Introduction

The genus Elizabethkingia comprises aerobic, non-fermenting, non-motile and non-spore-forming gram-negative rods that were previously named Flavobacterium or belonged to CDC group IIa and later reclassified as Chryseobacterium in 19941. In 2005, Chryseobacterium meningosepticum and C. miricola were transferred to a new genus, Elizabethkingia, on the basis of combined phenotypic and phylogenetic characteristics2. The genus comprises three medically important species, Elizabethkingia anophelis, E. meningoseptica and E. miricola. A novel species, E. endophytica, isolated from sweet corn, was also recently proposed3. E. meningoseptica, previously named Flavobacterium meningosepticum or C. meningosepticum, is the best known species among the genus. E. meningoseptica is a causative agent of nosocomial infections especially in immunocompromised patients, as well as neonatal meningitis and sepsis4. Besides soil, fresh water and plants, the bacterium can be found in hospital environments and may contaminate flushing solutions and medical devices5. Infections caused by E. meningoseptica can be difficult to treat and carry high mortalities, which may be partly explained by their intrinsic multidrug resistance towards commonly used antibiotics such as β-lactams and aminoglycosides6. Therefore, accurate diagnosis is important to guide appropriate antibiotic regimens which often consist of a combination of ciprofloxacin or rifampicin with piperacillin-tazobactam or vancomycin.

In contrast to E. meningoseptica, the epidemiology and pathogenicity of E. anophelis and E. miricola were less well understood. E. miricola, originally named C. miricola when first isolated from condensed water obtained from the Russian space station, Mir, only rarely causes nosocomial infections in human7,8. On the other hand, E. anophelis was first isolated from midgut of the mosquito Anopheles gambiae in 20119. Soon after its discovery, it was reported to cause neonatal meningitis in the Central African Republic and a nosocomial outbreak in an intensive-care unit in Singapore10,11. The first discovery of E. anophelis from mosquito gut has raised suspicion on mosquitoes as the source of neonatal meningitis cases in Africa10. However, our recent report on E. anophelis meningitis in two neonates and chorioamnionitis in a neonate’s mother in Hong Kong suggested that mosquitoes were unlikely the vehicles of transmission12. Since the transmission route was initially obscure, draft genome sequencing was performed and showed evidence for perinatal vertical transmission from a mother to her neonate12. The ultimate resolution power of genome sequencing also enabled species confirmation and discrimination from the phenotypically similar species, E. meningoseptica12.

Since E. anophelis was commonly misidentified as E. meningoseptica in previous reports10,11,12,13, we hypothesize that many previously described E. meningoseptica isolates were actually E. anophelis and that E. anophelis may account for a significant proportion of Elizabethkingia infections. To better understand the epidemiology and clinical disease spectrum of E. anophelis and Elizabethkingia as a whole, we determined the clinical and molecular epidemiology of bacteremia caused by Elizabethkingia-like species from five regional hospitals in Hong Kong. All bacteremia episodes caused by Elizabethkingia-like species identified by conventional phenotypic tests from 2004 to 2013 during the study period were included. For the 45 episodes of Elizabethkingia-like bacteremia identified, 16S rRNA gene sequencing was performed for species identification and clinical characteristics and outcomes were analyzed.

Results

Identification of Elizabethkingia-like bacteremia by 16S rRNA gene sequencing

Twenty-one of the 45 episodes of Elizabethkingia-like bacteremia were caused by Elizabethkingia, while 24 episodes were caused by diverse genera/species including Chryseobacterium (n = 15), Flavobacterium (n = 1), Planobacterium (n = 6), Sphingobacterium (n = 1) and Weeksella-like species (n = 1) according to 16S rRNA gene analysis (Fig. 1 and see Supplementary Table 1). Of the 21 episodes of Elizabethkingia bacteremia, 17 were caused by E. anophelis (99.0–99.9% nucleotide identity to E. anophelis type strain R26T), three by E. meningoseptica (99.4–99.8% nucleotide identity to E. meningoseptica type strain ATCC 13253T) and one by E. miricola (99.5% nucleotide identity to E. miricola type strain LMG 22470T).

