The long-term impacts of COVID-19 on confirmed cases at least 12 months post-infection in Wellington, New Zealand: an observational, cross-sectional study.

AIM: To explore the prevalence of ongoing symptoms and laboratory abnormalities in confirmed cases of COVID-19 from the first wave within the Greater Wellington Region, after at least 12 months post infection. METHOD: COVID-19 cases were obtained from EpiSurv. Eligible participants electronically completed questionnaires (Overall Health Survey, Patient Health Questionnaire-9 [PHQ-9], Generalised Anxiety Disorder-7 [GAD-7], Pittsburgh Sleep Quality Index, EuroQol 5 Dimension 5 Level [EQ-5D-5L], Fatigue Severity Scale [FSS], WHO Symptom Questionnaire, Modified Medical Research Council Dyspnoea Scale [mMRC Dyspnoea Scale]). Blood samples were analysed for cardiac, endocrine, haematological, liver, antibody, and inflammatory markers. RESULTS: Forty-two of 88 eligible cases undertook the study. Participants were enrolled at a median 628.5 days from symptom onset. Fifty-two point four percent felt that their current overall health was worse than it was prior to contracting COVID-19. Ninety percent of participants reported at least two ongoing symptoms since their acute illness. Between 45-72% of participants reported each of anxiety, depression, dyspnoea, pain/discomfort, and sleep difficulties, assessed using the GAD-7, PHQ-9, mMRC Dyspnoea Scale, EQ-5D-5L and FSS questionnaires respectively. There were minimal laboratory abnormalities. CONCLUSION: There is a high prevalence of ongoing symptoms following the first wave of COVID-19 infection in Aotearoa New Zealand. At a median of 1.7 years post infection, there is a wide spectrum of symptoms and symptom severity, although as an observational, cross-sectional study a causal relationship between symptoms or their severity and COVID-19 infection cannot be firmly established.

Genomic adaptations of Campylobacter jejuni to long-term human colonization.

BACKGROUND: Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract. RESULTS: There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. CONCLUSIONS: This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment.

Clinical and epidemiological characteristics of COVID-19 in Wellington, New Zealand: a retrospective, observational study.

AIMS: To review the demographic and clinical characteristics of confirmed COVID-19 cases within the Greater Wellington Region (GWR). METHODS: A retrospective, observational study of all 96 confirmed COVID-19 cases in the GWR. The primary outcome was time taken from onset to complete resolution of symptoms. Secondary outcomes were the epidemiological and clinical characteristics of cases. RESULTS: The mean (SD) time from symptom onset to complete resolution was 19.1 (1.1) days. The mean (SD) age was 43.1 (16.9). 51% were male. The majority were of European ethnicity (84%), resided in the top five decile neighbourhoods (76%) and had travelled to New Zealand (69%). The mean (SD) time from onset of symptoms to obtaining RT-PCR testing results was 5.3 (0.4) days. The most common symptoms at onset were cough (36%), sore throat (22%) and fatigue (21%); the overall most common symptoms were cough (65%), sore throat (43%), headache (43%) and fatigue (42%); many symptoms were late manifestations. The most common co-morbidity reported was asthma (20%), with no reported exacerbations. The rate of secondary infections within households was 0.05 per primary infection. CONCLUSION: The demography of COVID-19 cases reflected the imported nature of cases. The clinical presentation of COVID-19 was highly variable and there were no particular symptoms that could accurately predict infection.

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa).

The strategy in New Zealand (Aotearoa) to eliminate coronavirus disease requires that international arrivals undergo managed isolation and quarantine and mandatory testing for severe acute respiratory syndrome coronavirus 2. Combining genomic and epidemiologic data, we investigated the origin of an acute case of coronavirus disease identified in the community after the patient had spent 14 days in managed isolation and quarantine and had 2 negative test results. By combining genomic sequence analysis and epidemiologic investigations, we identified a multibranched chain of transmission of this virus, including on international and domestic flights, as well as a probable case of aerosol transmission without direct person-to-person contact. These findings show the power of integrating genomic and epidemiologic data to inform outbreak investigations.

