Detection of highly macrolide-resistant Legionella pneumophila strains from a hotel water network using systematic whole-genome sequencing

Occurrence of macrolides resistance in Legionella pneumophila ST188: Results of the Belgian epidemiology and resistome investigation of clinical isolates

OBJECTIVES

The incidence of Legionnaires' disease steadily increases worldwide. Although Legionella pneumophila is known as pathogenic, systematic investigations into antibiotic resistance are scarce, and reports of resistance in isolates are recently emerging.

METHODS

Clinical cases and metadata reported to the Belgian National Reference Centre between 2011 and 2022 were retrospectively analyzed. A total of 283 clinical isolates were typed by core genome multi-locus sequence typing (cgMLST). Acquired genes or mutations triggering resistance were extracted from all of them.

RESULTS

The number of Legionnaires' disease cases has increased in Belgium. Urinary antigen testing remains the main used test, but polymerase chain reaction and serology allow the diagnostic in 14.8% and 2.4% of cases, respectively. cgMLST showed a good discrimination between sequence typing (ST) and minimal variation for ST47 isolates, whereas ST1s were more diverse. Genotypic screening identified a 23S ribosomal RNA mutation linked to a high-level macrolide resistance in one isolate of ST188, which is genetically closed to resistant isolates from France.

CONCLUSION

The increase in incidence is of concern and likely an under-estimate due to the reliance on urine antigen testing. Routine typing by cgMLST allows good discrimination and the first clinical isolate reported as resistant for macrolides was cultured, underscoring the need to define resistance breakpoints and incorporate antimicrobial susceptibility testing as routine clinical investigation practice.

Antimicrobial susceptibility and epidemiological types of Legionella pneumophila human isolates from Italy (1987-2020)

OBJECTIVES

Although antimicrobial resistance has not yet emerged as an overarching problem for Legionella pneumophila (L. pneumophila) infection, the description of clinical and environmental strains resistant to fluoroquinolones and macrolides is a cause of concern. This study aimed to investigate the antimicrobial susceptibility of L. pneumophila human isolates in Italy.

METHODS

A total of 204 L. pneumophila clinical isolates were tested for sensitivity to 9 antibiotics using the broth microdilution assay (BMD). All isolates were typed by sequence-based typing, and Legionella pneumophila serogroup 1 (Lp1) isolates by monoclonal antibody subgrouping. Minimum inhibitory concentration (MIC) data were correlated with the possible source of infection and geographical distribution. The presence of the lpeAB efflux pump genes was also investigated. The genome sequences of a subpopulation of isolates showing reduced susceptibility to azithromycin were also analysed.

RESULTS

The L. pneumophila isolates did not show significant resistance to the tested antibiotics, although a trend toward reduced sensitivity to azithromycin was observed in a subpopulation of 46 strains, most of which belonged to sequence type 1 (ST1), the second most widespread ST in Italy. An amplicon of the expected size overlapping the lpeAB genes was obtained only in the 46-subpopulation above mentioned. In 4 of the 46 isolates, sequencing analysis showed the occurrence of amino-acid substitutions already described in other strains. No further mutation was found.

CONCLUSIONS

The presence of L. pneumophila strains with reduced susceptibility or resistance to azithromycin should be monitored to predict future trends and suggest to physicians a combined therapy with fluoroquinolones when a poor response to azithromycin is observed. © 2025 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.

Case report: The value of early application of mNGS technology in the diagnosis and treatment of severe Legionnaires' disease: reports of two cases with different outcomes

Background

Legionnaires' disease has a high clinical mortality rate, and early diagnosis and treatment are critical. Increasing evidence shows that metagenomic next-generation sequencing (mNGS) has excellent potential for the early identification of pathogens. To help clinicians better recognize Legionnaires' disease in its early stage and to illustrate the diagnostic value of mNGS technology, we reviewed and summarized two cases of severe Legionnaires' disease.

Methods and analysis

We selected two patients with severe Legionnaires' disease who were admitted to our department in recent years. We discuss experience with them and the shortcomings in their treatment by summarizing their medical history, disease evolution, tests, and diagnostic and therapeutic processes.

