Streptococcus pneumoniae is the most common bacteria found in viral secondary bacterial infections, and is particularly associated with causing high mortality and morbidity during influenza epidemics and pandemics (Brundage, 2006; Joseph et al., 2013). S. pneumoniae is a Gram-positive diplococci and is the most common cause of community-acquired pneumonia and invasive disease, i.e., sepsis and meningitis worldwide, as well as less severe acute disease such as otitis media (Bridy-Pappas et al., 2005; McCullers et al., 2010). S. pneumoniae is grouped into >97 immunologically distinctive serotypes based on a polysaccharide capsule (Bentley et al., 2006; Park et al., 2007; Jin et al., 2009; Calix and Nahm, 2010; Calix et al., 2012). A burden to public health in its’ own right, the WHO has reported that diseases caused by S. pneumoniae resulted in approximately 826,000 deaths in 2000 alone (Pittet and Posfay-Barbe, 2012). A more recent study shows that there are 4 million cases of disease caused by S. pneumoniae and 22,000 deaths annually in the United States (Huang et al., 2011). The current public health impact of S. pneumoniae infection is reduced by vaccine policies, with, for example, PCV-13 and PPV-23 being used for children and adults, respectively, in the United Kingdom (Pittet and Posfay-Barbe, 2012).

Many studies have shown that influenza infection facilitates the acquisition, colonization and development of disease from S. pneumoniae in people of all ages (Shrestha et al., 2013; Grijalva et al., 2014; Siegel et al., 2014). This is partly due to S. pneumoniae’s ability to catabolise sialic acid which is released from host cells and mucus by influenza’s NA. Influenza infection also results in increased mucus production, further increasing the amount of metabolite available for S. pneumoniae. The NA produced by S. pneumoniae also assists in the release of sialic acid (Siegel et al., 2014). Mouse models support the concept that influenza facilitates the development of disease from S. pneumoniae; they have provided evidence that influenza infection enhances secondary S. pneumoniae pneumonia (McCullers and Rehg, 2002; McCullers and Bartmess, 2003). Wu et al. (2011), showed that co-infection of a virus and a bacterium can either occur from mixed viral bacterial infection, or from a viral infection being sequentially followed by a bacterial infection. Sequential bacterial infection normally occurs within a 7-day period of the viral infection. Influenza infections and successive S. pneumoniae infections result is a time and dose dependent change in the host dendritic cells which produces enhanced inflammation. Berendt et al. (1975) inoculated squirrel monkeys with either influenza A, S. pneumoniae or influenza A and S. pneumoniae. Influenza alone caused minor illness such as mild tracheitis, with symptoms such as sneezing, coughing and fever (although some did develop bronchopneumonia) and had a 100% survival rate. S. pneumoniae again caused minor illness with a 100% survival rate. Co-infection of influenza A with S. pneumoniae resulted in severe morbidity with a 75% death rate within 40 h, clear evidence of the consequences of co/secondary bacterial infection (Berendt et al., 1975). These findings are reflected in several other studies, with some even showing that co-infection may assist in the spreading of S. pneumoniae infection to the lower respiratory tract (Takase et al., 1999; Seki et al., 2004).

An additional mouse model of infection provided comparable results whilst comparing the effect of different S. pneumoniae serotypes on co-infection (Sharma-Chawla et al., 2016). More cases of pneumonia and bacteraemia were observed in mice infected with both influenza A and S. pneumoniae than in mice infected with these pathogens individually. This was the case for all S. pneumoniae serotypes tested. More virulent pneumococcal serotypes caused a greater burden of disease in both the co-infected mice and those infected with S. pneumoniae alone. The highly invasive pneumococcal serotype 4 caused pneumonia in 58% of mice and bacteraemia in 21% in a single infection model. When co-infecting with influenza these figures increased to 100 and 90% for pneumonia and bacteraemia, respectively. Mortality rates increased from 0% for individual infection to 79% during co-infection. In comparison, individual infection with a carrier strain (of lower invasive potential) of serotype 19F, caused pneumonia in 91% of cases and bacteraemia in 0%. When co-infecting with influenza and 19F these figures increased to 100 and 33%. Mortality rose from 0% during individual infection to 63% during co-infection (Sharma-Chawla et al., 2016).

Pneumococcal vaccination has shown to ameliorate the risk of secondary bacterial pneumonia. During a vaccine efficacy study, the incidence of pneumonia in those with influenza reduced by 45% in groups vaccinated against S. pneumoniae (Madhi et al., 2007). However, whilst vaccine implementation has successfully reduced pneumococcal disease in a number of countries, lower levels of vaccine implementation in low and middle income countries coupled with fractional serotype coverage and increasing levels of antibiotic resistance, means the specter of influenza pandemic associated S. pneumoniae secondary infection remains a significant risk to global health.

