Appendix 4: Direct laboratory notification of communicable diseases flowcharts

Part of the Communicable Disease Control Manual

Appendix updated in April 2021. A description of changes can be found at Updates to the Communicable Disease Control Manual.


Contents

Section A – infectious diseases notifiable to a medical officer of health and local authority

Section B – infectious diseases notifiable to the medical officer of health

Section C – infectious diseases notifiable to the medical officer of health without identifying information of patient or deceased person

Diseases notifiable to the medical officer of health (other than notifiable infectious diseases)


Section A – infectious diseases notifiable to a medical officer of health and local authority

Campylobacteriosis

Updated 20 January 2020

Specimen: usually faeces, occasionally blood cultures, aspirated fluid or tissue Send for Antigen detectino (faeces), culture, NAAT. If reactive EIA, isolation of any Campylobacter species[1,2] or detection of Campylobacter nucleic acid, report to the medical officer of health. Click to enlarge

Notes:

  1. All species of Campylobacter should be notified. Diagnostic laboratories may choose to identify further than genus level but should refer isolates for confirmatory speciation to the Enteric Reference Laboratory at ESR.
  2. Please keep samples for two weeks in case culture is required for typing for public health purposes in an outbreak investigation.

Cholera1

Updated 20 January 2020

Specimen: usually faeces. Send for culture. If V. cholerae isolated[2], report to the medical officer of health and refer to the Enteric Reference laboratory at ESR for serotyping, toxin dection and confirmation. If Vibrio cholerae serogroup O1 or O139 and cholera toxin-producing, report to medical officer of health.

Notes:

  1. The notifiable condition is disease due to toxin-producing Vibrio cholerae O1 or O139.
  2. Vibrio should be identified to the species level.

Cryptosporidiosis

Updated 20 January 2020

Specimen: usually faeces, occasionally duodenal, ileal or bilary biopsies. Send for microscopy, direct fluorescence using monoclonal antibodies or rapid antigen test or enzyme immoassay, NAAT. If Cryptosporidium, Cryptosporidum antigen or Cryptosporidium nucleic acid detected, report to the medical officer of health. Click to enlarge

Giardiasis

Updated 20 January 2020

Specimen: usually faeces, occasionally duodenal aspirate. Send for microscopy, direct fluorescence using monoclonal antibodies or rapid antigen test or enzyme immoassay, NAAT. If Giardia cysts or trophozoites, Giardia antigen or Giardia nucleic acid detected, report to the medical officer of health. Click to enlarge

Hepatitis A

Updated 20 January 2020

Specimen: serum for antibody detection or NAAT, faeces for NAAT. Send for serology, NAAT. If anti-HAV IgM[1,2] detected and/or seroconversion between paired sera testing in the same laboratory [1,2] for serology, or detection of HAV nucleic acid[2] for NAAT, report result to the medical officer of health. Click to enlarge

Notes:

  1. In the absence of HAV vaccination in the preceding 12 weeks.
  2. Patient serum and/or faecal specimens (preferably both) should be sent to Specimen Reception at ESR Kenepuru Science Centre, Porirua for HAV genotyping by the ESR Enteric, Environmental and Food Virology Laboratory.

Legionellosis

Updated 20 January 2020

Specimen [1]: usually lower respiratory tract samples for NAAT with or without culture; occasionally aspirated fluid, tissue for NAAT with or without culture; urine for antigen detection, serum for antibody dection. Send for culture, urinary antigen assay, serology (acute and convalescent); NAAT. If isolation of Legionella on culture, report result to the medical officer of health and refer isolates to the Legionella Reference Lab, ESR, for speciation, sero-grouping with or without typing[4]. If detection of L. pneumophilia serogroup 1 antigen or L. longbeachae antigen[2] on urinary antigen assay, report result to the medical officer of health and if feasible obtain lower respiratory tract sample for NAAT and culture. If, on serology, seroconversion or 4-fold or greater increase in titre to specific species or serogroups or to multiple species between paired sera tested at the same laboratory or elevated Legionella species serology titres of 512 or greater[3], report result to the medical officer of health and refer to sera to the Legionella Reference Lab, ESR for single antigen testing[4]. If feasible, obtain lower respiratory tract sample for NAAT and culture, urine for antigen testing. If detection of Legionella nucleic acid on NAAT (amplification produce should be further characterised to attempt speciation), report result to the medical officer of health and attempt culture on lower respiratory tract sample. Click to enlarge

