In silico analyses of penicillin binding proteins in Burkholderia pseudomallei uncovers SNPs with utility for phylogeography, species differentiation, and sequence typing

Abstract

Burkholderia pseudomallei causes melioidosis. Sequence typing this pathogen can reveal geographical origin and uncover epidemiological associations. Here, we describe B. pseudomallei genes encoding putative penicillin binding proteins (PBPs) and investigate their utility for determining phylogeography and differentiating closely related species. We performed in silico analysis to characterize 10 PBP homologs in B. pseudomallei 1026b. As PBP active site mutations can confer β-lactam resistance in Gram-negative bacteria, PBP sequences in two resistant B. pseudomallei strains were examined for similar alterations. Sequence alignments revealed single amino acid polymorphisms (SAAPs) unique to the multidrug resistant strain Bp1651 in the transpeptidase domains of two PBPs, but not directly within the active sites. Using BLASTn analyses of complete assembled genomes in the NCBI database, we determined genes encoding PBPs were conserved among B. pseudomallei (n = 101) and Burkholderia mallei (n = 26) strains. Within these genes, single nucleotide polymorphisms (SNPs) useful for predicting geographic origin of B. pseudomallei were uncovered. SNPs unique to B. mallei were also identified. Based on 11 SNPs identified in two genes encoding predicted PBP-3s, a dual-locus sequence typing (DLST) scheme was developed. The robustness of this typing scheme was assessed using 1,523 RefSeq genomes from B. pseudomallei (n = 1,442) and B. mallei (n = 81) strains, resulting in 32 sequence types (STs). Compared to multi-locus sequence typing (MLST), the DLST scheme demonstrated less resolution to support the continental separation of Australian B. pseudomallei strains. However, several STs were unique to strains originating from a specific country or region. The phylogeography of Western Hemisphere B. pseudomallei strains was more highly resolved by DLST compared to internal transcribed spacer (ITS) typing, and all B. mallei strains formed a single ST. Conserved genes encoding PBPs in B. pseudomallei are useful for strain typing, can enhance predictions of geographic origin, and differentiate strains of closely related Burkholderia species.

Introduction

Melioidosis is an emerging but neglected infectious disease caused by the environmental Gram-negative bacterium Burkholderia pseudomallei. This soil- and surface water-dwelling microorganism is commonly found in tropical and subtropical regions of Southeast Asia and northern Australia, but also reported in other regions of the Western Hemisphere (WH) [1,2]. In August 2021, the US Centers for Disease Control and Prevention issued a Health Alert describing a multistate (GA, KS, MN, TX) investigation of non-travel associated melioidosis in four patients [3]. Naturally-acquired melioidosis infections can occur in humans and a wide range of other animals as a result of percutaneous inoculation, inhalation, or ingestion of B. pseudomallei [4]. In 2016, a global modeling study predicted that ~165,000 human melioidosis cases occur annually, and an estimated 89,000 result in death [1]. Infrequent laboratory diagnosis and clinical recognition due to unfamiliarity with the disease and the intrinsic resistance of B. pseudomallei to numerous antibiotics can cause delays in treatment leading to poor patient outcomes and mortality rates of up to 50% [5,6]. B. pseudomallei is also among a small group of high-consequence pathogens and toxins regulated in the US in which their misuse could pose a serious threat to public health and safety [7].

Clinically relevant β-lactams used to treat human melioidosis include the cephalosporin ceftazidime, the carbapenems meropenem and imipenem, and the β-lactam/ β-lactam inhibitor combination drug amoxicillin-clavulanic acid [8]. Mechanisms of resistance to these antibiotics have been described in B. pseudomallei and involve inactivation of β-lactams as well as modification of β-lactam targets. Mutations in penA, or its promoter region that results in overexpression of a β-lactamase, confers resistance to ceftazidime, imipenem, and amoxicillin-clavulanic acid [9–11]. For instance, B. pseudomallei isolated from a melioidosis patient in Thailand who succumbed to infection, developed resistance in vivo during ceftazidime treatment due to a PenA mutation (Pro167Ser) [12]. Acquired resistance to ceftazidime was also reported due to a reversible gene duplication and amplification event of the genomic region containing penA [13]. Understanding and rapidly identifying the mechanisms that contribute to β-lactam resistance in B. pseudomallei could inform treatment strategies and improve melioidosis patient outcomes.

Penicillin binding proteins (PBPs) are involved in the final stages of cell wall peptidoglycan synthesis and are conserved among bacteria, with several usually found per species. These proteins determine bacterial cell shape by regulating the localization, timing, and architecture of peptidoglycan polymerization [14]. PBPs are also well-known targets for β-lactams. The covalent binding of a β-lactam antibiotic to the catalytic serine residue at the PBP active site inactivates protein function resulting in inhibition of cell wall synthesis and cell lysis [15,16]. In bacteria such as Salmonella enterica, Streptococcus pneumoniae, and Helicobacter pylori, mutations in PBPs within or near conserved active site motifs can result in β-lactam antibiotic resistance by reducing antibiotic binding affinity [17–19]. Chantratita et al. demonstrated that the B. pseudomallei genome encodes three PBP-3 proteins [20]. Loss of one of these, PBP-3 (2) in this study, resulted in ceftazidime resistance. Except for PBP-3, very little is known about PBPs in B. pseudomallei. Recently, our group used an in silico approach to identify a suite of genes encoding 10 putative PBPs in the B. pseudomallei genome [21].

