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bioRxiv2022

Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA

The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 100 immunologically-distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally-disseminated strain, GPSC12 (CC180), which was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage {phi}OXC141. Prior to the introduction of PCV13, this clades composition shifted towards a {phi}OXC141-negative subpopulation in a systematically-sampled UK collection. In the post-PCV era, more rapidly-recombining non-Clade I isolates, also {phi}OXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the [~]100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage {phi}OXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in [~]30% of all pneumococci, and was particularly common in the unusually-clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR data demonstrated the altered csRNA3 was more effective at inhibiting production of the competence stimulating peptide pheromone. This interference with the quorum sensing needed to induce competence lowered the rate of spontaneous transformation, reducing the risk of the prophage being deleted by homologous recombination. Hence the selfish prophage-driven alteration of a regulatory RNA limits cell-cell communication and horizontal gene transfer, complicating the interpretation of post-vaccine population dynamics.

microbiology↗

bioRxiv2022

Genomic epidemiology of Corynebacterium diphtheriae in New Caledonia

ObjectivesAn increasing number of isolations of Corynebacterium diphtheriae has been observed in recent years in the archipelago of New Caledonia. We aimed to analyze the clinical and microbiological features of samples with C. diphtheriae. MethodsAll C. diphtheriae isolates identified in New Caledonia from May 2015 to May 2019 were included. For each case, a retrospective consultation of the patient files was conducted. Antimicrobial susceptibility phenotypes, tox gene and diphtheria toxin expression, biovar and the genomic sequence were determined. Core genome multilocus sequence typing (cgMLST), 7-gene MLST and search of genes of interest were performed from genomic assemblies. Results58 isolates were included, with a median age of patients of 28 years (range: 9 days to 78 years). Cutaneous origin accounted for 51 of 58 (87.9%) isolates, and C. diphtheriae was associated with Staphylococcus aureus and/or Streptococcus pyogenes in three quarters of cases. Half of cases came either from the main city Noumea (24%, 14/58) or from the sparsely populated island of Lifou (26%, 15/58). Six tox-positive isolates were identified, associated with recent travel to Vanuatu; 5 of these cases were linked and cgMLST confirmed recent transmission. Two cases of endocarditis in young female patients with a history of rheumatic fever involved tox-negative isolates. The 58 isolates were mostly susceptible to commonly used antibiotics. In particular, no isolate was resistant to the first-line molecules amoxicillin or erythromycin. Resistance to tetracycline was found in a genomic cluster of 17 (29%) isolates, 16 of which carried the tetO gene. There were 13 cgMLST sublineages, most of which were also observed in the neighboring country Australia. ConclusionsCutaneous infections may harbor non-toxigenic C. diphtheriae isolates, which circulate largely silently in non-specific wounds. The possible introduction of tox-positive strains from a neighboring island illustrates that diphtheria surveillance should be maintained in New Caledonia, and that immunization in neighboring islands must be improved. Genomic sequencing uncovers how genotypes circulate locally and across neighboring countries.

microbiology↗

bioRxiv2022

Leveraging PDE solver for predicting transient space-use dynamics in ecological and epidemiological systems

Model predictions of animal and human space-use patterns stemming from individual-level movement behaviors have not only contributed significantly to our understanding of population and community dynamics, but they could also inform the development of conservation, natural resource management, and disease control policies. The recent proliferation of high-resolution movement data has ushered in a paradigm shift in how space use is considered: instead of being defined narrowly as the stationary, long-term distribution of individual locations, there is a growing recognition of its transient dynamics, e.g.., how space-use pattern varies before it eventually stabilizes. However, movement models are slow to follow due to longstanding technical challenges in solving transient space-use dynamics. Here, we introduce a numerical framework that enables transient analysis of mechanistic movement models based on partial differential (Fokker-Planck) equations. We demonstrate its potential applications in the context of general research questions in movement ecology using classical and new case studies as illustrations. We demonstrate the frameworks applications and versatility in classical home range models, but also show how it may be extended to address new ecological questions.

ecology↗

bioRxiv2022

High growing season temperatures limit winter recovery of grapevines from Xylella fastidiosa infection: implications for epidemiology in hot climates

