Bordetella pertussis is a strict human pathogen which causes whooping cough, an endemic illness responsible of significant morbidity and mortality, especially in infants under 6 months old [1, 2, 5]. Although regional differences exist, Pertussis represents a considerable global disease burden that has been increasing, even in countries with high vaccination coverage [2, 5, 13]. In Peru, an alarming increase of cases has been observed in the last 5 years, and 56 % of cases are reported in infants under 1 year old [12, 14–16]. This have raise especial concern since infants under 6 months old are more vulnerable to disease related complications and carry a higher mortality [7, 21, 22].
The most common clinical manifestations of B. pertussis infections are prolonged and paroxysmal coughing, accompanied by inspiratory stridor [1, 3]. However, several factors are known to affect the disease presentation and Pertussis diagnosis may go unrecognized when other pathogens, such as respiratory syncytial virus (RSV) or Influenza virus circulate [10, 23, 24]. A retrospective study in Italy, from a group of infants hospitalized from October 2008 to April 2010 for acute respiratory symptoms reported that most of Pertussis cases were infants under 6 months with median of 71.5 days old and a male: female ratio of 6:13 . In our study pertussis toxin and IS481 genes were detected in 19.12 % (114/596) of the patients admitted with an acute respiratory infection and infants under 3 months old were the most frequently affected in 43 % (49/114) with a similar sex distribution.
Co-infection between Bordetella pertussis and RSV has been previously described to cause severe infections [10, 11]. A study conducted in a group of infants hospitalized for RSV bronchiolitis showed that almost 2 % of patients were co-infected with B. pertussis [25, 26]. In our series, co-infections were observed in 14 patients between B. pertussis and RSV-A and 1 sample was positive for B. pertussis and RSV-B. Moreover, 6 out of 9 cases of co-infections were clinically diagnosed as Bronquiolitis and B. pertussis was not suspected at the time of admission. Influenza virus and B. pertussis co-infections have been also identified as a possible pathogen present in children with community-acquired pneumonia; and the pertussis toxin-mediated suppression have been postulate to be responsible to produce more sever presentations [27, 28].
Multiple studies have reported Paroxysmal cough (76.5–91.1 %), cyanosis (46.7–81.7 %) and respiratory distress (47.8–55.7 %) as the most common symptoms in children [13, 29, 30]. However, several clinical features might help to suspect the diagnosis of pertussis in infants hospitalized for acute respiratory symptoms. 
One study in 2013, compared infants with Pertussis and confirmed RSV bronchiolitis; and the clinical characteristics showed that the percentage of infants with paroxysmal cough was significantly higher in infants with B. pertussis. Additionally, cough at admission lasted longer in infants with pertussis than in control infants. Also, fever was significantly lower in infants with pertussis, and more common in patients with bronchiolitis. In our study population, a similar clinical symptoms frequency was observed between patients with B. pertussis and RSV. The most frequently reported symptoms were fever, cough, rhinorrhea and respiratory distress, in more than 60 % of cases. However, the presence of rhinorrhea 88.35 %, respiratory distress 76.70 % and pharyngeal congestion 33.98 % was more common among patients with RSV. This higher frequency of symptoms in our study may be related to fact that more than 52 % of our patients were hospitalized infants under 6 months old.
The clinical diagnosis of Pertussis in infants can be challenging, especially in children with incomplete immunizations, and some patients may be catalogued as acute viral respiratory infections, before laboratory confirmation. Thus delaying the appropriate antibiotic treatment and isolation measures [11, 24]. In our series, pneumonia was clearly the most frequent diagnosis in 26.32 % (30/114) of the patients with positive B. Pertussis. However, other diagnosis were considered in this group, such as rhinopharingitis, bronchiolitis and influenza infections. In contrast, the diagnosis of Bronchiolitis was more common in 20.37 % (21/103) of children with a positive sample for RSV.
For Bordetella pertussis seasonality, a pattern corresponding to the summer and spring months have been reported in the southern hemisphere . Comparably, a previous study in infants under 6 month of age from 2003 to 2008 in Lima, registered more hospitalizations due to whooping cough during the months of February and September. In our study, a similar distribution was observed with an increase of B. pertussis cases from February to March and from October to November and a Seasonal index between 1.32 and 1.51 and 1.24–3.5 respectively.
Pertussis represents a considerable disease burden in Peru and the diagnosis is complicated by the limitations of currently available diagnostic tests. Therefore, the only diagnostic tests that are recommended for case confirmation in national reporting are culture and polymerase chain reaction (PCR) [7, 31]. However, in Peru the use of PCR for surveillance was started recently in 2012 and there is still evidence of a deficient report and registration of cases that limit the analysis of the real disease burden.