Notes:

  1. Improved PPV obtained by using more than one test type.
  2. Validated tests only.
  3. One or more elevated Legionella species serology titres of ≥ 512 tested using pooled antigen at a reference laboratory is considered suggestive evidence for probable case.
  4. Legionella Reference Lab, ESR, should report all results.

Listeriosis

Updated 20 January 2020

Specimen: blood, CSF, apirated fluid, tissue (eg, placenta, amniotic fluid); foetal gastrointestinal contents, foetal body swab. Send for culture, NAAT. If Listeria monocytogenes isolated on culture, report result to the medical officer of health and refer to the Special Bacterial Laboratory, ESR for further characterisation, and report that result to the medical officer of health. If Listeria monocytogenes nucleic acid detected on NAAT, report result to the medical officer of health and also send for culture.

Meningoencephalitis – primary amoebic

Updated 10 February 2021

Specimen: CSF for microscopy, culture or NAAT; brain tissue, usually post-mortem, for microscopy, immunofluorescent antibody stain or NAAT. Send for microscopy, amoebic culture, NAAT[2]. If directional movement of Naegleria flowleri in CSF, refer CSF, fresh brain tissue or histological sample to international referene laboratory for culture, immunofluorescent stains and NAAT[1], and report to the medical officer of health. If stained CSF smear or brain tissue histology, refer to the medical officer of health. If Naegleria fowleri trophozoites (+/- cysts from culture) detected on culture, report to the medical officer of health and sent for NAAT. If Naegleria fowleri nucleic acid detected on NAAT, report to the medical officer of health.

Notes:

  1. For further information on referring samples refer to the CDC website.
  2. NAAT testing is not available in New Zealand but samples can be sent to Australia. Discuss laboratory testing with the Institute of Environmental Science and Research (ESR).

Salmonellosis, typhoid and paratyphoid fever

Updated 20 January 2020

Specimen[1]: usually faeces; blood cultures, other sterile site specimen, urine. Send for culture, NAAT. If isolation of any Salmonella species on culture, refer to the Enteric Reference Lab, ESR for further characterisation, and report result to the medical officer of health once genus confirmed[2]. If detection of Salmonella nucleic acid on culture, notify and attempt to isolate Salmonella by culture, report result to the medical officer of health. Click to enlarge

Notes:

  1. Salmonella serology may provide evidence of past infection but is not useful for diagnosis of acute illness. Requests for Salmonella serology should be replaced by blood cultures if the patient has a febrile illness.
  2. Salmonella Paratyphi B var Java infections should still be notified as Salmonella cases rather than cases of Paratyphi.

Shigellosis

Updated 20 January 2020

Specimen: usually faeces; rarely isolated from blood cultures, other sterile site specimin, vaginal swabs. Send for culture, NAAT[1]. If any Shieglla species isolate on culture, report result to medical officer of health and refer isolates to the Enteric Reference Lab, ESR for further characterisation, and report that result to medical officer of health. If detection of Shigella/EIEC nucleic acid on NAAT, report result to medical officer of health and attempt to isolate Shigella by culture. Click to enlarge

Note:

  1. While NAAT may be used for screening, a positive NAAT does not meet the criteria for laboratory confirmation.

Yersiniosis

Updated 20 January 2020

Specimin: usually faeces, occasionally blood cultures, other streile site. Send for culture and NAAT. If Yersinia enterocolitica or Yersinia pseudotuberculosis isolated from culture, report result to the medical officer of health. All isolates must also be referred to the Enteric Reference Lab, ESR for further characterisation. If Yersinia nucleic acid detected by NAAT, notify to medical officer of health and also attempt to isolate Yersinia by culture. Click to enlarge


