Pyelonephritis: How a Kidney Infection Differs From Cystitis and Why the Antibiotic Choice Matters
Most urinary infections stay in the bladder. They burn, they make you run to the toilet, and a short course of antibiotics clears them. Pyelonephritis is what happens when the bacteria keep climbing, up the ureters and into the kidney itself.
At that point the illness changes character. It is no longer a local irritation but an infection of an organ with a rich blood supply, which means bacteria can reach the bloodstream. People feel properly ill: fever, shaking chills, pain in the back or side, sometimes vomiting. Treated promptly, most recover fully within a week or two. Left too long, or treated with the wrong tablet, it can lead to sepsis or kidney damage.
This guide covers how to recognise a kidney infection, why some common urinary antibiotics do not work for it, when hospital care is needed, and what recovery looks like. The wider picture of bladder infections is in our guide to urinary tract infections.
🧫 Bladder infection or kidney infection?
| Cystitis (bladder) | Pyelonephritis (kidney) | |
|---|---|---|
| Burning, urgency, frequency | Yes | Often, but can be absent |
| Fever | Usually none | Typical, often with shaking chills |
| Pain | Low in the pelvis | In the back or side, under the ribs, usually one side |
| Nausea or vomiting | Rare | Common |
| How you feel overall | Uncomfortable but well | Unwell, weak, feverish |
| Treatment length | 3 to 5 days | 5 to 14 days depending on the drug |
The single most useful clue is fever with pain in the side. A bladder infection that is followed a day or two later by a temperature and back pain has very likely moved up.
Kidney pain sits higher than most people expect: in the flank, just below the ribs at the back, often on one side. Pain lower down in the middle of the back is more likely to come from muscles. Tapping gently over the kidney area and finding it very tender is one of the signs doctors check.
🚨 Signs of sepsis: go now
🔴 Call emergency services or go to hospital immediately for a urinary infection with any of these:
- Confusion, slurred speech or unusual drowsiness
- Fast breathing or breathlessness
- Very fast heartbeat, feeling faint, or low blood pressure
- Cold, blotchy or very pale skin
- Passing little or no urine for a day
- Shaking so hard you cannot stop, with a high fever
- Vomiting so much that tablets and fluids cannot stay down
Older people may show none of the classic signs and simply become confused or fall. In them, a sudden change in behaviour with a urinary infection needs the same urgency.
🔬 How the infection gets there
In the vast majority of cases, bacteria from the gut, most often E. coli, enter the urethra, infect the bladder and travel upward. Anything that slows the flow of urine or lets it run backward makes this easier.
| Factor | Why it raises the risk |
|---|---|
| Being female | A short urethra close to the anus |
| Pregnancy | Hormones relax the ureters and the womb presses on them, so urine drains slowly |
| Kidney stones | Block drainage and shelter bacteria |
| Enlarged prostate | Leaves urine in the bladder |
| Diabetes | Sugar in urine feeds bacteria; immune defence is weaker |
| Urinary catheters | A direct route for bacteria |
| Reflux of urine in children | Urine flows back from bladder to kidney, carrying infection |
| Weakened immunity | Transplant medicines, chemotherapy, long-term steroids |
🧪 Tests
A urine sample goes for culture before the first antibiotic dose. This matters more than in simple cystitis. The culture shows which bacterium it is and which antibiotics will kill it, and with kidney infections there is little room for a wrong guess.
Blood tests check the white cell count, inflammation markers and kidney function, and blood cultures are taken if the person is feverish and unwell. Imaging, usually an ultrasound, is done straight away when a blockage such as a stone is suspected, in men, and in anyone who is very ill. It is also done if there is no improvement after two to three days of the right antibiotic.
💊 Which antibiotics work, and which do not
This is where kidney infections differ most from bladder infections. Some antibiotics that are excellent for cystitis reach high levels in the urine but almost none in the kidney tissue. They are useless here.
