A school-aged patient with a previous history of mild eczema developed a respiratory tract infection in October 2016, a couple of days after visiting a pig farm. The child had entered the pigsty but had not been in direct contact with pigs. Despite early prescription of antibiotics by the general practitioner the child’s clinical situation rapidly deteriorated. Within three days after onset of disease the child was transferred to a paediatric intensive care unit (PICU) for non-invasive ventilation support and intensive monitoring. Despite these efforts, the patient deteriorated further and was intubated in order to start mechanical ventilation. Bronchoscopy following intubation revealed large amounts of highly viscous mucus in the airways. Efforts to remove this mucus failed to improve ventilation. Mechanical ventilation became increasingly complex and it was decided to initiate veno-venous extracorporeal membrane oxygenation (ECMO) and to transfer to a quaternary PICU. Due to ECMO, blood oxygenation was secured and extensive bronchoscopy could be performed, during which topical DNAse (Dornase alpha, Pulmozyme, Roche) was instilled to decrease viscosity and facilitate removal of obstructing mucus plugs. On the following day, bronchoscopy was repeated and additional mucus was removed.

In the days following these procedures, the patient improved rapidly. ECMO was discontinued five days after start and the patient could be extubated. For the entire duration of hospitalisation, the patient had received broad-spectrum antibiotics, although all bacterial cultures remained negative. Throat swabs had been collected at initial admission and tested positive for influenza A virus, of which the quaternary PICU was informed on the day after the patient transfer. Oseltamivir treatment (60 mg twice daily) was started hours after initiation of ECMO and transport. It was continued for a total of 7 days when a nasal swab tested negative for influenza virus. At the time of submission of this report, the child was recovering well.

Influenza A virus (IAV) is a major animal and public health concern given the zoonotic nature of IAV (1–3). As a natural host to IAV, research on IAV in swine has relevance to both human and animal medicine. IAV is a segmented, negative-sense, single-stranded RNA virus. The surface glycoproteins, hemaggluttinin (HA) and neuraminidase (NA), are used to type IAV, and currently H1N1, H1N2, and H3N2 viruses circulate in pigs in the United States (4, 5). There are a large number of IAV H1 and H3 genetic and antigenic variants co-circulating, and continued antigenic drift and shift of circulating viruses has made control of IAV in swine very difficult (5). Live-attenuated influenza virus (LAIV) vaccination in swine has been shown to provide cross-protection against heterologous IAV of the same subtype, and partial protection against different subtypes [reviewed in Sandbulte et al. (6)]. LAIV is licensed for use in humans and was recently approved for use in swine, with numerous experimental studies documenting improved efficacy of LAIV over inactivated vaccines (7, 8). Several LAIV vaccines for use in swine have been developed; each with a different attenuation mechanism (9–11). Similar to humans, intranasal LAIV vaccination in pigs induces the production of IAV-specific mucosal IgA, but little peripheral IAV-specific IgG (8). The induction of immunity in the respiratory tract has been shown to be the mechanism by which LAIV vaccines provide significant cross-protection against heterologous strains of IAV, limiting viral replication throughout the respiratory tract [reviewed in Rose et al. (12)].

Bordetella bronchiseptica can colonize the respiratory tract of a large number of mammals, including mice, rabbits, dogs and pigs, among others. Respiratory disease associated with B. bronchiseptica covers a wide spectrum, including kennel cough in dogs and atrophic rhinitis in pigs (13, 14). In humans, B. pertussis infection can lead to whooping cough, though colonization without clinical presentation has been documented (15, 16). Similarly, B. bronchiseptica exposure to pigs can result in chronic, asymptomatic colonization of the respiratory tract and it is believed to be ubiquitous in swine production systems. Co-infection with IAV or coronavirus and B. bronchiseptica in pigs causes exacerbated pulmonary disease, indicating the negative impact of B. bronchiseptica colonization with viral infection (17, 18). Bordetella species encode for a number of virulence factors, including tracheal cytotoxin, dermonecrotic toxin, lipopolysaccharide, and a type III secretion system (19). While the gene locus controlling expression of many virulence factors, including the type III secretion system, has been highly investigated, factors that alter expression of virulence genes in vivo are not completely understood (20, 21).

In the past decade, the complex interaction between mucosal surfaces and colonizing microbiota has been recognized as important in modulating both health and disease states [reviewed in Esposito and principi (22)]. The commensal microbiota of the upper respiratory tract includes bacterial species in which colonization alone does not lead to clinical disease, but upon a stressful event (i.e., viral infection, immunosuppression) these bacteria play a major role in disease pathogenesis, often referred to as pathobionts. Administration of LAIV vaccine induces changes in the nasal microbiota and gene expression in nasal epithelium. In addition, LAIV administration alters colonization dynamics of important bacterial pathogens (23). Given the ubiquitous nature of B. bronchiseptica in swine and the documented increase in disease following B. bronchiseptica with IAV co-infection, we performed a study to determine if B. bronchiseptica colonization prior to LAIV vaccination altered LAIV immunogenicity and efficacy against heterologous IAV challenge, or the dynamics of B. bronchiseptica colonization.

Waterbirds and shorebirds of the orders Anseriformes (mainly ducks, geese and swans) and Charadriiformes (mainly gulls, terns and waders) are considered the natural host reservoirs of LPAI viruses (see Fig. 1). In wild birds LPAI viruses predominantly infect epithelial cells of the intestinal tract, and are subsequently excreted in the faeces. However, infection of wild birds with LPAI viruses is typically sub-clinical and occurs in the absence of obvious lesions,,. Every year, LPAI viruses cause outbreaks amongst waterbirds. These outbreaks are most commonly associated with the increased presence of juvenile, immunologically naïve birds in the population and occur during migration when contact rates between, and within, populations are high. The relatively high virus prevalence in waterbirds may be due, in part, to virus transmission through the faecal–oral route via surface waters.

Respiratory infections in pigs are very important factor affecting the profitability of pig production [1, 2]. Although various bacteria or viruses could induce the respiratory infection separately, it has commonly been caused by coinfection with more pathogens under field conditions [1–3]. The most important infectious agents responsible for infection of the respiratory tract in pigs are: swine influenza virus (SIV), porcine reproductive and respiratory syndrome virus (PRRSV), Pasteurella multocida (Pm), Actinobacillus pleuropneumoniae and Mycoplasma hyopneumoniae [2, 4–6]. Besides, the above mentioned pathogens, the Haemophilus parasuis (Hps) can also be recovered from the lungs of pigs with pneumonia [1, 7–10]. In these cases Hps is often isolated along with other bacterial or viral pathogens and, therefore, the role of Hps in producing pneumonia is not clear [8, 11].

