Floods: leptospirosis, wounds and contaminated water

Ten days after a major flood, the water has receded and the city is starting to clean up houses and streets. At the care station set up in a gymnasium, a forty-year-old man who spent the week removing mud from his house arrives with high fever, severe calf pain and red eyes. Next to him, a woman shows a cut on her foot from walking barefoot in the water, now red and swollen. A child has had diarrhea for two days. An older man who helped his neighbors has a wound on his hand and does not remember when he last had a tetanus shot. The scenes are fictional and were written for teaching. This text uses these scenarios as a setting for clinical reasoning: how exposure to floodwater changes the differential, which time windows help you think, and which shortcuts lead to error.

NEXO is a daily medical diagnosis game: one clinical case a day, up to six progressive clues, and ICD-10 proximity feedback across five levels.

The text avoids being a protocol. Antibiotics, vaccines, doses and admission criteria follow each service's protocols and local public health guidance, under supervision. The focus is on how to think. If you play the case of the day on NEXO, you will recognize the move: the exposure clue changes the weight of the others, and the time since exposure helps order the hypotheses.

Key points

• After a flood, the differential for fever, wounds and diarrhea changes, and the question about exposure to water enters every consultation.
• Leptospirosis is the hypothesis that demands the most attention in fever after contact with water or mud, because it can progress to severe forms with jaundice, kidney injury or pulmonary bleeding.
• Wounds exposed to floodwater can become infected with unusual bacteria, and tetanus vaccination status needs to be checked.
• Diarrhea and waterborne diseases depend heavily on people's displacement, access to safe water and sanitation.
• The most dangerous context bias is attributing everything to the flood and forgetting the common causes of fever, as well as chronic diseases that went untreated.

What the flood changes in clinical reasoning

Alderman, Turner and Tong reviewed the health effects of floods and describe increased mortality in the first year, outbreaks of hepatitis E, gastroenteritis and leptospirosis, especially where there is displacement and poor hygiene, and psychological distress that persists years later (Alderman et al., 2012). Paterson and colleagues add the immediate hazards of the water and the impact on chronic diseases and health services (Paterson et al., 2018). The World Health Organization page on floods summarizes the health risks and preparedness and response measures (WHO, Floods).

For clinicians, the flood adds a question to the history: did the person have contact with floodwater or mud, for how long, with what protection and how many days ago. This question changes the pre-test probability of several infectious diseases, but it does not eliminate the other causes of fever or diarrhea. The post on pre-test probability explains how context changes the reading of each finding.

Who is most exposed

The greatest exposure is usually among those cleaning houses and streets, first responders, those walking barefoot or in short clothing in the water, those with open wounds and those left displaced in crowded shelters. People with chronic diseases, such as diabetes or kidney disease, are at higher risk of complications and may also have gone without medication during the event.

A global problem

Floods happen on every continent, and the same clinical logic applies in very different places. What changes is the local epidemiology: which diseases circulate in the region, how vaccination coverage stands and what the health system's capacity is after the event. Paterson and colleagues reviewed the relationship between floods and infectious diseases and show that the risk depends both on the water and on local sanitation and housing conditions (Paterson et al., 2018).

Time windows: what to think at each stage

The time since exposure helps order the hypotheses. The table below is a teaching way to organize the reasoning and should be adjusted to local epidemiology and the service's protocol.

Phase after the flood	What else shows up	Useful questions
During and right after	Drowning, trauma, hypothermia, carbon monoxide poisoning from generators	Where the person was, what they used to heat or generate power
First days	Infected wounds, diarrhea, respiratory infections in shelters	Type of wound, water consumed, shelter conditions
One to four weeks	Leptospirosis and other waterborne and vector-borne fevers	Contact with water or mud, days since exposure
Weeks to months	Worsening of chronic diseases, mental health, vector-borne diseases	Interrupted medication, sleep, mood, losses

Carbon monoxide and other immediate risks

In the phase right after the water, one cause of malaise often goes unnoticed: carbon monoxide poisoning. Generators, stoves and combustion pumps used in closed spaces to dry houses or generate power produce a gas with no smell and no color, and the risk changes with the phase: generators and stoves during the power outage, pumps and dryers during cleanup, and damaged boilers or heaters months later (Waite et al., 2014). Headache, dizziness, nausea and confusion in several people in the same house are a strong clue. The question "what are you using to generate power or heat the house?" takes a few seconds and can change the approach.

