Diversity Of Pathogens Research Articles

Functional traits explain waterbirds' host status, subtype richness, and community-level infection risk for avian influenza.

Species functional traits can influence pathogen transmission processes, and consequently affect species' host status, pathogen diversity, and community-level infection risk. We here investigated, for 143 European waterbird species, effects of functional traits on host status and pathogen diversity (subtype richness) for avian influenza virus at species level. We then explored the association between functional diversity and HPAI H5Nx occurrence at the community level for 2016/17 and 2021/22 epidemics in Europe. We found that both host status and subtype richness were shaped by several traits, such as diet guild and dispersal ability, and that the community-weighted means of these traits were also correlated with community-level risk of H5Nx occurrence. Moreover, functional divergence was negatively associated with H5Nx occurrence, indicating that functional diversity can reduce infection risk. Our findings highlight the value of integrating trait-based ecology into the framework of diversity-disease relationship, and provide new insights for HPAI prediction and prevention.

Incidence, diversity and distribution of <i>Fusarium wilt</i> pathogens of eggplant in some major growing areas of Ashanti, Eastern and Volta Regions of Ghana

Fusarium wilt of eggplant is a major cause of losses to eggplant production globally. The disease is caused by many Fusarium species. In this study, incidence, diversity and distribution of Fusarium wilt pathogens of eggplants were determined in five communities each from Ashanti, Eastern and Volta Regions of Ghana during the 2017–2019 cropping seasons. Purposive sampling method was used to select 10 eggplant farms infected with Fusarium wilt from each community. Infected eggplants were sampled for isolation and identification of Fusarium species. Fusarium wilt incidence was below 10% in 57.3% of the sampled farms. Differences in disease incidence were significant (p ≤ 0.05) between the Regions. Volta Region recorded the highest disease incidence. A total of eight Fusarium species were isolated. These included F. accuminatum, F. culmorum, F. oxysporum, F. proliferatum, F. poae, F. solani, F. subglutinans, and F. verticillioides. Fusarium solani, F. oxysporum and F. culmorum were the most occurring species, representing 92.79% of the isolates. Six, five and eight Fusarium species were isolated respectively in Ashanti, Eastern and Volta Regions. Inoculum density of the Fusarium species was significantly (p ≤ 0.05) higher in the Ashanti and Eastern Regions than in the Volta Region.

The potential impact evaluation of climate changes on some sunflower pathogens

From domestication to the present time, agricultural crops have been constantly threatened by pathogens and pests that cause harvest losses, often leading to famine and social unrest. Global climate change, enhanced volume of trade and increased human mobility over the past 50 years are key risk factors in the introduction and establishment of non-native species in new areas. These invaders are a major threat worldwide due to their effect on human health, global food security and livelihoods, disruption of trade, biodiversity, habitat destruction, loss of agricultural productivity and high disease risk to crop plants. The given work have made an attempt to summarize the current knowledge with reference to the spread, frequency, genetics, evolution, diversity of pathogens, especially in sunflower, with some forecasts of the development of different diseases and recommendations for combating them in the context of climate change at the global level.

Modern technologies for studying the genome of mycobacteria

Molecular technologies play a leading role in the laboratory diagnosis of tuberculosis and mycobacteriosis. The successes in studying the genome of Mycobacterium have contributed to significant progress in understanding the evolution, variability, and genetic diversity of pathogens, as well as the development of diagnostic technologies, including research into resistance to anti-tuberculosis drugs.
 The aim of this research is to conduct a comparative study of the spectrum of modern technologies for studying the genomes of mycobacteria and their impact on the efficiency of the laboratory diagnosis of tuberculosis.
 Materials and methods: a search for sources of information was carried out in the PubMed, Medline, Web of Science, and Google Scholar databases. Materials related to the technology of molecular diagnosis of tuberculosis and mycobacteriosis and for determining the susceptibility of pathogens to anti-tuberculosis drugs were selected.
 Results: it was determined that the modern methods for studying the genome of mycobacteria include amplification technologies (PCR analysis), hybridization, restriction, spoligotyping, sequencing, and their various combinations. The main methods are standard and modified protocols of PCR (RAPD-PCR, AP-PCR, rep-PCR, Real-time PCR, Inverse PCR, TB-LAMP, HIP, LM-PCR). Genomic Restriction Analysis can be used in studies of MTBC and NTM strains (RFLP, AFLP analysis, MIRU-VNTR genotyping). The most effective method for genome analysis is WGS. Complex methods that utilize a combination of molecular technologies allow for the direct detection of mycobacteria in clinical samples.
 Conclusions: the widespread application of genomic technologies in the study of mycobacteria will contribute to the effective implementation of the global WHO strategy for the prevention, treatment, and control of tuberculosis and mycobacteriosis