Sequence variations within stable genetic markers in B. pseudomallei can be used for: species identification, differentiation of closely related species, characterization of isolates, and also phylogenetic and epidemiological investigations. Burkholderia mallei is considered a host-adapted deletion clone of B. pseudomallei. As the genes retained by B. mallei share ~99.5% nucleotide identity to corresponding homologs in B. pseudomallei [22], the accurate differentiation of these species using molecular-based laboratory tools is difficult but valuable for clinical applications. For example, 16S rRNA gene sequencing rapidly identifies B. pseudomallei based on a single nucleotide difference that can reliably discriminate it from B. mallei [23]. Polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS) have been used to investigate phylogenetic relationships within B. pseudomallei and among near-neighbor species [24]. ITS types C, E and CE represented the most endemic B. pseudomallei isolates and all isolates of the relative species B. thailandensis possessed ITS type A. The ITS allele of B. mallei appears monomorphic since all strains were found to have ITS type C [24]. A multi-locus sequence typing (MLST) scheme was also developed for B. pseudomallei and closely related species. This molecular typing method is based on sequence variations within seven conserved, housekeeping genes on chromosome I, the larger of its two replicons. MLST demonstrated utility for epidemiological studies and confirmed that B. mallei is a clone of B. pseudomallei, while the species Burkholderia thailandesis is distinct [25].

Despite having a highly recombinant genome, a strong geographic signal is encoded within B. pseudomallei and phylogeographic reconstruction of this population is possible [26]. Several factors have led to distinct Asian and Australasian B. pseudomallei populations that undergo regional evolution. These factors include the primary mode of transmission (via direct contact with contaminated environments), extremely rare human-to-human transmission, and substantial geographic barriers that restrict gene flow between populations [26]. While a large-scale comparative genomics approach is essential to determine fine-scale population structure and to confirm the true geographic origin of B. pseudomallei isolates [27–30], lower resolution typing methods such as ITS and MLST are useful tools for linking melioidosis cases to particular regions. Of the five ITS types exclusive to B. pseudomallei, type G was rare in Australia and Southeast Asia, and based on a small number of strains, this type was overrepresented for isolates originating from Africa and the Americas [24]. Testing of additional Western Hemisphere strains confirmed ITS type G was predominant and supported the original hypothesis that a genetic bottle neck took place during dispersal of B. pseudomallei to geographic locations outside endemic regions [24,31]. MLST can be used to define geographical segregation of B. pseudomallei by continent and provides a clear distinction between populations originating from Australia and Thailand [32,33]. However, occasional examples of ST homoplasy have been reported for isolates from different continents that are not actually related [34].

Despite the heavy disease burden and high mortality rate associated with melioidosis, even with aggressive antibiotic treatment [35], melioidosis is not included on the World Health Organization list of neglected tropical diseases and global strategies to address prevention and control are still needed. As the signs and symptoms of melioidosis frequently mimic other diseases, clinical or laboratory diagnosis can be challenging. Prompt diagnosis of this disease as well as timely treatment with appropriate antibiotics are crucial for positive patient outcomes. The genomes of B. pseudomallei, B. mallei, and B. thailandensis submitted by scientists from across the world to public databases could reveal important markers useful for speciation, predicting antibiotic resistance, phylogeny, or geographic origin.

Here, we utilized an in silico approach to characterize PBPs in B. pseudomallei and determined their conservation among B. pseudomallei isolates as well as closely related species, B. mallei and B. thailandensis. We also analyzed B. pseudomallei PBP sequences for i) amino acid mutations that may confer resistance to β-lactam antibiotics, ii) single nucleotide polymorphisms (SNPs) with utility for species differentiation, and iii) SNPs to infer phylogeographic origins.

Methods

In silico characterization of PBP homologs in B. pseudomallei 1026b

Ten PBP homologs were identified in B. pseudomallei 1026b (Table 1) using the UniProtKB database (https://www.uniprot.org/). Conserved protein domains were predicted using the Pfam database (http://pfam.xfam.org/) and theoretical molecular weight was calculated using ExPASy (https://web.expasy.org/compute_pi/). NCBI’s Protein BLAST was utilized to find the nearest PBP homologs in Pseudomonas aeruginosa PAO1 (taxid:208964) and Escherichia coli K-12 (taxid:83333). The nearest homologs produced the most significant alignments to B. pseudomallei 1026b PBPs with the lowest Expect (E)-value (NCBI, [36]). Geneious (v.11.1.4) was used to analyze PBP sequences and identify putative enzyme active sites (SXXK, SXN, and KS/TG).

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Table 1. PBP homologs in B. pseudomallei 1026b.

https://doi.org/10.1371/journal.pntd.0009882.t001

Identification of PBP homologs in genomes of an initial set of Burkholderia strains

The nucleotide sequences for the 10 genes encoding PBPs in B. pseudomallei 1026b were used as queries for BLASTn analysis. The search set included organisms B. pseudomallei (taxid:28450), B. mallei (taxid:13373) and B. thailandensis (taxid:57975). Default algorithm parameters were selected, with the exception of “max target sequences” which was set to 5,000. This initial set of 144 complete, assembled genomes, including 101 B. pseudomallei, 26 B. mallei, and 17 B. thailandensis, was examined to identify corresponding PBP homologs. These strains, along with their origin, epidemiological information, and NCBI accession numbers, are listed in S1 Table. Strain typing (MLST, ITS and whole-genome SNP typing) and phylogeography of B. pseudomallei from the Western Hemisphere was previously performed and reported by Gee et. al [37].

Analysis of SAAPs in PBP transpeptidase domains

The Pfam database was used to predict the transpeptidase domain (TD) location within each of the 10 PBP homologs in the B. pseudomallei 1026b reference strain. Gene sequences obtained from each BLASTn result for 101 B. pseudomallei strains were aligned, mapped to the reference strain, translated, and analyzed for single amino acid polymorphisms (SAAPs) within the predicted TDs using Geneious (v11.1.4). The amino acid position of SAAPs and the location of the putative enzyme active sites identified within the TDs are based on sequence alignment to the 1026b reference strain. The Protein Variation Effect Analyzer (PROVEAN) tool (v1.1) [38] was used to predict whether a SAAP affects protein function based on a generated PROVEAN score. A SAAP is predicted to have a ‘deleterious’ effect if the PROVEAN score is ≤ the predefined threshold of -2.5. A SAAP is predicted to have a ‘neutral’ effect if the score is greater than -2.5.

