Nanopore sequencing for identification and characterization of antimicrobial-resistant Escherichia coli and Salmonella spp. from tilapia and shrimp sold at wet markets in Dhaka, Bangladesh.

Wet markets in low-and middle-income countries are often reported to have inadequate sanitation resulting in fecal contamination of sold produce. Consumption of contaminated wet market-sourced foods has been linked to individual illness and disease outbreaks. This pilot study, conducted in two major wet markets in Dhaka city, Bangladesh during a 4-month period in 2021 aimed to assess the occurrence and characteristics of Escherichia coli and non-typhoidal Salmonella spp. (NTS) from tilapia (Oreochromis niloticus) and shrimp (Penaeus monodon). Fifty-four individuals of each species were collected. The identity of the bacterial isolates was confirmed by PCR and their susceptibility toward 15 antimicrobials was tested by disk diffusion. The whole genome of 15 E. coli and nine Salmonella spp. were sequenced using Oxford Nanopore Technology. E. coli was present in 60-74% of tilapia muscle tissue and 41-44% of shrimp muscle tissue. Salmonella spp. was found in skin (29%) and gills (26%) of tilapia, and occasionally in muscle and intestinal samples of shrimp. The E. coli had several Multilocus sequence typing and serotypes and limited antimicrobial resistance (AMR) determinants, such as point mutations on glpT and pmrB. One E. coli (BD17) from tilapia carried resistance genes for beta-lactams, quinolones, and tetracycline. All the E. coli belonged to commensal phylogroups B1 and A and showed no Shiga-toxin and other virulence genes, confirming their commensal non-pathogenic status. Among the Salmonella isolates, five belonged to Kentucky serovar and had similar AMR genes and phenotypic resistance patterns. Three strains of this serovar were ST198, often associated with human disease, carried the same resistance genes, and were genetically related to strains from the region. The two undetermined sequence types of S. Kentucky were distantly related and positioned in a separate phylogenetic clade. Two Brunei serovar isolates, one Augustenborg isolate, and one Hartford isolate showed different resistance profiles. This study revealed high fecal contamination levels in tilapia and shrimp sold at two main wet markets in Dhaka. Together with the occurrence of Salmonella spp., including S. Kentucky ST198, a well-known human pathogen, these results stress the need to improve hygienic practices and sanitation standards at markets to improve food safety and protect consumer health.

Rational use of inhaled corticosteroids for the treatment of COPD: a plain language summary.

WHAT IS THIS SUMMARY ABOUT?: Inhaled corticosteroids (ICS) are a type of medication delivered via an inhaler device that are commonly used in the treatment of asthma. ICS can also be used to treat chronic obstructive pulmonary disease (COPD), a progressive respiratory condition in which the lungs become worse over time. However, unlike in asthma, ICS are only effective in a small proportion of people with COPD. ICS can cause significant side effects in people with COPD, including pneumonia. Because of this, guidelines written by COPD experts recommend that ICS should largely be prescribed to people with COPD whose symptoms flare up frequently and become difficult to manage (episodes known as exacerbations). Despite this guidance, records collected from routine clinical practice suggest that many healthcare professionals prescribe ICS to people with COPD who do not have frequent exacerbations, putting them at unnecessary risk of side effects. The over-prescription of ICS in COPD may partly be due to the recent introduction of single-inhaler combination therapies, which combine ICS with other medicines (bronchodilators). This 'one inhaler for all' approach is a concerning trend as it goes against global COPD treatment guidelines, which recommend ICS use in only a small proportion of people. This is a plain language summary of a review article originally published in the journal NPJ Primary Care Respiratory Medicine. In this review, we investigate the benefits and risks of ICS use in COPD. Using data from both randomized controlled trials (RCTs) and observational studies, we explain which people benefit from ICS use, and why health regulatory bodies have concluded that ICS do not help people with COPD to live longer. Lastly, we provide practical guidance for doctors and people with COPD regarding when ICS should be prescribed and when they should be withdrawn.

Comparative genomics uncovered differences between clinical and environmental populations of Vibrio parahaemolyticus in New Zealand.