Section B – infectious diseases notifiable to the medical officer of health

Anthrax

Updated 4 February 2021

Click to enlarge

Arboviral infection other than yellow fever

Updated 4 February 2021

Click to enlarge

Note:

  1. Please e-notify results, including those done overseas.

Brucellosis

Updated 4 February 2021

Click to enlarge

Note:

  1. Consider the possibility of cross-reactivity.

Creutzfeldt-Jakob disease and other spongiform encephalopathies

Updated 4 February 2021

Cronobacter species (formerly Enterobacter sakazakii invasive disease) 

Updated 4 February 2021

Diphtheria

Updated 4 February 2021

Note: The diagnosis of diphtheria is primarily a clinical one. Tox-containing, nontoxigenic isolates have been described.

Haemophilus influenzae type b invasive disease

Updated 4 February 2021

Click to enlarge

Hepatitis B infection

Updated 4 February 2021

Specimen: serum for antigen or antibody detection. Send for serology. Report any of HBsAg positive in a <12 month old infant[1]; change from HBsAg neative to HBsAg positive within a 12 month period[1] (if testing performed at the same laboratory and cumulative history readily available within LIS); anti-HBcore IgM reactive (unless HBsAg positive >6 months ago and history readily available in laboratory information systems). Report result to the medical officer of health.

Note:

  1. Recent immunisation with HBV vaccine may also result in detectable HBsAg for a short period of time. Since laboratories do not necessarily have access to this information, all results consistent with possible Hepatitis B infection should be reported to the medical officer of health.

Hepatitis D

Updated 4 February 2021

Specimen from patient known to be HBV infected: serum for antibody detection or NAAT, liver biopsy for antigen detection. Send for serology, NAAT, antigen assay. If anti-HDV antibodies[1] detected on serology, report result to the medical officer of health. If HDV detected on NAAT, report result to the medical officer of health. If HDV antigen in liver biopsy by monoclonal antibody detected on antigen assay, report result to the medical officer of health.

Note:

  1. Report all positive antibody results so the medical officer of health can ensure that follow up testing is performed.

Hepatitis E

Updated 4 February 2021

Specimen: serum for antibody and/or NAAT, faeces for NAAT. Send for serology, NAAT. If anti-HEV antibodies[1,2] detected on serology, report result to the medical officer of health. If HEV nucleic acid detected on NAAT, report result to the medical officer of health. Click to enlarge

Notes:

  1. A positive IgM alone should be confirmed by either anti-HEV IgG or total antibodies or NAAT testing.
  2. Report all positive antibody results so the medical officer of health can ensure that follow up testing is performed.

Highly pathogenic avian influenza or non-seasonal influenza

Updated 4 February 2021

Click to enlarge

Note:

  1. Or other novel subtype of influenza A.

Hydatid disease

Updated 4 February 2021

Specimen: usually serum for antibody detection, cyst fluid for microscopy. Send for direct microscopy, serology. If Echinococcus scolices or hooklets detected on direct microscopy, report result to the medical officer of health. If Echinococcus antibodies detected on serology, report result to the medical officer of health. Click to enlarge

Leprosy

Updated 4 February 2021

Click to enlarge

Note:

  1. Where confirmed by sequencing or validated species-specific PCR.

Leptospirosis

Updated 4 February 2021

Click to enlarge

Malaria

Updated 4 February 2021

Click to enlarge

Note:

  1. Microscopy of P. knowlesi may resemble P. malariae or P. falciparum. If the patient has travelled to SE Asia or has severe malaria and has been diagnosed with P. malariae or P. falciparum, further testing by NAAT may be needed to confirm/exclude P. knowlesi.
  2. If possible, this result should be confirmed by microscopy or NAAT.

Measles

Updated 4 February 2021

Specimen: serum for antibody detection; nasopharyngeal/throat swab or aspirate, urine or blood for NAAT. Send for serology[1], NAAT[1]. If anti-measles IgM detected +/or seroconversion or significant increase in anti-measles IgG etected between paired sera tested at the same laboratory, report result to the medical officer of health. If measles virus nucleic acid detected on NAAT, report result to the medical officer of health. Click to enlarge

Note:

  1. Recent immunisation with MMR may also result in detectable anti-measles IgM, a significant increase in anti-measles IgG or a positive NAAT. Since laboratories do not necessarily have access to this information, all results consistent with possible measles infection should be reported to the medical officer of health. Further testing for vaccine strain will be arranged by the medical officer of health when appropriate.

