Characterising the microbial communities associated with the water distribution system of a broiler farm and their role in Campylobacter infection

Campylobacters are zoonotic pathogens with extensive animal and environmental reservoirs in spite of their fastidious nature. Campylobacter jejuni is the main bacterial cause of human gastroenteritis worldwide. Epidemiological studies have identified chicken meat as the main vehicle for human infection in industrialised countries. In some countries in the developing world, however, there is little information about Campylobacter prevalence in poultry and poultry meat. The dynamics of Campylobacter colonisation of chickens remain poorly understood. It is agreed that in most cases Campylobacter is transmitted to chickens horizontally from the farm environment. Different sources have been recognised, but their actual contribution to Campylobacter epidemiology remains a matter of debate. Water has rarely been identified as a possible source of Campylobacter contamination of chickens, but represents an understudied source. Research suggests that natural microbial communities might promote the survival of Campylobacter in environmental reservoirs by enabling incorporation into biofilms or interaction with protozoa. The aim of this study was to improve our understanding of Campylobacter ecology and epidemiology at the chicken farm level. The main objectives were to unravel the microbial communities associated with the drinking water system of broiler farms and their dynamics through the rearing cycle; to investigate the aerobic survival of the pathogen in co-culture with Pseudomonas environmental isolates and Acanthamoeba polyphaga; and to study Campylobacter prevalence in chicken farms in Uganda.A longitudinal study was conducted in a commercial broiler farm in the UK during a whole rearing cycle. The purpose of this study was to gain an understanding about the microbial communities that inhabit the drinking water system of the broiler farm, and their implication in Campylobacter ecology in the chicken farm. 16S and 18S rRNA profiling of bulk water and biofilm samples were carried out over a seven-week production cycle period. The same samples were screened for the presence of Campylobacter by culture-dependent methods and molecular techniques. Analysis of 16S and 18S rRNA profiles suggested that microbial communities in the water distribution system are niche specific. Biofilm and bulk water samples harboured distinct communities. Moreover, bulk water communities inside the broiler house were significantly different from those sampled from the source water (R=0.88, p<0.05). Inside the broiler house, microbial communities were found to vary across the rearing cycle. Similar changes in the dynamics of prokaryotic and eukaryotic communities were observed. Bacterial communities were dominated by the phylum Proteobacteria with a shift to Firmicutes towards the end of the cycle, mainly due to an increase in relative abundance of the genera Staphylococcus and Lactobacillus. Eukaryotic communities included a diversity of yeasts, fungi and protozoa.Campylobacter spp. were not detected on the UK broiler farm by culture-dependent techniques. However, the emerging gastrointestinal pathogen Helicobacter pullorum was isolated by culture towards the end of the rearing cycle. Another emerging pathogen C. ureolyticus was detected by both 16S rRNA amplicon sequencing and PCR in water samples and chicken faeces. This is the first report of C. ureolyticus in association with poultry. 16S rRNA reads belonging to the genus Campylobacter were also found in the sequencing data towards the end of the rearing cycle suggesting that the pathogen could be in a viable but non-culturable state in the water distribution system.Little information is available on the epidemiology of campylobacteriosis in Africa. In Uganda Campylobacter infections have been reported in children, and gorillas have been identified as carriers but no information is available on Campylobacter prevalence in chickens. Studies in neighbouring countries, however, have shown high Campylobacter prevalence in poultry. A pilot study, visiting three small-scale farms around Fort Portal, was conducted to investigate the prevalence of Campylobacter in chickens in W. Uganda. Through a combination of culture-dependent and culture-independent techniques Campylobacter was detected in all three farms with high prevalence. Mixed presence of C. jejuni and C. coli in the same farm were observed, suggesting that chickens and chicken meat can be a source of human infection in Uganda.Pseudomonas spp. and protozoa of the genus Acanthamoeba are ubiquitous organisms that commonly co-localise in water and in the farm environment with Campylobacter. In vitro assays were performed to investigate whether they could enhance C. jejuni survival under atmospheric conditions. Co-culture assays indicated that certain Pseudomonas ssp. and strains were able to enhance Campylobacter survival with an increase in viable cell recovery ranging from 0.8 LOG to 4.5 LOG depending on the strain after 24 hours of aerobic incubation, while others showed no interactive effect or even reduced Campylobacter survival. A. polyphaga was shown to internalize C. jejuni, protecting it from the oxygen in the atmosphere and thus enhancing its survival with an increase in viable cell recovery of 2 LOG.These studies have further shown the importance of chicken farms in Campylobacter ecology. It has been demonstrated that microorganisms that are capable of enhancing Campylobacter survival in vitro are found in the water distribution system of the farm studied in UK. The characterisation of these communities for a whole rearing cycle has led to the detection of emerging human pathogens in broiler chicken production showing how doing exploratory work targeting whole microbial communities can inform epidemiology

Carbapenem-resistant Enterobacteriaceae dispersal from sinks is linked to drain position and drainage rates in a laboratory model system.