Identification and selection of SNPs for the DLST scheme

The nucleotide sequences of B. pseudomallei 1026b genes I0276 and II1314, encoding PBP-3 (1) and PBP-3 (3), were used as queries for NCBI’s BLASTn analysis. Gene sequences obtained from BLASTn results for the initial set of 144 Burkholderia strains were aligned, mapped to the reference strain, B. pseudomallei 1026b, and analyzed for SNPs using Geneious (v11.1.4). Nine SNPs with utility to predict the geographic origin of B. pseudomallei, plus two SNPs useful for differentiating Burkholderia species (B. pseudomallei, B. mallei, and B. thailandensis) were identified and selected for DLST. The nucleotide positions described for the 11 DLST SNPs are based on alignment to the 1026b reference strain.

DLST performance for an expansive set of genomes

All RefSeq genomes of B. pseudomallei (n = 1525) and B. mallei (n = 83) were collected from NCBI on Oct. 28th, 2019 (S2 Table). All B. mallei assemblies (n = 83) and B. pseudomallei assemblies (n = 1446) with geographic information deposited in the NCBI BioSample database were evaluated for the presence of genes I0276 and II1314 with BLASTn v2.9.0+, using B. pseudomallei 1026b as a reference for each sequence. For both genes, the best alignment for each assembly, based on bitscore, was evaluated. A multiple record FastA file (GNU Awk, v4.1.4) was generated using aligned sequences saved from each BLASTn result. Both gene sequence sets were aligned using MUSCLE (v3.8.1551) [39] and visualized in ClustalX [40] to confirm the accuracy of the alignments. Of the 1446 B. pseudomallei II1314 sequences, 1442 shared >98% nucleotide identity to the 1026b reference strain and were included in the final number of assemblies evaluated in this study. The four remaining sequences in the II1314 alignment (B. pseudomallei strains 3001161896, A193, BP-6260, and BURK081) contained excessive SNPs and gaps, and were excluded based on poor alignment and low nucleotide identity (67%). I0276 sequences required no further filtering. The BioPython (v1.70) [41] library was used to extract nucleotide data at the 11 positions from both multiple record FastA files and SeqKit (v0.11.0) concatenated the two gene loci for subsequent DLST analysis. The discriminatory power (D) of the DLST scheme was calculated using the calculator (http://insilico.ehu.es/mini_tools/discriminatory_power/), where D is expressed by the formula of Simpson’s index of diversity [42].

Compilation of figures

Illustrations of the DLST SNP locations in B. pseudomallei 1026b and the DLST SNP-based phylogeographic tree for the initial set of B. pseudomallei and B. mallei strains (Figs 1 and 2) were generated in Microsoft PowerPoint for Microsoft 365 MSO (16.0.13801.20840) 64-bit. The more expansive phylogeographic tree (Fig 3), including 1442 B. pseudomallei strains resulting in 31 DLSTs, was generated using MPBoot (v1.1.0) [43]. The tree was visualized using the iTol webserver [44] and pie charts were created with the ggplot2 (v3.2.1) library in R (v3.4.4), then edited using InkScape (v0.92.4).

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Fig 1. DLST scheme based on 11 nucleotides in two genes (I0276 and II1314) encoding putative PBP-3s.

Nucleotide positions are based on sequence alignment to the B. pseudomallei 1026b reference strain. Nucleotides with phylogeographic utility (orange font) and utility for differentiating closely related Burkholderia species (purple font) are shown. PBP conserved domains (blue bubbles), amino acid position of domains (blue font), active site residues and positions (red font).

https://doi.org/10.1371/journal.pntd.0009882.g001

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Fig 2. DLST SNP-based phylogeographic tree for the initial set of B. pseudomallei (n = 101) and B. mallei (n = 26).

Each branch represents isolates with a distinct 11-nucleotide SNP signature determined by DLST. B. pseudomallei strains are color-coded by geographic origin and SNPs used to differentiate B. mallei strains are shown in dark yellow.

https://doi.org/10.1371/journal.pntd.0009882.g002

[Figure omitted. See PDF.]

Fig 3. DLST SNP-based phylogeographic tree for the expansive set of B. pseudomallei (n = 1,442, sequence types 1 to 31) and B. mallei (n = 81, sequence type 32).

B. pseudomallei strains are color-coded by geographic origin. Western Hemisphere (WH), asterisk indicates WH and European countries Mexico, Ecuador, Venezuela, Czech Republic, and Switzerland.

https://doi.org/10.1371/journal.pntd.0009882.g003

Results/Discussion

In silico characterization of predicted PBPs in B. pseudomallei 1026b

Bacterial species have distinctive suites of PBPs and variation exists in the number and redundancy of PBP homologs [45]. Four PBPs are encoded in the H. pylori genome, whereas eight and 12 PBPs have been identified in P. aeruginosa and E. coli, respectively [46–48]. Using the UniProtKB database, we previously identified 10 genes encoding putative PBPs in the B. pseudomallei reference strain 1026b [21]. S1 Fig illustrates the distribution of these genes within both chromosomes. Based on theoretical molecular weight (MW), conserved domains, and the nearest homologs in P. aeruginosa and E. coli, B. pseudomallei PBPs were classified as high molecular mass (HMM) or low molecular mass (LMM) (Table 1). Five HMM, Class-A PBP-1 homologs were identified in B. pseudomallei 1026b, each containing a transglycosylase and transpeptidase conserved domain. These proteins range from 713 to 906 amino acids in length with MWs of 95.3 to 76.0 kDa. The MWs of PBP-1 proteins for numerous Gram-negative species have been reported, ranging from 77 to 118 kDa [45]. Both genes encoding PBP-1A homologs (I3403 and I1297) are located on chromosome 1 of the B. pseudomallei 1026b genome and share 38.1 to 44.0% identity to PBP-1As in P. aeruginosa PAO1 and E. coli K-12, respectively. The predicted PBP-1C, encoded by II0898 on chromosome 2, was the largest HMM, Class-A protein, and shared 37.2% identity with PBP-1C in E. coli K-12.

