4 Identifying the key pathogens in global AMR surveillance

4.1 The thirteen key pathogens

Thirteen key bacterial pathogens in humans have been identified by the World Health Organization (WHO) as the focus of the GLASS surveillance programme for AMR (Table 3) (WHO, 2023). These are all pathogens that a hospital laboratory would normally be able to identify from one or more of four specimen types.

Table 3 WHO key pathogens for global AMR surveillance
Pathogen Gram reaction
Staphylococcus aureus Gram positive
Streptococcus pneumoniae
Acinetobacter species Gram negative
Escherichia coli
Haemophilus influenzae
Klebsiella pneumoniae
Neisseria gonorrhoeae
Neisseria meningitidis
Pseudomonas aeruginosa
Salmonella species (non-typhoidal)
Salmonella enterica serovar Typhi
Salmonella enterica serovar Paratyphi A
Shigella species

All of the GLASS target pathogens are listed on the WHO’s priority pathogen list (WHO, 2024). E. coli, K. pneumoniae and Acinetobacter all have globally widespread strains which are multi-drug resistant (MDR), even pan-resistant to antibiotics. Resistance can spread readily between the species and these organisms have proven capacity for outbreaks and spread between institutions. Such resistant strains are harder and more expensive to treat, wasting resources and posing a threat to modern medicine. For example, patients on chemotherapy need frequent antibiotics both for treatment and prophylaxis. If they encounter resistant organisms, then these patients have a high risk of dying from infection even if their cancer was curable.

Enteric pathogens like Salmonella and Shigella are of increasing AMR and public health importance. For Salmonella there are broadly two areas of concern: zoonotic infections causing diarrhoea, and sometimes invasive infection in patients with other infections such as HIV or malaria, and S. typhi and paratyphi causing enteric fever. For Shigella, these organisms are highly transmissible by the faeco-oral route, and AMR is a problem in areas with poor sanitation.

  • Why has N. gonorrhoeae been chosen out of all the pathogens causing sexually transmitted infection (STI) as a focus for surveillance?

  • Cephalosporin and/or fluorquinolone-resistant N. gonorrhoeae is listed as a high priority pathogen on the WHO’s priority pathogen list (WHO, 2024). Infection with N. gonorrhoeae leads to a lot of morbidity including pelvic inflammatory disease and infertility. Resistance is a big problem – especially to oral antibiotics. Some strains are already only sensitive to IV antibiotics, and untreatable strains are a becoming a possibility. N. gonorrhoeae can be cultured in a clinical laboratory whereas it is not possible to test the organisms that cause Chlamydia, Syphilis etc. for AMR. Resistance is, fortunately, less of an issue so far with these organisms.

Other GLASS target pathogens affect vulnerable populations; for example, H. influenzae, which can cause severe infections in children.

Activity 10: Usual isolation site of GLASS target pathogens

For each of the images below, can you identify the site you would expect them to be isolated from? Note: for some pathogens, there may be more than one site.

Click 'reveal discussion' to see the answer.

S. aureus tends to form grape-like clusters with each bacterium being up to 1 μm in diameter.

Which site or sites in the body is S. aureus isolated from?

Discussion

S. aureus is a common cause of infection in the community and of healthcare associated infection (HCAI). Sepsis or bloodstream infection mostly starts from an infective focus such as a wound, infected IV line or osteomyelitis. S. aureus can also cause skin and soft tissue infections such as boils and abscesses. MRSA strains of S. aureus are a particular threat in healthcare settings. A significant percentage of people carry S. aureus asymptomatically in their nose and on the skin. It can lead to infection if the body’s defences are breached, for example by a wound or medical procedure.

For GLASS, S. aureus isolated from bloodstream and lower respiratory tract samples are the focus of interest.

S. pneumoniae usually forms pairs (diplococci) or occasionally short chains.

Which site or sites in the body is S. pneumoniae isolated from?

Discussion

S. pneumoniae is a common cause of pneumonia, meningitis and ear infections, as well as infections in HIV patients. It is typically isolated from bloodstream samples in severe infections. It can also be found in upper respiratory and surface swabs, sputum and CSF cultures.

GLASS surveillance focuses on bloodstream, CSF and lower respiratory tract infection isolates.

A. baumannii

Acinetobacter are gram-negative, coccobacillary-shaped bacteria. A. baumannii accounts for most Acinetobacter infections in humans and is the species of concern. However, identification to species level is technically challenging so many sites report as Acinetobacter species only.

Which site or sites in the body are Acinetobacter species isolated from?

