Molecular validation of clinical Pantoea isolates identified by MALDI-TOF

Summary

The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.

Keywords:

Sequence analysis – Phylogenetics – Phylogenetic analysis – Urine – Matrix-assisted laser desorption ionization time-of-flight mass spectrometry – Ribosomal RNA – Erwinia – Texas

Introduction

Strains of Pantoea are frequently found in association with a wide variety of hosts, including plants, insects, animals, and humans [1,2]. Multiple Pantoea species are well-documented plant pathogens [3–5]; however, Pantoea species have also been isolated from clinical specimens. Pantoea agglomerans has been isolated from pediatric patients with bacteremia, osteomyelitis, peritonitis, pneumonia, septic arthritis, and septicemia [6]. The majority of P. agglomerans clinical cases are either the result of wound contamination with plant material or are hospital-acquired infections [7]. Likewise, other species such as Pantoea ananatis, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica have also been isolated from a variety of clinical sources including wounds, blood and other fluids, skin, stool, abscesses, cysts, fractures and body sites such as the urethra and trachea [2]. Pantoea has also been implicated in multiple outbreaks that resulted in the deaths of neonates [8,9]. Despite this, the human pathogenic potential of many Pantoea species is currently being debated as there is evidence to suggest that many clinical strains are not Pantoea at all [10]. Due in part to taxonomic and nomenclatural revisions many strains previously listed as Pantoea have been found to belong to other genera including Klebsiella and Enterobacter [11]. Furthermore, Pantoea strains are difficult to assign to a species group based on metabolic profiling alone, which has resulted in numerous Pantoea clinical isolates being incorrectly classified as Pantoea agglomerans [12].

Identification of clinical specimens of Pantoea is often achieved by the mass spectrometry-based approach matrix-assisted laser desorption ionization-time of flight (MALDI-TOF). MALDI-TOF involves the application of a laser to an isolated bacterial colony that has been treated with a matrix solution, leading to ionization of bacterial molecules that are then used as the signature for genus- and/or species-level identification via comparison to a reference database [13,14]. MALDI-TOF can achieve species-level identification with greater accuracy and speed than conventional biochemical methods [15,16]. However, as MALDI-TOF identification relies upon a database of profiles of known reference organisms, gaps in the database can lead to misidentification. Indeed, many reported MALDI-TOF misidentifications are the result of incomplete databases with most situations remedied by updating the reference database with additional organisms [15,17]. Likewise, novel and undescribed genera and species may not be discernible from the next closest relative. For the genus Pantoea, which continues to be revised with new species groups, the accuracy of MALDI-TOF-based identifications remains unknown.

Molecular typing methods can be used to help validate the accuracy of MALDI-TOF based clinical identifications of Pantoea. The 16S ribosomal RNA (rRNA) gene is considered to be a universal identifier for bacteria largely due to its conservation across Bacteria, and due to the phylogenetic signal provided by the approximately 1500 base pair (bp) locus [18]; however, this slowly-evolving locus often does not provide sufficient resolution for distinguishing between Pantoea species groups [19,20]. In contrast, the multi-locus sequence analysis (MLSA) approach has demonstrated reproducible typing of strains along with robust phylogenies for Pantoea [21]. Single-gene barcoding of Pantoea using leuS has also been proposed, which provides consistent species identification with some incongruencies only in the relative position of particular species groups in the tree [22]. The leuS gene, however, has not been developed as a universal marker for bacterial identification and classification, making comparisons across species and across studies considerably more difficult with this locus. In contrast, cpn60, known as groEL in E. coli, is a roughly 1650 bp chaperonin gene that has been shown to reliably provide robust species-level resolving power [23–25]. This gene is present in the genome of almost all bacteria and contains a region of close to 600 bp that has been designated a universal target for discriminating between closely related species [26]. In addition, a curated database of cpn60 sequences is available online [27].