💡 Nitrofurantoin and fosfomycin do not treat kidney infections. They are good first choices for simple bladder infections, but they do not reach the kidney. If you have been taking nitrofurantoin and develop fever and back pain, the treatment needs to change, not continue. In our catalogue nitrofurantoin is Macrobid (Nitrofurantoin), and it should be kept for bladder infections.
| Antibiotic | Typical course for kidney infection | Notes |
|---|---|---|
| Ciprofloxacin | 7 days | Reaches the kidney very well. First choice where local resistance is low |
| Levofloxacin | 5 to 7 days | Same family as ciprofloxacin, once daily |
| Co-trimoxazole | 14 days | Only if the culture shows the bacterium is sensitive |
| Amoxicillin with clavulanate, or oral cephalosporins | 10 to 14 days | Less effective by mouth; often used after a first injected dose, or in pregnancy |
| Nitrofurantoin, fosfomycin | Not suitable | Do not reach the kidney |
Where resistance to ciprofloxacin is common in the area, doctors often give a single injected dose of a stronger antibiotic first, then continue with tablets once the culture result is known. Oral options in our antibiotics category include Cipro (Ciprofloxacin), Levaquin (Levofloxacin), Bactrim (Trimethoprim) and Augmentin (Amoxicillin and Clavulanate). The interactions of co-trimoxazole are set out in our co-trimoxazole guide.
⚠️ What to know about ciprofloxacin and levofloxacin
These fluoroquinolones are the backbone of oral treatment for kidney infection because they work so well in kidney tissue. They also carry warnings that make them unsuitable for minor infections. For a kidney infection, the balance usually favours them.
- 🦵 Tendon pain or swelling, especially the Achilles. Stop and seek advice; the risk is higher over 60, with steroid tablets and after transplants
- 🧠 Tingling, numbness or burning in hands or feet, or unusual anxiety, confusion or sleep problems
- 🫀 Sudden severe chest, back or abdominal pain. Rarely these drugs are linked to tears in the main artery, so this is an emergency
- 🩸 Low or high blood sugar in people with diabetes
- 🥛 Dairy, calcium, iron, zinc and antacids block absorption. Take the tablet two hours before or six hours after them
- ☀️ Sun sensitivity
They are generally avoided in pregnancy and in children unless there is no suitable alternative.
🏥 When hospital is needed
Many adults with a kidney infection can be treated at home with tablets. Hospital care, usually with antibiotics through a drip at first, is needed when:
- there are signs of sepsis
- vomiting stops tablets staying down
- the person is pregnant
- there is a blocked kidney, for example from a stone. An infected, blocked kidney needs urgent drainage, not just antibiotics
- the person has only one kidney, a kidney transplant or significantly reduced kidney function
- there is no improvement after 48 to 72 hours of the right antibiotic
- the person is frail or elderly, or cannot manage at home
📅 What recovery looks like
| When | What to expect |
|---|---|
| First 24 to 48 hours | Fever may continue. Drink steadily, use paracetamol for fever and pain, rest |
| By day 3 | Fever settling, appetite returning. If not, contact the doctor |
| End of the course | Most symptoms gone. Finish every tablet |
| Following one to two weeks | Tiredness can linger; return to full activity gradually |
Paracetamol is the safer choice for pain and fever. Anti-inflammatory painkillers such as ibuprofen are best avoided while the kidney is inflamed, especially if you are dehydrated.
🤰 Pregnancy
Kidney infection is one of the most common reasons for hospital admission in pregnancy, and it can trigger early labour. For that reason, pregnant women are screened for bacteria in the urine and treated even without symptoms. A pregnant woman with fever and back pain should be seen the same day. Treatment usually starts in hospital with antibiotics safe in pregnancy, and urine is checked regularly for the rest of the pregnancy.
👶 Children
In babies and young children, a kidney infection may show up only as fever, poor feeding, vomiting, irritability or sleepiness, with no obvious urinary symptoms. Any baby under three months with a fever needs urgent assessment. A urine sample is essential. After a first kidney infection, many children have an ultrasound to look for a structural problem or reflux of urine, because repeated infections in young children can scar the kidneys.
👨 Men
Urinary infections are less common in men, so a kidney infection in a man is always investigated for a cause. That might be an enlarged prostate, a stone or a narrowing. Infection can involve the prostate as well, which needs a longer course, often two weeks or more. Our guide to urinary infections covers the bladder side in men.
🧬 Complications
Most people recover without lasting harm. Complications are more likely with delays, blockages, diabetes or a weak immune system:
- Sepsis
- Infection spreading into the bloodstream and affecting other organs. The most serious risk and the reason for urgency.
- Kidney abscess
- A pocket of pus that may need draining. Suspected when fever persists despite the right antibiotic.