Vibrio parahaemolyticus has been identified as an emerging human pathogen worldwide with cases undergoing a global expansion over recent decades in phase with climate change. New Zealand had remained free of outbreaks until 2019, but different outbreaks have been reported consecutively since then. To provide new insights into the recent emergence of cases associated with outbreak clones over recent years, a comparative genomic study was carried out using a selection of clinical (mostly outbreak) and environmental isolates of V. parahaemolyticus obtained in New Zealand between 1973 and 2021. Among 151 isolates of clinical (n=60) and environmental (n=91) origin, 47 sequence types (STs) were identified, including 31 novel STs. The population of environmental isolates generated 30 novel STs, whereas only 1 novel ST (ST2658) was identified among the population of clinical isolates. The novel clinical ST was a single-locus variant of the pandemic ST36 strain, indicating further evolution of this pandemic strain. The environmental isolates exhibited a significant genetic heterogeneity compared to the clinical isolates. The whole-genome phylogeny separated the population of clinical isolates from their environmental counterparts, clearly indicating their distant genetic relatedness. In addition to differences in ancestral profiles and genetic relatedness, these two groups of isolates exhibited a profound difference in their virulence profiles. While the entire population of clinical isolates harboured the thermostable direct haemolysin (tdh) and/or the thermostable-related haemolysin (trh), only a few isolates of environmental origin possessed the same virulence genes. In contrast to tdh and trh, adhesin-encoding genes, vpadF and MSHA, showed a significantly (P<0.001) greater association with the environmental isolates compared to the clinical isolates. The effectors, VopQ, VPA0450 and VopS, which belong to T3SS1, were ubiquitous, being present in each isolate regardless of its origin. The effectors VopC and VopA, which belong to T3SS2, were rarely detected in any of the examined isolates. Our data indicate that the clinical and environmental isolates of V. parahaemolyticus from New Zealand differ in their population structures, ancestral profiles, genetic relatedness and virulence profiles. In addition, we identified numerous unique non-synonymous single-nucleotide polymorphisms (nsSNPs) in adhesins and effectors, exclusively associated with the clinical isolates tested, which may suggest a possible role of these mutations in the overall virulence of the clinical isolates.

Marine water quality of a densely populated Pacific atoll (Tarawa, Kiribati): Cumulative pressures and resulting impacts on ecosystem and human health.

The resilience of coastal ecosystems and communities to poor environmental and health outcomes is threatened by cumulative anthropogenic pressures. In Kiribati, a developing Pacific Island country where human activities are closely connected with the ocean, both people and environment are particularly vulnerable to coastal pollution. We present a survey of environmental and human health water quality parameters around urban South Tarawa, and an overview of their impacts on the semi-enclosed atoll. Tarawa has significant water quality issues and decisions to guide improvements are hindered by a persistent lack of appropriate and sufficient observations. Our snapshot assessment identifies highest risk locations related to chronic focused and diffuse pollution inputs, and where mixing and dilution with ocean water is restricted. We demonstrate the importance of monitoring in the context of rapidly changing pressures. Our recommendations are relevant to other atoll ecosystems where land-based activities and ocean health are tightly interlinked.

Effectiveness of thicker hamstring or patella tendon grafts to reduce graft failure rate in anterior cruciate ligament reconstruction in young patients.

PURPOSE: The purpose of this study was to determine the anterior cruciate ligament reconstruction (ACLR) failure rate in young patients utilizing the New Zealand (NZ) anterior cruciate ligament (ACL) Registry. The hypothesis was that the ACLR rupture rate would be lower for thicker hamstring graft and bone patellar tendon bone (BPB) grafts in comparison to the classic hamstring technique. The ACLR failure rate was assessed according to graft type and patients' sex. METHODS: The NZ ACL registry was utilized to identify all patients aged 20 years or younger at the time of surgery who were skeletally mature and had a minimum 2-year follow-up. Graft ruptures, defined as an ACL revision, were identified according to graft type (traditional 4 strands hamstring semitendinosus and gracilis, 4 strands semitendinosus, 5-6 strands semitendinosus and gracilis, 7-8 strands semitendinosus and gracilis, bone-patella-bone graft). RESULTS: Nine-hundred and ninety-two patients were included. At a mean follow-up of 38 months, 52 cases of graft rupture were recorded, (overall failure rate: 5.2%). The failure rate was not statistically influenced by the graft diameter. Patients with a thinner graft (< 8 mm-196 patients) had a similar failure rate (6%) to patients with a thicker graft (8 mm or more-485 patients) (6.2%). There was a lower failure rate in the BPB group (3.1%) versus all hamstrings group (6%) (ns). Finally, BPB in females had a lower failure rate than all hamstring constructs together (0% versus 5.1%; p = 0.023) CONCLUSION: In a young population traditional four-strand hamstring grafts, multiple strand configurations or BPB ACLR, whatever their size (> or < 8 mm), showed no significant difference in the failure rate in the NZ ACL registry. Female patients who had an ACL reconstruction with BPB graft had a significant lower failure rate than patients who had a hamstring graft. LEVEL OF EVIDENCE: III.

