and c) residential proximity to cooling towers; however, for 2015, evidence points to hospital A only. Each source could be associated with only a proportion of cases. A focus on a single source may have delayed recognition and remediation of other significant sources of L. pneumophila. https://doi.org/10.1289/EHP5663.

Quantitative microbial risk assessment of Legionella pneumophila in a drinking water supply system in Israel

Legionella pneumophila cause human infections via inhalation of contaminated water aerosols, resulting in severe pneumonia. Legionella spp. prevalence was monitored in a drinking-water distribution system (DWDS) in Northern Israel. Five points (toilet faucets and showers) were sampled seasonally along a three years period. Toilet faucets and shower use, both generating aerosols, are known transmission routes for this pathogen and thus, present a potential health risk. Quantitative Microbial Risk Assessment (QMRA) was applied in order to assess the health risks posed by Legionella for these two exposure scenarios, while considering Legionella seasonality. The obtained results were compared with estimated tolerable risk levels of infection and of disease set by the USEPA and WHO. Both limits were expressed as Disability-Adjusted Life Years index (DALY) being 1 × 10^-4 and 1 × 10^-6, respectively. The QMRA revealed that the annual risk levels for both faucets and showers use exceeded the acceptable risk of infection with an average of 5.52 × 10^-4 and 2.37 × 10^-3 DALY'S per person per year, respectively. Annual risk levels were stable with no significant differences between the three years. Risk levels varied significantly between seasons by up to three orders of magnitude. Risk levels were highest during summer, autumn, and lowest during winter. The highest seasonal infection risk values were found in summer for both faucets and showers, which corresponded to 8.09 × 10^-4 and 2.75 × 10^-3 DALY'S per person per year, respectively. In conclusion, during summer and autumn there is a significant increase of the infection risk associated with exposure to Legionella-contaminated aerosols, in the studied water system. Public health assessment and prevention measures should focus on these seasons.

Legionella: a reemerging pathogen

PURPOSE OF REVIEW

The present review summarizes new knowledge about Legionella epidemiology, clinical characteristics, community-associated and hospital-based outbreaks, molecular typing and molecular epidemiology, prevention, and detection in environmental and clinical specimens.

RECENT FINDINGS

The incidence of Legionnaire's disease is rising and the mortality rate remains high, particularly for immunocompromised patients. Extracorporeal membrane oxygenation may help support patients with severe respiratory failure. Fluoroquinolones and macrolides appear to be equally efficacious for treating Legionnaires' disease. Whole genome sequencing is an important tool for determining the source for Legionella infections and for understanding routes of transmission and mechanisms by which new pathogenic clones emerge. Real-time quantitative polymerase chain reaction testing of respiratory specimens may improve our ability to diagnose Legionnaire's disease. The frequency of viable but nonculturable organisms is quite high in some water systems but their role in causing clinical disease has not been defined.

SUMMARY

Legionellosis remains an important public health threat. To prevent these infections, staff of municipalities and large buildings must implement effective water system management programs that reduce Legionella growth and transmission and all Medicare-certified healthcare facilities must have water management policies. In addition, we need better methods for detecting Legionella in water systems and in clinical specimens to improve prevention strategies and clinical diagnosis.

Factors associated with Legionnaires' disease recurrence in hotel and holiday rental accommodation sites

BackgroundThe detection of a cluster of travel-associated Legionnaires' disease (TALD) cases in any European Union/European Economic Area (EU/EEA) country prompts action at the accommodation, follow-up by health authorities and reporting of measures taken. Some accommodations incur further cases despite presumed implementation of adequate control measures.AimTo identify factors associated with the occurrence of a further TALD case after the implementation of control measures.MethodsWe conducted a retrospective cohort study of hotel and holiday rental accommodations in the EU/EEA associated with two or more TALD cases with onset dates less than 2 years apart (a 'cluster') and notification between 1 June 2011-31 December 2016. We fitted Cox regression models to estimate the association between accommodation characteristics and the occurrence of a further case, defined as any case with onset date after the report on measures taken.ResultsOf the 357 accommodations in the analysis, 90 (25%) were associated with at least one further case after the report on measures taken (12.4/100 accommodation-years). Accommodations associated with two or more cases before the cluster notification were more likely to be associated with a further case, compared with those not previously associated with any case (adjusted hazard ratio 1.85; 95% confidence interval: 1.14-3.02). Neither the detection of Legionella in the water system nor the type of disinfection were found to be associated with the risk of a further case.ConclusionAccommodation size and previous TALD cases were predictive of further Legionnaires' disease cases after implementation of control measures.

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.

