A case-control study and molecular epidemiology of yersiniosis in Aotearoa New Zealand.

The objective of this study was to determine risk factors and sources attributed to yersiniosis in Aotearoa New Zealand (NZ). A risk factor questionnaire was administered to 247 notified yersiniosis cases and 258 control participants from the Canterbury and/or Wellington regions of NZ. sp.

Metagenomic evaluation of bacteria in drinking water using full-length 16S rRNA amplicons.

and total coliforms are important tools for identifying potential faecal contamination in drinking water. However, metagenomics offers a powerful approach for delving deeper into a bacterial community when or total coliforms are detected. Metagenomics can identify microbes native to water systems, track community changes and potential pathogens introduced by contamination events, and evaluate the effectiveness of treatment processes.

Population structure and pathogen interaction of Escherichia coli in freshwater: Implications of land-use for water quality and public health in Aotearoa New Zealand.

Freshwater samples (n = 199) were obtained from 41 sites with contrasting land-uses (avian, low impact, dairy, urban, sheep and beef, and mixed sheep, beef and dairy) and the E. coli phylotype of 3980 isolates (20 per water sample enrichment) was determined. Eight phylotypes were identified with B1 (48.

When the implementation of water safety plans fail: rethinking the approach to water safety planning following a serious waterborne outbreak and implications for subsequent water sector reforms.

Water suppliers in New Zealand have been preparing the water safety plans (WSPs) since 2005; large drinking water-associated outbreaks of campylobacteriosis occurred in Darfield in 2012 and in Havelock North in 2016. This paper reviews the WSP that was in place for Havelock North, and analyses why it failed to prevent this outbreak. The risk assessment team completing the WSP underestimated the risks to human health of contamination events, while overestimating the security of the groundwater and bore heads.

Exploring the Bacterial Community in Aged Fecal Sources from Dairy Cows: Impacts on Fecal Source Tracking.

(1) Background: This paper discusses the impact of agricultural activities on stream health, particularly in relation to dairy cow fecal pollution. The study explores the fecal microbiome of cattle and the potential ecological implications of aging fecal pollution on waterways. (2) Methods: The study examines changes in the bacterial community available for mobilization from in-situ decomposing cowpats and the effects of simulated rainfall.

Diagnosis of protozoa diarrhoea in Campylobacter patients increases markedly with molecular techniques.

Cryptosporidium and Giardia are major causes of diarrhoea globally, and two of the most notified infectious diseases in New Zealand. Diagnosis requires laboratory confirmation carried out mostly via antigen or microscopy-based techniques. However, these methods are increasingly being superseded by molecular techniques.

Mobilization of Escherichia coli and fecal source markers from decomposing cowpats.

In rural environments, the sources of fecal contamination in freshwater environments are often diffuse and a mix of fresh and aged fecal sources. It is important for water monitoring purposes, therefore, to understand the impacts of weathering on detection of the fecal source markers available for mobilization from livestock sources. This study targets the impacts of rainfall events on the mobilization of fecal source tracking (FST) markers from simulated cowpats decomposing in situ for five-and-a-half-months.

A comparison of the performance of saliva and nasopharyngeal nucleic acid amplification testing for the detection of SARS-CoV-2 in New Zealand.

Aim: To compare detection of SARS-CoV-2 from paired nasopharyngeal swabs (NPS) and saliva using molecular methods in common use for testing swabs in New Zealand.

Method: Samples from individuals testing positive for SARS-CoV-2 in Auckland, Wellington and Dunedin were tested at the local laboratories using methods previously established for these sample types.

Results: One hundred and ninety-six paired samples from unique individuals were tested, with 46 (23%) positive from either sample type, of which 43/46 (93%) tested positive from NPS, and 42/46 (91%) from saliva, indicating no significant difference in performance between sample types (p=0.

Sensitivity of wastewater-based epidemiology for detection of SARS-CoV-2 RNA in a low prevalence setting.

To assist public health responses to COVID-19, wastewater-based epidemiology (WBE) is being utilised internationally to monitor SARS-CoV-2 infections at the community level. However, questions remain regarding the sensitivity of WBE and its use in low prevalence settings. In this study, we estimated the total number of COVID-19 cases required for detection of SARS-CoV-2 RNA in wastewater.

Emergence and global spread of main clinical clonal complex.

The bacterial foodborne pathogen clonal complex 1 (-CC1) is the most prevalent clonal group associated with human listeriosis and is strongly associated with cattle and dairy products. Here, we analyze 2021 isolates collected from 40 countries, covering -CC1 first isolation to present days, to define its evolutionary history and population dynamics. We show that -CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming and food industrialization in the 20th century.

Genome Typing and Epidemiology of Human Listeriosis in New Zealand, 1999 to 2018.

This study describes the epidemiology of listeriosis in New Zealand between 1999 and 2018 as well as the retrospective whole-genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population, and non-pregnancy-associated cases were more prevalent than pregnancy-associated cases (averages of 19 and 5 cases per annum, respectively).

Genomic diversity of Listeria monocytogenes isolates from seafood, horticulture and factory environments in New Zealand.

