Legionella in clinical specimens and hospital water supply facilities: molecular detection and genotyping of the isolates

Genotypic and phenotypic profiling of 127 Legionella pneumophila strains: Insights into regional spread

Given the recent global surge in Legionnaires' disease cases, the monitoring of Legionella pneumophila becomes increasingly crucial. Epidemiological cases often stem from local outbreaks rather than widespread dissemination, emphasizing the need to study the characteristics of this pathogen at a local level. This study focuses on isolates of L. pneumophila in the Italian region of Friuli Venezia Giulia to assess specific genotype and phenotype distribution over time and space. To this end, a total of 127 L. pneumophila strains isolated between 2005 and 2017 within national surveillance programs were analysed. Rep-PCR, RAPD, and Sau-PCR were used for genotypic characterization, while phenotypic characterization was conducted through fatty acids analysis. RAPD and Sau-PCR effectively assessed genetic characteristics, identifying different profiles for the isolates and excluding the presence of clones. Although Sau-PCR is rarely used to analyse this pathogen, it emerged as the most discriminatory technique. Phenotypically, hierarchical cluster analysis categorized strains into three groups based on varying membrane fatty acid percentages. However, both phenotypic and genotypic analyses revealed a ubiquitous profile distribution at a regional level. These results suggest an absence of correlations between strain profiles, geographical location, and isolation time, indicating instead high variability and strain dissemination within this region.

Whole Genome Sequencing: Applications in Clinical Bacteriology

The success in determining the whole genome sequence of a bacterial pathogen was first achieved in 1995 by determining the complete nucleotide sequence of Haemophilus influenzae Rd using the chain-termination method established by Sanger et al. in 1977 and automated by Hood et al. in 1987. However, this technology was laborious, costly, and time-consuming. Since 2004, high-throughput next-generation sequencing technologies have been developed, which are highly efficient, require less time, and are cost-effective for whole genome sequencing (WGS) of all organisms, including bacterial pathogens. In recent years, the data obtained using WGS technologies coupled with bioinformatics analyses of the sequenced genomes have been projected to revolutionize clinical bacteriology. WGS technologies have been used in the identification of bacterial species, strains, and genotypes from cultured organisms and directly from clinical specimens. WGS has also helped in determining resistance to antibiotics by the detection of antimicrobial resistance genes and point mutations. Furthermore, WGS data have helped in the epidemiological tracking and surveillance of pathogenic bacteria in healthcare settings as well as in communities. This review focuses on the applications of WGS in clinical bacteriology.

Contamination of Water Sources of Karaj Hospitals with Legionella pneumophila and Campylobacter jejuni

Background: One of the most common routes of infection development in humans is contaminated water. Legionella pneumophila and Campylobacter jejuni are the important causes of community- and hospital-acquired pneumonia and gastroenteritis that are transmitted to humans via the inhalation of contaminated water droplets and consumption of contaminated water, respectively. Thus, continuous monitoring of the water supply systems for these pathogens has great importance in public health. Objective: This study aimed to evaluate the water contamination of Karaj hospitals with these two bacterial species. Materials and Methods: In this study, 62 water samples were obtained from different parts of the hospitals of Karaj from April to September 2019, including air conditioning systems, dialysis equipment, ventilation tanks, and different wards of a hospital such as infectious diseases, pediatrics, gastroenterology, dialysis, and intensive and neonatal intensive care units. The samples were collected in sterile containers and immediately transferred to the laboratory for further analysis. The culture on specific media, staining, and biochemical tests were performed to identify the L. pneumophila and C. jejuni. Results: Out of 62 water samples, 25.8% (16 samples) were positive for L. pneumophila; 68.75% were observed in hot water samples, and 31.25% were attributed to cold water samples. Among 62 samples, 4.84% (3 samples) were positive for C. jejuni, which were all detected in hot water samples. Conclusion: Considering that the methods of water refinery of municipal water have no high efficiency, the quality improvement of the water sources of hospitals seems to be necessary.