Figure 1
figure 1

Phylogenetic tree showing the relationship of the 45 Elizabethkingia-like blood culture isolates to related bacterial species using 16S rRNA gene sequence analysis.

The tree was constructed by maximum likelihood method using General Time Reversible model and Escherichia coli (CP010304) as the root. A total of 1325 nucleotide positions were included in the analysis. Bootstrap values were calculated from 1000 replicates. The scale bar indicates the number of substitutions per site. Names and accession numbers are given as cited in GenBank database.

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Among the 24 episodes of non-Elizabethkingia bacteremia, 15 were caused by Chryseobacterium species, among which two (C13 and C15) represented two potentially novel Chryseobacterium species (≤98.4% nucleotide identity to existing Chryseobacterium species). One episode was caused by another potentially novel species most closely related to Weeksella (91.9% nucleotide identity to Weeksella virosa DSM 16922T). The other eight episodes were caused by Planobacterium (n = 6), Flavobacterium (n = 1) and Sphingobacterium (n = 1) species respectively.

Clinical characteristics of patients with Elizabethkingia-like bacteremia

The clinical characteristics of the 45 episodes of Elizabethkingia-like bacteremia were summarized in Tables 1, 2, 3. Of the 17 episodes of E. anophelis bacteremia, the male:female ratio was 11:6, with a median age of 58 years (range, 1 day to 104 years) (Table 2). Most patients had underlying diseases. Except two patients with pseudobacteremia, most cases were associated with clinically significant bacteremia, with 12 cases being hospital-acquired and three community-acquired. The most common diagnosis was pneumonia (n = 5), followed by catheter-related bacteremia (n = 4), neonatal meningitis (n = 3), nosocomial bacteremia (n = 2) and neutropenic fever (n = 1). Among the five cases of pneumonia, three were community-acquired, including one in a 51-year-old previously healthy man (case EA10). All three cases of neonatal meningitis were hospital-acquired. Details of two (HKU36 and HKU38) of the three neonatal meningitis cases have been reported previously12. They were included because they fell into the inclusion criteria during the study period. The source of E. anophelis in the two cases of nosocomial bacteremia and one case of neutropenic fever was obscure, although severe mucositis was present in the latter. Three of the 17 patients had multiple positive blood cultures. E. anophelis was concomitantly isolated from other body sites in seven patients, including cerebrospinal fluid (n = 3), respiratory samples (n = 3) and catheter tip (n = 1). Most patients survived, but four patients died despite appropriate antibiotics given in two of the four patients. Complications as a result of E. anophelis bacteremia included acute pulmonary edema, congestive heart failure, multi-organ failure, disseminated intravascular coagulation, septic shock, haematemesis, acute renal failure, metabolic acidosis and intraventricular haemorrhage. Various antibiotic regimens as single drug or combinations were used for empirical or definitive treatment, including quinolones, penicillins, cephalosporins, carbapenems, vancomycin and rifampicin. Removal of catheter was often required in catheter-related bacteremia cases in addition to antibiotic treatment.

Table 1 Characteristics of the 45 patients with bacteremia caused Elizabethkingia-like organisms
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Table 2 Clinical characteristics of patients with Elizabethkingia bacteremia.
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Table 3 Clinical characteristics of patients with non-Elizabethkingia bacteremia.
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All the four patients with E. meningoseptica or E. miricola bacteremia also had underlying disease and clinically significant infections (Table 2). Two patients with E. meningoseptica bacteremia had biliary tract infections, while one had nosocomial bacteremia. Interestingly, the only episode of E. miricola bacteremia (case EMI1) was detected in the same patient with E. anophelis nosocomial pneumonia (case EA1) which occurred more than one month previously during the same admission and was complicated by heart failure and acute pulmonary edema requiring intubation and inotropes. Five weeks after successful treatment with piperacillin-tazobactam, the patient developed another episode of bacteremia caused by E. miricola which was also isolated from central venous catheter. The patient recovered with levofloxacin and catheter removal.

