Evaluation ofLegionellareal-time PCR against traditional culture for routine and public health testing of water samples

Validation of quantitative real-time PCR for detection of Legionella pneumophila in hospital water networks

BACKGROUND

Rapid monitoring of Legionella pneumophila (Lp) is essential to reduce the risk of Legionnaires' disease in healthcare facilities. However, culture results take at least eight days, delaying the implementation of corrective measures. Here, we assessed the performance of a qPCR method and determined qPCR action thresholds for the detection of Lp in hospital hot water networks (HWNs).

METHODS

Hot water samples (n=459) were collected from a hospital HWNs. Lp were quantified using iQ-Check® Quanti real-time PCR Quantification kits (Bio-Rad) and the results were compared with those of culture. qPCR thresholds corresponding to the culture action thresholds of 10 and 1,000 CFU/L were determined on a training dataset and validated on an independent dataset.

RESULTS

Lp concentrations measured by culture and qPCR were correlated for both the training dataset (Spearman's correlation coefficient ρ = 0.687, p-value < 0.0001) and the validation dataset (ρ = 0.661, p-value < 0.0001). Lp qPCR positivity thresholds corresponding to culture action thresholds of 10 CFU/L was 91 genome units (GU) per liter (sensitivity, 86.4%; negative predictive value - NPV, 93.3%) and that corresponding to culture action thresholds of 1,000 CFU/L was 1,048 GU/L (sensitivity, 100%; NPV, 100%).

CONCLUSION

Detection of Lp by qPCR could be implemented with confidence in hospitals as a complement to culture in the monitoring strategy to speed up the implementation of corrective measures.

A Pilot Study for Legionella pneumophila Volatilome Characterization Using a Gas Sensor Array and GC/MS Techniques

Legionellosis is a generic term describing the pneumonic (Legionnaires' disease, LD) and non-pneumonic (Pontiac fever, PF) forms of infection with bacteria belonging to the genus Legionella. Currently, the techniques used to detect Legionella spp. in water samples have certain limitations and drawbacks, and thus, there is a need to identify new tools to carry out low-cost and rapid analysis. In this regard, several studies demonstrated that a volatolomics approach rapidly detects and discriminates different species of microorganisms via their volatile signature. In this paper, the volatile organic compounds (VOCs) pattern emitted in vitro by Legionella pneumophila cultures is characterized and compared to those produced by other Legionella species and by Pseudomonas aeruginosa, using a gas sensor array and gas chromatograph mass spectrometer (GC-MS). Bacterial cultures were measured at the 3rd and 7th day after the incubation. Sensor array data analyzed via the K-nearest neighbours (k-NN) algorithm showed a sensitivity to Legionella pneumophila identification at around 89%. On the other hand, GC-MS identified a bouquet of VOCs, mainly alcohols and ketones, that enable the differentiation of Legionella pneumophila in respect to other waterborne microorganisms.

Clinical and Laboratory Diagnosis of Legionella Pneumonia

Legionella pneumonia is a relatively rare but extremely progressive pulmonary infection with high mortality. Traditional cultural isolation remains the gold standard for the diagnosis of Legionella pneumonia. However, its harsh culture conditions, long turnaround time, and suboptimal sensitivity do not meet the clinical need for rapid and accurate diagnosis, especially for critically ill patients. So far, pathogenic detection techniques including serological assays, urinary antigen tests, and mass spectrometry, as well as nucleic acid amplification technique, have been developed, and each has its own advantages and limitations. This review summarizes the clinical characteristics and imaging findings of Legionella pneumonia, then discusses the advances, advantages, and limitations of the various pathogenetic detection techniques used for Legionella pneumonia diagnosis. The aim is to provide rapid and accurate guiding options for early identification and diagnosis of Legionella pneumonia in clinical practice, further easing healthcare burden.

Detection performance of PCR for Legionella pneumophila in environmental samples: a systematic review and meta-analysis

Background

Legionellosis remains a public health problem. The most common diagnostic method to detect Legionella pneumophila (L. pneumophila) is culture. Polymerase chain reaction (PCR) is a fast and accurate method for this detection in environmental samples.

