First two cases of severe multifocal infections caused by Klebsiella pneumoniae in Switzerland: characterization of an atypical non-K1/K2-serotype strain causing liver abscess and endocarditis

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Highlights

  • Hypervirulent K. pneumoniae infections in Europe are increasing.

  • We describe the first two cases in Switzerland: one was due to a typical K2 capsular strain.

  • The second one was due to an atypical strain (no capsular type associated with its wzi allele).

  • WGS was performed for the atypical strains and virulence factors were identified.

  • This work describes for the first time the WGS of an atypical non-K1-K2 strain.

Abstract

Background

We describe the first two multifocal invasive infections due to Klebsiella pneumoniae recently observed in Switzerland.

Methods

Phenotypic (MIC assays and string test) and molecular analyses (PCR/Sequencing for bla, virulence factor genes and whole genome sequencing for one strain) were performed to characterize the causative K. pneumoniae isolates.

Results

Both K. pneumoniae isolates (Kp1 and Kp2) were pan-susceptible to antibiotics and produced narrow-spectrum SHV β-lactamases. However, only Kp1 was string test positive. Kp1 was of ST380 and caused liver abscess as well as pneumonia and orbital phlegmon in an Eritrean patient. It belonged to the hypervirulent capsular serotype K2 and harboured the classic virulence-associated rmpA and aerobactin genes, fulfilling both the clinical and microbiological definitions for an invasive K. pneumoniae syndrome. Kp2 was of ST1043 and caused both liver abscess and endocarditis in a Swiss patient. Moreover, it did not possess the classic virulence-associated genes. Whole genome sequencing identified less well-known virulence factors in Kp2 that might have contributed to its virulence. Among these there were genes important for intestinal colonization and/or invasion, such as genes involved in adhesion (e.g., fimABCD and mrkABCD), regulation of capsule polysaccharide biosynthesis (e.g., evgS-evgA), as well as iron uptake (iroN), energy conversion, and metabolism.

Discussion

This report confirms the continuous dissemination of hypervirulent K. pneumoniae strains among patients of non-Asian descent in Europe. Moreover, it highlights the genetic background of an atypical hypervirulent K. pneumoniae causing a severe invasive infection despite not possessing the classical virulence characteristics of hypermucoviscous strains.

Introduction

Klebsiella pneumoniae (Kp) causes a wide variety of community-acquired and nosocomial infections typically affecting immunocompromised hosts [1], [2]. However, the recent advent of hypervirulent (hv) strains led to the emergence of highly invasive community-acquired infections in previously healthy and immunocompetent people. Commonly, the invasive syndrome due to hvKp implies a clinical presentation of liver abscess with metastatic spread (e.g., involving eyes, lungs, central nervous system) and/or causative strains of hypermucoviscous (hmv) phenotype usually belonging to the K1 or K2 serotypes [3], [4].

The mucoviscosity-associated gene A (magA) in the serotype-specific region of the K1 capsule gene cluster and the regulator of mucoid phenotype A (rmpA) are two extensively studied genes associated with the overexpression of the capsular serotypes K1 and K2 in hvKp, respectively [5], [6]. The siderophore aerobactin (iucA) is another virulence determinant that has been associated to hvKp strains [7]. Additionally, there are several less characterized factors (e.g., porins, efflux pumps, iron transport systems, and genes involved in the allantoin metabolism) which have been linked to the hvKp invasive syndrome in at least one in vivo infection model [6].

In the past, hmv/hvKp isolates were widely reported in Asia [8], [9]. However, cases are now increasingly observed in North America [10], [11], whereas in Europe reports are still scarce and no cases have been reported so far in Switzerland [12], [13], [14], [15], [16], [17], [18]. Notably, while most of the patients with an hmv/hvKp invasive syndrome reported from outside Asia were of Asian descent, growing cases among non-Asians are now being observed [12], [18], [19]. We also note that only few whole genome sequencing (WGS) analyses have been performed on typical hvKp strains (i.e., hmv and/or of capsular type K1/K2) for molecular epidemiology and virulence analysis [20], [21], [22], [23].

In this work, we present the first Swiss case of invasive liver abscess syndrome due to an hvKp which occurred in a non-Asian patient and a rare case of liver abscess and endocarditis due to an atypical hypervirulent Kp. State of the art phenotypic and molecular analyses (including WGS) were implemented to characterize the causative pathogens, contributing to the growing knowledge of the potential virulence factors responsible for the invasiveness of these strains.

Section snippets

Antimicrobial susceptibility testing (AST) and β-lactamase screening

The MICs for several antibiotics were determined using the microdilution Sentitre™ GNX2F plate (Trek Diagnostic Systems, East Grinstead, UK) and interpreted in accordance with the 2016 European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria (version 6.0, 2016), except for doxycycline and minocycline for which the Clinical & Laboratory Standards Institute (CLSI) guidelines were used (M100-S26, 2016). The string test was performed to define the hmv phenotype [4]. β-Lactamase (

Case 1

A 45-year-old Eritrean man living in Switzerland for eight years (without travel history to Asia and/or comorbidity/predisposing factors for infection) was referred to a community-hospital with a 7-day history of cough, fever, chills, and conjunctivitis. At presentation he was febrile, with a conjunctival erythema in the left eye, and both raised inflammatory markers and liver function parameters. CT scan showed a 60 × 54 mm multi-loculated liver abscess and bilateral lung infiltrates. Empirical

Discussion

In this work, we described the first two cases of multifocal invasive infections due to K. pneumoniae in Switzerland. The first case consisted of an invasive liver syndrome caused by a classic hvKp (Kp1), confirming the continuous dissemination of such strains among patients of non-Asian descent in Europe [12], [13], [14], [15], [16], [17]. The second case was due to an atypical hvKp (Kp2) causing community-acquired liver abscess and endocarditis, to which we applied WGS and screened for less

Conclusions

Kp2 highlights the new genetic background of an atypical hypervirulent Kp not belonging to the classical hvKp strains [3]. The bacterial virulence factors found in Kp2 probably play a major role in the invasiveness of this isolate. However, the lack of deposited WGS data for other atypical hypervirulent Kp, and the small numbers of available WGS for hvKp, make a comparison of the genetic virulence backgrounds belonging to the two groups of strains difficult. Furthermore, future investigations

Funding

This work was supported by the Swiss National Science Foundation (SNSF) with grant No. 171259 (due to BBF) and grant No. 153377 (due to AE).

Competing interests

None declared.

Ethical approval

Written informed consent was obtained from all individual participants included in the study.

Author contribution

Conception and design (BBF and AE); acquisition of data (BBF, VD, NB); analysis of data (BBF, VD, AE); drafting the work (BBF, VD, NB, AE); critical revision of the work (all authors); final approval of the manuscript (all authors).

Acknowledgments

We thank Prof. Stephen L. Leib (Director of the Institute for Infectious Diseases) for providing the laboratory space and equipment to perform this study. We also thank Prof. Andri Rauch and the colleagues of Department of Pneumology for providing us clinical data about the patients.

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