Bacterial pneumonia secondary to influenza is often observed in pigs. SIV is a significant contributor to the respiratory diseases and may predispose to secondary bacterial infection. Hps is an important and common respiratory pathogen of pigs. It can be a primary pathogen or be associated with other diseases such as SIV [3, 8]. It could be also isolated from nasal cavity, tonsils and trachea of apparently healthy pigs [8, 14]. Under favorable conditions, Hps can cause severe systemic infection characterized by fibrinous polyserositis, arthritis and meningitis [8, 11, 14]. Factors leading to systemic infection by Hps have not been clarified to date [9, 14].

Although there are previous reports of experimental reproduction of Hps or SIV infection in conventional pigs, little is known about the effect of concurrent infection with SIV and Hps on the disease severity and inflammatory response in pigs, even if this coinfection is common under field conditions [13, 15–17]. There are also limited data on the role of Hps in the production of pneumonia in the absence of other respiratory pathogens. Furthermore, the kinetics of acute phase protein (APP) response in SIV/Hps co-infected pigs has not been studied to date. As it has been shown for other pathogens, the exposure to several pathogens can lead to a stronger APP response, as compare to single infection [18–20]. Thus, in order to investigate the influence of SIV and Hps coinfection on clinical outcome, both local and systemic inflammatory response as well as pathogen shedding and load at various time points following intranasal inoculation, three experimental infections (Hps- and SIV-single infection, SIV/Hps co-infection) has been performed in the present study. The correlation between local concentration of cytokines and severity of infection (clinical score, lung score) as well as serum APP concentration has been also studied.

Influenza A viruses (Family Orthomyxoviridae) impose a large burden on both human and animal health worldwide. Influenza A viruses can be categorised into different subtypes based on genetic and antigenic differences in the two surface glycoproteins of the virus, the haemagglutinin (HA) and neuraminidase (NA). Wild waterfowl and shorebirds are the natural reservoirs of influenza A virus and can be infected with viruses harbouring combinations of 16 different HA subtypes and nine different NA subtypes. Recently, two novel influenza A virus subtypes (H17N10 and H18N11) have been identified in rectal swabs collected from the little yellow-shouldered bat [Sturnira lilium] and the flat-faced fruit-eating bat [Artibeus jamaicensis planirostris],,. Influenza viruses of this subtype have not been isolated from any other animal order and it is unknown whether these viruses might be able to cross the species barrier. In contrast, there is significant inter-species transmission of influenza viruses from waterbirds, such that animals ranging from domestic poultry to humans can also become infected. Accordingly, infection with influenza virus has wide-reaching ramifications. For example, whilst some influenza virus strains are largely asymptomatic in chickens (and are hence referred to as low pathogenic avian influenza [LPAI] viruses) others cause severe disease in chickens that is often fatal within 48 h (and are hence referred to as highly pathogenic avian influenza [HPAI] viruses). Outbreaks of HPAI viruses can cause devastation for the poultry industry resulting in the mass slaughter of millions of birds. Similarly, outbreaks of influenza viruses amongst thoroughbred horses have disrupted numerous race meetings and resulted in the death of infected horses. In humans, seasonal influenza viruses are a significant cause of morbidity and mortality and constitute an economic burden of $10.4 billion dollars per year in the U.S.A. alone. The diversity and complexity of influenza virus infections across so many different animal species suggests that a one-health approach is the only comprehensive way to reduce the burden of disease. Here, we seek to highlight how influenza viruses spread from their natural avian hosts to mammals, and what the virus needs to overcome in order to ensure the success of these inter-species transmission events. We highlight the consequences that this inter-species transmission has, not only for human health, but also for the health of wild animals and the success of industries such as poultry farming.

Small ruminants particularly sheep and goats contribute significantly to the economy of farmers in Mediterranean as well as African and Southeast Asian countries. These small ruminants are valuable assets because of their significant contribution to meat, milk, and wool production, and potential to replicate and grow rapidly. The great Indian leader and freedom fighter M. K. Gandhi “father of the nation” designated goats as “poor man's cow,” emphasizing the importance of small ruminants in poor countries. In India, sheep and goats play a vital role in the economy of poor, deprived, backward classes, and landless labours. To make this small ruminant based economy viable and sustainable, development of techniques for early and accurate diagnosis holds prime importance. Respiratory diseases of small ruminants are multifactorial and there are multiple etiological agents responsible for the respiratory disease complex. Out of them, bacterial diseases have drawn attention due to variable clinical manifestations, severity of diseases, and reemergence of strains resistant to a number of chemotherapeutic agents. However, sheep and goat suffer from numerous viral diseases, namely, foot-and-mouth disease, bluetongue disease, maedi-visna, orf, Tick-borne encephalomyelitis, peste des petits ruminants, sheep pox, and goat pox, as well as bacterial diseases, namely, blackleg, foot rot, caprine pleuropneumonia, contagious bovine pleuropneumonia, Pasteurellosis, mycoplasmosis, streptococcal infections, chlamydiosis, haemophilosis, Johne's disease, listeriosis, and fleece rot [3–10].

The respiratory diseases represent 5.6 per cent of all these diseases in small ruminants. Small ruminants are especially sensitive to respiratory infections, namely, viruses, bacteria, and fungi, mostly as a result of deficient management practices that make these animals more susceptible to infectious agents. The tendency of these animals to huddle and group rearing practices further predispose small ruminants to infectious and contagious diseases [6, 9]. In both sheep and goat flocks, respiratory diseases may be encountered affecting individuals or groups, resulting in poor live weight gain and high rate of mortality. This causes considerable financial losses to shepherds and goat keepers in the form of decreased meat, milk, and wool production along with reduced number of offspring. Adverse weather conditions leading to stress often contribute to onset and progression of such diseases. The condition becomes adverse when bacterial as well as viral infections are combined particularly under adverse weather conditions. Moreover, under stress, immunocompromised, pregnant, lactating, and older animals easily fall prey to respiratory habitats, namely, Streptococcus pneumoniae, Mannheimia haemolytica, Bordetella parapertussis, Mycoplasma species, Arcanobacterium pyogenes, and Pasteurella species [2, 4, 7–9, 12, 13]. Such infections pose a major obstacle to the intensive rearing of sheep and goat and diseases like PPR, bluetongue, and ovine pulmonary adenomatosis (Jaagsiekte) adversely affect international trade [2, 9, 10, 13], ultimately hampering the economy.

Depending upon the involvement of etiological agent, the infectious respiratory diseases of small ruminants can be categorized as follows [9, 14]:bacterial: Pasteurellosis, Ovine progressive pneumonia, mycoplasmosis, enzootic pneumonia, and caseous lymphadenitis,viral: PPR, parainfluenza, caprine arthritis encephalitis virus, and bluetongue,fungal: fungal pneumonia,parasitic: nasal myiasis and verminous pneumonia,others: enzootic nasal tumors and ovine pulmonary adenomatosis (Jaagsiekte).

