Laboratory-based surveillance

Referral of patient specimens and bacterial isolates

ESR undertakes laboratory-based surveillance of communicable diseases and pathogens of public health importance. For this surveillance, diagnostic laboratories throughout New Zealand refer specimens or bacterial isolates to ESR's national reference laboratories for strain identification and epidemiological typing.

Patient specimens and bacterial isolates from the communicable diseases and pathogens listed below should be referred routinely by diagnostic laboratories to the relevant ESR laboratory for typing/surveillance purposes1.

Invasive Pathogens Laboratory,
Kenepuru Science Centre, Porirua
  • Bordetella pertussis (isolates currently for storage only)
  • Haemophilus influenzae from cases of invasive disease
  • Neisseria meningitidis from sterile sites, conjunctiva, throat swabs from cases of meningococcal disease (where this is the only isolate available)  and NAAT positive DNA specimens
  • Streptococcus pneumoniae from cases of invasive disease
  • Streptococcus pyogenes (group A streptococcus)- from cases of invasive and other serious disease e.g. glomerulonephritis, necrotising fasciitis, rheumatic fever and septic arthritis, or outbreaks of infection
Legionella Reference Laboratory,
Kenepuru Science Centre, Porirua
  • Legionella isolates
  • Respiratory specimens from confirmed legionellosis cases
  • Extracted DNA from NAT-confirmed legionellosis cases
  • Paired (acute and convalescent) serum
  • Convalescent serum specimens from legionellosis cases confirmed by NAAT and/or urinary antigen testing or specifically where requested by the Medical Officer of Health
Special Bacteriology Laboratory,
Kenepuru Science Centre, Porirua
  • Corynebacterium diphtheriae and C. ulcerans
  • Listeria monocytogenes from cases of invasive disease
Antibiotic Reference Laboratory,
Kenepuru Science Centre, Porirua 
  • Carbapenemase-producingEnterobacteriaceae
  • Neisseria gonorrhoeae with decreased susceptibility to ceftriaxone or azithromycin resistance
  • Penicillin non-susceptible Streptococcus pyogenes
  • Tetracycline-resistant methicillin-resistant S.aureus (for the surveillance of the livestock-associated CC398 clone)
  • Vancomycin non-susceptible, daptomycin non-susceptible or linezolid non-susceptible Staphylococcus aureus
  • Vancomycin resistant or linezolid non-susceptible Enterococcus faecium and E.faecalis 
  • Organisms with other critical  emerging resistance mechanisms
  • Multidrug-resistant organisms associated with outbreaks (following consultation with ESR)
Enteric, Environmental and Food Virology Laboratory,
Kenepuru Science Centre, Porirua
  • Hepatitis A – serum or plasma (and faecal specimens where possible) from IgM positive or NAT-confirmed  confirmed cases
  • Norovirus - faecal specimens from suspected norovirus outbreaks with a corresponding outbreak number assigned by the local Public Health Unit
  • Rotavirus – faecal specimens from screening test positive cases
Enteric Reference Laboratory,
National Centre for Biosecurity and Infectious Diseases, Wallaceville
  • Cronobacter sakazakii from sterile sites
  • Salmonella species, including S. Typhi and S. Paratyphi
  • Shigatoxin/verotoxin producing E.coli
  • Shigella species
  • Yersinia species
  • Vibrio cholerae, V. albensis and V. parahaemolyticus from sterile sites or cases of acute gastroenteritis.
Leptospira Reference Laboratory,
National Centre for Biosecurity and Infectious Diseases, Wallaceville  
  • Leptospira cultures
  • Leptospira IgM- positive serum specimens
  • Paired or convalescent serum specimens from suspected/confirmed leptospirosis cases
Clinical Virology Laboratory,
National Centre for Biosecurity and Infectious Diseases, Wallaceville  
  • Acute flaccid paralysis/Polio – faecal specimens from cases/suspected cases
  • Dengue - specimens from NAAT and NS1 antigen-confirmed cases
  • Middle East respiratory syndrome coronavirus (MERS-CoV) - respiratory specimens from suspected cases
  • Non-seasonal (novel) influenza strains (i.e. non influenza A H3, A H1pdm, or B) – respiratory specimens from cases/suspected cases
  • Severe acute respiratory syndrome coronavirus (SARS-CoV) – respiratory specimens from suspected cases 

 Please note:

  • Measles confirmatory NAAT and genotype testing is now performed by Canterbury Health Laboratories, Christchurch
  • Identification of fungi and aerobic actinomycetes is performed by the Mycology Reference Laboratory, LabPlus, Auckland

1 This does not include specimens for diagnostic testing, nor for requests on a fee for test basis

Read more about ESR’s health laboratories (external link) .