Methods

Four databases were searched for studies that evaluated the detection efficiency of PCR in L. pneumophila. The quality evaluation was conducted using Review Manager 5.3. We used Meta-DiSc 1.4 software and the Stata 15.0 software to create forest plots, a meta-regression, a bivariate boxplot and a Deeks’ funnel plot.

Results

A total of 18 four-fold tables from 16 studies were analysed. The overall pooled sensitivity and specificity of PCR was 94% and 72%, respectively. The positive likelihood ratio (RLR) and negative likelihood ratio (NLR) was 2.73 and 0.12, respectively. The result of the diagnostic odds ratio (DOR) was 22.85 and the area under the curve (AUC) was 0.7884.

Conclusion

Establishing a laboratory diagnostic tool for L. pneumophila detection is important for epidemiological studies. In this work, PCR demonstrated a promising diagnostic accuracy for L. pneumophila.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00503-9.

Overview of the Clinical and Molecular Features of Legionella Pneumophila: Focus on Novel Surveillance and Diagnostic Strategies

Legionella pneumophila (L. pneumophila) is one of the most threatening nosocomial pathogens. The implementation of novel and more effective surveillance and diagnostic strategies is mandatory to prevent the occurrence of legionellosis outbreaks in hospital environments. On these bases, the present review is aimed to describe the main clinical and molecular features of L. pneumophila focusing attention on the latest findings on drug resistance mechanisms. In addition, a detailed description of the current guidelines for the disinfection and surveillance of the water systems is also provided. Finally, the diagnostic strategies available for the detection of Legionella spp. were critically reviewed, paying the attention to the description of the culture, serological and molecular methods as well as on the novel high-sensitive nucleic acid amplification systems, such as droplet digital PCR.

Assessing the viability of Legionella pneumophila in environmental samples: regarding the filter application of Ethidium Monoazide Bromide

Purpose

Analyses of 34 water samples from 13 healthcare structures revealed how culture method and quantitative PCR (qPCR) often differ in the detection of Legionella pneumophila (Lp). With these considerations in hand, culture method, PCR and Ethidium Monoazide Bromide (EMA) qPCR have all been compared in order to detect Lp in water samples, identify a method able to speed up the procedures, detect the “viable but not cultivable” bacteria (VBNC) and exclude non-viable bacteria using a commercial kit for extraction and amplification as well as modification of the protocol.

Methods

Pure water samples artificially spiked with viable, non-viable and VBNC Lp ATCC 33152 were analyzed using a commercial kit for both qPCR and EMA-qPCR, while ISO 11731-2-2004 was used for culture method.

Results

Only 35% (12/34) of the environmental samples were positive in both culture and qPCR methods. With regard to EMA-qPCR, results showed the absence of dye toxicity on viable and VBNC strains and an incomplete effectiveness on the non-viable ones. In both viable and VBNC strains, a decrease of bacterial DNA amplification was recorded as a function of sample dilution but not of EMA concentration.

Conclusions

Discrepancies between culture method and EMA-qPCR were observed and may be due to different causes such as membrane-dye interactions, presence of interfering compounds and the sensitivity of the kit used.

Study significance and impact

In the presence of one or more suspected cases of nosocomial legionellosis, the application of a rapid molecular method able to identify only the viable and VBNC Lp would be useful in order to quickly identify the source of infection and to intervene with sanitation treatments. However, seeing that in our experience EMA pretreatment on the filter membrane did not come up with the expected results, it would be necessary to proceed with other experiments and/or different dyes.

