Streptococcus pneumoniae and pandemic H1N1 severity – the data from Argentina

The influenza virus can kill directly. But it can also lower your immune defenses and open you up to bacterial infection. A study that examines the role of bacterial co-infections in the severity of pandemic H1N1 has recently been published in PLoS One.

This study was motivated by the apparently high case fatality rate reported in Argentina. From the paper:

Based on a study in the community of La Gloria, Mexico, where the virus was first detected early in 2009, and worldwide surveillance data and mathematical modeling, the CFR was estimated to be 0.6%. The first case in Argentina was reported on May 17, 2009; by July 16, 2009, just two months later, the number of cases in Argentina totaled 3056, with 137 deaths, representing a computed CFR of 4.5%. Although we could not exclude the possibility that this elevated CFR reflected underreporting of milder infections, the alternative, a bona fide increase due to differences at the level of host or pathogen, might have global implications.

Although some patient risk factors have been associated with a worse outcome, these were not at higher levels in Argentina than other countries, so this could not account for the apparently higher case fatality rates.

To determine whether severe cases had been infected with different strains than mild cases, the complete genomes of 26 viral samples collected from patients with a wide range of symptoms and outcomes were sequenced. No obvious differences were observed.

This left the possibility of bacterial co-infections. 199 samples from people infected with H1N1 were examined for the presence of a wide variety of bacteria and viruses. Many co-infections were found. Pathogens identified included:

…S. pneumoniae (n = 62); H. influenzae (n = 104); human respiratory syncytial virus (RSV) A (n = 11) and B (n = 1); human rhinovirus (HRV) A (n = 1) and B (n = 4); human coronavirus (HCoV) −229 (n = 1) and -OC43 (n = 2); K. pneumoniae (n = 2); A. baumannii (n = 2); S. marcescens (n = 1); and S. aureus (n = 35) and MRSA (n = 6)…

However, only one bacteria was associated with severe cases – S. pneumonia. Further, the effect of this bacteria on outcome was primarily observed in people aged 6 to 55, normally a low risk age group for severe influenza, but one which is at much higher risk with pandemic H1N1 than seasonal flu. This result is not entirely unexpected. As the authors point out:

…recent postmortem analyses indicated lower respiratory tract infection in 22 out of 77 lethal 2009 H1N1pdm cases in the United States (29%); S. pneumoniae was implicated in 10 of these cases.

From a practical standpoint, what do these results mean? Some might be tempted to conclude that treatment with antibiotics would be more effective than treatment with antivirals. However, when the authors examined this, they found the opposite:

Data concerning antiviral and antibiotic therapy were available for 120 subjects. Risk of severe disease was diminished in subjects who received only oseltamivir. Of 96 subjects receiving oseltamivir alone, 10 (10.4%) had severe disease. In contrast, 13 of 14 patients (92.9%) who received antibiotics without antiviral medication had severe disease (p<0.0001).

This is consistent with many other reports suggesting that treatment with Tamiflu (oseltamivir) is especially effective in limiting severity and preventing death from pandemic H1N1. The authors don’t speculate about why Tamiflu alone is more effective than antibiotic treatment alone, even though a bacterial agent appears to be correlated with severe disease. Perhaps the damage done by the virus gives bacteria such unusual access to lung tissue that antibiotics are not as effective as under normal circumstances. In any case, the results from this study clearly support the continued prescription of Tamiflu to limit damage from both the virus directly, and, perhaps, indirect damage from opportunistic bacteria.

Vaccines against Streptococcus pneumoniae are available. Whether they would reduce severe or fatal cases of pandemic H1N1 has not been demonstrated. However, the current paper provides further rationale for recommending such vaccination and study of its possible effectiveness.


Palaciaos et al. (2009) Streptococcus pneumoniae Coinfection Is Correlated with the Severity of H1N1 Pandemic Influenza. PLoS One.

CDC (2009) Bacterial coinfections in lung tissue specimens from fatal cases of 2009 pandemic influenza A (H1N1) – United States, May-August 2009. MMWR Morb Mortal Wkly Rep 58: 1071–1074.


One thought on “Streptococcus pneumoniae and pandemic H1N1 severity – the data from Argentina

  1. There are several types of streptococcus pneumoniae.
    Is it included in the pneumovax, is the pneumovax
    expected to help, has it been examined, were there
    victims that had the pneumovax ?

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