Group A Streptococcus was found in 6.5% of patients presenting with a sore throat and history of fever. This is lower than estimates from a meta-analysis of more than 495,000 patients presenting to primary care or emergency departments, where 24.1% of those presenting with symptoms of pharyngitis or URTI were found to have GAS on culture.29 They found higher prevalence in high-income countries than LMICs, at 24.3% and 17.6%, respectively.30 Our findings were similar to other studies from Thailand, which found GAS in 3.8–7.9% of patients presenting with URTI,3,31 and a study of influenza-like illnesses in Lao PDR (8.6%).32

All GAS isolates were sensitive to ceftriaxone and penicillin G. There were resistance to erythromycin in 2/11 (18.2%), clindamycin in 2/11 (18.2%), and chloramphenicol in 2/11 (18.2%) isolates. A single isolate (9.1%) was resistant to all three antibiotics. Intermediate sensitivity to erythromycin was found in 1/11 (9.1%) and to chloramphenicol in a different 1/11 (9.1%) isolate (see Table 2).

Clinical features of the patients with GAS are shown in Table 3. Of 11 patients with GAS, eight (72.7%) had abnormal throat examinations, four (36.4%) had pharyngitis, four (36.4%) had common colds, and three (27.3%) had tonsillitis.

Only four (36.4%) were prescribed an antibiotic at the index consultation, and one additional patient in the control group with high CRP was prescribed an antibiotic on the return visit at day 5. None of the patients sourced antibiotics from elsewhere during the 2 weeks of follow-up. Patients reported symptom resolution by day 14 in 10/11 (90.9%) cases. One patient had a persisting cough, but their other symptoms (fever, sore throat, and runny nose) had resolved.

Median CRP values for each swab result are shown in Table 4; there were two missing CRP values at enrollment into the main RCT. The median CRP levels were signficantly higher in patients with GAS than in those with no BHS isolated (P = 0.0302), and higher in those with any BHS isolated (P = 0.0516). C-reactive protein > 8 mg/L had a sensitivity of 81.8% (95% CI 52.3–94.8%) and specificity of 47.4% (95% CI 39.1–55.8%) for the detection of GAS compared with no BHS isolation. There were no significant statistical relationships between CRP values > 8 mg/L (P = 0.112), Centor scores ≥ 3 (P = 0.212), and FeverPAIN scores ≥ 4 (P = 1.000) and diagnosis of GAS compared with no BHS isolation.

Septicemia is a serious and life-threatening infection, in which a large amount of bacteria are present in the blood. It is commonly referred to as “blood poisoning” or “bacteremia with sepsis”.1 This disease often causes multi-organ failure by reducing the amount of blood reaching vital organs such as the liver and kidneys.1,48,75 In addition to the known bacterial pathogens (such as Staphylococcus) with capability of leading to septicemia with about 25% lethal rate,1,180 SS2 is also a causative agent of this disease.1 In general, SS2-caused septicemia arises as a result of the localized infection in the body, especially cut skin.1 In patients with septicemia, some of the following symptoms can be observed: fever and chills, rising heart/respiratory rate, cold and clammy feeling, fallen blood pressure, paled ,and petechial skin, and ultimately even unconsciousness. SS2 most likely releases some toxins into the blood that break down the walls of blood vessels which allows blood to leak out under the skin (it is this leaking that causes the rash or petechiae).33 In some cases, SS2 infects the bloodstream and the meninges at the same time, causing both septicemia and meningitis.33,181 Due to the rapidly progressive condition of septicemia, it can evolve into an irreversible toxic shock and even acute death if sufferers do not receive urgent treatment.33,181,182 Certainly, an antibiotic remedy could be altered quickly to treat the target bacteria agents, when medical tests have identified which bacteria cause the septicemia and which antibiotics are best effective.33,182 Of note, some medical treatments themselves are the inducers of septicemia, e.g., dental treatment, long-term use of intravenous needles, a colostomy, and so on.33,175 Collectively, septicemia is so serious and complex that it deserves a lot of attention worldwide.

Environmental stress associated with intense exercise, competition and prolonged transportation combined with canine vaccination may suppress the innate immune response to viral infections and subsequent S. equi subsp. zooepidemicus infection that only rarely cause pathology in dogs. Knowledge and alertness of early clinical signs of acute haemorrhagic pneumonia will enhance treatment success and shorten the rehabilitation period. However, caution should be taken to prevent athletes from return to the competition arena too fast. These high performance sled dogs recovered relatively fast and could prove their fitness by competing and winning international sled race championships three months later.

As a swine pathogen, S. suis was first reported by a vegetarian in 1954,2 while its zoonotic role could be traced to a human SS2 meningitis case in Denmark, in 1968.1 In light of the available literature with human S. suis infection recorded thus far, we expect that S. suis infections have been involved in no less than 30 countries and/or regions (Fig. 1), and resulted in around 1600 cases of severe human infections.2,8,48 In North America (United States49,50 and Canada51,52) and the South American countries (Argentina,53,54 Chile,55 and French Guiana56) only a very few cases of human SS2 infections were reported. Human SS2 infections are featuring with sporadic cases in Europe (Ireland,3 the United Kingdom [UK],3 France3,, Spain,57 Netherlands,58 Belgium,3 Poland,61 Sweden,3 Denmark,1 Germany,62 Hungary,3 Austria,63 Croatia,64 Italy65-67, Greece,68 and Portugal1), some Asian countries (Laos,1 Singapore,33,69 India,2,3,70 Korea,71-73 Japan,74 Hong Kong,75-80 Taiwan,33,81,82 and Philippine2,3), Australia,83,84 and New Zealand.85,86 So far, endemics of human SS2 infections was only observed in two Asian counties Vietnam2,7,16,37,38 and Thailand.6,11,14,87 Of particular note, coexistence of sporadic cases and epidemics of human SS2 infections were present in China.4,8,9,17-19,33,48 It seemed true that the majority of human SS2 infection cases occurred in southeast Asia (especially Vietnam, Thailand, and China), indicating an obvious geographic tropism (Fig. 1). Although we are not quite sure what mechanism can explain such kind of tropism, we anticipate that the following factors are probably correlated with frequent occurrence of human SS2 infections in above countries, which include (1) similar local climates and/or environments; (2) backyard cultivation of pigs; and (3) popular consumption of raw pork sold in the wet market.

