Klebsiella variicola: Infections, Causes, and Symptoms

Klebsiella variicola is a bacterium increasingly recognized as a cause of serious human infections, including bloodstream infections, pneumonia, and urinary tract infections, yet it has spent most of its known history hiding in plain sight. For years, clinical laboratories routinely misidentified it as its close relative Klebsiella pneumoniae, meaning that many infections attributed to K. pneumoniae were actually caused by K. variicola.¹ That misidentification problem has real consequences for treatment and for understanding how deadly the organism can be. As molecular tools have improved, a clearer and more concerning picture of K. variicola has emerged.

Why It So Often Goes Undetected

K. variicola was first described as a distinct species in 2004, isolated from banana plants in Mexico. It is genetically separate from K. pneumoniae, but the two look virtually identical under a microscope and behave similarly on the standard biochemical tests that most hospital labs rely on. Traditional culture-based identification methods almost always call it K. pneumoniae, because K. variicola ferments lactose and grows on the same media in the same way.² The practical result is that many hospitals have been treating K. variicola infections without knowing it.

Newer technology has started to change this. MALDI-TOF mass spectrometry, which identifies bacteria by their protein fingerprints rather than by how they grow on a plate, can now distinguish K. variicola from K. pneumoniae when the instrument’s reference database has been updated to include K. variicola profiles.¹ Whole-genome sequencing provides definitive species-level identification, using a method called average nucleotide identity to confirm that K. variicola is genetically distinct from both K. pneumoniae and a third close relative, K. quasipneumoniae.³ But many clinical labs worldwide still rely on older identification systems that cannot make the distinction, which means misidentification continues to be a routine problem.

This matters for more than academic taxonomy. Accurate identification affects which antibiotics are chosen, how outbreaks are tracked, and how we estimate the true burden of K. variicola disease. One research group put it plainly: species-level identification should be performed to improve patient outcomes during infection.⁴

Where K. variicola Comes From

Unlike many hospital-associated pathogens, K. variicola has a genuine dual life. It evolved as a plant-associated bacterium with the unusual ability to fix atmospheric nitrogen, meaning it can convert nitrogen gas into a form that plants can use. It lives in soil and the root zones of crops, where it promotes plant growth by producing plant hormones, dissolving phosphorus and potassium, and supplying nitrogen.⁵ In agricultural research, K. variicola is sometimes studied as a beneficial microbe.

But it also turns up in hospitals, wastewater, and the human gut. Genomic studies of K. variicola from wastewater treatment plants have confirmed that strains circulating in the environment carry many of the same resistance and capsule genes found in clinical isolates.⁶ A large-scale genomic analysis of K. variicola from around the world showed a star-like evolutionary pattern, with strains branching out from a common ancestor into different hosts, habitats, and geographic locations without clustering neatly by source.⁷ In other words, there is no clean division between “the plant strain” and “the human strain.” The organism moves between environments, and clinical infections can come from community exposure as well as healthcare settings.

Who Is Most at Risk

K. variicola can infect healthy people, but it overwhelmingly targets those whose defenses are already compromised. The conditions most frequently linked to K. variicola infections include diabetes, cancer, liver and biliary disease, organ transplantation, autoimmune conditions like lupus, and chronic alcohol use.⁸ These are the same comorbidities that predispose people to K. pneumoniae infections, which makes sense given the organisms’ overlapping biology.

Age appears to be a factor on its own. A Japanese study comparing bloodstream infections caused by K. variicola, K. pneumoniae, and K. quasipneumoniae found that K. variicola was more frequently isolated from patients over 80 years old than the other species.⁹ Why elderly patients seem especially susceptible is not entirely clear, though age-related immune decline is the most obvious explanation.

Newborns in intensive care units are another vulnerable group. Neonatal units have experienced outbreaks traced to K. variicola contamination of hospital sinks. In one New Zealand neonatal outbreak, rapid genome sequencing identified K. variicola in four infants and traced the source to two sink traps on the unit. After the sinks were disinfected and cleaning procedures were tightened, no further cases appeared.¹⁰

Types of Infections and Symptoms

K. variicola causes a range of infections that mirror those caused by K. pneumoniae. The symptoms depend on which body site is involved, and they are generally indistinguishable from infections caused by other Klebsiella species. There is nothing about a K. variicola infection that you would recognize at the bedside as “different” from K. pneumoniae without lab confirmation.