In contrast, 16 of the 24 patients with bacteremia due to non-Elizabethkingia species had pseudobacteremia (Table 3). The other eight patients were diagnosed to have nosocomial bacteremia (three cases), transfusion-related bacteremia (two cases), catheter-related bacteremia (one case), neutropenic fever (one case) and sepsis (one case). Except for a case of community-acquired sepsis in a 90-year-old man (case P1), all other cases were hospital-acquired. Only one episode of catheter-related bacteremia was complicated by septic shock, where C. arthrosphaerae was isolated from six blood cultures. All the eight patients survived.

Comparison between Elizabethkingia and non-Elizabethkingia cases showed that clinically significant infections were more common in patients with Elizabethkingia bacteremia than those with non-Elizabethkingia bacteremia (i.e. fewer pseudobacteremia cases were observed) (P < 0.01). Moreover, patients with Elizabethkingia bacteremia had more positive cultures from other sites (P < 0.05) and lower incidence of polymicrobial bacteremia (P < 0.01). They also showed higher complication (P < 0.05) and mortality (P < 0.05) rates than those with with non-Elizabethkingia bacteremia (Table 1).

Microbiological characteristics of Elizabethkingia isolates

All the 21 Elizabethkingia isolates were non-motile, oxidase-positive, catalase-positive, indole-positive, non-glucose-fermenting, Gram-negative bacilli. Growth on MacConkey agar, citrate utilization, urea hydrolysis and fermentation of cellobiose and melibiose fermentation were variable. All 21 isolates were identified as E. meningoseptica by Vitek 2 GNI system with 91–99% confidence. All 21 isolates were susceptible to ciprofloxacin, cefoperazone-sulbactam and vancomycin, but were resistant or intermediate-resistant to imipenem, amikacin, gentamicin and tobramycin. Susceptibilities to ceftazidime, piperacillin, rifampicin and cotrimoxazole were variable (see Supplementary Table 2).

MALDI-TOF MS using Reference Library Biotyper v3.1.2.0 (Bruker Daltonik, Germany) failed to identify the 17 E. anophelis isolates (10 misidentified as E. meningoseptica with score 2.073 to 2.403, two identified as Elizabethkingia species with score 1.952–1.971 and five unidentified with score 1.32 to 1.42 to E. meningoseptica). When the database was expanded with inclusion of mass spectra from seven E. anophelis isolates, all the other 10 E. anophelis isolates were correctly identified as E. anophelis with score 2.321 to 2.634. The three E. meningoseptica and one E. miricola strains were correctly identified by the Bruker reference library (see Supplementary Table 2). Hierarchical cluster analysis showed that the protein mass spectra of E. anophelis and E. miricola were clustered together but formed a distinct branch from E. meningoseptica (Fig. 2).

Figure 2
figure 2

Results of MALDI-TOF MS identification of the 21 Elizabethkingia strains.

In panel (A), representative MALDI-TOF MS spectra of the three Elizabethkingia species are shown. In panel (B), dendrogram was generated from hierarchical clustering of MALDI-TOF MS spectra of 21 Elizabethkingia isolates and reference strains of E. meningoseptica and E. miricola, using ClinProTools 3.0 (Bruker Daltonics, Germany). Distances are displayed in relative units.

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PFGE typing of E. anophelis

To determine the genetic relatedness of the 17 E. anophelis strains isolated from five different hospitals, PFGE was performed using the bacterial genomic and DNA restriction endonuclease XbaI. In general, the PFGE patterns among the 17 E. anophelis strains were distinct from each other and different from that of the type strain R26T. Dendrogram constructed using the PFGE images showed that some adjacently clustered strains were isolated from the same hospital (Fig. 3). For example, strains EA2, EA3 and EA4 were from hospital 5, while strains EA13 and EA15 were from hospital 6. However, no clear epidemiological linkage could be identified in terms of time and place of blood culture isolation. Specifically, strains EA2, EA3 and EA4 were isolated from different years. Strains EA13 and EA15 were isolated four months apart and the two patients were hospitalized in different wards of hospital 6.