The annual incidence of acute bronchitis increased significantly from 3836 (range, 1964-5665; mean, 3836) per 100,000 individuals in 2010 to 4612 (range, 2440-6034; mean, 4612) per 100,000 individuals in 2015 (p < 0.01) (Fig. 3a). The average incidences of acute bronchitis, acute tonsillitis, acute upper respiratory tract infections, and pneumonia were 4334, 1864, 1526, and 153 per 100,000 individuals, respectively (Fig. 3 (b)).

There was no difference in the rates of bacterial infections post-vaccination, (17.5% of the total) compared to 24% pre-vaccination (p=0.258). Overall, identified pneumococcal infections were not different between the studies (p=0.557). They represent 17.4% among children tested post-vaccination (14 (15%) out of 93 and 10 (22.2%) out of 45 in those aged <5 years and >5 years, respectively). This was compared to 14.7% pre-vaccination (28 (15.6%) out of 180 and seven (12%) out of 58 among those aged <5 years and >5 years, respectively). In the post-vaccine study, diagnosis of pneumococcal infection improved when PCR was used (21 (21.6%) out of 97) compared to culture (eight (6%) out of 132) (p=0.0004). A serotype was identified in 75% (18 out of 24) in the post-vaccine study. These were serotypes 1 (44.4%), 3 (27.8%), 19A (22.2%) and 7A/F (5.6%). The rate of positive blood culture post-vaccination was almost double (5.6%) that pre-vaccination (3.2%).

Group A streptococcal infections were confirmed in a greater proportion of children (10.5%) post-vaccination than in the pre-vaccination group (7%). These infections were associated with severe disease, and in two-thirds of cases with empyema. M. pneumoniae was identified from acute serology in 9.9% of children post-vaccination, with 4% (two out of 51) in those aged <5 years and 20% (six out of 30) in patients aged >5 years. The rate of detected mycoplasma infection was higher pre-vaccination (12.5%) when paired acute and convalescent samples were available, with 7% (nine out of 128) in those aged <5 years and 27% (13 out of 48) in those aged >5 years.

Monthly time series of antibiotic use, respiratory virus detection, and incidence of ARTIs are presented in Fig. 4. Seasonal antibiotic use clearly followed a similar oscillatory pattern to influenza virus detection. Antibiotic use also had a similar seasonal pattern as the incidences of acute bronchitis, acute upper respiratory tract infections, and acute tonsillitis.

The total monthly rate of antibiotic prescriptions was highly cross-correlated with the monthly detection rate of influenza virus (cross-correlation coefficient 0.47, p < 0.01). In bivariate analyses, antibiotic use rates for the 4 most commonly used antibiotics (penicillins, other beta-lactam antibacterials, macrolides, and fluoroquinolones) were significantly cross-correlated with influenza virus detection at the 0-month lag with cross-correlation coefficients of 0.45 (p < 0.01), 0.46 (p < 0.01), 0.40 (p < 0.01), and 0.35 (< 0.01), respectively (Table 1). However, no cross-correlation was found between antibiotic classes with lower-use rates (< 2 DID) and the influenza virus detection rate. There was significant cross-correlation between hRV and tetracycline with a 2-month lag (cross-correlation coefficient 0.24, p = 0.04).

For ARTIs, the correlation coefficiencts of antibiotic use and the incidence of acute bronchitis were 0.73 (p < 0.01) for penicillins, 0.69 (p < 0.01) for other beta-lactam antibacterials, 0.74 (p < 0.01) for macrolides and 0.45 (p < 0.01) for fluoroquinolones (Table 2). Acute upper respiratory infection was significantly correlated with penicillins (0.33, p < 0.01), other beta-lactam antibacterials (0.32, p < 0.01), macrolides (0.24, p = 0.04), and fluoroquinolones (0.31, p < 0.01) without a lag. Again, no cross-correlation was found between classes of antibiotics with lower-use rates (< 2 DID) and ARTIs.

For comparators that were more likely to require antibiotics than ARTIs, pneumonia was significantly correlated with penicillins (0.36, p < 0.01), macrolides (0.53, p < 0.01), aminoglycosides (0.38, p < 0.01), and other beta-lactam antibacterials (0.25, p < 0.03) without a lag. Furthermore, acute tonsillitis was significantly correlated with penicillin (0.69. p < 0.01), other beta-lactam antibacterials (0.68, p < 0.01), macrolides (0.59, p < 0.01), and fluoroquinolones (0.35, p < 0.01) without a lag.

Among 67 children enrolled during this period, the causative pathogen was identified in 37 (55%). S. pneumoniae was identified in 18.3% (11 out of 60) compared to 16.7% (13 out of 78) during the first year of PCV13 vaccination (p=0.824). Rates of infections were 22.4% bacterial, 22.4% viral and 10.5% mixed. The rate of bacterial infection is similar to the figures from the pre- and entire post-vaccine studies. There was no difference between the rates of viral infection before and after the introduction of PCV13 during the post-vaccine study (p=0.079).

