Molecular detection of Campylobacter spp. and fecal indicator bacteria during the northern migration of sandhill cranes (Grus canadensis) at the central Platte River

Assessing the defecation practices of unsheltered individuals and their contributions to microbial water quality in an arid, urban watershed

Outdoor defecation by people experiencing homelessness is frequently perceived as a potentially large source of human fecal pollution and a significant source of health risk in urban waterbodies with recreational contact. The goal of this study was to count the number of people experiencing homelessness and quantifies their sanitation habits in an urban river corridor setting, then use this information for estimating human fecal pollutant loading on a watershed scale. Two types of census counts were conducted including periodic point-in-time counts over six years and weekly counts of encampments. While the population census varied from count-to-count, the range of population estimates in the river corridor varied from 109 to 349 individuals during the six-year span, which mirrored the weekly counts of encampments. A face-to-face survey of people experiencing homelessness assessed the sanitation habits of the unsheltered population (N = 63), including outdoor defecation frequency and containment practices. Overall, 95 % of survey respondents reported defecating outdoors; 36 % practiced outdoor defecation between 4 and 7 days/week and 27 % practiced outdoor defecation <1 day/week. Of those that did practice outdoor defecation, 75 % contained their feces in a bucket or bag, thereby limiting fecal material contributions to the river; 6.7 % reported defecating on low ground near the river that could wash off when flood waters rise during a storm event. Only a single survey respondent reported defecating directly into the river. Based on literature values for average HF183 output for an adult human, and the average rainfall in the urban watershed, the total watershed contribution of HF183 averaged 1.2 × 1010 gene copies per storm event (95 % CI: 0.9 × 1010-1.6 × 1010) along the 41 km stretch of river in this study. This human fecal loading estimate is at least two orders of magnitude less than cumulative HF183 loading from all human sources measured at the bottom of the watershed.

Versatile dual-channel loop-mediated isothermal amplification assay featuring smartphone imaging enables determination of fecal indicator bacteria in environmental waters

Rapid diagnostic assays are often a critical tool for monitoring water quality in developing and developed countries. Conventional testing requires 24-48 h for incubation, resulting in delayed remediation and increasing the likelihood of negative outcomes. In this study, we report a workflow for detection of E. coli, a common indicator of fecal contamination. Following large volume filtration, E. coli is then solubilized enabling the facile isolation and recovery of genetic material by a thin film microextraction (TFME) device featuring a polymeric ionic liquid (PIL) sorbent. Rapid recovery of pure nucleic acids is achieved using a PIL sorbent with high affinity for DNA to significantly increase mass transfer and facilitate adsorption and desorption of DNA. Downstream detection is performed by a versatile, dual channel loop mediated isothermal amplification (LAMP) assay featuring a colorimetric dye and a sequence-specific molecular beacon. A portable LAMP companion box enables consistent isothermal heating and endpoint smartphone imaging while being powered by a single 12-V battery. Programmable LEDs are switched from white or blue light to facilitate the independent imaging of the colorimetric dye or fluorometric probe following amplification. The methodology positively identified E. coli in environmental samples spiked to concentrations of 6600 colony forming units (CFU) per milliliter and 660 CFU/mL with 100% and 22% positivity, respectively.

Effect of sex on the gut microbiota characteristics of passerine migratory birds

The gut microbiota, considered the “invisible organ” in the host animal, has been extensively studied recently. However, knowledge about the gut microbiota characteristics of passerine migratory birds during migration is limited. This study investigated the gut microbiota characteristics of three dominant migratory bird species (namely orange-flanked bluetail Tarsiger cyanurus, yellow-throated bunting Emberiza elegans, and black-faced bunting Emberiza spodocephala) in the same niche during spring migration and whether they were bird sex-specific. The compositions of gut microbiota species in these three migratory bird species and their male and female individuals were found to be similar. The main bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, and the main genera were Lactobacillus, Acinetobacter, Rickettsiella, and Mycobacterium; however, their relative abundance was different. Moreover, some potential pathogens and beneficial bacteria were found in all the three bird species. Alpha diversity analysis showed that in T. cyanurus, the richness and diversity of the gut microbiota were higher in male individuals than in female individuals, while the opposite was true for E. elegans and E. spodocephala. The alpha diversity analysis showed significant differences between male and female individuals of E. elegans (p < 0.05). The beta diversity analysis also revealed that the gut microbial community structure differed significantly between the male and female individuals of the three migratory bird species.