Management of widespread plant pathogens is challenging as climatic differences among crop growing regions may alter key aspects of pathogen spread and disease severity. Xylella fastidiosa is a xylem-limited bacterial pathogen that is transmitted by xylem sap feeding insects. Geographic distribution of X. fastidiosa is limited by winter climate and vines infected with X. fastidiosa can recover from infection when held at cold temperatures. California has a long history of research on Pierces disease, and significant geographic and climatic diversity among grape-growing regions. This background in combination with experimental disease studies under controlled temperature conditions can inform risk assessment for X. fastidiosa spread and epidemic severity across different regions and under changing climate conditions. Californias grape growing regions have considerable differences in summer and winter climate. In northern and coastal regions, summers are mild and winters cool, conditions favoring winter recovery of infected vines. In contrast, in inland and southern areas summers are hot and winters mild, reducing likelihood of winter recovery. Here, winter recovery of three table grape cultivars (Flame, Scarlet Royal, and Thompson seedless) and three wine grape cultivars (Sauvignon Blanc, Cabernet Sauvignon, and Zinfandel) were evaluated under temperature conditions representative of the San Joaquin Valley, an area with hot summers and mild winters that has been severely impacted by Pierces disease, and contains a large portion of California grape production. Mechanically inoculated vines were held in the greenhouse under one of three warming treatments to represent different seasonal inoculation dates prior to being moved into a cold chamber. Winter recovery under all treatments was generally limited, but with some cultivar variation. Given hot summer temperatures of many grape-growing regions worldwide, as well as increasing global temperatures overall, winter recovery of grapevines should not be considered a key factor affecting X. fastidiosa spread and epidemic severity in the majority of cases.

microbiology↗

bioRxiv2022

Genetic and structural data on the SARS-CoV-2 Omicron BQ.1 variant reveal its low potential for epidemiological expansion

The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 carries out some additional spike mutations in some key antigenic site which confer it further immune escape ability over other circulating lineage. In such a context, here we performed a genome-based survey aimed to obtain an as complete as possible nuance of this rapidly evolving Omicron subvariant. Genetic data suggests that BQ.1 represents an evolutionary blind background, lacking of the rapid diversification which is typical of a dangerous lineage. Indeed, the evolutionary rate of BQ.1 is very similar to that of BA.5 (7.6 x 10-4 and 7 x 10-4 subs/site/year, respectively), which is circulating by several months. Bayesian Skyline Plot reconstruction, indicates low level of genetic variability, suggesting that the peak has been reached around September 3, 2022. Structure analyses performed by comparing the properties of BQ.1 and BA.5 RBD indicated that the impact of the BQ.1 mutations on the affinity for ACE2 may be modest. Likewise, immunoinformatic analyses showed modest differences between the BQ.1 and the BA5 potential B-cells epitope. In conclusion, genetic and structural analysis on SARS-CoV-2 BQ.1 suggest that, it does not show evidence about its particular dangerous or high expansion capability. The monitoring genome-based must continue uninterrupted for a better understanding of its descendant and all other lineages.

molecular biology↗

bioRxiv2022

A la carte, Streptococcus pneumoniae capsular typing: using MALDI-TOF mass spectrometry and machine learning algorithms as complementary tools for the determination of PCV13 serotypes and the most prevalent NON PCV13 serotypes according to Argentina's epidemiology.

Laboratory surveillance of Streptococcus pneumoniae serotypes is crucial for the successful implementation of vaccines to prevent invasive pneumococcal diseases. The reference method of serotyping is the Quellung reaction, which is labor-intensive and expensive. In the last few years, the introduction of MALDI-TOF MS into the microbiology laboratory has been revolutionary. In brief, this new technology compares protein profiles by generating spectra based on the mass to charge ratio (m/z). We evaluated the performance of MALDI-TOF MS for typing serotypes of S. pneumoniae isolates included in the PCV13 vaccine using a machine learning approach. We challenged our classification algorithms in "real time" with a total of new 100 isolates of S. pneumoniae from Argentinian nationwide surveillance. Our best approach could correctly identify the isolates with a sensitivity of 58.33 % ([95%IC 40.7-71.7]); specificity of 81.48 % ([95%IC 53.6-79.7]); accuracy of 63.0% ([95%IC 61.9-93.7]); PPV of 80.77% ([95%IC 64.5-90.6]) and NPV of 59.46% ([95%IC 48.9-69.2]). In this work, it was possible to demonstrate that the combination of MALDI-TOF mass spectrometry and multivariate analysis allows the development of new strategies for the identification and characterization of Spn isolates of clinical importance; and we consider that by using AI, as more data becomes available the models will get better and more precise.