Graphical Abstract

Confirming the Presence of Legionella pneumophila in Your Water System: A Review of Current Legionella Testing Methods

Legionnaires' disease has been recognized since 1976 and Legionella pneumophila still accounts for more than 95% of cases. Approaches in countries, including France, suggest that focusing risk reduction specifically on L. pneumophila is an effective strategy, as detecting L. pneumophila has advantages over targeting multiple species of Legionella. In terms of assays, the historically accepted plate culture method takes 10 days for confirmed Legionella spp. results, has variabilities which affect trending and comparisons, requires highly trained personnel to identify colonies on a plate in specialist laboratories, and does not recover viable-but-non-culturable bacteria. PCR is sensitive, specific, provides results in less than 24 h, and determines the presence/absence of Legionella spp. and/or L. pneumophila DNA. Whilst specialist personnel and laboratories are generally required, there are now on-site PCR options, but there is no agreement on comparing genome units to colony forming units and action limits. Immunomagnetic separation assays are culture-independent, detect multiple Legionella species, and results are available in 24 h, with automated processing options. Field-use lateral flow devices provide presence/absence determination of L. pneumophila serogroup 1 where sufficient cells are present, but testing potable waters is problematic. Liquid culture most probable number (MPN) assays provide confirmed L. pneumophila results in 7 days that are equivalent to or exceed plate culture, are robust and reproducible, and can be performed in a variety of laboratory settings. MPN isolates can be obtained for epidemiological investigations. This accessible, non-technical review will be of particular interest to building owners, operators, risk managers, and water safety groups and will enable them to make informed decisions to reduce the risk of L. pneumophila.

Quantification of Legionella pneumophila by qPCR and culture in tap water with different concentrations of residual disinfectants and heterotrophic bacteria

Legionellosis prevalence is increasing in the United States. This disease is caused primarily by the bacterium Legionella pneumophila found in water and transmitted by aerosol inhalation. This pathogen has a slow growth rate and can "hide" in amoeba, making it difficult to monitor by the traditional culture method on selective media. Tap water samples (n = 358) collected across the United States were tested for L. pneumophila by both culture and quantitative Polymerase Chain Reaction (qPCR). The presence of other bacteria was quantified by heterotrophic plate counts (HPC). Residual disinfectant concentrations (free chlorine or monochloramine) were measured in all samples. Legionella pneumophila had the highest prevalence and concentration in the chlorinated water samples that had a free‑chlorine value of less than 0.2 mg Cl₂/L. In total, 24% (87/358) of the samples were positive for L. pneumophila either by qPCR or 3% (11/358) were positive by culture. In chloramine-treated samples, L. pneumophila was detected by qPCR in 21% (31/148) and 1% (2/148) by culture, despite a high monochloramine residual >1 mg Cl₂/L. Despite the presence of a high disinfectant residual (>1 mg Cl₂/L), HPC counts were substantial. This study indicates that both culture and qPCR methods have limitations when predicting a potential risk for disease associated with L. pneumophila in tap water. Measuring disinfectant residuals and quantifying HPC in water samples may be useful adjunct parameters for reducing Legionellosis' risk from public water supplies at high-risk locations.

Legionella and Biofilms-Integrated Surveillance to Bridge Science and Real-Field Demands

Legionella is responsible for the life-threatening pneumonia commonly known as Legionnaires’ disease or legionellosis. Legionellosis is known to be preventable if proper measures are put into practice. Despite the efforts to improve preventive approaches, Legionella control remains one of the most challenging issues in the water treatment industry. Legionellosis incidence is on the rise and is expected to keep increasing as global challenges become a reality. This puts great emphasis on prevention, which must be grounded in strengthened Legionella management practices. Herein, an overview of field-based studies (the system as a test rig) is provided to unravel the common roots of research and the main contributions to Legionella’s understanding. The perpetuation of a water-focused monitoring approach and the importance of protozoa and biofilms will then be discussed as bottom-line questions for reliable Legionella real-field surveillance. Finally, an integrated monitoring model is proposed to study and control Legionella in water systems by combining discrete and continuous information about water and biofilm. Although the successful implementation of such a model requires a broader discussion across the scientific community and practitioners, this might be a starting point to build more consistent Legionella management strategies that can effectively mitigate legionellosis risks by reinforcing a pro-active Legionella prevention philosophy.

