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m.l. devane, c. nicol, a. ball, j.d. klena, p. scholes, j.a. hudson, m.g. baker, b.j. gilpin, n. garrett and m.g. savill. 2005.To identify potential reservoirs and transmission routes of human pathogenicCampylobacterspp.An enrichment PCR method for the detection and identification ofCampylobacter jejuniand/orCampylobacter coliin faecal, food and river water samples was applied to 1450 samples of 12 matrix types obtained from a defined geographical area. PCR-positive samples were cultured to yield isolates for typing, and the data for 616C. jejuniisolates obtained.Serotyping andSmaI macrorestriction profiling using pulsed field gel electrophoresis revealed a high level of diversity within the isolates from each matrix.Campylobacter jejuniandC. colisubtypes indistinguishable from those obtained from human cases were detected in most of the matrices examined. NoCampylobacterisolates were isolated from possum faeces.Ten of the 12 matrices examined may be involved in the transmission of human campylobacteriosis as they containedCampylobactersubtypes also isolated from clinical cases.Results indicate that, for this rural population, a range of potential transmission routes that could lead to campylobacteriosis exist. Their relative importance needs to be assessed from an exposure assessment standpoint. [ABSTRACT FROM AUTHOR]

Understanding the composition of complex Escherichia coli populations from the environment is necessary for identifying strategies to reduce the impacts of fecal contamination and protect public health. Metabarcoding targeting the hypervariable gene gnd was used to reveal the complex population diversity of E. coli and phenotypically indistinct Escherichia species in water, soil, sediment, aquatic biofilm, and fecal samples from native forest and pastoral sites. The resulting amplicons were cross-referenced against a database containing over 700 different partial gnd sequences from E. coli/non-E. coli Escherichia species. Alpha and beta measures of diversity of Escherichia populations were lowest in feces, soil and sediment compared to water and aquatic biofilm samples. Escherichia populations recovered from extensive freshwater catchments dominated by sheep, beef and dairy farming were extremely diverse but well-separated from a wetland dairy site. In contrast, Escherichia populations from the low-impact native forest site with fewer fecal sources were less diverse. Metabarcoding distinguished E. coli populations important to fecal contamination monitoring from non-E. coli Escherichia environmental populations. These data represent in-depth analysis and geographic stability of Escherichia populations from environmental samples with extensive heterogeneity, and reveal links with diverse fecal sources, land-use and the overall burden of fecal contamination at sample sites., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

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 (48.04%), B2 (14.87%) and A (14.79%) the most abundant. Escherichia marmotae (n = 22), and Escherichia ruysiae (n = 1), were rare (0.68%) suggesting that these environmental strains are unlikely to confound water quality assessments. Phylotypes A and B1 were overrepresented in dairy and urban sites (p < 0.0001), whilst B2 were overrepresented in low impact sites (p < 0.0001). Pathogens ((Salmonella, Campylobacter, Cryptosporidium or Giardia) and the presence of diarrhoeagenic E. coli-associated genes (stx and eae) were detected in 89.9% (179/199) samples, including 80.5% (33/41) of samples with putative non-recent faecal inputs. Quantitative PCR to detect microbial source tracking targets from human, ruminant and avian contamination were concordant with land-use type and E. coli phylotype abundance. This study demonstrated that a potential recreational health risk remains where pathogens occurred in water samples with low E. coli concentration, potential non-recent faecal sources, low impact sites and where human, ruminant and avian faecal sources were absent., (© 2024 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.)

Escherichia coli is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500 Escherichia isolates including newly described Escherichia species, namely Escherichia marmotae , Escherichia ruysiae, and Escherichia whittamii , obtained from diverse environmental sources to assist with improved public health risk assessments., Competing Interests: The authors declare no conflict of interest.

Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Mākirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Moinet et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

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. The FST markers analysed were Escherichia coli, microbial source tracking (MST) markers, fecal steroids and a fecal ageing ratio based on the ratio between counts of river microflora and total coliforms. There was a substantial concentration of E. coli (10 4 /100 mL) released from the ageing cowpats suggesting a long-term reservoir of E. coli in the cowpat. Mobilization of fecal markers from rainfall-impacted cowpats, however, was markedly reduced compared with fecal markers in the cowpat. Overall, the Bacteroidales bovine-associated MST markers were less persistent than E. coli in the cowpat and rainfall runoff. The ten fecal steroids, including the major herbivore steroid, 24-ethylcoprostanol, are shown to be stable markers of bovine pollution due to statistically similar degradation rates among all steroids. The mobilizable fraction for each FST marker in the rainfall runoff allowed generation of mobilization decline curves and the derived decline rate constants can be incorporated into source attribution models for agricultural contaminants. Findings from this study of aged bovine pollution sources will enable water managers to improve attribution of elevated E. coli to the appropriate fecal source in rural environments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Generic Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates ( n  = 709) were isolated from water, sediment, soil, periphyton, and feces samples ( n  = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx 2 positive, 19 (2.7%) were eae positive, and stx 1 -positive isolates were absent. At the sample level, stx 2 -positive E. coli (5 of 189, 2.6%) and eae -positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments ( stx 1 , 23.9%; stx 2 , 31.4%; eae , 53.7%) and positively correlated with generic E. coli isolate numbers ( P  < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups. IMPORTANCE This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that "recreational exposure to water" is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.

