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Streptococcus suis is one of the most important bacterial swine pathogens affecting post-weaned piglets, causing mainly meningitis, arthritis and sudden death. It not only results in severe economic losses but also raises concerns over animal welfare and antimicrobial resistance and remains an important zoonotic agent in some countries. The definition and diagnosis of S. suis -associated diseases can be complex. Should S. suis be considered a primary or secondary pathogen? The situation is further complicated when referring to respiratory disease, since the pathogen has historically been considered as a secondary pathogen within the porcine respiratory disease complex (PRDC). Is S. suis a respiratory or strictly systemic pathogen? S. suis is a normal inhabitant of the upper respiratory tract, and the presence of potentially virulent strains alone does not guarantee the appearance of clinical signs. Within this unclear context, it has been largely proposed that co-infection with some viral and bacterial pathogens can significantly influence the severity of S. suis -associated diseases and may be the key to understanding how the infection behaves in the field. In this review, we critically addressed studies reporting an epidemiological link (mixed infections or presence of more than one pathogen at the same time), as well as in vitro and in vivo studies of co-infection of S. suis with other pathogens and discussed their limitations and possibilities for improvement and proposed recommendations for future studies.

In China, Tomato chlorosis virus (ToCV) and Tomato yellow leaf curl virus (TYLCV) are widely present in tomato plants. The epidemiology of these viruses is intimately associated with their vector, the whitefly ( Bemisia tabaci MED). However, how a ToCV+TYLCV mixed infection affects viral acquisition by their vector remains unknown. In this study, we examined the growth parameters of tomato seedlings, including disease symptoms and the heights and weights of non-infected, singly infected and mixed infected tomato plants. Additionally, the spatio-temporal dynamics of the viruses in tomato plants, and the viral acquisition and transmission by B. tabaci MED, were determined. The results demonstrated that: (i) ToCV+TYLCV mixed infections induced tomato disease synergism, resulting in a high disease severity index and decreased stem heights and weights; (ii) as the disease progressed, TYLCV accumulated more in upper leaves of TYLCV-infected tomato plants than in lower leaves, whereas ToCV accumulated less in upper leaves of ToCV-infected tomato plants than in lower leaves; (iii) viral accumulation in ToCV+TYLCV mixed infected plants was greater than in singly infected plants; and (iv) B. tabaci MED appeared to have a greater TYLCV, but a lower ToCV, acquisition rate from mixed infected plants compared with singly infected plants. However, mixed infections did not affect transmission by whiteflies. Thus, ToCV+TYLCV mixed infections may induce synergistic disease effects in tomato plants.

Viral diseases are a frequent problem in the agricultural sector, causing significant economic losses, so their management is a constant challenge for producers and researchers. One of the factors that often complicates the control of viral diseases in plants is mixed infections, which occur when two or more viruses are present in a plant, generating a complex expression of symptoms. During a mixed infection, the following types of interactions basically occur: complementation and interference, the effect of which produces synergism, antagonism, or no effect. However, there are also subcategories of effects. This makes early detection difficult, and this infection can also give a competitive advantage to the pathogens involved. This review presents updated information on mixed viral infections in plants, the interaction categories, the severity of symptoms, and the impact on plants and vectors. The intention is to share information to better understand the etiology of the diseases.

Respiratory diseases are a health and economic concern for poultry production worldwide. Given global economic exchanges and migratory bird flyways, respiratory viruses are likely to emerge continuously in new territories. The primary aim of this study was to investigate the major pathogens involved in respiratory disease in Tunisian broiler poultry and their epidemiology. Between 2018 and 2020, broilers farms in northeastern Tunisia were monitored, and 39 clinically diseased flocks were sampled. Samples were screened for five viral and three bacterial respiratory pathogens using a panel of real-time PCR assays. The reemergence of H9N2 low pathogenic avian influenza virus (LPAIV) in commercial poultry was reported, and the Northern and Western African GI lineage strain was typed. The infectious bronchitis virus (IBV) GI-23 lineage and the avian metapneumovirus (aMPV) subtype B also were detected for the first time in broilers in Tunisia. H9N2 LPAIV was the most detected pathogen in the flocks tested, but rarely alone, as 15 of the 16 H9N2 positive flocks were co-infected. Except for infectious laryngotracheitis virus (ILTV), all of the targeted pathogens were detected, and in 61% of the respiratory disease cases, a combination of pathogens was identified. The major combinations were H9N2 + aMPV (8/39) and H9N2 + IBV (6/39), showing the high contribution of H9N2 LPAIV to the multifactorial respiratory diseases. This field survey provided evidence of the emergence of new respiratory viruses and the complexity of respiratory disease in Tunisia. A comprehensive and continuous surveillance strategy therefore is needed to better control respiratory pathogens in Tunisia.