Genome Sequence Resource for Paramyrothecium foliicola, an Important Pathogenic Fungus Threatening Crop Production

Paramyrothecium foliicola is a species of ascomycete in the family Stachybotryaceae. In recent years, it has been reported as a threat to crop production in different countries. Because of its wide host range and high virulence, this pathogen may present as a major global concern in the near future. Despite its importance, there is no sufficient genomic information for P. foliicola. Our work introduces the initial PacBio-Illumina hybrid draft genome for TJWQPF1, the P. foliicola strain, together with the related annotations. This genome was assembled into 18 contigs, with the largest contig size of 8,042,417 bp. Genome annotation identified 13,330 protein-coding genes. The draft genome data will aid in understanding the pathogenic mechanism of P. foliicola, which is a valuable resource to explore the genetic diversity, pathogenicity, and evolution of this important pathogen. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Diversity of Colletotrichum species causing anthracnose on three oak species (Quercus acutissima, Q. mongolica and Q. variabilis) in China

AbstractAnthracnose of oak (Quercus) caused by Colletotrichum spp. is one of the most common diseases in oak forests. To investigate the species diversity of Colletotrichum associated with oak anthracnose, symptomatic leaf samples of three oak species (Q. acutissima, Q. mongolica and Q. variabilis) were collected from Anhui, Hainan, Henan, Shaanxi and Shandong Provinces, Inner Mongolia Autonomous Region, and Beijing City in China from 2019 to 2022. A total of 219 Colletotrichum isolates were obtained and identified by morphological and phylogenetic analyses of the rDNA internal transcribed spacer (ITS), glyceraldehyde‐3‐phosphate dehydrogenase (gapdh), chitin synthase 1 (chs‐1), actin (act) and β‐tubulin (tub2) sequences. Nine species were identified: C. fioriniae (two isolates, 0.9%), C. camellia‐japonicae (two isolates, 0.9%), C. karstii (three isolates, 1.4%), C. quercicola (two isolates, 0.9%), C. aenigma (three isolates, 1.4%), C. endophyticum (two isolates, 0.9%), C. fructicola (68 isolates, 31.1%), C. gloeosporioides sensu stricto (74 isolates, 33.8%) and C. siamense (63 isolates, 28.8%). Pathogenicity was confirmed using Koch's postulates, which showed that five species (C. camellia‐japonicae, C. endophyticum, C. fructicola, C. gloeosporioides s. s. and C. siamense) caused Q. acutissima anthracnose, four species (C. karstii, C. fructicola, C. gloeosporioides s. s. and C. siamense) caused Q. mongolica anthracnose and six species (C. fioriniae, C. quercicola, C. aenigma, C. fructicola, C. gloeosporioides s. s. and C. siamense) caused Q. variabilis anthracnose. This study demonstrates the pathogenic species diversity of Colletotrichum on Q. acutissima, Q. mongolica and Q. variabilis.

Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections

BackgroundSecondary bacterial infections and pneumonia are major mortality causes of respiratory viruses, and the disruption of the upper respiratory tract (URT) microbiota is a crucial component of this process. However, whether this URT dysbiosis associates with the viral species (in other words, is viral type-specific) is unclear.ResultsHere, we recruited 735 outpatients with upper respiratory symptoms, identified the infectious virus types in 349 participants using multiplex RT-PCR, and profiled their upper respiratory microbiome using the 16S ribosomal RNA gene and metagenomic gene sequencing. Microbial and viral data were subsequently used as inputs for multivariate analysis aimed at revealing viral type-specific disruption of the upper respiratory microbiota. We found that the oropharyngeal microbiota shaped by influenza A virus (FluA), influenza B virus (FluB), respiratory syncytial virus (RSV), and human rhinovirus (HRV) infections exhibited three distinct patterns of dysbiosis, and Veillonella was identified as a prominent biomarker for any type of respiratory viral infections. Influenza virus infections are significantly correlated with increased oropharynx microbiota diversity and enrichment of functional metabolic pathways such as L-arginine biosynthesis and tetracycline resistance gene tetW. We used the GRiD algorithm and found the predicted growth rate of common respiratory pathogens was increased upon influenza virus infection, while commensal bacteria, such as Streptococcus infantis and Streptococcus mitis, may act as a colonization resistance to the overgrowth of these pathogens.ConclusionsWe found that respiratory viral infections are linked with viral type-specific disruption of the upper respiratory microbiota, particularly, influenza infections uniquely associated with increased microbial diversity and growth rates of specific pathogens in URT. These findings are essential for clarifying the differences and dynamics of respiratory microbiota in healthy participants and acute respiratory viral infections, which contribute to elucidating the pathogenesis of viral-host-bacterial interactions to provide insights into future studies on effective prevention and treatment of respiratory tract infections.AxMbpzHUJuHXyJKsbr5ywRVideo

Natural foci of plague in Kazakhstan in the space-time continuum

The relevance of the problem of the stated topic lies in the fact that the causative agent of the plague infection demonstrates high survival while maintaining high virulence in the territories, which are enzootic in terms of the plague. The study aimed to investigate the geographic distribution and genetic diversity of the plague pathogen in endemic regions through molecular genetic research. The work included the results of laboratory studies of 3058 samples, including soil – 1154, burrow substrates – 549, the contents of the feeding chamber – 349, bone remains – 18, biological objects – 988 samples of sera and suspensions from carriers and vectors of plague infection collected from 14 autonomous plague foci of Kazakhstan for the period 2021–2022. The leading method in the study was a laboratory experiment, thanks to which, using a new advanced technology on a microbiological analyser VITEK 2 COMPACT 30, it was possible to study pathogenic and non-pathogenic strains of the genus Yersinia isolated during field experiment. As a result of experimental work, it was shown that during a long inter-epizootic period, the plague pathogen can persist in the soil in symbiosis with soil microorganisms, and in this area, it chooses soil with a low-quality index of 10 points, where soils with a low total microbial number and species landscape prevail.

Assessing Fungal Plant Pathogen Presence in Irrigation Water from the Rio Grande River in South Texas, USA

Irrigation is important in many crop production systems. However, irrigation water can be a carrier of plant pathogens that can enter the system and spread to fields, resulting in crop damage and yield losses. The Lower Rio Grande Valley of South Texas is an important area for agricultural production which depends on the Rio Grande River as a source of water for irrigation. Thus, the presence of plant pathogens in the Rio Grande River could have important implications for crop productivity in the region. Cultured-based methods and molecular identification methods are used for monitoring plant pathogens in irrigation water. However, these methods are labor-intensive and just detect targeted pathogens. To overcome these limitations, in this study, the ITS2 amplicon metagenomic method was applied for evaluating the fungal diversity, composition, and presence of fungal plant pathogens in irrigation water from the Rio Grande River as it leaves the water reservoir (WR) and it arrives at an irrigation valve at a farm (FA). Results from the Shannon (WR = 4.6 ± 0.043, FA = 3.63 ± 0.13) and Simpson indices (WR = 4.6 ± 0.043, FA = 3.63 ± 0.13) showed that there are significant differences in the fungal diversity and community structure between the two locations and the PCA analysis showed a clear differentiation between both fungal communities. Several OTUs identified in both locations included potential plant pathogens from diverse genera including Cladosporium, Exserohilum, and Nigrospora, while others such as Colletotrichum and Plectosphaerella were found only in one of the two locations assessed. This work indicates that microbes, including plant pathogens, may enter or exit throughout the irrigation-water distribution system, thereby modifying the microbial community composition along the way. Understanding the dynamics of plant pathogen movement in irrigation water systems can help growers identify risk factors to develop measures to mitigate those risks. This study also shows the usefulness of the metagenomic approach for detecting and monitoring plant pathogen in irrigation water.