In this study, we performed species-level identification of clinical and environmental candidate Pantoea isolates using a combination of MLSA and cpn60-based typing. We first generated and compared a cpn60 gene genealogy of Pantoea reference strains to a phylogeny generated by MLSA to demonstrate that cpn60 consistently recovers the Pantoea species groups with strong support. We used this robust clustering of species groups to type 64 candidate Pantoea strains from clinical and environmental sources, and show that 24% of clinical isolates were misidentified, with MALDI-TOF misidentifying one of every five strains. Of those strains that were correctly identified, the majority were P. agglomerans and P. septica. We also found clinical strains of the plant-associated, Pantoea allii and P. eucalypti.

Materials and methods

Bacterial strains

Clinical isolates were obtained from St. Boniface General Hospital in Winnipeg, Manitoba, Canada, the Texas Children's Hospital in Houston, Texas, USA, the Roy Romanow Provincial Laboratory in Regina, Saskatchewan, Canada, and the Regina General Hospital in Regina. Strain information provided included a tentative identification to genus, as well as anonymized patient information (Table 1). Clinical identification of isolates by St. Boniface General Hospital was achieved via a Bruker Biotyper microflex LT/SH MALDI-TOF system, which used the RUO MALDI Biotyper Reference Library (Bruker Ltd., Milton, Ontario, Canada). Texas Children's Hospital identified isolates using a combination of VITEK 2 [28] and 16S rRNA gene sequencing, the Roy Romanow Provincial Laboratory with MicroScan [29], biochemical typing, and 16S rRNA gene sequencing, and the Regina General Hospital with VITEK 2 ID cards. Environmental strains that were initially identified as Pantoea via phenotype-based methods were obtained from a variety of sources. Reference strain genomes were obtained from NCBI and our lab collection (S1 Table).

Sequence data

The gene sequences of atpD, fusA, gyrB, leuS, recA, rplB, and rpoB as well as cpn60 were extracted from Pantoea genomes from the National Centre for Biotechnology Information (NCBI) and from our collection [2] using an in-house Perl-based pipeline. Complete genomic data were not available for representatives of Pantoea beijingensis and coffeiphila so these were not included in the analysis. For new strains, the 16S rRNA and cpn60 genes were amplified using primers 16S+335 (ACTCCTACGGGAGGCAGC) and 16S-1400 (ACGGGCGGTGTGTACAA) in a colony PCR reaction with New England Biolabs Taq DNA polymerase (New England Biolabs Ltd., Whitby, Ontario, Canada) as per the manufacturer’s instructions, and cpn60_ent+1 (ATGGCAGCWAAAGACGTAAAATTCGG) and cpn60-1330 (CGCRACYTTRATACCSACGTTCTG) in a colony PCR reaction with GenedireX Taq DNA polymerase (GenedireX Inc., Taiwan) as per the manufacturer’s instructions. Amplicons were sequenced using Sanger sequencing by Genome Quebec (Montreal, Quebec, Canada). Forward and reverse reads were merged using the BBMap software package [30]. MLSA loci and cpn60 gene sequences have been deposited in Genbank under accession numbers MK909837-MK909900, MK928255-MK928322, and MK936803-MK936866.

Sequence analysis and phylogenetics

16S rRNA gene sequences were analyzed using the Ribosome Database Project (Training Set 16) Classifier [31]. cpn60 sequences were analyzed with a custom cpnDB database of Group I sequences [27] that included the cpn60 sequence of P. septica strains FF5, VB38951-A, and X44686, as well as Pantoea sp. PSNIH6, Pantoea sp. RIT388, Pantoea sp. UBA4389, Enterobacteriaceae bacterium IIIF5SW, Erwiniaceae bacterium IIIF1SW-P2, Izhakiella australiensis D4N98, Tatumella saanichensis NML 06–3099, Mixta calida LMG 25383 Pseudocitrobacter sp. RIT 415, Pseudocitrobacter faecalis DSM 27453, Erwinia gerundensis EM595, and Kosakonia cowanii Esp_Z (S1 Table). Alignments for phylogenies were generated using Clustal Omega version 1.2.1 using default parameters [32]. Alignments for the MLSA trees consisted of concatenated full-length fusA, gyrB, leuS, recA, rplB, rpoB, and atpD gene sequences, while cpn60 alignments contained sequences of at least 530 bp of the coding sequence. Maximum likelihood trees were constructed in MEGA version 7.0.26 [33] using models selected via Modeltest and 1000 bootstrap replicates. MLSA and cpn60 nucleotide sequences are available as supplementary data (S1 Dataset, S2 Dataset).