Towards elimination of tuberculosis in New Zealand.

New Zealand could be the first country in the world to eliminate tuberculosis (TB). We propose a TB elimination strategy based on the eight-point World Health Organization (WHO) action framework for low incidence countries. Priority actions recommended by the WHO include 1) ensure political commitment, funding and stewardship for planning and essential services; 2) address the most vulnerable and hard-to-reach groups; 3) address special needs of migrants and cross-border issues; 4) identify active TB and undertake screening for latent tuberculosis infection (LTBI) in recent TB contacts and selected high-risk groups, and provide appropriate treatment; 5) optimise the prevention and care of drug-resistant TB; 6) ensure continued surveillance, programme monitoring and evaluation and case-based data management; 7) invest in research and new tools; and 8) support global TB prevention, care and control. In New Zealand, central government needs to take greater responsibility for TB policy and programme governance. Urgent action is required to prevent TB in higher risk groups including Maori communities, and to enable immigration screening to detect and treat LTBI. Clinical services need to be supported to implement new guidelines for LTBI that enable better targeting of screening and shorter, safer treatment regimens. Access to WHO recommended treatment regimens needs to be guaranteed for drug-resistant TB. Better use of existing data could better define priority areas for action and assist in the evaluation of current control activities. Access to GeneXpert® MTB-RIF near the point of care and whole genome sequencing nationally would greatly improve clinical and public health management through early identification of drug resistance and outbreaks. New Zealand already has a world-class TB research community that could be better deployed to assist high-incidence countries through research and training.

Expert Elicitation for Estimation of the Proportion Foodborne for Selected Microbial Pathogens in New Zealand.

Objectives: To estimate the proportions of human cases of nine specific microbial diseases in New Zealand that were due to transmission by food and the proportion of the foodborne burden that was due to transmission by some specific foods. Materials and Methods: Subjective probability distributions were elicited from 10 food safety experts using a modified Delphi approach. In addition to uniform weighting of experts' opinions, two techniques were used to measure individual's expertise; self-assessment and performance-based weighting using Cooke's classical method. Aggregate estimates were derived by simulation. Results: Food was estimated to be the primary route of transmission for infections due to Campylobacter spp., Listeria monocytogenes, nontyphoid Salmonella spp., Vibrio parahaemolyticus, and Yersinia enterocolitica. Uncertainties were lowest for organisms where the self-assessed expertise level was highest. Conclusions: Foodborne proportion estimates were more "polarized" than for a similar elicitation in 2005. That is, where food was the primary transmission route the estimated proportion on account of food was higher (62.1-90.6% in the current study for self-assessed expertise weighted estimates, compared to 56.2-89.2% in 2005); where food was not the primary transmission route the estimated proportion because of food was lower (27.6-34.0% in the current study compared to 31.5-39.5% in 2005). These estimates represent an essential resource for determining the burden of foodborne disease in New Zealand.

Long-term Colonization by Campylobacter jejuni Within a Human Host: Evolution, Antimicrobial Resistance, and Adaptation.

Background: Campylobacteriosis is inflammation of the gastrointestinal tract as a result of Campylobacter infection. Most campylobacteriosis cases are acute and self-limiting, with Campylobacter excretion ceasing a few weeks after symptoms cease. We identified a patient with fecal specimens positive for Campylobacter jejuni (ST45) intermittently during a 10-year period. Methods: Sixteen Campylobacter isolates were collected from the patient during 2006-2016. The isolates' genomes were sequenced to determine their relatedness, and their antimicrobial susceptibility patterns and motility were measured to determine the effects of antibiotic therapy and long-term excretion on the Campylobacter population. Results: Phylogenetic analyses estimated that the isolates shared a date of common ancestor between 1998 and 2006, coinciding with the onset of symptoms for the patient. Genomic analysis identified selection for changes in motility, and antimicrobial susceptibility testing suggested that the Campylobacter population developed resistance to several antibiotics coinciding with periods of antibiotic therapy. Conclusions: The patient was consistently colonized with organisms from a Campylobacter population that adapted to the internal environment of the patient. Genomic and phylogenetic analyses can give insight into a patient's infection history and the effect of antimicrobial treatment on Campylobacter populations in this unusual situation of long-term colonization of an individual.

