Prevalence of pulmonary anthracosis in household dogs in southwest states in Nigeria: a sentinel for environmental pollution

Nigeria, stemming from vehicular traffic, generator sets, industrial sources, residential combustion, and road dust. Pulmonary anthracosis, the accumulation of carbon particles in the lungs, is a known risk factor for cancer. While this condition has been observed in stray dogs, data on its prevalence in household dogs is limited. This study aimed to determine the prevalence of pulmonary anthracosis in household dogs within three southwestern states of Nigeria over a decade (2011-2020) and to analyze the histopathological features of pulmonary anthracosis observed in canine lung tissue samples submitted for post-mortem examination. Lung tissue samples from 472 dog carcasses submitted to the Federal University of Agriculture, Abeokuta, and the University of Ibadan for post-mortem examination were analyzed in this study. Lesions suggestive of pulmonary anthracosis were identified through gross examination and further analyzed histologically to confirm their characteristics. The findings were presented using tables, charts, and chi-square to determine association between breed, age, and sex considering p < 0.05 as significant. Out of total lungs sampled, 150 (31.8%) were positive for pulmonary anthracosis. No significant association was found between breed (p = 0.95) or sex (p = 0.98) and anthracosis, but age was statistically significant (p = 0.01). Histopathological findings included bronchiolar smooth muscle hypertrophy (90%), severe fibrosis (80%), and bronchiolar epithelial hyperplasia (50%). The study concluded that pulmonary anthracosis is prevalent among household dogs in the region. The pathological changes highlighted the adverse effects associated with the condition in affected organs and that black carbon as a major air pollutant that poses health risks to humans and animals.

Diagnosis of bacteria from the CMNR group in farm animals

The CMNR group comprises bacteria of the genera Corynebacterium, Mycobacterium, Nocardia, and Rhodococcus and share cell wall and DNA content characteristics. Many pathogenic CMNR bacteria cause diseases such as mastitis, lymphadenitis, and pneumonia in farmed animals, which cause economic losses for breeders and represent a threat to public health. Traditional diagnosis in CMNR involves isolating target bacteria on general or selective media and conducting metabolic analyses with the assistance of laboratory biochemical identification systems. Advanced mass spectrometry may also support diagnosing these bacteria in the clinic's daily routine despite some challenges, such as the need for isolated bacteria. In difficult identification among some CMNR members, molecular methods using polymerase chain reaction (PCR) emerge as reliable options for correct specification that is sometimes achieved directly from clinical samples such as tracheobronchial aspirates and feces. On the other hand, immunological diagnostics such as the skin test or Enzyme-Linked Immunosorbent Assay (ELISA) for Mycobacterium tuberculosis yield promising results in subclinical infections with no bacterial growth involved. In this review, we present the methods most commonly used to diagnose pathogenic CMNR bacteria and discuss their advantages and limitations, as well as challenges and perspectives on adopting new technologies in diagnostics.

Photobacterium damselae subsp. damselae in Stranded Cetaceans: A 6-Year Monitoring of the Ligurian Sea in Italy

Photobacterium damselae subsp. damselae (Pdd) is an increasingly common bacterium in post-mortem diagnostics of beached marine mammals, but little is known about its precise etiological responsibility. To estimate the prevalence of Pdd in stranded cetaceans from 2017 to 2022 on the Ligurian coast (Pelagos Sanctuary), we tested tissues from 53 stranded individuals belonging to four cetacean species. DNA extracts from cetacean tissue were screened using a polymerase chain reaction (PCR) assay targeting the Pdd ureC gene. Positive samples were screened by PCR for dly, hlyApl and hlyAch hemolysin genes, which were confirmed by sequencing. Twenty-two out of 53 (41.5%) cetaceans analyzed by PCR were confirmed for Pdd DNA in at least one tissue among those analyzed. Five of these cetaceans were positive for at least one of the hemolysin genes tested. In all Pdd-positive cetaceans, other pathogens that were considered responsible for the causa mortis of the animals were also found. The results provide new information on the spread of Pdd in cetaceans and support the thesis that Pdd might be an opportunistic agent that could contribute to worsening health conditions in subjects already compromised by other pathogens. However, further studies are needed to investigate and deepen this hypothesis.

Miniaturized MXene-based electrochemical biosensors for virus detection

The timely control of infectious diseases can prevent the spread of infections and mitigate the significant socio-economic damage witnessed during recent pandemics. Diagnostic methods play a significant role in detecting highly contagious agents, such as viruses, to prevent further transmission. The emergence of advanced point-of-care techniques offers several advantages over conventional approaches for detecting infectious agents. These techniques are highly sensitive, rapid, can be miniaturized, and are cost-effective. Recently, MXene-based 2D nanocomposites have proven beneficial for fabricating electrochemical biosensors due to their suitable electrical, optical, and mechanical properties. This article covers electrochemical biosensors based on MXene nanocomposite for the detection of viruses, along with the associated challenges and future possibilities. Additionally, we highlight various conventional techniques for the detection of infectious agents, discussing their pros and cons. We delve into the challenges faced during the fabrication of MXene-based biosensors and explore future endeavors. It is anticipated that the information presented in this work will pave the way for the development of Point-of-Care (POC) devices capable of sensitive and selective virus detection, enhancing preparedness for ongoing and future pandemics.

Pattern analysis for the diagnosis of inflammatory skin lesions in domestic animals: An overview

Pattern analysis of inflammatory skin diseases is a technique that offers a systematic approach to the histologic diagnosis of skin diseases. First introduced to human dermatopathology in the 1970s, it was widely adopted by veterinary pathologists for the histologic diagnosis of skin diseases in animals. As the inflammatory pattern reflects, to varying extents, aspects of the underlying disease pathogenesis, its use has contributed to the recognition of novel skin diseases in domestic animals, particularly in dogs and cats. Alternative diagnostic approaches used in human dermatopathology, such as "tissue-reaction pattern" and a purely "anatomic approach" have not been as widely used in veterinary pathology. However, veterinary pathologists often combine pattern analysis with anatomic and etiologic factors. This overview outlines the technique, introduces the patterns, and discusses advantages and limitations of pattern analysis in veterinary diagnostic dermatopathology. While molecular analytic techniques and image informatics will undoubtedly prove to be revolutionary in many areas of diagnostic pathology, it is recognized in both human and veterinary arenas that the light microscopic interpretation of hematoxylin and eosin-stained tissue sections will remain the mainstay of routine dermatopathology diagnosis for the foreseeable future.

Scope of Onsite, Portable Prevention Diagnostic Strategies for Alternaria Infections in Medicinal Plants

Medicinal plants are constantly challenged by different biotic inconveniences, which not only cause yield and economic losses but also affect the quality of products derived from them. Among them, Alternaria pathogens are one of the harmful fungal pathogens in medicinal plants across the globe. Therefore, a fast and accurate detection method in the early stage is needed to avoid significant economic losses. Although traditional methods are available to detect Alternaria, they are more time-consuming and costly and need good expertise. Nevertheless, numerous biochemical- and molecular-based techniques are available for the detection of plant diseases, but their efficacy is constrained by differences in their accuracy, specificity, sensitivity, dependability, and speed in addition to being unsuitable for direct on-field studies. Considering the effect of Alternaria on medicinal plants, the development of novel and early detection measures is required to detect causal Alternaria species accurately, sensitively, and rapidly that can be further applied in fields to speed up the advancement process in detection strategies. In this regard, nanotechnology can be employed to develop portable biosensors suitable for early and correct pathogenic disease detection on the field. It also provides an efficient future scope to convert innovative nanoparticle-derived fabricated biomolecules and biosensor approaches in the diagnostics of disease-causing pathogens in important medicinal plants. In this review, we summarize the traditional methods, including immunological and molecular methods, utilized in plant-disease diagnostics. We also brief advanced automobile and efficient sensing technologies for diagnostics. Here we are proposing an idea with a focus on the development of electrochemical and/or colorimetric properties-based nano-biosensors that could be useful in the early detection of Alternaria and other plant pathogens in important medicinal plants. In addition, we discuss challenges faced during the fabrication of biosensors and new capabilities of the technology that provide information regarding disease management strategies.

Diagnosis of Bacterial Plant Diseases via a Nitroreductase-Activated Fluorescent Sensor

Plant diseases caused by bacteria have become one of the serious problems that threaten human food security, which led to the remarkable reduction of agricultural yields and economic loss. Nitroreductase (NTR), as an important biomarker, is highly expressed in bacteria, and the level of NTR is closely related to the progression of pathogen infection. Therefore, the design of small-molecule fluorescent sensors targeting NTR is of great significance for the detection and diagnosis of plant pathogenic bacteria. In this study, a new fluorescent sensor targeting NTR was discovered and then successfully applied to the imaging of zebrafish and pathogenic bacteria. Most importantly, the developed sensor achieved the real-time diagnosis of Brassica napus L. infected with bacteria, which provides a promising tool for examining the temporal and spatial infection of plant pathogens in precision agriculture.

A system-theoretic approach for image-based infectious plant disease severity estimation

The demand for high level of safety and superior quality in agricultural products is of prime concern. The introduction of new technologies for supporting crop management allows the efficiency and quality of production to be improved and, at the same time, reduces the environmental impact. Common strategies to disease control are mainly oriented on spraying pesticides uniformly over cropping areas at different times during the growth cycle. Even though these methodologies can be effective, they present a negative impact in ecological and economic terms, introducing new pests and elevating resistance of the pathogens. Therefore, consideration for new automatic and accurate along with inexpensive and efficient techniques for the detection and severity estimation of pathogenic diseases before proper control measures can be suggested is of great realistic significance and may reduce the likelihood of an infection spreading. In this work, we present a novel system-theoretic approach for leaf image-based automatic quantitative assessment of pathogenic disease severity regardless of disease type. The proposed method is based on a highly efficient and noise-rejecting positive non-linear dynamical system that recursively transforms the leaf image until only the symptomatic disease patterns are left. The proposed system does not require any training to automatically discover the discriminative features. The experimental setup allowed to assess the system ability to generalise symptoms detection beyond any previously seen conditions achieving excellent results. The main advantage of the approach relies in the robustness when dealing with low-resolution and noisy images. Indeed, an essential issue related to digital image processing is to effectively reduce noise from an image whilst keeping its features intact. The impact of noise is effectively reduced and does not affect the final result allowing the proposed system to ensure a high accuracy and reliability.

High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance

Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.

Bacteriological and pathological investigations on the preputial glands of one-year-old C57BL/6NCrl mice maintained in individually ventilated cages

Spontaneous infections of the preputial glands represent overlooked health problems in mice that could raise welfare concerns and potentially confound scientific experiments. Agents involved in preputial gland infections have rarely been investigated, with opportunistic pathogens of laboratory animals usually detected in inflamed preputial glands. The aim of this study was to investigate the prevalence of bacterial infection in the preputial glands and the relationship between haematological and pathological changes and infection status. We analysed 40 preputial glands from 20 one-year-old C57BL/6NCrl male mice by using bacteriology, haematology and pathology. Bacteria were isolated from 16/20 (80%) mice, for a total of 32/40 (80%) examined preputial glands. Enterobacter cloacae, Pasteurella spp., Klebsiella spp. and Staphylococcus aureus were identified in 35%, 17.5%, 15% and 12.5% of the examined glands, respectively. Preputial gland inflammation was identified in 29/40 (72.5%) glands and was classified as chronic interstitial adenitis in 27 cases and suppurative adenitis in the remaining two glands. No haematological changes were found in mice with infected glands. Histologically, the presence of intralesional bacteria, intraluminal necrotic material, intraluminal keratin accumulation, interstitial inflammatory cell infiltrate and granulocytes (intraluminal and/or interstitial), along with total inflammatory score and total histopathological score, were significantly increased in infected glands and correlated with the bacterial load. Most severe inflammatory changes were identified after S. aureus infection, while ductal hyperkeratosis was significantly increased in glands infected with Klebsiella spp. In conclusion, preputial gland infection was a common event in one-year-old C57BL/6NCrl mice, and bacterial load correlated with pathological findings, while systemic effects were not highlighted by haematology.

Histological Stains in the Past, Present, and Future

Certain contemporary histology stains and methods are not the same as those used in the past. This progression has delved into the requirement for more precise, less complex, and efficient staining procedures. The objective of this study is to assess historical and contemporary stains and procedures, as well as the challenges surrounding their improvement. Carmine, hematoxylin, silver nitrate, Giemsa, trichome stain, Gram stain, and mauveine were among the first histological stains discovered in nature. Aside from their utility in the study of tissues at the time, they also laid the groundwork for the development of commercial dyes that are still in use today. Hematoxylin and eosin, Ziehl-Nielsen (ZN) stain, periodic acid-Schiff stain, and Grocott-Gomori methenamine silver stain are some of the most recently developed histological stains. The future of histological stains and processes appears to be influenced by technological advancements and the demand for cost-effective diagnostic approaches in the healthcare system. Thus, currently used histological stains appear to be economical, quick, and reliable tools for interpreting, archiving, and delivering essential diagnoses that could not be achieved by any other means.

Microchip for continuous DNA analysis based on gel electrophoresis coupled with co-injection of size markers and in-channel staining

A continuous-flow microchip enabling high-accuracy DNA analysis was developed. Serial consecutive analysis for multiple amplified DNA samples was demonstrated. The sample segments were continuously introduced to the microchip from the PCR device which was interfaced to the microchip through capillary tubing. Electrokinetic co-injection of the DNA samples with size marker enabled reproducible and reliable injection of the DNAs into the gel-filled separation channel providing accurate size determination of the DNA samples. Cross-contamination between serially introduced DNA samples was minimized by plugging a washing solution segment following the previous sample segment between two sample plugs. Using this microchip, continuous separation of multiple samples was performed without any inconvenient and labor-intensive sample preparation steps such as sample mixing, staining, and gel loading which are necessary for conventional gel electrophoresis. It has taken about 4 min to separate single DNA sample and taken 37 min for three serially injected samples which implies that this microchip can be a platform device for fast as well as highly accurate DNA analysis.

Recent Developments in Smart Food Packaging Focused on Biobased and Biodegradable Polymers

Food packaging has a crucial function in the modern food industry. New food packaging technologies seek to meet consumers and industrial's demands. Changes related to food production, sale practices and consumers' lifestyles, along with environmental awareness and the advance in new areas of knowledge (such as nanotechnology or biotechnology), act as driving forces to develop smart packages that can extend food shelf-life, keeping and supervising their innocuousness and quality and also taking care of the environment. This review describes the main concepts and types of active and intelligent food packaging, focusing on recent progress and new trends using biodegradable and biobased polymers. Numerous studies show the great possibilities of these materials. Future research needs to focus on some important aspects such as possibilities to scale-up, costs, regulatory aspects, and consumers' acceptance, to make these systems commercially viable.

Fast and accurate protocol for histology and immunohistochemistry reactions in temporomandibular joint of rats

OBJECTIVE

Propose a standard, fast and accurate protocol for the processing of the temporomandibular joint (TMJ) of adults' rats for histology and immunohistochemistry reactions.

DESIGN

Wistar male rats were perfused with paraformaldehyde (4 %). The heads were fixed in formaldehyde 10 % solution for 48 h. After that, the heads were sectioned in a sagittal plane and fixed for plus 48 h. Decalcification was performed using 20 % formic acid for 96 h and delimitation of TMJ area was done. Detailed methodology to a standard extraction and processing of TMJ to histological sections is described. Different buffers, equipment, temperature and time were tested to optimize immunostaining. Morphological preservation and antigenicity were evaluated by hematoxylin and eosin staining and immunohistochemistry reaction.

RESULTS

The current findings demonstrated that TMJ fixed in 10 % formaldehyde and decalcified in 20 % formic acid optimized decalcification processing time with preservation of cell morphology. Antigen retrieval with citrate buffer in pressure cooker (2 min at 100 °C and 5 min at room temperature) demonstrated the best protocol to preservation of the structures of TMJ.

CONCLUSIONS

This work demonstrates in detail a methodology of a fast and accurate TMJ processing for histology and immunohistochemistry reactions that guarantee tissue integrity and quality of staining.

Improving sensitivity of single tube nested PCR to detect fastidious microorganisms

Single Tube Nested PCR (ST-nPCR) is of value to clinical laboratories with limited settings for the detection of fastidious microorganisms. The detection sensitivity of ST-nPCR is dependent on ensuring minimal leftovers of outer primers during the second round of the reaction. In this work, we investigated various approaches to optimize the performance of outer primers, including decreasing outer primer concentrations; using antisense oligonucleotides to block outer primers; using chemically modified inner primers; and using Q5 Taq polymerase that lacks 5′-3′ exonuclease and strand displacement capabilities. These solutions were tested on C. abortus and C. psittaci, which are both fastidious intracellular bacteria that are difficult to diagnose.

The best obtained result was by using Q5 Taq polymerase. A detection limit with a range between 0.1 and 1 ag was achieved, which corresponds to a range between 0.2 and 2 copies of the plasmid positive control. This level of sensitivity is comparable or even better than the sensitivity achieved by TaqMan probe based real-time PCR assays. The assay was validated using 70 veterinary clinical samples from small ruminant abortions and 10% of these samples gave positive results.

In conclusion, sensitivity of ST-nPCR to detect fastidious microorganisms can be improved by using Taq polymerases that lacks 5′-3′ exonuclease. The proposed assay is affordable and applicable to a wide range of fastidious pathogens and can be suitable for laboratories with limited settings.

Rapid detection of deformed wing virus in honeybee using ultra-rapid qPCR and a DNA-chip

Fast and accurate detection of viral RNA pathogens is important in apiculture. A polymerase chain reaction (PCR)-based detection method has been developed, which is simple, specific, and sensitive. In this study, we rapidly (in 1 min) synthesized cDNA from the RNA of deformed wing virus (DWV)-infected bees (Apis mellifera), and then, within 10 min, amplified the target cDNA by ultra-rapid qPCR. The PCR products were hybridized to a DNA-chip for confirmation of target gene specificity. The results of this study suggest that our method might be a useful tool for detecting DWV, as well as for the diagnosis of RNA virus-mediated diseases on-site.

Next-Generation Sequencing Coupled With in situ Hybridization: A Novel Diagnostic Platform to Investigate Swine Emerging Pathogens and New Variants of Endemic Viruses

Next generation sequencing (NGS) can be applied to identify and characterize the entire set of microbes within a sample. However, this platform does not provide a morphological context or specific association between the viral or bacterial sequences detected and the histological lesions. This limitation has generated uncertainty whether the sequences identified by NGS are actually contributing or not for the clinical outcome. Although in situ hybridization (ISH) and immunohistochemistry (IHC) can be used to detect pathogens in tissue samples, only ISH has the advantage of being rapidly developed in a context of an emerging disease, especially because it does not require development of specific primary antibodies against the target pathogen. Based on the sequence information provided by NGS, ISH is able to check the presence of a certain pathogen within histological lesions, by targeting its specific messenger RNA, helping to build the relationship between the pathogen and the clinical outcome. In this mini review we have compiled results of the application of NGS-ISH to the investigation of challenging diagnostic cases or emerging pathogens in pigs, that resulted in the detection of porcine circovirus type 3, porcine parvovirus type 2, Senecavirus A, and Mycoplasma hyorhinis.

Virus Size Analysis by Gas-Phase Mobility Measurements: Resolution Limits

Electrospraying (ES) dissolved viral particles, followed by charge reduction and size analysis with a differential mobility analyzer (DMA), offers a flexible size-analysis tool for small particles in solution. The technique relies on pioneering work by Kaufman and colleagues, commercialized by TSI, and often referred to as GEMMA. However, viral studies with TSI's GEMMA have suffered from limited resolving power, possibly because of imperfections in either the instrument (DMA or charge reduction) or the sample solution preparation. Here, we explore the limits of the resolution achievable by GEMMA, taking advantage of (i) cleaner charge reduction methods and (ii) DMAs of higher resolving power. Analysis of the literature provides indications that mobility peak widths (fwhm) of 2% or less may be achieved by combining careful sample preparation with improved instrumentation. Working with purified PP7 bacteriophage particles small enough to be classifiable by existing high-resolution DMAs, we confirm that fairly narrow viral mobility peaks may be obtained (relative full width at half-maximum fwhm <5%). Comparison of spectra of a given apian virus sample obtained with TSI's GEMMA and our improved instrumentation confirms that one critical limitation is the DMA. This is further verified by narrow peaks from murine parvovirus, norovirus, and encephalomyelitis virus samples, obtained in our improved GEMMA with little sample preparation, directly from infected cell cultures. Classification of purified large (60 nm) coliphage PR772 particles leads to broad peaks, due to both viral degradation and limited intrinsic resolution of the DMAs used to cover the range of such large particles. We conclude that improved DMAs suitable for high-resolution analysis of particles larger than 30 nm need to be developed to determine the intrinsic mobility width of viral particles.

Pasteurella canis infective endocarditis in a dog

Infective endocarditis, an infrequent clinical syndrome in dogs, is typically associated with nondescript clinical signs such as fever, malaise and loss of appetite. Although an uncommonly reported infection in dogs, Pasteurella canis is an emerging pathogen with increasing relevance in the human microbiology literature. The goal of this study is to detail the clinical presentation and microbiological findings associated with a novel causative agent of infective endocarditis in the dog. Diagnostic evaluation as well as conventional, automated and molecular microbiological methods are highlighted. The recent literature regarding P. canis and infective endocarditis in companion animals and humans is reviewed. Although an unusual etiologic agent of infective endocarditis, awareness of P. canis as a diagnostic possibility is crucial to accurate microbial surveillance.

Chemical and Biological Sensors for Food-Quality Monitoring and Smart Packaging

The growing interest in food quality and safety requires the development of sensitive and reliable methods of analysis as well as technology for freshness preservation and food quality. This review describes the status of chemical and biological sensors for food monitoring and smart packaging. Sensing designs and their analytical features for measuring freshness markers, allergens, pathogens, adulterants and toxicants are discussed with example of applications. Their potential implementation in smart packaging could facilitate food-status monitoring, reduce food waste, extend shelf-life, and improve overall food quality. However, most sensors are still in the development stage and need significant work before implementation in real-world applications. Issues like sensitivity, selectivity, robustness, and safety of the sensing materials due to potential contact or migration in food need to be established. The current development status of these technologies, along with a discussion of the challenges and opportunities for future research, are discussed.

Molecular Identification of Bacteria in Intra-abdominal Abscesses Using Deep Sequencing

Background

Intra-abdominal abscesses are localized collections of pus, which generally arise from a breach in the normal mucosal defense barrier that allows bacteria from gastrointestinal tract, and less commonly from the gynecologic or urinary tract, to induce inflammation, resulting in an infection. The microbiology of these abscesses is usually polymicrobial, associated with the primary disease process. However, the microbial identity, diversity and richness in intra-abdominal abscesses have not been well characterized, due in part to the difficulty in cultivating commensal organisms using standard culture-based techniques.

Methods

We used culture-independent 16S rRNA Illumina sequencing to characterize bacterial communities in intra-abdominal abscesses collected by percutaneous drainage. A total of 43 abscess samples, including 19 (44.2%) Gram stain and culture-negative specimens, were analyzed and compared with results from conventional microbiologic cultures.

Results

Microbial composition was determined in 8 of 19 culture-negative samples and 18 of 24 culture-positive samples, identifying a total of 221 bacterial taxa or operational taxonomic units (OTUs) and averaging 13.1 OTUs per sample (interquartile range, 8-16.5 OTUs). Microbial richness for monomicrobial and polymicrobial samples was significantly higher than culture-negative samples (17 and 15.2 OTUs vs 8 OTUs, respectively), with a trend toward a higher microbial diversity (Shannon diversity index of 0.87 and 1.18 vs 0.58, respectively).

Conclusions

The bacterial consortia identified by cultures correlated poorly with the microbial composition determined by 16S rRNA sequencing, and in most cases, the cultured isolates were minority constituents of the overall abscess microbiome. Intra-abdominal abscesses were generally polymicrobial with a surprisingly high microbial diversity, but standard culture-based techniques failed to reveal this diversity. These data suggest that molecular-based approaches may be helpful for documenting the presence of bacteria in intra-abdominal abscesses where standard cultures are unrevealing, particularly in the setting of prior antibiotic exposure.

Non-invasive in vivo imaging of fluorescence-labeled bacterial distributions in aquatic species

In vivo imaging is becoming an advanced tool for noninvasive distribution of longitudinal small animals. However, the aquatic species have been limited to the optical imaging of noninvasively tracking on pathogen distribution. The purpose of this study was to develop shell-less fish and shrimp models of non-invasive in vivo imaging technique for visualization of pathogens. This experiment was utilized Escherichia coli, Edwardsiella tarda, Vibrio alginolyticus and Vibrio harveyi labeled with fluorescence probes to imaging bacterial distributions by IVIS Lumina LT system. The study was traced the internal distribution of fluorescence probes labeled bacteria in systemic organs by quantified their fluorescence intensities. The ex vivo organ images were showed more obvious fluorescent signal in catfish intestine, liver, heart, kidney and the shrimp showed heart, hepatopancreas, and colon. Hence, the in vivo imaging methods using fluorescent labeled bacterial distribution were suggested to quantify by fluorescence intensity in whole pre-infected subjects. Therefore, it can offer the information about the localization and distribution of pathogens in the preclinical research, after immersion and injections.

Evaluation of a PCR assay on overgrown individual fecal samples cultured for Mycobacterium avium subsp. paratuberculosis

Microbial overgrowth can interfere with Mycobacterium avium subsp. paratuberculosis (MAP) growth and detection. We estimated the percentage of positive samples by PCR performed on the incubated media of individual fecal samples classified as non-interpretable (NI) by bacteriologic culture of liquid media. A total of 262 liquid cultures declared NI and 88 samples declared negative were included in the study. MAP DNA was detected in 7 NI samples (2.7%; 95% CI: 1.1–5.4%) and in 1 negative sample (1.1%; 95% CI: 0.3–6.2%). The PCR allowed the detection of MAP-positive samples that had been missed in the initial bacteriologic culture. However, the benefit of these few additional positive results must be weighed against the additional costs incurred. Using PCR to classify overgrown cultures optimizes the detection process and eliminates the NI outcome.

Detection of eight foodborne bacterial pathogens by oligonucleotide array hybridization

BACKGROUND

Simultaneous and rapid detection of multiple foodborne bacterial pathogens is important for the prevention of foodborne illnesses.

OBJECTIVE

The aim of this study was to evaluate the use of 16S rDNA and 23S rDNA sequences as targets for simultaneous detection of eight foodborne bacterial pathogens.

METHODS

Nineteen bacterial oligonucleotide probes were synthesized and applied to nylon membranes. Digoxygenin labeled 16S rDNA and 23S rDNA from bacteria were amplified by PCR using universal primers, and the amplicons were hybridized to the membrane array. Hybridization signals were visualized by NBT/BCIP color development.

RESULTS

The eight intestinal bacterial pathogens including Salmonella enterica, Escherichia coli, Bacillus cereus, Vibrio cholerae, Shigella dysenteriae, Staphylococcus aureus, Listeria monocytogenes, and Enterococcus faecalis were appropriately detected in a panel of oligonucleotide array hybridization. The experimental results showed that the method could discriminate the bacterial pathogens successfully. The sensitivity of oligonucleotide array was 10³ CFU/ml.

CONCLUSION

This study showed that 16S rDNA and 23S rDNA genes had sufficient sequence diversity for species identification and were useful for monitoring the populations of foodborne pathogenic bacteria. Furthermore, results obtained in this study revealed that oligonucleotide array hybridization had a powerful capability to detect and identify the bacterial pathogens simultaneously.

A comparative analysis and guidance for individualized chemotherapy of stage II and III colorectal cancer patients based on pathological markers

Adjuvant chemotherapy is considered the standard of care for patients with colorectal cancer after curative resection. Although current guidelines provide clear instructions for chemotherapy for stage II high-risk and stage III colorectal cancer, it is insufficient to individualize therapy. We analyzed the outcomes of 902 patients with colorectal cancer treated with or without chemotherapy in our hospital. We found Chinese survival benefit for chemotherapy was consistent with current guidelines. Moreover, our data added to the evidence that chemotherapy might be used for elderly patients with stage II high-risk colorectal cancer. Pathological markers could predict response to individualize therapy in a convenient, fast and inexpensive way. We compared survivals of patients with stage II high-risk and stage III colorectal cancer with chemotherapy in different pathological markers expression, and furthermore used 458 colon adenocarcinoma samples from The Cancer Genome Atlas to verify our preliminary results. We confirmed TOPIIα, EGFR and P170 may be sufficiently predictive markers to individualize chemotherapy. FOLFOX was the optimal adjuvant chemotherapy for patients with stage II high-risk and stage III colorectal cancer when TOPIIα was positive or EGFR or P170 was negative.

Semi-quantitative digital analysis of polymerase chain reaction-electrophoresis gel: Potential applications in low-income veterinary laboratories

Aim:

The interpretation of conventional polymerase chain reaction (PCR) assay results is often limited to either positive or negative (non-detectable). The more robust quantitative PCR (qPCR) method is mostly reserved for quantitation studies and not a readily accessible technology in laboratories across developing nations. The aim of this study was to evaluate a semi-quantitative method for conventional PCR amplicons using digital image analysis of electrophoretic gel. The potential applications are also discussed.

Materials and Methods:

This study describes standard conditions for the digital image analysis of PCR amplicons using the freely available ImageJ software and confirmed using the qPCR assay.

Results and Conclusion:

Comparison of ImageJ analysis of PCR-electrophoresis gel and qPCR methods showed similar trends in the Fusobacterium necrophorum DNA concentration associated with healthy and periodontal disease infected wallabies (p≤0.03). Based on these empirical data, this study adds descriptive attributes (“more” or “less”) to the interpretation of conventional PCR results. The potential applications in low-income veterinary laboratories are suggested, and guidelines for the adoption of the method are also highlighted.

Enhancement of wildlife disease surveillance using multiplex quantitative PCR: development of qPCR assays for major pathogens in UK squirrel populations

Rapid development in polymerase chain reaction (PCR) technology has revolutionised the speed and accuracy of many diagnostic assays. However, comparatively few wildlife epidemiological studies use quantitative PCR (qPCR) for pathogen detection, even fewer employ an internal control, to ensure confidence in negative results, and PCR's ability to multiplex and therefore detect several targets in a single reaction is underutilised. Here, we describe the development of two multiplex qPCR assays for the red and grey squirrel that detect the pathogens squirrelpox virus (SQPV) and adenovirus in squirrels (SADV), both of which cause mortality in the red squirrel. Both assays use a section of the squirrel phosphoglycerate kinase gene as an endogenous internal control that identifies and compensates for both, inadequate sampling or PCR inhibition. Tests on infected squirrel tissue demonstrate that simple swab samples (particularly from distal antebrachial skin) are sufficient to detect and identify the relative quantity of SQPV DNA in both squirrel species, while rectal swabs and blood cell pellets can be used to reliably indicate SADV infection. These assays are sensitive and specific with an endogenous internal control providing confidence in negative results and allowing comparison across laboratories. Using such assays should prove advantageous in wildlife studies with limited resources while allowing the maximum data yield.

A review of methods for nematode identification

Nematodes are non-segmented roundworms found in soil, aquatic environment, plants, or animals. Either useful or pathogenic, they greatly influence environmental equilibrium, human and animal health, as well as plant production. Knowledge on their taxonomy and biology are key issues to answer the different challenges associated to these organisms. Nowadays, most of the nematode taxonomy remains unknown or unclear. Several approaches are available for parasite identification, from the traditional morphology-based techniques to the sophisticated high-throughput sequencing technologies. All these techniques have advantages or drawbacks depending on the sample origin and the number of nematodes to be processed. This review proposes an overview of all newly available methods available to identify known and/or unknown nematodes with a specific focus on emerging high-throughput molecular techniques.

Biosensors based on modularly designed synthetic peptides for recognition, detection and live/dead differentiation of pathogenic bacteria

Rapid and sensitive detection of bacterial pathogens is critical for assessing public health, food and environmental safety. We report the use of modularly designed and site-specifically oriented synthetic antimicrobial peptides (sAMPs) as novel recognition agents enabling detection and quantification of bacterial pathogens. The oriented assembly of the synthetic peptides on electrode surfaces through an engineered cysteine residue coupled with impedimetric detection facilitated rapid and sensitive detection of bacterial pathogens with a detection limit of 10(2)CFU/mL for four bacterial strains including Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus) and Staphylococcus epidermidis (S. epidermidis). The approach enabled differentiation between live and dead bacteria. The fabrication of the sAMPs functionalized surface and the importance of the sAMPs orientation for providing optimum recognition and detection ability against pathogens are discussed. The proposed methodology provides a universal platform for the detection of bacterial pathogens based on engineered peptides, as alternative to the most commonly used immunological and gene based assays. The method can also be used to fabricate antimicrobial coatings and surfaces for inactivation and screening of viable bacteria.

Diagnostics and Resistance Profiling of Bacterial Pathogens

Worldwide infectious disease is one of the leading causes of death. Despite improvements in technology and healthcare services, morbidity and mortality due to infections have remained unchanged over the past few decades. The high and increasing rate of antibiotic resistance is further aggravating the situation. Growing resistance hampers the use of conventional antibiotics, and substantial higher mortality rates are reported in patients given ineffective empiric therapy mainly due to resistance to the agents used. These infections cause suffering, incapacity, and death and impose an enormous financial burden on both healthcare systems and on society in general. The accelerating development of multidrug resistance is one of the greatest diagnostic and therapeutic challenges to modern medicine. The lack of new antibiotic options underscores the need for optimization of current diagnostics, therapies, and prevention of the spread of multidrug-resistant organisms. The so-called -omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have yielded large-scale datasets that advanced the search for biomarkers of infectious diseases in the last decade. One can imagine that in the future the implementation of biomarker-driven molecular test systems will transform diagnostics of infectious diseases and will significantly accelerate the identification of the bacterial pathogens at the infected host site. Furthermore, molecular tests based on the identification of markers of antibiotic resistance will dramatically change resistance profiling. The replacement of culturing methods by molecular test systems for early diagnosis will provide the basis not only for a prompt and targeted therapy, but also for a much more effective stewardship of antibiotic agents and a reduction of the spread of multidrug resistance as well as the appearance of new antibiotic resistances.

Detection of feline upper respiratory tract disease pathogens using a commercially available real-time PCR test

Feline herpesvirus (FHV-1), feline calicivirus (FCV), Bordetella bronchiseptica (Bb), Chlamydia felis (Cf) and Mycoplasma felis (Mf) are common infectious agents identified in cats with upper respiratory tract disease (URTD). Each of these agents can either act as primary pathogens or cause subclinical infections, and pathogen identification can be used to prevent disease transmission in shelters, or to manage individual cats with recurrent URTD. The aim of this study was to compare pathogen detection rates using real-time PCR testing and virus isolation (VI) or bacterial culture in conjunctival, nasal and oropharyngeal swabs from 18 shelter-housed cats with clinical URTD. Co-infections were common; FHV-1 was most prevalent and Cf and FCV were least prevalent. Agents detected by PCR were FCV 2/18 (11%), FHV-1 17/18 (94%), Bb 8/18 (44%) and Mf 15/18 (83%). Agents detected by VI and bacterial culture were FCV 1/18 (6%), FHV-1 12/18 (67%), Bb 8/18 (44%) and Mf 12/18 (67%). Agreement between PCR results and the other two methods was: FHV-1, 57.4%; FCV, 98.1%; Bb, 75.0%; Mf, 60.0%. Discordancies included PCR-positive, VI-negative (FCV, n = 1/54, 1.9%; FHV-1, n = 23/54, 42.6%), PCR-positive, culture-negative (Bb, n = 6/36, 16.7%; Mf, n = 13/36, 36.1%) or PCR-negative, culture-positive (Bb, n = 3/36, 8.3%; Mf, n = 2/36, 5.6%) results. A combination of an oropharyngeal swab and either a conjunctival or a nasal swab submitted for PCR testing was able to detect all infectious agents tested for in each cat. PCR testing was a sensitive and convenient method of detection of infectious agents in cats with clinical signs of URTD.

Current and Prospective Methods for Plant Disease Detection

Food losses due to crop infections from pathogens such as bacteria, viruses and fungi are persistent issues in agriculture for centuries across the globe. In order to minimize the disease induced damage in crops during growth, harvest and postharvest processing, as well as to maximize productivity and ensure agricultural sustainability, advanced disease detection and prevention in crops are imperative. This paper reviews the direct and indirect disease identification methods currently used in agriculture. Laboratory-based techniques such as polymerase chain reaction (PCR), immunofluorescence (IF), fluorescence in-situ hybridization (FISH), enzyme-linked immunosorbent assay (ELISA), flow cytometry (FCM) and gas chromatography-mass spectrometry (GC-MS) are some of the direct detection methods. Indirect methods include thermography, fluorescence imaging and hyperspectral techniques. Finally, the review also provides a comprehensive overview of biosensors based on highly selective bio-recognition elements such as enzyme, antibody, DNA/RNA and bacteriophage as a new tool for the early identification of crop diseases.

Histological Stains: A Literature Review and Case Study

The history of histology indicates that there have been significant changes in the techniques used for histological staining through chemical, molecular biology assays and immunological techniques, collectively referred to as histochemistry. Early histologists used the readily available chemicals to prepare tissues for microscopic studies; these laboratory chemicals were potassium dichromate, alcohol and the mercuric chloride to harden cellular tissues. Staining techniques used were carmine, silver nitrate, Giemsa, Trichrome Stains, Gram Stain and Hematoxylin among others. The purpose of this research was to assess past and current literature reviews, as well as case studies, with the aim of informing ways in which histological stains have been improved in the modern age. Results from the literature review has indicated that there has been an improvement in histopathology and histotechnology in stains used. There has been a rising need for efficient, accurate and less complex staining procedures. Many stain procedures are still in use today, and many others have been replaced with new immunostaining, molecular, non-culture and other advanced staining techniques. Some staining methods have been abandoned because the chemicals required have been medically proven to be toxic. The case studies indicated that in modern histology a combination of different stain techniques are used to enhance the effectiveness of the staining process. Currently, improved histological stains, have been modified and combined with other stains to improve their effectiveness.

New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae

Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.