Bloodstream Infections

Bloodstream infections, or bacteremia, are the most studied and arguably the most dangerous presentation. Symptoms typically include fever, chills, rapid heart rate, low blood pressure, and confusion. These can progress rapidly to septic shock, where organ systems begin to fail. One case report described a 52-year-old man who developed fever and was initially treated with carbapenem antibiotics for what the lab identified as K. pneumoniae. The treatment failed, and he died within 72 hours of symptom onset from septic shock. Only after death did advanced sequencing reveal a mixed infection with K. variicola, and the clinical team concluded that K. variicola was the likely driver of his rapid deterioration.¹¹

K. variicola has also been identified as a cause of liver abscess, a hallmark of hypervirulent Klebsiella. Researchers in Japan documented two community-acquired liver abscess cases caused by K. variicola strains that carried hypervirulence-associated genes, representing the first genetically confirmed cases of that type in the country.¹²

Respiratory and Urinary Tract Infections

K. variicola has been recovered from sputum and tracheal aspirates in patients with pneumonia. In one community-acquired case, a 65-year-old man presented with pulmonary infection caused simultaneously by K. variicola and Acinetobacter baumannii. Both organisms were identified from sputum using MALDI-TOF mass spectrometry, and the patient was successfully treated with oral levofloxacin.¹³ Symptoms in respiratory infections follow the familiar pattern of cough, fever, shortness of breath, and sputum production.

Urinary tract infections are another common presentation. K. variicola has been found in routine urine cultures, including one case involving a 23-year-old pregnant woman whose urine culture grew an organism that MALDI-TOF identified as K. variicola.² Research on K. variicola’s behavior in the urinary tract has shown that clinical isolates can establish higher bacterial counts in the bladder than K. pneumoniae, suggesting the organism is well adapted to that environment.⁴

Neonatal and Sepsis Presentations

In neonatal units, K. variicola infections may present as late-onset sepsis, with nonspecific signs that include temperature instability, feeding intolerance, respiratory distress, and lethargy. These symptoms are common to many neonatal infections, which is why lab identification and outbreak investigation become critical. Genomic characterization of K. variicola from sepsis patients in Ethiopian hospitals confirmed the presence of biofilm-formation genes and iron-acquisition systems in clinical strains from both hospital sites studied.¹⁴

How It Compares to K. pneumoniae in Severity

The evidence on whether K. variicola is more or less dangerous than K. pneumoniae is genuinely mixed, and the answer may depend on which strain and which patient population you are looking at. One study from Stockholm found that K. variicola bloodstream infections had a 30-day mortality of about 29%, compared with roughly 14% for K. pneumoniae, a difference that held even after adjusting for age and other health conditions.¹⁵ That finding raised alarm.

But other studies have not replicated it. The Japanese comparative study mentioned earlier found no significant differences in clinical features or 30-day mortality between K. variicola, K. pneumoniae, and K. quasipneumoniae bloodstream infections.⁹ A more recent molecular epidemiology study similarly found no significant differences in 30-day mortality, though it noted that K. variicola strains carried certain virulence-associated genes less frequently than K. pneumoniae, suggesting the organism may be generally less virulent on a genetic level.¹²

The discrepancy likely reflects different patient populations, different strain compositions, and the small sample sizes in many of these studies. Rare hypervirulent K. variicola strains clearly exist and can cause devastating disease, but the “average” K. variicola infection may not be more lethal than its K. pneumoniae counterpart. The honest summary is that the field does not yet have a definitive answer on comparative mortality, and clinicians should treat both organisms with equal seriousness.

What Makes K. variicola Harmful

K. variicola shares many of its disease-causing tools with K. pneumoniae, but the details differ in ways that matter for how infections behave and respond to treatment. Like other Klebsiella species, K. variicola relies on a polysaccharide capsule that surrounds the bacterial cell and shields it from the immune system. The capsule type KL107-D1 appears to be especially common, found in about 88% of genomes compared in one study.⁶ Different capsule types may influence how well the immune system recognizes and fights the bacterium.