Legionellosis Associated with Recreational Waters: A Systematic Review of Cases and Outbreaks in Swimming Pools, Spa Pools, and Similar Environments

Legionella spp. is widespread in many natural and artificial water systems, such as hot water distribution networks, cooling towers, and spas. A particular risk factor has been identified in the use of whirlpools and hot tubs in spa facilities and public baths. However, there has been no systematic synthesis of the published literature reporting legionellosis cases or outbreaks related to swimming/spa pools or similar environments used for recreational purposes (hot springs, hot tubs, whirlpools, natural spas). This study presents the results of a systematic review of the literature on cases and outbreaks associated with these environments. Data were extracted from 47 articles, including 42 events (17 sporadic cases and 25 outbreaks) and 1079 cases, 57.5% of which were diagnosed as Pontiac fever, without any deaths, and 42.5% were of Legionnaires' disease, with a fatality rate of 6.3%. The results are presented in relation to the distribution of Legionella species involved in the events, clinical manifestations and diagnosis, predisposing conditions in the patients, favourable environmental factors, and quality of the epidemiological investigation, as well as in relation to the different types of recreational water sources involved. Based on the epidemiological and microbiological criteria, the strength of evidence linking a case/outbreak of legionellosis with a recreational water system was classified as strong, probable, and possible; in more than half of the events the resulting association was strong.

Electrophoretic mobility of Legionella pneumophila serogroups 1 to 14

Legionella pneumophila (Lp) is ubiquitous in the aquatic environment and can persist within drinking water distribution systems (DWDS) enabling these systems to serve as a potential source of human infections. Bacterial surface charge, deduced from electrophoretic mobility (EPM), is a well-recognized contributor to microorganism mobility, adherence and interactions with their surrounding environment. In this study, the EPM of 32 Lp strains representing serogroup (sg) 1 to 14 were measured, in 9.15 mM KH2PO4 at pH 8, to understand cell surface properties that may influence their occurrence within DWDS. EPM measurements indicated the charge of Lp varied widely between serogroups with five distinct clusters, from least to most negatively charged: (i) sg1 to 3, 5, and 12; (ii) sg6, 8, and 10; (iii) sg9 and 13; (iv) sg7, 11, and 14; and (v) sg4. The EPM of sg1 and 4 strains were pH dependent; however, values were constant between pH 6 and 9, a range typical of drinking water, suggesting that EPM differences between Lp serogroups could impact their survival within DWDS. Understanding the ecological importance of Lp surface properties (e.g. in mobility, colonization, resistance to disinfectants, etc.) within DWDS would aid in mitigation of health risks associated with this water-based pathogen.

Epidemiological information is key when interpreting whole genome sequence data - lessons learned from a large Legionella pneumophila outbreak in Warstein, Germany, 2013

Whole genome sequencing (WGS) is increasingly used in Legionnaires’ disease (LD) outbreak investigations, owing to its higher resolution than sequence-based typing, the gold standard typing method for Legionella pneumophila, in the analysis of endemic strains. Recently, a gene-by-gene typing approach based on 1,521 core genes called core genome multilocus sequence typing (cgMLST) was described that enables a robust and standardised typing of L. pneumophila. Methods: We applied this cgMLST scheme to isolates obtained during the largest outbreak of LD reported so far in Germany. In this outbreak, the epidemic clone ST345 had been isolated from patients and four different environmental sources. In total 42 clinical and environmental isolates were retrospectively typed. Results: Epidemiologically unrelated ST345 isolates were clearly distinguishable from the epidemic clone. Remarkably, epidemic isolates split up into two distinct clusters, ST345-A and ST345-B, each respectively containing a mix of clinical and epidemiologically-related environmental samples. Discussion/conclusion: The outbreak was therefore likely caused by both variants of the single sequence type, which pre-existed in the environmental reservoirs. The two clusters differed by 40 alleles located in two neighbouring genomic regions of ca 42 and 26 kb. Additional analysis supported horizontal gene transfer of the two regions as responsible for the difference between the variants. Both regions comprise virulence genes and have previously been reported to be involved in recombination events. This corroborates the notion that genomic outbreak investigations should always take epidemiological information into consideration when making inferences. Overall, cgMLST proved helpful in disentangling the complex genomic epidemiology of the outbreak.