Comparison of Updated Methods for Legionella Detection in Environmental Water Samples

The difficulty of cultivation of Legionella spp. from water samples remains a strenuous task even for experienced laboratories. The long incubation periods for Legionellae make isolation difficult. In addition, the water samples themselves are often contaminated with accompanying microbial flora, and therefore require complex cultivation methods from diagnostic laboratories. In addition to the recent update of the standard culture method ISO 11731:2017, new strategies such as quantitative PCR (qPCR) are often discussed as alternatives or additions to conventional Legionella culture approaches. In this study, we compared ISO 11731:2017 with qPCR assays targeting Legionella spp., Legionella pneumophila, and Legionella pneumophila serogroup 1. In samples with a high burden of accompanying microbial flora, qPCR shows an excellent negative predictive value for Legionella pneumophila, thus making qPCR an excellent tool for pre-selection of negative samples prior to work-intensive culture methods. This and its low limit of detection make qPCR a diagnostic asset in Legionellosis outbreak investigations, where quick-risk assessments are essential, and are a useful method for monitoring risk sites.

Comparison of the culture method with multiplex PCR for the confirmation of Legionella spp. and Legionella pneumophila

AIMS

The detection and enumeration of Legionella spp. in water samples are typically performed via a cultural technique standardized in ISO 11731. This method is time-consuming (up to 15 days), and the specificity of the confirmation step is questionable. This study proposes the use of multiplex polymerase chain reaction (PCR) to confirm presumptive Legionella colonies directly from the culture plate; this shortens the response time by 2-5 days while still reporting results in colony forming units (CFU).

METHODS AND RESULTS

Two laboratories analysed a total of 290 colonies to compare the confirmation step of Legionella spp. and Legionella pneumophila in accordance with ISO 11731 by culture growth and agglutination vs multiplex PCR. Discordant results were resolved by the swiss national reference laboratory. The data were evaluated following ISO 16140 and showed that the PCR-technique had higher specificity.

CONCLUSIONS

The confirmation of Legionella spp., L. pneumophila and L. pneumophila serogroup 1 by multiplex PCR allows detection of positive colonies more rapidly and with higher specificity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study highlights a possibility to shorten the response time significantly during the enumeration of Legionella spp. and achieving a higher specificity while adhering to the legally recognized reporting in CFU.

Evaluation of Legiolert™ for the Detection of Legionella pneumophila and Comparison with Spread-Plate Culture and qPCR Methods

Legionella pneumophila, the organism responsible for Legionnaires' disease, a potentially lethal pneumonia, is an opportunistic bacterium spread via inhalation of contaminated, aerosolized water. The detection and control of L. pneumophila is crucial to reduce the risk it poses to human health. L. pneumophila is generally detected and quantified by the plating method, ISO 11731:2017 and by qPCR. ISO 11731 is based on the filtration of the water sample through a membrane, which is placed on selective agar medium, and after colony growth, presumptive Legionella are then confirmed by subculturing, serology, or PCR. Quantitative Polymerase Chain Reaction (qPCR) is based on the amplification of a DNA sequence specific to L. pneumophila, usually within the mip gene. The objective of this study was to compare these methods to a new, liquid culture method based on the Most Probable Number (MPN) technique, Legiolert™/Quanti-Tray® with data obtained with ISO 11731 and a viability quantitative qPCR (v-qPCR), for quantification of L. pneumophila in potable and non-potable waters. Data showed that the Legiolert method revealed concentrations of L. pneumophila greater than ISO 11731 and generally similar results to those of v-qPCR. The Legiolert method was highly specific and easy to use, representing a significant advancement in the quantification of L. pneumophila from potable and non-potable waters.