BACKGROUND: Hospital sinks, waste traps and drains can harbour carbapenem-resistant Enterobacteriaceae (CRE). AIM: To investigate the dispersal of CRE from sinks in which water delivered from the tap flows directly into the drain and from clinical handwash basins with the drain at the rear. The effect of fast and slow drainage rates was also assessed. METHODS: Waste traps, known to be colonized with CRE, were taken from a hospital and installed within a model laboratory system. New waste traps were also installed and artificially inoculated with CRE. The potential for bacteria to be dispersed from sinks was assessed using cyclone air samplers and/or settle plates. FINDINGS: When the waste traps were artificially contaminated and CRE colonization was confined to the waste trap water, significantly fewer bacteria were dispersed from sinks that drained quickly (P = 0.004) and/or from rear-draining sinks (P = 0.002). When the waste traps were naturally contaminated and CRE colonized the trap, pipework and drain, there was significant interaction between sink drainage and position of the drain (P < 0.001). When drainage was slow, dispersal from rear-draining sinks was almost 30-fold less than from sinks with the drain underneath the tap (P < 0.001). When drainage was fast, rear-draining sinks again released comparatively fewer CRE, although, in this case, the difference was not statistically significant (P = 0.7). Contaminated splashes travelled up to 1 m from the sink. CONCLUSION: Slow drainage rates and sink designs with the drain directly underneath the tap increase the risk of CRE present in waste traps and drains contaminating the ward environment

Persistence of SARS-CoV-2 virus and viral RNA in relation to surface type and contamination concentration

The transmission of SARS-CoV-2 is likely to occur through a number of routes, including contact with contaminated surfaces. Many studies have used RT-PCR analysis to detect SARS-CoV-2 RNA on surfaces but seldom has viable virus been detected. This paper investigates the viability over time of SARS-CoV-2 dried onto a range of materials and compares viability of the virus to RNA copies recovered, and whether virus viability is concentration dependant. Viable virus persisted for the longest time on surgical mask material and stainless steel with a 99.9% reduction in viability by 122 and 114 hours respectively. Viability of SARS-CoV-2 reduced the fastest on a polyester shirt, with a 99.9% reduction within 2.5 hours. Viability on the bank note was reduced second fastest, with 99.9% reduction in 75 hours. RNA on all the surfaces exhibited a one log reduction in genome copy recovery over 21 days. The findings show that SARS-CoV-2 is most stable on non-porous hydrophobic surfaces. RNA is highly stable when dried on surfaces with only one log reduction in recovery over three weeks. In comparison, SARS-CoV-2 viability reduced more rapidly, but this loss in viability was found to be independent of starting concentration. Expected levels of SARS-CoV-2 viable environmental surface contamination would lead to undetectable levels within two days. Therefore, when RNA is detected on surfaces it does not directly indicate presence of viable virus even at high CT values

A 17-month longitudinal surface sampling study carried out on public transport vehicles operating in England during the COVID-19 pandemic identified low levels of SARS-CoV-2 RNA contamination

AIMS: To monitor severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA contamination in vehicles operating in England during the pandemic, to better understand transmission risk of SARS-CoV-2 on public transport. METHODS AND RESULTS: We collected 1 314 surface samples between December 2020 and April 2022 on trains and buses managed by five different transport operators. The presence of SARS-CoV-2 RNA was investigated through reverse transcription polymerase chain reaction (RT-PCR). SARS-CoV-2 RNA was found on 197 (15%) of the 1 314 surfaces sampled, including seat head rests, handholds, and air extract grilles, but the levels of RNA recovered on those samples (median value of 23.4, inter-quartile range: 14.3-35.4, N gene copies per extraction) made the presence of infectious virus at the time of sampling extremely unlikely. However, detection rates varied over time with peaks broadly coinciding with times of high community transmission, when it was more likely that people infected with SARS-CoV-2 were travelling on public transport. CONCLUSION: During the pandemic, and as in other public spaces, low levels of SARS-CoV-2 RNA were found on surfaces associated with public transport

Detection of SARS-CoV-2 within the healthcare environment: a multi-centre study conducted during the first wave of the COVID-19 outbreak in England

Background Understanding how severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is spread within the hospital setting is essential in order to protect staff, implement effective infection control measures, and prevent nosocomial transmission. Methods The presence of SARS-CoV-2 in the air and on environmental surfaces around hospitalized patients, with and without respiratory symptoms, was investigated. Environmental sampling was undertaken within eight hospitals in England during the first wave of the coronavirus disease 2019 outbreak. Samples were analysed using reverse transcription polymerase chain reaction (PCR) and virus isolation assays. Findings SARS-CoV-2 RNA was detected on 30 (8.9%) of 336 environmental surfaces. Cycle threshold values ranged from 28.8 to 39.1, equating to 2.2 x 105 to 59 genomic copies/swab. Concomitant bacterial counts were low, suggesting that the cleaning performed by nursing and domestic staff across all eight hospitals was effective. SARS-CoV-2 RNA was detected in four of 55 air samples taken <1 m from four different patients. In all cases, the concentration of viral RNA was low and ranged from <10 to 460 genomic copies/m3 air. Infectious virus was not recovered from any of the PCR-positive samples analysed. Conclusions Effective cleaning can reduce the risk of fomite (contact) transmission, but some surface types may facilitate the survival, persistence and/or dispersal of SARS-CoV-2. The presence of low or undetectable concentrations of viral RNA in the air supports current guidance on the use of specific personal protective equipment for aerosol-generating and non-aerosol-generating procedures