Shellfish growing waters contaminated with inadequately treated human wastewater is a major source of norovirus in shellfish and poses a significant human health risk to consumers. Microbial source tracking (MST) markers have been widely used to identify the source (s) of faecal contamination in water but data are limited on their use for shellfish safety. This study evaluated the source specificity, sensitivity, occurrence and concentration of three viral MST markers i.e. cross-assembly phage (crAssphage), F-specific RNA bacteriophage genogroup II (F-RNA phage GII) and pepper mild mottle virus (PMMoV) using animal faeces (n = 119; 16 animal groups), influent wastewater (n = 12), effluent wastewater (n = 16) and shellfish (n = 33). CrAssphage, F-RNA phage GII and PMMoV had source specific values of 0.97, 0.99 and 0.91, respectively. The sensitivity of MST markers was confirmed by their 100% detection frequency in influent wastewaters. The frequency of detection in effluent wastewater ranged from 81.3% (F-RNA phage GII) to 100% (PMMoV). Concentration of F-RNA phage GII was one log 10 (influent wastewater) and 2-3 log 10 (effluent wastewater) lower than crAssphage and PMMoV, respectively. Despite lower prevalence of F-RNA phage GII in oysters and mussels compared to crAssphage and PMMoV, concentrations of the three MST markers were similar in mussels. As an indicator of norovirus contamination in shellfish, crAssphage and PMMoV had greater predictive sensitivity (100%; [95% CI; 81.5%-100%)]) and F-RNA phage GII had greater predictive specificity (93.3%; [95% CI; 68.1%-99.8%]). In contrast, crAssphage and F-RNA phage GII have similar accuracy for predicting norovirus in shellfish, however, PMMoV significantly overestimated its presence. Therefore, a combination of crAssphage and F-RNA phage GII analysis of shellfish could provide a robust estimation of the presence of human faecal and norovirus contamination., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Objectives: To investigate the race-specific second primary bladder cancer (SPBC) risk following prostatic irradiation., Methods: Louisiana residents who were diagnosed with localized prostate cancer (PCa) in 1996-2013 and received surgery or radiation were included. Patients were followed until SPBC diagnosis, death, or Dec. 2018. The exposure variable was type of treatment (radiation only vs. surgery only). The outcome was time from PCa diagnosis to SPBC diagnosis, stratified by race. Fine and Gray's competing risk model was applied with death as a competing event and adjustment of sociodemographic and tumor characteristics. We used 5 years and 10 years as lag time in the analyses., Results: A total of 26,277 PCa patients with a median follow-up of 10.7 years were analyzed, including 18,598 white and 7679 black patients. About 42.9 % of whites and 45.7 % of blacks received radiation. SPBC counted for 1.84 % in the radiation group and 0.90 % in the surgery group among white patients and for 0.91 % and 0.58 %, respectively, among black patients. The adjusted subdistribution hazard ratio of SPBC was 1.80 (95 % CI: 1.30-2.48) for radiation recipients compared to surgery recipients among white patients; 1.93 (95 % CI: 1.36-2.74) if restricted to external beam radiation therapy (EBRT). The SPBC risk was not significantly different between irradiated and surgically treated among blacks., Conclusions: The SPBC risk is almost two-fold among white irradiated PCa patients compared to their counterparts treated surgically. Our findings highlight the need for enhanced surveillance for white PCa survivors receiving radiotherapy, especially those received EBRT., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Bivalve molluscan shellfish grown in areas impacted by human faecal pollution are at risk of being contaminated with multiple enteric viruses. To minimise the public health risks associated with shellfish consumption, determining the presence of faecal contamination in shellfish and their growing waters is crucial. In this study, we evaluated the use of pepper mild mottle virus (PMMoV) as an indicator of human faecal contamination in oysters, mussels, cockles and shellfish growing waters in New Zealand. Using reverse transcription quantitative polymerase chain reaction (RT-qPCR) the presence, and where applicable, the concentration of PMMoV was determined in faeces from 11 different animal species, influent (untreated) wastewater, shellfish and shellfish growing waters. Non-human faecal samples (from seagull, Canada goose, black swan and dog) were RT-qPCR positive for PMMoV. The faecal source specificity of PMMoV was 0.83 (maximum value of 1) when 'detected but not quantifiable' (DNQ) values were used. However, when 'lower limit of quantification' (LLOQ) values were used, the specificity increased to 0.92. The PMMoV concentration in influent wastewater (n = 10) ranged from 6.3 to 7.7 log 10 genome copies (GC)/L with a mean (±standard deviation) of 7.1 ± 0.5 log 10  GC/L. The overall occurrence of PMMoV in shellfish and shellfish growing waters from four different areas was 46/51 (90%) and 29/52 (56%), respectively. Of the cockles collected from an area known to be impacted by effluent wastewater, 14/14 (100%) contained PMMoV concentrations above the LLOQ. In contrast, only 13/37 (35%) shellfish and 6/52 (11.5%) growing water samples collected from three areas with low anthropogenic impact contained PMMoV concentrations above the LLOQ. The high concentration of PMMoV in influent wastewater indicates that PMMoV may be a promising indicator of human faecal contamination. The presence of PMMoV in shellfish and growing waters with a low anthropogenic impact may be of avian origin, and this needs to be considered if using PMMoV for monitoring shellfish and shellfish growing water quality in New Zealand., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Decay rates for sunlight inactivation of polymerase chain reaction (PCR) markers for total Bacteroidales, human-specific Bacteroidales, Escherichia coli, and Bifidobacterium adolescentis relative to cultured E. coli were investigated. The experiment used 100-L chambers of fresh water and seawater (paired with dark controls) seeded with human sewage and exposed to natural sunlight over three summer days. Culturable E. coli levels in sunlight-exposed chambers decreased by at least 3 logs on day 1, and by day 3 a total reduction of 4.5 to 5.5 logs was achieved in fresh water and seawater, respectively. In contrast, PCR detection of the four gene targets in sunlight-exposed chambers reduced by no more than 2 logs over the duration of the study (k(t) < 0.071 log(e) units h(-1)). Under these experimental conditions, PCR markers are considerably more conservative than culturable E. coli and can persist for extended periods of time following inactivation of E. coli.