Mumps

Updated 4 February 2021

Specimen: buccal/oral/saliva swab (taken from Stensen's duct following 30 seconds massage of parotid gland area), urine, CSF, seminal fluid. Send for culture, NAAT[1]. If mumps virus isolated on culture, report result to the medical officer of health. If mumps nucleic acid detected on NAAT, report result to the medical officer of health. Click to enlarge

Note:

  1. Recent immunisation with MMR may also result in a positive NAAT. Since laboratories do not necessarily have access to this information, all results consistent with possible mumps infection should be reported to the medical officer of health.  Further testing for vaccine strain will be arranged by the medical officer of health when appropriate.

Neisseria meningitidis invasive disease

Updated 4 February 2021

Specimen: blood, CSF[1], aspirated fluid, tissue; conjunctival swab[2]; throat swab (or other respiratory sample)[3]. Send for CSF microscopy, culture, NAAT. If gram-negative diplococci[1] detected on microscopy, report result to the medical officer of health. If Neisseria meningitidis[4,5] detected on culture, report result to the medical officer of health. If Neisseria meningitidis nucleic acid detected from sterile site, report result to the medical officer of health. Additionally all isolates or amplification products should be referred to the Invasive Pathogens Lab, ESR for further characterisation and result reported to the medical officer of health. Click to enlarge

Notes:

  1. Arrange for NAAT testing on CSF if cultures are sterile, so that amplification product can be further characterised by NRL. 
  2. Meningococcal conjunctivitis should be notified to the medical officer of health because of the potential for invasive disease in contacts of the case.
  3. Only if clinical details provided of meningococcal disease. 
  4. Meningococci isolated from genital swabs are not associated with systemic disease (except for rare neonatal meningitis in babies born to colonised mothers) and need not be reported to the medical officer of health.  
  5. If the primary laboratory is able to distinguish serogroup, this information is useful for the local PHU when planning vaccination of contacts.

Pertussis

Updated 4 February 2021

Specimen: nasopharyngeal swab or aspirate for culture; respiratory sample (usually upper respiratory tract sample) for NAAT; serum. Send for serology[1], culture, NAAT. If Bordella pertussis toxin IgG test of >100 IU/mL or significant increase in antibody levels between paired sera tested at the same laboratory on serology, report result to the medical officer of health. If Bordetella pertussis isolated on culture, report result to the medical officer of health. All isolates should be referred to the Invasive Pathogens Lab, ESR for storage and future characterisation, and result reported. If IS481 (Bordetella species) or Bordetella pertussis specifc nucleic acid detected on NAAT, report result to the medical officer of health. Click to enlarge

Note:

  1. Serology should only be requested after consultation between the medical officer of health and the microbiologist.

Plague

Updated 4 February 2021

Specimen: may include blood culture, aspirated bubo, CSF, respiratory tract samples. Send for culture, NAAT. If Yersinia pestis or non-lactose fermenting GNB that has pinpoint colonies after 24 hours on blood or MacConkey and is catalase positive, oxidase, indole and urease negative are isolated on culture, report result to the medical officer of health. If Yersinia pestis target genes detected on NAAT, report result to the medical officer of health. Additionally, all isoaltes/positive detections should be referred to the Enteric Reference Lab, ESR, for referral for further characterisation and result reported to the medical officer of health. Click to enlarge

Poliomyelitis

Updated 4 February 2021

Specimen from all AFP cases: usually faeces and throat swab for culture; faeces, CSF, nasopharyngeal swab or EDTA blood for PCR. Refer specimen to Virus Identification Reference Laboratory, ESR for culture, send for NAAT. If poliovirus isolated on culture, report result to the medical officer of health. Type to confirm wildtype or vaccine-associated poliovirus, and report result. If enterovirus PCR positive[1], original sample referred to the Virus Identification Laboratory, ESR. If typed as poliovirus, report result to the medical officer of health. Confirm if wildtype or vaccine-associated poliovirus and report result. Click to enlarge

Note:

  1. Enteroviral PCR performed on CSF, faeces or respiratory samples may detect an enterovirus potentially including poliovirus. Unless PCR amplification product has been further characterised because of the clinical scenario, positive enterovirus PCR results need to be notified to the medical officer of health.