Emergomycosis, an emerging dimorphic fungal infection caused by species, primarily affects immunocompromised individuals. has been reported in China, including rare cases in immunocompetent individuals. Diagnosis remains challenging due to the lack of typical clinical manifestations and radiological features. Co-infection with other pathogens further complicates management, with no prior global reports of concurrent and non-tuberculous mycobacterial (NTM) infections. A 21-year-old immunocompetent woman with occupational exposure to soil presented with cough, fever, and a mediastinal mass on chest CT. The initial biopsy specimens revealed granulomatous inflammation and yeast-like fungi. Metagenomic next-generation sequencing (mNGS) of endobronchial ultrasound (EBUS)-guided specimens confirmed (40 reads). Liposomal amphotericin B induction therapy initially relieved the symptoms. However, recurrence prompted repeat mNGS, which revealed elevated loads (791 reads). Combined with the patient's history of soil exposure, a diagnosis of mediastinal with co-infection was established based on the clinical presentation, the chest CT findings, histopathological observations of yeast-like fungi, the mNGS results, and the therapeutic response. Following confirmation of the co-infection, tailored adjustments to the antimicrobial regimen led to successful clinical management. To the best of our knowledge, this is the first study in which and were documented to coexist in the mediastinum. The dual pathogens were identified through a combination of EBUS-guided biopsy and mNGS. Accurate pathogen identification followed by tailored, pathogen-directed therapy is essential for the effective management of an and mixed infection.

It can be difficult to distinguish lung disease caused by nontuberculous mycobacteria (NTM), , and mixed infections (MIs) that include NTM. Metagenomic next generation sequencing (mNGS) is a highly sensitive method that can reliably identify lung pathogens. We retrospectively analyzed the records of patients who had MIs of the lungs that included NTM and received mNGS testing. The records of 36 patients who were diagnosed with NTM infection of the lungs at the Second Hospital of Jilin University from Nov 2023 to Jun 2024 were analyzed. Initial empirical treatments were ineffective in all patients, leading to the application of mNGS of bronchoalveolar lavage fluid (BALF). The average patient age was 62.4 years, 22 patients had one or more underlying chronic disease, and all patients had at least one respiratory symptom (cough, sputum production, fever, or dyspnea). Chest CT examinations showed that patients had different degrees of pneumonia and pleural effusion. Among tested patients, there were elevated levels of erythrocyte sedimentation rate in 81.8% (18/22) and elevated C-reactive protein in 90.5% (19/21). There were variable results from acid-fast staining of bronchoalveolar lavage fluid (BALF; 3/36, 8.3%), and transbronchial lung biopsy (TBLB; 5/14, 35.7%). mNGS identified seven NTM species. Treatment based on the mNGS results led to the resolution of clinical symptoms and absorption of lung lesions in all patients. Most of the 36 patients with MIs of the lungs that included NTM had underlying diseases. The results of traditional tests, including sputum or BALF culture and smear, acute phase markers, and TBLB pathological examination, were problematic. mNGS provides rapid and reliable diagnosis, allowing the rapid implementation of appropriate therapy in patients with MIs of the lungs that include NTM.

Blood parasites comprise some of the most prevalent pathogens in nature, and their detection and identification are major objectives in varied fields such as ecology and biomedicine. Two approaches were compared, one based on Sanger sequencing and the other next-generation sequencing (NGS) based, in terms of their performance in detecting avian blood parasites across tropical Southeast Asian birds. Across a panel of 528 bird individuals, 43 birds were ascertained to be infected with avian haemosporidians using a polymerase chain reaction-based detection method. Among these samples, NGS-based barcoding confirmed co-infections by multiple blood parasites in all eight cases where Sanger sequencing produced double peaks. Importantly however, the NGS-based method produced another five diagnoses of co-infections (62.5%) in which Sanger-based barcoding remained equivocal. In contrast to Sanger sequencing, the NGS-based method was able to identify co-infecting haemosporidian lineages via their barcodes. The accuracy of avian haemosporidian lineage identification was not compromised by the shorter length of NGS sequences, with ~94% of NGS barcodes producing matches identical to those of the Sanger barcodes. The application of NGS-based barcoding methods promises to enhance parasite identification and reduce erroneous inferences based on artefacts.