Temporal dynamics of Campylobacter and Arcobacter in a freshwater lake that receives fecal inputs from migratory geese

Migratory geese could influence the microbiological water quality; however, their impacts on pathogen dynamics remain largely unknown. In this study, we analyzed the population dynamics of Campylobacter and Arcobacter group bacteria (AGB) in a freshwater lake in Japan over two years. The bacteria were quantified by using both culture-dependent and -independent methods. The potential sources of these bacteria were examined by a high-throughput flaA sequencing approach. Campylobacter was abundantly detected both by culture-dependent and -independent methods in the lake, especially when migratory geese were present in the lake. High-throughput flaA sequencing suggests that geese were the likely source of Campylobacter in the lake. The viable population of Campylobacter exceeds the concentrations that can potentially cause 10^-4 infections per person per year when water is used to grow fresh vegetables. The occurrence of AGB, on the other hand, was not directly related to the population of migratory geese. AGB were not detected in geese fecal samples. Diverse AGB flaA genotypes occurred in the lake over multiple seasons. Our results suggest that AGB likely comprise a part of the indigenous microbial population of the lake and grow in response to high nutrient, warm temperature, and low dissolved oxygen concentrations in the lake. Geese therefore can indirectly impact the AGB population by providing nutrients to cause eutrophication and lower the dissolved oxygen concentration. Since geese travel long-distance and disperse their fecal microbiota and nutrients to wide areas, they may have significant impacts on water quality and public health.

Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use

Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences in the gut microbiome composition and the abundance of antibiotic resistance genes (ARGs) in faeces from four migratory waterbirds wintering in South-West Spain that differ in their habitat use. The white stork Ciconia ciconia and lesser black-backed gull Larus fuscus are omnivorous and opportunistic birds that use highly anthropogenic habitats such as landfills and urban areas. The greylag goose Anser anser and common crane Grus grus are herbivores and use more natural habitats. Fresh faeces from 15 individuals of each species were analysed to assess the composition of bacterial communities using 16S rRNA amplicon-targeted sequencing, and to quantify the abundance of the Class I integron integrase gene (intI1) as well as genes encoding resistance to sulfonamides (sul1), beta-lactams (bla_TEM, bla_KPC and bla_NDM), tetracyclines (tetW), fluoroquinolones (qnrS), and colistin (mcr-1) using qPCR. Bacterial communities in gull faeces were the richest and most diverse. Beta diversity analysis showed segregation in faecal communities between bird species, but those from storks and gulls were the most similar, these being the species that regularly feed in landfills. Potential bacterial pathogens identified in faeces differed significantly between bird species, with higher relative abundance in gulls. Faeces from birds that feed in landfills (stork and gull) contained a significantly higher abundance of ARGs (sul1, bla_TEM, and tetW). Genes conferring resistance to last resort antibiotics such as carbapenems (bla_KPC) and colistin (mcr-1) were only observed in faeces from gulls. These results show that these bird species are reservoirs of antimicrobial resistant bacteria and suggest that waterbirds may disseminate antibiotic resistance across environments (e.g., from landfills to ricefields or water supplies), and thus constitute a risk for their further spread to wildlife and humans.

Trends in the occurrence of large Whooping Crane groups during migration in the great plains, USA

Recent detections of large gatherings of Whooping Cranes suggest that flock sizes may be increasing at some stopover locations during both the spring and fall migrations. We used the public sightings database managed by the US Fish and Wildlife Service from 1942 to 2018 to analyze data for long-term trends in group size. We then examined the spatial distribution of large groups to explore potential explanations for these occurrences. The proportion of Whooping Crane groups comprised of 2, 3, and 4-6 individuals showed no trend over time. However, observations of individuals showed a declining trend and groups of 7-9 and ≥10 showed an increasing trend. The frequency of groups observed exceeding 5 and 10 individuals were better predicted by survey year than by Whooping Crane population size suggesting that an increasing population is not the sole driver of large group occurrences. Our results indicate that large groups occur disproportionately within the 50% migration corridor, at staging areas within the first or last 20-30% of the migration path, and near conservation-managed wetlands, particularly within the southern Great Plains. Our results suggest that in addition to population growth, conspecific attraction, location within the migration corridor, and habitat loss may be contributing to large group occurrences. Further research is needed to determine the degree to which these factors influence large Whooping Crane group formation. The gathering of large numbers of Whooping Cranes in a single location presents potential tradeoffs for the species. While increasing group sizes may improve threat detection and avoidance, it comes at a cost of increased disease and mass mortality risk.