Manytimes due to environmental stress, immunosuppression, and deficient managemental practices, secondary invaders more severely affect the diseased individuals; moreover, mixed infections with multiple aetiology are also common phenomena [5, 8, 13, 15].

These conditions involve respiratory tract as primary target and lesions remain confined to either upper or lower respiratory tract [7, 16]. Thus, these diseases can be grouped as follows [5, 8, 14, 17].Diseases of upper respiratory tract, namely, nasal myiasis and enzootic nasal tumors, mainly remain confined to sinus, nostrils, and nasal cavity. Various tumors like nasal polyps (adenopapillomas), squamous cell carcinomas, adenocarcinomas, lymphosarcomas, and adenomas are common in upper respiratory tracts of sheep and goats. However, the incidence rate is very low and only sporadic cases are reported.Diseases of lower respiratory tract, namely, PPR, parainfluenza, Pasteurellosis, Ovine progressive pneumonia, mycoplasmosis, caprine arthritis encephalitis virus, caseous lymphadenitis, verminous pneumonia, and many others which involve lungs and lesions, are observed in alveoli and bronchioles.

Depending upon the severity of the diseases and physical status of the infected animals, high morbidity and mortality can be recorded in animals of all age groups. These diseases alone or in combination with other associated conditions may have acute or chronic onset and are a significant cause of losses to the sheep industry [3, 10]. Thus, the respiratory diseases can also be classified on the basis of onset and duration of disease as mentioned below [3, 9, 14, 18]:acute: bluetongue, PPR, Pasteurellosis, and parainfluenza,chronic: mycoplasmosis, verminous pneumonia, nasal myiasis, and enzootic nasal tumors,progressive: Ovine progressive pneumonia, caprine arthritis encephalitis virus, caseous lymphadenitis, and pulmonary adenomatosis.

Respiratory illness is traditionally regarded as the disease of the growing pig, and has historically been associated with bacterial infections such as Mycoplasma hyopneumoniae [1–3] and Actinobacillus pleuropneumoniae [4–6]. These bacteria still are of great importance, but the continuously increasing herd sizes have complicated the clinical picture. As the number of transmission events between pigs in a population is equal to the number of pigs multiplied with the number of pigs minus one [x = n * (n − 1)], they will escalate as the herd size increase. Thus, the number of transmission events between pigs will increase with a factor of around four if a population is doubled and with a factor of around 100 if a population is enlarged ten times.

The increased number of transmissions between pigs may increase the influence of other microbes. M. hyopneumoniae and A. pleuropneumoniae are important pathogenic microbes, but co-infections may intensify or prolong clinical signs of respiratory disease [8–11]. It has also been observed that the incidence of respiratory illness may vary with season. Therefore, infections in the respiratory tract of grower pigs have become regarded as a syndrome rather than linked to single microorganisms [11, 13, 14]. This syndrome is referred to as the porcine respiratory disease complex (PRDC). As stated above PRDC is regarded to be dominated by bacterial species, and important primarily pathogenic bacterial species include M. hyopneumoniae [1–3] and A. pleuropneumoniae [4–6]. The frequent demonstration of interferon-α in serum in growers during the first week after arrival to fattening herds [15, 16] suggest that PRDC can be associated with viral infections, and that PRDC can also include the influence of secondary invaders such as Pasteurella spp [17, 18].

When Sweden in 1986 as the first country in the world banned the use of low dose antibiotics in animal feed for growth promotion, some introductory health disturbances were recorded. As a consequence, a strict age segregated rearing from birth to slaughter was implemented in a large scale, which improved health as well as productivity [19, 20]. As seen in Fig. 1, the incidence of recorded pathogenic lesions in the respiratory tract at slaughter decreased during the last decade of the twentieth century. The registrations of pneumonia at slaughter has remained stable at that level since then. In contrast, the incidence of recorded pleuritis at slaughter has continuously increased since the year 2000, as has the clinical evidence of actinobacillosis. Discussions concerning the reason for this increase has included suggestions of introduction of new strains, or mutation of existing strains of A. pleuropneumoniae. However, acute actinobacillosis has in Sweden historically been dominated by serotype 2, and is still dominated by that serotype. Further, Pulse Field Gel Electrophoreses has revealed that strains isolated in the twenty-first century were identical to strains isolated in the 1970s and 1980s. As a consequence, the increase of actinobacillosis and pleuritic recordings at slaughter has merely been linked to the continuously increasing herd sizes with increasing number of transmissions of microbes between pigs, within and between units.

The aim of this study was to validate the presence of A. pleuropneumoniae and M. hyopneumoniae, as well as the secondary invaders P. multocida and Streptococcus suis in pig herds with a high incidence of pleuritic lesions at slaughter.

Porcine respiratory disease complex (PRDC) is a syndrome caused by mixed viral and bacterial pathogens together with environmental, managerial and genetic factors. A combination of pathogens are involved, e.g. viruses such as porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV2), swine influenza virus (SIV), porcine respiratory coronavirus (PRCV), and various bacteria e.g. Actinobacillus pleuropneumoniae (APP), Mycoplasma hyopneumoniae (MHyo), Mycoplasma hyorhinis, Haemophilus parasuis (H.parasuis), Pasteurella multocida and Streptococcus suis [1–6]. Often it remains unclear which the primary pathogen is and which one is acting as a predisposing agent for other infections or as a secondary infection [2, 6, 7]. Many of these pathogens can also be found in clinically healthy pigs, but they are detected more often in pigs with respiratory symptoms. The pathogenesis of multifactorial PRDC is difficult to determine, because primary and opportunistic pathogens modify their impacts in different cases.

Pathogens involved in PRDC vary considerably in various countries, regions and herds over time. In Finland, the prevalence of porcine respiratory pathogens differs substantially from the situation in continental Europe. The country has been free of ADV, PRCV and PRRSV for decades. Also, Finland is nearly free of swine enzootic pneumonia. In 2015, MHyo was detected in only one Finnish pig herd, and most Finnish pig production (97%) is included in the national health programme requiring the absence of this pathogen. On the contrary, APP is a common pathogen causing respiratory problems. SIV is a newcomer in the country. Avian-like H1N1 swine influenza A virus was found in the Finnish pig population for the first time in 2008 and A(H1N1)pdm09 influenza virus in 2009. PCV2 is a pathogen commonly found in the Finnish pig population, and many herd owners control it by vaccination. However, its role in respiratory infections in Finland has not been studied earlier. Overall, assessing which respiratory pathogens are involved in acute respiratory disease outbreaks in a country lacking major viral pathogens is very important.