E. coli is a gram-negative, non-acid-fast, uniform staining, non-spore-forming bacillus that grows both aerobically and anaerobically and may be variable in size and shape. Many strains are motile and have peritrichous flagella. E. coli is considered as a member of the normal microflora of the poultry intestine, but certain strains, such as those designated as avian pathogenic E. coli (APEC), spread into various internal organs and cause colibacillosis characterized by systemic fatal disease. E. coli isolates pathogenic for poultry commonly belong to certain serogroups, particularly the serogroups O78, O1, and O2, and to some extent O15 and O55. In domestic poultry, avian colibacillosis is frequently associated with E. coli strains of serotypes O78:K80, O1:K1 and O2:K1 (2- Filali E). The avian colibacillosis was found widely prevalent in all age group of chickens (9.52 to 36.73%) with specially high prevalence rate in adult layer birds (36.73%).

The most important reservoir of E. coli is the intestinal tract of animals, including poultry. In chickens, there are about 109 colony forming units (CFU) of bacteria per gram of feces and of these, 106 CFU are E. coli. E. coli has also been commonly isolated from the upper respiratory tract. In addition, it is present on the bird’s skin and feathers. These strains always belong to both pathogenic and non-pathogenic types. In the caecal flora of healthy chickens, 10 to 15% of the E. coli strains may belong to an O-serotype that can also be isolated from colibacillosis lesions. As soon as the first hours after hatching, the birds start building up their E. coli flora. The bacteria drastically increase their numbers in the gut. In a single bird a large number of different E. coli types is present, obtained via horizontal contamination from the environment, more specifically from other birds, faeces, water and feed. Moreover, rodents may be carriers of APEC and hence a source of contamination for the birds.

The risk for colibacillosis increases with increasing infection pressure in the environment. A good housing hygiene and avoiding overcrowding are very important. Other principal risk factors are the duration of exposure, virulence of the strain, breed, and immune status of the bird [30–34]. Every damage to the respiratory system favours infection with APEC. Several pathogens, like NDV, IBV and MG, both wildtype and vaccine strains, may play a part in this process. An unfavourable housing climate, like an excess of ammonia or dust, renders the respiratory system more susceptible to APEC infections through deciliation of the upper respiratory tract.

Pulsed field gel electrophoresis (PFGE) is considered to be the most reliable molecular finger-printing technique to differentiate organisms but restriction fragment length polymorphism (RFLP) is the one that is used most frequently. However, both techniques require large quantities of DNA, are time consuming, and require expensive equipment. Other techniques such as ERIC–PCR and REP–PCR and random amplification of polymorphic DNA (RAPD)–PCR have been proposed as alternatives and used to characterize Escherichia coli isolates of avian origin. Other molecular techniques such as ribotyping and isoenzyme profile have also been used to evaluate the clonality of avian E. coli. Some clones are specific to APEC and a small-scale comparison of commensal and pathogenic isolates revealed that 83% of pathogenic strains belong to only five clones, whereas each of the 10 non-pathogenic strains belong to different clones. On the other hand, clonal relationships were found for O2:K1 isolates from humans and chickens and for O78 isolates from humans, cattle, sheep, pigs and chickens, indicating that these species too might act as a source of infection for chickens.

Even though certain O-types are more frequently detected in APEC than in commensal E. coli, the isolates are very heterogenous, both in their pheno- and genotype [43,45–47]. On the other hand, the prevalence of certain serotypes is linked with the geographical localisation of a flock.

Since avian pathogenic E. coli (APEC) and human uropathogenic E. coli (UPEC) may encounter similar challenges when establishing infection in extraintestinal locations, they may share a similar content of virulence genes and capacity to cause disease. In this regard, Rodriguez-Siek et al. compared 200 human uropathogenic E. coli (UPEC) and 524 avian pathogenic E. coli (APEC) isolates for their content of virulence genes (Table 1), including many implicated in extraintestinal pathogenic E. coli (ExPEC) virulence as well as those associated with APEC plasmids for assessing the potential of APEC to cause human extraintestinal diseases and a well-documented ability of avian E. coli to spread to human beings, the potential for APEC to act as human UPEC or as a reservoir of virulence genes for UPEC should be considered.

Avian pathogenic E. coli strains are often resistant to antimicrobials approved for poultry including cephradine, tetracyclines [66–70], chloramphenicol, sulfonamides [67,69–71], amino-glycosides [68–70,72,73] and β-lactam antibiotics. Resistance to fluoroquinolones was reported within several years of the approval of this class of drugs for use in poultry. There is reason for concern that genes conferring resistance to extended-spectrum beta-lactams will emerge in avian pathogenic E. coli strains and reduce the efficacy of ceftiofur, which is currently used on a limited basis in poultry breeding flocks and hatcheries. In one study, conducted at the University of Georgia, 97 of 100 avian pathogenic E. coli isolates were resistant to streptomycin and sulfonamide and 87% of these multiple antimicrobial resistant strains contained a class 1 integron, intI1, which carried multiple antibiotic resistance genes. Multiple antimicrobial resistance traits of avian pathogenic E. coli have also been associated with transmissible R-plasmids.

CPIV: Canine parainfluenza virus; ITB: Infectious tracheobronchitis; CIRD: Canine infectious respiratory disease; CAV-1: Canine adenovirus type 1; CAV-2: Canine adenovirus type 2; CDV: Canine distemper virus; CPV: Canine parvo virus; CCoV: Canine enteric coronavirus; CAP: Community-acquired pneumonia; NSVS: Norwegian School of Veterinary Science.