- Emphysematous pyelonephritis
- A rare, severe form with gas in the kidney, seen mostly in people with poorly controlled diabetes. A surgical emergency.
- Scarring
- Mainly after repeated infections in young children, and a cause of high blood pressure later in life.
🛡️ Preventing another one
Prevention is mostly about stopping bladder infections and treating them early. Drink enough to pass pale urine through the day. Pass urine after sex, and do not hold on for hours. Treat constipation, and keep diabetes well controlled. For women after menopause with repeated infections, vaginal oestrogen reduces recurrences. Cranberry products may slightly reduce bladder infections in some women but are not a treatment. If kidney infections recur, the urinary tract should be investigated for a cause, such as a stone.
📞 When to see a doctor
- Fever, shivers or back or side pain with a urinary infection — the same day
- Any sign of sepsis — emergency services
- Pregnancy with urinary symptoms or fever
- Baby or young child with unexplained fever
- No improvement after 48 to 72 hours of antibiotics
- Severe one-sided pain that comes in waves, which may be a stone
- Tendon pain, numbness or sudden severe chest or back pain while on ciprofloxacin or levofloxacin
❓ Frequently asked questions
How do I know if a UTI has spread to my kidneys?
The key signs are fever, often with shaking chills, pain in the back or side just below the ribs, and feeling generally unwell, sometimes with nausea or vomiting. Burning when passing urine may or may not be present. Fever with side pain after a bladder infection should be seen the same day.
Where is kidney infection pain felt?
In the flank, at the back just below the ribs, usually on one side, sometimes spreading to the side of the abdomen or groin. It is higher than most back pain and does not usually change with movement the way muscle pain does.
What is the best antibiotic for a kidney infection?
Where local resistance is low, ciprofloxacin for 7 days or levofloxacin for 5 to 7 days are common first choices because they reach kidney tissue well. Co-trimoxazole works if the bacterium is sensitive. The urine culture guides the final choice.
Does nitrofurantoin treat a kidney infection?
No. Nitrofurantoin reaches high levels in urine but not in kidney tissue, so it is only suitable for bladder infections. If fever and back pain develop while taking it, the treatment needs to change.
How long does it take to recover from a kidney infection?
Fever usually settles within two to three days of the right antibiotic, and most symptoms are gone by the end of the course. Tiredness can last another week or two. If there is no improvement after 48 to 72 hours, contact a doctor.
When does a kidney infection need hospital?
With signs of sepsis, vomiting that stops tablets staying down, pregnancy, a blocked kidney, a single or transplanted kidney, frailty, or no improvement after two to three days of treatment.
Can a kidney infection go away on its own?
It should not be left to do so. Untreated kidney infection can spread to the bloodstream and cause sepsis or kidney damage. It needs antibiotics chosen for kidney infection.
What painkiller can I take with a kidney infection?
Paracetamol is the safer choice for fever and pain. Anti-inflammatory painkillers such as ibuprofen are best avoided while the kidney is inflamed, especially if you are not drinking much.
Is a kidney infection dangerous in pregnancy?
It needs prompt care because it can trigger early labour and make the mother seriously ill. A pregnant woman with fever and back pain should be seen the same day, and treatment usually begins in hospital.
What are the side effects of ciprofloxacin to watch for?
Tendon pain or swelling, tingling or numbness in the hands or feet, unusual anxiety or confusion, and, rarely, sudden severe chest or back pain, which is an emergency. Dairy, calcium, iron and antacids reduce absorption, so keep them apart from the dose.
📑 Sources and editorial
- Guidelines on the treatment of acute uncomplicated pyelonephritis and complicated urinary tract infection
- Recommendations on antibiotic choice and duration based on tissue penetration and local resistance
- Guidance on sepsis recognition in urinary infection
- Guidance on urinary tract infection in pregnancy and in children, including imaging after a first febrile infection
- Regulatory safety communications on fluoroquinolone antibiotics
- Related reading: urinary tract infections, co-trimoxazole
- Related products: Cipro (Ciprofloxacin), Levaquin (Levofloxacin), antibiotics category
- RXshop Editorial Team — reviewed by Michael Reeves, MD, Urology
Medical Disclaimer: The information in this article is for educational and informational purposes only and is not a substitute for professional medical advice, diagnosis, or treatment. Always seek guidance from a qualified healthcare provider with any questions you may have regarding a medical condition, and before starting, stopping or changing any medication.