Isolation and characterization of potentially pathogenic Vibrio species in a temperate, higher latitude hotspot.

The recent emergence of Vibrio infections at high latitudes represents a clear human health risk attributable to climate change. Here, we investigate the population dynamics of three Vibrio species: Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae within a British coastal estuarine site, with contrasting salinity and temperature regimes during an intense heatwave event. Water samples were collected weekly through the summer of 2018 and 2019 and filtered using membrane filtration and subsequently grown on selective media. Suspected vibrios were confirmed using a conventional species-specific PCR assay and further analysed for potential pathogenic markers. Results showed that Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae were present at high concentrations throughout both years, with their populations at substantially greater abundances corresponding to conditions of higher water temperatures during the heatwave of 2018 and at lower salinity sites, which is comparable to the results of previous studies. A subset of strains isolated during the extreme heatwave event in 2018 (46 Vibrio parahaemolyticus, 11 Vibrio cholerae and 4 Vibrio vulnificus) were genomically sequenced. Analysis of these 63 sequenced strains revealed a broad phenotypic and genomic diversity of strains circulating in the environment. An analysis of pathogenicity attributes identified a broad array of virulence genes across all three species, including a variety of genes associated with human disease. This study highlights the importance of the need for an increased Vibrio spp. surveillance system in temperate regions and the potential impact warming events such as heatwaves may have on the abundance of potentially pathogenic bacteria in the environment.

New Invasive Nemertean Species (Cephalothrix Simula) in England with High Levels of Tetrodotoxin and a Microbiome Linked to Toxin Metabolism.

The marine nemertean Cephalothrix simula originates from the Pacific Ocean but in recent years has been discovered in northern Europe. The species has been associated with high levels of the marine neurotoxin Tetrodotoxin, traditionally associated with Pufferfish Poisoning. This study reports the first discovery of two organisms of C. simula in the UK, showing the geographical extent of this species is wider than originally described. Species identification was initially conducted morphologically, with confirmation by Cox 1 DNA sequencing. 16S gene sequencing enabled the taxonomic assignment of the microbiome, showing the prevalence of a large number of bacterial genera previously associated with TTX production including Alteromonas, Vibrio and Pseudomonas. LC-MS/MS analysis of the nemertean tissue revealed the presence of multiple analogues of TTX, dominated by the parent TTX, with a total toxin concentration quantified at 54 µg TTX per g of tissue. Pseudomonas luteola isolated from C. simula, together with Vibrio alginolyticus from the native nemertean Tubulanus annulatus, were cultured at low temperature and both found to contain TTX. Overall, this paper confirms the high toxicity of a newly discovered invasive nemertean species with links to toxin-producing marine bacteria and the potential risk to human safety. Further work is required to assess the geographical extent and toxicity range of C. simula along the UK coast in order to properly gauge the potential impacts on the environment and human safety.

Epidemic Dynamics of Vibrio parahaemolyticus Illness in a Hotspot of Disease Emergence, Galicia, Spain.

Galicia in northwestern Spain has been considered a hotspot for Vibrio parahaemolyticus infections. Infections abruptly emerged in 1998 and, over the next 15 years, were associated with large outbreaks caused by strains belonging to a single clone. We report a recent transition in the epidemiologic pattern in which cases throughout the region have been linked to different and unrelated strains. Global genome-wide phylogenetic analysis revealed that most of the pathogenic strains isolated from infections were associated with globally diverse isolates, indicating frequent episodic introductions from disparate and remote sources. Moreover, we identified that the 2 major switches in the epidemic dynamics of V. parahaemolyticus in the regions, the emergence of cases and an epidemiologic shift in 2015-2016, were associated with the rise of sea surface temperature in coastal areas of Galicia. This association may represent a fundamental contributing factor in the emergence of illness linked to these introduced pathogenic strains.