Avian colibacillosis is an infectious disease of birds caused by Escherichia coli, which is considered as one of the principal causes of morbidity and mortality, associated with heavy economic losses to the poultry industry by its association with various disease conditions, either as primary pathogen or as a secondary pathogen. It causes a variety of disease manifestations in poultry including yolk sac infection, omphalitis, respiratory tract infection, swollen head syndrome, septicemia, polyserositis, coligranuloma, enteritis, cellulitis and salpingitis. Colibacillosis of poultry is characterized in its acute form by septicemia resulting in death and in its subacute form by peri-carditis, airsacculitis and peri-hepatitis. On the other hand, Salmonella infection caused by a variety of Salmonella species is one of the most important bacterial diseases in poultry causing heavy economic losses through mortality and reduced production. Avian salmonella infection may occur in poultry either acute or chronic form by one or more member of genus Salmonella, under the family Enterobacteriaceae. Besides, motile Salmonellae (paratyphoid group) infection cause salmonellosis in chickens and have zoonotic significance.

Avian colibacillosis has been noticed to be a major infectious disease in birds of all ages. This disease has an important economic impact on poultry production worldwide. The majority of economic losses results from mortality and decrease in productivity of the affected birds. Infectious bursal disease (IBD), mycoplasmosis, coccidiosis, Newcastle disease or infectious bronchitis, as well as nutritional deficiencies all predispose the birds to this disease. However, faecal contamination of egg may result in the penetration of E. coli through the shell and may spread to the chickens during hatching and is often associated with high mortality rates, or it may give rise to yolk sac infection. On the other hand, with the great expansion of poultry rearing and farming, avian salmonellosis is the most devastating disease worldwide. The epidemiology of fowl typhoid and pullorum disease in poultry, particularly with regard to transmission from one generation to the next is known to be closely associated with infected eggs. The birds that survive from clinical disease when infected at a young stage may show few signs of infection but can become carriers.

At slaughter, resistant strains from the gut readily soil poultry carcasses and as a result poultry meats are often contaminated with multiresistant E. coli [ 8–14]; likewise eggs become contaminated during laying. Hence, resistant faecal E. coli from poultry can infect humans both directly and via food. These resistant bacteria may colonize the human intestinal tract and may also contribute resistance genes to human endogenous flora. Similarly, the emergence of multidrug resistance among Salmonella spp. is an increasing concern. Salmonella serovar Hadar has been reported as one of the most resistant Salmonella serotypes [17–19].

Microbial food safety is an increasing public health concern worldwide. Epidemiological reports suggest that poultry meat is still the primary cause of human food poisoning. Poultry meat is more popular in the consumer market because of advantages such as easy digestibility and acceptance by the majority of people. However, the presence of pathogenic and spoilage microorganisms in poultry meat and its by-products remains a significant concern for suppliers, consumers and public health officials worldwide. E. coli and Salmonella has been consistently associated with foodborne illnesses in most countries of the world.

There are many poultry diseases transmissible to human, among them avian colibacillosis and avian salmonellosis are the prime concerns. But the detailed information about avian colibacillosis and avian salmonellosis in connection to the public health concerns are not available yet in one place. So, I intend to write this review article focusing on the various aspects of avian colibacillosis and avain salmonellosis in connection to the public health concerns.

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).

All data generated or analyzed during this study are included in this manuscript.

This study verifies that Group A Streptococci still is to be considered the most important pathogen in pharyngotonsillitis, associated with a higher number of new visits within 30 days, and that F. necrophorum did not distinguish itself as a major cause of recurrent infection or complications. These results do not merit any expansion of the aetiological paradigm of pharyngotonsillitis as suggested by others. More studies, preferably treatment studies with the focus on the aetiology (and especially F. necrophorum) in adolescents with a sore throat, are needed before F. necrophorum can be confirmed or discarded as an important pathogen in pharyngotonsillitis.

Influenza A viruses belong to the family of Orthomyxoviridae and based on the antigenicity of their haemagglutinin (HA) and neuraminidase (NA) they are classified into 16 classical HA and 9 classical NA subtypes (Neumann et al., 2009). The 8-segmented genomes of influenza A viruses are characterized by a significant plasticity. Due to point mutations and re-assortment events new variants or strains with epidemic or pandemic potential emerge (Neumann et al., 2009). In addition, influenza can be transmitted between animals, including swine, birds, horses, and humans, making it a zoonotic disease (van der Meer et al., 2010). Seasonal influenza usually resolves without consequences in healthy individuals. However, it is estimated that seasonal influenza effects 5–10% of the world’s population resulting in about 250,000 to 500,000 deaths annually (Tjon-Kon-Fat et al., 2016). At greater risk to develop secondary bacterial pneumonia are individuals with comorbidities, elderly people (age > 65), pregnant women, and children under the age of one (Rothberg et al., 2008).