Haemophilus influenzae is another bacteria commonly found to co/secondarily infect viral infection, and has been associated with the complication of disease during influenza pandemics (Abrahams et al., 1919; Spooner et al., 1919; Brundage, 2006; Palacios et al., 2009). It is a Gram-negative fastidious coccobacillus. Typeable strains have a polysaccharide capsule and are categorized into six serotypes (A–F). H. influenzae serotype B was a major cause of invasive disease (Wenger, 1998; Murphy, 2003; Chin et al., 2005; Brouwer et al., 2010) although widespread implementation of the Hib vaccine has significantly reduced the burden of disease (Rosenstein and Perkins, 2000). Those H. influenzae that lack a capsule, denoted non-typeable H. influenzae (NTHi), remain a significant cause of bacterial meningitis, otitis media and exacerbations of chronic lung disease such as COPD worldwide (Langereis and de Jonge, 2015).

Various studies have shown the impact when H. influenzae co/secondarily infects with influenza, and some suggest a level of synergism. The effect of influenza and H. influenzae co-infection verses individual infection of both pathogens is tellingly different; Shope found that co-infection resulted in severe disease or death when on their own H. influenzae and influenza only caused mild infection or disease (Shope, 1931). More recently, Lee E.H. et al. (2010) undertook a similar study which provided comparable results and evidence that influenza and H. influenzae co-infection produces more epithelial cell destruction than single infection with either pathogen (Lee L.N. et al., 2010). Furthermore, they found individual infection caused mild bronchiolitis within 4 days of initial infection, from which the host lung was able to recover. Conversely, co-infection caused bronchial necrosis, bronchial inflammation and bronchitis within the same time period or less, and led to further complication such as epithelial erosion (Lee L.N. et al., 2010). It is now commonly accepted that co-infection results in more severe morbidity and poorer clinical outcome than infection of influenza or H. influenzae alone.

Further support of the impact of co-infection comes from Michaels et al. (1977), who dosed two groups of rats intranasally with H. influenzae with the intention of giving them meningitis. One group of rats were naive and the other had previously been dosed with influenza. In both groups ∼50% of the rats acquired meningitis, however, the naïve rats required a 100-fold larger dose of H. influenzae (Michaels et al., 1977).

As is the case for many bacterial and viral co-infections, mortality from H. influenzae and influenza co-infection is highly dependent on the timing of the introduction of the secondary microbe as well as density of bacterial colonization. Studies have shown that when influenza virus and H. influenzae are introduced at the same time there is no synergistic relationship. When H. influenzae is introduced 7 or more days after influenza there is again no synergistic relationship; however, high lethality is exhibited when H. influenzae and influenza are introduced 3 or 4 days apart (Lee L.N. et al., 2010).

Staphylococcus aureus is a Gram-positive cocci that has been found to complicate influenza infection; increasingly so in more recent years/pandemics (Hers et al., 1958; Palacios et al., 2009). S. aureus is transiently carried in the nose of 30% of the population, whilst 20% of the population have persistent nasal colonization (Wertheim et al., 2005). Like H. influenzae and S. pneumoniae, S. aureus is an opportunistic pathogen and a major cause of bacteraemia (Wertheim et al., 2005; Tong et al., 2015). It is also a common cause of pneumonia (Kollef et al., 2005); specifically necrotising pneumonia that is caused by community acquired Methicillin-resistant Staphylococcus aureus (MRSA) and has a 30% mortality rate (Murray et al., 2010). Necrotising pneumonia is highly associated with either the presence of Panton-Valentine leukocidin (PVL) or prior/co influenza infection (DeLeo and Musser, 2010). MRSA is a particularly problematic pathogen and concern for public health as it can be hard to treat due to its multidrug-resistant properties (Wu et al., 2005; Eom et al., 2014; Fishovitz et al., 2014).

Influenza infection has been shown to increase the adherence of S. aureus (as well as H. influenzae and S. pneumoniae) to host pharyngeal cells (Fainstein et al., 1980). In addition to this, mouse models have highlighted increased morbidity and mortality in mice that are pre-infected with influenza before they are exposed to S. aureus vs. those just exposed to S. aureus. Increased lung damage and bacterial density has also been shown (DeLeo and Musser, 2010; Lee M.H. et al., 2010; Iverson et al., 2011). Lee M.H. et al. (2010) showed that mice infected with low doses of influenza, low doses of S. aureus and high doses of S. aureus were able to survive. Those infected with high doses of influenza died within 4–7 days; however, all mice infected with a high dose of influenza and then a high dose S. aureus died within 2 days of bacterial exposure, showing how death can be accelerated by co-infection. When mice were infected with a low dose of influenza and then a high dose S. aureus they died at 7 days. The fact that the mice survived low influenza infection on its own, but could not survive co-infection with S. aureus shows the lethality of such co/secondary bacterial infection (Lee M.H. et al., 2010).