Results

cpn60 accurately constructs species groupings

A cpn60 phylogenetic tree was constructed and compared to a seven gene (fusA, gyrB, leuS, recA, rpoB, rplB, and atpD) MLSA phylogenetic tree from representative Pantoea genomes, along with representative genera of the Enterobacteriales. The majority of clades corresponding to individual Pantoea species groups were largely consistent between the two trees, and supported by strong bootstrap values, although the relative positions of some clades differed between the two trees (Fig 1). For example, the P. agglomerans group forms a sister group to P. eucalypti in the MLSA tree with P. vagans forming the basal group whereas in the cpn60 tree P. vagans is a sister group to P. eucalypti with P. agglomerans forming the basal group (Fig 1). There were similar incongruencies noted for the positions of the majority of Pantoea clades (Fig 1); however, in all these cases, taxa of the same species always formed monophyletic groups, but their recent common ancestor with other species varied.

One quarter of clinical strains labeled Pantoea are misidentified

The nucleotide sequence of the cpn60 gene from 64 bacterial isolates that had been received as Pantoea were added to the previously established cpn60 tree shown in Fig 1. Of these candidate Pantoea isolates, 54 were obtained from patients while 10 were collected from the environment (Table 1). Of the 54 clinical isolates, 47 were initially identified by MALDI-TOF, 4 were initially identified by a combination of VITEK 2 and 16S rRNA gene, 2 were initially identified via MicroScan combined with 16S rRNA gene and biochemical typing and a single isolate was initially identified using VITEK 2 ID cards. The 10 environmental isolates were initially identified visually by pigmentation. Based on the cpn60 phylogeny, 47 of the 64 isolates were confirmed to belong to the genus Pantoea (Fig 2, Table 1). These included 17 P. agglomerans, 1 P. allii, 1 P. dispersa, 1 P. eucalypti, 19 P. septica, 2 strains of the proposed species P. latae [34], and 6 Pantoea sp. with 3 found in the P. brenneri/P. conspicua lineage and 3 found in the P. septica/P. latae lineage possibly representing new species (Fig 2). Of the 17 P. agglomerans strains, 10 were clinical and were associated with sepsis, wound infection, and esophageal tracheal combitube contamination, while the other seven were isolated from flea beetles and various plant sources (Table 1). All of the other strains in the other species groups of Pantoea were clinical in origin. P. septica strains, which accounted for almost half of all Pantoea clinical isolates identified in this study were associated with a variety of medical conditions, including renal failure, febrile neutropenia, leg ulcer infection, foot ulcer infection, and conjunctivitis (Table 1). Strains identified as the proposed species P. latae were obtained from blood and sputum while the single P. dispersa strain was obtained from a contaminated esophageal tracheal combitube in a patient who had suffered cardiac arrest (Table 1). Of the three Pantoea sp. falling in the P. brenneri/P. conspicua lineage, 13BG284532 was obtained from the tracheal secretions of a premature infant while 17DB651035 and 17IE403177 were associated with urinary tract infection and endotracheal secretions (Table 1). The partial cpn60 sequence of 13BG284532 was more similar to the cpn60 sequence of the P. conspicua type strain than any P. brenneri strain (S2 Table) and therefore it may belong to P. conspicua. 17DB651035 and 17IE403177 share 99% nucleotide identity with the P. brenneri type strain over a 770 bp region of their 16S rRNA gene, suggesting they likely belong to the P. brenneri species group. There was also some ambiguity in the identity of the other three Pantoea sp. strains, 13DB433109, 16BF887461, and TX9, which grouped with reference Pantoea strains that have not been assigned to any existing species. Strains 13DB433109 and TX9, isolated from urine and a wound on the foot respectively, both grouped with Pantoea sp. PSNIH6 as part of a sister taxon to P. latae (Table 1, Fig 2). Strain 16BF887461, isolated from the blood of a 1 year old patient, grouped with Pantoea sp. UBA4389 and Pantoea sp. RIT388, forming a sister taxon to the P. septica/P. latae lineage (Table 1, Fig 2). These may represent more divergent P. latae strains or new species. Finally, one strain obtained from the maxillary sinus of a patient with chronic sinusitis (Table 1), forms a sister taxon to P. allii (Fig 2), and shares 99% identity to the P. allii type strain in a 721 bp region of the 16S rRNA gene, indicating that this strain belongs to the P. allii species group.