Epidemiological investigation of a foodborne outbreak in Spain associated with U.S. West Coast genotypes of Vibrio parahaemolyticus.

We describe an outbreak of seafood-associated Vibrio parahaemolyticus in Galicia, Spain in on 18th of August 2012 affecting 100 of the 114 passengers travelling on a food banquet cruise boat. Epidemiological information from 65 people was available from follow-on interviews, of which 51 cases showed symptoms of illness. The food items identified through the questionnaires as the most probable source of the infections was shrimp. This product was unique in showing a statistically significant and the highest OR with a value of 7.59 (1.52-37.71). All the nine strains isolated from stool samples were identified as V. parahaemolyticus, seven were positive for both virulence markers tdh and trh, a single strain was positive for trh only and the remaining strain tested negative for both trh and tdh. This is the largest foodborne Vibrio outbreak reported in Europe linked to domestically processed seafood. Moreover, this is the first instance of strains possessing both tdh+ and trh+ being implicated in an outbreak in Europe and that a combination of strains represent several pathogenicity groups and belonging to different genetic variants were isolated from a single outbreak. Clinical isolates were associated with a novel genetic variant of V. parahaemolyticus never detected before in Europe. Further analyses demonstrated that the outbreak isolates showed indistinguishable genetic profiles with hyper-virulent strains from the Pacific Northwest, USA, suggesting a recent transcontinental spread of these strains.

Fate of Human Noroviruses in Shellfish and Water Impacted by Frequent Sewage Pollution Events.

Knowledge of the fate of human noroviruses (NoV) in the marine environment is key to better controlling shellfish-related NoV gastroenteritis. We quantified NoV and Escherichia coli in sewage from storm tank discharges and treated effluent processed by a UV-disinfection plant following activated sludge treatment and studied the fate of these microorganisms in an oyster harvesting area impacted by frequent stormwater discharges and infrequent freshwater discharges. Oyster monitoring sites were positioned at intervals downstream from the wastewater treatment works (WwTW) outfall impacting the harvesting area. The decay rates of NoV in oysters as a function of the distance from the outfall were less rapid than those for E. coli that had concentrations of NoV of the same order of magnitude and were over 7 km away from the outfall. Levels of E. coli in oysters from more tidally influenced areas of the estuary were higher around high water than around low water, whereas tidal flows had no influence on NoV contamination in the oysters. The study provides comparative data on the contamination profiles and loadings of NoV and E. coli in a commercial oyster fishery impacted by a WwTW.

Novel application of high pressure processing for the production of shellfish toxin matrix reference materials.

The production of homogeneous and stable matrix reference materials for marine biotoxins is important for the validation and implementation of instrumental methods of analysis. High pressure processing was investigated to ascertain potential advantages this technique may have in stabilising paralytic shellfish poisoning toxins in shellfish tissues compared to untreated materials. Oyster tissues were subjected to a range of different temperatures and pressures, with results showing a significant reduction in biological activity in comparison to control samples, without significantly altering toxin profiles. Tissue subjected to pressures >600 MPa at 50 °C was assessed for homogeneity and stability. The sample homogeneity was determined using a pre-column oxidation LC-FLD method and shown to be within accepted levels of within batch repeatability. Short and long-term stability studies were conducted over a range of temperatures, with analysis by pre and post column oxidation LC-FLD demonstrating improved stability of toxins compared to the untreated materials and with epimerisation of toxins also notably reduced in treated materials. This study confirmed the technique of high pressure processing to improve the stability of PSP toxins compared to untreated wet tissues and highlighted its applicability in reference material preparation where removal of biological activity is of importance.

Feasibility studies into the production of gamma-irradiated oyster tissue reference materials for paralytic shellfish poisoning toxins.