In an act of synergism, S. aureus infection may actually assist influenza infection by increasing the infectivity of influenza; when the virion is being moved into the host cell within an endosome the low pH in the endosome causes a conformational change to the HA [HA₍₀₎] allowing it to be cleaved by host proteases into two subunits [HA₍₁₎ and HA₍₂₎]. This cleaving ‘activates’ the HA, mediating fusion between the virus and endosome membrane, ready for the opening of the M2 ion channel so the vRNP (viral ribonucleoproteins) can be released into the host cell where the viral RNA is replicated and transcribed. Several strains of S. aureus produce proteases that cleaves influenza HA; the more protease that is available, the more HA can be cleaved meaning more vRNP can get into host cells meaning overall more progeny virions (Tashiro et al., 1987; Steinhauer, 1999; Samji, 2009). This aspect contributes to the increased severity of disease caused by co-infection verses individual influenza infection. And although not all strains of S. aureus produce proteases that cleave influenza HA, the proteases they do produce indirectly enhance morbidity by causing host inflammatory responses which result in the production of host enzymes that are capable of cleaving HA (Tashiro et al., 1987).

The 1918 influenza pandemic was a result of influenza strain A (H1N1). It is considered the most devastating influenza pandemic ever recorded, infecting 50% of the world’s population and resulting in approximately 40–50 million deaths worldwide. India alone suffered 7 million deaths (Potter, 2001; Hilleman, 2002; Brundage, 2006; Michaelis et al., 2009). The main groups of individuals affected by this pandemic were those aged 20–40 years old, in addition to infants and those over 65. Ordinarily only young children and the elderly are the age groups most at risk from influenza, showing how distinctive pandemic strains can be (Potter, 2001). It is suggested that war time efforts meant that influenza easily spread through military camps, allowing the 20–40 years old age range to be more at risk than usual.

There are many published examples of co/secondary bacterial infections during the 1918 influenza pandemic, and pneumonia as a consequence of bacterial infection is estimated to have occurred in up to 95% of deaths during this pandemic (Morens et al., 2008). A majority of those deaths due to secondary S. pneumoniae infection (Brundage and Shanks, 2008; Morens et al., 2008). Many of the examples that detail co/secondary bacterial infection come from outbreaks within army camps. Within a 1-month period in 1918 at the military Camp Devens, a quarter of all troops were diagnosed with influenza. Of those infected, 17% developed pneumonia, of which 35% of cases were fatal. Out of 37 autopsies performed, 43% were positive for pure growth of H. influenzae in at least one lobe of the lung. Blood culture revealed 65% had S. pneumoniae, 2.5% had H. influenzae and 1.3% had S. aureus (Spooner et al., 1919; Brundage, 2006). This pattern of invasive bacterial co/secondary infection has also been documented for several other camps during the same year, including Camp Logan. Here 2,487 influenza-associated hospitalizations were recorded, 17% acquired pneumonia with 4% of these cases being fatal. Post-mortems found S. pneumoniae in the lungs of 44% and heart blood of 33% (Hall et al., 1918; Brundage, 2006). At Camp Jackson, 17% of influenza cases progressed to pneumonia with a further 31% of pneumonia cases proving fatal. Autopsies found S. pneumoniae to be the bacterial co-infection most associated with pneumonia, however, 155 of 312 lung cultures were positive for S. aureus (Michael, 1942; Brundage, 2006). At Camp Custer, 21% of influenza cases progressed to pneumonia, of which 28% died. Sputum cultures proved the presence of S. pneumoniae in 26% of cases. Further investigation found 28% of lung and blood cultures were positive for S. pneumoniae, again acting as supporting evidence of the invasive potential of such co-infections (Blanton and Irons, 1918; Brundage, 2006). Camp Fremont experienced 2418 hospitalizations, 17% had pneumonia of which 36% were fatal. Nasopharyngeal and sputum samples from 158 pneumonia cases found S. pneumoniae in 41% of cases, H. influenzae in 38%, and other Streptococcus spp. in 29% (Brem et al., 1918).