Of the 17 isolates that were not Pantoea, two were environmental isolates that grouped with the Gram-negative Acinetobacter and the Gram-positive Paenibacillus, and one was a clinical isolate identified as Bacillus by cpn60 (Fig 2, Table 1). The remaining 14 isolates included 13 clinical and 1 environmental isolate, all of which clustered within the Enterobacteriales. The identity of 9 of the 13 clinical strains was established by cpn60 and 16S rRNA gene analysis, as well as phylogenetic grouping (S2 Table). Among these were representatives of Citrobacter, Enterobacter, Erwinia, Klebsiella, Kosakonia and Mixta (Table 1). The identification of clinical Erwinia strains was unexpected, and these grouped within a newly defined species group, Erwinia gerundensis, which in both our MLSA and cpn60 trees was non-monophyletic with the other Erwinia. The 16S rRNA gene of our clinical E. gerundensis strains shared 100% identity with the E. gerundensis type strain 16S rRNA gene over approximately 800 bp. The identities of the other 4 of the 13 clinical strains and the lone remaining environmental isolate, ICMP12202, were ambiguous. Strains 10–854 and ICMP12202 matched different genera depending on whether cpn60 or 16S rRNA gene was used. 10–854 is identified by the RDP database with confidence as Pseudocitrobacter (92%), while cpnDB initially returned Leclercia and Klebsiella as best hits until Pseudocitrobacter representatives were included (S2 Table). ICMP12202, a strain previously identified as Kosakonia [35], and which our cpn60 analysis also confirms to be Kosakonia is identified as a weak Citrobacter (42%) by the RDP based on the 16S rRNA gene (S2 Table). Kosakonia is included in Training Set 16 of the RDP Classifier. Three strains, B012497, 12BT205805, and 07–703 also had conflicting 16S rRNA gene and cpn60 matches, and were categorized as “unclassified Enterobacteriaceae” by the RDP database. The groupings of these strains in our cpn60 phylogeny were ambiguous, and could not be used to assign identity with any confidence.

Discussion

This study identified clinical and environmental candidate Pantoea isolates to the species-level using cpn60. Our phylogenetic analysis examining the evolutionary history of cpn60 using representatives of each Pantoea species showed that these formed monophyletic groups consistent with those found in the MLSA trees, indicating largely vertical maintenance of the cpn60 locus within species groups. Notably, the relative position of each clade in the cpn60 tree differed from that of the MLSA tree (Fig 1), suggesting that at least for Pantoea, this locus may not accurately reconstruct the evolutionary history of the species groups. Similar results were obtained with previous studies evaluating the leuS gene, which has been suggested to have value as a single gene identification system for Pantoea isolates despite minor differences in species group relationships between MLSA phylogenies compared to leuS [22]. Other studies have also shown that cpn60 effectively identifies clinical isolates of Campylobacter to the species-level, as well as the opportunistically invasive Actinobacterium, Gardnerella vaginalis, which was consistent with the taxonomic classification obtained by whole-genome-based methods [36]. The congruence of our MLSA and cpn60 trees and the robust confidence values (Fig 1) indicates that cpn60 provides adequate phylogenetic information to accurately assign a given Pantoea isolate to a species group, or in the case of ambiguously positioned sequences, assign it to a specific multi-species lineage.

