Klebsiella pneumoniae is a type of bacteria found both in nature and in the human body, including the gut. It’s part of a group called Gram-negative bacteria and has a rod-like shape. In healthy people, it can live quietly without causing any problems. But in people with weak immune systems or an unhealthy balance of gut bacteria, it can turn harmful (Vornhagen et al., 2024).

In the gut, K. pneumoniae can stay in check as part of a normal, healthy mix of microbes. However, if it grows too much, it can cause infections not only in the gut but also in other parts of the body, such as the urinary tract, lungs, or even the bloodstream—especially in hospital patients. Some types can produce toxins or resist antibiotics, making them harder to treat and more dangerous (Vornhagen et al., 2024; Paczosa & Mecsas, 2016). This means it can be harmless in the right balance but a serious health risk when conditions allow it to overgrow.

✔ Type of bacteria: Gram-negative, rod-shaped bacterium in the Enterobacteriaceae family (Vornhagen et al., 2024).

✔ Where it’s found: Naturally present in soil, water, plants, and sometimes in the human gut, mouth, and skin.

✔ Part of the gut microbiome: Can live harmlessly in the gut of healthy people but may overgrow if the microbiome is disrupted.

✔ Opportunistic pathogen: Can cause infections, especially in people with weakened immune systems, chronic illness, or after antibiotic use.

✔ Common infections: Pneumonia, urinary tract infections, bloodstream infections, and wound infections (Paczosa & Mecsas, 2016).

✔ Antibiotic resistance risk: Some strains produce extended-spectrum β-lactamases (ESBLs) or carbapenemases, making them resistant to many antibiotics.

✔ Transmission: Spreads via contact with contaminated surfaces, equipment, or hands — particularly in healthcare settings.

While often considered a harmful pathogen, Klebsiella pneumoniae can also play a role in a balanced gut microbiome under healthy conditions. In a stable and diverse microbial community, it coexists with other bacteria without causing disease. Its presence can contribute to maintaining gut microbial diversity — an important factor in preventing the overgrowth of more harmful organisms (Vornhagen et al., 2024).

The gut immune system continuously monitors K. pneumoniae, helping train immune cells to distinguish between harmless colonisers and true pathogens. Low-level exposure may support immune resilience by maintaining mucosal immunity and promoting a controlled inflammatory response, which can act as a defence mechanism against more aggressive infections (Paczosa & Mecsas, 2016). However, this protective role is only seen when K. pneumoniae is kept in check by a healthy microbiome and host defences — disruptions such as antibiotic use or immune suppression can quickly shift it from a harmless commensal to a dangerous invader.

When Klebsiella pneumoniae overgrows or escapes the gut into other parts of the body, it can cause a range of health problems. Common symptoms and conditions linked to unhealthy levels include:

✔ Digestive disturbances: bloating, abdominal pain, diarrhoea, or constipation due to microbial imbalance.

✔ Recurrent urinary tract infections (UTIs): K. pneumoniae can migrate from the gut to the urinary tract.

✔ Respiratory issues: pneumonia, coughing, and difficulty breathing if the bacteria colonise the lungs.

✔ Systemic infections: fever, chills, fatigue, and sepsis if it enters the bloodstream (Vornhagen et al., 2024).

✔ Liver abscesses: especially in individuals with diabetes or weakened immunity (Paczosa & Mecsas, 2016).

✔ Antibiotic-resistant infections: certain strains can resist treatment, making recovery more difficult.

In healthy individuals, K. pneumoniae is usually kept under control by a diverse microbiome and strong immune system. However, factors like prolonged antibiotic use, chronic illness, or immune suppression can allow it to multiply unchecked, increasing the risk of serious infection.

In South Africa, Klebsiella pneumoniae is a growing public health concern due to its dual role as both a gut commensal and a serious pathogen. While it can live harmlessly in the intestines of healthy individuals, certain strains — particularly those carrying antibiotic resistance genes — can cause infections when the gut microbiome is disrupted or immunity is weakened. Overgrowth in the gut increases the risk of the bacteria migrating to the urinary tract, lungs, or bloodstream, leading to illnesses such as UTIs, pneumonia, and sepsis (Vornhagen et al., 2024).

South African hospitals have reported an increase in multidrug-resistant K. pneumoniae strains, making infections more challenging to treat and increasing the risk of outbreaks. These resistant strains can originate from the gut microbiome, especially after broad-spectrum antibiotic use, and are often linked to poor infection control in healthcare settings. People with chronic illnesses, such as diabetes, HIV, or cancer, are particularly vulnerable to severe disease. Maintaining a balanced gut microbiome through diet, cautious antibiotic use, and targeted probiotic or prebiotic support may help reduce the risk of colonisation and subsequent infection.

Keeping Klebsiella pneumoniae at harmless levels in your gut microbiome relies on maintaining microbial balance and preventing conditions that favour its overgrowth.

Use antibiotics cautiously: Overuse or inappropriate use of antibiotics can disrupt the gut microbiome, removing protective bacteria and creating an environment where K. pneumoniae can thrive (Martin & Bachman, 2018). Only take antibiotics when prescribed and follow the full course to reduce the risk of resistant strains.

Support gut microbial diversity: Diets high in fibre from vegetables, fruits, legumes, and whole grains promote beneficial bacteria, which compete with K. pneumoniae for resources and space in the gut (Vornhagen et al., 2024).

Consume probiotics and prebiotics: While K. pneumoniae is not a probiotic species, boosting beneficial strains like Bifidobacterium and Lactobacillus through fermented foods (yoghurt, kefir, sauerkraut) and prebiotic-rich foods (garlic, onions) can help maintain a healthy microbial balance (FIMM, 2020).

Manage chronic health conditions: Diseases such as diabetes, HIV, and cancer weaken immunity, increasing susceptibility to infections from K. pneumoniae (Paczosa & Mecsas, 2016). Effective management of these conditions reduces this risk.

Practise good hygiene: Rigorous handwashing, safe food preparation, and infection prevention measures in healthcare settings help limit the spread of multidrug-resistant K. pneumoniae strains (WHO, 2022).

Testing your gut microbiome with Epicentre’s Complete Gut Profile can identify K. pneumoniae colonisation early, allowing for targeted interventions before it progresses to urinary tract infections, pneumonia, or bloodstream infections, particularly in high-risk individuals.