A comprehensive study on the whole spectrum of viruses and viroids in five Iranian grapevine cultivars was carried out using sRNA libraries prepared from phloem tissue. A comparison of two approaches to virus detection from sRNAome data indicated a significant difference in the results and performance of the aligners in viral genome reconstruction. The results showed a complex virome in terms of viral composition, abundance, and richness. Thirteen viruses and viroids were identified in five Iranian grapevine cultivars, among which the grapevine red blotch virus and grapevine satellite virus were detected for the first time in Iranian vineyards. Grapevine leafroll-associated virus 1 (GLRaV1) and grapevine fanleaf virus (GFLV) were highly dominant in the virome. However, their frequency and abundance were somewhat different among grapevine cultivars. The results revealed a mixed infection of GLRaV1/grapevine yellow speckle viroid 1 (GYSVd1) and GFLV/GYSVd1 in grapevines that exhibited yellows and vein banding. We also propose a threshold of 14% of complete reconstruction as an appropriate threshold for detection of grapevine viruses that can be used as indicators for reliable grapevine virome profiling or in quarantine stations and certification programs.

Background Peritonitis caused by nontuberculous mycobacteria (NTM) is an infrequent but important complication in patients undergoing peritoneal dialysis (PD). There has been no report of mixed infections with multiple NTM. Peritoneal dialysis-associated peritonitis (PDAP) caused by Mycobacterium abscessus is more common than that caused by M. smegmatis and M. goodii . Case presentation This case concerns a patient with PDAP caused by gram-positive bacilli, which could not be identified at the species level in successive detections of initial peritoneal effluent. Later, M. smegmatis was detected with no sensitivity results in bacterial culture. However, metagenomic next-generation sequencing (mNGS) and first whole-genome sequences indicated that there were three species coexisting in the culture, including M. smegmatis (24,708 reads), M. abscessus (9224 reads), and M. goodii (8305 reads). This is the first case of PDAP with specific evidence that conventional detection methods isolated a poorly pathogenic NTM, whereas mNGS and first whole-genome sequences identified multiple NTM. Pathogenic bacteria might not be detected using conventional methods due to their lower abundance. This case report is the first description of mixed infections with more than two species of NTM during PDAP. Conclusions PDAP caused by multiple NTM is rare, and the diagnosis is difficult. When NTM are isolated by conventional tests in patients who are suspected of infection, clinicians should be vigilant, and further tests should be performed to determine the presence of rare or even previously unknown bacteria, for which the quantity is relatively low, but the pathogenicity is high. The rare pathogen may be a primary agent in causing such complications.

Many studies on the molecular epidemiology of tuberculosis (TB) have shown that 10-20% of patients may be infected with more than one strain of (MTB), during a single episode of the disease. However, data on the frequency of this phenomenon are underestimated, and methodological difficulties mean that most cases are not detected. Below we present the first case of polyclonal/mixed infection documented in Poland. We described the case of a 33-year-old Ukrainian man, imprisoned in a Polish prison, who was diagnosed with pulmonary TB confirmed by culture. During the 6-month therapy, the patient was treated in three Polish hospitals, but no negative sputum test result was obtained. In the course of microbiological and molecular diagnostics, conducted from June 2021 to February 2022, divergent results were obtained from drug susceptibility testing and genotyping of MTB strains isolated from clinical materials from the patient. In the final stage of the tests, it was confirmed that the patient was infected with two strains of MTB - one of them was drug-sensitive and belonged to the T1 267 genotype, the other was pre-extensively drug resistant (pre-XDR) and belonged to the Beijing 265 genotype. The existence of clonally complex TB infections resulting in heteroresistance to basic antituberculosis drugs has important implications for patient care. Established molecular methods complemented by routine microbiological diagnostics allow rapid detection of these infections and appropriate adjustment of therapy.