For a long time it was considered that the H1N1 strain, an avian-like H1N1 virus, directly caused most of the fatalities during the 1918–1919 pandemic (Spanish Flu), often from a hemorrhagic pneumonitis rapidly progressing to acute respiratory distress syndrome and death (Osterholm, 2005; Gerberding, 2006; Oxford et al., 2006). The pandemic killed around 50 million people worldwide and remains unique in its severity compared to other big outbreaks. However, many of the findings have been reinterpreted in recent years (Brundage and Shanks, 2007; Chien et al., 2009). It is estimated that around 95% of all severe cases and deaths were attributed to secondary infections with bacterial pathogens, most predominantly by Streptococcus pneumoniae (Morens et al., 2008). Individual studies limited to certain regions identified also other pathogens commonly colonizing the respiratory tract, including Staphylococcus aureus, group A streptococcus (GAS) and Haemophilus influenzae (Brundage and Shanks, 2008). During the next two pandemics (H2N2 Asian Flu 1957-1958 and H3N2 Hong Kong Flu 1968-1969) bacterial co-infections were less likely the cause of death compared to the Spanish Flu (Giles and Shuttleworth, 1957; Trotter et al., 1959). Still, pneumonia accounted for about 44% of deaths during the Asian Flu (Giles and Shuttleworth, 1957). Most fatalities resulting from pneumonia occurred in individuals with chronic conditions, i.e., chronic lung diseases, rheumatic carditis, and hypertension (Giles and Shuttleworth, 1957). In 1957–1958, S. aureus was predominantly isolated from fatal pneumonia cases (Hers et al., 1957, 1958; Robertson et al., 1958; Martin et al., 1959), whereas S. pneumoniae returned as predominant cause of severe pneumonia during the Hong Kong Flu (Sharrar, 1969; Bisno et al., 1971; Burk et al., 1971; Schwarzmann et al., 1971). Forty years later in 2009, a novel H1N1 virus of swine origin emerged and caused again a pandemic (Dawood et al., 2009, 2012). In contrast to Asian and Hong Kong Flu, mortality rates were rather low, but most deaths occurred in healthy young individuals with no underlying conditions (Reichert et al., 2010; Monsalvo et al., 2011; Dawood et al., 2012). About 25–50% of severe or fatal cases were linked to complications due to bacterial pneumonia (Dominguez-Cherit et al., 2009; Estenssoro et al., 2010; Mauad et al., 2010; Shieh et al., 2010). Although regional variations occurred, pneumococci and S. aureus were the most frequently isolated bacterial species (Mauad et al., 2010; Shieh et al., 2010; Rice et al., 2012). Group A streptococcus was absent in many local pneumonia outbreaks associated with viruses, but was predominant in others (Brundage and Shanks, 2008; Ampofo et al., 2010). When it does appear, it is typically third in incidence (Chaussee et al., 2011). Overall, data on pandemic outbreaks suggest that disease severity and mortality can be linked to secondary bacterial pathogens with variations depending on regions and state of immunity of the population (Brundage and Shanks, 2008; Shanks et al., 2010, 2011; McCullers, 2013).

Both surveys recruited LPMWs and CRs. The response rates for high-, moderate-, and low-risk groups of LPMWs and CRs in the stage I survey were 98 %, 95 %, 93 %, and 90 %, respectively. Such rates for LPMWs and CRs in the stage II survey were 80 % and 90 %, respectively. The response rates for LPM workers after the HPAI H5N2 outbreaks were lower than those after the LPAI H5N2 outbreaks.

In the first-stage survey after the LPAI H5N2 outbreaks but before the HPAI H5N2 outbreaks, a total of 848 questionnaires were administered, including 430 to LPMWs and 418 to CRs (Table 1). In stage I, there were significant differences in gender and education, but the results were comparable across age and geographical distributions, without statistical differences between these two groups [Tables 1 and 2]. However, workers in the wet markets had a significantly higher proportion of males [52.6 % (226/430)] as compared to the CRs [29.9 % (125/418)] (p < 0.001). Overall, the CRs had higher levels of education than the LPMWs (p < 0.001).

In the second stage survey (after the outbreaks of HPAI H5N2 in central Taiwan), 225 respondents (73 LPMWs and 152 CRs) completed the questionnaires. In this subgroup (Table 4), the LPMWs were significantly less educated (p < 0.001) and older [mean ± standard deviation (S.D.) of age (by years): 49.1 ± 14.6 vs. 32.2 ± 13.5, p < 0.001)] than those CRs of the same local areas with HPAI outbreaks.

Five hundred and twenty three children met the inclusion criteria and included. 285 [54.5%] boys and 238 [45.5%] girls. The mean ages for males and females were 1.7 [SD=1.98] and 1.8 [SD=2] years respectively, however 96.2% of cases were between 0-7 years. The most common condition diagnosed was non-specific URTI [285, 54.5 %] followed by the common cold [171, 32.7%]. Acute tonsillitis, acute otitis media and acute pharyngitis together accounted for only 8.4% of all children studied and no child had a diagnosis of sinusitis. Looking at the distribution of cases by age non-specific URTI was the most common diagnosis in patients 0-2 years [225/392, 57.4%] and 3-4 years [42/84, 50%]. In children less than 4 years the common cold [21/47, 44.7%] was most frequent. The common cold and non-specific URTI were also the only two diagnoses made in children over 9 years of age. Disease occurrence and gender were not associated except for otitis media in which 11(79%) of the 14 cases occurred in boys. Four patterns of prescribing were observed, (1) no drug therapy [10, 1.9%], (2) antibiotic therapy alone [32, 6.1%], (3) antibiotic therapy and symptomatic therapy [277, 53.0%] and (4) only symptomatic therapy [204, 39.0%]. A total of 309 [59.1%] patients received a single antibiotic; two or more antibiotics used in combination were never prescribed. Of patients diagnosed with the common cold 51.5% received an antibiotic and 58.2% of those diagnosed with a non-specific URTI received an antibiotic. Many patients (82.1%) with other diagnoses (acute tonsillitis, acute otitis media, viral URTI, influenza, and acute pharyngitis) also received an antibiotic. The most frequent antibiotics prescribed were amoxicillin [242, 78.3%], erythromycin [32, 10.4%] and amoxicillin/clavulanate [28, 9.1%]. The remaining 7 patients received different agents such as cefaclor, cefuroxime and co-trimoxazole. Irrespective of the diagnosis amoxicillin was the antibiotic of choice even among the 14 patients diagnosed with viral URTI, 4[28.6%]. In just over a third (204, 39%) of patients symptomatic therapy was recommended, one agent in 95, two in 101 and 3 in 8 patients. Both an antibiotic and symptomatic therapy were prescribed for 277 patients. Reported, 78.2% were treated with antibiotics and symptomatic agents and 6.4% were treated with an antibiotic alone The five symptomatic agents most frequently prescribed were paracetamol [40. 1%]; diphenhydramine [29. 1%]; normal saline nose drops [14.2%]; chlorpheniramine [7.3%]; and histatussin [3.1%]. There was a significant association between antibiotic prescribing and therapy for relief of symptoms [p=0.021] so that antibiotic prescription was likely to be given with a prescription for symptom relief. In 112 of the 523 cases studied throat swabs were analysed for culture and sensitivity. In 110 [98.2%] participants growth of commensals only was reported, and only two subjects had pathogenic organisms; one with streptococcus pyogenes and the other with Staphilococcus aureus. In children harbouring commensals, 52.7% were diagnosed with a non-specific URTI, and 34.8% had the common cold. In the one patient in whom Staphlococcus aureus was isolated, a diagnosis of the common cold was made, the patient received amoxicillin/clavulanate and the sensitivity report indicated resistance to ampicillin. In the patient with Streptococcus pyogenes, the child had non-specific URTI, received amoxicillin, and the sensitivity report indicated resistance to amoxicillin.

In the 110 participants in whom commensal growth was reported, 78.2% were treated with antibiotics and symptomatic agents and 6.4% were 168 treated with an antibiotic alone.

This was a retrospective observational study of paediatric patients with a physician diagnosis of an URTI during the period June 2003 to June 2005. Five public health facilities were randomly selected for this study, four of which had independent routine swab analysis performed by the National Surveillance Unit. A paediatric patient was a subject 12 years or below and an antibiotic was defined as a substance with bactericidal or bacteriostatic effects. The term is often extended however to include synthetic antibacterial agents, not produced by microbes 24, such as sulfonamides and quinolones, which was adopted in this study. The diagnoses of URTIs for the purposes of this study are: the common cold, acute pharyngitis, acute tonsillitis, sinusitis, acute otitis media, viral URTI, influenza and non-specific URTI. Exclusion criteria were (1) age equal or lower 13, (2) subjects immunocompromised, malnourished or infected by laboratory confirmed resistant strains of pathogens and chronic respiratory tract diseases and (3) a subject without a definite diagnosis of URTI. Data were analysed using Minitab version 14. 25 Data from throat swabs performed under the National Surveillance Programme conducted at four (4) of the health facilities studied were collected and used for analysis. Swabs were taken from children presenting with complaints of an upper respiratory tract infection and were obtained on the same day as the physician’s visit and were independent of physician consultation. These swabs were transported in commercially available transport media to the Microbiology department of the Port of Spain General Hospital where they were initially plated on blood agar containing antibiotic strips to detect sensitivity.

The results of the risk awareness, attitudes about, and protective behaviors against AI after the outbreak of HPAI H5N2 in Taiwan are summarized in Table 5. The older respondents were less likely to believe that Taiwan would be affected by the influenza outbreaks in mainland China (OR: 0.85, 95 % CI: 0.78–0.93, Question 1). Again, the impact of outbreaks of AI abroad as well as in Taiwan was further explored (Questions 1 and 2). Interestingly, there was a strong association between the respondents’ beliefs about Taiwan’s human outbreaks of AIV cases and influenza outbreaks in China (OR: 25.51, 95 % CI: 4.24–153.66). Moreover, the respondents who perceived that the outbreaks in China would lead to human infection of AIV in Taiwan and those who believed that Taiwan would face an AI threat reported that they had more willingness to take preventive measures against AIVs (OR, 6.83; 95 % CI, 2.10–22.26; OR, 3.88; 95 % CI, 1.16–12.98, respectively). Besides the impact of mainland China, the participants who were aware of the critical condition of the one H5N1 pediatric case in Hong Kong in June 2012 were more likely to have good knowledge of the new “Ten No’s, Five Needs” policy (Question 3, OR, 4.24; 95 % CI, 2.09–8.59).

For public health prevention, both personal protection and vaccination (Questions 4 and 5 of Table 5) were examined. The Taiwanese respondents knowing of the critical condition of the 2012 Hong Kong H5N1 pediatric case (OR: 5.85, 95 % CI: 1.45–23.56), or believing in the possibility of Taiwan’s domestic risk of future human infection of AIVs (OR: 4.09, 95 % CI: 1.15–14.62), or having knowledge of the severity of the threat posed by the AI viruses (OR: 6.62, 95 % CI: 1.54–28.55) all reported the habit of carrying out self-protection measures for preventing AI viral infection. For other preventive measures, only participants who believed in the effectiveness of seasonal influenza vaccines in protecting against either human or avian flu (OR: 5.51, 95 % CI: 1.97–15.42) or both types of flu (OR: 7.65, 95 % CI: 2.61–22.43) would consider receiving AI vaccination. Noteworthily, LPMWs were less likely to accept AI vaccine than those CRs in central Taiwan with HPAI outbreaks [61.6 % (45/73) vs. 75.0 % (114/152), p = 0.04] (Table 4).

The risk awareness of AI causing serious disease and even death was evaluated (Question 6 of Table 5). CRs of areas with documented chicken HPAI H5N2 outbreaks had higher awareness of AI leading to severe human clinical cases or fatalities (OR: 3.64, 95 % CI: 1.03–12.86) than CRs of other areas. These respondents with greater alertness of the AI severity not only had better knowledge of the new “Ten No’s, Five Needs” policy (OR, 4.10; 95 % CI, 1.19–14.12) but also were more likely to take preventive measures against AIVs (OR, 4.38; 95 % CI, 1.08–17.76).