Electric shocks during cleanup, falls, cuts and intense physical exertion in people with heart disease complete the list for the first days. For those providing care, the cleanup phase matters as much as the event itself.

The example of leptospirosis

Leptospirosis has an incubation period of a few days to a few weeks, so cases usually appear after the water recedes, in the cleanup phase. Haake and Levett describe the disease as a zoonosis in which human infection happens through contact with water or soil contaminated by animal urine, especially rodent urine (Haake and Levett, 2015). The review by Costa et al. estimated the global burden of the disease and showed that it is concentrated in tropical regions and among poor populations (Costa et al., 2015).

Fever after the water: leptospirosis in the differential

The scene of the forty-year-old man with fever, calf pain and red eyes is the center of this text. Haake and Levett describe the typical presentation of leptospirosis as an acute febrile illness with headache and muscle pain, and they call attention to conjunctival suffusion and calf pain as suggestive findings (Haake and Levett, 2015). Most cases are mild, but a portion progress to severe forms.

Signs of severity

Severe forms include the combination of jaundice, acute kidney injury and bleeding, known as Weil's disease, and pulmonary hemorrhage syndrome, which can progress quickly (Haake and Levett, 2015). For clinical reasoning, some findings change the urgency: shortness of breath or blood-streaked sputum, low urine output, jaundice, hypotension, bleeding and altered mental status. The presence of any of them calls for immediate assessment and follows the service protocol.

The differential that remains open

Leptospirosis shares space with other causes of fever that depend on the region: dengue and other arboviruses, malaria, typhoid fever, viral hepatitis and the common bacterial infections of any season. The question is not "is it leptospirosis or not", but "which hypotheses does this history make more likely and which need to be ruled out first". The post about differential diagnosis shows how to train this list with progressive clues.

• Was there contact with flood water or mud, and how many days ago?
• Does the person have skin wounds, did they walk barefoot or have prolonged contact with the water?
• Is there calf pain, red eyes, jaundice or low urine output?
• Which other fevers circulate in the region at this time of year?
• Are there signs of severity that call for immediate assessment?

Treatment and uncertainty

The Cochrane review on antibiotics for leptospirosis concluded that the evidence is insufficient to recommend or reject the use of antibiotics in the disease, with small, low-quality studies (Brett-Major and Coldren, 2012). In practice, the decision follows local protocols, which usually advise starting treatment early when there is clinical suspicion. The point for reasoning is to recognize that part of the management rests on consensus and experience, and that a well-founded suspicion weighs heavily in the decision.

Prophylaxis: what the evidence supports

In some places, antibiotic prophylaxis for leptospirosis is discussed for people with intense exposure. The Cochrane review by Win and colleagues concluded that the certainty of the evidence is low or very low and that the available data are insufficient to definitively support the use of antibiotics for prevention (Win and colleagues, 2024). The decision rests with health authorities and local protocols. For clinical reasoning, the point is that prophylaxis, when used, complements clinical suspicion and the advice to seek care in case of fever.

Advising those who will return to the cleanup

Many people seen with mild fever or with wounds go back to the mud the next day. Discharge advice is part of clinical reasoning: wear boots and gloves when possible, cover wounds, wash the skin after contact with the water and seek care at the first sign of fever, even if it seems like a cold. Explaining why fever matters helps the person come back in time. The sentence "if you have fever in the coming weeks, mention that you were in the flood" is simple and can shorten the path to diagnosis at another service.

Wounds and floodwater

The woman with the cut on her foot represents one of the most common complaints after a flood. The water carries soil, sewage and construction debris, and wounds can become infected with the usual skin bacteria and also with less common microorganisms. Baker-Austin and colleagues reviewed Vibrio infections and describe severe wound infections associated with exposure to warm, brackish water, with higher risk in people with liver disease, immunosuppression or other chronic conditions (Baker-Austin and colleagues, 2018).

What to look for in the wound

For clinical reasoning, a wound exposed to floodwater calls for three questions. What was the exposure: fresh, brackish or salt water, and for how long? How is the wound: clean, contaminated, with a foreign body or with signs of deep infection? Who is the person: do they have diabetes, liver disease, immunosuppression or another condition that raises the risk of severe infection? Disproportionate pain, rapid worsening, blisters or a change in skin color raise the hypothesis of necrotizing infection and call for immediate assessment.

