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AMR in the environment: extended learning
Calculating exposure in practice
Activity: Calculating exposure in practice
Let’s use ESBL-producing E. coli bacteria in water used for bathing as an example.
ESBL-producing E. coli is an Escherichia coli bacterium that produces Extended Spectrum Beta Lactamases (ESBLs), a group of enzymes capable of breaking down a broad spectrum of antibiotics, particularly penicillin and specific cephalosporins. ESBL-producing E. coli are very common in some countries, can be transmitted via water and can lead to difficult to treat urinary tract or other infections.
Imagine swimming in surface water contaminated with ESBL-producing E. coli. For one episode of recreational swimming, people are assumed to ingest some 30–50 ml of water. Supposing that the concentration of ESBL-producing E. coli was 2 CFU/L, what would the ingested dose of ESBL-producing E. coli be per year for someone swimming daily throughout the year?
Answer
The answer is up to 36 ESBL-producing E. coli per year.
Using the equation: D = c × V = 2 ESBL-producing E. coli per litre × 0.05 litre = 0.1 ESBL/day or 36 ESBL-producing E. coli per year if swimming daily throughout the year.
- D = c × V
- D = 2 ESBL-producing E. coli per litre × 0.05 litre
- D = 0.1 ESBL per day or 36 ESBL-producing E. coli per year if swimming daily throughout the year.
where:
- D = dose
- c = concentration of resistant bacterium/ARG in the compartment
- V = volume ingested or inhaled per time unit
Now that you understand the way to calculate the ingested dose, you can apply it to some real-world examples.
Thinking about your own lifestyle, try to estimate the quantity of water that you would ingest through bathing in surface water per year. Does this quantity differ much from the intake of other members of your family, or specific groups in your country? If so, suggest why this might be the case.
Discussion
Personal exposure can vary greatly depending on lifestyle. For example, if members of your family don’t swim at all, their exposure through this route could be negligible; that might be very different for smaller children who engage in water play, or in situations where suitable bathing water is nearby and used regularly. It can be difficult to capture such differences through a generic exposure assessment.
When you’ve tried this activity you should return to Section 3.1 of the course.
Wastewater treatment (part 1)
Activity: How effective are WWTPs?
You can now explore the scientific data that demonstrates the effectiveness of WWTPs. Study the following table and answer the questions below.
| Genes | WWTP | Concentration (copies/ml) in the influent | Concentration (copies/ml) in the effluent | References |
|---|---|---|---|---|
| sul1 | WWTP1 | 3 × 107 | 5 × 105 | Mao et al., 2015 |
| WWTP2 | 9 × 106 | 6 × 105 | Mao et al., 2015 | |
| WWTP3 | 1.19 × 108 | 4.52 × 106 | Zhang et al., 2017 |
- The sul1 gene confers resistance to sulfonamides. Does the treatment in the WWTP reduce or increase the concentrations of sul1?
- The removal efficiency of the treatment can be defined as:
-
where
influent is the raw wastewater before treatment in a WWTP and effluent is the wastewater after treatment in a WWTP, emitted to the environment.Using the equation, calculate the removal efficiency for sul1 in WWTPs 1–3.
- Which of the WWTPs shows the most effective treatment?
Answer
- The treatment reduces the concentration of sul1 at all three WWTP.
- The removal efficiencies for each plant are:
- WWTP1: efficiency = (3 × 107 – 5 × 105) / 3 × 107 = 2.95 × 107 / 3 × 107) = 0.98 or 98%
- WWTP2: efficiency = (9 × 106 – 6 × 105) / 9 × 106 = 8.4 × 106 / 9 × 106) = 0.93 or 93%
- WWTP3: efficiency = (1.19 × 108 – 4.52 × 106) / 1.19 × 108 = 1.14 × 108 / 1.19 × 108) = 0.96 or 96%
The first plant is most effective, with 98% removal. However, while a large proportion of the resistance gene is removed, there is still considerable discharge of this resistance gene with the effluent.
Removal efficiencies are often expressed on a log scale:
- Removal efficiency (log scale) = log10 (concentration in influent / concentration in effluent)
- So for WWTP1:
- removal efficiency (log scale) = log10 (3 × 107 / 5 × 105) = 1.78
- That is, removal is nearly 2 orders of magnitude.
When you’ve tried this activity you should return to Section 3.2 of the course.
Wastewater treatment (part 2)
Activity : Waste treatment in your country
Follow the steps below to investigate the sanitation data (that is, the human waste and sewage disposal routes) for your country and discover the most prevalent method of sanitation.
- Go to the data page on the WHO/ UNICEF Joint Monitoring Programme for Water Supply, Sanitation and Hygiene’s website (JMP, n.d.).
- Change the top menu from ‘World’ to ‘Country’ and select your own country from the list. If you can’t find your own country, select a country that interests you.
- Select ‘View data table’, and choose ‘Sanitation’ as the measure and ‘Analyse by facility type’ as the ladder type. You will now see a table with different columns such as ‘Country’, ‘Residence type’ and ‘Year’.
- Find the largest ‘Coverage’ (this means the proportion of the population having access to this sanitation method).
- Is this coverage larger or smaller in urban areas compared to rural areas?
Discussion
This activity gives you practice at searching databases. The result you obtained depends on your particular setting, but in general coverage is often higher in urban than in rural settings.
When you’ve tried this activity you should return to Section 3.2 of the course.