The objective of our study was to clinically and etiologically investigate acute outbreaks of respiratory disease in Finland. This field study also aimed to evaluate the clinical use of various methods in diagnosing the respiratory infections under field conditions and to describe the antimicrobial resistance profile of the main bacterial pathogen(s) found during our study.

During the last two decades, scientists have grown increasingly aware that viruses are emerging from the human–animal interface. In order to combat this increasingly complex problem, the One Health approach or initiative has been proposed as a way of working across disciplines to incorporate human, animal, and environmental health. Of particular concern are emerging respiratory virus infections; in a recent seminar given by the National Institute of Health on emerging and re-emerging pathogens, nearly 18% were respiratory viruses (1). Among the recently emerged respiratory pathogens contributing to the high burden of respiratory tract infection-related morbidity and mortality, displayed graphically in Figure 1, are influenza viruses, coronaviruses, enteroviruses (EVs), and adenoviruses (Ads). In this report, we summarize the emerging threat characteristics of these four groups of viruses.

The acute phase response is an unspecific systemic reaction of the organism that occurs after infection or inflammation. This reaction includes changes in the concentrations of some plasma proteins called acute phase proteins (APPs). Changes of APP concentration in pigs serum have been extensively investigated during last years 2–4 but, to the best of our knowledge, no studies related to the APP behavior following influenza virus and Pasteurella multocida (Pm) coinfection has been reported.

Respiratory diseases in pigs are often considered as multifactorial problems caused by various pathogens (viral and bacterial) in combination. The most common infectious agent responsible for respiratory infection in pigs are: swine influenza virus (SIV), porcine reproductive and respiratory syndrome virus (PRRSV), Pasteurella multocida (Pm), Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae. These pathogens may act together to increase the severity and duration of the disease. In pigs, as well as in humans, bacterial pneumonia secondary to influenza is often observed and SIV is an important contributor to the porcine respiratory disease complex (PRDC). The bacterial pathogens associated with PRDC are classified as primary or secondary pathogens, and Pm plays a key role as a secondary invader. Up to now the kinetics of acute phase response after experimental infection of pigs with SIV or Pm alone have been investigated. Exposure to multiple pathogens may result in different kinetics of APP response, as compare to monoinfection with SIV or Pm.

In this study the immune and C-reactive protein (CRP), haptoglobin (Hp), serum amyloid A (SAA) or/and pig major acute phase protein (Pig-MAP) responses after simultaneous co-infection with common porcine pathogens: SIV (H1N1 subtype) and Pm were evaluated in piglets. The correlation between concentration of investigated APP in serum and severity of infection (clinical score, lung score, turbinate score) were also studied, to estimate the utility of APP measurement in the evaluation of pigs health status.

In all coinfected pigs clinical sings including fever, coughing, nasal discharge, dyspnea and anorexia were observed. In all infected animals the rectal temperature increased over 40°C (Figure 1). Clinical score ranged between 1 and 5. In the control pigs no clinical signs of any disease were seen.

Swine influenza is a highly infectious acute respiratory viral disease of pigs that affects the respiratory tract and has considerable economic impacts. Three main subtypes of swine influenza virus (H1N1, H3N2, and H1N2), with H1N1 as the predominant subtype, have circulated in pigs worldwide [2, 3]. In March 2009, a new swine-origin H1N1 influenza virus became a pandemic. Pig infections with the new H1N1 virus have then been observed in multiple countries, showing that the pandemic H1N1 viruses have become established in swine populations [5–7]. Previous study has showed the new H1N1 viruses have spread from humans to pigs in China. Swine influenza virus replication is mainly restricted to the epithelial cells in the respiratory tract, with the lung being the major target organ. Although it is a highly contagious virus for pigs and has high-morbidity but low-mortality rates, secondary complications would substantially worsen the illness and increase death rate. In fact, swine influenza is one of the several significant contributors to the porcine respiratory disease complex (PRDC), which is caused by infection with more than one pathogen, such as the swine influenza virus and Streptococcus suis (S. suis) co-infection.

S. suis infections have been considered as a major problem worldwide in the swine industry and as a secondary agent of pneumonia, particularly in the past 20 years. Among the 35 serotypes, serotype 2 (SS2) is generally considered as the most prevalent and virulent type. S. suis infections in pigs often cause arthritis, meningitis, pneumonia, endocarditis, and septicemia with or without sudden death. Although S. suis is a major swine pathogen, it has been increasingly detected in wide range of mammalian species. Infections have been observed in humans in 2005 in China, which affected more than 200 people and had approximately 20% mortality. In clinical cases, co-infections of swine influenza virus and S. suis in pigs often contribute to severe pneumonia and can increase the mortality. Co-infection outbreaks have been recently reported in England.

Recently, several studies on the pathogenesis of the co-infection of influenza virus and Streptococcus pneumonia have been performed using mouse models [13–15]. Pro- and anti-inflammatory (IL-6, IL-1β, TNF-α, and IL-10) molecules were remarkably elevated in the blood in influenza virus and Streptococcus pneumonia co-infected mouse. However, fewer studies have examined swine influenza and S. suis co-infection in pigs, and its pathogenesis is not yet fully elucidated. In the present study, microarray assay was utilized to explore the global host responses of porcine lungs that suffered from H1N1 influenza virus, SS2, H1N1-SS2 co-infection, and phosphate-buffered saline (PBS) to enhance the understanding of the H1N1 and S. suis co-infection pathogenesis through a pig model. Stronger inflammatory and apoptosis responses were determined to be important contributors to the increased pathogenicity caused by swine H1N1 and SS2 co-infection. Our study would improve the understanding of the pathogenesis of H1N1 and SS2 co-infection in pigs.

Zoonotic diseases (ZD) are those infections that can be naturally transmitted from animals to humans with or without vector. In the past few decades, there has been a rise in the outbreaks of zoonotic diseases which have an enormous socioeconomic impact worldwide, for instance, all foodborne zoonoses occured in a single country costs about $1.3 billion annually. Additionally, ZD constitute 61% of all communicable diseases causing illness in humans and about 75% of emerging human pathogens. More than 75% of the diseases that affected humans have been transmitted from animals or animal products. Zoonotic diseases can be transferred from animals to humans by several ways such as the consumption of contaminated food and water (e.g., cryptosporidiosis), exposure to the pathogen during processing (e.g., campylobacteriosis and salmonellosis), direct contact with infected animals (e.g., avian influenza) and by pets scratches or bite (e.g., rabies). Some emerging zoonoses expanded their host range and their incidence increased (e.g., avian influenza). This expansion occurred as a result of global trade, increase poultry production, climate changes, bird migration, human movement, and the burgeoning global population. Several animal reservoirs of ZD have been identified, including ruminants, equines, poultry, rodents, dogs and cats, mosquitoes and ticks, which were considered a potential risk of disease transmission. Furthermore, antimicrobial resistance considered as an additional risk associated with exposure to zoonotic pathogens because it is potentially limits disease treatment options in both public health and veterinary settings. Therefore, prevention and control programs should be implemented by public health and veterinary officers to combat the sources and reservoirs of zoonoses especially after the development of antimicrobial resistance problem due to misuse of antibiotics.