Further lung tissue from fatalities of this pandemic were re-examined in 1919; S. pyogenes longus was found in 36% of cases, S. pneumoniae in 29% of cases and H. influenzae in 25% (Abrahams et al., 1919; Brundage, 2006). Additional post-mortems of lung tissue suggest that at least 90% of samples showed evidence of bacterial infection (Oxford et al., 2002; Morens et al., 2008; Chien et al., 2009). Overall 95% of deaths were due to co/secondary bacterial pneumonia (Opie et al., 1921; Morens et al., 2008).

Co-infection had also been reported as an issue prior to the official start of the pandemic. Influenza with secondary bacterial infection of S. pneumoniae (and other Streptococcus sp.), H. influenzae and/or Staphylococcus sp. was associated with major outbreaks of purulent bronchitis in 1916 and 1917 (Brundage, 2006; Joseph et al., 2013). Indeed in 1916–1917 British, Australian, Canadian, and American armed forces in England and France experienced an epidemic of purulent bronchitis. Out of 20 tested sputum specimens from a British army camp based in north France, 90% presented with H. influenzae, 65% presented with S. pneumoniae, 25% with other Streptococcus spp. and 15% with Staphylococcus spp. Out of the specimens positive for H. influenzae, many exhibited simultaneous H. influenzae and S. pneumoniae co-infection; with H. influenzae identified as the primary bacterial infector. S. pneumoniae infection first presented with low virulence, however, pathogenesis soon worsened, it has been suggested, as result of the symbiotic growth with H. influenzae (Brundage, 2006; Dennis Shanks et al., 2012). Of course it is known that there is a positive association between the colonization of H. influenzae and S. pneumoniae, and colonization is a prerequisite for disease, so the presence of such co-infection fits with current knowledge (Jacoby et al., 2007; Abdullahi et al., 2008).

This pandemic affected 40–50% of people worldwide. The cause was influenza strain A (H2N2) (Potter, 2001). Although global death toll estimates vary [between 1.5 million (Gatherer, 2009) and 2–4 million (Michaelis et al., 2009)], the death toll in the United States is accurately reported to have been 69, 800 (Klimov et al., 1999; Hilleman, 2002). Post-mortem cultures show evidence of bacterial infection in up to 80% of all severe and fatal cases (Hers et al., 1958; Morens et al., 2008; Gill et al., 2010).

During this pandemic the United States, and many other countries, experienced an increase in hospitalization rates. A majority were due to pneumonia, predominantly caused by S. pneumoniae, H. influenzae, and S. aureus infection (Petersdorf et al., 1959). There are similar documented reports from the Netherlands; of the 148 deaths presumed to be from the Asian pandemic influenza strain that were examined fully, 75% presented with bacterial pneumonia of which 15% were positive for S. pneumoniae and 59% were positive for S. aureus (Hers et al., 1958).

Robertson et al. (1958) unveiled similar findings when investigating the hospitalization of 140 people suffering pneumonia at Sheffield City General Hospital in 1957. A majority showed evidence of influenza A infection; 27% of those had co/secondary infection of S. aureus (which had a 47% death rate), 15% S. pneumoniae and 4% H. influenzae, although this is likely to be an underestimation as many patients had already started taking antibiotics (Robertson et al., 1958).

Worldwide 1–2 million people died during this pandemic which was caused by the influenza strain A(H3N2) (Michaelis et al., 2009). Although this is a lower death toll than engendered in previous pandemics, it is still an awfully high number of deaths. Overall 33,800 people died in the United States (Klimov et al., 1999) and the pandemic cost 3.9 billion dollars (Hilleman, 2002). In 1969, England and Wales saw a 55% increase in respiratory deaths, of which co/secondary bacterial infection was shown to be a major contributor (Tillett et al., 1983).

Staphylococcal pneumonia in particular was a major source of complication to influenza infection. A hospital in Atlanta suffered a threefold increase in cases of Staphylococcal pneumonia during this pandemic. Staphylococcal infection caused 26% of pneumonia cases during this period, and a high correlation was recognized between influenza infection and bacterial pneumonia (Schwarzmann et al., 1971). In addition, out of 79 cases of fatal influenza with pneumonia complications, 16% had bacterial co-infection with S. pneumoniae (6%), S. pyogenes (5%), and S. aureus (1%) being the main causes. More than one of these bacteria were present in 4% of cases (Schwarzmann et al., 1971; Metersky et al., 2012).

Another health care facility in the United States, the Mayo Clinic in Minnesota, also found S. aureus to be a major cause of complication. Of 129 adults diagnosed with pandemic influenza, pneumonia was established in 16%, of which 40% of these cases (6% of all 129 influenza cases) were fatal. S. aureus or P. aeruginosa bacterial infection was present in 75% of all fatal cases, indicating bacterial co/secondary infection was a major determinant of severe disease and death (Lindsay et al., 1970).