Four HMM, Class-B PBP homologs (one PBP-2 and three PBP-3s) were also identified in B. pseudomallei 1026b, each containing a transpeptidase conserved domain. The largest of the four, PBP-2, encoded by I3332 on chromosome 1, was 803 amino acids in length and had a MW of 85.66 kDa. The MWs calculated for the three PBP-3 homologs in B. pseudomallei 1026b, encoded by genes I0276, II1292 and II1314, ranged from 59.97 to 66.36 kDa and are comparable to 66 kDa reported previously for PBP-3 in E. coli [45]. Protein BLAST analyses revealed B. pseudomallei Class-B PBPs share 36.0 to 43.9% identity with the corresponding PBPs in P. aeruginosa and E. coli. Comparable sequence identity (42%) is reported between PBP-3 homologs of P. aeruginosa and E. coli [49]. One putative LMM, Class-C PBP-6, encoded by I3098, was found on chromosome 1 of B. pseudomallei 1026b. This putative serine-type D-Ala-D-Ala carboxypeptidase protein represents the smallest of the 10 predicted B. pseudomallei PBPs and shares >40% identity to PBP-5/6 and PBP-6 in P. aeruginosa PAO1 and E. coli K-12, respectively. Another gene, II1313, flanking II1314 and corresponding to BPSS1239 in strain K96243 [20], encodes a putative peptidase similar to PBP-5/6. While this gene was not identified in our initial UniProtKB database search and was not included for analysis herein, II1313 could represent an additional PBP candidate encoded in the B. pseudomallei genome.

The three conserved PBP sequence motifs that form that catalytic center of the active site (SXXK, SXN, and KS/TG) were identified in the transpeptidase domains for nine of the 10 PBP homologs in B. pseudomallei 1026b (Table 1). For each of these PBPs, the SXXK motifs were located between 54 and 62 residues upstream of the SXN motifs. Corresponding motifs in PBP-3 of P. aeruginosa PAO1 are similarly positioned, 55 residues apart [49]. For seven of the nine PBPs, the distance between the SXN and KS/TG motifs was ~130 residues. This is comparable to the 135 residues that separate the SSN motif from KSG in PBP-3 of P. aeruginosa PAO1 [49]. Only two of three active site motifs were found in the B. pseudomallei 1026b PBP-2, an STYK tetrad at site 342 and a KTG triad at position 559. It is unclear whether this predicted PBP-2 is functional despite missing the SXN active site sequence, as Tomberg et al. [50] demonstrated that an interaction involving the middle residue of this motif was necessary for the transpeptidase function, but not β-lactam binding, of PBP-2 in Neisseria gonorrhoeae.

Identification of PBP homologs among an initial set of Burkholderia strains analyzed

The nucleotide sequences for the 10 genes encoding PBPs in B. pseudomallei 1026b were used as queries for BLASTn analyses of three Burkholderia spp.; B. pseudomallei (taxid:28450), B. mallei (taxid:13373) and B. thailandensis (taxid:57975). An initial set of 143 publicly available, assembled genomes, including 100 additional B. pseudomallei, 26 B. mallei, and 17 B. thailandensis strains were examined to identify genes encoding corresponding PBP homologs. NCBI accession numbers and epidemiological information for these strains can be found in S1 Table. PBPs in B. pseudomallei were more homologous to PBPs in B. mallei compared to B. thailandensis. With 100% query coverage, BLASTn analysis revealed genes encoding PBPs in B. mallei were ≥99% identical to those in the B. pseudomallei 1026b genome. Gene sequences of predicted PBPs in B. thailandensis were ~95% identical with query coverages ranging from 85 to 100%.

All ten predicted PBPs identified in B. pseudomallei 1026b were conserved in the entire set of B. pseudomallei strains. Eight of 10 PBP homologs were conserved in all B. mallei genomes evaluated, and the remaining two homologs were present in 25 of 26 genomes. The two exceptions included: B. mallei 2002734306 missing one PBP-1A/B, and B. mallei SAVP1 missing PBP-1C. Genes encoding 9 of the 10 PBP homologs were present in all B. thailandensis genomes examined. However, the third PBP-3 homolog, encoded by II1314 in B. pseudomallei 1026b, was only present in 5 of the 17 B. thailandensis strains. Unique PBP profiles analyzed by SDS-PAGE have been used to distinguish species within the Enterococcus genus [51]. However, this type of analysis would not prove useful for differentiating B. pseudomallei from B. mallei and B. thailandensis, as several strains from each Burkholderia species possess an identical suite of predicted PBPs. While 10 putative PBPs were identified in the 1026b strain and shown to be conserved among this set of B. pseudomallei strains, the high recombination frequency of this species’ genome or use of other databases or functional protein assays could lend itself to the potential discovery of additional PBP homologs and/or variable numbers of PBPs among strains.

Examination of PBP transpeptidase domains for mutations in B. pseudomallei strains

Alterations in PBPs of Gram-negative bacteria can confer resistance to β-lactams by lowering the affinity of the antibiotic to the active site [17–19]. In this work, we examined the predicted transpeptidase domains (TDs) in B. pseudomallei PBPs for single amino acid polymorphisms (SAAPs) in or near active site sequence motifs. The Pfam database was used to predict conserved PBP TDs in B. pseudomallei reference strain 1026b. In the PBP-6 and five PBP-1 homologs, the TDs started 37 to 39 residues upstream of the predicted active-site serine residue in the first motif (SXXK). For the four HMM Class-B protein homologs, TDs were positioned ~47 and 59 residues upstream of the SXXK motif in the three PBP-3s and in PBP-2, respectively (Table 1).

The amino acid sequences of the ten putative PBP homologs in the set of 100 B. pseudomallei strains were aligned to the 1026b reference strain and examined for alterations. Two strains included in this set have known resistance to β-lactam antibiotics. Based on minimal inhibitory concentration interpretative criteria established by the Clinical Laboratory and Standards Institute, B. pseudomallei Bp1651 is considered resistant to amoxicillin-clavulanic acid (AMC), imipenem (IPM), and ceftazidime (CAZ), and B. pseudomallei MSHR1655 is resistant to AMC [52]. The reference strain B. pseudomallei 1026b is susceptible to all three β-lactams (AMC, IPM, CAZ). No SAAPs were identified directly within any of the three predicted active site motifs for any of the 101 B. pseudomallei strains analyzed. In addition, no SAAPs specific to the AMC-resistant strain MSHR1655 were found within the TD domains of the ten PBP homologs.

Antimicrobial resistance markers, including point mutations in the class A β-lactamase encoding penA gene, have been described for B. pseudomallei Bp1651 [9]. Here, analysis of the TDs in the PBP homologs of this multi-drug resistant strain revealed unique SAAPs that were not present in the other 100 B. pseudomallei strains evaluated (Table 2). To predict whether these SAAPs would affect protein function, the PROVEAN tool was used to score each mutation individually. The predicted effect was deleterious if the score was ≤ -2.5 and neutral if the score was > -2.5. Two potentially deleterious SAAPs exclusive to strain Bp1651 were found: G608D, located 49 residues downstream of the KTG active site motif in the PBP-2 homolog, and G530R, located 25 residues downstream of the SLN motif in the PBP-1C homolog. A neutral effect on protein function was calculated for the second amino acid substitution in the PBP-1C homolog at position 627. One additional predicted deleterious SAAP (G495S), 25 residues upstream of the second active site motif in a PBP-1A/B homolog, was found in B. pseudomallei strains Bp1651 and MSHR1153. Currently, the functional contributions of these SAAPs to β-lactam resistance in B. pseudomallei remain unknown, but future studies that include antimicrobial susceptibility testing of resistant clinical isolates may provide a link.

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Table 2. Single amino acid polymorphisms found in PBP transpeptidase domains of B. pseudomallei Bp1651.

https://doi.org/10.1371/journal.pntd.0009882.t002

Utility of PBP gene SNPs for differentiation of closely related Burkholderia species

As a result of the high degree of phenotypic and genotypic overlap between B. pseudomallei, B. mallei, and B. thailandensis, simple molecular approaches to differentiate these species are important for epidemiological studies and clinical applications. Some PCR-based methodologies targeting open reading frames including 16S rRNA, bimA, and fliC genes, have been described for the Burkholderia pseudomallei complex and were summarized by Lowe et al. [53]. As part of this work, gene sequences encoding each of the ten putative PBP homologs in the initial set of Burkholderia strains (S1 Table) were aligned to the B. pseudomallei 1026b reference strain and examined for species-specific SNPs. Several PBP gene homologs contained mutations with utility to differentiate the three closely related Burkholderia spp. (Table 3). The nucleotide positions for these mutations are reported based on sequence alignments to the 1026b reference strain. The combination of two SNPs at positions 888 and 1629 in the gene encoding the PBP-3 (1) homolog was found to be unique to each of the three Burkholderia spp. For 100% of the isolates analyzed at these two sites, we observed nucleotides C/T for B. pseudomallei (n = 101), T/C for B. mallei (n = 26) and C/C for B. thailandensis (n = 17).

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Table 3. PBP SNPs with utility for differentiation of Burkholderia species.

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SNPs unique to B. mallei were identified in genes encoding five predicted PBPs (Table 3). For instance, an adenine at position 217 in PBP-3 (2), a thymine at position 1177 in a PBP-1A, and two thymine nucleotides at positions 1239 and 1580 in a PBP-1A/B could be used to differentiate B. mallei from both B. pseudomallei and B. thailandensis. All B. mallei strains (26/26) also contained a three-nucleotide deletion starting at position 1340 in genes encoding the putative PBP-2 homolog. This mutation resulted in the deletion of a lysine for B. mallei, which was not observed in any of the 118 B. pseudomallei or B. thailandensis strains evaluated. Except for B. mallei strain SAVP1, which does not contain the gene encoding the predicted PBP-1C, a SNP at position 1941 could be used to differentiate B. pseudomallei from B. mallei. Compared to the 1026b reference strain, genes encoding PBP-1C homologs in B. thailandensis are missing ~400 nucleotides, including the portion of the gene surrounding the nucleotide at position 1941. Of the 10 predicted PBPs, PBP-3 (1) proved most useful in improving our ability to differentiate B. pseudomallei, B. mallei, and B. thailandensis.