Evolution of pathogens with cross-immunity in response to healthcare interventions

Cross-immunity, as an evolutionary driver, can contribute to pathogen evolution, particularly pathogen diversity. Healthcare interventions aimed at reducing disease severity or transmission are commonly used to control diseases and can also induce pathogen evolution. Understanding pathogen evolution in the context of cross-immunity and healthcare interventions is crucial for infection control.This study starts by modelling cross-immunity, the extent of which is determined by strain traits and host characteristics. Given that all hosts have the same characteristics, full cross-immunity between residents and mutants occurs when mutation step sizes are small enough. Cross-immunity can be partial when the step size is large. The presence of partial cross-immunity reduces pathogen load and shortens the infectious period inside hosts, reducing transmission between hosts and improving host population survival and recovery.This study focuses on how pathogens evolve through small and large mutational steps and how healthcare interventions affect pathogen evolution. Using the theory of adaptive dynamics, we found that when mutational steps are small (only full cross-immunity is present), pathogen diversity cannot occur because it maximises the basic reproduction number. This results in intermediate values for both pathogen growth and clearance rates. However, when large mutational steps are allowed (with full and partial cross-immunity present), pathogens can evolve into multiple strains and induce pathogen diversity. The study also shows that different healthcare interventions can have varying effects on pathogen evolution. Generally, low levels of intervention are more likely to induce strain diversity, while high levels are more likely to result in strain reduction.

Molecular characteristics and zoonotic potential of enteric protists in domestic dogs and cats in Egypt.

Domestic dogs and cats can be a source of human infection by a wide diversity of zoonotic pathogens including parasites. Genotyping and subtyping tools are useful in assessing the true public health relevance of canine and feline infections by these pathogens. This study investigated the occurrence, genetic diversity, and zoonotic potential of common diarrhea-causing enteric protist parasites in household dogs and cats in Egypt, a country where this information is particularly scarce. In this prospective, cross-sectional study a total of 352 individual fecal samples were collected from dogs (n = 218) and cats (n = 134) in three Egyptian governorates (Dakahlia, Gharbeya, and Giza) during July-December 2021. Detection and identification of Cryptosporidium spp., Giardia duodenalis, Enterocytozoon bieneusi, and Blastocystis sp. were carried out by PCR and Sanger sequencing. Basic epidemiological variables (geographical origin, sex, age, and breed) were examined for association with occurrence of infection by enteric protists. The overall prevalence rates of Cryptosporidium spp. and G. duodenalis were 1.8% (95% CI: 0.5-4.6) and 38.5% (95% CI: 32.0-45.3), respectively, in dogs, and 6.0% (95% CI: 2.6-11.4) and 32.1% (95% CI: 24.3-40.7), respectively, in cats. All canine and feline fecal samples analyzed tested negative for E. bieneusi and Blastocystis sp. Dogs from Giza governorate and cats from Dakahlia governorate were at higher risk of infection by Cryptosporidium spp. (p = 0.0006) and G. duodenalis (p = 0.00001), respectively. Sequence analyses identified host-adapted Cryptosporidium canis (n = 4, one of them belonging to novel subtype XXe2) and G. duodenalis assemblages C (n = 1) and D (n = 3) in dogs. In cats the zoonotic C. parvum (n = 5) was more prevalent than host-adapted C. felis (n = 1). Household dogs had a limited (but not negligible) role as source of human giardiasis and cryptosporidiosis, but the unexpected high frequency of zoonotic C. parvum in domestic cats might be a public health concern. This is the first molecular-based description of Cryptosporidium spp. infections in cats in the African continent to date. Molecular epidemiological data provided here can assist health authorities and policy makers in designing and implementing effective campaigns to minimize the transmission of enteric protists in Egypt.

Pathogenicity and Antibiotic Resistance Diversity in Clostridium perfringens Isolates from Poultry Affected by Necrotic Enteritis in Canada.

Necrotic enteritis (NE) caused by C. perfringens is one of the most common diseases of poultry and results in a huge economic loss to the poultry industry, with resistant clostridial strains being a serious concern and making the treatment difficult. Whole-genome sequencing approaches represent a good tool to determine resistance profiles and also shed light for a better understanding of the pathogen. The aim of this study was to characterize, at the genomic level, a collection of 20 C. perfringens isolates from poultry affected by NE, giving special emphasis to resistance mechanisms and production of bacteriocins. Antimicrobial resistance genes were found, with the tet genes (associated with tetracycline resistance) being the most prevalent. Interestingly, two isolates carried the erm(T) gene associated with erythromycin resistance, which has only been reported in other Gram-positive bacteria. Twelve of the isolates were toxinotyped as type A and seven as type G. Other virulence factors encoding hyaluronases and sialidases were frequently detected, as well as different plasmids. Sequence types (ST) revealed a high variability of the isolates, finding new allelic combinations. Among the isolates, C. perfringens MLG7307 showed unique characteristics; it presented a toxin combination that made it impossible to toxinotype, and, despite being identified as C. perfringens, it lacked the housekeeping gene colA. Genes encoding bacteriocin BCN5 were found in five isolates even though no antimicrobial activity could be detected in those isolates. The bcn5 gene of three of our isolates was similar to one previously reported, showing two polymorphisms. Concluding, this study provides insights into the genomic characteristics of C. perfringens and a better understanding of this avian pathogen.

Increased rat-borne zoonotic disease hazard in greener urban areas

Urban greening has benefits for both human and environmental health. However, urban greening might also have negative effects as the abundance of wild rats, which can host and spread a great diversity of zoonotic pathogens, increases with urban greenness. Studies on the effect of urban greening on rat-borne zoonotic pathogens are currently unavailable. Therefore, we investigated how urban greenness is associated with rat-borne zoonotic pathogen prevalence and diversity, and translated this to human disease hazard. We screened 412 wild rats (Rattus norvegicus and Rattus rattus) from three cities in the Netherlands for 18 different zoonotic pathogens: Bartonella spp., Leptospira spp., Borrelia spp., Rickettsia spp., Anaplasma phagocytophilum, Neoehrlichia mikurensis, Spiroplasma spp., Streptobacillus moniliformis, Coxiella burnetii, Salmonella spp., methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)/AmpC-producing Escherichia coli, rat hepatitis E virus (ratHEV), Seoul orthohantavirus, Cowpox virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Toxoplasma gondii and Babesia spp. We modelled the relationships between pathogen prevalence and diversity and urban greenness. We detected 13 different zoonotic pathogens. Rats from greener urban areas had a significantly higher prevalence of Bartonella spp. and Borrelia spp., and a significantly lower prevalence of ESBL/AmpC-producing E. coli and ratHEV. Rat age was positively correlated with pathogen diversity while greenness was not related to pathogen diversity. Additionally, Bartonella spp. occurrence was positively correlated with that of Leptospira spp., Borrelia spp. and Rickettsia spp., and Borrelia spp. occurrence was also positively correlated with that of Rickettsia spp. Our results show an increased rat-borne zoonotic disease hazard in greener urban areas, which for most pathogens was driven by the increase in rat abundance rather than pathogen prevalence. This highlights the importance of keeping rat densities low and investigating the effects of urban greening on the exposure to zoonotic pathogens in order to make informed decisions and to take appropriate countermeasures preventing zoonotic diseases.

Genetic diversity of vector-borne pathogens in ixodid ticks infesting dogs from Pakistan with notes on Ehrlichia canis, Rickettsia raoultii and Dirofilaria immitis detection

BackgroundVector-/tick-borne pathogens (V/TBPs) pose a potential threat to human and animal health globally. Information regarding canine V/TBPs is scarce and no specific study has been conducted so far to explore the microbial diversity within ticks infesting dogs from Pakistan. Herein, this knowledge gap is addressed by assessing the genetic diversity and prevalence pattern of V/TBPs in ixodid ticks with special implications for public and canine health.MethodsA total of 1150 hard ticks were collected from 300 dogs across central Khyber Pakhtunkhwa (KP), Pakistan. After morpho-molecular identification, 120 tick samples were screened for the presence of V/TBPs by amplifying 16S rRNA/gltA (Rickettsia/Ehrlichia and Wolbachia sp.), 18S rRNA (Theileria sp.) and cox1 (Dirofilaria sp.) genes through PCR followed by sequencing and phylogenetic study.ResultsIn toto, 50 ixodid ticks (50/120, 41.7%) were found positive for V/TBPs DNA. The detected V/TBPs were categorized into five genera and eight species, viz. Ehrlichia (E. canis and Ehrlichia sp.), Rickettsia (R. massiliae, R. raoultii and Rickettsia sp.), Theileria (T. annulata), Dirofilaria (D. immitis) and Wolbachia (Wolbachia sp.). The pathogen prevalence patterns showed that R. massiliae was the most prevalent zoonotic V/TBP (19.5%), followed by E. canis (10.8%), Rickettsia sp. (7.5%), R. raoultii (6.7%), T. annulata (5.8%), D. immitis (5.8%), Wolbachia sp. (4.2%) and Ehrlichia sp. (3.3%), respectively. Among the screened tick species, most Rhipicephalus sanguineus sensu lato samples were found positive for V/TBP DNA (20/20,100%) followed by Rh. turanicus sensu stricto (13/20, 65%), Hyalomma dromedarii (8/20, 40%), Rh. haemaphysaloides (6/20, 30%), Hy. excavatum (2/20, 10%) and Rh. microplus (1/20, 5%). Co-occurrence of V/TBP was also detected in tick specimens (single V/TBP infection: 32 ticks; double and triple: 13 and 5 tick samples). The detected pathogens shared a phylogenetic relationship with similar isolates published in NCBI GenBank from Old and New World countries.ConclusionIxodid ticks infesting dogs harbor a diverse array of V/TBPs including zoonotic agents from Pakistan. Furthermore, the presence of D. immitis in ticks that infest dogs raises the possibility that this parasite has either attained its dead-end host (i.e. the tick) while feeding on dogs or has expanded its range of intermediate/paratenic hosts. Further research work is needed to investigate the epidemiology and confirm the vector competence of screened tick species for these pathogens from Pakistan.Graphical

Hiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in Fusarium oxysporum f.sp. ciceris

Understanding the origins of variation in agricultural pathogens is of fundamental interest and practical importance, especially for diseases that threaten food security. Fusarium oxysporum is among the most important of soil-borne pathogens, with a global distribution and an extensive host range. The pathogen is considered to be asexual, with horizontal transfer of chromosomes providing an analog of assortment by meiotic recombination. Here, we challenge those assumptions based on the results of population genomic analyses, describing the pathogen's diversity and inferring its origins and functional consequences in the context of a single, long-standing agricultural system. We identify simultaneously low nucleotide distance among strains, and unexpectedly high levels of genetic and genomic variability. We determine that these features arise from a combination of genome-scale recombination, best explained by widespread sexual reproduction, and presence-absence variation consistent with chromosomal rearrangement. Pangenome analyses document an accessory genome more than twice the size of the core genome, with contrasting evolutionary dynamics. The core genome is stable, with low diversity and high genetic differentiation across geographic space, while the accessory genome is paradoxically more diverse and unstable but with lower genetic differentiation and hallmarks of contemporary gene flow at local scales. We suggest a model in which episodic sexual reproduction generates haplotypes that are selected and then maintained through clone-like dynamics, followed by contemporary genomic rearrangements that reassort the accessory genome among sympatric strains. Taken together, these processes contribute unique genome content, including reassortment of virulence determinants that may explain observed variation in pathogenic potential.

Potent antibacterial activity in surgical wounds with local administration of D-PLEX100

Despite significant advances in infection control guidelines and practices, surgical site infections remain a substantial cause of morbidity, prolonged hospitalization, and mortality. The most effective component of SSI reduction strategies is the preoperative administration of intravenous antibiotics; however, systemic antibiotics drug exposure diminishes rapidly and may result in insufficient prophylactic activity against susceptible and resistant SSI pathogens at the wound. D-PLEX100 (D-PLEX) is an antibiotic-releasing drug (doxycycline) that is supplied as a sterile powder for paste reconstitution with sterile saline. D-PLEX paste is administered locally into the incision site along the entire length of soft tissue and sternal bone wound surfaces prior to skin closure. A single D-PLEX administration is intended for 30 days of constant antimicrobial prophylaxis in the prevention of incisional SSIs. We evaluated D-PLEX minimal bactericidal concentration (MBC) against a panel of bacteria that is prevalent in the abdominal wall and sternal surgical procedures including doxycycline susceptible and resistant strains. D-PLEX in vivo efficacy was assessed in incisional infection rabbit models (abdominal wall and sternal) challenged with a similar bacterial panel. The D-PLEX drug exposure profile was determined by in vitro release assay, and in vivo by quantitative pharmacokinetic parameters of local and systemic doxycycline concentrations released from D-PLEX after local administration in incisional rabbit models. Analyses of pathogens and variations in antibiotic resistance from wound isolates were determined from patients who participated in a previously reported prospective randomized trial that assessed the SSI rate in D-PLEX plus standard of care (SOC) versus SOC alone in colorectal resection surgery. The D-PLEX MBC values demonstrated >3- Log10 reduction in all the organisms tested relative to untreated controls, including doxycycline-resistant bacteria (i.e., Methicillin-resistant Staphylococcus aureus (MRSA), K. pneumoniae, and P. aeruginosa). In vivo, D-PLEX significantly reduced the bacterial loads in all the bacteria tested in both animal models (p=0.0001) with a marked impact observed in E. Coli (>6.5 Log10 reduction). D-PLEX exhibited a zero-order release kinetics profile in vitro for 30 days (R2 = 0.971) and the matched in vivo release profile indicated a constant local release of protein-unbound doxycycline for 30 days at 3-5 mcg/mL with significantly lower (>3 orders of magnitudes) systemic levels. In colorectal surgery patients, where significant SSI reduction was observed, analysis of the positive cultures in the overall population indicated similar pathogen diversity and antibiotic resistance rates in both treatment arms. However, almost all the patients with positive culture in the SOC arm were adjudicated as SSI (94%) compared to only 28% in the D-PLEX arm. The SSI-adjudicated D-PLEX patients also exhibited lower resistance rates to the SOC antibiotics and to MDRs compared to patients in the SOC arm. Thus, D-PLEX provides safe and effective prophylaxis activity against the most prevalent SSI pathogens including doxycycline-susceptible and resistant bacteria. Our findings suggest that D-PLEX is a promising addition to SSI prophylactic bundles and may address the gaps in current SSI prophylaxis. D-PLEX is now evaluated in Phase 3 clinical trial.

ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data

BackgroundGenomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases’ prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual exploration of (large) phylogenetic trees and associated metadata, being time-consuming and difficult to reproduce.ResultsWe developed ReporTree, a flexible bioinformatics pipeline that allows diving into the complexity of pathogen diversity to rapidly identify genetic clusters at any (or all) distance threshold(s) or cluster stability regions and to generate surveillance-oriented reports based on the available metadata, such as timespan, geography, or vaccination/clinical status. ReporTree is able to maintain cluster nomenclature in subsequent analyses and to generate a nomenclature code combining cluster information at different hierarchical levels, thus facilitating the active surveillance of clusters of interest. By handling several input formats and clustering methods, ReporTree is applicable to multiple pathogens, constituting a flexible resource that can be smoothly deployed in routine surveillance bioinformatics workflows with negligible computational and time costs. This is demonstrated through a comprehensive benchmarking of (i) the cg/wgMLST workflow with large datasets of four foodborne bacterial pathogens and (ii) the alignment-based SNP workflow with a large dataset of Mycobacterium tuberculosis. To further validate this tool, we reproduced a previous large-scale study on Neisseria gonorrhoeae, demonstrating how ReporTree is able to rapidly identify the main species genogroups and characterize them with key surveillance metadata, such as antibiotic resistance data. By providing examples for SARS-CoV-2 and the foodborne bacterial pathogen Listeria monocytogenes, we show how this tool is currently a useful asset in genomics-informed routine surveillance and outbreak detection of a wide variety of species.ConclusionsIn summary, ReporTree is a pan-pathogen tool for automated and reproducible identification and characterization of genetic clusters that contributes to a sustainable and efficient public health genomics-informed pathogen surveillance. ReporTree is implemented in python 3.8 and is freely available at https://github.com/insapathogenomics/ReporTree.

The Genetic Diversity and Antimicrobial Resistance of Pyogenic Pathogens Isolated from Porcine Lymph Nodes