microbiology↗

bioRxiv2023

Long-term epidemiology and evolution of swine influenza viruses in Vietnam

Swine influenza virus (SwIV) surveillance in Hanoi, Vietnam from 2013-2019 found gene pool enrichment from imported swine from Asia and North America. Long-term maintenance, persistence and reassortment of SwIV lineages was observed. Co-circulation of H1-{delta}1a viruses with other SwIV genotypes raises concern due to its zoonotic potential.

microbiology↗

bioRxiv2023

The role of airborne particles in the epidemiology of clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus in commercial poultry production units

Since October 2021, Europe has experienced the largest avian influenza virus (AIV) epizootic, caused by clade 2.3.4.4b H5N1 high pathogenicity AIV (HPAIV), with over 320 poultry and captive bird infected premises (IPs) and 2480 dead H5N1 positive wild birds detected in Great Britain alone. Many IPs have been detected as geographical clusters, raising questions around potential lateral spread between premises by airborne particles. Airborne transmission over short distances has been reported for some AIVs strains. However, the risk of airborne spread of this strain remains to be elucidated. We conducted extensive sampling from IPs where clade 2.3.4.4b H5N1 HPAIVs was confirmed during the 2022/23 epizootic, each representing a major poultry species (ducks, turkeys, and chickens). A range of environmental samples were collected inside and outside houses, including deposited dust, feathers, and other potential fomites. Viral RNA (vRNA) and infectious virus were detected in air samples collected from inside and outside, but in close proximity, of infected houses, with vRNA alone being detected greater distances (>10m) outside. Some dust samples collected outside of the affected houses contained infectious virus, while feathers from the affected houses, located up to 60m away, only contained vRNA. Together, these data suggest that airborne particles harbouring infectious HPAIV can be translocated short distances (<10m) through the air, while particles containing vRNA might travel further (<50m). Therefore, the potential for airborne transmission of clade 2.3.4.4b H5N1 HPAIV between premises is considered low. Other factors, including indirect contact with wild birds, fomite spread and the efficiency of biosecurity represent greater importance in disease incursion. IMPORTANCEUnderstanding the routes of avian influenza virus incursion into poultry premises is critical to ensure the implementation of effective preventative measures, reducing the risk of spread of the virus. Extensive environmental sampling across three infected premises, representing the major global commercial poultry species, detected viral RNA and infectious virus in air samples, dust, and other fomites inside of the houses containing infected poultry, as well as within the immediate proximity of infected houses. This suggests that particles harbouring infectious virus may travel short distances outside of affected houses, which may potentially contribute to house-to-house transmission on the same premises, but not at distances likely to contribute to the transmission to another poultry premises. Consequently, control efforts should be focused on traditional, robust biosecurity measures at key barriers on poultry houses. Human behaviour in and around poultry houses as factors contributing to biosecurity risks should be considered.

microbiology↗

bioRxiv2023

Ancient methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection

Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes. We accessed 451 ancient (1965-1987) Swiss MRSA isolates, stored in the Culture Collection of Switzerland. We determined phenotypic antimicrobial resistance (AMR) and performed Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international genomes from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes. Among the 451 ancient Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-IIII. Early MRSA were predominantly from clonal complex (CC) 8. From 1980 to the end of the 20th century we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally. The combined analysis of 1761 ancient and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss and international MRSA across time.

microbiology↗

bioRxiv2023

Community phylogenetic structure shapes pathogen outbreak potential in an epidemiological multi-host model

Biodiversity loss and anthropogenic modifications to species communities are impacting the frequency and magnitude of disease emergence events. These changes may be related through mechanisms in which biodiversity either increases (amplifies) or decreases (dilutes) disease prevalence. Biodiversity effects can be direct, when contacts among competent hosts are substituted by contacts with sink hosts, or indirect through regulation of host abundances. Whether a disease is diluted or amplified depends on the competence of the host species in the community. Here, we introduce a multi-host compartmental disease model in which we assume that host competence is determined by evolutionary relatedness. By simulating communities of varying phylogenetic structure, and estimating community disease outbreak potential (R0), we show how differences in host phylogenetic relatedness can switch host communities from diluting to amplifying a disease, even when species richness is unchanged. We additionally show that phylogenetic dilution can occur simultaneously with amplification through species richness, highlighting the multidimensionality of the disease-diversity relationship. We illustrate our model using empirical data describing the relationship between phylogenetic distances separating hosts and their likelihood of disease sharing. Our study demonstrates how a phylogenetic dilution effect can emerge when we allow transmission to depend on host evolutionary histories.