In previous pandemics S. pneumoniae has been proposed as the major contributor of mortality and morbidity, however, during this 1968–1969 Hong Kong and the 1957 Asian influenza pandemic S. aureus clearly had a larger impact. This is possibly a reflection of increased antibiotic use and increased antibiotic resistance.

Within 4 weeks this outbreak of influenza A(H1N1) had spread to 41 countries resulting in 11,034 confirmed cases and 85 deaths (Michaelis et al., 2009; Wang and Palese, 2009). By the end of the pandemic it is thought that there were 284,000 deaths worldwide, with Mexico and the United States being most severely affected (Chertow and Memoli, 2013). Unlike other pandemics and yearly epidemics, during this pandemic it was predominantly children and young adults that were affected, particularly those aged 12–22 (Gill et al., 2010). Influenza A (H1N1) strains have been circulating amongst the human population for many years therefore this prior exposure could have provided many adults with some degree of immunity against the 2009 pandemic strain, particularly older groups who were more likely exposed during previous pandemics.

Surveillance by the New York City Department of Health and Mental Hygiene has shown that during the 2009 Swine Flu Pandemic almost 30% of the first 47 deaths showed invasive bacterial disease. S. pneumoniae was the most common causative agent identified (followed by S. pyogenes) (Lee E.H. et al., 2010). In the United Kingdom, of the 457 fatalities 68 were autopsied. Of these, 41% were shown to have complications associated with secondary bacterial infection, most commonly (25% of cases) due to S. pneumoniae (Lucas, 2010).

Further studies in the United States have reviewed 77 deaths during the period of May–August 2009 and found bacterial co-infection in almost 30% of cases; 46% of which were with S. pneumoniae, 9% with S. aureus and 1% with H. influenzae (Centers for Disease Control and Prevention, 2009). Studies based in Argentina produced similar evidence for the presence of bacterial infection, showing this wasn’t just a localized trend. Palacios et al. (2009) examined nasopharyngeal swab samples from almost 200 cases of pandemic influenza. H. influenzae was found in 52%, S. pneumoniae was found in 31% and S. aureus in 18% of samples. Although not the most common bacteria found, S. pneumoniae was the most strongly associated with severe disease (Palacios et al., 2009).

Additional research in pediatric intensive care units in the United States, investigated 838 critically ill children who were infected with pandemic influenza. Within 72 h of admission to the intensive care unit 33% exhibited bacterial co-infection; in 26% of these cases S. aureus was identified as the cause (48% of which were MRSA), 5.5% were positive for S. pneumoniae and 5% were positive for H. influenzae. Bacteraemia was observed in 5% of admissions, for which S. aureus was the main cause (Randolph et al., 2011). This study highlights how quickly co/secondary bacterial infection can become invasive particularly in at risk groups such as young children or the elderly. A point of concern is that almost half of the S. aureus were MRSA, and therefore inherently resistant to multiple antibiotics.

In another study of vulnerable and critically ill children in a pediatric intensive care unit in the United States, 51% of those with influenza infection had bacterial co/secondary infection. Of these 35% presented with S. aureus, 18% P. aeruginosa, 18% M. catarrhalis, 9% NTHI, 6% S. pneumoniae and 6% Group A Streptococcus. Those with S. aureus showed more severe morbidity and were more likely to develop disseminated intravascular coagulation which leads to a compromised blood flow within body tissue and therefore tissue damage (Nguyen et al., 2012).

In a retrospective study of 50 patients who were infected during pandemic influenza, 28% showed co/secondary bacterial infection (Dhanoa et al., 2011). Mycoplasma pneumoniae was found in 10%, making it the most common co/secondary infecting bacteria. This was followed by S. aureus found in 6%, K. pneumoniae and S. pneumoniae found in 4% and M. catarrhalis, P. aeruginosa, S. pyogenes, and Streptococcus agalactiae found in 2% of these patients (Dhanoa et al., 2011).