After the government declared the outbreaks of HPAI H5N2 in Taiwan in 2012, we found protective behaviors and shopping habits were different between LPMWs and CRs. Among the 221 respondents, 81 % of them washed their hands frequently (179/221) and 75.1 % of them (166/221, with 4 missing values) reported the intention to wear facemasks to protect themselves once AI outbreaks occur (Table 6). In this study, we did not differentiate surgical masks from cloth masks in our questionnaire on “facemasks”. However, most of the public can easily buy surgical masks in convenience stores or drug stores. Even among the CRs, high percentages of them intended to change their shopping behaviors such as avoiding both live-poultry markets (74/152, 48.7 %) and poultry purchases (56/152, 36.8 %).

Streptococcus suis serotype 2 (S. suis 2, SS2) is an important zoonotic pathogen that causes severe porcine infectious diseases, including arthritis, meningitis, and pneumonia. Virulent strains of SS2 can also be transmitted to humans (especially abattoir workers and pork handlers) by direct contact, causing meningitis, permanent hearing loss, septic shock, and even death. Two large-scale outbreaks of severe SS2 epidemics occurred in China in 1998 and 2005, causing great economic losses in the swine industry. These two outbreaks also posed serious public health risks from the newly emerging streptococcal toxin shock syndrome (STSS), which claimed 52 lives. Over the past decade, considerable attention has been given to the study of virulence factors (e.g., CPS, MRP, EF, and suilysin) and the pathogen-host interaction in this emerging pathogen. However, comparative studies at the whole-genome level had little done to decipher the evolutionary aspects by which the virulence and environmental adaptation of SS2 are shaped.

To shed light on the evolution of pathogenicity and potential genomic polymorphisms of SS2, several virulent strains were subjected to whole-genome sequencing and comparative genomic studies. Comparative analysis of the whole-genomic DNA sequence of the European S. suis strain P1/7 (by the Sanger Institute) and two representative highly virulent strains (98HAH12 and 05ZYH33) isolated from STSS patients during the two epidemic outbreaks in China uncovered a candidate pathogenicity island (PAI) named 89K, which has been confirmed to undergo horizontal gene transfer (HGT) by our recent work. Further analysis based on PCR amplification revealed that 89K exclusively present in the epidemic strains in these two Chinese SS2 outbreaks but not in other domestic clinical isolates or international virulent strains. However, analysis of the unfinished genomic sequence of SS2 strain 89/1591 (by the DOE Joint Genome Institute) revealed that a partial 89K sequence (~30 kb) is present in this typical North American virulent strain. Similarly, results from a recently published work suggest that S. suis strain BM407, which was isolated from a human meningitis case in Vietnam in 2004, contains two regions with extended similarity to 89K. These findings led us to hypothesize that the genome of SS2 would be highly polymorphic among different strains.

In this study, we employed the comparative genome re-sequencing (CGS) approach developed by Roche NimbleGen Systems to investigate genomic diversity in a collection of 18 SS2 strains, including isolates from the two outbreaks in China, other virulent strains from China (isolated before these outbreaks), virulent strains from European countries, and several avirulent strains. Although CGS cannot identify recently gained genes due to technical limitations, the DNA microarray-based comparative genome sequencing technique allows high resolution detection of sequence polymorphisms based on a reference genome. Using this technology, we identified a number of novel genetic polymorphisms in SS2 strains and several candidate virulence factors that may contribute to STSS. Our results provide new insight into the virulence mechanisms and genome dynamics of SS2, which will help to elucidate the evolution of SS2 strains and better monitor the incidence and spread of epidemic strains.

PCT is the peptide precursor of calcitonin, a hormone that is synthesized by the parafollicular C cells of the thyroid and regulates calcium homeostasis. Standard reference values of PCT in adults and children older than 72 hours are usually 0.15 ng/mL or less. In response to inflammation associated with bacterial endotoxin or inflammatory cytokines, PCT elevates within 2–6 hours, peaks at 12–24 hours, and has a half-life of 25–40 hours [37, 40]. Higher procalcitonin levels in patients with bacterial sepsis are associated with a greater likelihood of severe sepsis, septic shock, and decreased survival. Colonization or carrier states without a systemic host response do not significantly raise procalcitonin levels. Procalcitonin levels fall with successful treatment of either severe bacterial infection or noninfectious inflammatory stimuli.

URIs tend to cause modest elevations in PCT [42, 43]. Using a lower PCT threshold of 0.1 ng/mL in association with polymerase chain reaction–confirmed bacterial cultures of common oral pathogens such as GABHS or atypical pathogens such as Chlamydophila or Mycoplasma, would suggest a true active bacterial infection. Higher PCT cutoffs of 0.15–0.25 ng/mL could be used in association with growth of typical bacterial colonizers or in association with a negative bacterial culture to suggest active bacterial infection in patients without another confirmed source of infection, such as a viral infection [8, 40]. The PCT response to viral infections and noninfectious inflammatory stimuli such as autoimmune disease and chronic inflammatory processes typically do not exceed 0.75 ng/mL [44, 45]. Branch et al. found that 17% of viral infections had a PCT >0.25 ng/mL. At low concentrations (<1.0 ng/mL), PCT is inadequate by itself to differentiate viral from bacterial etiology [8, 47, 48].

In this study, we followed a well-described cohort of patients with pharyngotonsillitis and non-infected controls in primary healthcare for 2 years after inclusion, with special focus on the aetiology. We observed a high tendency in patients to return with a sore throat within 2 years irrespective of microbiological finding at inclusion, while patients with GAS more often returned within 30 days as compared to patients with other possible aetiology of their disease. Only one complication was recorded (sinusitis) and 2.8% of the patients underwent tonsillectomy within 2 years after inclusion.