An outbreak of multiple serotypes of salmonella in New Zealand linked to consumption of contaminated tahini imported from Turkey.

A widespread salmonellosis outbreak linked to consumption of hummus made from contaminated tahini imported from Turkey occurred in New Zealand in November 2012. This article summarizes the outbreak detection, investigation, and control. The New Zealand Enteric Reference Laboratory alerted public health units regarding a cluster of 11 persons with Salmonella Montevideo infection identified from different regions of the North Island of New Zealand. A multiagency outbreak investigation commenced to determine the source of illness and prevent further transmission. Salmonellosis is a notifiable disease in New Zealand. Outbreak cases were identified through routine salmonellosis notifications, and interviewed using a standardized questionnaire to identify common exposures. Clinical and food isolates were initially characterized by serotyping and then further typed by pulsed-field gel electrophoresis (PFGE). PFGE profiles were sent to PulseNet and international alerts were posted. The scope of the investigation widened to include persons with either Salmonella Maastricht and Salmonella Mbandaka infection following detection of these serotypes in tahini epidemiologically linked to laboratory-confirmed cases. All three of the tahini-associated serotypes were detected in people who had consumed tahini, and these were found to have PFGE profiles indistinguishable from the tahini isolates. Twenty-seven salmonellosis cases infected with at least one of the three tahini-associated Salmonella serotypes were detected between September 1 and December 31, 2012; of these, 16 (59%) cases (12 with Salmonella Montevideo, 3 with Salmonella Mbandaka, and 1 with Salmonella Maastricht infection) had PFGE patterns indistinguishable from the outbreak profile. The investigation led to a trade withdrawal and consumer recall for tahini sesame paste from the consignment and products containing this tahini. The outbreak ceased following the recall. The importer of the implicated tahini was reminded of his duties as a food importer, including ensuring appropriate product testing. Changes to New Zealand legislation strengthened food safety responsibilities of food importers.

Recurring norovirus transmission on an airplane.

BACKGROUND: Previously reported outbreaks of norovirus gastroenteritis associated with aircraft have been limited to transmission during a single flight sector. During October 2009, an outbreak of diarrhea and vomiting occurred among different groups of flight attendants who had worked on separate flight sectors on the same airplane. We investigated the cause of the outbreak and whether the illnesses were attributable to work on the airplane. METHODS: Information was obtained from flight attendants on demographic characteristics, symptoms, and possible transmission risk factors. Case patients were defined as flight attendants with diarrhea or vomiting <51 hours after the end of their first flight sector on the airplane during 13-18 October 2009. Stool samples were tested for norovirus RNA. RESULTS: A passenger had vomited on the Boeing 777-200 airplane on the 13 October flight sector. Sixty-three (82%) of 77 flight attendants who worked on the airplane during 13-18 October provided information, and 27 (43%) met the case definition. The attack rate among flight attendants decreased significantly over successive flight sectors from 13 October onward (P < .001). Working as a supervisor was independently associated with development of illness (adjusted odds ratio, 5.8; 95% confidence interval, 1.3-25.6). Norovirus genotype GI.6 was detected in stool samples from 2 case patients who worked on different flight sectors. CONCLUSIONS: Sustained transmission of norovirus is likely to have occurred because of exposures on this airplane during successive flight sectors. Airlines should make provision for adequate disinfection of airplanes with use of products effective against norovirus and other common infectious agents after vomiting has occurred.

Two New Zealand outbreaks of norovirus gastroenteritis linked to commercially farmed oysters.