ecology↗

bioRxiv2023

Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms

Control measures are being introduced globally to reduce the prevalence of antibiotic resistant (ABR) bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in key opportunistic human pathogens such as Escherichia coli on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin resistance (3GC-R) in E. coli. 3GC-R isolates were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from faecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal transmission of 3GC-R mechanisms. Despite this, mechanisms such as CTX-M-15 and CTX-M-2 were detected more often in dairy farms, while CTX-M-8 and CMY-2, and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more commonly detected in pig farms. This suggests different selective pressures of antibiotic use in these two animal types, particularly the balance of fourth-versus third-generation cephalosporin use, and of amoxicillin/clavulanate and florfenicol use. We identified the {beta}-lactamase gene blaROB in 3GC-R E. coli, which has previously only been reported in the family Pasteurellaceae, including farmed animal pathogens. blaROB was found alongside a novel florfenicol resistance gene - ydhC - also mobilised from a pig pathogen as part of a new plasmid-mediated composite transposon, which is already widely disseminated. These data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate zoonotic transmission of resistant bacteria in this region. ImportanceLittle is known about the ecology of critically important antibiotic resistance among opportunistic human pathogens (e.g. Escherichia coli) on South American farms. By studying 70 farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species (pigs or dairy cattle) and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli were highly phylogenetically variable and we identified the de novo mobilisation of the resistance gene blaROB, alongside a novel florfenicol resistance gene, from pig pathogens into E. coli on a mobile genetic element that was widespread in the study region. Overall, this shows the importance of surveying poorly studied regions for critically important antibiotic resistance which might impact human health.

microbiology↗

bioRxiv2023

Molecular epidemiological study of Scrub Typhus in residence, farm and forest habitats from Yunnan Province, China

The number of people suffering from scrub typhus, which is not of concern, is increasing year by year, especially in Yunnan Province, China. From June 1, 2021 to August 15, 2022, a total of 505 mammalian samples were collected from farm, forest, and residential habitats with high incidence of scrub typhus in Yunnan, China, for nPCR (nested PCR) and qPCR (quantitative real-time PCR) detection of Orientia tsutsugamushi. A total of 4 orders of murine-like animals, Rodentia (87.52%, n=442), Insectivora (10.29%, n=52), Lagomorpha (1.79%, n=9) and Scandentia (0.40%, n=2) were trapped. Comparing the qPCR infection rates in the three habitats, it was no significant difference that the infection rate of residential habitat (44.44%) and that of the farm habitat (45.05%, P>0.05), which is much larger than that of the forest habitat (3.08%) (P<0.001). Three genotypes (Karp, Kato and TA763) of O. tsutsugamushi were found from Yunnan, China in this study. We found a tendency for scrub typhus to migrate from forests to residential habitats. Author SummaryScrub typhus is acute febrile infectious disease caused by Orientia tsutsugamushi that threatens nearly 1 billion people. According to the data we have obtained, the incidence rate of infected people has reached 23.84/100,000 population until December 2022 in Yunnan, China. The incidence rate has increased non-negligibly Compared with 0.65/100,000 population in 2006. Among them, the incidence rate has increased by 71.14% from 2019 to 2022. Scrub typhus is transmitted by the bite of chigger larvae with murine-like animals as the main source of infection Rodentia are the most important reservoir hosts, followed by Insectivora. Therefore, in view of the influencing factor of human habitat, we used qPCR (quantitative real-time PCR) and nPCR (nested PCR) techniques to analyze the prevalence of O. tsutsugamushi in hosts of different human habitats from June 2021 to August 2022. Our research shows that the diversity of O. tsutsugamushi genotypes in Yunnan Province provides guidance for the prevention and Control of scrub typhus. And it was found that the infection rate of O. tsutsugamushi in murine-like animals is quite different in different human habitats, especially the high infection rate in residential habitat and farm habitat, suggesting that O. tsutsugamushi can be infected without wilderness history.

molecular biology↗

bioRxiv2023

Phylogenetics, Epidemiology and Temporal Patterns of Dengue Virus type 1 in Araraquara, Sao Paulo State