Beyond the capsule, K. variicola uses several strategies to establish and sustain infection:

Biofilm formation: K. variicola strains carry mrk gene clusters that produce sticky structures called fimbriae, allowing the bacteria to cling to surfaces like catheters and sink drains and to form biofilms that are much harder for antibiotics and immune cells to penetrate.¹⁴
Iron theft: Bacteria need iron to grow, and the human body actively withholds it from invaders. K. variicola produces siderophores, small molecules that scavenge iron from host tissues. Some strains carry the yersiniabactin system, a particularly effective iron-capture mechanism first identified in plague-causing bacteria and acquired through horizontal gene transfer.¹⁶
Serum survival: Laboratory experiments have shown that classical K. variicola strains can survive and even multiply in human blood serum, especially when certain sugars are available. Sorbitol, galactose, and maltose all enhanced biofilm production, siderophore output, and serum survival in tested strains.¹⁷

A small proportion of K. variicola strains are hypermucoviscous, producing an extra-thick, gooey capsule that is the hallmark of hypervirulent Klebsiella. These strains can cause invasive infections even in people without underlying health problems, including the liver abscesses described earlier. But most K. variicola strains are not hypermucoviscous, and the frequency of full hypervirulence gene sets appears to be lower in K. variicola than in K. pneumoniae.¹²

Antibiotic Resistance

K. variicola carries a built-in beta-lactamase gene called blaLEN that provides low-level resistance to certain penicillins. This gene is found in the vast majority of K. variicola strains, roughly three-quarters of genomes in one comparative analysis.⁶ The organism also typically carries the oqxAB genes, which confer reduced susceptibility to certain fluoroquinolone antibiotics.⁴ These intrinsic resistance genes mean that even wild-type K. variicola strains are not susceptible to the most basic antibiotics used against bacterial infections.

The bigger worry is acquired resistance. K. variicola strains from around the world have picked up genes that make them resistant to much more powerful drugs:

Extended-spectrum beta-lactamases: Strains carrying blaCTX-M-15, a gene that breaks down third-generation cephalosporin antibiotics, have been found in clinical isolates from South Korea and elsewhere.¹⁸
Carbapenem resistance: Carbapenems are often considered last-resort antibiotics for serious Gram-negative infections. K. variicola strains carrying blaKPC-2 and blaKPC-3 carbapenemase genes have been isolated on multiple continents. In one South Korean isolate, blaKPC-2 was found on a transferable plasmid, meaning it can potentially pass the gene to other bacteria.¹⁸
Novel carbapenemases: A K. variicola strain from China carried blaOXA-484, a carbapenemase gene that appears to have evolved from a related gene through a series of mutations, raising concerns about the ongoing diversification of resistance mechanisms.¹⁹

One genomic study found carbapenem resistance genes in about 10 out of 145 K. variicola genomes examined, drawn from clinical isolates across multiple geographic regions.⁴ That proportion is still modest compared to some K. pneumoniae lineages, but these resistance genes sit on mobile plasmids that can spread between species, and the trend is clearly upward.

Hospital Outbreaks and the Sink Problem

K. variicola has featured in several hospital outbreak investigations in recent years, and a recurring theme is hospital plumbing. In one acute care hospital in Virginia, 18 cases of carbapenemase-producing Enterobacterales were identified over about six months, and K. variicola accounted for 14 of them. The infections showed up mostly in urine specimens and rectal surveillance swabs. Investigators found the same KPC-3-producing K. variicola in a sink drain and a faucet aerator in a patient room, and clinical isolates were genetically near-identical to the environmental ones.²⁰ The investigation also identified gaps in hand hygiene, antibiotics being dumped into handwashing sinks, and patient care supplies stored within splash range of sinks.

A South Korean hospital outbreak told a similar story, with both K. pneumoniae and K. variicola carrying the same carbapenemase genes persisting in hospital sinks.²¹ And the New Zealand neonatal outbreak traced transmission to contaminated sink traps, which served as a reservoir for the clonal K. variicola strain infecting babies.¹⁰

K. variicola’s ability to form biofilms is central to this problem. Biofilms in drain pipes and faucet components are extremely difficult to eradicate with routine cleaning. The bacteria embed themselves in a self-produced matrix that protects them from disinfectants and drying. Even after apparent decontamination, regrowth from residual biofilm can restart transmission. Hospitals increasingly recognize that sink design and plumbing management are infection-control concerns, not just facilities issues.