Listeria monocytogenes is a foodborne human pathogen that causes systemic infection, fetal-placental infection in pregnant women causing abortion and stillbirth and meningoencephalitis in elderly and immunocompromised individuals. This study aimed to analyse L. monocytogenes from different sources from New Zealand (NZ) and to compare them with international strains.

Prevalence and Genotyping of Campylobacter jejuni and Campylobacter coli from Ovine Carcasses in New Zealand.

Abstract: A pilot survey was performed to determine the prevalence of Campylobacter jejuni and Campylobacter coli on three age classes (lamb, hogget, and mutton) of ovine carcass trim postdressing and prechill. Sampling of hogget carcasses was undertaken 6 months before sampling of lamb and mutton carcasses. A total of 120 trim samples were collected from 11 processing plants across New Zealand.

Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring.

In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E.

A large scale waterborne Campylobacteriosis outbreak, Havelock North, New Zealand.

Background: We describe the investigation of a Campylobacter outbreak linked to contamination of an untreated, groundwater derived drinking water supply.

Methods: We analysed epidemiological data collected from clinician-confirmed diarrheal cases and estimated the total burden of Havelock North cases using an age-adjusted cross-sectional telephone survey. Campylobacter isolates from case fecal specimens, groundwater samples, and sheep fecal specimens from paddocks adjacent to the drinking water source were whole genome sequenced.

Genomic Analysis of Fluoroquinolone- and Tetracycline-Resistant Campylobacter jejuni Sequence Type 6964 in Humans and Poultry, New Zealand, 2014-2016.

In 2014, antimicrobial drug-resistant Campylobacter jejuni sequence type 6964 emerged contemporaneously in poultry from 3 supply companies in the North Island of New Zealand and as a major cause of campylobacteriosis in humans in New Zealand. This lineage, not previously identified in New Zealand, was resistant to tetracycline and fluoroquinolones. Genomic analysis revealed divergence into 2 major clades; both clades were associated with human infection, 1 with poultry companies A and B and the other with company C.

Relationships between chemical and microbial faecal source tracking markers in urban river water and sediments during and post-discharge of human sewage.

This study explores the relationships between faecal source tracking (FST) markers (quantitative Polymerase Chain Reaction (qPCR) markers and steroids), microbial indicators, the faecal ageing ratio of atypical colonies/total coliforms (AC/TC) and potential human pathogens (Giardia, Cryptosporidium and Campylobacter). Faecal source PCR markers tested were GenBac3, HumM3, HumBac (HF183-Bac708R); Bifidobacterium adolescentis, wildfowl and canine-associated markers. Sediment and water samples from the Avon River were collected during and post-discharge of untreated human sewage inputs, following a series of earthquakes, which severely damaged the Christchurch sewerage system.

Fecal source tracking methods to elucidate critical sources of pathogens and contaminant microbial transport through New Zealand agricultural watersheds - A review.

In New Zealand, there is substantial potential for microbial contaminants from agricultural fecal sources to be transported into waterways. The flow and transport pathways for fecal contaminants vary at a range of scales and is dependent on chemical, physical and biological attributes of pathways, soils, microorganisms and landscape characteristics. Understanding contaminant transport pathways from catchment to stream can aid water management strategies.

Concentrations of spp., , Enterococci, and spp. in the Feces of Farmed Red Deer in New Zealand.

Intensive deer farming can cause environmental issues, mainly by its impact on soils and water quality. In particular, there is a risk to the microbial quality of water, as high quantities of suspended sediment and fecal bacteria can enter into water systems. The feces of farmed red deer (, = 206) from Canterbury and Southland, New Zealand, were analyzed with regard to the presence of spp.

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.

PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives.

Draft Genome Sequences: Resources for Food Safety and Public Health.

is a major foodborne pathogen that infects humans and nonhuman primates and is the major cause of dysentery and reactive arthritis worldwide. This is the initial public release of 16 genome sequences from four species sequenced as part of the 100K Pathogen Genome Project.

Large-Scale Release of Campylobacter Draft Genomes: Resources for Food Safety and Public Health from the 100K Pathogen Genome Project.

Campylobacter is a food-associated bacterium and a leading cause of foodborne illness worldwide, being associated with poultry in the food supply. This is the initial public release of 202 Campylobacter genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in the Campylobacter genus.

Statistical Considerations in Environmental Microbial Forensics.

In environmental microbial forensics, as in other pursuits, statistical calculations are sometimes inappropriately applied, giving rise to the appearance of support for a particular conclusion or failing to support an innately obvious conclusion. This is a reflection of issues related to dealing with sample sizes, the methodologies involved, and the difficulty of communicating uncertainties. In this brief review, we attempt to illustrate ways to minimize such problems.

Field study of the composition of greywater and comparison of microbiological indicators of water quality in on-site systems.

Thirty on-site greywater systems were sampled to determine greywater characteristics and practices in the field. Kitchen greywater was present at eight sites and urine was included at seven sites. These non-traditional sources resulted in significantly higher concentrations of enterococci and 5-day biochemical oxygen demand (BOD5) in greywater.