Figure 3
figure 3

Pulsed-field gel electrophoresis (PFGE) analysis of the 17 E. anophelis isolates and E. anophelis type strain R26T.

(lane 1 = EA1, lane 2 = EA2, lane 3 = EA3, lane 4 = EA4, lane 5 = EA5, lane 6 = EA6, lane 7 = EA7, lane 8 = EA8, lane 9 = EA9, lane 10 = EA10, lane 11 = EA11, lane 12 = EA12, lane 13 = EA13, lane 14 = EA14, lane 15 = EA15, lane 16 = HKU38, lane 17 = HKU36, lane 18 = R26T, M = lambda marker). In Panel (A), PFGE was performed using CHEF Mapper XA system (Bio-Rad) and restriction endonuclease XbaI. Results showed that the 17 isolates possessed distinct PFGE patterns. In Panel (B), dendrogram was constructed with PFGE data by similarity and clustering analysis using the Dice coefficient (1% tolerance and 0.5% optimization) and unweighted pair-group method using average linkages with GelCompar II.

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Discussion

E. anophelis bacteremia should be considered clinically significant unless proven otherwise and should prompt appropriate antibiotic therapy. In contrast to the traditional belief that E. meningoseptica was the most important Elizabethkingia species associated with bacteremia, the present study showed that the majority of Elizabethkingia bacteremia cases were caused by E. anophelis. In particular, neonatal meningitis was associated exclusively with E. anophelis in this study. In the present series, E. anophelis bacteremia mainly occurred in neonates or adults with underlying medical illnesses and was most commonly associated with pneumonia and hospital-acquired infections such as catheter-related bacteremia and neonatal meningitis. Notably, community-acquired pneumonia occurred in three patients including a healthy middle-aged adult, where the infective source remained obscure. Apart from the two previous reported cases of neonatal meningitis (HKU36 and HKU38) which were most likely acquired from maternal-to-infant transmission based on comparative genomics12, no obvious epidemiological linkage or genetic relatedness was identified among the other cases. Nevertheless, some potentially genetically related strains upon PFGE analysis may have circulated in the same hospital. Further studies should be performed to better understand the disease spectrum and transmission routes of E. anophelis.

E. anophelis bacteremia carries significant morbidity and mortality. Various complications were observed and four patients died, giving a mortality rate of 23.5%. This is in line with previous reports of E. anophelis neonatal meningitis being associated with poor outcomes10. Nevertheless, all the three present cases of neonatal meningitis were cured with early use of appropriate antibiotics12. Although E. anophelis usually confers resistance to multiple antibiotics such as ceftazidime, imipenem and aminoglycosides12, all the 17 isolates were susceptible to ciprofloxacin, cefoperazone-sulbactam and vancomycin, which should be considered in empirical treatment while awaiting susceptibility results. In cases of catheter-related bacteremia, infected catheters should be removed in addition to antibiotic treatment. Future prospective studies with population-based data should be performed to determine the prevalence or incidence of E. anophelis bacteremia.

E. meningoseptica and E. miricola appeared to be much less prevalent than E. anophelis, although similar studies in other countries are required to more accurately assess their relative importance. Similar to E. anophelis, E. meningoseptica and E. miricola bacteremia were associated with clinically significant infections. Besides one case of E. meningoseptica nosocomial bacteremia and one case of E. miricola catheter-related bacteremia, biliary tract infections were also noted in two cases of E. meningoseptica bacteremia. It remains to be determined if E. meningoseptica may have the propensity to cause biliary tract infections among the genus. Given their similar antibiotic susceptibility profiles to that of E. anophelis, ciprofloxacin, cefoperazone-sulbactam and vancomycin should also be included in treatment regimens for E. meningoseptica and E. miricola bacteremia.