Rapid Testing and Interventions to Control Legionella Proliferation following a Legionnaires' Disease Outbreak Associated with Cooling Towers

Most literature to date on the use of rapid Legionella tests have compared different sampling and analytical techniques, with few studies on real-world experiences using such methods. Rapid tests offer a significantly shorter feedback loop on the effectiveness of the controls. This study involved a complex of five factories, three of which had a history of Legionella contamination in their cooling water distribution system. Multiple sampling locations were utilised to take monthly water samples over 39 months to analyse for Legionella by both culture and quantitative polymerase chain reaction (qPCR). Routine monitoring gave no positive Legionella results by culture (n = 330); however, samples were frequently (68%) positive by qPCR for Legionella spp. (n = 1564). Legionella spp. qPCR assay was thus found to be a good indicator of cooling tower system health and suitable as a routine monitoring tool. An in-house qPCR limit of 5000 genomic units (GU)/L Legionella spp. was established to trigger investigation and remedial action. This approach facilitated swift remedial action to prevent Legionella proliferation to levels that may represent a public health risk. Cooling tower operators may have to set their own action levels for their own systems; however, in this study, 5000 GU/L was deemed appropriate and pragmatic.

Polymerase chain reaction thermal cycling using the programmed tilt displacements of capillary tubes

A thermal cycling method, whereby capillary tubes holding polymerase chain reactions are subjected to programmed tilt displacements so that they are moved using gravity over three spatial regions (I, II, and III) kept at different constant temperatures to facilitate deoxyribonucleic acid (DNA) denaturation, annealing, and extension, is described. At tilt speeds in excess of 0.2 rad/s, the standard deviation of static coefficient of friction values was below 0.03, indicating in sync movement of multiple capillary tubes over the holding platform. The travel time during the acceleration phase and under constant velocity between adjacent regions (I to II and II to III) and distant regions (III to I) was 0.03 s and 0.31 s, respectively. The deviations in temperature did not exceed 0.05 °C from the average at the prescribed denaturing, annealing, and extension temperatures applied. DNA amplification was determined by optical readings, the fluorescence signal was found to increase twofold after 30 thermal cycles, and 1.16 × 10⁶ DNA copies/μl could be detected. The approach also overcomes problems associated with thermal inertia, sample adhesion, sample blockage, and handling of the reaction vessels encountered in the other thermal cycling schemes used.

Evaluation of GVPC and BCYE Media for Legionella Detection and Enumeration in Water Samples by ISO 11731: Does Plating on BCYE Medium Really Improve Yield?

Legionella spp are the causative agents of Legionnaires’ diseases, which is a pneumonia of important public health concern. Ubiquitous freshwater and soil inhabitants can reach man-made water systems and cause illness. Legionella enumeration and quantification in water systems is crucial for risk assessment and culture examination is the gold standard method. In this study, Legionella recovery from potable water samples, at presumably a low concentration of interfering microorganisms, was compared by plating on buffered charcoal yeast extract (BCYE) and glycine, vancomycin, polymyxin B, cycloheximide (GVPC) Legionella agar media, according to the International Standard Organization (ISO) 11731: 2017. Overall, 556 potable water samples were analyzed and 151 (27.1%) were positive for Legionella. Legionella grew on both BCYE and GVPC agar plates in 85/151 (56.3%) water samples, in 65/151 (43%) on only GVPC agar plates, and in 1/151 (0.7%) on only BCYE agar plates. In addition, GVPC medium identified Legionella species other than pneumophila in six more samples as compared with the culture on BCYE. Although the medians of colony forming units per liter (CFU/L) detected on the BCYE and GVPC agar plates were 2500 and 1350, respectively (p-value < 0.0001), the difference did not exceed one logarithm, and therefore is not relevant for Legionella risk assessment. These results make questionable the need to utilize BCYE agar plates to analyze potable water samples.