Are we overestimating risk of enteric pathogen spillover from wild birds to humans?

Enteric illnesses remain the second largest source of communicable diseases worldwide, and wild birds are suspected sources for human infection. This has led to efforts to reduce pathogen spillover through deterrence of wildlife and removal of wildlife habitat, particularly within farming systems, which can compromise conservation efforts and the ecosystem services wild birds provide. Further, Salmonella spp. are a significant cause of avian mortality, leading to additional conservation concerns. Despite numerous studies of enteric bacteria in wild birds and policies to discourage birds from food systems, we lack a comprehensive understanding of wild bird involvement in transmission of enteric bacteria to humans. Here, we propose a framework for understanding spillover of enteric pathogens from wild birds to humans, which includes pathogen acquisition, reservoir competence and bacterial shedding, contact with people and food, and pathogen survival in the environment. We place the literature into this framework to identify important knowledge gaps. Second, we conduct a meta‐analysis of prevalence data for three human enteric pathogens, Campylobacter spp., E. coli, and Salmonella spp., in 431 North American breeding bird species. Our literature review revealed that only 3% of studies addressed the complete system of pathogen transmission. In our meta‐analysis, we found a Campylobacter spp. prevalence of 27% across wild birds, while prevalence estimates of pathogenic E. coli (20%) and Salmonella spp. (6.4%) were lower. There was significant bias in which bird species have been tested, with most studies focusing on a small number of taxa that are common near people (e.g. European starlings Sturnus vulgaris and rock pigeons Columba livia) or commonly in contact with human waste (e.g. gulls). No pathogen prevalence data were available for 65% of North American breeding bird species, including many commonly in contact with humans (e.g. black‐billed magpie Pica hudsonia and great blue heron Ardea herodias), and our metadata suggest that some under‐studied species, taxonomic groups, and guilds may represent equivalent or greater risk to human infection than heavily studied species. We conclude that current data do not provide sufficient information to determine the likelihood of enteric pathogen spillover from wild birds to humans and thus preclude management solutions. The primary focus in the literature on pathogen prevalence likely overestimates the probability of enteric pathogen spillover from wild birds to humans because a pathogen must survive long enough at an infectious dose and be a strain that is able to colonize humans to cause infection. We propose that future research should focus on the large number of under‐studied species commonly in contact with people and food production and demonstrate shedding of bacterial strains pathogenic to humans into the environment where people may contact them. Finally, studies assessing the duration and intensity of bacterial shedding and survival of bacteria in the environment in bird faeces will help provide crucial missing information necessary to calculate spillover probability. Addressing these essential knowledge gaps will support policy to reduce enteric pathogen spillover to humans and enhance bird conservation efforts that are currently undermined by unsupported fears of pathogen spillover from wild birds.

Campylobacter in an Urban Estuary: Public Health Insights from Occurrence, HeLa Cytotoxicity, and Caco-2 Attachment Cum Invasion