Egypt is located in the north-eastern part of Africa connecting the three old-world continents Africa, Asia and Europe. It is the county with the highest population density in the Middle East, North Africa and the Mediterranean basin with about 90 million inhabitants. Egypt has 27 governorates and over 90% of the population live in 10% of the whole area along the River Nile and Nile Delta in the northern part of the country. A number of zoonotic pathogens have been reported in Egypt. The burden of ZD is provoked by factors such as the method of control, environmental factors, behavioral factors, social factors, clinical manifestations, the socioeconomic impact of such diseases and mode of transmission. The highest incidence and prevalence of zoonotic diseases in Egypt may be attributed to the deficiency of suitable control mechanisms, inadequate infrastructure and lack of information on their significance and distribution. However, there is a marked decrease in the prevalence of some ZD (e.g., schistosomiasis). In this review, we will focus on the most important and prevalent emerging and re-emerging ZD in Egypt including the current situation, reservoirs, sources of human infection and control regimes, if available.

In recent years the human microbiota is more and more recognized to play a crucial role in pathogenesis of many diseases (Weinstock, 2012). The upper respiratory tract is a natural niche for potentially pathogenic bacteria embedded in commensal communities forming the nasopharyngeal microbiome. In particular, the microbial communities of the nasopharynx (Hilty et al., 2012) are associated with respiratory diseases, i.e., severe pneumonia, which are responsible for substantial mortality and morbidity in humans worldwide (Prina et al., 2016). The composition of the nasopharyngeal microbiome is highly dynamic (Biesbroek et al., 2014a,b,c) and many factors, including environmental and host factors, can affect microbial colonization (Koppen et al., 2015). Recent studies on neonates have shown that the respiratory microbiota develops from initially maternally transmitted mixed flora with predominance of Streptococcus viridans species to niche-specific bacterial profiles containing mostly Staphylococcus aureus at around 1 week of age (Bosch et al., 2016a). Between 2 weeks and 6 months after birth, the staphylococcal predominance declines and colonization with Streptococcus pneumoniae (pneumococci) as a predominant pathobiont emerges (Miller et al., 2011; Bosch et al., 2016a,b). The dynamic microbiome composition is guaranteed through the interplay between bacterial species, other microbes, and changing environmental conditions, as well as host–bacteria interactions (Blaser and Falkow, 2009). Most of the time, the microbiome and its interplay with the human host are believed to be beneficial for both (Pettigrew et al., 2008; Murphy et al., 2009). However, imbalances in microbial composition can lead to acquisition of new viral or bacterial species and invasion of potential pathogens, which in turn can become detrimental, especially in elderly people and children with an exhausted or immature immune system (Pettigrew et al., 2008; Blaser and Falkow, 2009; Murphy et al., 2009).

One particular example showing imbalances introduced by single dosage of antibiotics was demonstrated by Ichinohe and colleagues (Ichinohe et al., 2011). While commensal respiratory microbiota facilitated immune-support against Influenza A virus infection (IAV), oral treatment with antibiotics resulted not only in a shift of bacterial composition, but also in impaired CD4 T-, CD8 T-, and B-cell immunity following infection with IAV in mice (Ichinohe et al., 2011). Analyses of human oropharyngeal microbiomes during the 2009 H1N1 IAV pandemic revealed that at the phylum level, the abundance of Fermicutes and Proteobacteria was augmented in pneumonia patients as compared to healthy controls (Leung et al., 2013). However, another study published in the same year contradicted these results (Chaban et al., 2013). Chaban and colleagues analyzed microbiomes of 65 patients from H1N1 IAV outbreak in 2009. Although the phylogenetic composition of pneumonia patients was dominated by Fermicutes, Proteobacteria, and Actinobacteria, no significant differences between the patients and healthy controls or any other variables tested, including age and gender, were observed (Chaban et al., 2013).

In this review we discuss secondary bacterial infections of the respiratory tract after primary infection by IAV with a focus on mechanisms by which these interactions are potentially mediated, and we will provide insight into the host contribution and immunological consequences. We further focus on potential animal models suitable for mimicking asymptomatic bacterial colonization and disease progression and thus, enabling to study adaptation strategies, viral-bacterial interactions, and immune responses in these highly lethal co-infections.

Swine influenza A viruses (SIVs) are enzootic in most European pig populations. The SIV H1N1 and H3N2 subtypes have been circulating for more than 30 years, and the SIV subtype H1N2 has been circulating since it was first isolated in Great Britain in 1994 [2, 3]. In April 2009, a new influenza A virus of subtype H1N1 emerged in the human population in Mexico and the United States. This was a multiple reassortant virus containing genes from North American and Eurasian lineages [4, 5]. The virus spread rapidly across the world by human-to-human transmission. Human-to-pig transmission was first reported in Canada in late April 2009, then in European pig population in early September 2009, and has since been reported in several countries all over the world [6–9]. In October 2009, SIV was reported for the first time in Norway when an integrated pig herd tested positive for pandemic (H1N1) 2009 virus after showing mild clinical signs of respiratory disease.

The clinical picture of pandemic (H1N1) 2009 infections in experimentally and naturally infected pigs was described as mild respiratory illness, increased temperature, and decreased appetite [6, 11, 12]. In some infected herds, clinical signs were not detected. Studies have shown that immunological naïve pigs experimentally infected with pandemic (H1N1) 2009 virus could transmit the virus efficiently to other naïve pigs [11, 14, 15]. Although pandemic (H1N1) 2009 virus contains gene segment genetically related to other swine influenza virus strains circulating in Europe and North America, it shows antigenetic differences in the major glycoproteins of the virus. However, it has been shown that pigs infected or vaccinated with H1N1 European avian-like swine influenza virus could produce cross-reactive antibodies against pandemic (H1N1) 2009 virus which protected pigs against the infection of pandemic (H1N1) 2009 virus [13, 16].

The pig production in Norway consists of approximately 2500 herds, mainly small family farms, with about 1.5 million slaughtered pigs in 2010. National surveillance and control program shows that the pig population is free for Aujeszky's disease (AD), transmissible gastroenteritis (TGE), porcine respiratory corona virus (PRCV), porcine reproductive and respiratory syndrome (PRRS), and Mycoplasma hyopneumoniae [17, 18]. The Norwegian Food Safety Authority has been running annual surveillance programs to document the status since 1994. SIV was added to the program in 1997. Under the surveillance, blood samples from about 500 randomly selected herds are collected annually for specific disease surveillance. The surveillance has never detected SIV infection in Norway until October 2009, except for pigs in one herd that tested seropositive for subtype H3N2 in 1998 without showing clinical signs or further spread of the infection.