Dengue virus is a prominent arbovirus with global spread, causing approximately 390 million infections each year. In Brazil, yearly epidemics follow a well-documented pattern of serotype replacement every three to four years on average. Araraquara, located in the state of Sao Paulo, has faced significant impacts from DENV epidemics since the emergence of DENV-1 in 2010. The municipality then transitioned from low to moderate endemicity in less than 10 years. Yet, there remains an insufficient understanding of the virus circulation dynamics, particularly concerning DENV-1, in the region, as well as the genetic characteristics of the virus. To address this, we generated 37 complete or partial DENV-1 genomes sampled from 2015 to 2022 in Araraquara. Then, using also Brazilian and worldwide DENV-1 sequences we reconstructed the evolutionary history of DENV-1 in Araraquara and estimated the time to the most recent common ancestor (tMRCA) for the serotype 1, for the genotype V and its main lineages. Within the last ten years, there were at least three introductions of genotype V in Araraquara, distributed in the two main lineages (LIa and LIb, and LII). The tMRCA for the first sampled lineage (2015/2016 epidemics) was approximately 15 years ago (in 2008). Crucially, our analysis challenges existing assumptions regarding emergence time of the DENV-1 genotypes, suggesting that genotype V might have diverged more recently than previously described. The presence of the two lineages of genotype V in the municipality might have contributed to the extended persistence of DENV-1 in the region.

genomics↗

bioRxiv2023

Molecular epidemiology of Candida africana isolates collected from vagina swabs in French Guiana.

Candida africana corresponds to the clade 13 of Candia albicans. It has been mostly involved in vulvovaginal candidiasis worldwide but few data exist in South America. The aim of our study was to investigate the prevalence of C. africana in women living in French Guiana. For this, we first set up a fluorescent-intercalating-dye-real time PCR targeting the hyphal wall protein 1 gene. The test was applied to 212 C. albicans isolates collected from May to August 2019 from vaginal swabs, allowing the identification of 6 women harboring C. africana (8 isolates). No demographics or clinical-specific features could be demonstrated. Genetic diversity of those isolates was analyzed through multilocus sequence typing and showed that diploid sequence type 182 was predominant (n=6) and allowed the report of a new diploid sequence type.

microbiology↗

bioRxiv2024

Epidemiological, Serological, and Virological Analysis of an Outbreak of Elephant Hemorrhagic Disease in Switzerland

Elephant hemorrhagic disease (EHD), caused by several Elephant endotheliotropic herpesviruses (EEHV), represents a frequently lethal syndrome, affecting both captive and free-living elephants. In summer 2022, three young Asian elephants (Elephas maximus) succumbed to EHD in a zoo in Switzerland, despite of considerable preventive efforts and early detection of EEHV1A viremia. In this communication, we describe the extent of preventive measures in terms of prior virus detection, active survey of viremia, and antibody status. In the course of the outbreak, the causative virus was concomitantly analyzed and eventually fully sequenced and compared to other EEHV types and strains. The conclusions from these analyses may be summarized in three points: (1) A previously undetected EEHV1A strain had remained unrecognized among these elephants. Probably, the new virus re-emerged after almost 40 years of latency from one of the oldest elephants in the zoo. (2) While two of the three affected animals had prior immune responses against EEHV1, their strain-specific immunity proved insufficient to prevent EHD. (3) There is an urgent need to develop efficient antiviral drugs and protective vaccines. In particular, ways need to be found to circumvent the present unavailability of appropriate cell cultures and animal models.

microbiology↗

bioRxiv2024

Genomic epidemiology of ESBL-producing Escherichia coli from humans and an Aotearoa New Zealand river

In Aotearoa New Zealand, urinary tract infections in humans are commonly caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. This group of antimicrobial resistant bacteria are often multidrug resistant. However, there is limited information on ESBL-producing E. coli found in the environment and their link with human clinical isolates. In this study, we examined the genetic relationship of environmental and human clinical ESBL-producing E. coli and isolates collected in parallel within the same area over 14 months. Environmental samples were collected from treated effluent, stormwater and multiple locations along an Aotearoa New Zealand river. Treated effluent, stormwater and river water sourced downstream of the treated outflow point were the main sources of ESBL-producing E. coli (7/14 samples, 50.0%; 3/6 samples, 50%; and 15/28 samples, 54% respectively). Whole genome sequence comparison was carried out on 307 human clinical and 45 environmental ESBL-producing E. coli isolates. Sequence type 131 was dominant for both clinical (147/307, 47.9%) and environmental isolates (11/45, 24.4%). The most prevalent ESBL genes were both blaCTX-M-27 and blaCTX-M-15 for the clinical isolates (134/307, 43.6%) and blaCTX-M-15 for the environmental isolates (28/45, 62.2%). A core single nucleotide polymorphism analysis of these isolates suggested that some strains were shared between humans and the local river. These results highlight the importance of understanding different transmission pathways for the spread of ESBL-producing E. coli. 2. Impact statementExtended spectrum beta lactamase (ESBL)-producing E. coli frequently cause urinary tract infections that exhibit multidrug resistance. Surveillance studies have identified the predominant strains and resistance genes associated with urinary tract infections. However, there is limited information on the extent of spread beyond the patient. We describe the genetic relatedness of ESBL-producing environmental and clinical E. coli isolated during the same temporal-spatial period in Aotearoa New Zealand. Comparative genomic analyses of these bacteria provide evidence of clonal spread between humans and the environment, highlighting the need to integrate environmental surveillance into antimicrobial resistance monitoring. 3. Data summaryAll Illumina sequence reads for this study have been deposited in GenBank under BioProject PRJNA1032159, except for strain SB0283h1, whose data can be found under BioProject PRJNA715472. The sequence read accessions for each genome are provided in the supplementary material. The code used for the genomic and statistical analyses is available from the GitHub repository https://github.com/sburgess1/Manawat-_ESBL. The authors confirm all supporting data and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2024