A study was conducted to assess the feasibility for the production of sterile, stable and homogenous shellfish reference materials containing known concentrations of paralytic shellfish poisoning (PSP) toxins. Pacific oysters were contaminated with toxins following mass culturing of toxic algae and shellfish feeding experiments. Live oysters were shucked and tissues homogenised, before measuring into multiple aliquots, with one batch subjected to gamma irradiation treatment and the other remaining untreated. The homogeneity of both batches of samples was assessed using a pre-column oxidation liquid chromatography with fluorescence detection (Pre-COX LC-FLD) method and shown to be within the limits of normal within-batch repeatability. A twelve-month stability experiment was conducted for both untreated and gamma irradiated batches, specifically examining the effects of long term storage at -20 °C, +4 °C and +40 °C. Results indicated mostly good stability of PSP toxins in both materials when stored frozen at -20 °C, but with the instability of GTX2&3 concentrations in the untreated tissues eliminated in the irradiated tissues. Analysis using a post-column oxidation (PCOX) LC-FLD method also showed epimerisation in both GTX1&4 and GTX2&3 epimeric pairs in untreated samples after only 6 months frozen storage. This issue was not present in the tissues irradiated before long term storage. Biological activity testing confirmed the absence of bacteria in the irradiated samples throughout the 12 month study period. With such results there was clear evidence for the potential of increasing the scale of the mass culturing and shellfish feeding for the production of large batches of tissue suitable for the preparation of a certified matrix reference material. Overall results demonstrated the feasibility for production of oyster reference materials for PSTs, with evidence for prolonged stability following gamma irradiation treatment and storage at -20 °C.

Isolation of pandemic Vibrio parahaemolyticus from UK water and shellfish produce.

Vibrio parahaemolyticus is a Gram-negative, halophilic bacterium found commonly in temperate and warm estuarine waters worldwide. V. parahaemolyticus is considered an emerging bacterial pathogen in Europe and has been responsible for several recent seafood-associated outbreaks. During ad hoc testing of raw shellfish produce in May 2012, pandemic group (O3:K6) V. parahaemolyticus was isolated from Pacific oysters (Crassostrea gigas), harvested in Southern England. Follow-on testing of water and shellfish, encompassing a small number geographically diverse sites, also retrieved pandemic group isolates. These strains are amongst the most northerly pandemic strains described to date and represent the first instance of pandemic V. parahaemolyticus isolated in the UK, highlighting the expanding geographical distribution of these foodborne pathogens in the environment.

Flexible services for the support of research.

Cloud computing has been increasingly adopted by users and providers to promote a flexible, scalable and tailored access to computing resources. Nonetheless, the consolidation of this paradigm has uncovered some of its limitations. Initially devised by corporations with direct control over large amounts of computational resources, cloud computing is now being endorsed by organizations with limited resources or with a more articulated, less direct control over these resources. The challenge for these organizations is to leverage the benefits of cloud computing while dealing with limited and often widely distributed computing resources. This study focuses on the adoption of cloud computing by higher education institutions and addresses two main issues: flexible and on-demand access to a large amount of storage resources, and scalability across a heterogeneous set of cloud infrastructures. The proposed solutions leverage a federated approach to cloud resources in which users access multiple and largely independent cloud infrastructures through a highly customizable broker layer. This approach allows for a uniform authentication and authorization infrastructure, a fine-grained policy specification and the aggregation of accounting and monitoring. Within a loosely coupled federation of cloud infrastructures, users can access vast amount of data without copying them across cloud infrastructures and can scale their resource provisions when the local cloud resources become insufficient.

Potential use of gamma irradiation in the production of mussel and oyster reference materials for paralytic shellfish poisoning toxins.

Bivalve shellfish samples containing paralytic shellfish poisoning toxins were subjected to gamma irradiation dosage trials in order to assess the potential suitability of the technique in the production of toxin reference materials. Two candidate reference materials of tissue homogenates, mussels (Mytilus sp.) and native oysters (Ostrea edulis), were prepared in-house. Both were subjected to gamma irradiation at four different dose levels, 3.0, 6.0, 13.0 and 18.1 kGy. Bacterial levels were shown to be eliminated in the mussels and significantly reduced in the oysters following irradiation at all four dose levels. Paralytic shellfish poisoning (PSP) toxin concentrations were not significantly reduced in any of the samples indicating the treatment had no adverse affect on the initial stability of any of the PSP toxins monitored. Chromatographic results showed near-identical profiles for treated and non-treated samples inferring that no fluorescent toxin degradation products or matrix interferences were produced during the irradiation process. Results therefore proved that gamma irradiation treatment reduced bacterial levels within paralytic shellfish poisoning reference materials without compromising analyte content, with the subsequent potential to enhance the stability of future candidate reference materials treated in this manner.