This paper consists of studies that describe the initial spread of pandemic (H1N1) 2009 virus amongst Norwegian pig herds, the control measures initiated, and the infection status 20 months after the introduction. The paper also discusses the manifestation of the infection in the Norwegian pigs given that they had no prior immunity to any influenza A viruses and are free from most other viral respiratory diseases.

There is increasing evidence that the nasopharyngeal microbiota plays an important role in the pathogenesis of acute viral respiratory infections (Teo et al., 2015; de Steenhuijsen Piters et al., 2016; Rosas-Salazar et al., 2016a,b). Respiratory viruses, including IAV, have been shown to alter bacterial adherence and colonization leading to an increased risk of secondary bacterial infections (Tregoning and Schwarze, 2010). Pneumococci, S. aureus, and GAS are important human Gram-positive pathogens. All of them are frequent colonizers of the human nasopharynx and they share many features including pathogenic mechanisms and clinical aspects (Figure 1). However, they also have unique properties.

Staphylococcus aureus colonizes persistently about 30% of the human population and typical niches include nares, axillae, and skin (Peacock et al., 2001; von Eiff et al., 2001; van Belkum et al., 2009). They cause a variety of clinical manifestations ranging from mild skin infections to fatal necrotizing pneumonia. In the last decades, the pathogen became resistant to an increasing number of antibiotics and methicillin-resistant S. aureus (MRSA) is now a major cause of hospital acquired infections (Hartman and Tomasz, 1984; Ubukata et al., 1989; Zetola et al., 2005). Also the rise of community-acquired S. aureus strains is of special concern, because certain clones are associated with very severe infections (Rasigade et al., 2010). Recent prospective studies demonstrated an increase in proportion of community-acquired methicillin-sensitive S. aureus in severe pneumonia cases (McCaskill et al., 2007; Sicot et al., 2013).

The pneumococcus is a typical colonizer of the human nasopharynx. About 20–50% of healthy children and 8–30% of healthy adults are asymptomatically colonized (McCullers, 2006). Pneumococci cause diseases ranging from mild, i.e., sinusitis, conjunctivitis, and otitis media, to more severe and potentially life-threatening infections, including community-acquired pneumonia, bacteraemia, and meningitis (Bogaert et al., 2004; Valles et al., 2016). This bacterium is associated with high morbidity and mortality rates in risk groups such as immunocompromised individuals, children, and elderly (Black et al., 2010; Valles et al., 2016).

Group A streptococci colonize the mouth and upper respiratory tract in about 2–5% of world’s population (Okumura and Nizet, 2014). The most common, non-invasive and mild infections caused by GAS are tonsillitis and pharyngitis with estimated 600 million cases per year (Carapetis et al., 2005). Listed as number nine in the list of global killers with around 500,000 deaths annually (Carapetis et al., 2005), it is obvious that this pathogen can cause severe invasive infections, including pneumonia, sepsis, streptococcal toxic shock syndrome, and necrotizing skin infections (Cunningham, 2000; Carapetis et al., 2005).

Although all three pathogens are able to cause highly lethal diseases, the most fatal remains the pneumococcus, estimated to cause ca. 10% of all deaths in children below 5 years of age (O’Brien et al., 2009), in the elderly (Marrie et al., 2017), and in immuno-compromised individuals (Baxter et al., 2016).

The genus Ebolavirus of the Filoviridae family includes five species: Bundibugyo ebolavirus, Reston ebolavirus, Sudan ebolavirus, Tai Forest ebolavirus, and Zaire ebolavirus. Among them, the Zaire ebolavirus, usually called Ebola virus (EBOV), is the main causative agent of human outbreaks, causing the Ebola virus disease (EVD). EVD is a disease of human and non-human primates that is characterized by a high fatality rate (30–90%). EBOV persists in the environment in a still unidentified animal reservoir, most likely the fruit bats, which maintains the virus in an enzootic cycle. Recently, a new ebolavirus, the Bombali virus, has been detected in free-tailed bats in Sierra Leone while in China a new filovirus (Měnglà virus) was identified in rousettus bats further supporting the role of bats in filovirus ecology. Occasionally, EBOV can be transmitted to non-human primates and duikers in an epizootic cycle causing outbreaks with high mortality. Human infection represents a sporadic event taking place in the context of a human animal interface. Transmission is mainly due to the contact with blood or body fluids from infected humans or animals. EVD begins with nonspecific symptoms involving fever, fatigue, and muscle ache, and evolves to a severe condition associated with vomiting, diarrhea, infrequent hemorrhaging, and mental disorder leading to a comatose state and death. The convalescence phase of survivor patients lasts several months and is characterized by fatigue, joint pain as well as loss of appetite and memory. Viral RNA can be detected in specific organs, such as the testis, for more than one year after symptoms resolution.

Until 2014, EVD was considered a neglected disease, causing small outbreaks in remote African villages. EBOV research was focused mainly on biology aspects of viral infection or preparedness due to its potential use as bioweapon, and was limited to few laboratories equipped with biosafety level-4 (BSL-4) facilities. However, the recent large outbreak of EVD (Western Africa, 2013–2016) characterized by 28,616 cases and 11,310 deaths, highlighted the worldwide danger of this disease and its impact on global public health and economy.

Thus, research on the molecular dissection of EBOV life cycle received a strong stimulus and financial support with the ultimate goal of developing effective preventive and therapeutic approaches. In this review, we summarize the current knowledge of a specific step of the EBOV life cycle, the entry process, and the compounds identified so far capable of interfering with it, as well as the molecular models used to these purposes.

The case herds were classified according to the pathology, bacteriology and virology of the three lung samples examined from each herd and the nasal swab samples examined for SIV.

A herd was considered to suffer from acute respiratory disease caused by APP (coded as CL-APP) when pigs examined pathologically exhibited either 1) typical pathological gross lesions for APP (various sizes of consolidated dark or grayish well-demarcated pneumonic areas or a consolidation with necrotic areas often together with local pleurisy) in at least two out of the three lung samples together with isolation of APP bacteria in two or three lung samples, or 2) characteristic pathological lesions in at least one lung sample and either a necrotic area indicative of APP infection or mild consolidated lesions in another lung sample combined with isolation of APP bacteria in all three lung samples.