AIM: We report on the investigations of two gastroenteritis outbreaks, which were linked to a common source. METHODS: Retrospective cohort studies were conducted for two gastroenteritis outbreaks which occurred in Auckland and in Waikato. Faecal samples and samples of oyster meat were analysed. Environmental surveys of implicated areas were conducted. RESULTS: 10 out of 16 people who had eaten at a catered event in Auckland, and 3 out of 15 people who had eaten at a Waikato restaurant, experienced gastroenteritis. The symptoms, duration of illness and incubation periods were consistent with norovirus gastroenteritis in both outbreaks. The consumption of oysters was strongly associated with an increased risk of illness. Faecal samples were positive for norovirus. Oysters from both outbreaks were traced back to the same growing area. Samples of oyster meat from one of the restaurants and from the growing area were positive for norovirus. The growing area was closed for further investigation. A pipe from a waste water treatment plant was later found to be leaking partially treated effluent into a stream discharging near the implicated growing area. CONCLUSION: Investigation of these two outbreaks led to the discovery of a common source of norovirus at a commercial oyster growing area.

Transmission of pandemic A/H1N1 2009 influenza on passenger aircraft: retrospective cohort study.

OBJECTIVES: To assess the risk of transmission of pandemic A/H1N1 2009 influenza (pandemic A/H1N1) from an infected high school group to other passengers on an airline flight and the effectiveness of screening and follow-up of exposed passengers. DESIGN: Retrospective cohort investigation using a questionnaire administered to passengers and laboratory investigation of those with symptoms. SETTING: Auckland, New Zealand, with national and international follow-up of passengers. PARTICIPANTS: Passengers seated in the rear section of a Boeing 747-400 long haul flight that arrived on 25 April 2009, including a group of 24 students and teachers and 97 (out of 102) other passengers in the same section of the plane who agreed to be interviewed. MAIN OUTCOME MEASURES: Laboratory confirmed pandemic A/H1N1 infection in susceptible passengers within 3.2 days of arrival; sensitivity and specificity of influenza symptoms for confirmed infection; and completeness and timeliness of contact tracing. RESULTS: Nine members of the school group were laboratory confirmed cases of pandemic A/H1N1 infection and had symptoms during the flight. Two other passengers developed confirmed pandemic A/H1N1 infection, 12 and 48 hours after the flight. They reported no other potential sources of infection. Their seating was within two rows of infected passengers, implying a risk of infection of about 3.5% for the 57 passengers in those rows. All but one of the confirmed pandemic A/H1N1 infected travellers reported cough, but more complex definitions of influenza cases had relatively low sensitivity. Rigorous follow-up by public health workers located 93% of passengers, but only 52% were contacted within 72 hours of arrival. CONCLUSIONS: A low but measurable risk of transmission of pandemic A/H1N1 exists during modern commercial air travel. This risk is concentrated close to infected passengers with symptoms. Follow-up and screening of exposed passengers is slow and difficult once they have left the airport.

Migrants and tuberculosis: analysing epidemiological data with ethnography.

OBJECTIVE: Media portrayals of tuberculosis (TB) in New Zealand are of immigrants who enter the country with active disease and pose a threat to inhabitants, which fosters a popular perception that border control is the best and only response to disease control. This paper reviews both New Zealand and international data on TB rates, causes and transmission among migrant populations to elucidate the precise nature of the link between immigration and TB rates. METHODS: Recent information from scholarly journals on immigration and TB was reviewed. Surveillance data from New Zealand and comparable information from other low-incidence countries were reviewed. CONCLUSIONS AND IMPLICATIONS: The importation of active TB is only a minor part of the total TB burden. While effective border control is essential, equally, if not more important, are the circumstances that promote the reactivation of latent TB infection in migrant communities, including migrants' experiences in transit and after arrival, structural conditions, and personal characteristics. For sound prevention strategies, attention needs to be paid to the existence of transnational communities and the conditions for migrants, rather than placing a singular focus on place of birth.

A Legionnaires' disease outbreak: a water blaster and roof-collected rainwater systems.