An unexpected result was the identification of two clinical isolates of the recently proposed E. gerundensis, a species group whose type strain was isolated from the leaves of a pear tree [37]. The members of the genus Erwinia have not been documented as opportunistic human pathogens, and when coupled with the non-monophyly of E. gerundensis with the other Erwinia species in either tree (Fig 1), the placement of E. gerundensis within the genus Erwinia remains uncertain. In addition, the cpn60 gene of E. gerundensis is more similar to that of members of Pantoea than it is to other members of Erwinia. This could account for why E. gerundensis appeared within the Pantoea lineage of the candidate isolate-containing cpn60 phylogeny, albeit with low branch support (Fig 2). The reliability of cpn60 for the identification of Erwinia strains should therefore be explored further.

Using cpn60 we determined that of the 64 candidate Pantoea strains (54 clinical, 10 environmental), 47 were confirmed to be Pantoea. Of the 54 clinical strains, 41 were correctly identified, leaving one quarter misidentified. 81% (38/47) of clinical isolates initially identified via MALDI-TOF were correctly identified while 3 of 4 strains initially identified using VITEK combined with 16S rRNA gene typing were correctly identified. The remaining 3 clinical isolates, initially identified with other methodological combinations, were misidentified. Because these strains were classified prior to the description of the proposed Mixta calida, we considered the single M. calida strain found in our study to be correctly identified [38]. Three non-Pantoea strains, 07–703, 12BT205805, and B012497 are sufficiently divergent that they remain unclassified. Of the clinical strains that were confirmed to be Pantoea, the vast majority belonged to P. agglomerans (10 strains) and P. septica (19 strains). P. agglomerans has been previously identified as a human pathogen [6,39,40]; however, it has been suggested that P. agglomerans may be incorrectly considered a human pathogen due to inaccurate identification of clinical isolates and nomenclatural confusion [10]. Strains that were misidentified as Pantoea tended to be other closely related enteric species (S2 Table), many of which are genera that contain opportunistic, multi-drug resistant human pathogens [41,42]; however, many clinical strains identified were confirmed to be P. agglomerans. The recurrent isolation of strains implicated in sepsis, esophageal tracheal combitube contamination, and various wound infections suggests that P. agglomerans is not simply guilty by association (Table 1) [1]. In contrast, P. septica appears to be largely clinical in origin [1,43], so it was not surprising that 19 strains were recovered from patients suffering from a variety of conditions, including renal failure, respiratory failure, ulcers, infected wounds, and conjunctivitis (Table 1). Other species of Pantoea that were recovered included P. dispersa and strains within the P. brenneri/P. conspicua lineage, with all three aforementioned species having been noted by the scientific community to be human-associated species groups that have been isolated from the clinical environment previously [1,43–45]. For example, P. dispersa has been implicated as the cause of bacteremia and multiple cases of neonatal sepsis while P. brenneri and P. conspicua have been isolated from human sputum and blood respectively [43,46,47].