Rabies and other lyssaviruses

Updated 4 February 2021

Specimen: saliva, CSF, tissue (eg, brain or nuchal biopsy) for culture and NAAT). Send for culture, NAAT. If lyssavirus isolated on culture, report result to the medical officer of health. If lyssavirus nuleic acid detected on NAAT, report result to the medical officer of health. Click to enlarge

Rheumatic fever

Updated 4 February 2021

The diagnosis is clinical.

Detection of pharyngeal S. pyogenes or changing streptococcal serology does not make the diagnosis.

No action is required for laboratories.

Tetanus

Updated 4 February 2021

The diagnosis is clinical. 

Neither culture of the organism nor presence of antibodies to the toxin is proof of disease. 

No action is required for laboratories.

Tuberculosis, active (new case, reactivation)

Updated 4 February 2021

Specimen: usually respiratory sample, aspirated fluid, tissue, CSF; occassionally urine. Send for direct microscopy (histology or microbial sample), histology, culture, NAAT. If acid-fast bacilli[1] detected on microscopy, report result to the medical officer of health. If histology suggestive of tuberculosis, eg, necrotising granulomatous inflammationp1[, report result to the medical officer of health, send for direct microscopy and cultures. If M. tuberculosis isolated on cultures, report result to the medical officer of health and all isolates should be referred to LabPLUS for genotyping and result reported. If M. tuberculosis complex[1] detected on NAAT, report result to medical officer of health and all isolates should be referred to LabPLUS for genotyping and result reported. Click to enlarge

Note:

  1. Samples should be collected for mycobacterial culture, if not already done.

Latent tuberculosis 

Latent tuberculosis (LTBI) is only reported when there is a decision to treat, and with permission of the case. Therefore, no action is required by laboratories.

Verocytotoxin- or Shiga toxin-producing Escherichia coli (VTEC/STEC)

Updated 4 February 2021

Specimen: usually faeces, occasionally blood cultures. Send for culture, NAAT. If shiga-toxin producing E. coli isolated on culture, report result to the medical officer of health. All isolates should be referred to the Enteric Reference Lab, ESR for further characterisation, and report result to the medical officer of health. If PCR detection of the genes (stx1 and/or stx2) associated with the production of shiga toxin in E. coli on NAAT, report result to the medical officer of health and send for culture.


Section C – infectious diseases notifiable to the medical officer of health without identifying information of patient or deceased person

Acquired immunodeficiency syndrome (AIDS)

AIDS is a clinical syndrome. No action is required by laboratories.

Gonorrhoeal infection

Updated 18 January 2020

Specimen: first void urine; swab from vagina, cervix, uretha; swab from throat, rectum, conjunctiva[1]; blood culture, aspirated fluid, tissue. Send for NAAT[1] and culture. If N. gonorrhoeae DNA detected or N. gonorrhoeae isolated, report result to the medical officer of health. Click to enlarge

Note:

  1. It is recommended that culture negative, reactive NAAT results on specimens from extra-genital sites be confirmed by supplementary testing, using a different nucleic acid target, before reporting depending on the test method used.
  2. Given difficulties in the implementation of gonorrhoea and syphilis notification system, the reporting to medical officer do not yet apply to the laboratory notification process. Laboratories will be advised when this issue is solved.