Infections Beyond Humans

K. variicola is not exclusively a human pathogen. It has been identified as a cause of bovine mastitis, an inflammation of the udder that causes economic losses on dairy farms. Genome sequences of K. variicola isolated from cows with clinical mastitis on a Canadian dairy farm confirmed the species identity and demonstrated that the organism can infect agricultural animals as well.²² The genomic analysis showing that strains do not cluster by host type raises the possibility that animal and human strains are not fundamentally separate populations, though direct animal-to-human transmission has not been definitively demonstrated for K. variicola.⁷

The broader picture is of an organism that lives comfortably in soil, water, plants, animals, and humans, moving between these niches more fluidly than many traditional pathogens. That ecological flexibility, combined with its ability to acquire antibiotic resistance genes on mobile genetic elements and its talent for forming persistent biofilms in hospital plumbing, makes K. variicola a pathogen that infection-control teams and microbiologists are paying closer attention to each year. As diagnostic tools continue to improve and more labs routinely distinguish it from K. pneumoniae, the recorded burden of K. variicola disease will almost certainly continue to rise.

1
PubMed Central. Accurate Identification of Klebsiella variicola by MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories
2
INTERNATIONAL JOURNAL OF SCIENTIFIC RESEARCH. KLEBSIELLA VARIICOLA URINARY TRACT INFECTION: A MISIDENTIFIED PATHOGEN
3
Journal of Basic Microbiology. Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae
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PubMed Central. Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella variicola
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PubMed Central. Exploring the environmental traits and applications of Klebsiella variicola
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BMC Genomics. Genomic insight on Klebsiella variicola isolated from wastewater treatment plant has uncovered a novel bacteriophage
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bioRxiv. Genome Analyses of A Worldwide Multisource Collection of Klebsiella variicola Reveal Adaptation Relevant for Human Infection
8
PubMed Central. Klebsiella variicola: an emerging pathogen in humans
9
PubMed Central. Clinical characteristics in blood stream infections caused by Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae: a comparative study, Japan, 2014-2017
10
PubMed Central. The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing
11
PubMed Central. Fatal community-acquired bloodstream infection caused by Klebsiella variicola: A case report
12
PubMed Central. Molecular epidemiology and clinical features of Klebsiella variicola bloodstream infection compared with infection with other Klebsiella pneumoniae species complex strains
13
PubMed Central. Lung Infection Due to Species Infrequently Isolated in the Community Setting: Klebsiella variicola and Acinetobacter baumannii
14
PubMed Central. Genomic characterizations of Klebsiella variicola: emerging pathogens identified from sepsis patients in Ethiopian referral hospitals
15
PLoS ONE. Klebsiella variicola Is a Frequent Cause of Bloodstream Infection in the Stockholm Area, and Associated with Higher Mortality Compared to K. pneumoniae
16
The Microbe. Multidrug-resistant Klebsiella pneumoniae and Klebsiella variicola isolated from patients in Portuguese hospitals: Genomic and phenotypic characterization
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PubMed Central. The Influence of Carbohydrates on the Virulence Potential of Klebsiella variicola Isolates
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PubMed Central. Characterization of Antimicrobial Resistance and Hypervirulent Traits of Klebsiella variicola Isolates Collected in South Korea
19
PubMed Central. Emergence of OXA-484-Producing Klebsiella variicola in China
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Open Forum Infectious Diseases. Multispecies Outbreak of Klebsiella pneumoniae Carbapenemase-3 (KPC-3)-producing Enterobacterales in an Acute Care Hospital – Virginia, 2023-2024
21
PubMed Central. An outbreak of bla(KPC-4)- and bla(VIM-1)-producing Klebsiella pneumoniae and Klebsiella variicola at a single hospital in South Korea
22
PubMed Central. Genome Sequences of Klebsiella variicola Isolates from Dairy Animals with Bovine Mastitis from Newfoundland, Canada