Moraxella catarrhalis is a bacteria of increasing importance being now acknowledged as the third most common cause of otitis media (OM), after S. pneumoniae and H. influenzae (Bluestone, 1986; Faden et al., 1994; Kilpi et al., 2001; Dupont et al., 2010) and the second most common cause of exacerbations in COPD, accounting for up to 4 million exacerbations per year in the United States alone (Murphy et al., 2005). M. catarrhalis is a cause of pneumonia (Berg and Bartley, 1987; Hager et al., 1987; Marchant, 1990; Verduin et al., 2002) and invasive disease such as bacteraemia (Ioannidis et al., 1995) and meningitis (Newing and Christie, 1947), with bacteraemia being a common complication of pneumonia, particularly in adults (Collazos et al., 1992; Ioannidis et al., 1995). Although this review has focused on S. pneumoniae, H. influenzae, and S. aureus, it has cited other bacteria seen as a source of co-infection during the various pandemics described. In early influenza pandemics such as the 1918 Spanish pandemic, M. catarrhalis rarely appears to be a noted cause of co-infection. However, in the 2009 pandemic it is seen in up to 18% of cases (Nguyen et al., 2012). We have therefore considered the importance of this. Data produced toward the end of the 1970’s and throughout the 1980’s demonstrated M. catarrhalis’ potential to cause disease, however, before this M. catarrhalis was considered a non-pathogenic harmless commensal (McNeely et al., 1976; Johnson et al., 1981; Onofrio et al., 1981; McLeod et al., 1983; Feder and Garibaldi, 1984; Hager et al., 1987; Catlin, 1990). Therefore there are two possibilities to consider; perhaps M. catarrhalis wasn’t present in early pandemics as a cause of co-infection and has become more of an issue in recent years; possibly as a result of vaccines, i.e., Hib and PCV, reducing the disease burden of other bacteria such as S. pneumonia and H. influenzae. Alternatively, we must consider that as M. catarrhalis was not considered a pathogen it was therefore missed or not commented upon prior to the 1980’s. Retrospective studies may be able to address this. For example, autopsies from the 1918 pandemic were reviewed and it was found that S. pneumoniae was the most common co-infector, followed by S hemolytic, S. aureus, and H. influenzae. ‘Other bacteria’ were also highlighted within which M. catarrhalis was grouped (Morens et al., 2008).

Another point of consideration are changes of methodology. Pre-1983 laboratories would only undertake bacterial culture, however, in 2009 more sensitive methodology, i.e., PCR were available and commonly used in laboratories worldwide. The use of sensitive methods such as PCR, may have increased the likelihood of M. catarrhalis being detected, and as a known respiratory pathogen it would have been tested for, where as previously it may not have been. Alternatively maybe PCR detects bacteria that may have been out grown/not shown on a culture plate?

In contrast to S. pneumoniae and H. influenzae little research has been undertaken looking at influenza and M. catarrhalis co-infection and the dynamics and mechanisms of such infection. This is therefore an area worthy of future research. M. catarrhalis has been highlighted as a frequent source of co-infection for influenza since the early 1980’s (Klein et al., 2016). In the setting of a pandemic it may therefore have a major public health impact.

It has become clear that influenza, as well as other upper respiratory tract viral infections, leads not only to a greater risk of infection from bacterial pathobionts but also an increased likelihood that an individual may become colonized with bacteria such as S. pneumoniae, H. influenzae and S. aureus (Hament et al., 1999; Hilleman, 2002). Plotkowski et al. (1986) found enhanced colonization and adherence of S. pneumoniae to the tracheal cells of mice when they were infected with influenza (Plotkowski et al., 1986). Other studies have intranasally inoculated ferrets with influenza, finding prior viral infection increases colonization and adherence of S. aureus (Sanford and Ramsay, 1987). Furthermore, poor disease outcome has been linked to lost lung repair function and loss of basal epithelial cells, including alveolar epithelial cells; which is associated with increased bacterial attachment and apoptosis (Kash et al., 2011). Wadowsky et al. (1995) conducted a study in which adult subjects were inoculated with influenza and then screened for bacterial colonization. After 6 days 15% of the subjects were heavily colonized by S. pneumoniae (Wadowsky et al., 1995). Additionally, the effect of viral prevention methods further supports the idea of viruses predisposing a host to secondary bacterial infection (Peltola and McCullers, 2004; Lee et al., 2008). Studies have shown that influenza vaccination can reduce the occurrence of bacterial pneumonia (Fedson et al., 1993; Nichol et al., 1998).