Next Day Legionella PCR: a highly reliable negative screen for Legionella in the built environment

The opportunistic, waterborne pathogen Legionella caused 9,933 cases of Legionnaires' disease in 2018 in the United States (CDC.gov). The incidence of Legionnaires' disease can be reduced by maintaining clean building water systems through water management programs (WMPs). WMPs often include validation testing to confirm the control of bacteria, but the traditional culture method for enumerating Legionella requires 10-14 days to obtain results. A rapid DNA extraction developed by Phigenics and a real-time PCR negative screen for the genus Legionella provided results the day after sampling. This study evaluated the Next Day Legionella PCR (Phigenics, LLC) compared with the traditional culture method (ISO 11731) on 11,125 building water samples for approximately 1 year. Two DNA extraction methods (Methods 1 and 2) were compared. The negative predictive value (NPV) of the Next Day Legionella PCR in comparison to traditional culture for Method 1 was 99.95%, 99.92%, 99.85%, and 99.17% at >10, >2, >1, and >0.1 CFU/ml limits of detection, respectively. The improved DNA extraction (Method 2) increased the NPV to 100% and 99.88% at >1 and >0.1 CFU/ml, respectively. These results demonstrate the reliability of the genus-level Legionella PCR negative screen to predict culture-negative water samples.

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.

Biofilm growth and control in cooling water industrial systems

Matrix-embedded, surface-attached microbial communities, known as biofilms, profusely colonise industrial cooling water systems, where the availability of nutrients and organic matter favours rapid microbial proliferation and their adhesion to surfaces in the evaporative fill material, heat exchangers, water reservoir and cooling water sections and pipelines. The extensive growth of biofilms can promote micro-biofouling and microbially induced corrosion (MIC) as well as pose health problems associated with the presence of pathogens like Legionella pneumophila. This review examines critically biofilm occurrence in cooling water systems and the main factors potentially affecting biofilm growth, biodiversity and structure. A broad evaluation of the most relevant biofilm monitoring and control strategies currently used or potentially useful in cooling water systems is also provided.

Validation and in-field testing of a new on-site qPCR system for quantification of Legionella pneumophila according to ISO/TS 12869:2012 in HVAC cooling towers

Legionella pneumophila, found in engineered water systems such as HVAC cooling towers, poses a significant public health risk. Culture, though routinely used to quantify L. pneumophila, has several disadvantages including long turnaround time, low sensitivity, and inter-laboratory variability. In this study, we validated the performance of an on-site quantitative polymerase chain reaction (qPCR) detection system for L. pneumophila in accordance with International Standards Organization Technical Specification 12869:2012. We evaluated specificity, limit of detection and quantification, and calibration curve linearity. Additionally, we evaluated whole system recovery and robustness using samples taken from taps and evaporative cooling towers. We then compared the system's performance against laboratory culture and laboratory qPCR across 53 cooling towers in a 12-week in-field study. We found that concordance between on-site qPCR and culture was both laboratory- and site/sample-dependent. Comparison of laboratory qPCR with on-site qPCR revealed that laboratory results were highly variable and showed little concordance. Some discordance may be explained by time delay between sample collection and testing ('shipping effect') which may lead to inaccurate reporting. Overall, our study highlights the value of on-site qPCR detection of L. pneumophila, demonstrates that laboratories are prone to misreporting results due to shipping effects, and reveals significant discordance between laboratory qPCR and culture.

Legionella Detection in Environmental Samples as an Example for Successful Implementation of qPCR

Waterborne diseases are a serious threat because of their ability to infect a high number of individuals in a short time span, such as during outbreaks of Legionellosis. This significantly highlights the need for the rapid detection and quantification of bacteria in environmental water samples. The aim of this study was to investigate the feasibility of quantitative Polymerase Chain Reaction (qPCR) for the detection of Legionellapneumophila (L. pneumophila) in environmental water samples and comparison of standard culture methods for Legionella detection with qPCR. Our study reached a negative predictive value (NPV) for L. pneumophila of 80.7% and for L. pneumophila serogroup 1 (sg1) the calculated NPV was 87.0%. The positive predictive value (PPV) for L. pneumophila was 53.9% and for L. pneumophila sg1 PPV was 21.4%. Results showed a correlation between qPCR and culture with an R2 value of 0.8973 for L. pneumophila, whereas no correlation was observed for the detection of L. pneumophila sg1. In our study, qPCR proved useful for the identification of L. pneumophila negative samples. However, despite the obvious benefits (sample handling, rapid generation of results), qPCR needs to be improved regarding the PPV before it can replace culture in water quality assessment.