A herd was considered to suffer from respiratory disease caused by an acute Ascaris suum (coded as CL-ASC) infestation when the following two criteria were fulfilled: 1) at least two out of the three pigs examined pathologically in these herds had compatible gross lesions (typically heavy, wet and mottled red lungs) compatible with an A. suum infestation, and 2) detection of gross ascarid larvae in the tracheal froth and/or in the histological sections of these lung samples. The lung samples defined as having lesions caused by an A. suum infestation had no other gross lesions characteristic of another specific respiratory pathogen.

A case herd was considered to suffer from acute swine influenza infection (coded as CL-SIV) if SIV was detected by PCR in at least one of the three examined lungs or in at least one of the 20 nasal swab samples.

Miscellaneous etiology (coded as CL-MISC) was considered if variable pneumonic lesions in the lung samples were observed and the abovementioned criteria were not fulfilled.

All the inoculated pigs showed typical clinical symptoms, namely, sneezing and coughing. They also developed a high fever, and their average rectal temperature exceeded 40.0°C between PID 2 and 4. In contrast, control pigs exhibited no clinical symptoms throughout the experiment. The three groups infected with H1N1, H1N2, and H3N2-infected groups did not differ significantly in their clinical appearance that included sneezing, coughing, rectal temperature, and respiratory rate (data not shown).

The viral RNA of H1N1 was detected in lung samples from the infected pigs at PID 2 (2/3; number of positive pigs/number of pigs tested), PID 4 (3/3), PID 7 (2/3), and PID 14 (1/3), while the viral RNA was detected in the pigs infected with H1N2 or H3N2 at PID 2 (1/3 or 3/3), PID 4 (3/3 or 3/3), and PID 7 (2/3 or 2/3), respectively. However, pigs of the control group remained negative for the viral RNA throughout the study period.

The gross lung lesions of infected pigs ranged from multifocal lesions to a coalescing reddish-tan consolidation of the lung, particularly affected the cranial lobes, but these lesions were not detected in the control pigs (Figure 1). The three infected groups differed in their gross lesion scores following post inoculation. The H3N2 infected pigs showed significantly higher lung lesion score than other groups (P < 0.05) at PID 2, and this then progressively decreased. Both the H1N1 and H1N2 infected pigs lacked gross lesions at PID 2, but they showed minimal to mild pneumonia lesions on PID 4, 7 and 14. The pigs infected with H1N1 had significant scores (P < 0.05) of gross lesions when compared with the other pigs infected with H1N2, H3N2, and control at PID 14 (Figure 2A.).

The histological lesions were limited to the bronchi, bronchioles, and alveoli, but no lesions were observed in the tissues of control pigs. The pigs infected with H1N1, H1N2, and H3N2 all shared the following histopathological features; bronchial/bronchiolar necrosis, thickening of the alveolar septa due to the infiltration of inflammatory leukocytes, and pulmonary hemorrhage and atelectasis (Figure 3). The H3N2 infected pigs had severe histological lesions at PID 2, while, in the other sub-type infected pigs, the lesions were milder at PID 2. However, at PID 14, these lung lesions of H1N1-infected pigs had a significantly higher mean histological score (5.3, P < 0.05) than those from the lungs of H1N2 (0) and H3N2 (2.1) infected pigs (Figure 2B).

SIV was detected in the lung tissue following IHC staining. Influenza viral antigens were predominantly found in the bronchial and bronchiolar epithelium. In addition, numerous necrotic epithelial cells that underwent phagocytosis by alveolar macrophages were detected in the lumen. In the three infected groups, mean antigen-positive score of the viral antigens of H3N2-infected pigs was higher than those of the other group’s pigs at PID 2. The mean antigen scores of pigs infected with H1N2 and H3N2 were rarely detected from PID 7. However, an increased amount of viral antigens in H1N1infected pigs were found in the bronchioles and alveolar epithelium, and the mean score was significantly higher (P < 0.05) than those of H1N2 and H3N2 infected pigs at PID 14 (Figures 4 and 5).

Despite the announcement of the successful eradication of smallpox in 1979, the last case of rinderpest in 2008 and the current campaigns to eradicate poliomyelitis and measles through mass-immunization programmes, we still face the prospect of emerging or reemerging viral pathogens that exploit changing anthropological behavioural patterns. These include intravenous drug abuse, unregulated marketing of domestic and wild animals, expanding human population densities, increasing human mobility, and dispersion of livestock, arthropods and commercial goods via expanding transportation systems. Consequently, the World Health Organization concluded that acquired immune deficiency syndrome, tuberculosis, malaria, and neglected tropical diseases will remain challenges for the foreseeable future.1 Understandably, the high human fatality rates reported during the recent epidemics of Ebola, severe acute respiratory syndrome and Middle East respiratory syndrome have attracted high levels of publicity. However, many other RNA viruses have emerged or reemerged and dispersed globally despite being considered to be neglected diseases.2,3 Chikungunya virus (CHIKV), West Nile virus (WNV) and dengue virus (DENV) are three of a large number of neglected human pathogenic arthropod-borne viruses (arboviruses) whose combined figures for morbidity and mortality far exceed those for Ebola, severe acute respiratory syndrome and Middle East respiratory syndrome viruses. For instance, for DENV, the number of cases of dengue fever/hemorrhagic fever is between 300–400 million annually, of which an estimated 22 000 humans die.4 Moreover, in the New World, within 12 months of its introduction, CHIKV caused more than a million cases of chikungunya fever according to Pan American Health Organization/World Health Organization, with sequelae that include persistent arthralgia, rheumatoid arthritis and lifelong chronic pain.5 Likewise, within two months of its introduction, to Polynesia, the number of reported cases exceeded 40 0006 and is currently believed to be approaching 200000 cases. Alarmingly, this rapid dispersion and epidemicity of CHIKV (and DENV or Zika virus in Oceania) is now threatening Europe and parts of Asia through infected individuals returning from these newly endemic regions. This is an increasingly worrying trend. For example, in France, from 1 May to 30 November, 2014, 1492 suspected cases of dengue or chikungunya fever were reported.7 Accordingly, this review focuses on the emergence or reemergence of arboviruses and their requirements and limitations for controlling these viruses in the future.

First discovered in 1953 by Rowe et al., Ads are non-enveloped, double-stranded DNA viruses with 57 unique serotypes, some of which are specific for attacking the respiratory track, conjunctiva, or gastrointestinal track (40). Key features of Ad infections include various symptoms of disease, including rhinorrhea, nasal congestion, cough, sneezing, pharyngitis, keratoconjunctivitis, pneumonia, meningitis, gastroenteritis, cystitis, and encephalitis. Illnesses may be asymptomatic, mild, or severe; however, immunocompromised patients and infants are at increased risk of severe morbidity and death.