Genome Sequencing Links Persistent Outbreak of Legionellosis in Sydney (New South Wales, Australia) to an Emerging Clone of Legionella pneumophila Sequence Type 211

The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions, the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using single-nucleotide polymorphism (SNP)-based core-genome multilocus sequencing typing (MLST) and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and those in suburb 1. These isolates were designated the "main cluster" and consisted of isolates from two patients from the CBD March outbreak, one patient and one tower isolate from suburb 1, and isolates from two cooling towers and three patients from the CBD May outbreak. All main cluster isolates were sequence type 211 (ST211), which previously has only been reported in Canada. Significantly, pangenome analysis identified mobile genetic elements containing a unique type IV A F-type secretion system (T4ASS), which was specific to the main cluster, and cocirculating clinical strains, suggesting a potential mechanism for increased fitness and persistence of the outbreak clone. Genome sequencing enabled linking of the geographically dispersed environmental sources of infection among the spatially and temporally coinciding cases of legionellosis in a highly populated urban setting. The discovery of a unique T4ASS emphasizes the role of genome recombination in the emergence of successful Lp1 clones.IMPORTANCE A new emerging clone has been responsible for a prolonged legionellosis outbreak in Sydney, Australia. The use of whole-genome sequencing linked two outbreaks thought to be unrelated and confirmed the outliers. These findings led to the resampling and subsequent identification of the source, guiding public health actions and bringing the outbreak to a close. Significantly, the outbreak clone was identified as sequence type 211 (ST211). Our study reports this ST in the Southern Hemisphere and presents a description of ST211 genomes from both clinical and environmental isolates. A unique mobile genetic element containing a type IV secretion system was identified in Lp1 ST211 isolates linked to the main cluster and Lp1 ST42 isolates that were cocirculating at the time of the outbreak.

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.

Street Cleaning Trucks as Potential Sources of Legionella pneumophila

In 2015, Legionnaires’ disease was diagnosed in a street cleaning worker. We found Legionella pneumophila serogroup 1 in the water and internal foam from the tanks of 2 trucks used by the worker during the incubation period. The internal foam was removed, and a Legionella prevention program was implemented.

A Supervised Statistical Learning Approach for Accurate Legionella pneumophila Source Attribution during Outbreaks

Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure, with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based on L. pneumophila core genome single nucleotide polymorphism (SNP) comparisons eliminates ambiguity for defining outbreak clusters and accurately predicts exposure sources for clinical cases. We illustrate the performance of our method by genome comparisons of 234 L. pneumophila isolates obtained from patients and cooling towers in Melbourne, Australia, between 1994 and 2014. This collection included one of the largest reported Legionnaires' disease outbreaks, which involved 125 cases at an aquarium. Using only sequence data from L. pneumophila cooling tower isolates and including all core genome variation, we built a multivariate model using discriminant analysis of principal components (DAPC) to find cooling tower-specific genomic signatures and then used it to predict the origin of clinical isolates. Model assignments were 93% congruent with epidemiological data, including the aquarium Legionnaires' disease outbreak and three other unrelated outbreak investigations. We applied the same approach to a recently described investigation of Legionnaires' disease within a UK hospital and observed a model predictive ability of 86%. We have developed a promising means to breach L. pneumophila genetic diversity extremes and provide objective source attribution data for outbreak investigations.IMPORTANCE Microbial outbreak investigations are moving to a paradigm where whole-genome sequencing and phylogenetic trees are used to support epidemiological investigations. It is critical that outbreak source predictions are accurate, particularly for pathogens, like Legionella pneumophila, which can spread widely and rapidly via cooling system aerosols, causing Legionnaires' disease. Here, by studying hundreds of Legionella pneumophila genomes collected over 21 years around a major Australian city, we uncovered limitations with the phylogenetic approach that could lead to a misidentification of outbreak sources. We implement instead a statistical learning technique that eliminates the ambiguity of inferring disease transmission from phylogenies. Our approach takes geolocation information and core genome variation from environmental L. pneumophila isolates to build statistical models that predict with high confidence the environmental source of clinical L. pneumophila during disease outbreaks. We show the versatility of the technique by applying it to unrelated Legionnaires' disease outbreaks in Australia and the UK.

Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila

Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires' disease. Previous genomic studies have shown that recombination accounts for a high proportion (>96%) of diversity within several major disease-associated sequence types (STs) of L. pneumophila. This suggests that recombination represents a potentially important force shaping adaptation and virulence. Despite this, little is known about the biological effects of recombination in L. pneumophila, particularly with regards to homologous recombination (whereby genes are replaced with alternative allelic variants). Using newly available population genomic data, we have disentangled events arising from homologous and non-homologous recombination in six major disease-associated STs of L. pneumophila (subsp. pneumophila), and subsequently performed a detailed characterisation of the dynamics and impact of homologous recombination. We identified genomic "hotspots" of homologous recombination that include regions containing outer membrane proteins, the lipopolysaccharide (LPS) region and Dot/Icm effectors, which provide interesting clues to the selection pressures faced by L. pneumophila. Inference of the origin of the recombined regions showed that isolates have most frequently imported DNA from isolates belonging to their own clade, but also occasionally from other major clades of the same subspecies. This supports the hypothesis that the possibility for horizontal exchange of new adaptations between major clades of the subspecies may have been a critical factor in the recent emergence of several clinically important STs from diverse genomic backgrounds. However, acquisition of recombined regions from another subspecies, L. pneumophila subsp. fraseri, was rarely observed, suggesting the existence of a recombination barrier and/or the possibility of ongoing speciation between the two subspecies. Finally, we suggest that multi-fragment recombination may occur in L. pneumophila, whereby multiple non-contiguous segments that originate from the same molecule of donor DNA are imported into a recipient genome during a single episode of recombination.

High Prevalence and Genetic Polymorphisms of Legionella in Natural and Man-Made Aquatic Environments in Wenzhou, China

Natural and engineered water systems are the main sources of Legionnaires’ disease. It is essential from a public health perspective to survey water environments for the existence of Legionella. To analyze the main serogroups, genotypes and pathogenicity of the pathogen, a stratified sampling method was adopted to collect water samples randomly from shower water, cooling tower water, and local public hot springs in Wenzhou, China. Suspected strains were isolated from concentrated water samples. Serum agglutination assay and real-time PCR (Polymerase chain reaction) were used to identify L. pneumophila. Sequence-based typing (SBT) and pulsed-field gel electrophoresis (PFGE) were used to elucidate the genetic polymorphisms in the collected isolates. The intracellular growth ability of the isolates was determined through their interaction with J774 cells and plating them onto BCYE (Buffered Charcoal Yeast Extract) agar plates. Overall, 25.56% (46/180) of water samples were Legionella-positive; fifty-two strains were isolated and two kinds of serogroups were co-detected from six water samples from 2015 to 2016. Bacterial concentrations ranged from 20 CFU/100 mL to 10,720 CFU/100 mL. In detail, the Legionella-positive rates of shower water, cooling tower water and hot springs water were 15.45%, 13.33%, and 62.5%, respectively. The main serogroups were LP1 (30.69%) and LP3 (28.85%) and all strains carried the dot gene. Among them, 52 isolates and another 10 former isolates were analyzed by PFGE. Nineteen distinct patterns were observed in 52 strains isolated from 2015 to 2016 with three patterns being observed in 10 strains isolated from 2009 to 2014. Seventy-three strains containing 52 from this study and 21 former isolates were selected for SBT analysis and divided into 25 different sequence types in 4 main clonal groups belonging to 4 homomorphic types. Ten strains were chosen to show their abilities to grow and multiply in J744 cells. Taken together, our results demonstrate a high prevalence and genetic polymorphism of Legionella in Wenzhou’s environmental water system. The investigated environmental water sources pose a potential threat to the public where intervention could help to prevent the occurrence of Legionnaires’ disease.

Legionnaires' Disease Outbreak at a Resort in Cozumel, Mexico

An investigation of a Legionnaires' disease outbreak at a Cozumel Island resort identified the source of the first reported Legionnaires' disease outbreak in Mexico and highlighted the need for all countries to make Legionnaires' disease a reportable disease.

Background. A Legionnaires' disease (LD) outbreak at a resort on Cozumel Island in Mexico was investigated by a joint Mexico-United States team in 2010. This is the first reported LD outbreak in Mexico, where LD is not a reportable disease.

Methods. Reports of LD among travelers were solicited from US health departments and the European Working Group for Legionella Infections. Records from the resort and Cozumel Island health facilities were searched for possible LD cases. In April 2010, the resort was searched for possible Legionella exposure sources. The temperature and total chlorine of the water at 38 sites in the resort were measured, and samples from those sites were tested for Legionella.

Results. Nine travelers became ill with laboratory-confirmed LD within 2 weeks of staying at the resort between May 2008 and April 2010. The resort and its potable water system were the only common exposures. No possible LD cases were identified among resort workers. Legionellae were found to have extensively colonized the resort's potable water system. Legionellae matching a case isolate were found in the resort's potable water system.

Conclusions. Medical providers should test for LD when treating community-acquired pneumonia that is severe or affecting patients who traveled in the 2 weeks before the onset of symptoms. When an LD outbreak is detected, the source should be identified and then aggressively remediated. Because LD can occur in tropical and temperate areas, all countries should consider making LD a reportable disease if they have not already done so.

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current "gold standard" typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method. L. pneumophila serogroup 1 isolates (n = 106) from the standard "typing panel," previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ∼50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila.