Exploring the environmental traits and applications of Klebsiella variicola

Genomic characterizations of Klebsiella variicola: emerging pathogens identified from sepsis patients in Ethiopian referral hospitals

Healthcare in low- and middle-income countries is becoming problematic due to the emergence of multidrug-resistant bacteria causing serious morbidity and mortality. Klebsiella variicola carrying multiple antimicrobial resistance (AMR) genes were found significantly among sepsis patients in a study done between October 2019 and September 2020 at four Ethiopian hospitals located in the central (Tikur Anbessa and Yekatit 12), southern (Hawassa), and northern (Dessie) parts. Among 1416 sepsis patients, 74 K. variicola isolates were identified using MALDI-TOF, most of them at Dessie (n = 44) and Hawassa (n = 28) hospitals. Whole genome sequencing showed that K. variicola strains identified at Dessie Hospital displayed phylogenetic clonality, carried an IncM1 plasmid and the majority were ST3924. Many K. variicola identified at Hawassa Hospital were clonally clustered and the majority belonged to novel STs and carried IncFIB(K) and IncFII(K) plasmids concurrently. Fifty K. variicola carried ESBL genes while 2 isolates harboured AmpC. Other frequently found genes were aac(3)-lla, blaCTX-M-15, blaTEM-1B, blaLEN2, blaOXA-1, blaSCO-1, catB3, dfrA14, QnrB1, aac(6')-lb-cr and sul2. Virulence genes detected at both sites were mrk operons for biofilm formation and siderophore ABC transporter operons for iron uptake. Capsular alleles varied, with wzi 269 at Dessie and wzi 582 at Hawassa. The isolation of multidrug-resistant K. variicola as an emerging sepsis pathogen calls for strong infection prevention strategies and antimicrobial stewardship supported by advanced bacterial identification techniques.

The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure

Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.

Mechanism of metabolites distribution between 2,3-butanediol and branched-chain amino acid synthesis pathways in Klebsiella pneumoniae

Klebsiella pneumoniae is a commonly known 2,3-butanediol producer. 2,3-Butanediol synthesis and branched-chain amino acid (BCAA) synthesis pathways share the same step of α-acetolactate synthesis from pyruvate. Those two pathways do not interfere with each other in the wild-type strain. Knocking out budA (encoding α-acetolactate decarboxylase) blocks the 2,3-butanediol synthesis pathway. Meanwhile, metabolites of the BCAA synthesis pathway (valine, 2-ketoisovalerate, 2,3-dihydroxyisovalerate and 2-hydroxyisovalerate) are accumulated. However, the mechanism underlying the metabolite changes resulting from the inactivation of budA remains unclear. In this study, both ex vivo and in vitro experiments were conducted to elucidate this mechanism. Kinetic parameters of BudA and acetohydroxy acid isomeroreductase (IlvC) were determined. BudA has a higher affinity toward α-acetolactate and has a higher catalytic constant (Km = 3.66 mM, kcat = 7.8 s-1) compared to IlvC (Km = 17.98 mM, kcat = 0.68 s-1). ex vivo experiments showed that IlvC activities were not influenced by knocking out budA and vice versa. IlvC activities were improved in the cells in which ilvC was overexpressed, but this did not lead to the accumulation of metabolites of the BCAA synthesis pathway. The activities of IlvC in the cell were not affected by the accumulation of 2,3-dihydroxyisovalerate, 2-ketoisovalerate, or valine in the broth. These results indicated that the competitiveness of BudA and IlvC in the cell determines the metabolites distribution between those two pathways. The inactivation of BudA and intact IlvC led to the exceeded α-acetolactate flow into the BCAA synthesis pathway, which caused the accumulation of metabolites of the BCAA synthesis pathway.

Environmental Applications of GM Microorganisms: Tiny Critters Posing Huge Challenges for Risk Assessment and Governance

In recent years, the interest in developing genetically modified microorganisms (GMMs), including GMMs developed by genome editing, for use in the environment has significantly increased. However, the scientific knowledge on the ecology of such GMMs is severely limited. There is also little experience at the hands of regulators on how to evaluate the environmental safety of GMMs and on how to assess whether they provide sustainable alternatives to current (agricultural) production systems. This review analyzes two different GMM applications, GM microalgae for biofuel production and nitrogen-fixing GM soil bacteria for use as biofertilizers. We assess the challenges posed by such GMMs for regulatory environmental risk assessment (ERA) against the background of the GMO legislation existing in the European Union (EU). Based on our analysis, we present recommendations for ERA and the monitoring of GMM applications, and in particular for the improvement of the existing EU guidance. We also explore whether existing approaches for technology assessment can provide a framework for the broader assessment of GMM applications. To this end, we recommend developing and implementing an evidence-based sustainability analysis and other methods of technology assessment to support decision making and to address broader societal concerns linked to the use of GMM applications in the environment.

Systematic review and meta-analysis of the potential effects of endophytic bacteria Klebsiella on plant growth promotion and biocontrol of pathogens

Klebsiella is a bacterial genus widely recognized in the medical field but with underexplored potential in agriculture. This study employed a systematic review and meta-analysis to investigate scientific articles on plant growth promotion effects associated with endophytic bacteria Klebsiella species. A total of 39 relevant studies, published between 2012 and 2024, were identified based on strict inclusion and exclusion criteria. The analysis revealed that Klebsiella sp., K. pneumoniae, and K. variicola are cosmopolitan species that have functional versatility in phytohormone production, nutrient solubilization, and pathogen control in agricultural systems in both tropical and temperate zones. The data showed a significant correlation between the use of Klebsiella sp. and plant growth, highlighting the positive impact of these species in controlling aggressive pathogens. These findings underscore the potential of Klebsiella as a biotechnological tool for sustainable agricultural practices, enhancing plant growth and reducing the reliance on chemical inputs. The study further emphasizes the need for future research to deepen genomic characterization and expand the agricultural applications of these bacteria.

Native CRISPR-Cas-based programmable multiplex gene repression in Klebsiella variicola

Klebsiella variicola is a Gram-negative bacterium that is frequently isolated from a wide variety of natural niches. It is a ubiquitous opportunistic pathogen that can cause diverse infections in plants, animals, and humans. It also has significant biotechnological potential. However, due to the lack of efficient genetic tools, the molecular basis contributing to the pathogenesis and beneficial activities of K. variicola remains poorly understood. In this study, we found and characterized a native type I-E CRISPR-Cas system in a recently isolated K. variicola strain KV-1. The system cannot cleave target DNA sequences due to the inactivation of the Cas3 nuclease by a transposable element but retains the activity of the crRNA-guided Cascade binding to the target DNA sequence. A targeting plasmid carrying a mini-CRISPR to encode a crRNA was designed and introduced into the KV-1 strain, which successfully repurposed the native type I-E CRISPR-Cas system to inhibit the expression of the target gene efficiently and specifically. Moreover, by creating a mini-CRISPR to encode multiple crRNAs, multiplex gene repression was achieved by providing a single targeting plasmid. This work provides the first native CRISPR-Cas-based tool for programmable multiplex gene repression in K. variicola, which will facilitate studying the pathogenic mechanism of K. variicola and enable metabolic engineering to produce valuable bioproducts.

Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize

Increasing biological nitrogen (N) fixation (BNF) in maize production could reduce the environmental impacts of N fertilizer use, but reactive N in the rhizosphere of maize limits the BNF process. Using non-transgenic methods, we developed gene-edited strains of Klebsiella variicola (Kv137-2253) and Kosakonia sacchari (Ks6-5687) bacteria optimized for root-associated BNF and ammonium excretion in N-rich conditions. The aim of this research was to elucidate the mechanism of action of these strains. We present evidence from in vitro, in planta and field experiments that confirms that our genetic remodeling strategy derepresses BNF activity in N-rich systems and increases ammonium excretion by orders of magnitude above the respective wildtype strains. BNF is demonstrated in controlled environments by the transfer of labeled 15N2 gas from the rhizosphere to the chlorophyll of inoculated maize plants. This was corroborated in several 15N isotope tracer field experiments where inoculation with the formulated, commercial-grade product derived from the gene-edited strains (PIVOT BIO PROVEN® 40) provided on average 21 kg N ha-1 to the plant by the VT-R1 growth stages. Data from small-plot and on-farm trials suggest that this technology can improve crop N status pre-flowering and has potential to mitigate the risk of yield loss associated with a reduction in synthetic N fertilizer inputs.

Clinical course of Klebsiella variicola peritonitis in end-stage kidney disease patients receiving peritoneal dialysis

Klebsiella variicola is part of the K. pneumoniae complex and has been recently identified to have pathogenic properties. Emerging reports show that it can cause bloodstream, respiratory and urinary tract infections. It has been shown to be an important causative agent in immunocompromised individuals. We report here three cases of K. variicola peritonitis encountered in our peritoneal dialysis patients.

Genomic insight on Klebsiella variicola isolated from wastewater treatment plant has uncovered a novel bacteriophage

Klebsiella variicola is considered an emerging pathogen, which may colonize a variety of hosts, including environmental sources. Klebsiella variicola investigated in this study was obtained from an influent wastewater treatment plant in the North-West Province, South Africa. Whole genome sequencing was conducted to unravel the genetic diversity and antibiotic resistance patterns of K. variicola. Whole genome core SNP phylogeny was employed on publicly available 170 genomes. Furthermore, capsule types and antibiotic resistance genes, particularly beta-lactamase and carbapenems genes were investigated from the compared genomes. A 38 099 bp bacteriophage was uncovered alongside with K. variicola genome. Whole genome sequencing revealed that the extended beta-lactamase blaLEN (75.3%) of the beta-lactamase is dominant among compared K. variicola strains. The identified IncF plasmid AA035 confers resistance genes of metal and heat element subtypes, i.e., silver, copper, and tellurium. The capsule type KL107-D1 is a predominant capsule type present in 88.2% of the compared K. variicola genomes. The phage was determined to be integrase-deficient consisting of a fosB gene associated with fosfomycin resistance and clusters with the Wbeta genus Bacillus phage group. In silico analysis showed that the phage genome interacts with B. cereus as opposed to K. variicola strain T2. The phage has anti-repressor proteins involved in the lysis-lysogeny decision. This phage will enhance our understanding of its impact on bacterial dissemination and how it may affect disease development and antibiotic resistance mechanisms in wastewater treatment plants. This study highlights the need for ongoing genomic epidemiological surveillance of environmental K. variicola isolates.

2-Hydroxyisovalerate production by Klebsiella pneumoniae

2-Hydroxyisovalerate is a valuable chemical that can be used in the production of biodegradable polyesters. In nature, it was only produced at a very low level by Lactococcus lactis. 2-Ketoisovalerate is an intermediate metabolite of the branched-chain amino acid biosynthesis pathway, and Klebsiella pneumoniae ΔbudAΔldhA (Kp ΔbudAΔldhA) was a 2-ketoisovalerate producing strain. In this research, 2-hydroxyisovalerate was identified as a metabolite of Kp ΔbudAΔldhA, and its synthesis pathway was revealed. It was found that 2-ketoisovalerate and 2-hydroxyisovalerate were produced by Kp ΔbudA and Kp ΔbudAΔldhA, but not by Kp ΔbudAΔldhAΔilvD in which the 2-ketoisovalerate synthesis was blocked. budA, ldhA, and ilvD encode α-acetolactate decarboxylase, lactate dehydrogenase, and dihydroxy acid dehydratase, respectively. Thus, it was deduced that 2-hydroxyisovalerate was synthesized from 2-ketoisovalerate. Isoenzymes of ketopantoate reductase PanE, PanE2, and IlvC were suspected of being responsible for this reaction. Kinetic parameters of these enzymes were detected, and they all hold the 2-ketoisovalerate reductase activities. PanE and PanE2 use both NADH and NADPH as co-factors. While IlvC only uses NADH as a co-factor. Over-expression of panE, panE2, or ilvC in Kp ΔbudAΔldhA all enhanced the production of 2-hydroxyisovalerate. Accordingly, 2-hydroxyisovalerate levels were reduced by knocking out panE or panE2. In fed-batch fermentation, 14.41 g/L of 2-hydroxyisovalerate was produced by Kp ΔbudAΔldhA-panE, with a substrate conversion ratio of 0.13 g/g glucose.

Plasmids of the incompatibility group FIBK occur in Klebsiella variicola from diverse ecological niches

Plasmids play a fundamental role in the evolution of bacteria by allowing them to adapt to different environments and acquire, through horizontal transfer, genes that confer resistance to different classes of antibiotics. Using the available in vitro and in silico plasmid typing systems, we analyzed a set of isolates and public genomes of K. variicola to study its plasmid diversity. The resistome, the plasmid multilocus sequence typing (pMLST), and molecular epidemiology using the MLST system were also studied. A high frequency of IncF plasmids from human isolates but lower frequency from plant isolates were found in our strain collection. In silico detection revealed 297 incompatibility (Inc) groups, but the IncFIBK (216/297) predominated in plasmids from human and environmental samples, followed by IncFIIK (89/297) and IncFIA/FIA(HI1) (75/297). These Inc groups were associated with clinically important ESBL (CTX-M-15), carbapenemases (KPC-2 and NDM-1), and colistin-resistant genes which were associated with major sequence types (ST): ST60, ST20, and ST10. In silico MOB typing showed 76% (311/404) of the genomes contained one or more of the six relaxase families with MOBF being most abundant. We identified untypeable plasmids carrying blaKPC-2, blaIMP-1, and blaSHV-187 but for which a relaxase was found; this may suggest that novel plasmid structures could be emerging in this bacterial species. The plasmid content in K. variicola has limited diversity, predominantly composed of IncFIBK plasmids dispersed in different STs. Plasmid detection using the replicon and MOB typing scheme provide a broader context of the plasmids in K. variicola. This study showed that whole-sequence-based typing provides current insights of the prevalence of plasmid types and their association with antimicrobial resistant genes in K. variicola obtained from humans and environmental niches.

Metataxonomic Characterization of Enriched Consortia Derived from Oil Spill-Contaminated Sites in Guimaras, Philippines, Reveals Major Role of Klebsiella sp. in Hydrocarbon Degradation

Oil spills are major anthropogenic disasters that cause serious harm to marine environments. In the Philippines, traditional methods of rehabilitating oil-polluted areas were proven to be less efficient and cause further damage to the environment. Microbial degradation has poised itself to be a promising alternative to those traditional methods in remediating oil spills. Hence, the present study aimed to enrich and characterize hydrocarbon-degrading microbial consortia from oil-contaminated regions in Guimaras Island for potential use in bioremediation. A total of 75 soil samples were obtained and used as inoculum for the enrichment for hydrocarbon degraders. Afterwards, 32 consortia were recovered and subjected to the 2,6-DCPIP assay for biodegradation ability on four types of hydrocarbons: diesel, xylene, hexane, and hexadecane. The consortia that obtained the highest percent degradation for each of the four hydrocarbons were "B2" (92.34% diesel degraded), "A5" (85.55% hexadecane degraded), "B1" (74.33% hexane degraded), and "B7" (63.38% xylene degraded). Illumina MiSeq 16S rRNA gene amplicon sequencing revealed that the dominant phyla in all consortia are Pseudomonadota (previously Proteobacteria), followed by Bacillota (previously Firmicutes). Overall, the amplicon sequence variants (ASVs) retrieved were mainly from the Gammaproteobacteria class, in which many hydrocarbon-degrading bacteria are found. Predictive functional profiling of the consortium showed the presence of genes involved in the degradation of recalcitrant hydrocarbon pollutants. Fatty acid metabolism, which includes alkB (alkane-1-monooxygenase) and genes for beta oxidation, was inferred to be the most abundant amongst all hydrocarbon degradation pathways. Klebsiella sp. is the predominant ASV in all the sequenced consortia as well as the major contributor of hydrocarbon degradation genes. The findings of the study can serve as groundwork for the development of hydrocarbon-degrading bacterial consortia for the bioremediation of oil spill-affected areas in the Philippines. Likewise, this paper provides a basis for further investigation into the role of Klebsiella sp. in the bioremediation of hydrocarbon pollutants.

Pathogen Profile of Klebsiella variicola, the Causative Agent of Banana Sheath Rot

Banana (Musa spp.) is an important fruit and food crop worldwide. In recent years, banana sheath rot has become a major problem in banana cultivation, causing plant death and substantial economic losses. Nevertheless, the pathogen profile of this disease has not been fully characterized. Klebsiella variicola is a versatile bacterium capable of colonizing different hosts, such as plants, humans, insects, and animals, and is recognized as an emerging pathogen in various hosts. In this study, we obtained 12 bacterial isolates from 12 different banana samples showing banana sheath rot in Guangdong and Guangxi Provinces, China. Phylogenetic analysis based on 16S rRNA sequences confirmed that all 12 isolates were K. variicola strains. We sequenced the genomes of these strains, performed comparative genomic analysis with other sequenced K. variicola strains, and found a lack of consistency in accessory gene content among these K. variicola strains. However, prediction based on the pan-genome of K. variicola revealed 22 unique virulence factors carried by the 12 pathogenic K. variicola isolates. Microbiome and microbial interaction network analysis of endophytes between the healthy tissues of diseased plants and healthy plants of two cultivars showed that Methanobacterium negatively interacts with Klebsiella in banana plants and that Herbaspirillum might indirectly inhibit Methanobacterium to promote Klebsiella growth. These results suggest that banana sheath rot is caused by the imbalance of plant endophytes and opportunistic pathogenic bacteria, providing an important basis for research and control of this disease.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants

Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.

Dynamic Analysis of the Bacterial Community and Determination of Antioxidant Capacity during the Fermentation of Sour Tea

The imbalance of the redox state caused by extra reactive oxygen species is closely related to many diseases. Therefore, it is necessary for people to ingest antioxidants through food. The safety of some synthetic antioxidants has been questioned. In this context, it is worth exploring natural and safe antioxidants from biological sources. Tea has good antioxidant activity, and the antioxidant activity of fermented sour tea is better than that of other types. It is necessary to clarify the antioxidant capacity of sour tea during fermentation, as well as the microbial community and its sources. Nonculture and culture-dependent methods were adopted to track the changes in the microbial population and community structure during the fermentation of sour tea. Sequence analysis of 16S rRNA gene amplification revealed significant differences in community complexity and structure at different fermentation times. The highest proportion of operational taxonomic units (OTU s) in all samples was Latilactobacillus, which was determined to be Lactiplantibacillus plantarum by further analysis. The second highest proportion of OTUs was Enterobacter. With the fermentation of sour tea, the antioxidant capacity increased, and all isolated Lb. plantarum had good DPPH clearance rates. Our findings suggest that Lb. plantarum plays a crucial role in the fermentation process of sour tea. The possibility of discovering new antioxidants was provided by the determination of the antioxidant capacity and bacterial community during the fermentation of sour tea.

Immobilization of bacterial mixture of Klebsiella variicola FH-1 and Arthrobacter sp. NJ-1 enhances the bioremediation of atrazine-polluted soil environments

In this study, the effects of the immobilized bacterial mixture (IM-FN) of Arthrobacter sp. NJ-1 and Klebsiella variicola strain FH-1 using sodium alginate-CaCl2 on the degradation of atrazine were investigated. The results showed that the optimal ratio of three types of carrier materials (i.e., rice straw powder, rice husk, and wheat bran) was 1:1:1 with the highest adsorption capacity for atrazine (i.e., 3774.47 mg/kg) obtained at 30°C. On day 9, the degradation efficiency of atrazine (50 mg/L) reached 98.23% with cell concentration of 1.6 × 108  cfu/ml at pH 9 and 30°C. The Box-Behnken method was used to further optimize the culture conditions for the degradation of atrazine by the immobilized bacterial mixture. The IM-FN could be reused for 2-3 times with the degradation efficiency of atrazine maintained at 73.0% after being stored for 80 days at 25°C. The population dynamics of IM-FN was explored with the total soil DNA samples specifically analyzed by real-time PCR. In 7 days, the copy numbers of both PydC and estD genes in the IM-FN were significantly higher than those of bacterial suspensions in the soil. Compared with bacterial suspensions, the IM-FN significantly accelerated the degradation of atrazine (20 mg/kg) in soil with the half-life shortened from 19.80 to 7.96 days. The plant heights of two atrazine-sensitive crops (wheat and soybean) were increased by 14.99 and 64.74%, respectively, in the soil restored by immobilized bacterial mixture, indicating that the IM-FN significantly reduced the phytotoxicity of atrazine on the plants. Our study evidently demonstrated that the IM-FN could significantly increase the degradation of atrazine, providing a potentially effective bioremediation technique for the treatment of atrazine-polluted soil environment and providing experimental support for the wide application of immobilized microorganism technology in agriculture.

Recent Developments in Biological Processing Technology for Palm Oil Mill Effluent Treatment-A Review

POME is the most voluminous waste generated from palm oil milling activities. The discharge of POME into the environment without any treatment processing could inflict an undesirable hazard to humans and the environment due to its high amount of toxins, organic, and inorganic materials. The treatment of POME prior to discharge into the environment is utmost required to protect the liability for human health and the environment. Biological treatments are preferable due to eco-friendly attributes that are technically and economically feasible. The goal of this review article is to highlight the current state of development in the biological processing technologies for POME treatment. These biological processing technologies are conducted in the presence of fungi, bacteria, microalgae, and a consortium of microorganisms. Numerous microbes are listed to identify the most efficient strain by monitoring the BOD, COD, working volume of the reactor, and treatment time. The most effective processing technology for POME treatment uses an upflow anaerobic sludge blanket reactor with the COD value of 99%, hydraulic retention time of 7.2 days, and a working volume of 4.7 litres. Biological processing technologies are mooted as an efficient and sustainable management practice of POME waste.

PCR system for the correct differentiation of the main bacterial species of the Klebsiella pneumoniae complex

Accurate recognition of the closely related species Klebsiella pneumoniae, Klebsiella quasipneumoniae and Klebsiella variicola by phenotypic, biochemical and automated tests is notoriously unreliable in hospitals' diagnostic laboratories. A comparative genomics approach was conducted for the correct differentiation of the main bacterial species in the K. pneumoniae complex. Analysis of the deduced proteomes of 87 unique genomes of the Klebsiella in public databases, was used for the identification of unique protein family members. This allowed the design of a multiplex-PCR assay for the correct differentiation of these three species from different origins. This system allowed us to determine the prevalence of K. pneumoniae, K. quasipneumoniae and K. variicola among a collection of 552 clinical isolates. Of these, 87.3% (482/552) isolates corresponded to K. pneumoniae, 6.7% (33/552) to K. quasipneumoniae and 5.9% (33/552) to K. variicola. The multiplex-PCR results showed a 100% accuracy for the correct identification of the three species evaluated, which was validated with rpoB phylogenetic sequence analysis.