Utility of PBP SNPs for predicting geographic origin of B. pseudomallei

Phylogeographic reconstruction of B. pseudomallei has been demonstrated using both high resolution comparative genomics and lower resolution typing methods such as ITS [24, 27]. To investigate whether isolates could be assigned to a geographic region gene sequences encoding each of the ten putative PBP homologs in 100 B. pseudomallei genomes were aligned to the B. pseudomallei 1026b reference strain and examined for SNPs useful for phylogeography. In the initial set of 101 B. pseudomallei genomes analyzed (S1 Table), 75 strains originated from the Eastern Hemisphere (EH); 33 strains from Australia and Papua New Guinea, and 42 strains from 8 countries in Asia and Southeast Asia. The remaining 26 B. pseudomallei strains were isolated from clinical or environmental samples in the Western Hemisphere (WH); 23 of which have ITS type G, common to strains from the WH, and 3 isolates have ITS type C or CE, supporting an original origin outside the WH, most likely Asia [37].

Several SNPs with phylogeographic utility were identified in genes encoding putative PBPs in the initial set of B. pseudomallei strains. For example, analysis of predicted PBP-1A/B gene homologs, aligned to II0265 in the B. pseudomallei 1026b reference strain, revealed a SNP at position 168 shared by all ITS type G, WH strains (23/23). Only 4 strains originating from the EH shared the same SNP. A SNP unique to WH strains originating from Puerto Rico and Florida was also identified in gene sequences encoding PBP-2 homologs at position 108. Another SNP more prevalent to strains originating from Australia and Papua New Guinea (27/33) was identified in gene sequences encoding the second predicted PBP-1A/B homolog found at nucleotide position 2,330. However, the two genes containing the most SNPs with utility to predict geographic origin of B. pseudomallei encode the predicted PBP-3 (1) and PBP-3 (3) homologs. Furthermore, as SNPs in the first PBP-3 gene homolog could also be used to differentiate B. pseudomallei from B. mallei and B. thailandensis, these two loci were selected for the Dual-Locus Sequence Typing (DLST) approach.

Development of a Dual-Locus Sequence Typing approach

DLST is a molecular biology technique that uses unique allelic profiles in two loci to characterize and type bacterial species. Implementation of DLST typing schemes has been demonstrated for bacterial pathogens such as methicillin-resistant Staphylococcus aureus and P. aeruginosa [54,55]. Here, a DLST scheme was developed using polymorphic sites at 11 nucleotide positions in two conserved B. pseudomallei loci encoding PBP-3 homologs (Table 4 and Fig 1). The nucleotide positions reported herein are based on sequence alignment to the I0276 and II1314 genes, encoding PBP-3 (1) and PBP-3 (3), respectively, in the B. pseudomallei 1026b reference strain. SNPs at 9 of the 11 positions were chosen for their phylogeographic utility, and the other 2 SNPs were useful in differentiating Burkholderia spp. The DLST approach was first tested using gene sequences encoding PBP-3 (1) and PBP-3 (3) homologs in the initial set of B. pseudomallei (n = 101) and B. mallei (n = 26) strains.

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Table 4. Dual-locus sequence typing scheme.

https://doi.org/10.1371/journal.pntd.0009882.t004

The DLST scheme is based on 11 nucleotides in two genes encoding putative PBP-3s. Nucleotide (nt) positions are based on sequence alignment to the 1026b reference strain. Nucleotides with phylogeographic utility are shown in black font and nucleotides used to differentiate Burkholderia species are shown in gray font.

DLST results for the initial set of 127 Burkholderia strains are depicted in a phylogeographic SNP tree (Fig 2) and summarized in S3 Table. Each branch of the SNP tree represents a group of strains with a distinct 11-nucleotide SNP signature. Directly adjacent branches differ by one SNP (underlined), as indicated by the size bar. In Fig 2, B. pseudomallei strains are color-coded by geographic origin and SNPs used to differentiate B. mallei strains are shown in dark yellow. All B. mallei strains (26/26) shared the same SNP signature (CTTCC-AGCCGC) and clustered together. At the initial bifurcation point of the SNP tree, B. pseudomallei strains originating from India and Sri Lanka (in green) group together. Geographically, these countries are in proximity, sharing a maritime border. The other three isolates from Sri Lanka (Bps 111, 110, and 123) share 10 of 11 DLST signature SNPs (Fig 2).

A SNP unique to B. pseudomallei strains from Papua New Guinea was identified at nucleotide position 1473 in the first DLST locus, and as a result these three strains formed their own branch on the tree (CCCTT-GGCCGC) (Fig 2). The majority of B. pseudomallei strains originating from Australia (26/30), located just south of Papua New Guinea, share 2 DLST signatures and differ from Papua New Guinea strains by only one or two SNPs. MLST has been used to study the origins of isolates from Papua New Guinea [56]; three unique sequence types (STs) were resolved and phylogenetic analysis revealed they were located in clades mainly dominated by isolates of Australian origin. The six DLST signatures in the lower portion of the phylogeographic SNP tree mainly consisted of B. pseudomallei strains originating from Southeast Asia (Vietnam, Thailand, and Malaysia), China, and Taiwan (Fig 2). One of which, CCCCT-GGTTAA, contained the most isolates from Thailand (6), including the 1026b reference strain (in bold). Outliers included Australian strains MSHR840 and TSV202 which were assigned to a DLST branch along with five Asian isolates. However, B. pseudomallei strains with ITS type C and CE; CA2010, OH2013, and PB08298010 from the WH, and the Australian strain MSHR5858 have all been shown to be more closely related to strains originating in Asia [29,37,57]; indeed, these four clinical isolates shared SNP signatures with strains from several Asian countries.