Tetanus

The older man with the wound on his hand recalls the question that cannot be left out. Yen and Thwaites reviewed tetanus and describe a vaccine-preventable disease that still occurs where vaccine coverage is incomplete, transmitted through wounds contaminated with spores present in the soil (Yen and Thwaites, 2019). Checking vaccination status and indicating prophylaxis according to the protocol is part of the care of any wound after a flood. Older adults and people with no vaccination record deserve special attention.

Diarrhea, water and shelters

The child with diarrhea recalls that the risk of waterborne diseases depends on what happens after the flood. Watson, Gayer and Connolly reviewed epidemics after natural disasters and showed that the risk of an outbreak is linked mainly to population displacement, the lack of safe water and sanitation and the conditions of shelters, more than to the disaster itself (Watson and colleagues, 2007).

For clinical reasoning, this changes the questions in the history. Where is the family living now? Where does the drinking water come from? Are there other cases in the same shelter? The answer guides both individual care and the alert to health surveillance. In young children and older adults, the immediate focus is hydration and recognition of signs of dehydration.

When the case is a matter for surveillance

An isolated case of diarrhea calls for individual care. Several cases in the same shelter, on the same street or linked to the same water source also call for rapid communication with health surveillance. Watson and colleagues show that rapid outbreak detection depends on surveillance systems working in the period after the disaster (Watson and colleagues, 2007). For those providing care, recording where the person is and the water source they consumed makes each consultation a clue for the public health team.

The same reasoning applies to fevers. A rise in fever cases with muscle pain in a specific area may indicate a cluster of leptospirosis cases, and a rise in fever with spots may indicate another disease in circulation. The baseline rate changes over the weeks, and those providing care need to update their own estimate with this information. The post on baseline rate in diagnosis explains why the local frequency of the disease weighs so heavily in interpreting each case.

Respiratory and skin diseases in shelters

Crowded shelters favor respiratory infections, conjunctivitis and skin diseases. Mold in homes that were flooded can worsen asthma and other respiratory diseases when families return. These complaints are common and, in most cases, mild, but they call for the same reasoning as always: recognize the expected picture and look for what does not fit.

When the flood hides another diagnosis

In the week after the flood, the explanation "it was the water" is available for almost any fever or malaise. That availability is the problem. The flood does not change the frequency of pneumonia, urinary infection, appendicitis or meningitis, and people with chronic diseases may arrive decompensated because they lost medications, appointments and dialysis.

Graber, Franklin and Gordon studied diagnostic errors in internal medicine and showed that premature closure, accepting a diagnosis before considering the alternatives, was the most frequent cognitive error (Graber and colleagues, 2005). In a flood scenario, premature closure often has a name: leptospirosis for every fever, gastroenteritis for every abdominal pain, stress for every vague complaint.

Interrupted chronic diseases

The person with diabetes who lost their insulin in the flood, the person on dialysis who could not get to the session and the person with mental illness who was left without medication are expected cases in the following weeks. Asking what the person was using before the flood and what they managed to keep is part of the care. The post on signs, symptoms and history helps organize this conversation.

Mental health

Alderman and colleagues note that the mental health effects after a flood can persist for years after the flood (Alderman and colleagues, 2012). Insomnia, anxiety, grief and symptoms of post-traumatic stress appear frequently. Recognizing these pictures, asking directly and offering referral is part of clinical reasoning after the disaster.

The biases of the flood scenario

The week after the flood brings together excess demand, tired teams, a lack of tests and a ready explanation for almost everything. Pat Croskerry describes the most frequent cognitive errors in diagnosis and proposes metacognition, stopping and examining one's own reasoning, as the main way to reduce them (Croskerry, 2003).

The first bias is attribution to context, when the flood becomes a universal explanation. The second is anchoring on the first hypothesis, which leads the team to treat every fever as leptospirosis and stop investigating dengue, malaria or pneumonia. The third is availability bias, which gives excessive weight to the severe case seen the day before. A simple way to reduce them is the diagnostic pause before each discharge: what else could it be, what does not fit, what would I do if there had been no flood. The post on diagnostic pause describes the method, and the post on diagnostic uncertainty brings strategies for deciding without all the tests.

How NEXO helps train this reasoning

In NEXO, the case of the day is fictional, with a real clinical presentation and up to six progressive clues. You propose a diagnosis by looking for the ICD-10 code and receive feedback on proximity in five levels, which shows whether your guess landed on the exact code, the same category, the same group, the same chapter or a different chapter. This format connects with the theme of this text: when the exposure clue points to an infectious disease, the feedback shows whether you stayed in the right chapter or anchored too early.