Urinary antigene and PCR can both be used to detect Legionella pneumophila in children's hospital-acquired pneumonia

Legionella pneumophila is the causative agent of more than 95% cases of severe Legionella pneumonia. Nosocomial pneumonias in different hospital wards is an important medical and pharmaceutical concern. This study aimed to detect Legionella with two methods: polymerase chain reaction (PCR) and detection of urine antigenic test (UAT) in patients suffering from nosocomial pneumonia admitted to pediatric intensive care unit (PICU) of children hospitals. This study was conducted in PICU wards of Rasool Akram and Bahrami children hospitals, Tehran, Iran during 2013-2014. In patients diagnosed with hospital-acquired pneumonia, intratracheal secretion samples for PCR and urine sample for UAT were taken. Simultaneously, PCR and urinary antigen test were conducted using commercial kits. The results of urinary antigen test and PCR were analyzed by SPSS v.19 for statistical comparison. In this study, 96 patients aging 2.77 years on average with two age peaks of less than 1 year and 7-8 year were enrolled. More than half of the patients were under 1 year old. The most common underlying diseases were seizure, Acute Lymphoblastic Lymphoma, Down syndrome and metabolic syndromes. The positivity rate of Legionella urinary antigen test was 16.7% and positivity rate of PCR test was 19.8%. There were no significant associations between the results obtained by both assays with age, gender or underlying diseases. In conclusion, PCR is a better detection method for Legionella infection than urinary antigen test, but the difference between the two methods was not significant.

Comparison of in situ sequence type analysis of Legionella pneumophila in respiratory tract secretions and environmental samples of a hospital in East Jerusalem

Legionella pneumophila genotyping is important for epidemiological investigation of nosocomial and community-acquired outbreaks of legionellosis. The prevalence of legionellosis in pneumonia patients in the West Bank was monitored for the first time, and the sequence types (STs) from respiratory samples were compared with STs of environmental samples from different wards of the hospital. Sputum (n = 121) and bronchoalveolar lavage (BAL) (n = 74) specimens were cultured for L. pneumophila; genomic DNA was tested by 16S rRNA polymerase chain reaction (PCR) amplification. Nested PCR sequence-based typing (NPSBT) was implemented on DNA of the respiratory and environmental PCR-positive samples. Only one respiratory specimen was positive for L. pneumophila by culture. BAL gave a higher percentage of L. pneumophila-positive samples, 35% (26/74) than sputum, 15% (18/121) by PCR. NPSBT revealed the following STs: ST 1 (29%, 7/24), ST 461 (21%, 5/24), ST 1037 (4%, 1/24) from respiratory samples, STs from environmental samples: ST 1 (28.5%, 4/14), ST 187 (21.4%, 3/14) and ST 2070, ST 461, ST 1482 (7.1%, 1/14) each. This study emphasises the advantage of PCR over culture for the detection of L. pneumophila in countries where antibiotics are indiscriminately used prior to hospital admission. ST 1 was the predominant ST in both respiratory and environmental samples.

Dendrimers and Polyamino-Phenolic Ligands: Activity of New Molecules Against Legionella pneumophila Biofilms

Legionnaires’ disease is a potentially fatal pneumonia caused by Legionella pneumophila, an aquatic bacterium often found within the biofilm niche. In man-made water systems microbial biofilms increase the resistance of legionella to disinfection, posing a significant threat to public health. Disinfection methods currently used in water systems have been shown to be ineffective against legionella over the long-term, allowing recolonization by the biofilm-protected microorganisms. In this study, the anti-biofilm activity of previously fabricated polyamino-phenolic ligands and polyamidoamine dendrimers was investigated against legionella mono-species and multi-species biofilms formed by L. pneumophila in association with other bacteria that can be found in tap water (Aeromonas hydrophila, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae). Bacterial ability to form biofilms was verified using a crystal violet colorimetric assay and testing cell viability by real-time quantitative PCR and Plate Count assay. The concentration of the chemicals tested as anti-biofilm agents was chosen based on cytotoxicity assays: the highest non-cytotoxic chemical concentration was used for biofilm inhibition assays, with dendrimer concentration 10-fold higher than polyamino-phenolic ligands. While Macrophen and Double Macrophen were the most active substances among polyamino-phenolic ligands, dendrimers were overall twofold more effective than all other compounds with a reduction up to 85 and 73% of legionella and multi-species biofilms, respectively. Chemical interaction with matrix molecules is hypothesized, based on SEM images and considering the low or absent anti-microbial activity on planktonic bacteria showed by flow cytometry. These data suggest that the studied compounds, especially dendrimers, could be considered as novel molecules in the design of research projects aimed at the development of efficacious anti-biofilm disinfection treatments of water systems in order to minimize legionellosis outbreaks.