For WH B. pseudomallei strains, the DLST system demonstrated higher resolution compared to ITS typing and some DLST groups could be associated with geographic origin. Based on DLST SNP signatures, B. pseudomallei ITS Type G isolates from the WH (in blue) could be differentiated into several distinct groups (Fig 2). All WH strains evaluated in this study that originated from Puerto Rico and Florida (6/6) populated a single branch on the SNP tree (CTCCT-GTTTAA). This is consistent with core genome SNP analysis results which showed these six isolates made up a distinct subclade within the WH clade [37]. Moreover, two MLST type 518 B. pseudomallei strains, CA2007 and CA2013a, both isolated from pet iguanas in California [37], clustered together using the DLST approach (CTCCT-GGTCAA). The largest DLST group, with SNP signature CTCCT-GGTTAA, consisted of seven WH B. pseudomallei strains. One outlier was an ITS Type G isolate from a California patient (MX2013). DLST placed this WH strain in a group with B. pseudomallei strains from Southeast Asia and Taiwan. Interestingly, this patient had travel history or residence in Mexico and had prior military service in Vietnam [37] (S1 Table).

Testing DLST performance with an expansive set of B. pseudomallei and B. mallei genomes

The DLST approach was challenged using an extensive set of B. pseudomallei and B. mallei RefSeq genomes collected from NCBI. All B. pseudomallei assemblies (n = 1,446) with geographic information deposited in the NCBI BioSample database and B. mallei assemblies (n = 83) were evaluated for the presence of genes encoding predicted PBP-3 (1) and PBP-3 (3) homologs (I0276 and II1314) with BLASTn, using B. pseudomallei 1026b as a reference for each sequence. Both loci were highly conserved in B. pseudomallei, each exhibiting ≥98.8% nucleotide identity to the reference. Only four of 1,446 B. pseudomallei strains were excluded from subsequent DLST analysis based on poor alignment and low nucleotide identity to the second locus, II1314 (S4 Table). Similarities of the other eight genes encoding predicted PBPs among the 1,446 B. pseudomallei strains can be found in S4 Table. The two putative PBP-3 gene homologs were also highly conserved in B. mallei, with only two of 83 strains missing the second locus. As a result, DLST typing performance was ultimately assessed using gene sequences from 1,442 B. pseudomallei and 81 B. mallei strains. Both gene sequence sets were aligned to the B. pseudomallei 1026b reference strain, and nucleotide data at the 11 polymorphic positions were extracted and concatenated for subsequent DLST analysis.

DLST of 1,523 Burkholderia strains resulted in 32 sequence types (STs); 31 STs for B. pseudomallei strains and one ST (ST-32) for all B. mallei strains (S5 Table). B. pseudomallei STs were assigned in numerical order in accordance with the number of strains in each ST, highest to lowest. Based on this typing nomenclature, STs were assigned in retrospect to the initial set of 101 B. pseudomallei and 26 B. mallei strains used to develop the DLST approach (S3 Table). To assess the discriminatory power (D) of the DLST method, a single numerical index of discrimination [42] was calculated based on the probability that two unrelated, randomly sampled B. pseudomallei or B. mallei strains from our test population (n = 1,523) would be placed in different typing groups. Predicated on 32 STs, the D value of this DLST was 0.8512.

DLST data was used to construct a phylogeographic tree (Fig 3). Individual branches depict the unique SNP signature, or allelic profile, for each ST. The geographic origins of strains assigned to each ST are represented by color-coded pie charts at each terminal node. The largest number of B. pseudomallei strains (n = 451) was assigned to ST-1, of which ~98% (n = 440) geographically originate from Southeast Asia (Thailand, Singapore, Malaysia and Vietnam). No Australian isolates were assigned to ST-1, and the four ST-1 strains described as originating from the United Kingdom are in fact laboratory cultures of the Thai B. pseudomallei strain K96243 (S5 Table). The B. pseudomallei 1026b reference strain is among the 416 isolates from Thailand that belong this DLST profile.

DLST revealed only B. pseudomallei strains with Southeast and East Asian origin (n = 157) belonged to ST-4 (S5 Table). Nine STs unique to isolates from Thailand (n = 63) were also resolved using DLST profiling. These STs are depicted in tree branches with entirely red pie charts (Fig 3). Additionally, a tenth ST (ST-5) included 91 B. pseudomallei from Thailand and one strain from the USA; the latter, CA2010, is ITS Type C and is more closely related to B. pseudomallei strains from Southeast Asia [37]. ST-18 consisted of five isolates specifically from Papua New Guinea; three from our initial set of B. pseudomallei genomes analyzed (strains K42, B03, and A79A) and two additional isolates from this more expansive DLST analysis (S3 and S5 Tables). One other Papua New Guinean B. pseudomallei strain (MSHR139) was profiled by DLST and assigned to ST-3. Only the country of isolation is listed in the SAMN02443743 sample information on NCBI, so it is unknown whether this strain was isolated from a melioidosis patient with travel history to other geographic locations. All B. pseudomallei strains with French (n = 5) and Pakistani (n = 3) origin clustered together in ST-3.

While the majority of B. pseudomallei isolates separate into 2 phylogenetic groups, Australia and Southeast Asia/rest of the world, a single strain (MSHR5858) with a unique MLST sequence type (ST-562) is present in northern Australia, Taiwan, and southern China [58]. Although we observe four STs specific to a small number of Australian isolates (n = 6), this DLST scheme does not completely support the separation of Australasian and Asian B. pseudomallei clades. Comparable to ITS typing [24], we observed several STs (7) populated with strains originating from both Thailand and Australia (Fig 3 and S5 Table). Two of these types, ST-7 and ST-9, were more common to Australia, encompassing 94% and 72% of the total number of strains. Twelve of 13 B. pseudomallei isolates belonging to ST-11 were from Australia and the other was an outlier, CA2009, an ITS type G strain from the WH. Prior to this more extensive DLST analysis, strain CA2009 resided alone on its own branch in the phylogeographic SNP tree based on the initial set of 101 B. pseudomallei strains (Fig 2).