A single clinical isolate of P. allii was identified in our study, which to our knowledge is the first instance of this plant-pathogenic species being isolated from the clinical environment. P. allii has been characterized as a plant pathogen able to cause disease in onion and is most closely related to P. ananatis and P. stewartii [48]. As P. allii is closely related to P. ananatis, a species group that has also been isolated from the clinical environment and has been described as an opportunist [5,49,50], it is possible that P. allii also carries host-association and virulence factors that may enable opportunism. Similarly, P. eucalypti has been isolated predominantly from diseased plants [4] and is generally considered a plant-associated species, yet our study has identified one clinical isolate of P. eucalypti, marking the third clinical strain of P. eucalypti that we have reported [1]. While the isolation of P. allii from the clinical environment has been the exception rather than the rule, species like P. eucalypti are becoming more frequently identified among clinical specimens. Similarly, we identified two clinical strains of the proposed species, P. latae, the type strain of which had been isolated from the rhizosphere of cycad plants and forms a sister group to the P. septica lineage [34]. Both of these clinical strains fall, with confidence, within the P. latae species group (Fig 2). Although P. latae has previously only been isolated from plants, the identification of clinical isolates in our study is not necessarily surprising given that P. septica is so closely related to P. latae (Fig 1). It is possible that some of the factors responsible for the ability of P. septica to persist in the clinical environment are shared with P. latae. This could also explain the clinical origin of 13DB433109, 16BF887461, and TX9 which grouped with reference Pantoea strains related to the P. septica/P. latae lineage that have yet to be assigned to a species (Fig 2).

There is mounting evidence that clinical specimens of Pantoea are not simply misidentifications caused by incomplete MALDI-TOF spectral databases; rather, it is possible that the genetic factors used by Pantoea strains for environmental persistence and for association with plants, insects and other hosts are being co-opted and used for establishing opportunistic human infections [51,52]. For example, in the closely related clinically-isolated species M. calida, a plant type III secretion system was identified suggesting that some of these strains may have other primary hosts [53]. Although there is little information on the genetic determinants that may be used by Pantoea strains for opportunistic association with humans, some factors have been identified that may play a role in infection. Many strains secrete a diversity of natural products, some having antimicrobial activity against clinically relevant pathogens [54,55], while others are biosurfactants that exhibit cytotoxicity toward animal cells [56]. It has recently been reported that P. septica and the P. ananatis/P. stewartii lineage have horizontally acquired the biosynthetic gene cluster responsible for production of the iron-gathering siderophore, aerobactin, which is absent in other Pantoea species [57]. Aerobactin is a known virulence factor and has been demonstrated to be essential for the virulence of hypervirulent, Klebsiella pneumoniae [58,59]. While these genetic factors may have evolved to exploit very specific niches, they may provide a competitive edge in other environments as well, which may include the human host environment.

Although we were able to successfully identify the isolates in our study to the species level using cpn60, there are several limitations to single gene identification methods including limited phylogenetic signal, and misleading evolutionary histories due to horizontal transfer events. Using multiple gene or whole genome-based identification methods would likely yield more accurate and precise results; however, this requires additional time and resources with currently available technologies. These constraints, particularly in the clinical setting, are easily overcome by MALDI-TOF, since it is relatively inexpensive, fast and accurate. Still, our work has demonstrated that Pantoea isolates continue to be misidentified by MALDI-TOF, although this may continue to improve as MALDI-TOF spectra for Pantoea are expanded with additional representatives of the species groups and their close relatives. This also raises questions about the frequency of isolates that are Pantoea, but are being incorrectly identified as other genera. Our work has shown that P. septica and P. agglomerans continue to account for a large portion of clinical Pantoea isolations from urinary tract infections, wound infections, conjunctivitis, sepsis, renal failure, sinusitis, ulcers, and febrile neutropenia. Furthermore, our work shows that species of Pantoea considered primarily plant pathogens can be isolated from humans, although their specific involvement in disease establishment and pathology still requires further investigation.

Supporting information

S1 Dataset [txt]
Nucleotide sequences of concatenated MLSA genes in FASTA format.

S2 Dataset [txt]
Nucleotide sequences of genes in FASTA format.

S1 Table [xlsx]
Accession numbers of reference strains used for phylogenetic and cpnDB analyses.

S2 Table [xlsx]
Strain identification based on and 16S rRNA typing.