In contrast to Elizabethkingia species, isolation of non-Elizabethkingia species from blood cultures should raise suspicion of their clinical significance. In this study, non-Elizabethkingia bacteremia is associated with higher incidence of pseudobacteremia and polymicrobial bacteremia than Elizabethkiniga bacteremia. In particular, all six isolates of C. indologenes and the three potentially novel species were associated with pseudobacteremia. Bacteremia caused by non-Elizabethkingia species is also associated with lower incidence of complications and mortality than Elizabethkingia bacteremia, suggesting that these bacterial species may be less virulent than Elizabethkingia. Moreover, these environmental, non-Elizabethkingia bacterial species may contaminate blood cultures when aseptic techniques during blood taking are breached. Careful clinical assessment is required to determine the clinical significance and the need for antibiotics when these bacteria are isolated from blood cultures.

Although the two E. anophelis strains, HKU36 and EA14, are phylogenetically genetically close to E. endophytica strain JM-87T, they should belong to E. anophelis instead of E. endophytica or a novel species. The two strains possessed 99.9% nucleotide identities to both the newly proposed species, E. endophytica strain JM-87T and E. anophelis R26T in their 16S rRNA gene sequences. Although strain JM-87T was reported to possess 51–52% similarities to E. anophelis R26T by DNA-DNA hybridization3, our previous study showed that the draft genome of strain HKU36 possessed 78.3% nucleotide identity to the genome of E. anophelis R26T by estimation of intergenomic distance12. Given the close relatedness of strains HKU36, EA14 and JM-87T in their 16S rRNA genes (Fig. 1), it is likely that the genome sequences of strain JM-87T and EA14 may also possess >70% identity to that of E. anophelis R26T. Since genome-based comparison can offer ultimate resolution for species delineation which is superior to traditional DNA-DNA hybridization methods, genome sequencing of strain JM-87T and related strains such as EA14 should be performed to more accurately define their taxonomic positions.

The present results confirmed our suspicion that E. anophelis was a previously under-reported bacterium which can be easily misidentified as E. meningoseptica12. Although E. anophelis was first discovered from mosquito gut10, we previously showed that maternal chorioamnionitis, instead of mosquitoes, was more likely the source of neonatal meningitis12. Similarly, mosquitoes are unlikely the route of transmission in other E. anophelis infections. We speculate that contaminated environments, such as infected catheters, are the source of infection in most cases, as in the case of previously described “E. meningoseptica” infections. Given their similar phenotypic characteristics, E. anophelis isolates from previous reports were often mistaken as E. meningoseptica initially10,11,12,14. Phenotypic tests, such as acid production from cellobiose and citrate utilization, previously reported as potentially useful for species discrimination12, were unlikely to be reliable. In our previous study, the three E. anophelis strains were also initially misidentified as E. meningoseptica even with MALDI-TOF MS, owing to the absence of E. anophelis spectra in commercial databases12. The 16S rRNA genes of E. anophelis possessed >98% nucleotide identity to those of E. meningoseptica and E. miricola, which should offer sufficient discriminative power12. However, some “E. meningoseptica” strains with 16S rRNA sequences deposited in GenBank, such as strains G3-1-08 and 50215,16, should belong to E. anophelis based on phylogenetic analysis12. These “misidentified” strains in GenBank may confuse the interpretation of 16S rRNA gene sequencing results and should be rectified12. While E. anophelis can be distinguished from E. meningoseptica by MALDI-TOF MS when the database is expanded with mass spectra from E. anophelis strains, E. anophelis and E. miricola appear to be indistinguishable from each other. With an expanded database using E. anophelis isolates, MALDI-TOF MS is the method of choice for rapid and accurate diagnosis of E. anophelis infections, which is crucial to better understand its epidemiology and clinical disease spectrum.

Methods

Ethics statement

The use of blood culture isolates and anonymous clinical data were approved by Institute Review Board, The University of Hong Kong/Hospital Authority, Hong Kong (reference UW 04-278 T/600). The methods and all experimental protocols were carried out in accordance with the approved guidelines. Since this study does not involve experimentation on human subjects or the use of tissue samples from human subjects, written informed consent has been waived by our institutional review board.

