Airborne antibiotic-resistant ESKAPE bacteria detected at South African inner-city clinic

Researchers at the University of Johannesburg have identified antibiotic-resistant ESKAPE bacteria circulating in the air of a clinic situated in a densely populated inner-city area of South Africa. The team sampled the clinic's air, identified the bacteria present, and then tested how those bacteria survived exposure to a range of antibiotic medicines. Their findings, published in the peer-reviewed journal Indoor Air, show that a wide variety of dangerous ESKAPE bacteria from the clinic's air resist first-line drugs, that many are highly resistant to multiple first-line drugs, and that some already survive drugs of last resort — the medicines reserved for use when nothing else is effective.

The bacteria recovered from the clinic's air are capable of causing lower respiratory tract infections such as bronchitis, bronchiolitis and pneumonia, including community-acquired, hospital-acquired and ventilator-associated pneumonia. All of these infections can be fatal, because ESKAPE bacteria tend to be multidrug-resistant or even extensively drug-resistant. Dr Lee Heine, the lead author of the study and a researcher at the Water and Health Research Centre within the UJ Faculty of Health Sciences, explained that the high HIV and TB infection rates in South Africa increase the risk of lower respiratory tract infections caused by these bacteria.

If patients are already immunocompromised, the risk of death from pneumonia caused by a multidrug-resistant strain increases, because such bacteria are likely to spread to the bloodstream and cause sepsis. The Gram-negative bacteria analysed in the study included Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species and E. coli collected from the clinic. Among these Gram-negative organisms, the researchers found a highly concerning resistance to both first-line antibiotics and drugs of last resort.

Colistin, a toxic 'last defence' used only in critical situations where all other drugs have already failed, was survived by 80.5 percent of the Gram-negative bacteria from the clinic. Ertapenem and meropenem, members of the carbapenem class of advanced broad-spectrum antibiotics used only after first-line antibiotics fail, were survived by 31.2 percent and 26 percent of the Gram-negative bacteria respectively. Resistance to first-line treatments was even more widespread.

All of the Gram-negative bacteria showed resistance to at least one drug in three or more antibiotic categories. When exposed to cefuroxime, a common first-line treatment, 85.71 percent of the bacteria survived; with ceftazidime, 67.53 percent survived. All of these organisms were classified as multidrug-resistant (MDR) in the study.

More worrying still, 3.9 percent of the Gram-negative bacteria were classified as extensively drug resistant (XDR), meaning they survived at least one drug in all except one or two antibiotic categories. The study's findings on Methicillin-Resistant Staphylococcus aureus, better known as MRSA, were described as highly concerning. This bacterium can rapidly infect even intact skin and can easily be spread from person to person.

Dr Heine noted that worldwide, ten percent of people carry S. aureus in their nasal passages or armpits, and that healthcare workers identified as carriers need to be treated with appropriate antibiotics to clear the MRSA from their bodies before they are allowed to be in contact with patients again. In the clinic air samples, exposure to a variety of single drugs led to survival rates for this species ranging between 71.8 percent and 94.8 percent. Only vancomycin, a reserved or last-resort drug, was about 95 percent effective in killing the bacteria.

For this species, the multidrug-resistant rate was 6.3 percent and the extensively drug-resistant rate was 5.6 percent. The ESKAPE pathogens are grouped under this name because of their ability to 'escape' the activity of an increasing number of antibiotics. According to Dr Heine, these bacteria are very effective at causing infections and are specifically associated with infections contracted at hospitals and clinics.

Treating infection with antibiotics relies on an intact immune system: the body works with the antibiotics to eliminate bacteria, and without an intact immune system, treatment can be prolonged or unsuccessful. This is particularly relevant in South Africa, which has one of the highest rates of TB and HIV co-infection in the world, leaving many people vulnerable to lung infections and living with suppressed immune systems. The vulnerability of the South African population is underscored by national mortality statistics.

According to the September 2026 Stats SA mortality report, tuberculosis was the fourth leading cause of natural deaths among all age groups in South Africa in 2024, HIV-related diseases were fifth, and influenza and pneumonia combined ranked sixth. In a related study, Professor Tobias (TG) Barnard, Director of the UJ Water and Health Research Centre, and Dr Heine identified ESKAPE bacteria in the intensive care unit for newborn babies of a public hospital in the same city as the clinic. That study, published in Infection Prevention in Practice, involved collecting hundreds of surface swabs from incubators as well as handwash samples from nurses, doctors, cleaners and clerks working in the neonatal intensive care unit.

The clinic and the NICU examined in these studies are among the many medical facilities worldwide struggling to reduce the number of patients who fall ill with lower respiratory tract infections during their treatment. Antimicrobial resistance, or AMR, is the phenomenon in which bacteria are unaffected — not killed or neutralised — when exposed to the usual dose or concentration of antibiotic used to treat infection. Dr Heine stated that AMR is increasing for all bacteria in South Africa and globally, and that resistant bacteria thrive in hospital and clinic environments because the use of antibiotics and disinfectants selects for their reproduction over less resistant bacteria.

This selective pressure means that the very measures used to control infection can, over time, favour the survival of the hardiest organisms. A regulatory gap compounds the problem. Global guidelines for allowable numbers of bacteria, both pathogenic and non-pathogenic, exist for water quality, and comparable standards exist for surfaces in food preparation facilities and for surfaces in healthcare facilities.

However, there are no comparable standards for airborne bacteria and fungi in indoor environments. Given the increasing rate of bacterial resistance to antibiotics, Dr Heine argues that indoor quality standards for bacterial counts need to be established in South Africa. There are currently no stipulated allowable numbers of respiratory pathogens for a given volume of air, and she concludes that monitoring bacterial and fungal air quality should be mandatory in healthcare facilities, that medical facilities should adhere to infection prevention and control protocols at all times, and that routine air quality monitoring needs to be added to those protocols.

The study was funded by the University Research Council of the University of Johannesburg, and the authors declared no conflicts of interest.

Subject of Research: Airborne multidrug-resistant ESKAPE respiratory bacteria isolated from a South African inner-city clinic

Article Title: Airborne ESKAPE pathogens at inner-city clinic resist advanced antibiotics

Article References: Airborne ESKAPE pathogens at inner-city clinic resist advanced antibiotics. Original publication (Bibliographic details unavailable.)

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Keywords: antimicrobial resistance, ESKAPE pathogens, airborne bacteria, Johannesburg clinic, MRSA, colistin resistance, carbapenems, lower respiratory tract infections, South Africa, indoor air quality, neonatal intensive care, multidrug resistance