According to the Food and Agriculture Organization of the United Nations, pork remains the most consumed meat in the world. Consequently, it is very important to ensure that it is of the highest microbiological quality. Many of the pathogens that cause lymph node lesions in pigs are zoonotic agents, and the most commonly isolated bacteria are Mycobacterium spp., Streptococcus spp., Staphylococcus aureus and Rhodococcus equi (synonymous with Prescottella equi). The prevention and treatment of zoonotic infections caused by these bacteria are mainly based on antimicrobials. However, an overuse of antimicrobials contributes to the emergence and high prevalence of antimicrobial-resistant strains, which are becoming a serious challenge in many countries. The aim of this study was to evaluate the genetic diversity and antimicrobial resistance of the Streptococcus spp. (n = 48), S. aureus (n = 5) and R. equi (n = 17) strains isolated from swine lymph nodes with and without lesions. All isolates of S. dysgalactiae, S. aureus and R. equi were subjected to PFGE analysis, which showed the genetic relatedness of the tested bacteria in the studied pig populations. Additionally, selected tetracycline and macrolide resistance genes in the streptococcal strains were also studied. The results obtained in the present study provide valuable data on the prevalence, diversity, and antimicrobial resistance of the studied bacteria. Numerous isolated bacterial Streptococcus spp. strains presented resistance to doxycycline, and almost half of them carried tetracycline resistance genes. In addition, R. equi and S. aureus bacteria presented a high level of resistance to beta-lactam antibiotics and to cefotaxime, respectively.

Real-time detection and analysis of foodborne pathogens via machine learning based fiber-optic Raman sensor

Food safety is a critical concern worldwide, and in recent years, it has become a growing public concern in the United States due to mass production and multi-channel distribution of high-nutrient and fresh-cut foods that have increased the prevalence and diversity of foodborne pathogens (e.g., Escherichia coli, Salmonella, Listeria, etc.). Traditional methods for the detection of these pathogens rely heavily on low-efficiency techniques, which may expose the public to contaminated foods that have not been tested or identified. Therefore, rapid, simple, sensitive, and inexpensive detection methods are urgently needed for food safety investigations with higher efficiency and accuracy. One of the promising methods for the detection of foodborne pathogens is Raman spectroscopy, which is a molecular-level analytical tool with the advantages of high selectivity and sensitivity and simple operation at a relatively low cost. In this study, a novel fiber-optic-based portable Raman probe was developed and used for real-time detection of a panel of pathogen-specific molecular fingerprint volatile organic compounds (VOCs). Furthermore, machine learning (ML) algorithms were applied to assist in the extraction of molecular information from the raw Raman spectra, resulting in high accuracy prediction of complex VOC mixtures, even at high dilution folds (100x). The developed ML-assisted Raman probe has immense potential for rapid on-site detection of complex chemical mixtures in food safety and beyond. This innovative approach achieves high accuracy in comprehensively sorting mixed chemicals with varying concentrations and provides several advantages over previous studies, including speed, portability, non-contact operation, and precise classification of foodborne pathogen VOCs.

Triplex qPCR assay for Campylobacter jejuni and Campylobacter coli monitoring in wastewater

Campylobacter spp. is one of the most frequent pathogens of bacterial gastroenteritis recorded worldwide. Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli) are the two major disease-associated species, accounting for >95 % of infections, and thus have been selected for disease surveillance. Monitoring temporal variations in pathogen concentration and diversity excreted from community wastewater allows the early detection of outbreaks. Multiplex real-time/quantitative PCR (qPCR) enables multi-target quantification of pathogens in various types of samples including wastewater. Also, an internal amplification control (IAC) is required for each sample when adopting PCR-based methods for pathogen detection and quantification in wastewater to exclude the inhibition of the wastewater matrix. To achieve reliable quantification of C. jejuni and C. coli towards wastewater samples, this study developed and optimized a triplex qPCR assay by combining three qPCR primer-probe sets targeting Campylobacter jejuni subsp. jejuni, Campylobacter coli, and Campylobacter sputorum biovar sputorum (C. sputorum), respectively. This triplex qPCR assay not only can directly and simultaneously detect the concentration of C. jejuni and C. coli in wastewater but also can achieve the PCR inhibition control using C. sputorum primer-probe set. This is the first developed triplex qPCR assay with IAC for C. jejuni and C. coli, to be used in the wastewater-based epidemiology (WBE) applications. The optimized triplex qPCR assay enables the detection limit of the assay (ALOD100%) and wastewater (PLOD80%) as 10 gene copy/μL and 2 log10 cells/mL (2 gene copies/μL of extracted DNA), respectively. The application of this triplex qPCR to 52 real raw wastewater samples from 13 wastewater treatment plants demonstrated its potential as a high-throughput and economically viable tool for the long-term monitoring of C. jejuni and C. coli prevalence in communities and the surrounding environments. This study provided an accessible methodology and a solid foundation for WBE-based monitoring of Campylobacter spp. relevant diseases and paved the road for future WBE back-estimation of C. jejuni and C. coli prevalence.