The main strength of this study is that it links the aetiological study on pharyngotonsillitis, where modern techniques were used, with both short- (30 days) and long-term (2-year) follow-up data.

The medical file review was carried out in a comprehensive electronic medical record system that covered both general practice and hospital care in the county. This increased the possibility to catch all relevant events. Possibly, a few patients may have sought medical advice outside the county.

The main weakness of this study, however, is its small size, being powered rather for the aetiological mapping than for prospective follow-up of uncommon events. This has increased the risk of missing true differences between groups, as well as it prevented from adjusting for confounders such as smoking, age, socioeconomic status and morbidity. Hedin et al. did, however, only find smoking and tonsillar coating to be associated with F. necrophorum at inclusion. The rate of complications and surgery was also in line with previous reports.

Research on children has suggested that immediate prescription increases the risk of both relapse and recurrent infections, and Little et al. found that prescribing antibiotics lead to medicalisation and increased re-attendance in patients with sore throat. In our study, the group of patients with only GAS had the highest proportion of reconsultations within 30 days. In Swedish primary care, rapid antigen detection tests for GAS are readily available, and one hypothesis could be that the mere identification of GAS changes the way physicians communicate with their patients. This may in turn affect the patients’ view on relapsing symptoms and hence lower their threshold for re-attendance. The fact that most patients with GAS were prescribed antibiotics, and equally often regardless of Centor score, could reflect both an excessive use of rapid antigen tests and GP’s making treatment decisions based on microbiological findings rather than clinical severity. The high prescription rate among patients with GAS and F. necrophorum (despite the physicians being unaware of the latter) may have reduced the number of complications observed in this study. However, a study on respiratory tract infections in general practice found that even a large reduction in antibiotic prescribing was only associated with a small increase in the number of complications.

While F. necrophorum was the second most prevalent pathogen in the aetiological study, it does not seem to compete with GAS aetiology regarding new visits in the short-term perspective. Rather, the patients with F. necrophorum were positioned with the groups with “only viruses” and “no pathogen” detected. However, the power of this result was somewhat diminished by 4 young patients with F. necrophorum leaving the county before follow-up.

As the proportion of patients with new visits evened out between groups over time, the aetiology did not seem to matter in the long perspective. This finding, together with the finding that the patients had more new visits than the controls, might suggest that a subset of the general population more often than the average experience a sore throat (as subjectively reported in the background characteristics) and/or have a lower threshold for attending medical care. The proportion of controls that re-attended was higher than we had anticipated. It must also be pointed out that a sore throat can have non-infectious causes, and that this study might have miss-classified some of the new visits as infectious.

According to current guidelines, the main reason for treating an acute sore throat with antibiotics is to alleviate symptoms in patients with more severe presentations, rather than preventing complications or surgery. This study does not contradict these recommendations.

The significance of F. necrophorum in an acute sore throat has been debated: we saw previously that the bacterium was highly prevalent (15%) in the studied cohort, only outnumbered by GAS, and Centor found it to be even more common (20% prevalence) in a student population aged 15 to 30. Similarly, other researchers have identified F. necrophorum more often in patients than in controls [5, 8, 17] and Klug states that the role of F. necrophorum in acute tonsillitis seems significant but has to be clarified. These studies were all focused on the acute illness and did not include a follow-up study. Jensen, however, analysed throat swabs retrospectively among patients aged 10 to 40 and found F. necrophorum in 11% of patients with acute non-streptococcal group A tonsillitis, but in 23% of patients with recurrent tonsillitis, which supports the view that the bacterium could be especially involved in such conditions. Similarly, our group has found F. necrophorum to be common before tonsillectomy but also prevalent (16%) six months post-tonsillectomy, despite the fact that all these patients were then asymptomatic. This emphasizes the hypothesis that F. necrophorum may only cause a throat infection under certain circumstances. In this study, we have not found any support for F. necrophorum as a more pathogenic finding than other pathogens in patients with pharyngotonsillitis with regard to new visits, complications or surgery within 2 years of infection.

For the bactericidal assay, AMC 0.6 mg, DCBA 1.2 mg lozenges (Strepsils Honey and Lemon, Reckitt Benckiser Healthcare Ltd, Slough, UK) were dissolved into 5 mL of artificial saliva medium (0.1% meat extract [VWR International, Lutterworth, UK], 0.2% yeast extract [VWR International], 0.5% protease peptone [Oxoid, Basingstoke, UK], 0.02% potassium chloride [Fisher Scientific, Loughborough, UK], 0.02% sodium chloride [Fisher Scientific], 0.03% calcium carbonate [Fisher Scientific], 0.2% glucose [VWR International], 0.2% mucin from porcine stomach Type II [Sigma Aldrich, Gillingham, Dorset, UK], pH 6.7±0.3) at 44°C±1°C.

The following outcome measures were used to summarize the findings:

Average AIV-prevalence before (Ppre) or after (Ppost) the intervention:•Ppre = total nr. of positive samples before the intervention/total nr. of samples tested before the intervention•Ppost = total nr. of positive samples after the intervention/total nr. of samples tested after the intervention

Relative risk (RR):RR=Ppost/Ppre

Relative risk reduction (RRR) for studies with AIV-prevalence as an outcome:RRR=1−RR

The 95% confidence intervals for the RRR were calculated as 1 minus the confidence limits of the relative risk.

Incidence rate ratio (IRR) for studies with H7N9-incidence as an outcome:

IRR = incidence rate after the intervention / incidence rate before the intervention

LPM closure effectiveness was calculated as one minus the incidence rate ratio.

The statistical analysis was conducted with SPSS statistical software, version 20.