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.

Role of biofilm in protection of the replicative form of Legionella pneumophila

The dual nature of Legionella pneumophila enables its survival in free and intracellular environments and underpins its infection and spread mechanisms. Experiments using bacterial cultures and improved RTqPCR protocols were devised to gain fresh insights into the role of biofilm in protecting the replicative form of L. pneumophila. mip gene expression was used as a marker of virulence in sessile (biofilm-bound) and planktonic (free-floating) cells of L. pneumophila serotype 1 ATCC 33152. The ratio of mip gene expression to transcriptionally active Legionella cells increased both in sessile and free-floating cells demonstrating an up-regulation of mip gene under nutrient depletion. However, a different trend was observed between the two forms, in planktonic cells the mip gene expression/transcriptionally active Legionella cells increased until the end of the experiment, while in the biofilm such increase was observed at the end of the experiment. These findings suggest a possible association between the switch to the transmissive phase of Legionella and a mip up-regulation and a role for biofilm in preserving Legionella cells in replicative form. Moreover, it has been shown that improved RTqPCR protocols are valuable tools to explore bacterial virulence.

Legionella detection by culture and qPCR: Comparing apples and oranges

Legionella spp. are the causative agent of Legionnaire's disease and an opportunistic pathogen of significant public health concern. Identification and quantification from environmental sources is crucial for identifying outbreak origins and providing sufficient information for risk assessment and disease prevention. Currently there are a range of methods for Legionella spp. quantification from environmental sources, but the two most widely used and accepted are culture and real-time polymerase chain reaction (qPCR). This paper provides a review of these two methods and outlines their advantages and limitations. Studies from the last 10 years which have concurrently used culture and qPCR to quantify Legionella spp. from environmental sources have been compiled. 26/28 studies detected Legionella at a higher rate using qPCR compared to culture, whilst only one study detected equivalent levels of Legionella spp. using both qPCR and culture. Aggregating the environmental samples from all 28 studies, 2856/3967 (72%) tested positive for the presence of Legionella spp. using qPCR and 1331/3967 (34%) using culture. The lack of correlation between methods highlights the need to develop an acceptable standardized method for quantification that is sufficient for risk assessment and management of this human pathogen.

Application of three uniplex polymerase chain reaction assays for the detection of atypical bacteria in asthmatic patients in Kuwait

BACKGROUND

Respiratory infections are known to exacerbate wheezing in many asthmatic patients. We aimed to use molecular methods for the fast detection of Mycoplasma pneumoniae, Chlamydia pneumoniae and Legionella pneumophila in respiratory specimens from asthmatic patients in Kuwait.

METHODS

We used uniplex PCR assays to detect the three atypical bacteria in clinical specimens from 235 asthmatic and non-asthmatic patients in Kuwait. A regression analysis was used to identify the risk factors related to the bacterial type. Group comparisons for similarity were conducted and correlation coefficients were calculated using SPSS statistical software.

RESULTS

The detection limits using uniplex PCR for C. pneumoniae, L. pneumophila and M. pneumoniae were approximately 1pg, 2.4fg and 12pg of DNA, respectively. M. pneumoniae PCR positivity was more common in asthmatic patients (15%) than in non-asthmatic subjects (9%) (P<0.05). A marked difference was observed between patients with acute asthma exacerbation (11%) and patients with chronic (stable) asthma (7%) among Kuwaiti patients; these percentages were 16% for non-Kuwaiti acute asthma patients and 14% for non-Kuwaiti chronic asthma patients (P<0.201). There was a weak positive correlation between asthma severity and PCR positivity for M. pneumoniae. The PCR results for C. pneumoniae and L. pneumoniae were found to be statistically insignificant.