Discussion

Acinetobacter are classic HCAI pathogens, for example affecting patients in intensive care, particularly with open wounds or on a ventilator. Acinetobacter are typically isolated from the bloodstream, wound swabs, sputum and rarely from urine.

For GLASS, bloodstream and lower respiratory tract isolates are the focus of interest.

E. coli is a typical rod-shaped, Gram-negative bacterium, about 2 µm long.

Which site or sites in the body is E. coli isolated from?

Discussion

E. coli is the most common cause of UTI and a leading cause of bloodstream infection. Some strains have specific virulence factors allowing them to infect the urinary tract (Sarowski et al., 2019). Different pathogenic strains of E. coli are a common cause of diarrhoeal disease, for example as a result of food poisoning. E. coli are also a common cause of intra-abdominal infections such as Cholecystitis.

E. coli is typically isolated from bloodstream and urine. They can also be isolated from stools, but this requires special techniques to distinguish the pathogenic strains from commensal E. coli which is prevalent in the gut.

For GLASS, isolates from bloodstream and urine are the focus of interest.

K. pneumoniae is a typical rod-shaped, Gram-negative bacterium about 2 µm long.

Which site or sites in the body is K. pneumoniae isolated from?

Discussion

K. pneumoniae is a common cause of HCAI including UTI, pneumonia, and bloodstream and wound infections.

K. pneumoniae is typically isolated from bloodstream and urine samples and GLASS focuses on these as well as lower respiratory tract specimens. It can also be found in swabs and sputum samples, but it is harder to be sure it is acting as a pathogen rather than colonising these sites.

N. gonorrhoeae forms Gram-negative diplococci, 0.6–1 μm in diameter.

Which site or sites in the body is N. gonorrhoeae isolated from?

Discussion

N. gonorrhoeae causes the STI gonorrhoea and is commonly isolated from genital samples, and occasionally bloodstream samples in cases of disseminated infection.

For GLASS, N. gonorrhoeae isolated from genital samples are the focus.

S. typhimurium is an example of Salmonella species. Salmonella are Gram-negative, rod-shaped bacteria about 1–3 µm in length.

Which site or sites in the body are Salmonella species isolated from?

Discussion

Enteric fever is caused by S. typhi/paratyphi with the other non-typhoidal strains causing diarrhoeal disease. Enteric fever strains only affect humans, but the other strains can also be transmitted via animals and animal products. This is important in the One Health context.

For GLASS, Salmonella spp. (non-typhoidal) isolated from both stool and blood samples are the focus. For Salmonella enterica serovars blood samples are the focus.

Shigella are Gram-negative, rod-shaped bacteria typically 1–3 μm in length.

Which site or sites in the body are Shigella species isolated from?

Discussion

Shigella species cause diarrhoeal disease and cause significant morbidity in young children.

For GLASS, Shigella isolated from stool samples are the focus.

H. influenzae are gram-negative, coccobacillary-shaped bacteria

Which site or sites in the body is H. influenzae isolated from?

Discussion

H. influenzae can cause many different types of infections. These infections range from mild (ear infections in children) to serious (bloodstream infections). The most common serious infections caused by H. influenzae are pneumonia, bloodstream infections and meningitis.

For GLASS, H. influenzae isolated from CSF and the lower respiratory tract are the focus.

Neisseria meningitidis are Gram-negative diplococcus that looks like a kidney beans under a microscope

Which site or sites in the body is Neisseria meningitidis isolated from?

Discussion

Neisseria meningitidis cause meningococcal disease. The two most common types of meningococcal infections are meningitis and bloodstream infections.

For GLASS, Neisseria meningitidis isolated from blood and CSF are the focus.

P. aeruginosa are gram negative rod shaped bacteria

Which site or sites in the body is P. aeurginosa isolated from?

Discussion

P. aeruginosa can cause infections in the blood, lungs, urinary tract or other parts of the body after surgery. Patients in healthcare settings are at highest risk.

For GLASS, P. aeurginosa isolated from blood and the lower respiratory tract are the focus.

Your laboratory is almost certainly identifying other organisms than the ones listed in Activity 10. However, the focus of this course is on some of the issues around identifying the eight key GLASS pathogens under global AMR surveillance. Your laboratory should have comprehensive standard operating procedures (SOPs) for isolating and identifying these organisms. SOPs are unambiguous written instructions covering routine laboratory operations as well as the organisation and management of the laboratory. In the section that follows we discuss some important considerations about the identification of different types of bacteria.

3.3 Advanced testing

4.2 Identifying Gram-positive cocci