Research shows that influenza A is the type most commonly associated with co/secondary bacterial infection and subtypes with NA2 traditionally result in more severe infection (Peltola et al., 2005). Although reported less, influenza B has also been associated with severe bacterial co/secondary infection (Finelli et al., 2008; Aebi et al., 2010). Various factors are known to impact the severity of viral infection, which in turn increases the likelihood of bacterial co/secondary infections; these include the type of HA and NA surface antigen. As mentioned previously, HA mediates virion binding to the host cell via sialic acid receptors. Binding is followed by endocytosis and the movement of the virion into the host cell within an endosome (Samji, 2009). HA binds to sialylated glycans found on the surface of human epithelial cells; traditionally seasonal influenza A virus binds to α2-6 sialylated glycans on cells in the upper respiratory tract whereas the highly pathogenic avian H5N1 strain binds to α2-3 sialylated glycans on type 2 pneumocytes lining lung alveoli (Shinya et al., 2006). Clearly the type of HA impacts on the site and development of infection. The low pH in the endosome causes a conformational change to the HA allowing it to be cleaved, an important step in penetrating into the host cell. Therefore HA and the availability of appropriate host proteases are determinants of infectivity (Steinhauer, 1999; Samji, 2009). Interestingly non-pathogenic and mammalian influenza HA undergoes cleavage outside of the host cell where as highly pathogenic strains are cleaved inside host cells (Steinhauer, 1999). Another example of how the type of HA can make a difference to infection, and therefore the impact of an epi- or pandemic, is that traditionally trypsin-like protease cleaves influenza HA; however, some HA types (i.e., types 5 and 7) have the ability to acquire insertional mutations at the cleavage site which changes their recognition site in such a way that specificity is broadened so more proteases are recognized (Kash and Taubenberger, 2015).

Neuraminidase enables the release of newly formed progeny virions; by hydrolysing the sialic acid and detaching it from the HA the virion becomes liberated from the host cell (Zambon, 2001). To be truly effective the NA must be complementary and share the same receptor specificity as HA, so if the viral HA binds to α2-3 sialic acid then the NA should hydrolyse α2-3 sialic acid (Baum and Paulson, 1991).

The production of viral toxins that impact host cell integrity is another important factor in the development of co/secondary bacterial infection. Influenza A virus can produce a viral cytotoxin PB1-F2 (Conenello and Palese, 2007; Iverson et al., 2011) which plays a role in increasing inflammation and therefore host cell damage and bacterial adherence, increasing mortality and morbidity (Lee et al., 2016). It also helps reduce bacterial clearance, increasing the occurrence and severity of co/secondary bacterial infection, by causing cell death in host monocytes (Conenello and Palese, 2007; Iverson et al., 2011).

Following bacterial colonization, disease develops due to specific characteristics of viral infection that facilitate bacterial adhesion and penetration (Selinger et al., 1981). Influenza produces NA, which increases adhesion of some bacterial species by removing sialic acid to expose host cell receptors (McCullers and Bartmess, 2003; Peltola and McCullers, 2004). Alternatively some bacteria, i.e., group B Streptococci, contain sialic acid which allows for direct binding to the viral HA expressed by influenza infected host cells (Okamoto et al., 2003; Peltola and McCullers, 2004). Damaged host cells, whether damaged directly by the virus or by inflammation and immune cell responses, provide additional adhesion sites allowing for increased bacterial adhesion. For example the exposure of apical receptors like integrins permit the adhesion of bacteria such as S. aureus and P. aeruginosa (Sanford et al., 1978; Davison and Sanford, 1981; Bucior et al., 2012; Smith and McCullers, 2014). In response to viral infection, host inflammatory responses may cause an up-regulation in the expression of host receptor molecules and other molecules that bacteria can use as a receptors (Hakansson et al., 1994; Peltola and McCullers, 2004). For example Cundell et al. (1995) showed an increased presentation of G-protein-coupled platelet-activating factor (PAF) receptor, which certain bacteria, i.e., S. pneumoniae, can utilize for cell attachment and colonization in endothelial cells (Cundell et al., 1995; van der Sluijs et al., 2010). In contrast it has been suggested that the PAF receptor does not affect initial bacterial adherence and colonization but is more involved with assisting bacterial transition/spread into the blood and thus the development of invasive disease (McCullers et al., 2008).