To use the case of the day as training, try three habits. Before each guess, write down how many days have passed since the exposure and what that makes more likely. When a clue seems to explain everything, ask which common cause it leaves out. After the result, note which clue you overvalued.

Three exercises with cases

Sort by time. In cases with environmental exposure, write the time since exposure and the hypotheses that fit that window.

Open the chapter. In each fever case, write one infectious hypothesis linked to the context and one common one from any time.

Remember the chronic. In disaster cases, ask which underlying disease may have decompensated from lack of treatment.

The post about case-based learning in clinical practice shows why training with cases helps fix this type of decision.

The limits on using the game are described on the NEXO economy page. If you research the teaching of clinical reasoning, the page for researchers explains how to get in touch. Professionals who write or review cases find information on curation and creators, and institutions can learn about the proposal on the partnerships page.

Frequently asked questions

When should you think of leptospirosis after a flood?

In acute fever with muscle pain, especially in the calves, in someone who had contact with flood water or mud in the previous days or weeks. Red eyes, jaundice and low urine output reinforce the hypothesis and may indicate severity.

Which signs call for immediate care?

Shortness of breath, blood in sputum, low urine output, jaundice, bleeding, low blood pressure and altered mental state. In wounds, pain out of proportion, rapid worsening, blisters or a change in skin color also call for immediate assessment.

What should be done with a wound exposed to flood water?

Assess the wound, clean it according to the service protocol, check tetanus vaccination status and give guidance on signs of infection. People with diabetes, liver disease or immunosuppression deserve closer monitoring.

Is prophylaxis against leptospirosis recommended for everyone?

Decisions about prophylaxis rest with health authorities and local protocols. The most recent Cochrane review considers the evidence to be of low certainty. For everyone exposed, the central guidance is to seek care in case of fever.

Why does diarrhea increase after some floods?

Because the risk of an outbreak follows the displacement of people, the lack of safe water and sanitation and the conditions in shelters. Asking where the family is staying and where the water comes from helps individual care and surveillance.

What should you remember beyond infections?

Chronic diseases left untreated, carbon monoxide poisoning from generators and mental health. All of them appear in the following weeks and call for direct questions.

Final checklist

• I asked about contact with water or mud, protection used and days since exposure.
• I considered leptospirosis in fever with muscle pain and looked for signs of severity.
• I kept fevers from the region and common infections from any time in the differential.
• I assessed wounds, the patient's risk factors and tetanus vaccination status.
• I asked about water consumed, shelter and other nearby cases in diarrhea.
• I reviewed chronic diseases, interrupted medication and mental health before discharge.

Want to practice reasoning with progressive clues? Play the case of the day.

References

1. Alderman K, Turner LR, Tong S. Floods and human health: a systematic review. Environ Int. 2012. PMID 22750033.
2. Baker-Austin C, Oliver JD, Alam M, et al. Vibrio spp. infections. Nat Rev Dis Primers. 2018. PMID 30002421.
3. Brett-Major DM, Coldren R. Antibiotics for leptospirosis. Cochrane Database Syst Rev. 2012. PMID 22336839.
4. Costa F, Hagan JE, Calcagno J, et al. Global Morbidity and Mortality of Leptospirosis: A Systematic Review. PLoS Negl Trop Dis. 2015. PMID 26379143.
5. Croskerry P. The importance of cognitive errors in diagnosis and strategies to minimize them. Acad Med. 2003. PMID 12915363.
6. Graber ML, Franklin N, Gordon R. Diagnostic error in internal medicine. Arch Intern Med. 2005. PMID 16009864.
7. Haake DA, Levett PN. Leptospirosis in humans. Curr Top Microbiol Immunol. 2015. PMID 25388133.
8. Paterson DL, Wright H, Harris PNA. Health Risks of Flood Disasters. Clin Infect Dis. 2018. PMID 30986298.
9. Waite T, Murray V, Baker D. Carbon monoxide poisoning and flooding: changes in risk before, during and after flooding require appropriate public health interventions. PLoS Curr. 2014. PMID 25045587.
10. Watson JT, Gayer M, Connolly MA. Epidemics after natural disasters. Emerg Infect Dis. 2007. PMID 17370508.
11. Win TZ, Perinpanathan T, Mukadi P, et al. Antibiotic prophylaxis for leptospirosis. Cochrane Database Syst Rev. 2024. PMID 38483067.
12. World Health Organization. Floods. who.int.
13. Yen LM, Thwaites CL. Tetanus. Lancet. 2019. PMID 30935736.