Unravelling the Dynamics of Bacterial-Laden Respiratory Droplets: Epidemiological Transfer from Fomites to Susceptible Host

This study provides the first comprehensive investigation into how pathogen-laden respiratory droplets transfer diseases via inanimate surfaces. Respiratory fluid ejections containing pathogens pose a significant health threat, especially in high-traffic areas like hospitals, public transport, restaurants, and schools. When these droplets dry on surfaces, they form deposits that can transfer pathogens to healthy individuals through contact and can be ingested via the oral or nasal route. The study examined the effects of varying salt and mucin concentrations in respiratory fluid droplets containing Pseudomonas aeruginosa (PA). Results showed that PA viability increased tenfold at elevated mucin concentrations, while changes in salt concentration had minimal impact. Adhesive properties of the deposits were analysed using atomic force spectroscopy and scotch tape test. Pathogen transfer from the deposit to a fingerprint patterned model thumb at different relative humidity (RH) levels was assessed using confocal microscopy, showing significant pathogen transfer at elevated RH. Out of 106 CFU/ml pathogens in deposits, 17% to 38% are potentially transferable, with most of the transfer occurring from the droplets edge deposits. The study also explored evaporation, internal flow, and precipitation dynamics, with deposit and pathogen distribution characterized by optical profilometry, scanning electron microscopy, and confocal microscopy.

microbiology↗

bioRxiv2024

Epidemiological Study Of Foot And Mouth Diseases Through Serological And Molecular Investigation In Cattle Of Selected Districts, Jimma Zone, Southwest Ethiopia

Foot and mouth disease is highly contagious and notifiable transboundary disease of cattle that can cause a huge cattle productivity and production loss. A cross-sectional study was performed to estimate sero prevalence, assess associated risk factors and molecular detection of FMDV in cattle. Cluster sampling technique was employed for the selection of sampling units for the seroprevalence study. A total of 245 blood samples were collected using plain vacutainer tubes and the obtained sera were tested by 3ABC-Ab ELISA at the Animal Health institute. Twenty nine (29) epithelial tissue and vesicular fluid samples were collected purposively from outbreak cases for the molecular detection of FMDV. Kebeles and individual cattle were randomly selected, while households were designated using systematic random sampling method. An overall prevalence of 22.45% (95%, CI=17.22%-27.67%) was recorded. Multivariable logistic regression analysis indicated that herd size, age, new animal introduction into the herd and management system were the major risk factors, significantly associated with FMD sero positivity (P<0.05). The large herd size had 4-times (OR=3.97; P=0.000) more odds of FMD sero-positivity compared to the small herd sizes. The FMD seropositivity decreases 0.11013 as the Cattle age increases by 5years with the (coefficient=-0.11; P=0.172). The animals from herd to which new animals was introduced had nearly 9-times more odds (OR=9.40; P=0.000) of sero positivity than the animals sampled from no new animal introduction. Likewise, cattle those reared under extensive management system were 4-times (OR=4.10; P=0.009) at higher chance of being sero-positive compared to the intensive one. From outbreak cases, 27 (93.1%) were identified positive for FMDV serotype SAT 2. A total of 124 individuals were interviewed, and the majority responded that there is no practice of reporting disease outbreak, free animal movement, free rangeland grazing and they use traditional case management as a means of controlling the disease. The finding of FMD virus antibodies in cattle from all study areas indicate endemic circulation of the virus. The implementation of regular vaccination could minimize the occurrence and further molecular characterization should be needed to identify other serotypes of FMD virus that could inform to supply an appropriate vaccine to the area.

immunology↗