In February 2006, an outbreak of Legionnaires' disease (LD) was identified in Beachlands, a small, isolated east Auckland suburb. It was investigated through case finding, a case-control study, sampling potential sources of infection and by molecular typing (using sequence-based typing (SBT) of all Legionella pneumophila serogroup 1 (Lp1) isolates). Lp1 was isolated from the respiratory tract of one case, the roof-collected rainwater systems of five households (three associated with cases) and from a water blaster at a nearby marina. All isolates were indistinguishable, exhibiting the same SBT allele pattern. Three LD cases lived within 500m of the water blaster (the fourth case within 1250m) and downwind in prevailing conditions. Another domestic roof-collected rainwater supply contaminated by Lp1 (identical SBT pattern) was incidentally identified in another suburb 4km east of Beachlands. This is the first outbreak of LD linked to roof-collected rainwater supplies and the first isolation of Legionella from these systems in New Zealand. Aerosols containing Legionella discharged to air by the marina water blaster may have infected some cases directly or may have seeded roof-collected rainwater systems. Some cases may have been exposed by contaminated bathroom showers. Roof-collected rainwater systems need appropriate design, careful cleaning and the maintenance of hot water temperatures at a minimum of 60 degrees C to reduce the chances of Legionella multiplying. Further research into the ecology of Legionella in roof-collected rain water systems is indicated.

Paediatric tuberculosis in a Pacific Islands community in New Zealand.

OBJECTIVES: To describe the demographic, clinical and management aspects of an outbreak of tuberculosis (TB) within a paediatric Pacific Island community in Auckland, New Zealand, in 2002-2003. METHODS: The index and source case are described along with details of the extensive contact tracing that was undertaken in this community. RESULTS: A total of 24 children were diagnosed with TB over an 11-month period. All cases were found to be epidemiologically linked to the one source case, mother of the index case. This total included 22 children with pulmonary disease, 1 case of miliary disease (index case) and 1 of cervical adenitis. Only 58% had symptoms at diagnosis and only 5 presented to medical attention with symptoms, the remainder had symptoms disclosed after contact tracing occurred. The Mycobacterium tuberculosis isolate was fully sensitive and all children (excluding the child with miliary disease) received short course directly observed therapy. One child developed hepatotoxicity requiring modification of his drug regimen. CONCLUSIONS: Children are at high risk of developing active disease after exposure to TB. The study describes the minimal symptoms manifested in many of the children with significant radiological changes consistent with pulmonary TB. This highlights the need to consider Mantoux testing and chest X-rays for children presenting with persistent respiratory symptoms in high-risk populations. Issues of contact tracing and adherence were also a problem in this population.

A community and workplace outbreak of tuberculosis in Hawke's Bay in 2002.

AIMS: To describe a community and workplace outbreak of tuberculosis in Hawke's Bay in 2002. METHODS: Contact tracing and case definitions used in this study followed New Zealand guidelines for tuberculosis control. DNA fingerprinting of Mycobacterium tuberculosis isolates was performed by restriction fragment length polymorphism (RFLP). RESULTS: 19 new cases of active tuberculosis disease (TBD) and 42 cases of latent tuberculosis infection (LTBI) were diagnosed. 55 family and close associates of the index case were investigated, of whom 9 (16.4%) had TBD disease and 11 (20.0%) had LTBI. 139 co-workers on the same work shift were investigated of whom 8 (5.8%) had TBD and 27 (19.4%) had LTBI. DNA typing of Mycobacterium isolates (from 4 TBD cases) confirmed that this was an outbreak of 'Rangipo'-strain TB. CONCLUSIONS: High infection rates were observed among family, close associates, and workplace contacts. Several factors may have contributed to this high infection rate--ie, delays in presentation and contact tracing, the use of positive pressure ventilation and re-circulated unfiltered air, and virulence of this strain of Mycobacterium tuberculosis. Inadequate adherence to TBD treatment precipitated this outbreak and reinforces the recommendation that TBD cases (in whom risk factors for non-adherence are present) should receive directly observed therapy (DOT) or at least by close supervision. Further research into strain characteristics is required in order to determine if the Rangipo-strain of TB is truly more virulent and if contact tracing or treatment regimes need to be modified accordingly.

First incursion of Salmonella enterica serotype typhimurium DT160 into New Zealand.

An outbreak of human Salmonella enterica serotype Typhimurium DT160 infection in New Zealand was investigated from May to August 2001. Handling of dead wild birds, contact with persons with diarrheal illness, and consumption of fast food were associated with infection. Contaminated roof-collected rainwater was also detected.