Human immunodeficiency virus (HIV) infection

Updated 18 January 2020

Specimin: serum – serological testing; plasma – qualitative or quantitative NAAT. For adults and children over 18 months, sent for reactive HIV point of care test, for HIV antibody or p24 antigen/antibody screening EIA. If repeatedly reactive, sent for western blot assay or antibody differentiation immunoassay, and HIV NAAT[1]. If indeterminate or negative western blot/antibody differentiation immunoassay, refer HIV NAAT. If specific HIV-1 or HIV-2 antibodies detected on assay, or following HIV NAAT, report result to the medical officer of health[2]. For children under 18 months, send for HIV NAAT, if positive, confirm on second specimin from different date. Report result to the medical officer of health[2]. For both groups, reported results will then be passed on to the AEG to process. Click to enlarge

Notes:

  1. Whether positive or negative, the result of the first NAAT/viral load test performed must be notified for surveillance purposes. Subsequent new positive results on an individual for whom all previous results have been negative, also require notification. Subsequent results (positive or negative) on the same individual do not require notification. (Note: All subsequent results may be requested separately for other purposes, such as cascade of care monitoring, but this would not be done through the e-notification system.)
  2. Any known cases previously diagnosed in New Zealand and having a viral load test, will be filtered by the AEG.

Syphilis

Updated 18 January 2020

Specimins (all ages, including neonatal/infant/child): serum or CSF for serological testing; tissue specimin or body fluid, eg, placenta and umbilical cord, amniotic fluid, neonatal nasal discharge, CSF, mucocutaneous ulcers – genital or oral (NAAT, direct fluorescent antibody [DFA]). In the context of congenital syphilis, this should be from a normally sterile specimin, eg, CSF, placental tissue. Sent for T. pallidum EIA (enzyme IgG immunoassay) (specific treponemal antibody test); specific treponemal antibody test (TPPA, TPHA, FTA-ABS, IgM immunoassay); NAAT; DFA. If T. pallidum EIA reactive, send for non-specific treponemal test (RPR, VDRL) as well as specific. If non-specific treponemal test reactive (serum or CSF) at any titre, report result to the medical officer of health, and comment if your records show there has been a fourfold or greater increase within the past 2 years. Following specific treponemal antibody test, send for different specific treponemal antibody test, report result to medical officer of health. For NAAT, on detection of T. pallidum DNA, report result to medical officer of health. For DFA, if T. pallidum visualised, report result to the medical officer of health. Click to enlarge

Note:

  1. Given difficulties in the implementation of gonorrhoea and syphilis notification system, the reporting to medical officer do not yet apply to the laboratory notification process. Laboratories will be advised when this issue is solved.

Diseases notifiable to the medical officer of health (other than notifiable infectious diseases)

Cysticercosis

Updated 18 January 2020

  • Cysticercosis is caused by the larval stage of T. solium after ingestion of eggs (rather than encysted larvae) from contaminated food, water or via faecal-oral autoinoculation.
  • Stool examinations can be performed; however, eggs are typically not found, since the majority of people diagnosed with cysticercosis do not have a viable T. solium tapeworm in their intestines.
  • Serology is available through reference laboratories for patients with suggestive radiological findings. Occasionally, the diagnosis of extraneural cysticercosis is made by finding a larval scolex in an excisional biopsy of a skin or muscle lesion.

Specimen: serum or CSF for antibody detection, tissue. Sent for serology and histological examination. On detection of T.solium antibodies or larval scolex, report to the medical officer of health.

Taeniasis

Updated 18 January 2020

  • Taeniasis (adult tapeworm infection) occurs after the ingestion of inadequately cooked pork containing encysted T. solium larvae.

Specimin[1]: usually faeces. Sent for direct microscopy. On detection of Taenia eggs or proglottids[1], report to the medical officer of health.

Notes:

  1. If cysticercosis is also suspected, possible use of serology should be discussed with the clinical microbiologist.
  2. It is not possible to differentiate the eggs of T. solium from the beef tapeworm T. saginata. Identification to species level requires examination of proglottid segments passed in the stool.

Trichinosis

Updated 18 January 2020

Specimin: usually muscle biopsy[1], serum[2] for antibody detection. Sent for histology and serology. On detection of larvae in muscle or of Trichinella antibodies, report result to the medical officer of health. Click to enlarge

Notes:

  1. Muscle biopsy for histology collected at least 10 days and ideally ~4 weeks after infection.
  2. Eosinophilia is supportive but not diagnostic.
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