Results

In both patients, the diagnosis of Legionnaires' disease was confirmed through analysis of the bronchoalveolar lavage fluid (BALF). The middle-aged male patient was cured and discharged due to early detection and diagnosis. The elderly immunocompromised patient died due to a delay in diagnosis.

Conclusion

This study highlights the importance of the early recognition and diagnosis of severe Legionnaires' disease and the advantages of mNGS in identifying the pathogen.

Broth microdilution protocol for determining antimicrobial susceptibility of Legionella pneumophila to clinically relevant antimicrobials

Currently there is no detailed, internationally agreed protocol defined to evaluate antimicrobial susceptibility testing (AST) for Legionella pneumophila (required to establish epidemiological cut-off value or "ECOFF" boundaries); therefore, antimicrobial resistance in these isolates cannot be defined. AST methods utilising media containing activated charcoal as an ingredient, to enable Legionella growth, are unreliable as noted in an internationally authored opinion paper and a new gold standard is required. Here we define a detailed protocol for broth microdilution (BMD) using defined cell culture collection-deposited control reference strains (Philadelphia-1 and Knoxville-1) as well as two accessible reference strains with moderately (lpeAB-carrying) and markedly (23S rRNA mutation-carrying) elevated azithromycin minimum inhibitory concentration (MIC). The defined protocol enables up to eight L. pneumophila strains to be set up on a single 96-well plate per antimicrobial tested. Initial ranges to routinely capture an MIC for these reference strains using clinically relevant antimicrobials azithromycin (0.01-0.25 mg/L), levofloxacin (0.008-0.03 mg/L), lefamulin (0.01-2 mg/L), rifampicin (0.0002-0.0008 mg/L) and doxycycline (0.25-16 mg/L) following incubation for 48 h at 37 °C in a shaking incubator have been empirically determined. Establishment of this internationally agreed protocol sets the scene for the next step: validation and comparison of antimicrobial ranges between international Legionella reference laboratories to establish putative resistance cut-off thresholds for these clinically relevant antimicrobials.

Expect the unexpected: endocarditis caused by Legionella feeleii

We report a fatal case of Legionella feeleii endocarditis in a post-lung transplant patient. The diagnosis was delayed, as routine microbiological testing of nonrespiratory specimens does not account for extrapulmonary Legionella, and urine antigen testing only reliably detects Legionella pneumophila serogroup 1. This case also illustrates the utility of molecular sequencing for blood culture-negative endocarditis.

Antimicrobial susceptibility testing reveals reduced susceptibility to azithromycin and other antibiotics in Legionella pneumophila serogroup 1 isolates from Portugal

BACKGROUD

Although not fully investigated, studies show that Legionella pneumophila can develop antibiotic resistance. As there is limited data available for Portugal, we determined the antibiotic susceptibility profile of Portuguese L. pneumophila serogroup 1 (LpnSg1) isolates against antibiotics used in the clinical practice in Portugal.

METHODS

Minimum inhibitory concentrations (MICs) were determined for LpnSg1 clinical (n = 100) and related environmental (n = 7) isolates, collected between 2006-2022 in the context of the National Legionnaire´s Disease Surveillance Programme, against azithromycin, clarithromycin, erythromycin, levofloxacin, ciprofloxacin, moxifloxacin, rifampicin, doxycycline, tigecycline, and amoxicillin/clavulanic acid, using three different assays. Isolates were also PCR-screened for the presence of the lpeAB gene.

RESULTS

Twelve isolates had azithromycin MICs above the EUCAST tentative highest WT MIC, 9 of which were lpeAB negative; for erythromycin and clarithromycin, all isolates tested within the susceptible range. The number of isolates with MICs above the tentative highest WT MIC for the remaining antibiotics was: ciprofloxacin: 7; levofloxacin: 17; moxifloxacin: 8; rifampicin: 11; doxycycline: 82; tigecycline: 4. EUCAST breakpoints are not available for amoxicillin/clavulanic acid. We estimated the ECOFFs and one isolate had a MIC eightfold higher than the E-test ECOFF. Additionally, a clinical isolate generated three colonies growing on the E-test inhibition zone that resulted in MICs fourfold higher than for the parental isolate.