CONCLUSIONS

The results of this study suggest that infection with M. pneumoniae may be related to the exacerbation of asthma symptoms and could possibly be a factor that induces wheezing.

Detection and Quantification of Legionella pneumophila from Water Systems in Kuwait Residential Facilities

The prevalence of Legionella pneumophilia in water systems of residential facilities in Kuwait was performed during the period from November 2007 to November 2011. A total of 204 water samples collected from faucets and showerheads in bathrooms (n = 82), taps in kitchens (n = 51), and water tanks (n = 71), from different locations of residential facilities in Kuwait were screened for Legionella pneumophila by the standard culture method and by real time polymerase chain reaction (RT-PCR). Out of the 204 samples, 89 (43.6%) samples were positive for Legionella spp., 48 (23.5%) samples were detected by the standard culture method, and 85 (41.7%) were detected by RT-PCR. Of the culture positive Legionella samples, counts ranged between 10 to 2250 CFU/L. Serological typing of 48 Legionella isolates revealed that 6 (12.5%) of these isolates belonged to Legionella pneumophila serogroup 1, 37 (77.1%) isolates to Legionella pneumophila serogroup 3, and 1 isolate each (2.1%) belonged to serogroups 4, 7, and 10. The minimum inhibitory concentration (MICs) of the 46 environmental L. pneumophila isolates against the 10 antimicrobials commonly used for Legionella infection treatments were determined. Rifampicin was found to be the most active against L. pneumophila serogroups isolates in vitro.

Optimization of pulsed-field gel electrophoresis for Legionella pneumophila subtyping

A total of 32 strains of Legionella pneumophila were used to optimize pulsed-field gel electrophoresis (PFGE) for subtyping of L. pneumophila. Twenty-six isolates of L. pneumophila with various origins and 11 isolates from five different water systems were used as the panels. For optimization of electrophoretic parameters (EPs) of SfiI PFGE, 26 isolates were analyzed with SfiI digestion, using four EPs yielding the same D value. The EP of a switch time of 5 to 50 s for 21 h had the smallest similarity coefficients and was declared the optimal EP for SfiI PFGE of L. pneumophila. By software analysis and pilot study, AscI was chosen as another PFGE enzyme. AscI PFGE could cluster the isolates from each water system into the same or very similar patterns and had a high degree of typing concordance with other molecular methods. In evaluating the discriminatory power of AscI with the panel of 26 isolates, AscI PFGE gave one single pattern and a D value of 100%. AscI PFGE had a high discriminatory power and a high degree of consistency with epidemiological data and other molecular typing methods for L. pneumophila subtyping, and hence, AscI could be used as a restriction enzyme in PFGE subtyping of L. pneumophila.

Molecular investigation of Streptococcus agalactiae isolates from environmental samples and fish specimens during a massive fish kill in Kuwait Bay

This study was undertaken to identify and characterize bacterial isolates obtained simultaneously from dead fish samples during a massive fish kill in Kuwait Bay and sewage-water samples running into Kuwait Bay using conventional and molecular techniques. Of the 71 bacterial isolates studied; 66 were recovered from 7 different fish species and 5 strains were isolated from sewage samples. The species-specific identity of the isolates was established by phenotypic characteristics and by PCR amplification of 16S rRNA by using Streptococcus agalactiae-specific primers. The genotyping of 12 isolates from fish samples and all 5 isolates from sewage samples was performed by random amplification of polymorphic DNA (RAPD) analysis. Culture methods identified 44 of 66 (67%) and 4 of 5 (80%) isolates obtained from fish and sewage samples, respectively, as S. agalactiae. The PCR amplification of 16S rRNA not only confirmed the results of conventional methods but also resulted in additional identification of 14 of 66 (21%) isolates obtained from fish samples and the remaining isolate recovered from sewage sample, as S. agalactiae. A total of 9 RAPD patterns were observed among the 17 isolates studied; these RAPD patterns were grouped into three clusters. Interestingly, four of the isolates recovered from sewage samples produced nearly identical RAPD band patterns (85-100% similarity) with some of the S. agalactiae strains isolated from Mullet kidney and brain indicting the possibility of sewage being the source of infection.