Aquatic recreation in urban estuaries worldwide is often restricted by fecal pollution. Variability in the occurrence of fecal pathogens and their differential virulence potentials within these estuaries may result in variable public health risks. To address this hypothesis, Campylobacter were isolated from the Yarra River estuary, Australia and then characterized via HeLa cell cytotoxicity and attachment to and the invasion of Caco-2 monolayers. Overall, 54% (n=216) of estuarine samples (water and sediment combined) yielded biochemically confirmed culturable Campylobacter; higher detection was recorded in water (92%, n=90) than in the bank and bed sediments combined (27%, n=126). The seasonality of occurrence was not significant. HeLa cell cytotoxicity revealed that estuarine Campylobacter had low cytotoxin titers; the 95% confidence interval (CI) ranged between 61 and 85, which was markedly lower than the mean value (~386) for the C. jejuni 11168 reference pathogenic strain. The Caco-2 attachment of estuarine Campylobacter isolates (n=189) revealed that the 95%CI for the attachment efficiency of the test strains ranged between 0.09 and 0.1%, with only 3.7% having a higher efficiency than the 5^th percentile value for C. jejuni 11168. None of the estuarine strains exhibited Caco-2 invasion capabilities. In contrast to the common assumption during quantitative microbial/risk assessments (QMRAs) that all environmental strains are pathogenic, the present results revealed that Campylobacter within the Yarra River estuary had very low virulence potential. Since this is the first study to use human epithelial cell lines to characterize estuary-borne pathogens, these results generate valuable insights for a better understanding of the public health risks in urban estuaries that will underpin more robust QMRAs.

A Gallus gallus Model for Determining Infectivity of Zoonotic Campylobacter

To better understand public health implications of waterfowl as reservoirs for zoonotic sources of Campylobacter in recreational waters, we developed a Gallus gallus (chick) model of infection to assess the pathogenicity of environmental isolates of Campylobacter. This method involved exposure of 1-day-old chicks through ingestion of water, the natural route of infection. Viable Campylobacter from laboratory-infected animals were monitored by using a modified non-invasive sampling of fresh chick excreta followed by a passive polycarbonate-filter migration culture assay. The method was used to evaluate the infectivities of three laboratory strains of Campylobacter spp. (Campylobacter coli, Campylobacter jejuni, and Campylobacter lari), three clinical isolates of C. jejuni, and four environmental Campylobacter spp. isolated from California gulls (Larus californicus). The results revealed that chicks were successfully infected with all laboratory and clinical isolates of Campylobacter spp. through ingestion of Campylobacter-spiked water, with infection rates ranging from <10 to >90% in a dose-dependent manner. More importantly, exposure of chicks with Campylobacter spp. isolated from Gallus gallus excreta also resulted in successful establishment of infection (≤90%). Each monitored Campylobacter spp. contained ≥7.5 × 10⁴ CFU⋅g^–1 of feces 7 days post-exposure. These results suggest that a G. gallus model can be used to assess infectivity of Campylobacter isolates, including gull and human clinical isolates. Use of an avian animal model can be applied to assess the importance of birds, such as the G. gallus, as potential contributors of waterborne-associated outbreaks of campylobacteriosis.

Validation and application of quantitative PCR assays using host-specific Bacteroidales genetic markers for swine fecal pollution tracking

Genome fragment enrichment (GFE) method was applied to identify host-specific bacterial genetic markers that differ among different fecal metagenomes. To enrich for swine-specific DNA fragments, swine fecal DNA composite (n = 34) was challenged against a DNA composite consisting of cow, human, goat, sheep, chicken, duck and goose fecal DNA extracts (n = 83). Bioinformatic analyses of 384 non-redundant swine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode metabolism-associated, cellular processes and information storage and processing. After challenged against fecal DNA extracted from different animal sources, four sequences from the clone libraries targeting two Bacteroidales- (genes 1-38 and 3-53), a Clostridia- (gene 2-109) as well as a Bacilli-like sequence (gene 2-95), respectively, showed high specificity to swine feces based on PCR analysis. Host-specificity and host-sensitivity analysis confirmed that oligonucleotide primers and probes capable of annealing to select Bacteroidales-like sequences (1-38 and 3-53) exhibited high specificity (>90%) in quantitative PCR assays with 71 fecal DNAs from non-target animal sources. The two assays also demonstrated broad distributions of corresponding genetic markers (>94% positive) among 72 swine feces. After evaluation with environmental water samples from different areas, swine-targeted assays based on two Bacteroidales-like GFE sequences appear to be suitable quantitative tracing tools for swine fecal pollution.