CONCLUSIONS

We report, for the first time, elevated MICs against first-line and other antibiotics (including azithromycin, fluoroquinolones and amoxicillin/clavulanic acid commonly used to treat pneumonia patients in Portugal) in Portuguese L. pneumophila strains. Results point towards decreased susceptibility in circulating strains, justifying further investigation.

Severe Legionnaires' disease

BACKGROUND

Legionnaires' disease (LD) is a common but under-diagnosed cause of community-acquired pneumonia (CAP), although rapid detection of urine antigen testing (UAT) and advances in molecular testing have improved the diagnosis. LD entails intensive care unit (ICU) admission in almost one-third of cases, and the mortality rate ranges from 4% to 40%. This review aims to discuss recent advances in the study of this condition and to provide an update on the diagnosis, pathogenesis and management of severe LD.

RESULTS

The overall incidence of LD has increased worldwide in recent years due to the higher number of patients with risk factors, especially immunosuppression, and to improvements in diagnostic methods. Although LD is responsible for only around 5% of all-cause CAP, it is one of the three most common causes of CAP requiring ICU admission. Mortality in ICU patients, immunocompromised patients or patients with a nosocomial source of LD can reach 40% despite appropriate antimicrobial therapy. Regarding pathogenesis, no Legionella-specific virulence factors have been associated with severity; however, recent reports have found high pulmonary Legionella DNA loads, and impairments in immune response and lung microbiome in the most severe cases. The clinical picture includes severe lung injury requiring respiratory and/or hemodynamic support, extrapulmonary symptoms and non-specific laboratory findings. LD diagnostic methods have improved due to the broad use of UAT and the development of molecular methods allowing the detection of all Lp serogroups. Therapy is currently based on macrolides, quinolones, or a combination of the two, with prolonged treatment in severe cases.

CONCLUSIONS

Numerous factors influence the mortality rate of LD, such as ICU admission, the underlying immune status, and the nosocomial source of the infection. The host immune response (hyperinflammation and/or immunoparalysis) may also be associated with increased severity. Given that the incidence of LD is rising, studies on specific biomarkers of severity may be of great interest. Further assessments comparing different regimens and/or evaluating host-directed therapies are nowadays needed.

Bacterial persistence in Legionella pneumophila clinical isolates from patients with recurring legionellosis

Bacterial persisters are a transient subpopulation of non-growing, antibiotic-tolerant cells. There is increasing evidence that bacterial persisters play an important role in treatment failure leading to recurring infections and promoting the development of antibiotic resistance. Current research reveals that recurring legionellosis is often the result of relapse rather than reinfection and suggests that the mechanism of bacterial persistence may play a role. The development of single-cell techniques such as the Timerbac system allows us to identify potential persister cells and investigate their physiology. Here, we tested the persister forming capacity of 7 pairs of Legionella pneumophila (Lp) clinical isolates, with isolate pairs corresponding to two episodes of legionellosis in the same patient. We distinguished non-growing subpopulations from their replicating counterparts during infection in an amoeba model. Imaging flow cytometry allowed us to identify single non-growing bacteria within amoeba cells 17 h post-infection, thus corresponding to this subpopulation of potential persister cells. Interestingly the magnitude of this subpopulation varies between the 7 pairs of Lp clinical isolates. Biphasic killing kinetics using ofloxacin stress confirmed the persister development capacity of ST1 clinical isolates, highlighting enhanced persister formation during the host cell infection. Thus, persister formation appears to be strain or ST (sequence type) dependent. Genome sequence analysis was carried out between ST1 clinical isolates and ST1 Paris. No genetic microevolution (SNP) linked to possible increase of persistence capacity was revealed among all the clones tested, even in clones issued from two persistence cycle experiments, confirming the transient reversible phenotypic status of persistence. Treatment failure in legionellosis is a serious issue as infections have a 5-10% mortality rate, and investigations into persistence in a clinical context and the mechanisms involved may allow us to combat this issue.