Most of the ZIKV cases are either in-apparent infections (about 80%) or mild ‘dengue-like’ syndrome.14 Symptomatic case usually presents with abrupt onset of mild fever, joint pain, headaches, retro-orbital pain, maculo-papular rash usually with itching, and conjunctivitis. Oedema of extremities, vertigo, myalgia and digestive disorder may also occur. These symptoms are usually mild and last for 2-7 days and the incubation period ranged 3-12 days.7,19 The cause of phobia about Zika is due to its suspected implication with increased neonatal microcephaly (as discussed), and other neurological conditions as Guillain-Barré syndrome.4,7

Laboratory diagnosis, Infection with ZIKV can be diagnosed by PCR or by IgG and IgM antibodies detection.7,20

Rabies is caused by neurotropic viruses in the genus Lyssavirus, family Rhabdoviridae, and is transmissible to all mammals. Dogs are the main hosts responsible for human rabies in Africa, Latin Americas and Asia, especially in China, where rabies is re-emerging as a major public health threat, and its severity is only second to HIV and tuberculosis (TB) among all reportable infectious diseases. From the annual ~3000 human deaths, southeast China counts for most cases, with more than 90% attributed to rabid dog bites. Notably, both human population and dog density are high in the region with low rabies vaccination coverage in dogs. Given that the program of dog rabies elimination has not been listed in the priority of governmental agenda, it is possible that long term dog rabies enzootics will lead to spillover events of dog-associated rabies into wildlife species. In addition to rabies transmitted by rabid dogs, other sources of rabies exposure to humans, such as cats, ferret badgers (FB), and pigs, have been continuously reported in China. Interestingly, in provinces like Zhejiang, Jiangxi and Anhui, the percentage of dog-associated human rabies is relatively low. Meanwhile, up to 80% of the reported human rabies cases were inferred to be caused by FB bites in some districts in Zhejiang province from 1994 to 2004. Although rabies in badgers was previously recorded in other countries, FB-associated human rabies has never been reported except in China. The frequent occurrence of FB-associated human rabies cases in southeast China highlights the lack of laboratory-based surveillance and urges revisiting the potential importance of this animal in rabies transmission. Nevertheless, management of such animal bites in humans needs a clear guideline on post-exposure prophylaxis (PEP) for rabies. Currently, FB trading and its meat consumption are common in the related areas, resulting in a frequent source of FB bite to humans. Similar to severe acute respiratory syndrome (SARS) outbreaks through consumption of civet in south china, the close and frequent contact of FB by humans could be an important factor in human rabies cases in southeast China.

To determine if the FB actually contributes to human and dog rabies cases, and the possible origin of the FB-associated rabies in the region, we conducted an expanded retrospective/prospective epidemiological survey, which encompassed both descriptive and molecular epidemiological approaches.

Influenza A viruses (IAV) cause an acute respiratory disease in humans and animals. Annual outbreaks and occasional pandemics of influenza result in millions of deaths, suffering, and economic losses. In the US alone, since 2010 influenza viruses have caused 140,000–710,000 hospitalizations resulting in 12,000–56,000 deaths annually (https://www.cdc.gov/flu/about/disease/burden.htm). The elderly, infants, and people with underlying conditions are at high risk of influenza-associated mortality. In addition to seasonal and pandemic viruses, highly pathogenic avian influenza (HPAI) H5N1 virus has been repeatedly transmitted directly from avian species to humans. In humans, H5N1 virus is associated with severe disease resulting in multi-organ failure and high mortality rates [1, 2]. As of 30 October 2017, HPAI H5N1 viruses have caused 860 human infections resulting in 454 deaths since 2003 (http://www.who.int/influenza/human_animal_interface/2017_10_30_tableH5N1.pdf?ua = 1) Severe cases of influenza cause significant mortality due to their ability to induce cytokine-mediated immune lung pathology with features of moderate to severe acute respiratory distress syndrome (ARDS).

Influenza virus infections are generally controlled by annual vaccination. However, these vaccines provide limited protection against new reassortants which are genetically different from the vaccine virus. In the event of a pandemic, generation of a new vaccine containing circulating viruses takes approximately 6 months. Moreover, influenza viruses continually undergo mutations resulting in the generation of new viral strains that can become resistant to currently available antiviral drugs. Thus, alternative therapies capable of inhibiting influenza virus replication and attenuating the inflammatory response of the host are needed.

Mesenchymal stem (stromal) cells (MSCs) are multipotent cells that were first identified in bone marrow (BM) as plastic adherent fibroblast-like cells. MSCs possess multilineage differentiation, and immunomodulatory and tissue repair properties. Due to these properties MSCs are attractive as cellular therapy for inflammatory and autoimmune diseases, and regenerative medicine. Several studies of ARDS in animal models have shown beneficial effects of MSC administration, and clinical trials have shown the feasibility of MSC administration in patients with ARDS [5–7]. Therapeutic studies are underway. Similarly to ARDS, severe influenza virus infections in humans and animal models show acute inflammatory response and lung damage. As MSCs suppress inflammation and have tissue repair and regenerative ability, ARDS and influenza are appropriate targets for MSC therapy. However, MSC therapy in mice models of influenza show inconsistent results [9–12]. Also, we and others have shown that influenza virus infects MSCs and that infection may alter the immunoregulatory and differentiation properties of MSCs [13–15].

Several studies indicated that the beneficial actions of MSCs are due to release of paracrine factors since only a few transplanted MSCs engraft at the site of injury. Recently, extracellular vesicles (EVs) that include exosomes (Exo) which are released from multivesicular bodies and microvesicles (MVs) that are shed from the cell surface, and apoptotic bodies were identified in MSC secretions. In this paper EVs, Exo, and MVs will be collectively referred to as EVs. MSC-derived EVs have similar expression of surface molecules and contain MSC-specific proteins, mRNAs, microRNAs (miRNAs), organelles, and lipids [18–20]. In diseased tissue, MSC-EVs interact with injured cells and transfer proteins, mRNA, and bioactive lipids from MSCs to injured cells resulting in tissue repair [21, 22]. In rodent models, these EVs were as therapeutically efficacious as MSCs in E. coli endotoxin-induced acute lung injury (ALI) and E. coli-induced severe pneumonia in mice [20, 23].

Due to their close similarity in anatomy, physiology, and immunology to humans, pigs are used as a large animal preclinical model for several human diseases, including respiratory diseases and regenerative medicine [24, 25]. In addition, pigs are naturally infected with influenza virus as the respiratory epithelium of pigs expresses receptors utilized by avian and mammalian influenza viruses. Influenza virus pathogenesis and clinical signs in pigs are also similar to those observed in humans. Thus, pigs are a suitable large animal model to study human influenza virus pathogenesis and to test the efficacy of therapeutics including MSCs or their derivatives for influenza.