Five STs were observed that were unique to 34 B. pseudomallei strains from the WH. ST-10 was the most common DLST profile for WH isolates (n = 13) followed by ST-12 (n = 11). Consistent with our preliminary DLST analysis which included six B. pseudomallei strains isolated from clinical and environmental samples in Puerto Rico and Florida, 6 additional strains from this same geographical region all clustered together in ST-12 (Figs 2 and 3 and S5 Table). DLST sequence type ST-22 contained three WH strains, two originating from Mexico and the other, strain TX2015, isolated from a melioidosis patient with travel history to Mexico [37]. Strains CA2007 and CA2013a, which were both isolated from Iguana iguana, remain the only two of 1,442 strains assigned to ST-25. The two WH B. pseudomallei strains, designated as American in origin, that fall into ST-2 along with 218 strains from the EH are strain Bp1651, which formerly comes from Australia and 2014002816, which is a clinical isolate from a patient in Maryland with travel history to Africa.

Conclusions

The true global burden of B. pseudomallei infections is likely underestimated due to several factors including difficulty of diagnosis, insufficient methods for conventional identification, and limited diagnostic facilities [59]. Diagnosis and epidemiological analysis of B. pseudomallei are critical to ensure positive patient outcomes and investigate outbreaks, however, resource constraints may limit the laboratory techniques employed for routine testing. Rapid, low-cost, and easy to perform methods that produce unambiguous results, portable between laboratories, may be more feasible to implement in such settings.

We characterized genes encoding 10 predicted PBPs that were conserved among sequenced B. pseudomallei and B. mallei strains. Within these genes, SNPs with utility for phylogeography and species differentiation were uncovered, markedly in those encoding the predicted PBP-3 (1) and PBP-3 (3) homologs. Using 11 polymorphic nucleotides identified within these two loci, a simple DLST typing scheme was developed and challenged with sequence data from over 1500 B. pseudomallei and B. mallei strains. The willingness of research scientists worldwide to share B. pseudomallei and B. mallei genome sequences in publicly accessible databases strengthened this work. While WGS offers the most comprehensive (and therefore has the potential to be the most accurate) method for determining the geographic origin of B. pseudomallei, lower resolution techniques such as MLST and ITS typing are useful tools for associating melioidosis cases to particular regions. A limitation of the DLST described herein is the reduced discriminatory power compared to WGS and MLST. However, the DLST approach relies on only two gene targets and could be easily operationalized into a PCR test from a culture isolate (or optimized for testing directly from certain clinical specimens). This simple test could be used to rapidly discern strains of closely related Burkholderia spp. and perform some phylogeographic reconstruction, most notably for WH B. pseudomallei isolates. In summary, sequence typing methods based on conserved genes encoding PBPs in B. pseudomallei may be used to improve our current, targeted typing schemes, enhance our ability to link genetic data with geographic origin, and help differentiate closely related Burkholderia species, especially in settings where WGS may not be feasible.

Supporting information

S1 Fig. Distribution of the 10 genes encoding putative PBPs in the B. pseudomallei 1026b reference strain genome.

Loci tags are shown in green outside circular chromosomes. Loci positions within each chromosome are shown in green and have been rounded to the nearest decimal (Mb).

https://doi.org/10.1371/journal.pntd.0009882.s001

(TIF)

S1 Table. Summary of epidemiological data and assembled genome sequences publicly available (GenBank, NCBI) for the initial set of B. pseudomallei (101), B. mallei (26) and B. thailandensis (17) strains used for SNP analyses of PBPs.

Information not available (--), Australia, Northern Territory (NT).

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(DOCX)

S2 Table. B. pseudomallei (1525) and B. mallei (83) RefSeq genomes collected from NCBI and used for DLST analysis.

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(XLSX)

S3 Table. DLST typing results for the initial set of Burkholderia strains analyzed and reported in Fig 2.

Nucleotides with phylogeographic utility are shown in black font and nucleotides used to differentiate Burkholderia species are shown in gray font.

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(DOCX)

S4 Table. Based on alignment results, minimum, maximum, and mean ± standard deviation for percent identity and bit-score are presented for each PBP homolog.

99.7% (1,442/1,446) B. pseudomallei strains exhibited a minimum of ≥98.8% identity to II1314 encoding the PBP-3 (3) homolog in B. pseudomallei 1026b. (*) The remaining four strains (3001161869, BP-6260, BP-6887, RNS8-BP1) demonstrated poor alignment and low sequence identity to II1314, accounting for the lower minimum percent identity of 67.7%. These strains were excluded from DLST analysis.

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(DOCX)

S5 Table. Sequence typing results and epidemiological data for 1,523 Burkholderia strains used to assess the performance of the DLST approach.

All RefSeq genomes are publicly available (NCBI) and geographic information was acquired from the BioSample database. DLSTs were assigned in numerical order based on the number of strains in each ST, highest to lowest. (+) UK laboratory cultures of B. pseudomallei K96243, originally from Thailand [60]. (*) ITS Type C. (#) 1 of 2 strains is Bp1651, Australian in origin.

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(DOCX)

Acknowledgments

We thank Zachary Weiner, Jay Gee, and Mindy Glass Elrod in the Division of High-Consequence Pathogens and Pathology at the Centers for Disease Control and Prevention for their technical expertise and review of this manuscript.

Disclaimer

The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention. Use of trade names is for identification only and does not imply endorsement by the Centers for Disease Control and Prevention.

Citation: McLaughlin HP, Gulvik CA, Sue D (2022) In silico analyses of penicillin binding proteins in Burkholderia pseudomallei uncovers SNPs with utility for phylogeography, species differentiation, and sequence typing. PLoS Negl Trop Dis 16(4): e0009882. https://doi.org/10.1371/journal.pntd.0009882

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