Further examples of water surveillance
Activity: Further examples of water surveillance
Extended learning example 1: Drinking water monitoring in Ireland
The following extract summarises a study of AMR in drinking water from private wells in Ireland (Alawi et al., 2024). Read the extract and then answer the questions below.
In Europe, data on AMR in drinking water is scarce. In Ireland, as in many countries, household drinking water is supplied via mains, private wells or water schemes. We identified Irish private drinking water supplies as reservoirs of antimicrobial resistant bacteria (ARB), including both Gram-negative (n = 464) and Gram-positive (n = 72). For example, we isolated linezolid-resistant Enterococcus. Linezolid is a last-resort antibiotic used to treat vancomycin-resistant Enterococcus sp (VRE). Our work suggests that private drinking water is a potential sink and source of AMR pathogens.
This highlights a value of drinking water surveillance as the surveillance would provide information regarding the movement and persistence of ARB and ARGs that are able to survive in drinking water and subsequently have the opportunity to be mobilised through humans.
- What environmental compartment was studied?
- What was the main finding of the study?
Answer
- The environmental compartment was drinking water from private wells.
- The study found a significant level of contamination and AMR bacteria in the drinking water wells, showing possible contamination of private wells by human or animal faeces.
Extended learning example 2: Surveillance of antibiotics in wastewater in South Africa
Wastewater surveillance is used for monitoring resistant bacteria. It can also be used to generate information on antibiotic use in situations where there is limited data on quantities of antibiotics used.
A study in South Africa tested different antibiotics and their degradation products in wastewater from a WWTP and from an informal settlement, finding that the quantities of specific antibiotics measured in sewage exceeded the quantities that were expected based on existing prescription data (Holton et al., 2023). Incomplete data on prescriptions was put forward as one of the reasons for this difference, as well as other methodological difficulties such as estimates of the population size contributing to the wastewater samples and stability of the residues analysed.
Can you suggest another reason for the disparity?
Answer
It is also possible that antibiotics are purchased and used without prescriptions.
When you’ve tried this activity you should return to Section 7.2 of the course.
The place and time of sampling for environmental surveillance
The options for sampling sites, frequency and timing depend on the environmental compartment of interest. For all environmental compartments it is important to consider the parameters explored below.
Position with respect to the point of emission
Because many of the study objectives are related to measuring AMR from human activities or exposure to AMR in the environment, mapping the study area and identifying potential sources of contamination is vital for environmental studies. These emissions are a result of human activities such as:
- farming where antimicrobials are used
- factories that produce antimicrobials
- hospitals that take care of patients carrying AMR and residues
- surface water receiving treated or untreated sewage from abattoirs or wet markets.
-
What control could you consider including in your sampling of a potential contamination source?
-
A sample upstream of the prospective source of contamination (if a river is studied), or from a site not under the influence of the studied point source. This gives you a baseline to assess the level of hazardous emission.
Time of the day or year
Daily and yearly (seasonal) patterns can significantly influence the presence, spread and behaviour of AMR microbes in the environment. The main factors related to time of the day or year affecting these patterns are:
- temperature
- precipitation
- human and animal activity.
The following table summarises how each of these factors affects AMR dynamics.
| Factor | How it affects AMR dynamics |
|---|---|
| Temperature | Bacterial growth is affected by temperature: bacteria multiply faster in warmer temperatures. On the other hand, bacteria are also inactivated more quickly at higher temperatures. Time of the day and season exhibit different temperatures. |
| Precipitation | Rainfall, flooding or droughts. Excess water can overwhelm sewerage systems, causing release of polluted water. Droughts lessen water flows so limit the spread of water-borne resistance, but can also lead to higher concentrations of AMR bacteria due to a reduction of dilution by rainwater. Precipitation varies across seasons and regions. |
| Human and animal activity | Human and animal activity is not stable over time of the day or year but is clustered at times (e.g. mornings) or places (e.g. urban vs rural areas). Activity is a source of emission of AMR and/or residues. The more humans and animals are locally active the more faeces they produce. |
All these factors can either promote or limit the spread of AMR microbes. Understanding these variations in the area and time of study allows for more discriminating hypotheses to be formulated, and better planning of the surveillance. This knowledge also suggests which AMR indicators to assess and their potential prevalence. It also helps to identify high-risk periods/peaks.
Another important aspect to consider is that all these factors are being affected by climate change, both now and possibly more so in the future.
When you’ve read this section you should return to Section 9 of the course.
Metric and air sampling
Soil assessment
The metric for assessing contamination of soil is the number of bacteria or genes per gram of soil or per millilitre (in a dilution made of 1 gram of soil).
Soil is full of bacteria and can therefore be a complex compartment to measure. When sampling soil, it is imperative to pool soil subsamples to obtain a representative sample. Furthermore, because soil is often analysed to assess the role of fertilisation with animal manure, information on the state of fertilisation (such as the last fertilisation event or the type of manure) is needed.
Standardised soil sampling is described in ISO 18400-104:2018. Detection of AMR is often carried out using molecular techniques identifying ARGs.
Air assessment
The metric for assessing contamination of air is bacteria or genes per cubic metre (m3) air or per time collected.
Sampling air often takes considerable time to collect enough DNA or bacteria to be able to analyse in the lab. Air can be sampled actively with pumps or passively with dust collectors or agar settle plates that, when left uncovered, will be colonised by bacteria falling from the air.
During the hours of sampling, many litres of air or fresh settled dust will be sampled: this amount is needed to have enough bacteria or genes to measure.
When you’ve read this section you should return to Section 9.1 of the course.