Identifying avian sources of faecal contamination using sterol analysis

Discrimination of the source of faecal pollution in water bodies is an important step in the assessment and mitigation of public health risk. One tool for faecal source tracking is the analysis of faecal sterols which are present in faeces of animals in a range of distinctive ratios. Published ratios are able to discriminate between human and herbivore mammal faecal inputs but are of less value for identifying pollution from wildfowl, which can be a common cause of elevated bacterial indicators in rivers and streams. In this study, the sterol profiles of 50 avian-derived faecal specimens (seagulls, ducks and chickens) were examined alongside those of 57 ruminant faeces and previously published sterol profiles of human wastewater, chicken effluent and animal meatwork effluent. Two novel sterol ratios were identified as specific to avian faecal scats, which, when incorporated into a decision tree with human and herbivore mammal indicative ratios, were able to identify sterols from avian-polluted waterways. For samples where the sterol profile was not consistent with herbivore mammal or human pollution, avian pollution is indicated when the ratio of 24-ethylcholestanol/(24-ethylcholestanol + 24-ethylcoprostanol + 24-ethylepicoprostanol) is ≥0.4 (avian ratio 1) and the ratio of cholestanol/(cholestanol + coprostanol + epicoprostanol) is ≥0.5 (avian ratio 2). When avian pollution is indicated, further confirmation by targeted PCR specific markers can be employed if greater confidence in the pollution source is required. A 66% concordance between sterol ratios and current avian PCR markers was achieved when 56 water samples from polluted waterways were analysed.

Water quality monitoring and risk assessment by simultaneous multipathogen quantification

Water quality monitoring and microbial risk assessment are important to ensure safe water for drinking, recreational, and agricultural purposes. In this study, we applied a microfluidic quantitative PCR (MFQPCR) approach to simultaneously quantify multiple waterborne pathogens in a natural freshwater lake in Hokkaido, Japan, from April to November, 2012. Tens of thousands of geese stopped over at this lake during their migration in spring and fall. Because lake water is used for irrigation of the surrounding agricultural area, we assessed infection risks through irrigation water usage based on pathogen concentrations directly measured by MFQPCR. We detected various pathogens in the lake water, particularly during the bird migration seasons, suggesting that migratory birds were the main source of the pathogens. However, neither counts of geese nor fecal indicator bacteria were good predictors of pathogen concentrations. On the basis of quantitative microbial risk assessment, concentrations of Campylobacter jejuni and Shigella spp. in water samples were above the concentrations that can potentially cause 10(-4) infections per person per year when water is used to grow fresh vegetables. These results suggest that direct and simultaneous multipathogen quantification can provide more reliable and comprehensive information for risk assessment than the current fecal indicator-based approach.

Intestinal microbiota and species diversity of Campylobacter and Helicobacter spp. in migrating shorebirds in Delaware Bay

Using 16S rRNA gene sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e., Campylobacter and Helicobacter) in red knot (Calidris canutus; n = 40), ruddy turnstone (Arenaria interpres; n = 35), and semipalmated sandpiper (Calidris pusilla; n = 22) fecal samples collected during a migratory stopover in Delaware Bay. Additionally, we studied the occurrence of Campylobacter spp., enterococci, and waterfowl fecal source markers using quantitative PCR (qPCR) assays. Of 3,889 16S rRNA clone sequences analyzed, the bacterial community was mostly composed of Bacilli (63.5%), Fusobacteria (12.7%), Epsilonproteobacteria (6.5%), and Clostridia (5.8%). When epsilonproteobacterium-specific 23S rRNA gene clone libraries (i.e., 1,414 sequences) were analyzed, the sequences were identified as Campylobacter (82.3%) or Helicobacter (17.7%) spp. Specifically, 38.4%, 10.1%, and 26.0% of clone sequences were identified as C. lari (>99% sequence identity) in ruddy turnstone, red knot, and semipalmated sandpiper clone libraries, respectively. Other pathogenic species of Campylobacter, such as C. jejuni and C. coli, were not detected in excreta of any of the three bird species. Most Helicobacter-like sequences identified were closely related to H. pametensis (>99% sequence identity) and H. anseris (92% sequence identity). qPCR results showed that the occurrence and abundance of Campylobacter spp. was relatively high compared to those of fecal indicator bacteria, such as Enterococcus spp., E. faecalis, and Catellicoccus marimammalium. Overall, the results provide insights into the complexity of the shorebird gut microbial community and suggest that these migratory birds are important reservoirs of pathogenic Campylobacter species.