Influenza infection appears to prime the host airways for bacterial infection, whilst modifying and impairing immune responses in a number of ways (Joseph et al., 2013). Viral induced immunosuppression can allow for a bacterial super infection, as host immune responses can be suppressed when immunologic cells are impaired during influenza infection and immune cell dysfunction can reduce the host’s ability to fight bacteria (Peltola and McCullers, 2004; Brundage, 2006; Wu et al., 2011). Many studies involving animal models have shown that influenza infection increases and prolongs bacterial growth, due to reduced macrophage accumulation and decreased bacterial clearance due to reduced phagocytic activity (Kleinerman et al., 1976; Wyde et al., 1989; Sun and Metzger, 2008). Additionally it has recently been shown that S. pneumoniae and influenza co-infection results in a reduction in the number of local alveolar macrophages, this due to increased death of these macrophages by apoptosis and necrosis (Sharma-Chawla et al., 2016). This reduction is likely to hinder bacterial clearance, hence the increased bacterial load found during co-infection during this study, and results in prolonged inflammatory response increasing morbidity. Even after influenza is cleared, S. pneumoniae bacterial clearance is affected. This study has highlighted some serotype dependent differences, suggesting different treatment programs would be beneficial for different serotypes. Evidence that it is worth further looking into co-infection of influenza with different serotypes of S. pneumoniae and other bacteria of interest (Sharma-Chawla et al., 2016). Impaired neutrophils have been shown to correlate with secondary bacterial infection in Chinchillas, due to the importance of phagocytosis during innate immunity (Abramson et al., 1981). Influenza infection is known to result in the production of IFN; pulmonary IFNγ pro-inflammatory cytokines are produced by natural killer (NK) cells as part of innate immunity and by CD4 and CD8 NK T cells as part of adaptive immunity (Schoenborn and Wilson, 2007). They increase macrophage activation during innate immunity (Scott et al., 2004) however, during T cell responses to viral infection they have been shown to inhibit bacterial clearance from the respiratory system by macrophages. It is thought that as they assist in the induction of specific anti-influenza adaptive immunity they down regulate innate immunity. The resulting suppression of phagocytosis paves the way for successful bacterial infection (Sun and Metzger, 2008). Additionally, Type I IFNs inhibit interleukin 23 (IL-23) dependent induction of T helper cell 17 (Th17) immunity, and therefore there is a reduction in the levels of CD4+ T cells and gamma delta T cells and hence a reduction in the production of IL-17 and IL-22, preventing the clearance of bacteria (Shahangian et al., 2009; Kudva et al., 2011; Mulcahy and McLoughlin, 2016). Robinson et al. (2013) have also shown that influenza A infection significantly decreased IL-1β production; IL-1β has been shown to play a role in Th17 polarization, therefore further hindering this pathway of immunity (Robinson et al., 2013). During co/secondary S. pneumoniae infection, type I IFNs have been shown to inhibit the production of specific chemokines (KC/CXCL1 and Mip2/CXCL2) resulting in an attenuated neutrophil response (Shahangian et al., 2009). Viral and bacterial co-infection of monocyte derived macrophages synergistically induces a pro-inflammatory response related to the type-I IFN and JAK-STAT signaling pathways (Hoffmann et al., 2016). Inflammation causes tissue damage, revealing more attachment sites for increased/developed bacterial infection. Co-infection also results in a synergistic increase in type II IFN (IFNγ) when compared to individual infection of influenza or S. pneumoniae, CXCL10 (aka IFNγ-induced protein 10/IP-10) is secreted in response. IP-10 attracts various immune cells including activated T cells, monocytes and macrophages, therefore causing inflammation (Dufour et al., 2002; Hoffmann et al., 2016). Patients suffering severe pneumonia show significantly higher levels of IP-10 than those with minor cases of pneumonia. IP-10 is increased during H. influenzae and S. aureus co-infection as well, and like with S. pneumoniae, correlates with/highlights pneumonia etiology (Hoffmann et al., 2016). In addition, when S. pneumoniae successively co-infects with influenza it leads to severe clinical complications; partly due to an increase in apoptosis of dendritic cells, which therefore reduces T cell priming impairing the development of adaptive immunity. Influenza and S. pneumoniae infections can also lead to synergistic and non-synergistic dysregulation of cytokine responses (Wu et al., 2011).

As previously described influenza infection results in a reduction in the production of IL-17 and 22. IL-17 is important in the clearance of S. aureus by neutrophils (Archer et al., 2013). IL-22 in involved in controlling the production of antimicrobial peptides as well as staphylococcal ligand expression (Robinson et al., 2014; Mulcahy et al., 2016). In addition to this, influenza positively affects the colonization of S. aureus by causing increased type III- IFN expression, which alters the IL-22 responses impairing host expression of antimicrobial peptides (Mulcahy and McLoughlin, 2016). Distress signals, such as ATP and norepinephrine, produced by damaged influenza also have several effects on S. aureus; namely the instigation of biofilm dispersal which helps the spread of S. aureus into the lungs, assisting in the development of pneumonia and invasive disease (Mulcahy and McLoughlin, 2016).

Of course viral infection doesn’t just benefit bacteria; several mechanisms of synergism between viruses and bacteria have been suggested. A number of studies have documented an increase in viral load as viral clearance is reduced during bacterial co-infection. It is, however, unclear whether this is from bacterial and viral cooperation/interactions or simply from bacteria burdening the host immune system resulting in the reduction of viral eradication. Therefore further research is required to develop our understanding of the interaction between bacteria and viruses within co-infection (Peltola and McCullers, 2004; Iverson et al., 2011; Smith and McCullers, 2014).