Settings and Patients

Patients were hospitalized in five regional hospitals located in different areas of Hong Kong from 2004 to 2013. To identify potential cases of Elizabethkingia bacteremia, all bacteremia episodes caused by oxidase-positive, non-glucose fermenters that were identified as Elizabethkingia, Flavobacterium or Chryseobacterium species by conventional phenotypic tests during the study period were included with clinical data analyzed17. Bacteremia was categorized as clinically significant or pseudobacteremia (contamination of blood culture) by clinical and laboratory criteria18. The criteria include the patient’s clinical presentation, physical examination findings, body temperature at the time of the blood culture, leukocyte and differential cell counts, imaging or operative results, histopathological findings, number of positive blood cultures out of the total number performed and response to treatment.

Bacterial isolates

Collection of clinical specimens, bacterial cultures and conventional phenotypic identification were performed according to standard protocols19. Two of the 45 Elizabethkingia-like isolates from two neonates (HKU36 and HKU38) have been reported previously12. The same isolate recovered from the same patient was counted only once.

16S rRNA gene sequencing for species identification

The 45 blood culture isolates were subject to 16S rRNA gene sequencing according to previously published protocols with modifications, using primers LPW57 (5′-AGTTTGATCCTGGCTCAG-3′) and LPW58 (5′-AGGCCCGGGAACGTATTCAC-3′)12,20. The sequences of PCR products were compared to known gene sequences in GenBank by multiple sequence alignment using CLUSTAL_W in MEGA version 621. Phylogenetic tree was constructed by maximum likelihood method using MEGA version 621.

Statistical analysis

A comparison of characteristics was made between patients with Elizabethkingia and non-Elizabethkingia bacteremia using Chi-square test (IBM SPSS Statistics version 19). P < 0.05 was regarded as statistically significant.

Phenotypic characterization and matrix-assisted laser-desorption ionization-time-of-flight mass-spectrometry (MALDI-TOF MS) of Elizabethkingia isolates

The 21 Elizabethkinigia isolates were characterized by phenotypic tests, Vitek 2 GNI system (bioMérieux, France) and MALDI-TOF MS. MALDI-TOF MS was performed by ethanol formic acid extraction method as described previously, using Bruker Daltonics microflex LT system with Reference Library Biotyper v3.1.2.0 (Bruker Daltonik, Germany)22,23. Since E. anophelis is not included in the Bruker reference, mass spectra generated from seven E. anophelis strains with identity confirmed by 16S rRNA gene sequencing were later added to the database. Obtained spectra were subject to hierarchical cluster analysis as described previously24. Antibiotic susceptibility testing was performed by Kirby Bauer disk diffusion method with results interpreted according to Clinical and Laboratory Standards Institute for Staphylococcus aureus (vancomycin) and Pseudomonas aeruginosa (other drugs), because of the lack of interpretative criteria for Elizabethkingia25.

Pulsed-field gel electrophoresis (PFGE)

The 17 E. anophelis isolates were characterized by PFGE using CHEF Mapper XA system (Bio-Rad, CA, USA) and restriction endonuclease XbaI as described previously12,26. After PFGE, the gel was stained with ethidium bromide (1 μg/ml) for 30 minutes and the patterns of the genomic DNA digest were visualized with a UV transilluminator. Digital images were stored electronically as TIFF files and analyzed visually and with GelCompar II (version 3.0; Applied Maths, Kortrijk, Belgium) and represented by UPGMA method.

Nucleotide sequence accession number

The 16S rRNA gene sequences of the 45 blood culture isolates have been deposited in the GenBank sequence database under accession no. KP875383 to KP875427.

Additional Information

How to cite this article: Lau, S. K. P. et al. Elizabethkingia anophelis bacteremia is associated with clinically significant infections and high mortality. Sci. Rep. 6, 26045; doi: 10.1038/srep26045 (2016).